COL28A1 collagen type XXVIII alpha 1 chain [Homo sapiens (human)] - Gene

Summary

Official Symbol: COL28A1provided by HGNC
Official Full Name: collagen type XXVIII alpha 1 chainprovided by HGNC
Primary source: HGNC:HGNC:22442
See related: Ensembl:ENSG00000215018 MIM:609996; AllianceGenome:HGNC:22442
Gene type: protein coding
RefSeq status: VALIDATED
Organism: Homo sapiens
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as: COL28
Summary: COL28A1 belongs to a class of collagens containing von Willebrand factor (VWF; MIM 613160) type A (VWFA) domains (Veit et al., 2006 [PubMed 16330543]).[supplied by OMIM, Nov 2010]
Expression: Broad expression in salivary gland (RPKM 1.1), adrenal (RPKM 0.6) and 20 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 7p21.3

Exon count:: 47

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	7	NC_000007.14 (7338194..7543870, complement)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	7	NC_060931.1 (7477054..7655035, complement)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	7	NC_000007.13 (7397506..7575504, complement)

Chromosome 7 - NC_000007.14 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: HPA RNA-seq normal tissues
Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
BioProject: PRJEB4337
Publication: PMID 24309898
Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

COL28 promotes proliferation, migration, and EMT of renal tubular epithelial cells.
Title: COL28 promotes proliferation, migration, and EMT of renal tubular epithelial cells.
Observational study of gene-disease association, gene-environment interaction, and pharmacogenomic / toxicogenomic. (HuGE Navigator)
Title: Variation at the NFATC2 locus increases the risk of thiazolidinedione-induced edema in the Diabetes REduction Assessment with ramipril and rosiglitazone Medication (DREAM) study.
Observational study of gene-disease association. (HuGE Navigator)
Title: Gene-centric association signals for lipids and apolipoproteins identified via the HumanCVD BeadChip.
Clinical trial of gene-disease association and gene-environment interaction. (HuGE Navigator)
Title: Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score.
Collagen XXVIII is a novel von Willebrand factor A domain-containing protein with many imperfections in the collagenous domain
Title: Collagen XXVIII, a novel von Willebrand factor A domain-containing protein with many imperfections in the collagenous domain.

Submit: New GeneRIF Correction

Phenotypes

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Review eQTL and phenotype association data in this region using PheGenI

EBI GWAS Catalog

Description
A genome-wide meta-analysis identifies novel loci associated with schizophrenia and bipolar disorder. EBI GWAS Catalog EBI GWAS CatalogPubMed
Genome-wide analysis of polymorphisms associated with cytokine responses in smallpox vaccine recipients. EBI GWAS Catalog EBI GWAS CatalogPubMed

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

GDB:1317716 (e-PCR)
- UniSTS:55584

GDB:3778193 (e-PCR)
- UniSTS:53052

GDB:193196 (e-PCR)
- UniSTS:155746

SHGC-82101 (e-PCR)
- UniSTS:103027

RH36519 (e-PCR)
- UniSTS:53112

RH122425 (e-PCR)
- UniSTS:135296

GDB:1317600 (e-PCR)
- UniSTS:22187

D7S2553 (e-PCR), detects polymorphism
- UniSTS:79545

D7S2553 (e-PCR), detects polymorphism
- UniSTS:79324

D7S1984 (e-PCR)
- UniSTS:44532

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables extracellular matrix structural constituent conferring tensile strength	IBA Inferred from Biological aspect of Ancestor more info
enables extracellular matrix structural constituent conferring tensile strength	RCA inferred from Reviewed Computational Analysis more info	PubMed
enables heparin binding	IBA Inferred from Biological aspect of Ancestor more info
enables serine-type endopeptidase inhibitor activity	IEA Inferred from Electronic Annotation more info

Process	Evidence Code	Pubs
involved_in extracellular matrix organization	IBA Inferred from Biological aspect of Ancestor more info

Component	Evidence Code	Pubs
located_in basement membrane	IEA Inferred from Electronic Annotation more info
part_of collagen type XI trimer	IBA Inferred from Biological aspect of Ancestor more info
located_in collagen-containing extracellular matrix	HDA more info	PubMed
is_active_in collagen-containing extracellular matrix	IBA Inferred from Biological aspect of Ancestor more info
located_in endoplasmic reticulum lumen	TAS Traceable Author Statement more info
located_in extracellular region	TAS Traceable Author Statement more info
is_active_in extracellular space	IBA Inferred from Biological aspect of Ancestor more info

General protein information

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Preferred Names: collagen alpha-1(XXVIII) chain

Names: collagen, type XXVIII, alpha 1

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

mRNA and Protein(s)

NM_001037763.3 → NP_001032852.2 collagen alpha-1(XXVIII) chain precursor

See identical proteins and their annotated locations for NP_001032852.2

Status: VALIDATED

Source sequence(s)

AC004982, AC006356, AJ890451

Consensus CDS

CCDS43553.1

UniProtKB/Swiss-Prot

A4D101, A4D106, A4D107, A8MVR2, B9EGX9, Q2UY07, Q2UY08, Q2UY09

Related

ENSP00000382356.3, ENST00000399429.8

Conserved Domains (4) summary

cd00109
Location:1070 → 1123

KU; BPTI/Kunitz family of serine protease inhibitors; Structure is a disulfide rich alpha+beta fold. BPTI (bovine pancreatic trypsin inhibitor) is an extensively studied model structure.

cd01450
Location:47 → 209

vWFA_subfamily_ECM; Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of ...

pfam00092
Location:799 → 974

VWA; von Willebrand factor type A domain

pfam01391
Location:360 → 419

Collagen; Collagen triple helix repeat (20 copies)

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

NC_000007.14 Reference GRCh38.p14 Primary Assembly

Range

7338194..7543870 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_011515360.3 → XP_011513662.1 collagen alpha-1(XXVIII) chain isoform X1

See identical proteins and their annotated locations for XP_011513662.1

UniProtKB/Swiss-Prot

A4D101, A4D106, A4D107, A8MVR2, B9EGX9, Q2UY07, Q2UY08, Q2UY09

Conserved Domains (4) summary

cd00109
Location:1070 → 1123

KU; BPTI/Kunitz family of serine protease inhibitors; Structure is a disulfide rich alpha+beta fold. BPTI (bovine pancreatic trypsin inhibitor) is an extensively studied model structure.

cd01450
Location:47 → 209

vWFA_subfamily_ECM; Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of ...

pfam00092
Location:799 → 974

VWA; von Willebrand factor type A domain

pfam01391
Location:360 → 419

Collagen; Collagen triple helix repeat (20 copies)
XM_011515358.4 → XP_011513660.1 collagen alpha-1(XXVIII) chain isoform X1

See identical proteins and their annotated locations for XP_011513660.1

UniProtKB/Swiss-Prot

A4D101, A4D106, A4D107, A8MVR2, B9EGX9, Q2UY07, Q2UY08, Q2UY09

Conserved Domains (4) summary

cd00109
Location:1070 → 1123

KU; BPTI/Kunitz family of serine protease inhibitors; Structure is a disulfide rich alpha+beta fold. BPTI (bovine pancreatic trypsin inhibitor) is an extensively studied model structure.

cd01450
Location:47 → 209

vWFA_subfamily_ECM; Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of ...

pfam00092
Location:799 → 974

VWA; von Willebrand factor type A domain

pfam01391
Location:360 → 419

Collagen; Collagen triple helix repeat (20 copies)
XM_011515359.2 → XP_011513661.1 collagen alpha-1(XXVIII) chain isoform X1

See identical proteins and their annotated locations for XP_011513661.1

UniProtKB/Swiss-Prot

A4D101, A4D106, A4D107, A8MVR2, B9EGX9, Q2UY07, Q2UY08, Q2UY09

Conserved Domains (4) summary

cd00109
Location:1070 → 1123

KU; BPTI/Kunitz family of serine protease inhibitors; Structure is a disulfide rich alpha+beta fold. BPTI (bovine pancreatic trypsin inhibitor) is an extensively studied model structure.

cd01450
Location:47 → 209

vWFA_subfamily_ECM; Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of ...

pfam00092
Location:799 → 974

VWA; von Willebrand factor type A domain

pfam01391
Location:360 → 419

Collagen; Collagen triple helix repeat (20 copies)
XM_047420314.1 → XP_047276270.1 collagen alpha-1(XXVIII) chain isoform X5
XM_011515362.2 → XP_011513664.1 collagen alpha-1(XXVIII) chain isoform X3

Conserved Domains (3) summary

pfam01391
Location:198 → 253

Collagen; Collagen triple helix repeat (20 copies)

cd00109
Location:687 → 740

KU; BPTI/Kunitz family of serine protease inhibitors; Structure is a disulfide rich alpha+beta fold. BPTI (bovine pancreatic trypsin inhibitor) is an extensively studied model structure.

pfam00092
Location:416 → 591

VWA; von Willebrand factor type A domain
XM_047420313.1 → XP_047276269.1 collagen alpha-1(XXVIII) chain isoform X2
XM_011515364.3 → XP_011513666.1 collagen alpha-1(XXVIII) chain isoform X6

Conserved Domains (2) summary

pfam01391
Location:383 → 442

Collagen; Collagen triple helix repeat (20 copies)

cd01450
Location:47 → 209

vWFA_subfamily_ECM; Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of ...
XM_011515363.3 → XP_011513665.1 collagen alpha-1(XXVIII) chain isoform X4

See identical proteins and their annotated locations for XP_011513665.1

UniProtKB/Swiss-Prot

Q2UY09

Conserved Domains (2) summary

pfam01391
Location:383 → 442

Collagen; Collagen triple helix repeat (20 copies)

cd01450
Location:47 → 209

vWFA_subfamily_ECM; Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of ...
XM_011515365.3 → XP_011513667.1 collagen alpha-1(XXVIII) chain isoform X8

Conserved Domains (2) summary

pfam01391
Location:383 → 442

Collagen; Collagen triple helix repeat (20 copies)

cd01450
Location:47 → 209

vWFA_subfamily_ECM; Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of ...
XM_017012133.2 → XP_016867622.1 collagen alpha-1(XXVIII) chain isoform X7
XM_011515366.3 → XP_011513668.1 collagen alpha-1(XXVIII) chain isoform X9

Conserved Domains (2) summary

pfam01391
Location:383 → 442

Collagen; Collagen triple helix repeat (20 copies)

cd01450
Location:47 → 209

vWFA_subfamily_ECM; Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of ...