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Aliases for BRDT Gene

Aliases for BRDT Gene

  • Bromodomain Testis Associated 2 3 5
  • Cancer/Testis Antigen 9 2 3 4
  • Bromodomain, Testis-Specific 2 3
  • RING3-Like Protein 3 4
  • CT9 3 4
  • Bromodomain Testis-Specific Protein 3
  • SPGF21 3
  • BRD6 3

External Ids for BRDT Gene

Previous GeneCards Identifiers for BRDT Gene

  • GC01P092874
  • GC01P091615
  • GC01P091752
  • GC01P091886
  • GC01P092126
  • GC01P092414
  • GC01P090535

Summaries for BRDT Gene

Entrez Gene Summary for BRDT Gene

  • BRDT is similar to the RING3 protein family. It possesses 2 bromodomain motifs and a PEST sequence (a cluster of proline, glutamic acid, serine, and threonine residues), characteristic of proteins that undergo rapid intracellular degradation. The bromodomain is found in proteins that regulate transcription. Several transcript variants encoding multiple isoforms have been found for this gene. [provided by RefSeq, Jun 2011]

GeneCards Summary for BRDT Gene

BRDT (Bromodomain Testis Associated) is a Protein Coding gene. Diseases associated with BRDT include Spermatogenic Failure 21 and Retinitis Pigmentosa 30. Among its related pathways are Chromatin Regulation / Acetylation. Gene Ontology (GO) annotations related to this gene include transcription coactivator activity and lysine-acetylated histone binding. An important paralog of this gene is BRD4.

UniProtKB/Swiss-Prot for BRDT Gene

  • Testis-specific chromatin protein that specifically binds histone H4 acetylated at Lys-5 and Lys-8 (H4K5ac and H4K8ac, respectively) and plays a key role in spermatogenesis (PubMed:22464331, PubMed:22901802). Required in late pachytene spermatocytes: plays a role in meiotic and post-meiotic cells by binding to acetylated histones at the promoter of specific meiotic and post-meiotic genes, facilitating their activation at the appropriate time (PubMed:22901802). In the post-meiotic phase of spermatogenesis, binds to hyperacetylated histones and participates in their general removal from DNA (PubMed:22901802). Also recognizes and binds a subset of butyrylated histones: able to bind histone H4 butyrylated at Lys-8 (H4K8ac), while it is not able to bind H4 butyrylated at Lys-5 (H4K5ac) (By similarity). Also acts as a component of the splicing machinery in pachytene spermatocytes and round spermatids and participates in 3-UTR truncation of specific mRNAs in post-meiotic spermatids (By similarity). Required for chromocenter organization, a structure comprised of peri-centromeric heterochromatin.

Gene Wiki entry for BRDT Gene

Additional gene information for BRDT Gene

No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for BRDT Gene

Genomics for BRDT Gene

GeneHancer (GH) Regulatory Elements for BRDT Gene

Promoters and enhancers for BRDT Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH01I091947 Promoter/Enhancer 1.1 EPDnew ENCODE 550.8 -0.7 -687 1.5 USF1 CEBPB USF2 MITF RAD51 PRDM10 ZBTB33 NFE2 CBFA2T2 BRDT EVI5 GC01P091939
GH01I091952 Promoter 0.5 EPDnew 550.8 +2.8 2803 0.1 BRDT GC01P091968
GH01I091912 Enhancer 0.5 ENCODE 11.6 -35.6 -35640 2.3 MEIS2 ZNF121 JUN MAFK BRDT GLMN TGFBR3 GC01P091939
GH01I091856 Enhancer 0.4 dbSUPER 10.2 -92.5 -92544 1.1 ZBTB33 ZIC2 ZNF18 BRDT CDC7 EVI5 GC01P091842 GC01M091855 TGFBR3
GH01I091854 Enhancer 0.2 dbSUPER 10.2 -94.2 -94150 0.7 BRDT CDC7 GC01P091842 GC01M091855 TGFBR3
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around BRDT on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the BRDT gene promoter:

Genomic Locations for BRDT Gene

Genomic Locations for BRDT Gene
chr1:91,949,371-92,014,428
(GRCh38/hg38)
Size:
65,058 bases
Orientation:
Plus strand
chr1:92,414,928-92,479,985
(GRCh37/hg19)

Genomic View for BRDT Gene

Genes around BRDT on UCSC Golden Path with GeneCards custom track

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

RefSeq DNA sequence for BRDT Gene

Proteins for BRDT Gene

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

    Protein Symbol:
    Q58F21-BRDT_HUMAN
    Recommended name:
    Bromodomain testis-specific protein
    Protein Accession:
    Q58F21
    Secondary Accessions:
    • A6NF68
    • B7Z811
    • B7Z890
    • B7ZAX7
    • D3DT32
    • O14789
    • Q05DQ4
    • Q6P5T1
    • Q7Z4A6
    • Q8IWI6

    Protein attributes for BRDT Gene

    Size:
    947 amino acids
    Molecular mass:
    107954 Da
    Quaternary structure:
    • Interacts with mRNA splicing machinery proteins SRSF2, DDX5, HNRNPK and TARDBP. Interacts with the acetylated N-terminus of histone H1, H2, H3 and H4. Interacts with P-TEFb components CDK9 and CCNT1/cyclin-T1. Interacts with SMARCE1 (By similarity). Interacts with the acetylated N-terminus of histone H1.4, H2A, H2B, H3 and H4.
    Miscellaneous:
    • BRDT is a promising target for male contraception. Inhibition by thienodiazepine inhibitor (+)-JQ1 that binds Asn-109, prevents recognition of acetylated histone H4, causing a complete and reversible contraceptive effect in male mice (PubMed:22901802).
    SequenceCaution:
    • Sequence=AAH05281.1; Type=Miscellaneous discrepancy; Note=Contaminating sequence. Potential poly-A sequence.; Evidence={ECO:0000305}; Sequence=AAH47900.1; Type=Miscellaneous discrepancy; Note=Contaminating sequence. Potential poly-A sequence.; Evidence={ECO:0000305}; Sequence=AAH62700.1; Type=Miscellaneous discrepancy; Note=Contaminating sequence. Potential poly-A sequence.; Evidence={ECO:0000305};

    Three dimensional structures from OCA and Proteopedia for BRDT Gene

    Alternative splice isoforms for BRDT Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for BRDT Gene

Post-translational modifications for BRDT Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

No data available for DME Specific Peptides for BRDT Gene

Domains & Families for BRDT Gene

Gene Families for BRDT Gene

HGNC:
Human Protein Atlas (HPA):
  • Predicted intracellular proteins

Protein Domains for BRDT Gene

Suggested Antigen Peptide Sequences for BRDT Gene

Graphical View of Domain Structure for InterPro Entry

Q58F21

UniProtKB/Swiss-Prot:

BRDT_HUMAN :
  • Bromo domains mediate interaction with histones that have acetylated lysine residues at specific positions (PubMed:22464331). Bromo domain 1 mediates binding with histone H4 acetylated at Lys-5 and Lys-8 (H4K5ac and H4K8ac, respectively) (PubMed:22901802). The bromo domains also recognize and bind a subset of butyrylated histones: able to bind histone H4 butyrylated at Lys-8 (H4K8ac), while it is not able to bind H4 butyrylated at Lys-5 (H4K5ac) (By similarity).
Domain:
  • Bromo domains mediate interaction with histones that have acetylated lysine residues at specific positions (PubMed:22464331). Bromo domain 1 mediates binding with histone H4 acetylated at Lys-5 and Lys-8 (H4K5ac and H4K8ac, respectively) (PubMed:22901802). The bromo domains also recognize and bind a subset of butyrylated histones: able to bind histone H4 butyrylated at Lys-8 (H4K8ac), while it is not able to bind H4 butyrylated at Lys-5 (H4K5ac) (By similarity).
genes like me logo Genes that share domains with BRDT: view

Function for BRDT Gene

Molecular function for BRDT Gene

GENATLAS Biochemistry:
bromodomain testis specific gene,with homology to RING3 (D6S113E) and Drosophila fsh
UniProtKB/Swiss-Prot Function:
Testis-specific chromatin protein that specifically binds histone H4 acetylated at Lys-5 and Lys-8 (H4K5ac and H4K8ac, respectively) and plays a key role in spermatogenesis (PubMed:22464331, PubMed:22901802). Required in late pachytene spermatocytes: plays a role in meiotic and post-meiotic cells by binding to acetylated histones at the promoter of specific meiotic and post-meiotic genes, facilitating their activation at the appropriate time (PubMed:22901802). In the post-meiotic phase of spermatogenesis, binds to hyperacetylated histones and participates in their general removal from DNA (PubMed:22901802). Also recognizes and binds a subset of butyrylated histones: able to bind histone H4 butyrylated at Lys-8 (H4K8ac), while it is not able to bind H4 butyrylated at Lys-5 (H4K5ac) (By similarity). Also acts as a component of the splicing machinery in pachytene spermatocytes and round spermatids and participates in 3-UTR truncation of specific mRNAs in post-meiotic spermatids (By similarity). Required for chromocenter organization, a structure comprised of peri-centromeric heterochromatin.

Phenotypes From GWAS Catalog for BRDT Gene

Gene Ontology (GO) - Molecular Function for BRDT Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003713 transcription coactivator activity TAS 10365964
GO:0042393 histone binding IDA,IEA 22464331
GO:0070577 lysine-acetylated histone binding IEA,ISS --
genes like me logo Genes that share ontologies with BRDT: view
genes like me logo Genes that share phenotypes with BRDT: view

Animal Models for BRDT Gene

MGI Knock Outs for BRDT:
  • Brdt tm1a(EUCOMM)Wtsi

miRNA for BRDT Gene

miRTarBase miRNAs that target BRDT

Clone Products

  • Addgene plasmids for BRDT

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

Localization for BRDT Gene

Subcellular locations from UniProtKB/Swiss-Prot for BRDT Gene

Nucleus. Note=Detected on chromatin. {ECO:0000250 UniProtKB:Q91Y44}.

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 BRDT gene
Compartment Confidence
nucleus 5

Gene Ontology (GO) - Cellular Components for BRDT Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus ISS --
genes like me logo Genes that share ontologies with BRDT: view

No data available for Subcellular locations from the Human Protein Atlas (HPA) for BRDT Gene

Pathways & Interactions for BRDT Gene

genes like me logo Genes that share pathways with BRDT: view

Pathways by source for BRDT Gene

1 Cell Signaling Technology pathway for BRDT Gene

Gene Ontology (GO) - Biological Process for BRDT Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0001207 histone displacement ISS --
GO:0006338 chromatin remodeling ISS,IEA --
GO:0006351 transcription, DNA-templated IEA --
GO:0006355 regulation of transcription, DNA-templated IMP 28199965
GO:0006397 mRNA processing IEA --
genes like me logo Genes that share ontologies with BRDT: view

No data available for SIGNOR curated interactions for BRDT Gene

Drugs & Compounds for BRDT Gene

(2) Drugs for BRDT Gene - From: DGIdb

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
(+)-JQ1 Pharma Potent, selective BET bromodomain inhibitor; cell permeable 0
XD14 Pharma 0
genes like me logo Genes that share compounds with BRDT: view

Transcripts for BRDT Gene

Unigene Clusters for BRDT Gene

Bromodomain, testis-specific:
Representative Sequences:

Clone Products

  • Addgene plasmids for BRDT

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

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

ExUns: 13 ^ 14 ^ 15 ^ 16 ^ 17 ^ 18 ^ 19 ^ 20
SP1:
SP2:
SP3:
SP4:
SP5:
SP6:
SP7:
SP8:
SP9:
SP10:
SP11:
SP12:
SP13:
SP14:
SP15:

Relevant External Links for BRDT Gene

GeneLoc Exon Structure for
BRDT
ECgene alternative splicing isoforms for
BRDT

Expression for BRDT Gene

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

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

This gene is overexpressed in Testis (x51.6).

Protein differential expression in normal tissues from HIPED for BRDT Gene

This gene is overexpressed in Plasma (47.7), Monocytes (10.2), and Testis (9.4).

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



Protein tissue co-expression partners for BRDT Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of BRDT Gene:

BRDT

SOURCE GeneReport for Unigene cluster for BRDT Gene:

Hs.482520

mRNA Expression by UniProt/SwissProt for BRDT Gene:

Q58F21-BRDT_HUMAN
Tissue specificity: Testis-specific. A 3-fold higher expression is seen in adult testis than in embryo testis. Expression seems to be correlated with histone H4 hyperacetylation during the haploid phase of spermatogenesis (spermiogenesis). No expression, or very low expression is seen in patients testes with abnormal spermatogenesis. Expressed in cancers such as non-small cell lung cancer and squamous cell carcinomas of the head and neck as well as of esophagus, but not in melanoma or in cancers of the colon, breast, kidney and bladder.

Evidence on tissue expression from TISSUES for BRDT Gene

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

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery and Phenotype-based relationships between genes and organs from Gene ORGANizer for BRDT Gene

Orthologs for BRDT Gene

This gene was present in the common ancestor of animals and fungi.

Orthologs for BRDT Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia BRDT 33 34
  • 99.27 (n)
dog
(Canis familiaris)
Mammalia BRDT 33 34
  • 87.09 (n)
cow
(Bos Taurus)
Mammalia BRDT 34
  • 81 (a)
OneToOne
rat
(Rattus norvegicus)
Mammalia Brdt 33
  • 77.33 (n)
mouse
(Mus musculus)
Mammalia Brdt 33 16 34
  • 77.14 (n)
platypus
(Ornithorhynchus anatinus)
Mammalia BRDT 34
  • 69 (a)
OneToOne
oppossum
(Monodelphis domestica)
Mammalia BRDT 34
  • 63 (a)
OneToOne
chicken
(Gallus gallus)
Aves BRDT 33 34
  • 64.47 (n)
lizard
(Anolis carolinensis)
Reptilia BRDT 34
  • 44 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia brdt 33
  • 60.44 (n)
zebrafish
(Danio rerio)
Actinopterygii brdt 33 34
  • 59.45 (n)
fruit fly
(Drosophila melanogaster)
Insecta fs(1)h 35 34
  • 47 (a)
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes BDF2 36
Species where no ortholog for BRDT 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)
  • 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)
  • 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 squirt (Ciona intestinalis)
  • sea squirt (Ciona savignyi)
  • 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)
  • worm (Caenorhabditis elegans)

Evolution for BRDT Gene

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

Paralogs for BRDT Gene

Paralogs for BRDT Gene

Pseudogenes.org Pseudogenes for BRDT Gene

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

Variants for BRDT Gene

Sequence variations from dbSNP and Humsavar for BRDT Gene

SNP ID Clin Chr 01 pos Variation AA Info Type
rs754258809 pathogenic, SPERMATOGENIC FAILURE 21, Spermatogenic failure 21 (SPGF21) [MIM:617644] 92,014,213(+) G/A coding_sequence_variant, missense_variant
rs781375003 A gastric adenocarcinoma sample 91,964,700(+) C/T coding_sequence_variant, intron_variant, missense_variant
VAR_041927 A lung neuroendocrine carcinoma sample p.His288Tyr
rs1000024324 -- 92,004,277(+) C/G intron_variant
rs1000048026 -- 91,983,501(+) A/G intron_variant

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

Variant ID Type Subtype PubMed ID
dgv365n54 CNV gain 21841781
esv2659029 CNV deletion 23128226
esv2714684 CNV deletion 23290073
esv2750842 CNV gain 17911159
nsv1002730 CNV gain 25217958
nsv1006318 CNV gain 25217958
nsv462517 CNV gain 19166990
nsv524845 CNV gain 19592680
nsv830581 CNV loss 17160897
nsv950207 CNV duplication 24416366

Variation tolerance for BRDT Gene

Residual Variation Intolerance Score: 78% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 10.16; 90.37% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for BRDT Gene

Human Gene Mutation Database (HGMD)
BRDT
SNPedia medical, phenotypic, and genealogical associations of SNPs for
BRDT

SNP Genotyping and Copy Number Assay Products

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

Disorders for BRDT Gene

MalaCards: The human disease database

(2) MalaCards diseases for BRDT Gene - From: HGMD, OMIM, ClinVar, DISEASES, and GeneCards

Disorder Aliases PubMed IDs
spermatogenic failure 21
  • spgf21
retinitis pigmentosa 30
  • rp30
- elite association - COSMIC cancer census association via MalaCards
Search BRDT in MalaCards View complete list of genes associated with diseases

UniProtKB/Swiss-Prot

BRDT_HUMAN
  • Spermatogenic failure 21 (SPGF21) [MIM:617644]: An infertility disorder caused by spermatogenesis defects and characterized by acephalic spermatozoa in the semen of affected individuals. SPGF21 inheritance is autosomal recessive. {ECO:0000269 PubMed:28199965}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Additional Disease Information for BRDT

Genetic Association Database
(GAD)
Human Genome Epidemiology Navigator
(HuGE)
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
genes like me logo Genes that share disorders with BRDT: view

No data available for Genatlas for BRDT Gene

Publications for BRDT Gene

  1. Identification and characterization of BRDT: A testis-specific gene related to the bromodomain genes RING3 and Drosophila fsh. (PMID: 9367677) Jones MH … Shimane M (Genomics 1997) 2 3 4 22 58
  2. Molecular cloning and expression of a novel alternative splice variant of BRDT gene. (PMID: 15647849) Zheng Y … Sha JH (International journal of molecular medicine 2005) 3 4 22 58
  3. Expression of cancer-testis antigens in lung cancer: definition of bromodomain testis-specific gene (BRDT) as a new CT gene, CT9. (PMID: 10704737) Scanlan MJ … Old LJ (Cancer letters 2000) 3 4 22 58
  4. Whole-exome sequencing identified a homozygous BRDT mutation in a patient with acephalic spermatozoa. (PMID: 28199965) Li L … Wang B (Oncotarget 2017) 3 4 58
  5. Histone recognition and large-scale structural analysis of the human bromodomain family. (PMID: 22464331) Filippakopoulos P … Knapp S (Cell 2012) 3 4 58

Products for BRDT Gene

  • Addgene plasmids for BRDT

Sources for BRDT Gene

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