COL28A1 (collagen type XXVIII alpha 1 chain) - Rat Genome Database

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Gene: COL28A1 (collagen type XXVIII alpha 1 chain) Chlorocebus sabaeus
Analyze
Symbol: COL28A1
Name: collagen type XXVIII alpha 1 chain
RGD ID: 18560764
Description: ENCODES a protein that exhibits extracellular matrix structural constituent conferring tensile strength (inferred); serine-type endopeptidase inhibitor activity (inferred); INVOLVED IN cell adhesion (inferred); extracellular matrix organization (inferred); ASSOCIATED WITH amphetamine abuse (ortholog); FOUND IN basement membrane (inferred); collagen trimer (inferred); collagen-containing extracellular matrix (inferred)
Type: protein-coding
RefSeq Status: MODEL
Previously known as: collagen alpha-1(XXVIII) chain
RGD Orthologs
Human
Mouse
Rat
Chinchilla
Bonobo
Dog
Squirrel
Pig
Naked Mole-Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: ChlSab1.1 - Green Monkey 1.1 Assembly
Position:
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.12150,667,287 - 50,844,773 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl2150,671,247 - 50,843,083 (+)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366604253,554,465 - 53,718,863 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component

Molecular Function

References

Genomics

Comparative Map Data
COL28A1
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.12150,667,287 - 50,844,773 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl2150,671,247 - 50,843,083 (+)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366604253,554,465 - 53,718,863 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
COL28A1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh3877,338,194 - 7,543,870 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl77,356,203 - 7,535,873 (-)EnsemblGRCh38hg38GRCh38
GRCh3777,397,506 - 7,575,504 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 3677,364,769 - 7,541,985 (-)NCBINCBI36Build 36hg18NCBI36
Celera77,367,965 - 7,545,230 (-)NCBICelera
Cytogenetic Map7p21.3NCBI
HuRef77,246,816 - 7,425,461 (-)NCBIHuRef
CHM1_177,398,239 - 7,575,464 (-)NCBICHM1_1
T2T-CHM13v2.077,477,054 - 7,655,035 (-)NCBIT2T-CHM13v2.0
CRA_TCAGchr7v277,445,378 - 7,622,650 (-)NCBI
Col28a1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm3967,997,100 - 8,193,709 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl67,997,808 - 8,192,617 (-)EnsemblGRCm39 Ensembl
GRCm3867,997,100 - 8,193,709 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl67,997,808 - 8,192,617 (-)EnsemblGRCm38mm10GRCm38
MGSCv3767,947,808 - 8,142,617 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv3667,947,808 - 8,142,617 (-)NCBIMGSCv36mm8
Celera68,140,497 - 8,334,541 (-)NCBICelera
Cytogenetic Map6A1NCBI
cM Map63.44NCBI
Col28a1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8437,036,303 - 37,189,435 (-)NCBIGRCr8
mRatBN7.2436,069,980 - 36,223,128 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl436,069,970 - 36,223,220 (-)EnsemblmRatBN7.2 Ensembl
Rnor_6.0434,048,074 - 34,198,558 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl434,048,533 - 34,194,764 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0433,904,586 - 34,058,707 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4433,043,706 - 33,216,862 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera431,574,414 - 31,727,219 (-)NCBICelera
Cytogenetic Map4q21NCBI
Col28a1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495543214,462,226 - 14,633,236 (-)EnsemblChiLan1.0
ChiLan1.0NW_00495543214,462,226 - 14,634,396 (-)NCBIChiLan1.0ChiLan1.0
COL28A1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v2612,265,932 - 12,465,411 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan1760,590,644 - 60,790,729 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v078,093,060 - 8,260,276 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.177,446,107 - 7,611,876 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl77,446,107 - 7,611,876 (-)Ensemblpanpan1.1panPan2
COL28A1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.11422,991,469 - 23,153,333 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl1422,993,286 - 23,153,305 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha1422,566,580 - 22,728,366 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.01422,805,409 - 22,967,559 (-)NCBIROS_Cfam_1.0
UMICH_Zoey_3.11422,958,432 - 23,120,179 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.01422,690,951 - 22,852,986 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.01422,948,432 - 23,110,560 (-)NCBIUU_Cfam_GSD_1.0
Col28a1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440511836,314,965 - 36,475,876 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049365852,390,414 - 2,546,366 (+)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_0049365852,390,383 - 2,547,859 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
COL28A1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl977,666,282 - 77,833,806 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1977,670,890 - 77,841,939 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2985,201,979 - 85,497,584 (-)NCBISscrofa10.2Sscrofa10.2susScr3
Col28a1
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046248134,947,301 - 5,152,632 (-)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_0046248134,945,733 - 5,180,098 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2


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

endocrine system hemolymphoid system nervous system
High
Medium
Low 36 13 38
Below cutoff 4 22

Sequence


Reference Sequences
RefSeq Acc Id: ENSCSAT00000011145   ⟹   ENSCSAP00000009227
Type: CODING
Position:
Green Monkey AssemblyChrPosition (strand)Source
ChlSab1.1 Ensembl2150,671,247 - 50,843,083 (+)Ensembl
RefSeq Acc Id: XM_038004365   ⟹   XP_037860293
Type: CODING
Position:
Green Monkey AssemblyChrPosition (strand)Source
Vero_WHO_p1.0NW_02366604253,554,465 - 53,718,863 (-)NCBI
Protein Sequences
Protein RefSeqs XP_037860293 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSCSAP00000009227.1
Reference Protein Sequences
RefSeq Acc Id: ENSCSAP00000009227   ⟸   ENSCSAT00000011145
RefSeq Acc Id: XP_037860293   ⟸   XM_038004365
- UniProtKB: A0A0D9RKT8 (UniProtKB/TrEMBL)


Additional Information

Database Acc Id Source(s)
Ensembl Genes ENSCSAG00000013070 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSCSAT00000011145.1 UniProtKB/TrEMBL
Gene3D-CATH 3.40.50.410 UniProtKB/TrEMBL
  4.10.410.10 UniProtKB/TrEMBL
InterPro Collagen UniProtKB/TrEMBL
  Kunitz_BPTI UniProtKB/TrEMBL
  Kunitz_BPTI_sf UniProtKB/TrEMBL
  Prtase_inh_Kunz-CS UniProtKB/TrEMBL
  VWF_A UniProtKB/TrEMBL
  vWFA_dom_sf UniProtKB/TrEMBL
KEGG Report csab:103226501 UniProtKB/TrEMBL
NCBI Gene COL28A1 ENTREZGENE
PANTHER COLLAGEN ALPHA UniProtKB/TrEMBL
  COLLAGEN ALPHA-1(XXVIII) CHAIN UniProtKB/TrEMBL
Pfam Collagen UniProtKB/TrEMBL
  Kunitz_BPTI UniProtKB/TrEMBL
  VWA UniProtKB/TrEMBL
PRINTS VWFADOMAIN UniProtKB/TrEMBL
PROSITE BPTI_KUNITZ_1 UniProtKB/TrEMBL
  BPTI_KUNITZ_2 UniProtKB/TrEMBL
  VWFA UniProtKB/TrEMBL
SMART SM00131 UniProtKB/TrEMBL
  VWA UniProtKB/TrEMBL
Superfamily-SCOP SSF53300 UniProtKB/TrEMBL
  SSF57362 UniProtKB/TrEMBL
UniProt A0A0D9RKT8 ENTREZGENE, UniProtKB/TrEMBL