Col28a1 (collagen type XXVIII alpha 1 chain) - Rat Genome Database

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Gene: Col28a1 (collagen type XXVIII alpha 1 chain) Rattus norvegicus
Analyze
Symbol: Col28a1
Name: collagen type XXVIII alpha 1 chain
RGD ID: 1564680
Description: Predicted to be an extracellular matrix structural constituent conferring tensile strength. Predicted to be involved in cell adhesion. Predicted to be located in basement membrane. Predicted to be part of collagen trimer. Predicted to be active in extracellular matrix. Orthologous to human COL28A1 (collagen type XXVIII alpha 1 chain); INTERACTS WITH 17beta-estradiol; 2,3,7,8-tetrachlorodibenzodioxine; atrazine.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: collagen alpha-1(XXVIII) chain; collagen, type XXVIII, alpha 1; LOC312115; RGD1564680; similar to matrilin 2 precursor
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: GRCr8 - GRCr8 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8437,036,303 - 37,189,435 (-)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl437,035,761 - 37,189,494 (-)EnsemblGRCr8
mRatBN7.2436,069,980 - 36,223,128 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl436,069,970 - 36,223,220 (-)EnsemblmRatBN7.2
Rnor_6.0434,048,074 - 34,198,558 (-)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl434,048,533 - 34,194,764 (-)Ensemblrn6Rnor6.0
Rnor_5.0433,904,586 - 34,058,707 (-)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.4433,043,706 - 33,216,862 (-)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera431,574,414 - 31,727,219 (-)NCBICelera
Cytogenetic Map4q21NCBI
JBrowse:




Disease Annotations     Click to see Annotation Detail View

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

Biological Process

Cellular Component

References

References - curated
# Reference Title Reference Citation
1. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
2. GOA pipeline RGD automated data pipeline
3. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
4. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:16330543   PMID:20830809   PMID:27559042  


Genomics

Comparative Map Data
Col28a1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8437,036,303 - 37,189,435 (-)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl437,035,761 - 37,189,494 (-)EnsemblGRCr8
mRatBN7.2436,069,980 - 36,223,128 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl436,069,970 - 36,223,220 (-)EnsemblmRatBN7.2
Rnor_6.0434,048,074 - 34,198,558 (-)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl434,048,533 - 34,194,764 (-)Ensemblrn6Rnor6.0
Rnor_5.0433,904,586 - 34,058,707 (-)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.4433,043,706 - 33,216,862 (-)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera431,574,414 - 31,727,219 (-)NCBICelera
Cytogenetic Map4q21NCBI
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 (-)Ensemblhg38GRCh38
GRCh3777,397,506 - 7,575,504 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 3677,364,769 - 7,541,985 (-)NCBIBuild 36Build 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 EnsemblGRCm39
GRCm3867,997,100 - 8,193,709 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl67,997,808 - 8,192,617 (-)Ensemblmm10GRCm38
MGSCv3767,947,808 - 8,142,617 (-)NCBIMGSCv37MGSCv37mm9NCBIm37
MGSCv3667,947,808 - 8,142,617 (-)NCBIMGSCv36mm8
Celera68,140,497 - 8,334,541 (-)NCBICelera
Cytogenetic Map6A1NCBI
cM Map63.44NCBI
Col28a1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495543214,462,226 - 14,633,236 (-)Ensembl
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 (-)EnsemblpanPan2panpan1.1
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 (-)EnsemblcanFam3CanFam3.1
Dog10K_Boxer_Tasha1422,566,580 - 22,728,366 (-)NCBIDog10K_Boxer_TashaDog10K_Boxer_Tasha
ROS_Cfam_1.01422,805,409 - 22,967,559 (-)NCBIROS_Cfam_1.0ROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl1422,807,226 - 22,967,511 (-)EnsemblROS_Cfam_1.0 Ensembl
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_1.0UU_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 (+)EnsemblSpeTri2.0 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 (-)EnsemblsusScr11Sscrofa11.1
Sscrofa11.1977,670,890 - 77,841,939 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2985,201,979 - 85,497,584 (-)NCBISscrofa10.2Sscrofa10.2susScr3
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 (+)EnsemblChlSab1.1 EnsemblchlSab2Vervet-AGM
Vero_WHO_p1.0NW_02366604253,554,465 - 53,718,863 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
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_1.0 EnsemblhetGla2HetGla_female_1.0 Ensembl
HetGla 1.0NW_0046248134,945,733 - 5,180,098 (-)NCBIHetGla 1.0HetGla 1.0hetGla2

Variants

.
Variants in Col28a1
879 total Variants
miRNA Target Status (No longer updated)

Predicted Target Of
Summary Value
Count of predictions:96
Count of miRNA genes:83
Interacting mature miRNAs:85
Transcripts:ENSRNOT00000045270
Prediction methods:Microtar, Miranda, Rnahybrid
Result types:miRGate_prediction

The detailed report is available here: Full Report CSV TAB Printer

miRNA Target Status data imported from miRGate (http://mirgate.bioinfo.cnio.es/).
For more information about miRGate, see PMID:25858286 or access the full paper here.


QTLs in Region (GRCr8)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
2302371Stl22Serum triglyceride level QTL 225.15blood triglyceride amount (VT:0002644)serum triglyceride level (CMO:0000360)41308014658080146Rat
2303585Bw86Body weight QTL 864body mass (VT:0001259)body weight (CMO:0000012)41564430960644309Rat
5685012Bmd87Bone mineral density QTL 875.1tibia mineral mass (VT:1000283)bone mineral content (CMO:0001554)43511329080113290Rat
8552906Pigfal3Plasma insulin-like growth factor 1 level QTL 3blood insulin-like growth factor amount (VT:0010479)plasma insulin-like growth factor 1 level (CMO:0001299)41103870656038706Rat
10755501Bp390Blood pressure QTL 3902.5arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)427730518170099664Rat
8655949Rf62Renal function QTL 6222blood urea nitrogen amount (VT:0005265)plasma urea nitrogen level (CMO:0000586)43539660045429897Rat
6478766Anxrr47Anxiety related response QTL 470.09637locomotor behavior trait (VT:0001392)number of entries into a discrete space in an experimental apparatus (CMO:0000960)41103870656038706Rat
70222Eae2Experimental allergic encephalomyelitis QTL 24.3nervous system integrity trait (VT:0010566)experimental autoimmune encephalomyelitis incidence/prevalence measurement (CMO:0001046)42228845340471598Rat
61330Eau1Experimental allergic uveoretinitis QTL 10.0003uvea integrity trait (VT:0010551)experimental autoimmune uveitis score (CMO:0001504)426234499134199155Rat
631642Stl2Serum triglyceride level QTL 23.3blood triglyceride amount (VT:0002644)serum triglyceride level (CMO:0000360)4589457557613242Rat
6478769Anxrr48Anxiety related response QTL 480.02514locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)41103870656038706Rat
631261Tcas3Tongue tumor susceptibility QTL 36.88tongue integrity trait (VT:0010553)number of squamous cell tumors of the tongue with diameter greater than 3 mm (CMO:0001950)41170660492690519Rat
2313401Anxrr27Anxiety related response QTL 27aggression-related behavior trait (VT:0015014)tameness/aggressiveness composite score (CMO:0002136)41890069763900697Rat
631209Bw2Body weight QTL24.2retroperitoneal fat pad mass (VT:0010430)retroperitoneal fat pad weight to body weight ratio (CMO:0000635)4145429897Rat
6909128Pancm4Pancreatic morphology QTL 411.35pancreas mass (VT:0010144)pancreas wet weight (CMO:0000626)427862204126119996Rat
8694374Bw155Body weight QTL 1553.390.001body lean mass (VT:0010483)lean tissue morphological measurement (CMO:0002184)41103870656038706Rat
2303168Bp330Blood pressure QTL 3304.250.017arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)45889999148002343Rat
61412Pia2Pristane induced arthritis QTL 23.9joint integrity trait (VT:0010548)post-insult time to onset of experimental arthritis (CMO:0001450)42228845363245191Rat
8552807Vie4Viral induced encephalitis QTL 47.3brain integrity trait (VT:0010579)encephalitis incidence/prevalence measurement (CMO:0002361)41890069763900697Rat
6478724Anxrr35Anxiety related response QTL 350.00449defecation behavior trait (VT:0010462)defecation measurement (CMO:0000997)41103870656038706Rat
8655906Rf60Renal function QTL 603.8blood creatinine amount (VT:0005328)creatinine clearance (CMO:0000765)43044896182336920Rat
61415Eae11Experimental allergic encephalomyelitis QTL 112.9nervous system integrity trait (VT:0010566)post-insult time to onset of experimental autoimmune encephalomyelitis (CMO:0001422)4140471598Rat
619616Bp79Blood pressure QTL 790.0292arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)4588999950889999Rat
7387227Uae40Urinary albumin excretion QTL 402.90.0052urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)41891315163913151Rat
6909122Insul22Insulin level QTL 224.63blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)42786220462997402Rat
1358203Stl19Serum triglyceride level QTL 192.80.002blood triglyceride amount (VT:0002644)serum triglyceride level (CMO:0000360)42192515166925151Rat
70192BpQTLcluster5Blood pressure QTL cluster 54.183arterial blood pressure trait (VT:2000000)absolute change in mean arterial blood pressure (CMO:0000533)4163900697Rat
9590304Scort17Serum corticosterone level QTL 174.960.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)41103870656038706Rat
12798520Anxrr55Anxiety related response QTL 554.450.01locomotor behavior trait (VT:0001392)number of rearing movements with lid-pushing in an experimental apparatus (CMO:0002715)433538597116185060Rat
11530004Niddm71Non-insulin dependent diabetes mellitus QTL 710.001blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)43353881653719714Rat
2316958Gluco58Glucose level QTL 5810blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)412212457182430611Rat
1354665Stl10Serum triglyceride level QTL 103.57blood triglyceride amount (VT:0002644)serum triglyceride level (CMO:0000360)42228845345429897Rat
1300141Bp178Blood pressure QTL 178arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)41075870140490708Rat

Markers in Region
RH132505  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2436,070,074 - 36,070,274 (+)MAPPERmRatBN7.2
Rnor_6.0434,048,169 - 34,048,368NCBIRnor6.0
Rnor_5.0433,904,681 - 33,904,880UniSTSRnor5.0
RGSC_v3.4433,043,801 - 33,044,000UniSTSRGSC3.4
Celera431,574,509 - 31,574,708UniSTS
RH 3.4 Map4211.9UniSTS
Cytogenetic Map4q21UniSTS


Expression

RNA-SEQ Expression

alimentary part of gastrointestinal system
appendage
circulatory system
ectoderm
endocrine system
endoderm
exocrine system
hemolymphoid system
hepatobiliary system
integumental system
mesenchyme
mesoderm
musculoskeletal system
nervous system
renal system
reproductive system
respiratory system
sensory system
visual system
16 12 47 131 67 65 35 38 35 6 240 118 10 110 63 88 30 6 6

Sequence


Ensembl Acc Id: ENSRNOT00000045270   ⟹   ENSRNOP00000046298
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl437,035,761 - 37,189,494 (-)Ensembl
mRatBN7.2 Ensembl436,069,970 - 36,223,220 (-)Ensembl
Rnor_6.0 Ensembl434,048,533 - 34,194,764 (-)Ensembl
RefSeq Acc Id: XM_039108604   ⟹   XP_038964532
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8437,036,303 - 37,189,435 (-)NCBI
mRatBN7.2436,069,980 - 36,223,128 (-)NCBI
RefSeq Acc Id: XM_039108605   ⟹   XP_038964533
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8437,036,303 - 37,184,667 (-)NCBI
mRatBN7.2436,069,980 - 36,218,349 (-)NCBI
Protein Sequences
Protein RefSeqs NP_001418648 (Get FASTA)   NCBI Sequence Viewer  
  XP_038964532 (Get FASTA)   NCBI Sequence Viewer  
  XP_038964533 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000046298
  ENSRNOP00000046298.6
Ensembl Acc Id: ENSRNOP00000046298   ⟸   ENSRNOT00000045270
RefSeq Acc Id: XP_038964532   ⟸   XM_039108604
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038964533   ⟸   XM_039108605
- Peptide Label: isoform X2
Protein Domains
BPTI/Kunitz inhibitor   VWFA

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-D3ZN64-F1-model_v2 AlphaFold D3ZN64 1-1142 view protein structure

Transcriptome

eQTL   View at Phenogen
WGCNA   View at Phenogen
Tissue/Strain Expression   View at Phenogen


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1564680 AgrOrtholog
BioCyc Gene G2FUF-45662 BioCyc
Ensembl Genes ENSRNOG00000033618 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000045270 ENTREZGENE
  ENSRNOT00000045270.6 UniProtKB/TrEMBL
Gene3D-CATH 3.40.50.410 UniProtKB/TrEMBL
  4.10.410.10 UniProtKB/TrEMBL
InterPro Collagen UniProtKB/TrEMBL
  Collagen_superfamily UniProtKB/TrEMBL
  Kunitz_BPTI_sf UniProtKB/TrEMBL
  Prot_inh_Kunz-m UniProtKB/TrEMBL
  Prtase_inh_Kunz-CS UniProtKB/TrEMBL
  VWF_A UniProtKB/TrEMBL
  vWFA_dom_sf UniProtKB/TrEMBL
NCBI Gene 312115 ENTREZGENE
PANTHER COLLAGEN ALPHA UniProtKB/TrEMBL
  COLLAGEN TRIPLE HELIX REPEAT UniProtKB/TrEMBL
Pfam Collagen UniProtKB/TrEMBL
  Kunitz_BPTI UniProtKB/TrEMBL
  VWA UniProtKB/TrEMBL
PhenoGen Col28a1 PhenoGen
PRINTS VWFADOMAIN UniProtKB/TrEMBL
PROSITE BPTI_KUNITZ_1 UniProtKB/TrEMBL
  BPTI_KUNITZ_2 UniProtKB/TrEMBL
  VWFA UniProtKB/TrEMBL
RatGTEx ENSRNOG00000033618 RatGTEx
SMART SM00131 UniProtKB/TrEMBL
  VWA UniProtKB/TrEMBL
Superfamily-SCOP Prot_inh_Kunz-m UniProtKB/TrEMBL
  SSF53300 UniProtKB/TrEMBL
UniProt D3ZN64 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2016-06-01 Col28a1  collagen type XXVIII alpha 1 chain  Col28a1  collagen, type XXVIII, alpha 1  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2013-11-25 Col28a1  collagen, type XXVIII, alpha 1  RGD1564680  similar to matrilin 2 precursor  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-04-30 RGD1564680  similar to matrilin 2 precursor   RGD1564680_predicted  similar to matrilin 2 precursor (predicted)  'predicted' is removed 2292626 APPROVED
2006-03-07 RGD1564680_predicted  similar to matrilin 2 precursor (predicted)  LOC312115  similar to matrilin 2 precursor  Symbol and Name status set to approved 1299863 APPROVED
2006-02-09 LOC312115  similar to matrilin 2 precursor      Symbol and Name status set to provisional 70820 PROVISIONAL