Col4a2 (collagen type IV alpha 2 chain) - Rat Genome Database

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Gene: Col4a2 (collagen type IV alpha 2 chain) Chinchilla lanigera
Analyze
Symbol: Col4a2
Name: collagen type IV alpha 2 chain
RGD ID: 8982471
Description: INVOLVED IN aging (ortholog); cellular response to transforming growth factor beta stimulus (ortholog); collagen-activated tyrosine kinase receptor signaling pathway (ortholog); ASSOCIATED WITH Anal Atresia, Hypospadias, and Penoscrotal Inversion (ortholog); atherosclerosis (ortholog); brain small vessel disease 1 (ortholog); FOUND IN basement membrane; collagen type IV trimer (ortholog)
Type: protein-coding
RefSeq Status: MODEL
Previously known as: collagen alpha-2(IV) chain; collagen, type IV, alpha 2
RGD Orthologs
Human
Mouse
Rat
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: ChiLan1.0 - Chinchilla ChiLan1.0 Assembly
NCBI Annotation Information: Annotation category: partial on reference assembly
Position:
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554042,092,184 - 2,178,079 (-)EnsemblChiLan1.0
ChiLan1.0NW_0049554042,092,184 - 2,178,079 (-)NCBIChiLan1.0ChiLan1.0
JBrowse: View Region in Genome Browser (JBrowse)
Model


References

References - curated
# Reference Title Reference Citation
1. Transitive Annotation Pipeline Automated assignment of GO, PW and RDO ISS annotations to Chinchilla, Squirrel, Bonobo and/or Dog genes from Human gene annotations
2. OMIM Disease Annotation Pipeline OMIM Disease Annotation Pipeline
3. Proteoglycan arrays in the cochlear basement membrane. Tsuprun V and Santi P, Hear Res. 2001 Jul;157(1-2):65-76.

Genomics

Comparative Map Data
Col4a2
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554042,092,184 - 2,178,079 (-)EnsemblChiLan1.0
ChiLan1.0NW_0049554042,092,184 - 2,178,079 (-)NCBIChiLan1.0ChiLan1.0
COL4A2
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh3813110,307,284 - 110,513,209 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p13 Ensembl13110,305,812 - 110,513,209 (+)EnsemblGRCh38hg38GRCh38
GRCh3713110,959,631 - 111,165,556 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 3613109,757,632 - 109,963,375 (+)NCBINCBI36hg18NCBI36
Build 3413109,757,631 - 109,963,372NCBI
Celera1391,803,804 - 92,011,436 (+)NCBI
Cytogenetic Map13q34NCBI
HuRef1391,559,092 - 91,764,904 (+)NCBIHuRef
CHM1_113110,928,062 - 111,133,226 (+)NCBICHM1_1
T2T-CHM13v2.013109,536,748 - 109,743,647 (+)NCBI
Col4a2
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39811,362,805 - 11,499,287 (+)NCBIGRCm39mm39
GRCm39 Ensembl811,362,805 - 11,499,287 (+)Ensembl
GRCm38811,312,805 - 11,449,287 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl811,312,805 - 11,449,287 (+)EnsemblGRCm38mm10GRCm38
MGSCv37811,312,829 - 11,449,287 (+)NCBIGRCm37mm9NCBIm37
MGSCv36811,312,996 - 11,449,187 (+)NCBImm8
Celera811,487,441 - 11,623,992 (+)NCBICelera
Cytogenetic Map8A1.1NCBI
cM Map85.62NCBI
Col4a2
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21678,047,591 - 78,183,360 (-)NCBImRatBN7.2
mRatBN7.2 Ensembl1678,047,602 - 78,183,839 (-)Ensembl
Rnor_6.01683,386,388 - 83,522,169 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1683,387,364 - 83,438,561 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01682,852,230 - 82,987,790 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41682,899,206 - 83,045,102 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11682,871,435 - 83,006,872 (-)NCBI
Celera1675,846,004 - 75,981,238 (-)NCBICelera
Cytogenetic Map16q12.5NCBI
COL4A2
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.113110,562,681 - 110,768,362 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl13110,563,119 - 110,767,530 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v01391,440,314 - 91,650,138 (+)NCBIMhudiblu_PPA_v0panPan3
COL4A2
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.12258,656,579 - 58,820,560 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl2258,697,175 - 58,773,297 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha2258,360,350 - 58,530,121 (+)NCBI
ROS_Cfam_1.02259,273,416 - 59,443,367 (+)NCBI
ROS_Cfam_1.0 Ensembl2259,273,522 - 59,443,348 (+)Ensembl
UMICH_Zoey_3.12258,775,158 - 58,944,081 (+)NCBI
UNSW_CanFamBas_1.02258,766,023 - 58,936,137 (+)NCBI
UU_Cfam_GSD_1.02258,801,350 - 58,971,538 (+)NCBI
Col4a2
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024404945193,535,946 - 193,681,319 (+)NCBI
SpeTri2.0NW_0049364722,270,836 - 2,416,324 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
COL4A2
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1176,997,516 - 77,161,614 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11176,996,885 - 77,161,617 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21184,613,792 - 84,675,826 (+)NCBISscrofa10.2Sscrofa10.2susScr3
COL4A2
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1388,564,328 - 88,760,191 (+)NCBIChlSab1.1chlSab2
ChlSab1.1 Ensembl388,563,903 - 88,760,411 (+)EnsemblChlSab1.1chlSab2
Vero_WHO_p1.0NW_02366604645,280,036 - 45,477,365 (+)NCBIVero_WHO_p1.0
Col4a2
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046247932,202,244 - 2,324,507 (-)EnsemblHetGla_female_1.0hetGla2
HetGla 1.0NW_0046247932,201,815 - 2,325,002 (-)NCBIHetGla_female_1.0hetGla2


Expression


Sequence


Reference Sequences
RefSeq Acc Id: ENSCLAT00000003771   ⟹   ENSCLAP00000003695
RefSeq Status:
Type: CODING
Position:
Chinchilla AssemblyChrPosition (strand)Source
ChiLan1.0 EnsemblNW_0049554042,092,184 - 2,178,079 (-)Ensembl
RefSeq Acc Id: XM_013516801   ⟹   XP_013372255
RefSeq Status:
Type: CODING
Position:
Chinchilla AssemblyChrPosition (strand)Source
ChiLan1.0NW_0049554042,092,184 - 2,178,079 (-)NCBI
Sequence:
Protein Sequences
Protein RefSeqs XP_013372255 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: XP_013372255   ⟸   XM_013516801
- Sequence:
RefSeq Acc Id: ENSCLAP00000003695   ⟸   ENSCLAT00000003771
Protein Domains
Collagen IV NC1


Additional Information

Database Acc Id Source(s)
Ensembl Genes ENSCLAG00000002637 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSCLAP00000003695 ENTREZGENE
  ENSCLAP00000003695.1 UniProtKB/TrEMBL
Ensembl Transcript ENSCLAT00000003771 ENTREZGENE
  ENSCLAT00000003771.1 UniProtKB/TrEMBL
Gene3D-CATH 2.170.240.10 UniProtKB/TrEMBL
InterPro Collagen UniProtKB/TrEMBL
  Collagen_IV_NC UniProtKB/TrEMBL
  Collagen_IV_NC_sf UniProtKB/TrEMBL
  CTDL_fold UniProtKB/TrEMBL
NCBI Gene Col4a2 ENTREZGENE
Pfam Collagen UniProtKB/TrEMBL
  PF01413 UniProtKB/TrEMBL
PROSITE NC1_IV UniProtKB/TrEMBL
SMART SM00111 UniProtKB/TrEMBL
Superfamily-SCOP SSF56436 UniProtKB/TrEMBL
UniProt A0A8C2YJQ6_CHILA UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2016-08-03 Col4a2  collagen type IV alpha 2 chain    collagen, type IV, alpha 2  Symbol and/or name change 5135510 APPROVED