LOC100623720 (collagen alpha-1(VI) chain) - Rat Genome Database
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Gene: LOC100623720 (collagen alpha-1(VI) chain) Sus scrofa
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Symbol: LOC100623720
Name: collagen alpha-1(VI) chain
RGD ID: 14128523
Description: ENCODES a protein that exhibits collagen binding (inferred); platelet-derived growth factor binding (inferred); INVOLVED IN cellular response to amino acid stimulus (ortholog); PARTICIPATES IN syndecan signaling pathway; ASSOCIATED WITH autistic disorder (ortholog); Axenfeld-Rieger syndrome type 3 (ortholog); Bethlem myopathy (ortholog); FOUND IN extracellular matrix (ortholog); extracellular region (ortholog); sarcolemma (ortholog); INTERACTS WITH 3,3',5,5'-tetrabromobisphenol A; bisphenol A; Tetrachlorobisphenol A
Type: protein-coding
RefSeq Status: MODEL
Also known as: COL6A1; collagen type VI alpha 1 chain; collagen, type VI, alpha 1; type VI collagen alpha-1 chain
RGD Orthologs
Human
Mouse
Rat
Chinchilla
Bonobo
Dog
Squirrel
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: Sscrofa11.1 - Pig Sscrofa11.1 Assembly
Position:
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl13208,295,240 - 208,313,127 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.113208,295,245 - 208,321,789 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component

Molecular Function

Molecular Pathway Annotations     Click to see Annotation Detail View
References

Genomics

Comparative Map Data
LOC100623720
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl13208,295,240 - 208,313,127 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.113208,295,245 - 208,321,789 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
COL6A1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl2145,981,737 - 46,005,050 (+)EnsemblGRCh38hg38GRCh38
GRCh38.p13 Ensembl2145,981,769 - 46,005,050 (+)EnsemblGRCh38hg38GRCh38
GRCh382145,981,770 - 46,005,048 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh372147,401,684 - 47,424,962 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 362146,226,091 - 46,249,391 (+)NCBINCBI36hg18NCBI36
Build 342146,226,095 - 46,249,390NCBI
Celera2132,514,265 - 32,537,566 (+)NCBI
Cytogenetic Map21q22.3NCBI
HuRef2132,782,505 - 32,806,491 (+)NCBIHuRef
CHM1_12146,962,501 - 46,985,646 (+)NCBICHM1_1
Col6a1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391076,544,626 - 76,561,878 (-)NCBIGRCm39mm39
GRCm39 Ensembl1076,544,626 - 76,562,002 (-)Ensembl
GRCm381076,708,792 - 76,726,044 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1076,708,792 - 76,726,168 (-)EnsemblGRCm38mm10GRCm38
MGSCv371076,171,537 - 76,188,789 (-)NCBIGRCm37mm9NCBIm37
MGSCv361076,152,508 - 76,169,760 (-)NCBImm8
Celera1077,753,031 - 77,770,283 (-)NCBICelera
Cytogenetic Map10C1NCBI
cM Map1039.71NCBI
Col6a1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.22011,906,105 - 11,924,599 (+)NCBI
Rnor_6.0 Ensembl2012,658,065 - 12,675,561 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.02012,657,913 - 12,676,370 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.02014,817,411 - 14,835,868 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.42012,320,102 - 12,338,500 (+)NCBIRGSC3.4rn4RGSC3.4
Celera2013,404,454 - 13,422,911 (+)NCBICelera
Cytogenetic Map20p12NCBI
Col6a1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495540742,461,952 - 42,478,261 (+)EnsemblChiLan1.0
ChiLan1.0NW_00495540742,461,837 - 42,479,048 (+)NCBIChiLan1.0ChiLan1.0
COL6A1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.12145,583,978 - 45,608,233 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl2145,584,096 - 45,607,240 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v02132,322,185 - 32,346,850 (+)NCBIMhudiblu_PPA_v0panPan3
COL6A1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1 Ensembl3139,301,748 - 39,448,062 (+)EnsemblCanFam3.1canFam3CanFam3.1
CanFam3.13139,301,718 - 39,319,895 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
Col6a1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
SpeTri2.0NW_004936778515,600 - 530,828 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
COL6A1
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1289,608,525 - 89,649,823 (+)NCBI
Col6a1
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462474531,125,136 - 31,140,126 (+)NCBI


Expression


RNA-SEQ Expression
High: > 1000 TPM value   Medium: Between 11 and 1000 TPM
Low: Between 0.5 and 10 TPM   Below Cutoff: < 0.5 TPM

alimentary part of gastrointestinal system circulatory system endocrine system hemolymphoid system musculoskeletal system nervous system renal system reproductive system respiratory system
High
Medium 9 4 5 2 3 1
Low 1 3 23 2
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: ENSSSCT00000024347   ⟹   ENSSSCP00000026963
RefSeq Status:
Type: CODING
Position:
Pig AssemblyChrPosition (strand)Source
Sscrofa11.1 Ensembl13208,295,467 - 208,313,127 (+)Ensembl
RefSeq Acc Id: ENSSSCT00000039559   ⟹   ENSSSCP00000051801
RefSeq Status:
Type: CODING
Position:
Pig AssemblyChrPosition (strand)Source
Sscrofa11.1 Ensembl13208,295,479 - 208,313,127 (+)Ensembl
RefSeq Acc Id: ENSSSCT00000073546   ⟹   ENSSSCP00000066198
RefSeq Status:
Type: CODING
Position:
Pig AssemblyChrPosition (strand)Source
Sscrofa11.1 Ensembl13208,295,240 - 208,312,440 (+)Ensembl
RefSeq Acc Id: ENSSSCT00000083024   ⟹   ENSSSCP00000060149
RefSeq Status:
Type: CODING
Position:
Pig AssemblyChrPosition (strand)Source
Sscrofa11.1 Ensembl13208,295,240 - 208,312,440 (+)Ensembl
RefSeq Acc Id: XM_021071094   ⟹   XP_020926753
RefSeq Status:
Type: CODING
Position:
Pig AssemblyChrPosition (strand)Source
Sscrofa11.113208,295,245 - 208,313,132 (+)NCBI
Sequence:
RefSeq Acc Id: XM_021071095   ⟹   XP_020926754
RefSeq Status:
Type: CODING
Position:
Pig AssemblyChrPosition (strand)Source
Sscrofa11.113208,295,432 - 208,313,132 (+)NCBI
Sequence:
RefSeq Acc Id: XM_021071096   ⟹   XP_020926755
RefSeq Status:
Type: CODING
Position:
Pig AssemblyChrPosition (strand)Source
Sscrofa11.113208,295,432 - 208,321,789 (+)NCBI
Sequence:
Protein Sequences
Protein RefSeqs XP_020926753 (Get FASTA)   NCBI Sequence Viewer  
  XP_020926754 (Get FASTA)   NCBI Sequence Viewer  
  XP_020926755 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein BAE93248 (Get FASTA)   NCBI Sequence Viewer  
  BAE93249 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: XP_020926753   ⟸   XM_021071094
- Sequence:
RefSeq Acc Id: XP_020926755   ⟸   XM_021071096
- Sequence:
RefSeq Acc Id: XP_020926754   ⟸   XM_021071095
- Sequence:
RefSeq Acc Id: ENSSSCP00000051801   ⟸   ENSSSCT00000039559
RefSeq Acc Id: ENSSSCP00000066198   ⟸   ENSSSCT00000073546
RefSeq Acc Id: ENSSSCP00000060149   ⟸   ENSSSCT00000083024
RefSeq Acc Id: ENSSSCP00000026963   ⟸   ENSSSCT00000024347
Protein Domains
VWFA


Additional Information

Database Acc Id Source(s)
Ensembl Genes ENSSSCG00000022506 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
  ENSSSCG00070006690 UniProtKB/TrEMBL
Ensembl Protein ENSSSCP00000026963 UniProtKB/TrEMBL
  ENSSSCP00000051801 UniProtKB/TrEMBL
  ENSSSCP00000060149 UniProtKB/TrEMBL
  ENSSSCP00000066198 ENTREZGENE, UniProtKB/TrEMBL
  ENSSSCP00070010593 UniProtKB/TrEMBL
  ENSSSCP00070010644 UniProtKB/TrEMBL
Ensembl Transcript ENSSSCT00000024347 UniProtKB/TrEMBL
  ENSSSCT00000039559 UniProtKB/TrEMBL
  ENSSSCT00000073546 ENTREZGENE, UniProtKB/TrEMBL
  ENSSSCT00000083024 UniProtKB/TrEMBL
  ENSSSCT00070012872 UniProtKB/TrEMBL
  ENSSSCT00070012927 UniProtKB/TrEMBL
Gene3D-CATH 3.40.50.410 UniProtKB/TrEMBL
InterPro Collagen UniProtKB/TrEMBL
  VWF_A UniProtKB/TrEMBL
  vWFA_dom_sf UniProtKB/TrEMBL
NCBI Gene LOC100623720 ENTREZGENE
Pfam Collagen UniProtKB/TrEMBL
  VWA UniProtKB/TrEMBL
PROSITE VWFA UniProtKB/TrEMBL
SMART VWA UniProtKB/TrEMBL
Superfamily-SCOP SSF53300 UniProtKB/TrEMBL
UniProt A0A287B5M9_PIG UniProtKB/TrEMBL
  A0A4X1T5C8_PIG UniProtKB/TrEMBL
  A0A4X1T5I1_PIG UniProtKB/TrEMBL
  A0A5G2Q7R0_PIG UniProtKB/TrEMBL
  A0A5G2QW87_PIG UniProtKB/TrEMBL
  I3LS72_PIG UniProtKB/TrEMBL