CCDC88B coiled-coil domain containing 88B [Homo sapiens (human)] - Gene

Summary

Official Symbol: CCDC88Bprovided by HGNC
Official Full Name: coiled-coil domain containing 88Bprovided by HGNC
Primary source: HGNC:HGNC:26757
See related: Ensembl:ENSG00000168071 MIM:611205; AllianceGenome:HGNC:26757
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: BRLZ; HKRP3; gipie; CCDC88
Summary: This gene encodes a member of the hook-related protein family. Members of this family are characterized by an N-terminal potential microtubule binding domain, a central coiled-coiled and a C-terminal Hook-related domain. The encoded protein may be involved in linking organelles to microtubules. [provided by RefSeq, Oct 2009]
Expression: Biased expression in bone marrow (RPKM 19.8), spleen (RPKM 16.5) and 13 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 11q13.1

Exon count:: 27

Annotation release	Status	Assembly	Chr	Location
RS_2023_10	current	GRCh38.p14 (GCF_000001405.40)	11	NC_000011.10 (64340204..64357534)
RS_2023_10	current	T2T-CHM13v2.0 (GCF_009914755.1)	11	NC_060935.1 (64330213..64347539)
105.20220307	previous assembly	GRCh37.p13 (GCF_000001405.25)	11	NC_000011.9 (64107676..64125006)

Chromosome 11 - NC_000011.10 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?

A critical function of CCDC88B in colonic inflammation and inflammatory bowel disease
Title: CCDC88B is required for pathogenesis of inflammatory bowel disease.
results demonstrate an important role for HkRP3 in regulating the clustering of lytic granules and MTOC repositioning during the development of NK cell-mediated killing.
Title: HkRP3 is a microtubule-binding protein regulating lytic granule clustering and NK cell killing.
A genotype dataset found a sarcoidosis risk locus on chromosome 11q13.1, a risk region for Crohn disease. An allele-dependent expression of CCDC88B was found in bronchoalveolar lavage samples of German, Swedish and Czech patients with sarcoidosis.
Title: A novel sarcoidosis risk locus for Europeans on chromosome 11q13.1.
Data show that a novel Girdin family protein, Gipie, is expressed in endothelial cells, where it interacts with GRP78, a master regulator of the UPR, and that Gipie/GRP78 interaction controls the IRE1-JNK signaling pathway.
Title: Protective role of Gipie, a Girdin family protein, in endoplasmic reticulum stress responses in endothelial cells.

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Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

EBI GWAS Catalog

Description
A novel sarcoidosis risk locus for Europeans on chromosome 11q13.1. EBI GWAS Catalog EBI GWAS CatalogPubMed
Discovery of six new susceptibility loci and analysis of pleiotropic effects in leprosy. EBI GWAS Catalog EBI GWAS CatalogPubMed
Host-microbe interactions have shaped the genetic architecture of inflammatory bowel disease. 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

G33078 (e-PCR)
- UniSTS:9063

D1S1425 (e-PCR)
- UniSTS:149621

D20S984 (e-PCR)
- UniSTS:154596

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables dynein light intermediate chain binding	IBA Inferred from Biological aspect of Ancestor more info
enables microtubule binding	IBA Inferred from Biological aspect of Ancestor more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed

Process	Evidence Code	Pubs
involved_in cytoplasmic microtubule organization	IBA Inferred from Biological aspect of Ancestor more info
involved_in cytoskeleton-dependent intracellular transport	IBA Inferred from Biological aspect of Ancestor more info
involved_in defense response to protozoan	IEA Inferred from Electronic Annotation more info
involved_in positive regulation of T cell activation	ISS Inferred from Sequence or Structural Similarity more info
involved_in positive regulation of T cell proliferation	ISS Inferred from Sequence or Structural Similarity more info
involved_in positive regulation of cytokine production	ISS Inferred from Sequence or Structural Similarity more info

Component	Evidence Code	Pubs
located_in Golgi apparatus	IEA Inferred from Electronic Annotation more info
is_active_in centrosome	IBA Inferred from Biological aspect of Ancestor more info
located_in centrosome	IDA Inferred from Direct Assay more info
is_active_in cytoplasm	IBA Inferred from Biological aspect of Ancestor more info
located_in cytosol	IDA Inferred from Direct Assay more info
located_in endoplasmic reticulum	IEA Inferred from Electronic Annotation more info
located_in membrane	HDA more info	PubMed
located_in nucleoplasm	IDA Inferred from Direct Assay more info

General protein information

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Preferred Names: coiled-coil domain-containing protein 88B

Names: 78 kDa glucose-regulated protein [GRP78]-interacting protein induced by ER stress; GRP78-interacting protein induced by ER stress; brain leucine zipper domain-containing protein; brain leucine zipper protein; coiled-coil domain containing 88; hook-related protein 3

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_032251.6 → NP_115627.6 coiled-coil domain-containing protein 88B

See identical proteins and their annotated locations for NP_115627.6

Status: REVIEWED

Source sequence(s)

AP003774, BC140822, BC141866, BC151222, BE222756

Consensus CDS

CCDS8072.2

UniProtKB/Swiss-Prot

A5D8Y5, A6NC98, B5MDM2, Q05BL2, Q6RUV3, Q8N1Q6, Q8NF44, Q9H0H1

UniProtKB/TrEMBL

B2RTU8

Related

ENSP00000349238.5, ENST00000356786.10

Conserved Domains (2) summary

TIGR02168
Location:728 → 1295

SMC_prok_B; chromosome segregation protein SMC, common bacterial type

cd22230
Location:10 → 180

HkD_Gipie; Hook domain found in Gipie (GRP78-interacting protein induced by ER stress) and similar proteins