Col28a1 collagen, type XXVIII, alpha 1 [Mus musculus (house mouse)] - Gene

Summary

Official Symbol: Col28a1provided by MGI
Official Full Name: collagen, type XXVIII, alpha 1provided by MGI
Primary source: MGI:MGI:2685312
See related: Ensembl:ENSMUSG00000068794 AllianceGenome:MGI:2685312
Gene type: protein coding
RefSeq status: PROVISIONAL
Organism: Mus musculus
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
Also known as: Col28; Gm466
Summary: Predicted to be an extracellular matrix structural constituent. Predicted to be involved in extracellular matrix organization. Predicted to act upstream of or within cell adhesion and negative regulation of peptidase activity. Located in basement membrane. Is expressed in several structures, including main olfactory bulb; metapodial pad; peripheral nervous system; skeletal muscle; and skin. Orthologous to human COL28A1 (collagen type XXVIII alpha 1 chain). [provided by Alliance of Genome Resources, Apr 2022]
Expression: Biased expression in bladder adult (RPKM 1.7), mammary gland adult (RPKM 0.6) and 14 other tissues See more
Orthologs: human all
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Genomic context

Location:: 6 A1; 6 3.44 cM

Exon count:: 39

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCm39 (GCF_000001635.27)	6	NC_000072.7 (7997100..8193709, complement)
108.20200622	previous assembly	GRCm38.p6 (GCF_000001635.26)	6	NC_000072.6 (7997100..8193709, complement)

Chromosome 6 - NC_000072.7 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: Mouse ENCODE transcriptome data
Description: RNA profiling data sets generated by the Mouse ENCODE project.
BioProject: PRJNA66167
Publication: PMID 25409824
Analysis date: n/a

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.
Type XXVIII Collagen Regulates Renal Interstitial Fibrosis and Epithelial-Mesenchymal Transition by SREBP1-Mediated HKDC1 Expression.
Title: Type XXVIII Collagen Regulates Renal Interstitial Fibrosis and Epithelial-Mesenchymal Transition by SREBP1-Mediated HKDC1 Expression.
The correlation between the absence of myelin and the presence of collagen XXVIII is confirmed in a mouse model of Charcot-Marie-Tooth characterized by dysmyelinated nerve fibers, in which enhancement of collagen XXVIII labeling is observed
Title: Collagen XXVIII is a distinctive component of the peripheral nervous system nodes of ranvier and surrounds nonmyelinating glial cells.
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

Variation

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Alleles

Alleles of this type are documented at Mouse Genome Informatics (MGI)

Endonuclease-mediated (2)

General gene information

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Markers

D6Mit348 (e-PCR), detects polymorphism
- UniSTS:116583

Gene Ontology Provided by MGI

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 peptidase inhibitor activity	IEA Inferred from Electronic Annotation more info
enables serine-type endopeptidase inhibitor activity	IEA Inferred from Electronic Annotation more info

Process	Evidence Code	Pubs
involved_in cell adhesion	IBA Inferred from Biological aspect of Ancestor more info
involved_in collagen fibril organization	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within negative regulation of peptidase activity	IEA Inferred from Electronic Annotation more info

Component	Evidence Code	Pubs
located_in basement membrane	IDA Inferred from Direct Assay more info	PubMed
part_of collagen trimer	IEA Inferred from Electronic Annotation more info
part_of collagen type V 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 extracellular region	IEA Inferred from Electronic Annotation 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 28

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_001037865.1 → NP_001032954.1 collagen alpha-1(XXVIII) chain precursor

See identical proteins and their annotated locations for NP_001032954.1

Status: PROVISIONAL

Source sequence(s)

AJ890449

Consensus CDS

CCDS39424.1

UniProtKB/Swiss-Prot

Q2UY10, Q2UY11

Related

ENSMUSP00000111199.2, ENSMUST00000115537.2

Conserved Domains (5) summary

pfam01391
Location:575 → 636

Collagen; Collagen triple helix repeat (20 copies)

cd00109
Location:1086 → 1139

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 → 212

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

pfam03157
Location:361 → 763

Glutenin_hmw; High molecular weight glutenin subunit

RefSeqs of Annotated Genomes: GCF_000001635.27-RS_2024_02

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

Reference GRCm39 C57BL/6J

Genomic

NC_000072.7 Reference GRCm39 C57BL/6J

Range

7997100..8193709 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_017321502.1 → XP_017176991.1 collagen alpha-1(XXVIII) chain isoform X1

UniProtKB/Swiss-Prot

Q2UY10, Q2UY11

Conserved Domains (5) summary

pfam01391
Location:575 → 636

Collagen; Collagen triple helix repeat (20 copies)

cd00109
Location:1086 → 1139

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 → 212

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

pfam03157
Location:361 → 763

Glutenin_hmw; High molecular weight glutenin subunit
XM_036166011.1 → XP_036021904.1 collagen alpha-1(XXVIII) chain isoform X2

Conserved Domains (4) summary

cd00109
Location:1017 → 1070

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 → 212

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:730 → 905

VWA; von Willebrand factor type A domain

pfam01391
Location:500 → 567

Collagen; Collagen triple helix repeat (20 copies)
XM_006505031.2 → XP_006505094.1 collagen alpha-1(XXVIII) chain isoform X1

See identical proteins and their annotated locations for XP_006505094.1

UniProtKB/Swiss-Prot

Q2UY10, Q2UY11

Conserved Domains (5) summary

pfam01391
Location:575 → 636

Collagen; Collagen triple helix repeat (20 copies)

cd00109
Location:1086 → 1139

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 → 212

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

pfam03157
Location:361 → 763

Glutenin_hmw; High molecular weight glutenin subunit
XM_006505033.4 → XP_006505096.1 collagen alpha-1(XXVIII) chain isoform X3

Conserved Domains (4) summary

pfam01391
Location:32 → 96

Collagen; Collagen triple helix repeat (20 copies)

cd00109
Location:861 → 914

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.

pfam09606
Location:162 → 411

Med15; ARC105 or Med15 subunit of Mediator complex non-fungal

pfam00092
Location:574 → 749

VWA; von Willebrand factor type A domain
XM_017321503.3 → XP_017176992.1 collagen alpha-1(XXVIII) chain isoform X3

Conserved Domains (4) summary

pfam01391
Location:32 → 96

Collagen; Collagen triple helix repeat (20 copies)

cd00109
Location:861 → 914

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.

pfam09606
Location:162 → 411

Med15; ARC105 or Med15 subunit of Mediator complex non-fungal

pfam00092
Location:574 → 749

VWA; von Willebrand factor type A domain