SpermatogenesisOnline 1.0

Tag Content
SG ID
SG00004652 
UniProt Accession
Theoretical PI
5.92  
Molecular Weight
110334 Da  
Genbank Nucleotide ID
Genbank Protein ID
Gene Name
Col6a2 
Gene Synonyms/Alias
 
Protein Name
Collagen alpha-2(VI) chain 
Protein Synonyms/Alias
Flags: Precursor 
Organism
Mus musculus (Mouse) 
NCBI Taxonomy ID
10090 
Chromosome Location
chr:10;76058507-76086375;-1
View in Ensembl genome browser  
Function in Stage
Uncertain 
Function in Cell Type
Uncertain 
Probability (GAS) of Function in Spermatogenesis
0.142457117 
The probability was calculated by GAS algorithm, ranging from 0 to 1. The closer it is to 1, the more possibly it functions in spermatogenesis.
Description
Temporarily unavailable 
Abstract of related literatures
1. The National Institutes of Health's Mammalian Gene Collection (MGC) project was designed to generate and sequence a publicly accessible cDNA resource containing a complete open reading frame (ORF) for every human and mouse gene. The project initially used a random strategy to select clones from a large number of cDNA libraries from diverse tissues. Candidate clones were chosen based on 5'-EST sequences, and then fully sequenced to high accuracy and analyzed by algorithms developed for this project. Currently, more than 11,000 human and 10,000 mouse genes are represented in MGC by at least one clone with a full ORF. The random selection approach is now reaching a saturation point, and a transition to protocols targeted at the missing transcripts is now required to complete the mouse and human collections. Comparison of the sequence of the MGC clones to reference genome sequences reveals that most cDNA clones are of very high sequence quality, although it is likely that some cDNAs may carry missense variants as a consequence of experimental artifact, such as PCR, cloning, or reverse transcriptase errors. Recently, a rat cDNA component was added to the project, and ongoing frog (Xenopus) and zebrafish (Danio) cDNA projects were expanded to take advantage of the high-throughput MGC pipeline. PMID: [15489334] 

2. This study describes comprehensive polling of transcription start and termination sites and analysis of previously unidentified full-length complementary DNAs derived from the mouse genome. We identify the 5' and 3' boundaries of 181,047 transcripts with extensive variation in transcripts arising from alternative promoter usage, splicing, and polyadenylation. There are 16,247 new mouse protein-coding transcripts, including 5154 encoding previously unidentified proteins. Genomic mapping of the transcriptome reveals transcriptional forests, with overlapping transcription on both strands, separated by deserts in which few transcripts are observed. The data provide a comprehensive platform for the comparative analysis of mammalian transcriptional regulation in differentiation and development. PMID: [16141072] 

3. We have previously described the molecular cloning of a cDNA probe which detects a 6 kb mRNA termed pOb24. pOb24 mRNA appeared to be a marker of the preadipose state both in vitro and in vivo. A pOb24 genomic fragment was isolated and used to screen cDNA libraries in order to isolate the full-length pOb24 cDNA and to identify the corresponding protein. The screening yielded a new cDNA clone which detected a 3.7 kb mRNA species in addition to the 6 kb mRNA species. Sequences at the 3' end of the 6 kb and 3.7 kb mRNAs indicate that both mRNAs are generated from the same gene through the use of two different polyadenylation sites. The protein encoded by the 3.7 kb mRNA appeared to be homologous to the human alpha 2 chain of type VI collagen (A2COL6). The expression of the A2COL6 gene was not confined to adipose tissue; mRNA species can be detected in ovaries, adrenal glands and lungs but not in liver and skeletal muscle. The expression appeared specific for initial phase(s) of cell differentiation since it is parallel to that of the MyoD1 gene during muscle embryogenesis in vivo. In the myogenic C2C12 cell line, the A2COL6 gene exhibited the same regulation as MyoD1 and myogenin genes. These results indicate that A2COL6 gene expression is a marker of the preadipose state, but may also be a marker of other differentiation programmes such as that of muscle. PMID: [8380980] 

4. Type VI collagen cDNAs of human and avian origin were recently obtained and characterized by screening cDNA libraries in lambda phage. Based on the published sequences of these cDNAs, we constructed partially degenerate oligonucleotide primers that we used in polymerase chain reactions for the generation of alpha 2(VI) collagen clones of murine origin. As template, we used cDNA derived from murine total RNA. We amplified, cloned and sequenced a 1043-bp fragment that contains the coding sequence for the entire triple-helical domain except for the first two amino acids that are Gly-Pro in both man and chicken. Comparison of the nucleotide and derived amino acid sequences revealed 84.6% and 92.5% identity between mouse and man at the DNA and protein levels, respectively. Comparison with chicken sequences showed 72% and 79.1% identity. The third base usage showed a distinct preference for A in the glycine codons for the three species; whereas, U is preferred in all human fibrillar collagen genes previously defined. The preference for third base codon in Y position prolines is U for the alpha 2(VI) collagen as it is for the human fibrillar collagen genes. A single cysteine at position 89, two Arg-Gly-Asp sequences, and one triple helix-interruption are conserved in mouse, man and chicken. Comparison of hydropathy plots showed great similarity between those of murine and human alpha 2(VI) collagen chains and to a lesser extent between murine and chick. Northern blot hybridization of murine poly A+ RNA with a nick-translated radiolabeled alpha 2(VI) collagen probe detected one major transcript of 3.7 kb.(ABSTRACT TRUNCATED AT 250 WORDS) PMID: [1709252] 

5. cDNA clones encoding the alpha 1, alpha 2 and alpha 3 chains of mouse collagen VI have been isolated by screening cDNA libraries with the corresponding human probes. The composite cDNAs for the alpha 1, alpha 2, and alpha 3 chains are 2.5, 1.6 and 2.9 kb in size respectively. The alpha 1 and alpha 2 cDNAs encode the C-terminal portions of the chains as well as the entire 3'-untranslated regions, while the alpha 3 cDNAs encode a central segment of 959 amino acids flanking the triple-helical domain. The deduced amino acid sequences share 86-88% identity with the human counterparts and 67-73% identity with the chicken equivalents. Alignment of the deduced amino acid sequences of mouse, human and chicken collagens reveal that the key features of the protein, including the cysteine residues, imperfections in the Gly-Xaa-Xaa regions, Arg-Gly-Asp sequences and potential N-glycosylation sites, are mostly conserved. PMID: [8489506] 

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Function
Collagen VI acts as a cell-binding protein. 
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Subcellular Location
Secreted, extracellular space, extracellularmatrix (By similarity). Membrane; Peripheral membrane protein (Bysimilarity). Note=Recruited on membranes by CSPG4 (By similarity). 
Tissue Specificity
Highly expressed in adipose tissue, lung,adrenal glands and ovary. Lower levels in testis, tongue, skin,kidney, heart, intestine and spleen. No expression in skeletalmuscle or liver. 
Gene Ontology
GO IDGO termEvidence
GO:0005581 C:collagen IEA:UniProtKB-KW.
GO:0031012 C:extracellular matrix IDA:MGI.
GO:0005576 C:extracellular region ISO:MGI.
GO:0043234 C:protein complex ISO:MGI.
GO:0042383 C:sarcolemma IDA:MGI.
GO:0007155 P:cell adhesion IEA:UniProtKB-KW.
GO:0070208 P:protein heterotrimerization ISO:MGI.
GO:0009749 P:response to glucose stimulus IEA:Compara.
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Interpro
IPR008160;    Collagen.
IPR002035;    VWF_A.
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Pfam
PF01391;    Collagen;    5.
PF00092;    VWA;    3.
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SMART
SM00327;    VWA;    3.
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PROSITE
PS50234;    VWFA;    3.
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PRINTS
Created Date
18-Oct-2012 
Record Type
GAS predicted 
Sequence Annotation
SIGNAL        1     25       Potential.
CHAIN        26   1034       Collagen alpha-2(VI) chain.
                             /FTId=PRO_0000005833.
DOMAIN       61    249       VWFA 1.
DOMAIN      630    820       VWFA 2.
DOMAIN      848   1029       VWFA 3.
REGION       26    270       Nonhelical region.
REGION      271    605       Triple-helical region.
REGION      606   1034       Nonhelical region.
MOTIF       381    383       Cell attachment site (Potential).
MOTIF       441    443       Cell attachment site (Potential).
MOTIF       504    506       Cell attachment site (Potential).
MOTIF       513    515       Cell attachment site (Potential).
MOTIF       554    556       Cell attachment site (Potential).
MOD_RES     612    612       Phosphotyrosine (By similarity).
MOD_RES     680    680       Phosphotyrosine (By similarity).
CARBOHYD    155    155       N-linked (GlcNAc...) (Potential).
CARBOHYD    342    342       N-linked (GlcNAc...) (Potential).
CARBOHYD    645    645       N-linked (GlcNAc...) (Potential).
CARBOHYD    800    800       N-linked (GlcNAc...) (Potential).
CARBOHYD    912    912       N-linked (GlcNAc...) (Potential).
CONFLICT     12     12       S -> P (in Ref. 1; CAA46541).
CONFLICT    205    205       V -> L (in Ref. 1; CAA46541).
CONFLICT    273    273       H -> S (in Ref. 5; AAA37441).
CONFLICT    809    809       A -> S (in Ref. 6; CAA79153).
CONFLICT    853    853       L -> Q (in Ref. 1; CAA46541 and 4;
                             CAA44206).
CONFLICT    967    971       TGNDS -> GNDSL (in Ref. 1; CAA46541 and
                             4; CAA44206).
CONFLICT    981    982       KQ -> TR (in Ref. 1; CAA46541 and 4;
                             CAA44206).
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Nucleotide Sequence
Length: 3571 bp   Go to nucleotide: FASTA
Protein Sequence
Length: 1034 bp   Go to amino acid: FASTA
The verified Protein-Protein interaction information
UniProt
 Gene Symbol Ref Databases
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