Gene: [01p32/SCPRP] sterol carrier precursor protein SCP-X/SCP-2; 3-ketoacyl-CoA thiolase?, peroxisomal (SCP2);


COM

 [1] As it follows from 'Summary' of the current entry, Seedorf U &:1994b suggested that SCP-X may manifest 3-ketoacyl-CoA thiolase activity in peroxisomes. This enzymatic function have been already assigned to an- other human protein encoded by a distinctive gene (GEM:03p2/ACAA). No a meaningful structural similarity between amino acid sequences of the two proteins was found in a homology analysis of the sequences, except a short segment (see a GEM expert's note on the mentioned citation, in the Summary).
[2] An initial suggestion that a mutation in SCPX/SCP2 can be a cause of infantile neuronal ceroid lipofuscinosis, INCL, was not confirmed in further studies of the subject matter by the same research group (Vesa J &:1994; GEM:01p32/PPT). Also see a note on the swp:P22307 entry in the section 'Refer_1' ('Protein_structure', 'SCP-2 isoform').
[3] Public Sequence databases currently contain above fifty entries rel- evant to the human SCPX/SCP2 genes/proteins, including many modified and truncated copies created by NCBI. Some of the entries contain sequences with multiple errors, as well as very confusing descriptors or comments: !USER ATTENTION ADVISED! in citations these sources."

SUM

 <*> [INTRODUCTORY NOTES] Findings accumulated to date support the earlier suggestions that the mechanism of differential splicing is involved in expression of the SCPX /SCP2 gene. So far, two major translation products of the gene have been identified - the 143 aa SCP-2 isoform and the 547 aa SCP-X/SCP-2 precur- sor. SCP-2 is nonspecific lipid-transfer protein mediating the transfer of common phospholipids,cholesterol,gangliosides between cell membranes. Also, it probably plays a role in regulating steroidogenesis. According to Van Heusden GP &:1990, the SCP2 protein is presented in various sub- cellular organelles, particularly cytosol (in the liver), microsomes,and mitochondria as well as on the surface of peroxisomes in steroidogenic tissues. The function of another form, SCP-X, is still unclear, but this protein has been found in the matrix of peroxisomes (see further in this this 'Summary'). Tissue specificity: liver, fibroblasts, placenta. %-------------------------- <* > [MORE ABOUT EXPRESSION]
[1] YAMAMOTO R &:1991a showed that expressed SCP2 cDNAs in COS-7 cells yielded a 15.3 kDa-polypeptide and increased amounts of a 13.2kDa-poly- peptide. The relevant cDNA probe hybridized with 3.2 & 1.8 kb-mRNA in species in liver polyA+ RNA.The latter of the two mRNA species was most abundant in fibroblasts and placenta. Using Southern blot experiments, the authors suggested that'either there are multiple copies of the SCP2 gene in the human genome or that the SCP2 gene is very large.'They also suggested that alternate splicing of the primary SCP-2 transcript may lead to the expression of pre-SCP2/SCPX (58 kDa) from a single gene. %-------------------------------
[2] UNUSUALLY COMPLEX EXPRESSION of SCP2 in mice was reported by Seedorf U &:1993. The authors detected at least four SCP2-related transcripts in MOUSE liver: two (1.6 & 3.0 kb) are expressed to high levels, while the other two (0.9 & 2.2 kb) revealed relatively low expression. The authors isolated two overlapping SCPX cDNAs which were shown to be de- rived from alternatively polyadenylated transcripts spanning approxi- mately 2.2 and 2.9 kb. The predicted ORF consisting of 547 codons was composed of 143 C-terminal amino acids essentially identical with mouse preSCP2, and 404 N-terminal residues specific for SCP-X.To that moment, the authors could not determine whether all SCP2-related transcripts were transcribed from a single gene. Since they also isolated a genomic clone containing an SCP2-related sequence, with some of the character- istics expected for a processed pseudogene, the authors suggested that at least some of the multiple restriction bands detected by Southern hybridization with SCPX cDNA-derived probes could be explained by cross- hybridization with a pseudogene. %----------------------
[3] SEEDORF U &:1994b (Institut fur Arterioskleroseforschung, Westfali- schen Wilhelms Universitat, Munster, Federal Rep of Germany) and other researchers found several SCP2-encoding cDNAs containing in-frame 5'- extensions of up to 1250 nt upstream of the initiator ATG codon of the pre-SCP2 cDNA. Such transcripts are primarily expressed in liver and are predicted to encode a previously undescribed 'fusion' protein - sterol carrier protein X, SCP-X, consisting of two parts: (i) a 143 aa C-terminal domain completely identical to SCP2; and (ii) a 404 aa N- terminal domain with unknown biochemical activity. The authors showed that SCP-X epitopes are primarily detected within peroxisomes, and the protein cleaves 3-oxoacyl(n)-CoA to yield acetyl-CoA and acyl(n-2)- -CoA. In addition, like SCP-2, SCP-X also stimulates (in vitro) the microsomal conversion of 7-dehydrocholesterol to cholesterol and trans- fers phosphatidylcholine and 7-dehydrocholesterol from small unilamel- lar vesicles to acceptor membranes, i.e., SCP-X manifests previously undescribed peroxisomal 3-ketoacyl-CoA thiolase activity (EC:2.3.1.16?) with intrinsic sterol carrier and lipid transfer function. /NOTE: Because of the mentioned enzymatic function have been already assigned to another human protein (GEM:03p2/ACAA), a search for some kind of structural homology between SCP-X and ACAA may be important. An alignment of the two sequences, perform by a GEM expert, showed that the proteins share one short motif presented below - 16 matched residues within a 20 aa-segment that resides in the C-terminal third of ACAA and the intermediate one of SCP-X: ----------------------------- SCPX(=547 aa): 383=GAKVALQHNLGIGGA-VVVTL=402 gnb:M75883 ||*|||*|:||*:||**|:|| ACAA(=424 aa): 371=GA-VALGHPLGCTGARQVITL=390 swp:P09110 ----------------------------- This finding may support, at least partially, the Seedorf U &:1994's suggestion, as well as indicate on a functionally specific region in the two enzymes\ %--------------------- <* > [IN THE 3D STUDY,] Szyperski T &:1993(Institut fur Molekularbiologie und Biophysik, Eidgenossische Technische Hochschule-Hong-gerberg,Zurich, Switzerland), the authors used NMR spectroscopy to determine the three- -dimensional (3D) polypeptide backbone fold of the mature SCP2 (123 aa). Three alpha-helices (the residues 9-22, 25-30, 78-84)and a five-stranded beta-sheet (the residues 33-41, 47-54, 60-62, 71-76, 100-102) were iden- tified. The authors concluded that the beta-sheet is 'a central feature of the molecular architecture' - the first three strands are arranged in an antiparallel manner and the polypeptide crosses over this 3-stranded sheet in a right-handed manner so that the fourth strand is become paral- lel to the first one; the fifth strand runs anti-parallel to the fourth one (i.e., the overall topology is +1, +1, -3x, -1). /Note_3: Some materials used in this study, in particular, a previously isolated cDNA encoding pre-SCP2 polypeptide, as well as a PCR ampli- fication of the cDNA followed by cloning/sequencing of the amplified DNA) were previously described by the same authors in other publica- tions (Smith DB, Johnson KS: Gene, 67, 31, 40, 1988; Johnson KS &: Nature, 338, 585-587, 1989)\"

PRT

 "<* > [SCP-2 ISOFORM]
<** SOURCES:> [Published & Submitted/Cited_in DBs]
%---------------------------------
<*** REFER_1:> [Yamamoto R &:1991a]
%-----------
/IDP: Yamamoto R, Kallen CB, Babalola GO, Rennert H, Billheimer JT,
Strauss JF III;
'Cloning and expression of a cDNA encoding human sterol carrier
protein 2';
PNAS, 88, 463-467, 1991\
%---------
/IDC_1.1: gnb:M55421^HUMSTEAA| cDNA= 1219 bp;
'Human sterol carrier protein-2 (SCP-2) mRNA,
complete cds'; //: seq_from human female liver\
/Date: Dec-06-1993\
/Duplicate: cbi:432973 & cbi:432978\
/Features:
seg(84..515) == CDS //: incl STOP codon;
seg(84..143) == SIGNAL_peptide;
seg(144..512 == MATURE_peptide;
seg(782..787) == polyA_signal //: putative;
seg(1062..1067) == polyA_signal //: putative;
seg(1107..1112) == polyA_signal //: putative;
seg(1190..1195) == polyA_signal //: putative;
pos:1219(=a) == polyA_site //: experimental\
/User_ATTN: This sequence differs from that presented in the duplicate
entry emb:M55421^HSSTEAA(=1218 bp) and its 'orthologous' entry swp:
:P22307(=143 aa) at several positions. A comparative analysis of
all entries relevant to 'Yamamoto R &:1991a' & 'Yamamoto R &:1992'
is presented in the next section 'Coding_region'.\
/Note: This gnb:entry also refers to 'Vesa J &:Unpubl' that was pub-
lished later, 1994, and submitted as a separate entry, gnb:M75883
(=2572 bp); see 'Refer_4' below.\
%---------
/IDC_1.2: emb:M55421^HSSTEAA| cDNA= 1218 bp;
'Human sterol carrier protein-2 (SCP-2) mRNA,
complete cds'; //: seq_from human liver\
/Date: Aug-01-1991^Nov-06-1993\
/CrRf: swp:P22307^NLTP_HUMAN\
/Features:
seg(84..515) == CDS //: incl STOP codon;
seg(84..143) == SIGNAL_peptide;
seg(144..512 == MATURE_peptide\
/User_ATTN: This sequence differs from that presented in the duplicate
entry gnb:M55421^HUMSTEAA(=1219 bp) and its 'orthologous' entry swp:
:P22307(=143 aa) at several positions. A comparative analysis of
all entries relevant to 'Yamamoto R &:1991a' & 'Yamamoto R &:1992'
is presented in the next section 'Coding_region'.\
%---------
/IDC_1.3: swp:P22307^NLTP_HUMAN| prt= 143 aa (MW= 15370);
'Nonspecific lipid-transfer protein precursor (sterol
carrier protein 2, SCP-2)'\
/Date: Aug-01-1991^Apr-01-1993\
/Duplicate: cbi:128386\
/CrRf: emb:M55421^HSSTEAA; pir:A39010^-\
/Note: The following is selected from the 'Comments' field of this swp:
entry - 'SCP2 is present in low levels in subjects with Zellweger
syndrome (cerebro-hepatic-renal syndrome), whose cells are deficient
in peroxisomes and who have an associated impairment in plasmalogen
and bile acid synthesis & catabolism of phytanic acid and very-long-
chain fatty acids.'
//: the mentioned data relating to SCP2 are apparently a secondary
phenomenon occasionally found in Zellweger syndrome (for details,
see GEM:07q11/ZWS1)\
/Features:
seg(1..20) == mitochondrion (potential);
seg(21..143) == nonspecific lipid-transfer protein;
pos:90 == essential for transport of lipids;
seg(141..143) == microbody targeting signal (similar)\
/User_ATTN: The amino acid sequence presented in this swp:entry was ac-
tually derived from 1229 bp-cDNA (prt=143 aa) published by 'Yamamoto
R &:1992' (see 'Refer_2'), i.e., the sequence entirely identical to
that translated in gnb:S52450. Nucleotide and amino acid sequences
presented in these entries contain multiple errors (see further)\
%------------------------------
<*** REFER_2:> [Yamamoto R:1992]
/IDP: Yamamoto R;
'Localization of human sterol carrier protein 2 gene and cDNA
expression in COS-7 cell';
Hokkaido Igaku Zasshi, 67, N6, 839-848, 1992\
%-------
/IDC_2: gnb:S52450^cbi:122504| cDNA= 1229 bp;
'Sterol carrier protein 2 (human liver mRNA);
//: map_location 1\
/Date: Mar-08-1993\
/Duplicate: cbi:263550-551\
/Features:
seg(84..515) == CDS //: incl STOP codon)\
/User_ATTN: A translation product (143 aa) derived from this cDNA is
entirely identical to that presented in swp:P22307 although the
latter entry refers to another source - 'Yamamoto R &:1991a' con-
taining actually a distinctive version of the sequence in question.
Both nucleotide and amino acid sequences presented in these entries
contain multiple errors (see further)\
%---------------------------------
<*** REFER_6:> [Szyperski T &:1993]
/IDP: Szyperski T, Scheek S, Johansson J, Assmann G, Seedorf U,
Wuthrich K;
'NMR determination of the secondary structure and the three-
-dimensional polypeptide backbone fold of the human sterol
carrier protein 2';
FEBS Lett, 335, N1 (Nov 29), 18-26, 1993\
%----
/IDC_6: cbi:128386^-| prt= 143 aa (MW= ?)
'Nonspecific lipid-transfer protein precursor (sterol
carrier protein 2, SCP-2'\
/Date: Feb-01-1994\
/CrRf: swp:P22307^NLTP_HUMAN; pir:A39010; gnb:M55421; HSSP:P00805\
/Features:
seg(1..20) == transit_peptide (mitochondrion, putative);
seg(21..143) == mature_chain (nonspecif lipid-transfer prot);
pos:90 == lipids_transport (specific function);
seg(141..143) == microbody targeting_signal (putative)\
/User_ATTN: The actually published sequence differs from that presented
in the cbi:entry by one amino acid substitution (Gln -> Arg) at the
position #pos:91(=Q) which corresponds to #pos:111(=R) in Refer_6\
%---------------------------------------
<** SEQUENCE:> [PROT= 143 aa, MW= 15370?]
%---------------------------------------
{//: 1......... ........20 .......... ........40 ........50;
Signal polypeptide | Mature protein | |;
| | | | |\
pep: 1=MGFPEAASSF RTHQIEAVPT SSASDGFKAN LVFKEIEKKL EEEGEQFVKK=
pep: 51=IGGIFAFKVK DGPGGKEATW VVDVKNGKGS VLPNSDKKAD CTITMADSDF=
pep:101=LALMTGKMNP QSAFFQGKLK ITGNMGLAMK LQNLQLQPGN AKL=143\}
%------------
<*** CONFLICTS>
{pos:68 A -> D in Yamamoto R &: 1992 //: sequencing error?;
pos:78 K -> Q in Yamamoto R &: 1992 //: sequencing error?;
pos:91 Q -> R in Szyperski T &:1993 //: PCR-copying error;
pos:97 D -> A in Yamamoto R &: 1992 //: sequencing error?;
pos:118 K -> P in Yamamoto R &: 1992 //: sequencing error?}
%------------
<*** LANDMARKS>
{seg(1..20) == transit_SIGNAL //: binding_MITOCHONDRION?;
seg(21..143) == MATURE_protein;
seg(29..42) == alpha-helix 1 //: (9..22) in mature form;
seg(45..50) == alpha-helix 2 //: (25..30) in mature form;
seg(53..61) == beta-sheet strand 1 //: (33..41) in mature form;
seg(67..74) == beta-sheet strand 2 //: (47..54) in mature form;
seg(80..82) == beta-sheet strand 3 //: (60..62) in mature form;
pos:90=D/Asp == lipids_TRANSPORT //: specific function;
seg(91..96) == beta-sheet strand 4 //: (71..76) in mature form;
seg(98..104) == alpha-helix 3 //: (78..84) in mature form;
seg(120..122) == beta-sheet strand 5 //: (100..102), mature form;
pos:124=N/Asn == lipids_TRANSPORT //: specific function;
seg(141..143) == targeting_SIGNAL //: binding_PEROXISOME?}
%----------------------------------------------------------------------
<** > [DISCUSSION]
[1] Two SCP2 cDNA seqs published by Yamamoto R &:1991a/1992 contained
multiple errors (see Table_1) both in coding and 3'-UTL regions. Some
additional complications came from the above-mentioned confusing cita-
tions of the sequences in the EMBL and SwissPROT Databases. In fact,
two 'duplicate' entries - GNB:M55421 (cDNA= 1219 bp) and EMB:M55421
(cDNA= 1218 bp), differ from each other at 13 positions of which four
are single nucleotide insertions/deletions and nine are single substi-
tutions including one in the coding region - #pos:373(=a/c). However,
the major complications came from the 1229 bp-cDNA published by 'Yama-
moto R:1992' (GNB:S52450) and incorrectly cited as 'Yamamoto R &:1991'
(1219 bp-cDNA) in EMB:M55421 and SWP:P22307. As a result,the sequences
presented in the two latter entries differ both from each other and
that presented in GNB:S52450 at many positions, especially in the 3'-
-untranslated region.
%---------------------
[2] /Table_1: Alignment of the Yamamoto R &:1991a/1992 cDNA
sequences cited in the relevant Database entries;
//: numericals presented in columns of this Table are
numbers of the corresponding nucleotide positions
in different aligned versions of the sequence in
question; nucleotides occurring at those positions
are marked by '*' when they are not matched.\
------------------------------------------------------------
GNB:S52450 281=agaggacacc 311=tggccaagga 431=aggcccattg
# |||||*|||| ||||*||||| ||||**||||
EMB:M55421 281=agaggccacc 311=tggcaaagga 431=aggcaaattg
GNB:M55421 281=agaggccacc 311=tggcaaagga 431=aggcaaattg
............................................................
GNB:S52450 371=tgcctcagac 601=actacacatc
EMB:M55421 371=tgcctcagac <- CDS | 601=actacacatc
# ||*||||||| | 3'-UTL -> |||||||||*
GNB:M55421 371=tgactcagac 601=actacacatt
------------------------------------------------------------
GNB:S52450 621=gtgggataga 661=tttttcctaa 671=gctgcgggtg
EMB:M55421 621=gtgggataga 661=tttttcctaa 671=gctgcgggtg
# ||||****|| |||||||||* |||**|||||
GNB:M55421 621=gtggatagga 661=tttttcctat 671=gctctgggtg
............................................................
GNB:S52450 691=gactggtata 711=gcg-aattgc 1000=gattaaaaat
EMB:M55421 691=gactggtata 711=gcg-aattgc 1000=gattaaaaat
# ||*||||||| |||*|||||| |||*||||||
GNB:M55421 691=ga-tggtata 710=gcggaattgc 1000=gat-aaaaat
............................................................
GNB:M55421 1200=gctttcagat gcagttttca=1219\
GNB:S52450 1201=gctttcagat gcagttttca aaaaaaaaa=1229\
# |||||||||| |||||||*|\
EMB:M55421 1201=gctttcagat gcagttt-c=1218\
------------------------------------------
<* > [SCP-X/SCP-2 PRECURSOR|= 547 aa]
<** SOURCES:> [Published & Submitted/Cited_in DBs]
%--------------------------
<*** REFER_3:> [He Z &:1991]
/IDP: He Z, Yamamoto R, Furth EA, Schantz LJ, Naylor SL, George H,
Billheimer JT, Strauss JF III;
'cDNAs encoding members of a family of proteins related to
human sterol carrier protein 2 and assignment of the gene
to human chromosome 1p21-pter';
DNA Cell Biol, 10, 559-569, 1991\
/Note: According to a note in another publication by partly the same
research group, this cDNA sequence contains 27 single nucleotide
differences from the SCPX/SCP2 cDNA published by 'Vesa J &:1994'
(see Refer_4).\
%-------
/IDC_3: gnb:M75884^HUMSCP2B| cDNA= 1500 bp;
'Human sterol carrier protein 2 mRNA, complete cds';
//: seq_from liver; clone_l:HL-1115b\
/Date: Dec-06-1993\
/Duplicate: cbi:432976-977\
/Features:
seg(82..951) == CDS //: incl STOP codon;
seg(1218..1223) == polyA_signal (putative);
//: 'no polyA or polyA signal was found at the end of this
cDNA clone, indicating that the mRNA sequence may be
partial at the 3' end'\
%-------------------------------
<*** REFER_4:> [Vesa J &:1994]
/IDP: Vesa J, Hellsten E, Branoski BL, Emanuel BS, Billheimer JT,
Mead S, Cowell JK, Strauss JF III, Peltonen L;
'Assignment of sterol carrier protein X/sterol carrier
protein 2 to 1p32 and its exclusion as the causative
gene for infantile neuronal ceroid lipofuscinosis';
Hum Mol Genet, 3, N2, 341-346, 1994\
%-------
/IDC_4: gnb:M75883^HUMSCP2A| cDNA= 2572 bp;
'Human sterol carrier protein X/sterol carrier
protein 2 mRNA, complete cds';
//: seq_from liver; clone_l:HL-1115b\
/Date: Dec-06-1993\
/Duplicate: cbi:432974-975\
/Features:
seg(22..1665) == CDS //: incl STOP codon;
seg(1932..1937) == polyA_signal (putative);
seg(2213..2218) == polyA_signal (putative);
seg(2258..2263) == polyA_signal (putative);
seg(2341..2346) == polyA_signal (putative);
seg(2550..2555) == polyA_signal (putative);
pos:2572(=a) == polyA_site (experimental)\
%------------------------------------------------------------
<** ALIGNMENT:> [Matches & Conflicts]
/Note: The following sequences of the SCPX/SCP2 precursor and SCP2
isoform are conceptual translation products derived from cDNAs
described in 'Refer_1-4' above. 'Refer_5' (Ohba T &:1994) is
described in the the section 'Gene_structure'. The two latter,
Refer_4 and _5, are denoted as one entity 'ref4/5' in the cur-
rent alignment since their amino acid sequences are identical.\
------------------------------------------------------------------
/Table_2: Alignment of all SCP-X/SCP-2 amino acid sequences
cited in the relevant Database entries\
------------------------------------------------------------------
{//: +1 SCP-X/SCP-2 precursor is as follows;
|\
{ref4/5: 1=MSSSPWEPAT LRRVFVVGVG MTKFVKPGAE NSRDYPDLAE EAGKKALADA=
ref4/5: 51=QIPYSAVDQA CVGYVFGDST CGQRAIYHSL GMTGIPIINV NNNCATGSTA=
ref4/5: 101=LFMARQLIQG GVAECVLALG FEKMSKGSLG IKFSDRTIPT DKHVDLLINK=
ref4/5: 151=YGLSAHPVAP QMFGYAGKEH MEKYGTKIEH FAKIGWKNHK HSVNNPYSQF=
ref4/5: 201=QDEYSLDEVM ASKEVFDFLT ILQCCPTSDG AAAAILASEA FVQKYGLQSK=
ref3: -21=sea fl........}
-------------------------------------------------------------------
{//: +1? (Unknown isoform?);
|\
ref4/5: 251=AVEILAQEMM TDLPSSFEEK SIIKMVGFDM SKEAARKCYE KSGLTPNDID=
ref3: -8=........M ........... .......... .......... ..........}
%-----------
{ref4/5: 301=VIELHDCFST NELLTYEALG LCPEGQGATL VDRGDNTYGG KWVINPSGGL=
ref3: 43=.......... .......... .......... .......... ..........}
%-----------
{ref4/5: 351=ISKGHPLGAT GLAQCAELCW QLRGEAGKRQ VPGAKVALQH NLGIGGAVVV=
ref3: 93=.......... .......... .......KRQ .......... ..........;
ref2: -27=krq .......... ..........;
ref1: -27=krq .......... ..........}
-------------------------------------------------------------------
{//: SCP-2 +1:Signal_sequence; +21:Mature_polypeptide;
| |\
ref4/5: 401=TLYKMGFPEA ASSFRTHQIE AVPTSSASDG FKANLVFKEI EKKLEEEGEQ=
ref3: 143=....M..... .......... .......... .......... ..........;
ref2: -4=....M..... .......... .......... .......... ..........;
ref1: -4=....M..... .......... .......... .......... ..........}
%-----------
{ref4/5: 451=FVKKIGGIFA FKVKDGPGGK EATWVVDVKN GKGSVLPNSD KKADCTITMA=
ref3: 193=.......... .......... .A........ .K........ ..........;
ref1: 47=.......... .......... .A........ .K........ ..........;
#ref2: 47=.......... .......... .D........ .Q........ ..........}
%-----------
{ref4/5: 501=DSDFLALMTG KMNPQSAFFQ GKLKITGNMG LAMKLQNLQL QPGNAKL=547\;
ref3: 243=D......... .......... .K........ .......... .......=289\;
ref1: 97=D......... .......... .K........ .......... .......=143\;
#ref2: 97=A......... .......... .P........ .......... .......=143\}"

COD

 "<* TITLE:> [PROT= 547 aa (MW= ?) from cDNA= 2571 bp]
<* SOURCES:> [Published & Submitted/Cited_in DBs]
/Note: All sources used in an analysis of the SCPX/SCP2 coding region
follow below, in a short format:
ref1 - 1219 bp-cDNA (Yamamoto R &:1991, gnb:M55421, Dec-06-1993);
ref2 - 1229 bp-cDNA (Yamamoto R:1992, gnb:S52450, Mar-08-1993);
ref3 - 1500 bp-cDNA (He Z &:1991, gnb:M75884, Dec-06-1993);
ref4 - 2572 bp-cDNA (Vesa J &:1994, gnb:M75883, Dec-06-1993);
ref5 - 2571 bp-cDNA (Ohba T &:1994, emb:U11298..313, Aug-24-1994);
gem: - inferred/corrected by the current GEM expert from all above.\
<* FEATURES>
/Note_1: The ref5 & ref4 cDNAs both start within the contig_1 sequence
(see 'Gene-structure') at the same position #contig_1:501(=a); their
translation starts 21 bp downstream at #pos:contig_1:622(=atg).\
/Note_2: The ref3 cDNA starts within exon_9 at #pos:contig_9:47(=a);the
translation starts 79 bp downstream at #pos:contig_9:126(=atg).\
/Note_3: The ref2 & ref1 cDNAs both start within exon_12 at the same
position #contig_12:74(=g); the translation starts 83 bp downstream
at #pos:contig_12:157(=atg).\
%--------------------------------------------
<** ALIGNMENT:>
{/Table_3: Alignment of all SCPX/SCP2 cDNA sequences presented
in the relevant Database entries;
//: numericals presented in columns of this Table are numbers of
the corresponding nucleotide positions in different aligned
versions of the sequence in question; nucleotides themselves
occurring at those positions are only presented in case of a
conflict between the versions (false nucleotides and amino
acids are marked by '*'\
<*** MATCHES>
-----------------------------------------------------------------------
{//: Cap2? Cap3?;
5'-NTC Cap1 (ATG...|......atg....|.......ATG....)TGA;
| | | | | | | |\
GEM_correct: _1:1 _1:501 _1:622 _9:47 _9:126 _12:74 _12:157 _16:119;
ref5^U11298> - 1 22 717 796 1151 1234 1663;
ref4^M75883: - 1 22 717 796 1151 1234 1663;
ref3^M75884: - - - 1 82 437 520 949;
ref2^S52450: - - - - - 1 84 513;
ref1^M55421: - - - - - 1 84 513}
-----------------------------------------------------------------------
{//: 3'-UnTransLated TCT 3'-NTC;
| | |\
GEM_correct: _16:670 _16:826 _16:835 _16:1027 _16:1028 _16:1052\end;
ref5^U11298> 2214 2370 2379 2571\end;
ref4^M75883: 2214 2370 2379 2571 2572\end;
ref3^M75884: 1500\end;
ref2^S52450: 1064 1220 1229\end;
ref1^M55421: 1063 1219\end}
------------------------------------------------------------------------
<*** CONFLICTS_1:> [Coding_segment]
---------------------------------
{GEM_correct: _9:47=agcagcaatt ttggccagtg aagca=_9:71 _9:75=gta;
ref5^U11298> 717=agcagcaatt ttggccagtg aagc--a=741 745=gta;
ref4^M75883: 717=agcagcaatt ttggccagtg aagc--a=741 745=gta;
ref3^M75884: *1=GTcaATaaAA tAtATcagtg aagcCAa=*27 *31=Tta}
%----------
{GEM_correct: _10:82=t _14:102=c _14:131=a _15:59=a _16:41=aa;
ref5^U11298> 993=T 1436=c 1465=a 1523=a 1585=aa;
ref4^M75883: *993=g 1436=c 1465=a 1523=a 1585=aa;
ref3^M75884: *189=g 722=c 751=a 809=a 871=aa;
ref1^M55421: - 286=c 315=a 373=a 435=aa;
ref2^S52450: - *286=A *315=C *373=C *435=CC}
-----------------------------------------------------------------
{/Table_4: Nucleotide and amino acid differences in coding regions
of the SCPX/SCP2 sequences presented in the relevant
Database entries;
//: columns 1 and 2 correspond to the above comparison between the
ref3 and ref5 sequences while columns 3-6 to that between the
ref2 and ref5 ones\
.........................................................
1 2 | 3 4 5 6
-----------------------|-------------------------------------------
242=V/Val 294=L/Leu | 472=A/Ala 482=K/Lys 501=D/Asp 522=K/Lys
1 745=| 993=| | 1436=| 1465=| 1523=| 1585=||
______ gta ____ ctt | ___ gcc _______ aaa _____ gac _______ aaa
Tta ctG | gAc Caa gCc CCa
2 31=* 189=* | 286=* 315=* 373=* 435=**
-17=L/Leu 36=L/Leu | 68=D/Asp 78=Q/Gln 97=A/Ala 118=P/Pro}
--------------------------------------------------------------------
<*** CONFLICTS_2:> [3'-UTL region]
%----------
{GEM_correct: _16:216=c _16:231=atag _16:276=t _16:280=ct;
ref5^U11298> 1760=c 1775=atag 1820=t 1824=ct;
ref4^M75883: *1760=T 1775=atag 1820=t 1824=ct;
ref3^M75884: *1046=T 1061=atag 1106=t 1110=ct;
ref1^M55421: * 610=T 625=atag 670=t 674=ct;
ref2^S52450: 610=c *625=GATA *670=A *674=GC}
%----------
{GEM_correct: _16:299=_ _16:319=g _16:609=t _16:614=a;
ref5^U11298> 1843=_ 1863=g 2153=t 2158=a;
ref4^M75883: 1843=_ 1863=g 2153=t 2158=a;
ref3^M75884: 1129=_ 1149=g 1439=t 1444=a;
ref1^M55421: 693=_ 713=g *1003=A *1008=_;
ref2^S52450: *693=C *714=_ 1003=t 1008=a}}"

REF

 CLO,SEQ,COD,EXP,LOC,MOL "He Z &: DNA Cell Biol, 10, N8, 559-569, 1991
GEN,SEQ,STR "Ohba T &: Genomics, 24, N2 (Nov 15), 370-374, 1994
FUN,MEB,MAM,REV "Reinhart MP: Experientia, 46, 599-611, 1990
PEP,FUN,STR,ENG "Seedorf U &: JBC, 269, N4 (Jan 28), 2613-2618, 1994a
PEP,FUN,STR,ENG "Seedorf U &: JBC, 269, N33 (Aug 19), 21277-21283, 1994b
CLO,SEQ,COD,EXP,MOU "Seedorf U &: Gene, 123, N2 (Jan 30), 165-172, 1993
PEP,SEQ,STR "Szyperski T &: FEBS Lett, 335, N1 (Nov 29), 18-26, 1993
FUN,MEB,EVO "Tan H &: Eur J Biochem, 190, 107-112, 1990
FUN,MEB,MAM,REV "Vahouny GV &: Adv Lipid Res, 22, 83-113, 1987
FUN,MEB,MAM,REV "Van Heusden GP &: BBA, 1046, 315-321, 1990
LOC,CYG,MOL,PRO "Vesa J &: Hum Mol Genet, 3, N2, 341-346, 1994
FUN,MEB,MAM,REV "Wirtz KWA: Annu Rev Biochem, 60, 73-99, 1991
FUN,MEB,MAM,REV "Wirtz KWA, Gadella TWJ: Experientia, 46, 592-599, 1990
CLO,SEQ,COD,EXP "Yamamoto R &: Hokkaido Igaku Zasshi, 67, N6, 839-848, 1992
CLO,SEQ,COD,EXP,LOC,MOL "Yamamoto R &: PNAS, 88, N2, 463-467, 1991a
LOC,CYG,MOL,PRO "Yamamoto R &: CCG, 58 (HGM11), N1-4, 1866-1867, 1991b

KEY

 lip, ats, ster, trp

CLA

 coding, basic

LOC

 01 p32

MIM

 MIM: 184755

EZN

 ENZYME: 2.3.1.16?