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CRB1 crumbs 1, cell polarity complex component [ Homo sapiens (human) ]

Gene ID: 23418, updated on 3-Jun-2018
Official Symbol
CRB1provided by HGNC
Official Full Name
crumbs 1, cell polarity complex componentprovided by HGNC
Primary source
HGNC:HGNC:2343
See related
Ensembl:ENSG00000134376 MIM:604210; Vega:OTTHUMG00000035663
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
LCA8; RP12
Summary
This gene encodes a protein which is similar to the Drosophila crumbs protein and localizes to the inner segment of mammalian photoreceptors. In Drosophila crumbs localizes to the stalk of the fly photoreceptor and may be a component of the molecular scaffold that controls proper development of polarity in the eye. Mutations in this gene are associated with a severe form of retinitis pigmentosa, RP12, and with Leber congenital amaurosis. Alternate splicing results in multiple transcript variants, some protein coding and some non-protein coding.[provided by RefSeq, Apr 2012]
Expression
Biased expression in brain (RPKM 4.0) and testis (RPKM 1.3) See more
Orthologs
See CRB1 in Genome Data Viewer
Location:
1q31.3
Exon count:
18
Annotation release Status Assembly Chr Location
109 current GRCh38.p12 (GCF_000001405.38) 1 NC_000001.11 (197201462..197478455)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (197170592..197447585)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene abnormal spindle microtubule assembly Neighboring gene septin 14 pseudogene 12 Neighboring gene zinc finger and BTB domain containing 41 Neighboring gene ATPase H+ transporting accessory protein 2 pseudogene Neighboring gene mitochondrial ribosomal protein S21 pseudogene 3 Neighboring gene DENN domain containing 1B Neighboring gene eukaryotic translation elongation factor 1 alpha 1 pseudogene 32 Neighboring gene ribosomal protein L24 pseudogene 5

  • 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 Jun 15 11:32:44 2016

GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

NHGRI GWAS Catalog

Description
Lupus nephritis susceptibility Loci in women with systemic lupus erythematosus.
NHGRI GWA Catalog
Variants of DENND1B associated with asthma in children.
NHGRI GWA Catalog
  • Hippo signaling pathway, organism-specific biosystem (from KEGG)
    Hippo signaling pathway, organism-specific biosystemHippo signaling is an evolutionarily conserved signaling pathway that controls organ size from flies to humans. In humans and mice, the pathway consists of the MST1 and MST2 kinases, their cofactor S...
  • Hippo signaling pathway, conserved biosystem (from KEGG)
    Hippo signaling pathway, conserved biosystemHippo signaling is an evolutionarily conserved signaling pathway that controls organ size from flies to humans. In humans and mice, the pathway consists of the MST1 and MST2 kinases, their cofactor S...
Products Interactant Other Gene Complex Source Pubs Description

Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
calcium ion binding IEA
Inferred from Electronic Annotation
more info
 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
scavenger receptor activity IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
Process Evidence Code Pubs
cell-cell signaling TAS
Traceable Author Statement
more info
PubMed 
establishment or maintenance of cell polarity TAS
Traceable Author Statement
more info
PubMed 
establishment or maintenance of epithelial cell apical/basal polarity IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
eye photoreceptor cell development IEA
Inferred from Electronic Annotation
more info
 
heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
plasma membrane organization IEA
Inferred from Electronic Annotation
more info
 
Component Evidence Code Pubs
apical plasma membrane IEA
Inferred from Electronic Annotation
more info
 
cell-cell adherens junction IDA
Inferred from Direct Assay
more info
PubMed 
extracellular region IEA
Inferred from Electronic Annotation
more info
 
integral component of membrane IEA
Inferred from Electronic Annotation
more info
 
microvillus IEA
Inferred from Electronic Annotation
more info
 
photoreceptor inner segment IEA
Inferred from Electronic Annotation
more info
 
plasma membrane IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
protein-containing complex IDA
Inferred from Direct Assay
more info
PubMed 
Preferred Names
protein crumbs homolog 1
Names
crumbs family member 1, photoreceptor morphogenesis associated

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_008483.2 RefSeqGene

    Range
    71743..281994
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001193640.1NP_001180569.1  protein crumbs homolog 1 isoform 2 precursor

    See identical proteins and their annotated locations for NP_001180569.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) lacks two in-frame exons compared to variant 1. The resulting isoform (2) has the same N- and C-termini but is shorter compared to isoform 1.
    Source sequence(s)
    AJ748821, AY043325, DC370545, DC370777
    Consensus CDS
    CCDS53454.1
    UniProtKB/Swiss-Prot
    P82279
    Related
    ENSP00000356369.2, OTTHUMP00000180665, ENST00000367399.6, OTTHUMT00000280653
    Conserved Domains (3) summary
    smart00179
    Location:285326
    EGF_CA; Calcium-binding EGF-like domain
    cd00054
    Location:148183
    EGF_CA; Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the ...
    pfam02210
    Location:402537
    Laminin_G_2; Laminin G domain
  2. NM_001257965.1NP_001244894.1  protein crumbs homolog 1 isoform 3

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) contains three noncoding exons in place of the first exon and contains an alternate in-frame exon compared to variant 1. The resulting isoform (3) is shorter at the N- terminus and contains an alternate internal segment compared to isoform 1.
    Source sequence(s)
    AK289733, AK302826, AL136322, AY043325
    Consensus CDS
    CCDS58053.1
    UniProtKB/Swiss-Prot
    P82279
    UniProtKB/TrEMBL
    A8K118, B7Z826, F5H0L2
    Related
    ENSP00000438786.1, ENST00000535699.5
    Conserved Domains (3) summary
    smart00179
    Location:328369
    EGF_CA; Calcium-binding EGF-like domain
    cd00054
    Location:79114
    EGF_CA; Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the ...
    pfam02210
    Location:445580
    Laminin_G_2; Laminin G domain
  3. NM_001257966.1NP_001244895.1  protein crumbs homolog 1 isoform 4 precursor

    See identical proteins and their annotated locations for NP_001244895.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (4) lacks an alternate in-frame segment of two coding exons and most of a third compared to variant 1. The resulting isoform (4) has the same N- and C-termini but lacks an alternate internal segment compared to isoform 1.
    Source sequence(s)
    AK299368, AL513325, AY043325, DC370545
    Consensus CDS
    CCDS58052.1
    UniProtKB/Swiss-Prot
    P82279
    Related
    ENSP00000438091.1, ENST00000538660.5
    Conserved Domains (3) summary
    smart00179
    Location:397438
    EGF_CA; Calcium-binding EGF-like domain
    cd00054
    Location:148183
    EGF_CA; Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the ...
    pfam02210
    Location:514649
    Laminin_G_2; Laminin G domain
  4. NM_201253.2NP_957705.1  protein crumbs homolog 1 isoform 1 precursor

    See identical proteins and their annotated locations for NP_957705.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) encodes the longest isoform (1).
    Source sequence(s)
    AY043325, BC136271, DC370545, DC370777
    Consensus CDS
    CCDS1390.1
    UniProtKB/Swiss-Prot
    P82279
    Related
    ENSP00000356370.3, OTTHUMP00000033690, ENST00000367400.7, OTTHUMT00000086565
    Conserved Domains (3) summary
    smart00179
    Location:397438
    EGF_CA; Calcium-binding EGF-like domain
    cd00054
    Location:148183
    EGF_CA; Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the ...
    pfam02210
    Location:514649
    Laminin_G_2; Laminin G domain

RNA

  1. NR_047563.1 RNA Sequence

    Status: REVIEWED

    Description
    Transcript Variant: This variant (5) lacks an alternate internal segment of a coding exon compared to variant 1, that causes a frameshift. The resulting transcript is a candidate for nonsense-mediated mRNA decay (NMD) and is thought to be non-protein coding.
    Source sequence(s)
    AL513325, AY043325, BC143726, DC370545
  2. NR_047564.1 RNA Sequence

    Status: REVIEWED

    Description
    Transcript Variant: This variant (6) uses an alternate splice junction at the 3' end of a coding exon compared to variant 1, that causes a frameshift. The resulting transcript is a candidate for nonsense-mediated mRNA decay (NMD) and is thought to be non-protein coding.
    Source sequence(s)
    AL513325, AY043324, DC370545
    Related
    ENST00000484075.5, OTTHUMT00000086562

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109 details...Open this link in a new tab

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

Reference GRCh38.p12 Primary Assembly

Genomic

  1. NC_000001.11 Reference GRCh38.p12 Primary Assembly

    Range
    197201462..197478455
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_017000852.1XP_016856341.1  protein crumbs homolog 1 isoform X5

  2. XM_011509367.1XP_011507669.1  protein crumbs homolog 1 isoform X2

    Conserved Domains (3) summary
    smart00179
    Location:397438
    EGF_CA; Calcium-binding EGF-like domain
    cd00054
    Location:148183
    EGF_CA; Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the ...
    pfam02210
    Location:514649
    Laminin_G_2; Laminin G domain
  3. XM_011509365.2XP_011507667.1  protein crumbs homolog 1 isoform X1

    Related
    ENSP00000491102.1, ENST00000638467.1
    Conserved Domains (3) summary
    smart00179
    Location:397438
    EGF_CA; Calcium-binding EGF-like domain
    cd00054
    Location:148183
    EGF_CA; Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the ...
    pfam02210
    Location:514649
    Laminin_G_2; Laminin G domain
  4. XM_017000851.1XP_016856340.1  protein crumbs homolog 1 isoform X3

  5. XM_011509369.2XP_011507671.1  protein crumbs homolog 1 isoform X4

    See identical proteins and their annotated locations for XP_011507671.1

    UniProtKB/TrEMBL
    B7Z824
    Conserved Domains (2) summary
    cd00054
    Location:627656
    EGF_CA; Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the ...
    pfam02210
    Location:461586
    Laminin_G_2; Laminin G domain

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

  1. NM_012076.2: Suppressed sequence

    Description
    NM_012076.2: This RefSeq was permanently suppressed because it is a nonsense-mediated mRNA decay (NMD) candidate.
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