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Aliases for CCDC88B Gene

Aliases for CCDC88B Gene

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

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. An important paralog of this gene is CCDC88C.

UniProtKB/Swiss-Prot 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 , fRNAdb sequence ontologies and piRNA Summary for CCDC88B Gene

Genomics for CCDC88B Gene

Regulatory Elements for CCDC88B Gene

Enhancers for CCDC88B Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH11G064338 1.3 ENCODE dbSUPER 22.1 +0.9 877 4.4 HDGF ATF1 PKNOX1 CREB3L1 AGO1 ARID4B SIN3A ELK1 ZNF207 ZNF143 LOC102723878 CCDC88B PLCB3 TRMT112 MIR7155
GH11G064205 1.4 ENCODE dbSUPER 8.6 -132.6 -132602 4.4 HDGF PKNOX1 CREB3L1 ARNT AGO1 ARID4B SIN3A DMAP1 ZNF2 YY1 ZFPL1 TRPT1 ENSG00000257086 PLCB3 TRMT112 GPR137 BAD KCNK4-TEX40 KCNK4 ENSG00000207024
GH11G064180 1.2 Ensembl ENCODE 8.5 -158.6 -158640 2.1 HDGF PKNOX1 ATF1 ARNT ARID4B SIN3A ZNF2 ZNF48 SLC30A9 ZNF121 TRPT1 FERMT3 PLCB3 ENSG00000257086 ENSG00000256341 NAA40 CCDC88B STIP1 PIR62169
GH11G064097 1.1 ENCODE dbSUPER 8.7 -241.7 -241694 1.5 PKNOX1 BMI1 NFXL1 FEZF1 ZBTB40 RARA ZNF121 ZSCAN5C ETV6 RELB TRMT112 VEGFB CCDC88B PIR46997 ENSG00000256481
GH11G064163 1.1 ENCODE 8.5 -174.8 -174774 4.0 HDGF PKNOX1 FOXA2 CREB3L1 ARID4B SIN3A DMAP1 YY1 SLC30A9 ZNF766 TRPT1 TRMT112 ENSG00000256481 ENSG00000256341 NAA40 CCDC88B ENSG00000256116 TM7SF2 MACROD1 PIR54353
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around CCDC88B on UCSC Golden Path with GeneCards custom track

Promoters for CCDC88B Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00000040657 203 401 HDGF CTCF PKNOX1 MXI1 BACH1 EBF1 ZBTB40 RELA ELK1 POLR2A

Genomic Location for CCDC88B Gene

Chromosome:
11
Start:
64,340,197 bp from pter
End:
64,357,534 bp from pter
Size:
17,338 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

Protein Domains for CCDC88B Gene

InterPro:
ProtoNet:

Suggested Antigen Peptide Sequences for CCDC88B Gene

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

No data available for Gene Families for CCDC88B Gene

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.

Gene Ontology (GO) - Molecular Function for CCDC88B Gene

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

Phenotypes for CCDC88B Gene

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

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
cytosol 2
extracellular 1
mitochondrion 1
peroxisome 1
lysosome 1

Gene Ontology (GO) - Cellular Components for CCDC88B Gene

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

Pathways & Interactions for CCDC88B Gene

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 --
GO:0031122 cytoplasmic microtubule organization IBA --
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

Unigene Clusters for CCDC88B Gene

Coiled-coil domain containing 88B:
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

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
ECgene alternative splicing isoforms for
CCDC88B

Expression for CCDC88B Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP 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, PaxDb, and MOPED for CCDC88B Gene



Protein tissue co-expression partners for CCDC88B Gene

NURSA nuclear receptor signaling pathways regulating expression of CCDC88B Gene:

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(4.3)
  • Liver(4.2)
  • Nervous system(4.2)
genes like me logo Genes that share expression patterns with CCDC88B: view

Primer Products

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 34 35
  • 99.46 (n)
cow
(Bos Taurus)
Mammalia CCDC88B 34 35
  • 85.5 (n)
dog
(Canis familiaris)
Mammalia CCDC88B 34 35
  • 84.52 (n)
mouse
(Mus musculus)
Mammalia Ccdc88b 34 16 35
  • 80.48 (n)
rat
(Rattus norvegicus)
Mammalia Ccdc88b 34
  • 80.46 (n)
oppossum
(Monodelphis domestica)
Mammalia CCDC88B 35
  • 75 (a)
OneToOne
lizard
(Anolis carolinensis)
Reptilia CCDC88B 35
  • 28 (a)
OneToOne
zebrafish
(Danio rerio)
Actinopterygii ccdc88b 34 35
  • 51.77 (n)
fruit fly
(Drosophila melanogaster)
Insecta Girdin 35
  • 22 (a)
OneToMany
worm
(Caenorhabditis elegans)
Secernentea grdn-1 35
  • 18 (a)
OneToMany
sea squirt
(Ciona savignyi)
Ascidiacea CSA.3137 35
  • 23 (a)
OneToMany
Species where no ortholog for CCDC88B was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya 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 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)

Paralogs for CCDC88B Gene

Paralogs for CCDC88B Gene

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

genes like me logo Genes that share paralogs with CCDC88B: view

Variants for CCDC88B Gene

Sequence variations from dbSNP and Humsavar for CCDC88B Gene

SNP ID Clin Chr 11 pos Sequence Context AA Info Type
rs1000167890 -- 64,342,443(+) CCTCC(C/T)TCCCA intron-variant, upstream-variant-2KB
rs1000173374 -- 64,349,207(+) CCCAA(A/G)GGCTT intron-variant
rs1000383749 -- 64,343,798(+) CGGCC(A/C)CCTCG nc-transcript-variant, upstream-variant-2KB, reference, missense
rs1000436154 -- 64,355,197(+) AGGGT(A/C)CCCTT nc-transcript-variant, reference, missense
rs1000475294 -- 64,354,960(+) CCCCC(C/T)CCCTG intron-variant

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)

Relevant External Links 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

Relevant External Links for CCDC88B

Atlas of Genetics and Cytogenetics in Oncology and Haematology:
CCDC88B

No disorders were found for CCDC88B Gene.

No data available for MalaCards , 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. (Mol. Biol. Cell 2011) 2 3 4 64
  2. HkRP3 is a microtubule-binding protein regulating lytic granule clustering and NK cell killing. (PMID: 25762780) Ham H. … Billadeau D.D. (J. Immunol. 2015) 3 4 64
  3. A novel hook-related protein family and the characterization of hook- related protein 1. (PMID: 15882442) Simpson F. … Wicking C. (Traffic 2005) 2 3 64
  4. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T. … Sugano S. (Nat. Genet. 2004) 3 4 64
  5. Towards 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 Res. 2001) 3 4 64

Products for CCDC88B Gene

Sources for CCDC88B Gene

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