SpermatogenesisOnline 1.0

Tag Content
SG ID
SG00006019 
UniProt Accession
Theoretical PI
6.1  
Molecular Weight
141973 Da  
Genbank Nucleotide ID
Genbank Protein ID
Gene Name
Col2a1 
Gene Synonyms/Alias
 
Protein Name
Collagen alpha-1(II) chain Collagen alpha-1(II) chain Chondrocalcin 
Protein Synonyms/Alias
Alpha-1 type II collagen;Contains:Contains:Flags: Precursor 
Organism
Mus musculus (Mouse) 
NCBI Taxonomy ID
10090 
Chromosome Location
chr:15;97806033-97835155;-1
View in Ensembl genome browser  
Function in Stage
Uncertain 
Function in Cell Type
Uncertain 
Probability (GAS) of Function in Spermatogenesis
0.117971819 
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. Several overlapping clones covering the entire mouse type II collagen gene including 10 kilobases (kb) of 5'- and 15 kb of 3'-flanking sequences were isolated from a cosmid library. The overall gene structure was determined by restriction mapping and sequencing. The gene spans 28.9 kb from the start of transcription to the polyadenylation site and contains 54 exons. It codes for a major mRNA species of 4910 bases which translates into a polypeptide of 1419 amino acids. A less abundant RNA species of 5110 bases contains additional sequences corresponding to an alternatively spliced exon 2. Except for the amino-terminal propeptide (N-propeptide) domain the exon-intron organization of the mouse pro alpha 1(II) collagen gene is remarkably similar to genes for other fibrillar collagen types. The overall identity of the coding sequences of the mouse and human type II collagen genes is 89% at the nucleotide level, but only 37 amino acid changes occur within the mature alpha 1(II) collagen chains between mouse and man. Intron sizes are also conserved between the mouse and human genes but not with the chick alpha 1(II) gene. The promoter of the mouse type II collagen gene is similar to those of the rat and human genes containing a TATA box and several G + C-rich elements but no CCAAT box. The 3'-untranslated sequence contains two regions of high homology between chick, mouse, bovine, and human genes preceding the major polyadenylation site. Additional size variation in the mRNA arises from the use of a minor polyadenylation signal. Information on conserved noncoding sequences will help in studies on the regulation of the pro alpha 1(II) collagen gene. Detailed knowledge of the gene is also necessary for site-directed mutagenesis and work with transgenic mice. PMID: [1885613] 

2. 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] 

3. The mouse alpha 1(II) collagen gene has been isolated and a 5' portion of the gene which has low homology to other collagen genes was used to study the pattern of expression during mouse embryogenesis. In situ hybridization studies show that in the mouse, like the chick, alpha 1(II) collagen is expressed in chondrogenic tissues in advance of chondrocyte differentiation. The gene is expressed early in embryogenesis at 9.5 days both in the cranial mesenchyme destined for the chondrocranium, and the sclerotome of the somites, and at 12.5 days in the primordia of the hyoid and the laryngeal cartilage. Type II collagen gene transcripts were found in all the chondrogenic tissues of the axial and appendicular skeleton until the onset of endochondral ossification. Expression of alpha 1(II) collagen mRNA was also observed in non-chondrogenic tissues such as the notochord which may be responsible for inducing chondrogenesis in somitic mesoderm, neural retina, the corneal and conjunctival epithelia and sclera of the developing eye. Expression in the tail tendon was late, at 16.5-18.5 days. Transient expression was also found in the heart at 9.5-12.5 days, the epidermis at 10.5-14.5 days, the calvarial mesenchyme at 12.5-16.5 days, the inner ear at 14.5 days and the fetal brain from 9.5-14.5 days. Within the neural tube, alpha 1(II) collagen mRNA was localized in the proliferative ventricular cells of the forebrain and midbrain of 9.5- to 10.5-day embryos. Subsequently, transcription of the alpha 1(II) collagen gene was confined to restricted areas of the rhombencephalic basal plate, the ventricular layer of the hindbrain and the cervical spinal cord. These examples of expression of the type II collagen gene in the developing nervous system seem to suggest that active transcription of this gene might be associated with early stages of neuroblast differentiation. Type II collagen may therefore have additional roles in development unrelated to chondrogenesis. PMID: [1879363] 

4. Type II collagen is the major extracellular matrix component of cartilage and correct expression of the alpha 1(II) collagen gene is important for vertebrate skeletal development. In order to provide the basis for studying the control of type II collagen gene expression in embryogenesis and in mouse models of human connective tissue disease, the complete mouse Col2-a1 gene has been isolated in a single cosmid clone, cosMco1.2, and partially characterized. The gene is approximately 30 kb and is highly conserved in exon/intron structure and nucleotide and amino acid sequence (greater than 80% homology) when compared with the human, rat, bovine and chicken equivalents. A high degree of conservation was also found in the 5' flanking region of the rat, human and mouse alpha 1(II) collagen genes, including the presence of several G + C and C + T rich, direct repeat motifs. The sites of transcription start, termination codon and polyadenylation have also been identified. Unlike chicken, bovine and human, where polyA attachment is at a single site, for the mouse Col2a-1 gene two polyadenylation sites are utilized. Col2a-1 has also been localized by interspecies backcross analysis to the central portion of mouse Chromosome (Chr) 15, approximately 8 centiMorgans (cM) proximal of Int-1 and 18 cM distal of Myc. Col2a-1 is therefore included in a linkage group which is conserved on human Chr 12q. PMID: [1797232] 

5. 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] 

6. We have constructed DNA probes for the specific detection of mouse pro alpha 1(I), pro alpha 1(II), pro alpha 1(III) and alpha 1(IX) collagen transcripts. To avoid cross-hybridization the probes for fibrillar collagens cover mainly sequences in the 3' untranslated region of the gene. Sequencing and Northern analysis confirmed that the clones share minimal sequence similarity and detect only the specific mRNAs under normal hybridization and washing conditions. The clone for mouse alpha 1(IX) collagen covers coding sequences but is sufficiently divergent from other collagen transcripts to allow specific detection of the corresponding mRNA. PMID: [2054384] 

7. A missense mutation in the mouse Col2a1 gene has been discovered, resulting in a mouse phenotype with similarities to human spondyloepiphyseal dysplasia (SED) congenita. In addition, SED patients have been identified with a similar molecular mutation in human COL2A1. This mouse model offers a useful tool for molecular and biological studies of bone development and pathology. PMID: [12968670] 

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Function
Type II collagen is specific for cartilaginous tissues.It is essential for the normal embryonic development of theskeleton, for linear growth and for the ability of cartilage toresist compressive forces. 
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Subcellular Location
Secreted, extracellular space, extracellularmatrix (By similarity). 
Tissue Specificity
 
Gene Ontology
GO IDGO termEvidence
GO:0005604 C:basement membrane IDA:MGI.
GO:0005585 C:collagen type II IDA:MGI.
GO:0005737 C:cytoplasm IDA:MGI.
GO:0005615 C:extracellular space IDA:MGI.
GO:0005201 F:extracellular matrix structural constituent IEA:InterPro.
GO:0001502 P:cartilage condensation IMP:MGI.
GO:0060351 P:cartilage development involved in endochondral bone morphogenesis IMP:MGI.
GO:0071773 P:cellular response to BMP stimulus IDA:MGI.
GO:0007417 P:central nervous system development IEP:UniProtKB.
GO:0002062 P:chondrocyte differentiation IEP:UniProtKB.
GO:0030199 P:collagen fibril organization IMP:MGI.
GO:0060272 P:embryonic skeletal joint morphogenesis IEA:Compara.
GO:0001958 P:endochondral ossification IMP:MGI.
GO:0003007 P:heart morphogenesis IMP:MGI.
GO:0042472 P:inner ear morphogenesis IMP:MGI.
GO:0060174 P:limb bud formation IEP:UniProtKB.
GO:0043066 P:negative regulation of apoptotic process IMP:MGI.
GO:0030903 P:notochord development IEP:UniProtKB.
GO:0071599 P:otic vesicle development IEP:UniProtKB.
GO:0060021 P:palate development IMP:MGI.
GO:0006029 P:proteoglycan metabolic process IMP:MGI.
GO:0010468 P:regulation of gene expression IMP:MGI.
GO:0007605 P:sensory perception of sound IEA:Compara.
GO:0001894 P:tissue homeostasis IMP:MGI.
GO:0007601 P:visual perception IEA:Compara.
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Interpro
IPR008160;    Collagen.
IPR000885;    Fib_collagen_C.
IPR001007;    VWF_C.
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Pfam
PF01410;    COLFI;    1.
PF01391;    Collagen;    11.
PF00093;    VWC;    1.
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SMART
SM00038;    COLFI;    1.
SM00214;    VWC;    1.
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PROSITE
PS51461;    NC1_FIB;    1.
PS01208;    VWFC_1;    1.
PS50184;    VWFC_2;    1.
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PRINTS
Created Date
18-Oct-2012 
Record Type
GAS predicted 
Sequence Annotation
SIGNAL        1     25       Potential.
PROPEP       26    181       N-terminal propeptide (By similarity).
                             /FTId=PRO_0000005732.
CHAIN       182   1241       Collagen alpha-1(II) chain.
                             /FTId=PRO_0000005733.
CHAIN      1242   1487       Chondrocalcin.
                             /FTId=PRO_0000005734.
DOMAIN       32     89       VWFC.
DOMAIN     1253   1487       Fibrillar collagen NC1.
REGION      201   1214       Triple-helical region.
REGION     1215   1241       Nonhelical region (C-terminal).
SITE        181    182       Cleavage; by procollagen N-endopeptidase
                             (By similarity).
SITE       1241   1242       Cleavage; by procollagen C-endopeptidase
                             (By similarity).
MOD_RES     190    190       5-hydroxylysine (By similarity).
MOD_RES     287    287       5-hydroxylysine (By similarity).
MOD_RES     299    299       5-hydroxylysine (By similarity).
MOD_RES     308    308       5-hydroxylysine (By similarity).
MOD_RES     374    374       5-hydroxylysine (By similarity).
MOD_RES     608    608       5-hydroxylysine (By similarity).
MOD_RES     620    620       5-hydroxylysine (By similarity).
MOD_RES     670    670       3-hydroxyproline (By similarity).
MOD_RES     907    907       3-hydroxyproline (By similarity).
MOD_RES    1144   1144       3-hydroxyproline (By similarity).
MOD_RES    1186   1186       3-hydroxyproline (By similarity).
MOD_RES    1201   1201       3-hydroxyproline (By similarity).
MOD_RES    1207   1207       3-hydroxyproline (By similarity).
MOD_RES    1213   1213       3-hydroxyproline (By similarity).
CARBOHYD    190    190       O-linked (Gal...) (By similarity).
CARBOHYD    287    287       O-linked (Gal...) (By similarity).
CARBOHYD    299    299       O-linked (Gal...) (By similarity).
CARBOHYD    308    308       O-linked (Gal...) (By similarity).
CARBOHYD    374    374       O-linked (Gal...) (By similarity).
CARBOHYD    608    608       O-linked (Gal...) (By similarity).
CARBOHYD    620    620       O-linked (Gal...) (By similarity).
VAR_SEQ      29     97       QEAGSCLQNGQRYKDKDVWKPSSCRICVCDTGNVLCDDIIC
                             EDPDCLNPEIPFGECCPICPADLATASG -> R (in
                             isoform 3 and isoform 7).
                             /FTId=VSP_022780.
VAR_SEQ     103    113       Missing (in isoform 4 and isoform 6).
                             /FTId=VSP_022781.
VAR_SEQ     114    142       Missing (in isoform 2 and isoform 3).
                             /FTId=VSP_022782.
VAR_SEQ     114    124       Missing (in isoform 5).
                             /FTId=VSP_022783.
VAR_SEQ     125    142       Missing (in isoform 4).
                             /FTId=VSP_022784.
VAR_SEQ     143    177       Missing (in isoform 5 and isoform 6).
                             /FTId=VSP_022785.
VARIANT     989    989       R -> C (in sedc mice).
CONFLICT     97     97       G -> GR (in Ref. 1; AAA68100/AAA68101/
                             AAA68099/AAA68102).
CONFLICT    272    272       Q -> M (in Ref. 1; AAA68100/AAA68101/
                             AAA68099/AAA68102).
CONFLICT    539    539       T -> A (in Ref. 1; AAA68100/AAA68101/
                             AAA68099/AAA68102).
CONFLICT    806    806       V -> A (in Ref. 1; AAA68100/AAA68101/
                             AAA68099/AAA68102).
CONFLICT    824    824       R -> P (in Ref. 1; AAA68100/AAA68101/
                             AAA68099).
CONFLICT    947    947       Q -> E (in Ref. 1; AAA68100/AAA68101/
                             AAA68099/AAA68102).
CONFLICT   1119   1119       G -> R (in Ref. 2; AAH51383).
CONFLICT   1141   1145       LPGPP -> SAWPS (in Ref. 4; AAC06113).
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Nucleotide Sequence
Length: 32492 bp   Go to nucleotide: FASTA
Protein Sequence
Length: 1487 bp   Go to amino acid: FASTA
The verified Protein-Protein interaction information
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