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COL4A3BP collagen type IV alpha 3 binding protein [ Homo sapiens (human) ]

Gene ID: 10087, updated on 8-Dec-2018

Summary

Official Symbol
COL4A3BPprovided by HGNC
Official Full Name
collagen type IV alpha 3 binding proteinprovided by HGNC
Primary source
HGNC:HGNC:2205
See related
Ensembl:ENSG00000113163 MIM:604677
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
CERT; GPBP; CERTL; MRD34; STARD11
Summary
This gene encodes a kinase that specifically phosphorylates the N-terminal region of the non-collagenous domain of the alpha 3 chain of type IV collagen, known as the Goodpasture antigen. Goodpasture disease is the result of an autoimmune response directed at this antigen. One isoform of this protein is also involved in ceramide intracellular transport. Three transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2008]
Expression
Ubiquitous expression in thyroid (RPKM 18.3), fat (RPKM 18.1) and 25 other tissues See more
Orthologs

Genomic context

See COL4A3BP in Genome Data Viewer
Location:
5q13.3
Exon count:
20
Annotation release Status Assembly Chr Location
109 current GRCh38.p12 (GCF_000001405.38) 5 NC_000005.10 (75368486..75511981, complement)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 5 NC_000005.9 (74666928..74807806, complement)

Chromosome 5 - NC_000005.10Genomic Context describing neighboring genes Neighboring gene ankyrin repeat domain 31 Neighboring gene SUMO2 pseudogene 5 Neighboring gene 3-hydroxy-3-methylglutaryl-CoA reductase Neighboring gene ribosomal protein S26 pseudogene 26 Neighboring gene RNA, U7 small nuclear 175 pseudogene Neighboring gene DNA polymerase kappa Neighboring gene ankyrin repeat and death domain containing 1B Neighboring gene uncharacterized LOC107986424

Genomic regions, transcripts, and products

Expression

  • 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

GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

Phenotypes

Associated conditions

Description Tests
Mental retardation, autosomal dominant 34
MedGen: C4225156 OMIM: 616351 GeneReviews: Not available
not available

NHGRI GWAS Catalog

Description
Genome-wide association studies in an isolated founder population from the Pacific Island of Kosrae.
NHGRI GWA Catalog

Pathways from BioSystems

  • Metabolism, organism-specific biosystem (from REACTOME)
    Metabolism, organism-specific biosystemMetabolic processes in human cells generate energy through the oxidation of molecules consumed in the diet and mediate the synthesis of diverse essential molecules not taken in the diet as well as th...
  • Metabolism of lipids and lipoproteins, organism-specific biosystem (from REACTOME)
    Metabolism of lipids and lipoproteins, organism-specific biosystemLipids are hydrophobic but otherwise chemically diverse molecules that play a wide variety of roles in human biology. They include ketone bodies, fatty acids, triacylglycerols, phospholipids and sphi...
  • Sphingolipid de novo biosynthesis, organism-specific biosystem (from REACTOME)
    Sphingolipid de novo biosynthesis, organism-specific biosystemThe main steps involved in de novo sphingolipid synthesis are annotated here (Merrill 2002, Gault et al. 2010).
  • Sphingolipid metabolism, organism-specific biosystem (from REACTOME)
    Sphingolipid metabolism, organism-specific biosystemSphingolipids are derivatives of long chain sphingoid bases such as sphingosine (trans-1,3-dihydroxy 2-amino-4-octadecene), an 18-carbon unsaturated amino alcohol which is the most abundant sphingoid...

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Clone Names

  • FLJ20597

Gene Ontology Provided by GOA

Function Evidence Code Pubs
ceramide 1-phosphate binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
ceramide 1-phosphate transporter activity IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
ceramide binding IDA
Inferred from Direct Assay
more info
PubMed 
intermembrane ceramide transfer activity IDA
Inferred from Direct Assay
more info
PubMed 
kinase activity IEA
Inferred from Electronic Annotation
more info
 
lipid binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
phosphatidylinositol-4-phosphate binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
Process Evidence Code Pubs
ER to Golgi ceramide transport IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
ER to Golgi ceramide transport IMP
Inferred from Mutant Phenotype
more info
PubMed 
cell morphogenesis IEA
Inferred from Electronic Annotation
more info
 
cell proliferation IEA
Inferred from Electronic Annotation
more info
 
ceramide 1-phosphate transport IEA
Inferred from Electronic Annotation
more info
 
ceramide metabolic process IEA
Inferred from Electronic Annotation
more info
 
ceramide transport IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
endoplasmic reticulum organization IEA
Inferred from Electronic Annotation
more info
 
heart morphogenesis IEA
Inferred from Electronic Annotation
more info
 
immune response NAS
Non-traceable Author Statement
more info
PubMed 
in utero embryonic development IEA
Inferred from Electronic Annotation
more info
 
intermembrane lipid transfer IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
intermembrane sphingolipid transfer IDA
Inferred from Direct Assay
more info
PubMed 
lipid homeostasis IEA
Inferred from Electronic Annotation
more info
 
mitochondrion morphogenesis IEA
Inferred from Electronic Annotation
more info
 
muscle contraction IEA
Inferred from Electronic Annotation
more info
 
phosphorylation IEA
Inferred from Electronic Annotation
more info
 
response to endoplasmic reticulum stress IEA
Inferred from Electronic Annotation
more info
 
signal transduction IEA
Inferred from Electronic Annotation
more info
 
sphingolipid biosynthetic process TAS
Traceable Author Statement
more info
 
Component Evidence Code Pubs
Golgi apparatus IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
Golgi apparatus IDA
Inferred from Direct Assay
more info
PubMed 
cytosol IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
cytosol TAS
Traceable Author Statement
more info
 
endoplasmic reticulum membrane TAS
Traceable Author Statement
more info
 
membrane IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
mitochondrion IEA
Inferred from Electronic Annotation
more info
 
nucleoplasm IDA
Inferred from Direct Assay
more info
 
colocalizes_with perinuclear region of cytoplasm IDA
Inferred from Direct Assay
more info
PubMed 

General protein information

Preferred Names
collagen type IV alpha-3-binding protein
Names
StAR-related lipid transfer (START) domain containing 11
ceramide transfer protein
ceramide transporter
collagen, type IV, alpha 3 (Goodpasture antigen) binding protein
hCERT
lipid-transfer protein CERTL
NP_001123577.1
NP_005704.1
NP_112729.1
XP_006714576.1
XP_011541392.1
XP_011541393.1
XP_016864408.1

NCBI Reference Sequences (RefSeq)

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.

Genomic

  1. NG_029492.1 RefSeqGene

    Range
    5001..145879
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001130105.1NP_001123577.1  collagen type IV alpha-3-binding protein isoform 3

    See identical proteins and their annotated locations for NP_001123577.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) represents the longest transcript and encodes the longest isoform (3).
    Source sequence(s)
    AC008897, AK000604, AK096854
    Consensus CDS
    CCDS47235.1
    UniProtKB/Swiss-Prot
    Q9Y5P4
    Related
    ENSP00000494110.1, ENST00000644072.1
    Conserved Domains (2) summary
    cd08872
    Location:519752
    START_STARD11-like; Ceramide-binding START domain of mammalian STARD11 and related domains
    cd13283
    Location:154253
    PH_GPBP; Goodpasture antigen binding protein Pleckstrin homology (PH) domain
  2. NM_005713.2NP_005704.1  collagen type IV alpha-3-binding protein isoform 1

    See identical proteins and their annotated locations for NP_005704.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) differs in the 5' UTR and coding region compared to variant 3. The resulting isoform (1) is shorter at the N-terminus compared to isoform 3.
    Source sequence(s)
    AC008897, AK000604, AK292087, AY453386
    Consensus CDS
    CCDS4028.1
    UniProtKB/Swiss-Prot
    Q9Y5P4
    Related
    ENSP00000383996.3, ENST00000405807.9
    Conserved Domains (2) summary
    cd08872
    Location:391624
    START_STARD11-like; Ceramide-binding START domain of mammalian STARD11 and related domains
    cd13283
    Location:26125
    PH_GPBP; Goodpasture antigen binding protein Pleckstrin homology (PH) domain
  3. NM_031361.2NP_112729.1  collagen type IV alpha-3-binding protein isoform 2

    See identical proteins and their annotated locations for NP_112729.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) differs in the 5' UTR and coding region and lacks an alternate in-frame exon compared to variant 3. The resulting isoform (2) is shorter at the N-terminus and lacks an internal segment compared to isoform 3. The absence of the in-frame exon results in the loss of a protein motif and less phosphorylation activity. This isoform also mediates intracellular transport of ceramide from the endoplasmic reticulum to the Golgi apparatus.
    Source sequence(s)
    AC008897, AK000604, AK292087, AY453385
    Consensus CDS
    CCDS4029.1
    UniProtKB/Swiss-Prot
    Q9Y5P4
    UniProtKB/TrEMBL
    A0A024RAJ5
    Related
    ENSP00000493563.1, ENST00000645483.1
    Conserved Domains (2) summary
    cd08872
    Location:364598
    START_STARD11-like; Ceramide-binding START domain of mammalian STARD11 and related domains
    cd13283
    Location:26125
    PH_GPBP; Goodpasture antigen binding protein Pleckstrin homology (PH) domain

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109

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

Reference GRCh38.p12 Primary Assembly

Genomic

  1. NC_000005.10 Reference GRCh38.p12 Primary Assembly

    Range
    75368486..75511981 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_017008919.2XP_016864408.1  collagen type IV alpha-3-binding protein isoform X4

    UniProtKB/Swiss-Prot
    Q9Y5P4
    UniProtKB/TrEMBL
    A0A024RAJ5
    Related
    ENSP00000496243.1, ENST00000644445.1
    Conserved Domains (2) summary
    cd08872
    Location:364598
    START_STARD11-like; Ceramide-binding START domain of mammalian STARD11 and related domains
    cd13283
    Location:26125
    PH_GPBP; Goodpasture antigen binding protein Pleckstrin homology (PH) domain
  2. XM_006714513.3XP_006714576.1  collagen type IV alpha-3-binding protein isoform X2

    See identical proteins and their annotated locations for XP_006714576.1

    UniProtKB/Swiss-Prot
    Q9Y5P4
    Related
    ENSP00000261415.8, ENST00000261415.12
    Conserved Domains (2) summary
    cd08872
    Location:391624
    START_STARD11-like; Ceramide-binding START domain of mammalian STARD11 and related domains
    cd13283
    Location:26125
    PH_GPBP; Goodpasture antigen binding protein Pleckstrin homology (PH) domain
  3. XM_011543090.3XP_011541392.1  collagen type IV alpha-3-binding protein isoform X1

    Conserved Domains (3) summary
    cd13283
    Location:26125
    PH_GPBP; Goodpasture antigen binding protein Pleckstrin homology (PH) domain
    pfam00169
    Location:24114
    PH; PH domain
    cl14643
    Location:391583
    SRPBCC; START/RHO_alpha_C/PITP/Bet_v1/CoxG/CalC (SRPBCC) ligand-binding domain superfamily
  4. XM_011543091.3XP_011541393.1  collagen type IV alpha-3-binding protein isoform X3

    Related
    ENSP00000496016.1, ENST00000642556.1
    Conserved Domains (3) summary
    cd13283
    Location:26125
    PH_GPBP; Goodpasture antigen binding protein Pleckstrin homology (PH) domain
    pfam00169
    Location:24114
    PH; PH domain
    cl14643
    Location:364557
    SRPBCC; START/RHO_alpha_C/PITP/Bet_v1/CoxG/CalC (SRPBCC) ligand-binding domain superfamily
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