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] See more...

Aliases for CCDC88B Gene

Aliases for CCDC88B Gene

  • Coiled-Coil Domain Containing 88B 2 3 5
  • BRLZ 2 3 4
  • GRP78-Interacting Protein Induced By ER Stress 2 3
  • Brain Leucine Zipper Domain-Containing Protein 3 4
  • Coiled-Coil Domain-Containing Protein 88B 3 4
  • Coiled-Coil Domain Containing 88 2 3
  • Brain Leucine Zipper Protein 2 3
  • Hook-Related Protein 3 3 4
  • Gipie 3 4
  • HkRP3 2 4
  • 78 KDa Glucose-Regulated Protein [GRP78]-Interacting Protein Induced By ER Stress 3
  • FLJ37970 2
  • FLJ00354 2
  • CCDC88B 5
  • CCDC88 3
  • HKRP3 3
  • GIPIE 2

External Ids for CCDC88B Gene

Previous HGNC Symbols for CCDC88B Gene

  • CCDC88

Previous GeneCards Identifiers for CCDC88B Gene

  • GC11P063866
  • GC11P064107
  • GC11P060435

Summaries for CCDC88B Gene

Entrez Gene Summary for CCDC88B Gene

  • 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]

GeneCards Summary for CCDC88B Gene

CCDC88B (Coiled-Coil Domain Containing 88B) is a Protein Coding gene. Diseases associated with CCDC88B include Aarskog-Scott Syndrome and Leprosy 3. An important paralog of this gene is CCDC88C.

UniProtKB/Swiss-Prot Summary for CCDC88B Gene

  • Acts as a positive regulator of T-cell maturation and inflammatory function. Required for several functions of T-cells, in both the CD4(+) and the CD8(+) compartments and this includes expression of cell surface markers of activation, proliferation, and cytokine production in response to specific or non-specific stimulation (By similarity). Enhances NK cell cytotoxicity by positively regulating polarization of microtubule-organizing center (MTOC) to cytotoxic synapse, lytic granule transport along microtubules, and dynein-mediated clustering to MTOC (PubMed:25762780). Interacts with HSPA5 and stabilizes the interaction between HSPA5 and ERN1, leading to suppression of ERN1-induced JNK activation and endoplasmic reticulum stress-induced apoptosis (PubMed:21289099).

No data available for CIViC Summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for CCDC88B Gene

Genomics for CCDC88B Gene

GeneHancer (GH) Regulatory Elements Pubs

Promoters and enhancers for CCDC88B Gene
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around CCDC88B on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for CCDC88B

Top Transcription factor binding sites by QIAGEN in the CCDC88B gene promoter:
  • CREB
  • deltaCREB
  • E47
  • Tal-1

Genomic Locations for CCDC88B Gene

Genomic Locations for CCDC88B Gene
chr11:64,340,203-64,357,534
(GRCh38/hg38)
Size:
17,332 bases
Orientation:
Plus strand
chr11:64,107,690-64,125,006
(GRCh37/hg19)
Size:
17,317 bases
Orientation:
Plus strand

Genomic View for CCDC88B Gene

Genes around CCDC88B on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
CCDC88B Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for CCDC88B Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for CCDC88B Gene

Proteins for CCDC88B Gene

  • Protein details for CCDC88B Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    A6NC98-CC88B_HUMAN
    Recommended name:
    Coiled-coil domain-containing protein 88B
    Protein Accession:
    A6NC98
    Secondary Accessions:
    • A5D8Y5
    • B5MDM2
    • Q05BL2
    • Q6RUV3
    • Q8N1Q6
    • Q8NF44
    • Q9H0H1

    Protein attributes for CCDC88B Gene

    Size:
    1476 amino acids
    Molecular mass:
    164809 Da
    Quaternary structure:
    • Homodimer (PubMed:25762780). Interacts with DOCK8 (PubMed:25762780). Interacts (via C-terminus) with intact microtubules (PubMed:25762780). Interacts with dynein-dynactin motor complex (PubMed:25762780). Interacts (via C-terminus) with HSPA5 (PubMed:21289099).
    SequenceCaution:
    • Sequence=BAC03417.1; Type=Erroneous initiation; Evidence={ECO:0000305};

    Alternative splice isoforms for CCDC88B Gene

neXtProt entry for CCDC88B Gene

Post-translational modifications for CCDC88B Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

No data available for DME Specific Peptides for CCDC88B Gene

Domains & Families for CCDC88B Gene

Gene Families for CCDC88B Gene

Human Protein Atlas (HPA):
  • Predicted intracellular proteins

Protein Domains for CCDC88B Gene

InterPro:
ProtoNet:

Suggested Antigen Peptide Sequences for CCDC88B Gene

GenScript: Design optimal peptide antigens:
  • Coiled-coil domain containing 88B (B2RTU8_HUMAN)
  • Hook-related protein 3 (CC88B_HUMAN)

Graphical View of Domain Structure for InterPro Entry

A6NC98

UniProtKB/Swiss-Prot:

CC88B_HUMAN :
  • Belongs to the CCDC88 family.
Family:
  • Belongs to the CCDC88 family.
genes like me logo Genes that share domains with CCDC88B: view

Function for CCDC88B Gene

Molecular function for CCDC88B Gene

UniProtKB/Swiss-Prot Function:
Acts as a positive regulator of T-cell maturation and inflammatory function. Required for several functions of T-cells, in both the CD4(+) and the CD8(+) compartments and this includes expression of cell surface markers of activation, proliferation, and cytokine production in response to specific or non-specific stimulation (By similarity). Enhances NK cell cytotoxicity by positively regulating polarization of microtubule-organizing center (MTOC) to cytotoxic synapse, lytic granule transport along microtubules, and dynein-mediated clustering to MTOC (PubMed:25762780). Interacts with HSPA5 and stabilizes the interaction between HSPA5 and ERN1, leading to suppression of ERN1-induced JNK activation and endoplasmic reticulum stress-induced apoptosis (PubMed:21289099).
UniProtKB/Swiss-Prot Induction:
By endoplasmic reticulum stress.

Phenotypes From GWAS Catalog for CCDC88B Gene

Gene Ontology (GO) - Molecular Function for CCDC88B Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0008017 microtubule binding IBA 21873635
GO:0051959 dynein light intermediate chain binding IBA 21873635
genes like me logo Genes that share ontologies with CCDC88B: view
genes like me logo Genes that share phenotypes with CCDC88B: view

Animal Model Products

CRISPR Products

miRNA for CCDC88B Gene

miRTarBase miRNAs that target CCDC88B

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for CCDC88B

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for CCDC88B Gene

Localization for CCDC88B Gene

Subcellular locations from UniProtKB/Swiss-Prot for CCDC88B Gene

Membrane. Peripheral membrane protein. Cytoplasm, cytoskeleton, microtubule organizing center. Endoplasmic reticulum. Golgi apparatus. Cytoplasm.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for CCDC88B gene
Compartment Confidence
endoplasmic reticulum 4
cytoskeleton 3
golgi apparatus 3
nucleus 2
plasma membrane 1
extracellular 1
mitochondrion 1
endosome 1
cytosol 1
lysosome 1
peroxisome 0

Subcellular locations from the

Human Protein Atlas (HPA)
  • Centrosome (2)
  • Cytosol (2)
  • Nucleoplasm (2)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for CCDC88B Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005737 cytoplasm IBA 21873635
GO:0005783 endoplasmic reticulum IEA --
GO:0005794 Golgi apparatus IEA --
GO:0005813 centrosome IBA 21873635
GO:0005856 cytoskeleton IEA --
genes like me logo Genes that share ontologies with CCDC88B: view

Pathways & Interactions for CCDC88B Gene

PathCards logo

SuperPathways for CCDC88B Gene

No Data Available

Gene Ontology (GO) - Biological Process for CCDC88B Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0001819 positive regulation of cytokine production ISS --
GO:0030705 cytoskeleton-dependent intracellular transport IBA 21873635
GO:0031122 cytoplasmic microtubule organization IBA 21873635
GO:0042102 positive regulation of T cell proliferation ISS --
GO:0042832 defense response to protozoan IEA --
genes like me logo Genes that share ontologies with CCDC88B: view

No data available for Pathways by source and SIGNOR curated interactions for CCDC88B Gene

Drugs & Compounds for CCDC88B Gene

No Compound Related Data Available

Transcripts for CCDC88B Gene

mRNA/cDNA for CCDC88B Gene

1 REFSEQ mRNAs :
14 NCBI additional mRNA sequence :
10 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for CCDC88B

Alternative Splicing Database (ASD) splice patterns (SP) for CCDC88B Gene

ExUns: 1 ^ 2a · 2b ^ 3 ^ 4 ^ 5 ^ 6a · 6b ^ 7a · 7b ^ 8 ^ 9 ^ 10a · 10b · 10c ^ 11 ^ 12a · 12b ^ 13 ^ 14 ^ 15a · 15b ^ 16 ^ 17a · 17b ^ 18a ·
SP1: -
SP2:
SP3: - -
SP4: -
SP5:
SP6:
SP7:
SP8:
SP9:
SP10: - -
SP11:
SP12: - - -
SP13:
SP14:
SP15:

ExUns: 18b ^ 19 ^ 20 ^ 21a · 21b · 21c ^ 22a · 22b ^ 23a · 23b · 23c · 23d
SP1:
SP2:
SP3:
SP4:
SP5:
SP6: - - -
SP7:
SP8:
SP9: -
SP10:
SP11:
SP12:
SP13:
SP14:
SP15:

Relevant External Links for CCDC88B Gene

GeneLoc Exon Structure for
CCDC88B

Expression for CCDC88B Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for CCDC88B Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for CCDC88B Gene

This gene is overexpressed in Whole Blood (x14.3), Brain - Cerebellum (x5.4), Brain - Cerebellar Hemisphere (x5.3), and Spleen (x4.2).

Protein differential expression in normal tissues from HIPED for CCDC88B Gene

This gene is overexpressed in Islet of Langerhans (15.9), Urinary Bladder (13.4), and Peripheral blood mononuclear cells (10.8).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB and MOPED for CCDC88B Gene



Protein tissue co-expression partners for CCDC88B Gene

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for CCDC88B

SOURCE GeneReport for Unigene cluster for CCDC88B Gene:

Hs.98564

mRNA Expression by UniProt/SwissProt for CCDC88B Gene:

A6NC98-CC88B_HUMAN
Tissue specificity: Expressed in endothelium (at protein level) (PubMed:21289099). Expressed in NK cells (at protein level) (PubMed:25762780).

Evidence on tissue expression from TISSUES for CCDC88B Gene

  • Spleen(4.4)
  • Liver(4.3)
  • Nervous system(4.3)
  • Bone marrow(2.1)
genes like me logo Genes that share expression patterns with CCDC88B: view

No data available for Phenotype-based relationships between genes and organs from Gene ORGANizer for CCDC88B Gene

Orthologs for CCDC88B Gene

This gene was present in the common ancestor of animals.

Orthologs for CCDC88B Gene

Organism Taxonomy Gene Similarity Type Details
Chimpanzee
(Pan troglodytes)
Mammalia CCDC88B 30 31
  • 99.46 (n)
OneToOne
Cow
(Bos Taurus)
Mammalia CCDC88B 30 31
  • 85.5 (n)
OneToOne
Dog
(Canis familiaris)
Mammalia CCDC88B 30 31
  • 84.52 (n)
OneToOne
Mouse
(Mus musculus)
Mammalia Ccdc88b 30 17 31
  • 80.48 (n)
OneToOne
Rat
(Rattus norvegicus)
Mammalia Ccdc88b 30
  • 80.46 (n)
Oppossum
(Monodelphis domestica)
Mammalia CCDC88B 31
  • 75 (a)
OneToOne
Lizard
(Anolis carolinensis)
Reptilia CCDC88B 31
  • 28 (a)
OneToOne
Zebrafish
(Danio rerio)
Actinopterygii ccdc88b 30 31
  • 51.77 (n)
OneToOne
Fruit Fly
(Drosophila melanogaster)
Insecta Girdin 31
  • 22 (a)
OneToMany
Worm
(Caenorhabditis elegans)
Secernentea grdn-1 31
  • 18 (a)
OneToMany
Sea Squirt
(Ciona savignyi)
Ascidiacea CSA.3137 31
  • 23 (a)
OneToMany
Species where no ortholog for CCDC88B was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Eremothecium gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • Alpha proteobacteria (Wolbachia pipientis)
  • Amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • Baker's yeast (Saccharomyces cerevisiae)
  • Barley (Hordeum vulgare)
  • Beta proteobacteria (Neisseria meningitidis)
  • Bread mold (Neurospora crassa)
  • Chicken (Gallus gallus)
  • Chromalveolata (Phytophthora infestans)
  • Common water flea (Daphnia pulex)
  • Corn (Zea mays)
  • E. coli (Escherichia coli)
  • Filamentous fungi (Aspergillus nidulans)
  • Firmicute Bacteria (Streptococcus pneumoniae)
  • Fission Yeast (Schizosaccharomyces pombe)
  • Green Algae (Chlamydomonas reinhardtii)
  • Honey Bee (Apis mellifera)
  • K. Lactis Yeast (Kluyveromyces lactis)
  • Loblloly Pine (Pinus taeda)
  • Malaria Parasite (Plasmodium falciparum)
  • Medicago Trunc (Medicago Truncatula)
  • Moss (Physcomitrella patens)
  • Orangutan (Pongo pygmaeus)
  • Pig (Sus scrofa)
  • Platypus (Ornithorhynchus anatinus)
  • Rainbow Trout (Oncorhynchus mykiss)
  • Rice (Oryza sativa)
  • Rice Blast Fungus (Magnaporthe grisea)
  • Schistosome Parasite (Schistosoma mansoni)
  • Sea Anemone (Nematostella vectensis)
  • Sea Vase (Ciona intestinalis)
  • Sea Urchin (Strongylocentrotus purpuratus)
  • Sorghum (Sorghum bicolor)
  • Soybean (Glycine max)
  • Stem Rust Fungus (Puccinia graminis)
  • Sugarcane (Saccharum officinarum)
  • Thale Cress (Arabidopsis thaliana)
  • Tomato (Lycopersicon esculentum)
  • Toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • Tropical Clawed Frog (Silurana tropicalis)
  • Wheat (Triticum aestivum)

Evolution for CCDC88B Gene

ENSEMBL:
Gene Tree for CCDC88B (if available)
TreeFam:
Gene Tree for CCDC88B (if available)
Aminode:
Evolutionary constrained regions (ECRs) for CCDC88B: view image

Paralogs for CCDC88B Gene

Paralogs for CCDC88B Gene

(3) SIMAP similar genes for CCDC88B Gene using alignment to 3 proteins:

  • CC88B_HUMAN
  • B2RTU8_HUMAN
  • H7BY33_HUMAN
genes like me logo Genes that share paralogs with CCDC88B: view

Variants for CCDC88B Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for CCDC88B Gene

SNP ID Clinical significance and condition Chr 11 pos Variation AA Info Type
771746 Benign: not provided 64,353,363(+) C/T SYNONYMOUS_VARIANT
rs1318165 - p.Asp886Ala
rs647152 - p.Asp193Glu
rs685870 - p.Trp639Arg

Additional dbSNP identifiers (rs#s) for CCDC88B Gene

Structural Variations from Database of Genomic Variants (DGV) for CCDC88B Gene

Variant ID Type Subtype PubMed ID
dgv13n64 CNV loss 17921354
nsv1069590 CNV deletion 25765185
nsv1113398 CNV deletion 24896259
nsv1119885 CNV deletion 24896259
nsv358 CNV insertion 18451855
nsv555192 CNV loss 21841781
nsv555193 CNV loss 21841781
nsv832186 CNV loss 17160897
nsv832187 CNV loss 17160897
nsv951010 CNV deletion 24416366

Variation tolerance for CCDC88B Gene

Residual Variation Intolerance Score: 98.5% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 8.46; 85.73% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for CCDC88B Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
CCDC88B

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for CCDC88B Gene

Disorders for CCDC88B Gene

MalaCards: The human disease database

(2) MalaCards diseases for CCDC88B Gene - From: DISEASES

Disorder Aliases PubMed IDs
aarskog-scott syndrome
  • aas
leprosy 3
  • leprosy, susceptibility to, 3
- elite association - COSMIC cancer census association via MalaCards
genes like me logo Genes that share disorders with CCDC88B: view

No data available for UniProtKB/Swiss-Prot and Genatlas for CCDC88B Gene

Publications for CCDC88B Gene

  1. Protective role of Gipie, a Girdin family protein, in endoplasmic reticulum stress responses in endothelial cells. (PMID: 21289099) Matsushita E … Takahashi M (Molecular biology of the cell 2011) 2 3 4
  2. HkRP3 is a microtubule-binding protein regulating lytic granule clustering and NK cell killing. (PMID: 25762780) Ham H … Billadeau DD (Journal of immunology (Baltimore, Md. : 1950) 2015) 3 4
  3. A novel hook-related protein family and the characterization of hook-related protein 1. (PMID: 15882442) Simpson F … Wicking C (Traffic (Copenhagen, Denmark) 2005) 2 3
  4. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T … Sugano S (Nature genetics 2004) 3 4
  5. Toward a catalog of human genes and proteins: sequencing and analysis of 500 novel complete protein coding human cDNAs. (PMID: 11230166) Wiemann S … Poustka A (Genome research 2001) 3 4

Products for CCDC88B Gene

Sources for CCDC88B Gene