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Aliases for TTC39B Gene

Aliases for TTC39B Gene

  • Tetratricopeptide Repeat Domain 39B 2 3 5
  • TPR Repeat Protein 39B 3 4
  • C9orf52 3 4
  • Tetratricopeptide Repeat Protein 39B 3
  • Chromosome 9 Open Reading Frame 52 2

External Ids for TTC39B Gene

Previous HGNC Symbols for TTC39B Gene

  • C9orf52

Previous GeneCards Identifiers for TTC39B Gene

  • GC09M015162

Summaries for TTC39B Gene

GeneCards Summary for TTC39B Gene

TTC39B (Tetratricopeptide Repeat Domain 39B) is a Protein Coding gene. An important paralog of this gene is TTC39A.

No data available for Entrez Gene Summary , CIViC summary , UniProtKB/Swiss-Prot , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for TTC39B Gene

Genomics for TTC39B Gene

Regulatory Elements for TTC39B Gene

Enhancers for TTC39B 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
GH09G015304 1.6 FANTOM5 ENCODE dbSUPER 29.3 +0.5 526 4.7 PKNOX1 ARID4B SIN3A DMAP1 ZNF48 YY1 GLIS2 FOS SP3 SP5 TTC39B PIR49655
GH09G015293 1.7 FANTOM5 Ensembl ENCODE dbSUPER 22 +10.2 10187 8.2 ATF1 PKNOX1 ZNF133 ZBTB40 RAD21 YY1 ZNF335 FOS ETV6 CREM TTC39B PSIP1 PIR49655
GH09G015285 0.9 ENCODE dbSUPER 16.5 +20.5 20503 1.8 ZNF639 HDAC1 ATF1 L3MBTL2 USF2 MNT FOXA1 ZNF217 RAD51 GATA3 TTC39B PIR49655
GH09G015275 1 ENCODE dbSUPER 11.7 +30.0 30002 3.1 HNRNPUL1 CTCF NFIB ZMYM3 ZBTB40 RAD21 GATA3 CTBP1 ADNP SMC3 TTC39B PSIP1 PIR49655
GH09G015331 0.9 ENCODE 11.2 -25.7 -25682 3.1 ELF3 HNRNPUL1 ATF1 MLX ARID4B THRB ZSCAN9 RAD21 YY1 RARA TTC39B GC09P015350
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around TTC39B on UCSC Golden Path with GeneCards custom track

Promoters for TTC39B Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00000233379 460 1801 PKNOX1 ARID4B SIN3A DMAP1 ZNF48 YY1 GLIS2 SP3 SP5 MXD4

Genomic Location for TTC39B Gene

Chromosome:
9
Start:
15,163,622 bp from pter
End:
15,307,360 bp from pter
Size:
143,739 bases
Orientation:
Minus strand

Genomic View for TTC39B Gene

Genes around TTC39B on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
TTC39B Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for TTC39B Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for TTC39B Gene

Proteins for TTC39B Gene

  • Protein details for TTC39B Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q5VTQ0-TT39B_HUMAN
    Recommended name:
    Tetratricopeptide repeat protein 39B
    Protein Accession:
    Q5VTQ0
    Secondary Accessions:
    • A5PLN1
    • B4DQ10
    • B4DQX4
    • B4DW93
    • Q8IVR7
    • Q8IXZ6
    • Q8N267

    Protein attributes for TTC39B Gene

    Size:
    682 amino acids
    Molecular mass:
    76956 Da
    Quaternary structure:
    No Data Available
    SequenceCaution:
    • Sequence=AAH42417.1; Type=Erroneous initiation; Note=Translation N-terminally shortened.; Evidence={ECO:0000305}; Sequence=AAI42986.1; Type=Erroneous initiation; Note=Translation N-terminally extended.; Evidence={ECO:0000305}; Sequence=BAC03603.1; Type=Erroneous initiation; Note=Translation N-terminally extended.; Evidence={ECO:0000305}; Sequence=BAG60772.1; Type=Erroneous initiation; Note=Translation N-terminally extended.; Evidence={ECO:0000305}; Sequence=CAH71481.1; Type=Erroneous initiation; Note=Translation N-terminally extended.; Evidence={ECO:0000305};

    Alternative splice isoforms for TTC39B Gene

neXtProt entry for TTC39B Gene

Post-translational modifications for TTC39B Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

No data available for DME Specific Peptides for TTC39B Gene

Domains & Families for TTC39B Gene

Gene Families for TTC39B Gene

Protein Domains for TTC39B Gene

Graphical View of Domain Structure for InterPro Entry

Q5VTQ0

UniProtKB/Swiss-Prot:

TT39B_HUMAN :
  • Belongs to the TTC39 family.
Family:
  • Belongs to the TTC39 family.
genes like me logo Genes that share domains with TTC39B: view

Function for TTC39B Gene

genes like me logo Genes that share phenotypes with TTC39B: view

Animal Models for TTC39B Gene

MGI Knock Outs for TTC39B:

Animal Model Products

  • Taconic Biosciences Mouse Models for TTC39B

CRISPR Products

miRNA for TTC39B Gene

miRTarBase miRNAs that target TTC39B

No data available for Molecular function , Enzyme Numbers (IUBMB) , Gene Ontology (GO) - Molecular Function , Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for TTC39B Gene

Localization for TTC39B Gene

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 TTC39B gene
Compartment Confidence
extracellular 1
peroxisome 1
cytosol 1

No data available for Subcellular locations from UniProtKB/Swiss-Prot and Gene Ontology (GO) - Cellular Components for TTC39B Gene

Pathways & Interactions for TTC39B Gene

SuperPathways for TTC39B Gene

No Data Available

Gene Ontology (GO) - Biological Process for TTC39B Gene

None

No data available for Pathways by source and SIGNOR curated interactions for TTC39B Gene

Drugs & Compounds for TTC39B Gene

No Compound Related Data Available

Transcripts for TTC39B Gene

Unigene Clusters for TTC39B Gene

Tetratricopeptide repeat domain 39B:
Representative Sequences:

CRISPR Products

Alternative Splicing Database (ASD) splice patterns (SP) for TTC39B Gene

ExUns: 1 ^ 2 ^ 3 ^ 4 ^ 5 ^ 6a · 6b · 6c ^ 7 ^ 8 ^ 9a · 9b ^ 10 ^ 11 ^ 12 ^ 13 ^ 14 ^ 15 ^ 16 ^ 17 ^ 18 ^ 19 ^ 20 ^ 21 ^ 22 ^ 23 ^
SP1: - - - - -
SP2: -
SP3:
SP4:
SP5:

ExUns: 24a · 24b
SP1:
SP2:
SP3:
SP4:
SP5:

Relevant External Links for TTC39B Gene

GeneLoc Exon Structure for
TTC39B
ECgene alternative splicing isoforms for
TTC39B

Expression for TTC39B Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for TTC39B Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Protein differential expression in normal tissues from HIPED for TTC39B Gene

This gene is overexpressed in Urine (32.1), Peripheral blood mononuclear cells (22.6), and Heart (6.4).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MaxQB, and MOPED for TTC39B Gene



Protein tissue co-expression partners for TTC39B Gene

NURSA nuclear receptor signaling pathways regulating expression of TTC39B Gene:

TTC39B

SOURCE GeneReport for Unigene cluster for TTC39B Gene:

Hs.563630

Evidence on tissue expression from TISSUES for TTC39B Gene

  • Nervous system(2.9)
genes like me logo Genes that share expression patterns with TTC39B: view

Primer Products

No data available for mRNA differential expression in normal tissues , mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for TTC39B Gene

Orthologs for TTC39B Gene

This gene was present in the common ancestor of animals.

Orthologs for TTC39B Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia TTC39B 34 35
  • 99.27 (n)
dog
(Canis familiaris)
Mammalia TTC39B 34 35
  • 90.49 (n)
cow
(Bos Taurus)
Mammalia TTC39B 34 35
  • 87.94 (n)
rat
(Rattus norvegicus)
Mammalia Ttc39b 34
  • 85.31 (n)
mouse
(Mus musculus)
Mammalia Ttc39b 34 16 35
  • 84.55 (n)
platypus
(Ornithorhynchus anatinus)
Mammalia TTC39B 35
  • 70 (a)
OneToOne
oppossum
(Monodelphis domestica)
Mammalia TTC39B 35
  • 69 (a)
OneToOne
chicken
(Gallus gallus)
Aves TTC39B 34 35
  • 74.65 (n)
lizard
(Anolis carolinensis)
Reptilia TTC39B 35
  • 70 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia ttc39b 34
  • 69.41 (n)
African clawed frog
(Xenopus laevis)
Amphibia Xl.18685 34
zebrafish
(Danio rerio)
Actinopterygii zgc:158403 35
  • 52 (a)
ManyToMany
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP010417 34
  • 50.4 (n)
worm
(Caenorhabditis elegans)
Secernentea C32D5.6 34 35
  • 49.34 (n)
sea squirt
(Ciona savignyi)
Ascidiacea -- 35
  • 42 (a)
OneToMany
Species where no ortholog for TTC39B was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • 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)
  • 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)
  • fruit fly (Drosophila melanogaster)
  • 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)
  • 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)
  • wheat (Triticum aestivum)

Evolution for TTC39B Gene

ENSEMBL:
Gene Tree for TTC39B (if available)
TreeFam:
Gene Tree for TTC39B (if available)

Paralogs for TTC39B Gene

Paralogs for TTC39B Gene

(1) SIMAP similar genes for TTC39B Gene using alignment to 3 proteins:

Pseudogenes.org Pseudogenes for TTC39B Gene

genes like me logo Genes that share paralogs with TTC39B: view

Variants for TTC39B Gene

Sequence variations from dbSNP and Humsavar for TTC39B Gene

SNP ID Clin Chr 09 pos Sequence Context AA Info Type
rs1000013287 -- 15,211,046(+) GAAAT(-/C)CCCCC intron-variant
rs1000018578 -- 15,216,672(+) TATAG(A/G)CCCAT intron-variant
rs1000030042 -- 15,216,437(+) GGAGG(A/G)CTAAG intron-variant
rs1000044345 -- 15,284,457(+) GAAAT(C/T)AGAAT intron-variant
rs1000061952 -- 15,199,936(+) AATAA(C/T)TCAGT intron-variant

Structural Variations from Database of Genomic Variants (DGV) for TTC39B Gene

Variant ID Type Subtype PubMed ID
dgv12573n54 CNV loss 21841781
esv2677212 CNV deletion 23128226
esv2761504 CNV loss 21179565
esv2761505 CNV gain 21179565
esv2762797 CNV loss 21179565
esv3619762 CNV loss 21293372
esv3619763 CNV gain 21293372
esv3619765 CNV loss 21293372
esv3619766 CNV gain 21293372
esv3619768 CNV loss 21293372
esv3619769 CNV gain 21293372
esv3619771 CNV loss 21293372
esv3619772 CNV loss 21293372
esv3619774 CNV loss 21293372
esv3619775 CNV loss 21293372
nsv1015960 CNV loss 25217958
nsv436610 CNV deletion 17901297
nsv517975 CNV loss 19592680
nsv521191 CNV loss 19592680
nsv524381 CNV gain 19592680
nsv524849 CNV loss 19592680
nsv831519 CNV loss 17160897

Variation tolerance for TTC39B Gene

Residual Variation Intolerance Score: 35.3% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 3.08; 50.74% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for TTC39B Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
TTC39B

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for TTC39B Gene

Disorders for TTC39B Gene

Relevant External Links for TTC39B

Genetic Association Database (GAD)
TTC39B
Human Genome Epidemiology (HuGE) Navigator
TTC39B
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
TTC39B

No disorders were found for TTC39B Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for TTC39B Gene

Publications for TTC39B Gene

  1. Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score. (PMID: 20379614) Rose J.E. … Uhl G.R. (Mol. Med. 2010) 3 46 64
  2. Evaluating the discriminative power of multi-trait genetic risk scores for type 2 diabetes in a northern Swedish population. (PMID: 20571754) Fontaine-Bisson B. … Franks P.W. (Diabetologia 2010) 3 46 64
  3. Biological, clinical and population relevance of 95 loci for blood lipids. (PMID: 20686565) Teslovich T.M. … Kathiresan S. (Nature 2010) 3 46 64
  4. Genetic variants influencing circulating lipid levels and risk of coronary artery disease. (PMID: 20864672) Waterworth D.M. … Sandhu M.S. (Arterioscler. Thromb. Vasc. Biol. 2010) 3 46 64
  5. Common variants at 30 loci contribute to polygenic dyslipidemia. (PMID: 19060906) Kathiresan S. … Cupples L.A. (Nat. Genet. 2009) 3 46 64

Products for TTC39B Gene

Sources for TTC39B Gene

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