TDRD9 tudor domain containing 9 [Homo sapiens (human)] - Gene

Summary

Official Symbol: TDRD9provided by HGNC
Official Full Name: tudor domain containing 9provided by HGNC
Primary source: HGNC:HGNC:20122
See related: Ensembl:ENSG00000156414 MIM:617963; AllianceGenome:HGNC:20122
Gene type: protein coding
RefSeq status: VALIDATED
Organism: Homo sapiens
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as: HLS; SPNE; HIG-1; NET54; SPGF30; C14orf75
Summary: Predicted to enable RNA binding activity. Involved in spermatogenesis. Located in cytoplasm and nucleus. Implicated in spermatogenic failure 30. [provided by Alliance of Genome Resources, Apr 2022]
Expression: Biased expression in testis (RPKM 26.4) and thyroid (RPKM 5.7) See more
Orthologs: mouse all
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Genomic context

Location:: 14q32.33

Exon count:: 38

Annotation release	Status	Assembly	Chr	Location
RS_2023_10	current	GRCh38.p14 (GCF_000001405.40)	14	NC_000014.9 (103928456..104052667)
RS_2023_10	current	T2T-CHM13v2.0 (GCF_009914755.1)	14	NC_060938.1 (98165768..98289910)
105.20220307	previous assembly	GRCh37.p13 (GCF_000001405.25)	14	NC_000014.8 (104394793..104519004)

Chromosome 14 - NC_000014.9 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?

Mutational alterations of TDRD 1, 4 and 9 genes in colorectal cancers.
Title: Mutational alterations of TDRD 1, 4 and 9 genes in colorectal cancers.
Here we evaluate gene and protein expression levels of four key TDRDs (TDRD1, TDRD5, TDRD9 and TDRD12) in testicular biopsy samples obtained from men with obstructive azoospermia (OA, n = 29), as controls, and various types of non-obstructive azoospermia containing hypospermatogenesis (HP, 28), maturation arrest (MA, n = 30), and Sertoli cell-only syndrome (SCOS, n = 32) as cases.
Title: Testicular expression of TDRD1, TDRD5, TDRD9 and TDRD12 in azoospermia.
first report of a recessive deleterious mutation in TDRD9 in humans; study demonstrates that non-obstructive azoospermia can be caused by a mutation in TDRD9
Title: Mutation in TDRD9 causes non-obstructive azoospermia in infertile men.
Observational study and genome-wide association study of gene-disease association. (HuGE Navigator)
Title: Genome-wide searching of rare genetic variants in WTCCC data.
Observational study of gene-disease association. (HuGE Navigator)
Title: Family-based association study for bipolar affective disorder.

Submit: New GeneRIF Correction

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

Associated conditions

Description	Tests
Spermatogenic failure 30 MedGen: C4748224 OMIM: 618110 GeneReviews: Not available	Compare labs

EBI GWAS Catalog

Description
Genome-wide association study of 14,000 cases of seven common diseases and 3,000 shared controls. EBI GWAS Catalog EBI GWAS CatalogPubMed
Propensity score-based nonparametric test revealing genetic variants underlying bipolar disorder. 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

NoName (e-PCR)
- UniSTS:487171

G35738 (e-PCR)
- UniSTS:30497

RH104332 (e-PCR)
- UniSTS:98657

G35566 (e-PCR)
- UniSTS:19814

D14S940 (e-PCR)
- UniSTS:2685

G35533 (e-PCR)
- UniSTS:59291

G35706 (e-PCR)
- UniSTS:31389

G36281 (e-PCR)
- UniSTS:40114

TDRD9__5236 (e-PCR)
- UniSTS:464599

G35366 (e-PCR)
- UniSTS:29940

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables ATP binding	IEA Inferred from Electronic Annotation more info
enables ATP hydrolysis activity	ISS Inferred from Sequence or Structural Similarity more info
enables RNA binding	IBA Inferred from Biological aspect of Ancestor more info
enables RNA helicase activity	IEA Inferred from Electronic Annotation more info
enables helicase activity	IBA Inferred from Biological aspect of Ancestor more info

Process	Evidence Code	Pubs
involved_in cell differentiation	IEA Inferred from Electronic Annotation more info
involved_in fertilization	ISS Inferred from Sequence or Structural Similarity more info
involved_in male meiosis I	ISS Inferred from Sequence or Structural Similarity more info
involved_in male meiotic nuclear division	ISS Inferred from Sequence or Structural Similarity more info
involved_in piRNA processing	ISS Inferred from Sequence or Structural Similarity more info
involved_in piRNA-mediated retrotransposon silencing by heterochromatin formation	ISS Inferred from Sequence or Structural Similarity more info
involved_in siRNA-mediated retrotransposon silencing by heterochromatin formation	ISS Inferred from Sequence or Structural Similarity more info
involved_in spermatogenesis	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in spermatogenesis	ISS Inferred from Sequence or Structural Similarity more info

Component	Evidence Code	Pubs
located_in cytoplasm	IDA Inferred from Direct Assay more info	PubMed
is_active_in intracellular anatomical structure	IBA Inferred from Biological aspect of Ancestor more info
located_in nucleus	IDA Inferred from Direct Assay more info	PubMed
located_in piP-body	ISS Inferred from Sequence or Structural Similarity more info

General protein information

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Preferred Names: ATP-dependent RNA helicase TDRD9

Names: hypoxia-inducible HIG-1; putative ATP-dependent RNA helicase TDRD9; tudor domain-containing protein 9

NP_694591.2

EC 3.6.4.13

XP_005267366.1

EC 3.6.4.13

XP_006720082.1

EC 3.6.4.13

XP_006720083.1

EC 3.6.4.13

XP_011534699.1

EC 3.6.4.13

XP_011534700.1

EC 3.6.4.13

XP_011534702.1

EC 3.6.4.13

XP_011534704.1

EC 3.6.4.13

XP_047286865.1

EC 3.6.4.13

XP_047286866.1

EC 3.6.4.13

XP_047286867.1

EC 3.6.4.13

XP_047286868.1

EC 3.6.4.13

XP_054231303.1

EC 3.6.4.13

XP_054231304.1

EC 3.6.4.13

XP_054231305.1

EC 3.6.4.13

XP_054231306.1

EC 3.6.4.13

XP_054231307.1

EC 3.6.4.13

XP_054231308.1

EC 3.6.4.13

XP_054231309.1

EC 3.6.4.13

XP_054231310.1

EC 3.6.4.13

XP_054231311.1

EC 3.6.4.13

XP_054231312.1

EC 3.6.4.13

XP_054231313.1

EC 3.6.4.13

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_153046.3 → NP_694591.2 ATP-dependent RNA helicase TDRD9

See identical proteins and their annotated locations for NP_694591.2

Status: VALIDATED

Source sequence(s)

AL132712, AL136001

Consensus CDS

CCDS9987.2

UniProtKB/Swiss-Prot

A1A4S7, Q6ZU54, Q8N7T3, Q8N827, Q8N9V5, Q8NDG6, Q96AS9

Related

ENSP00000387303.4, ENST00000409874.9

Conserved Domains (2) summary

COG1643
Location:132 → 716

HrpA; HrpA-like RNA helicase [Translation, ribosomal structure and biogenesis]

cd20431
Location:905 → 1005

Tudor_TDRD9; Tudor domain found in Tudor domain-containing protein 9 (TDRD9) and similar proteins

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

NC_000014.9 Reference GRCh38.p14 Primary Assembly

Range

103928456..104052667

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_006720019.4 → XP_006720082.1 ATP-dependent RNA helicase TDRD9 isoform X1

Conserved Domains (6) summary

cd04508
Location:949 → 996

TUDOR; Tudor domains are found in many eukaryotic organisms and have been implicated in protein-protein interactions in which methylated protein substrates bind to these domains. For example, the Tudor domain of Survival of Motor Neuron (SMN) binds to ...

smart00847
Location:588 → 665

HA2; Helicase associated domain (HA2) Add an annotation

COG1643
Location:132 → 716

HrpA; HrpA-like RNA helicase [Translation, ribosomal structure and biogenesis]

cd00046
Location:149 → 290

DEXDc; DEAD-like helicases superfamily. A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.

pfam00271
Location:383 → 500

Helicase_C; Helicase conserved C-terminal domain

pfam00567
Location:904 → 1013

TUDOR; Tudor domain
XM_005267309.5 → XP_005267366.1 ATP-dependent RNA helicase TDRD9 isoform X5

Conserved Domains (6) summary

cd04508
Location:949 → 996

TUDOR; Tudor domains are found in many eukaryotic organisms and have been implicated in protein-protein interactions in which methylated protein substrates bind to these domains. For example, the Tudor domain of Survival of Motor Neuron (SMN) binds to ...

smart00847
Location:588 → 665

HA2; Helicase associated domain (HA2) Add an annotation

COG1643
Location:132 → 716

HrpA; HrpA-like RNA helicase [Translation, ribosomal structure and biogenesis]

cd00046
Location:149 → 290

DEXDc; DEAD-like helicases superfamily. A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.

pfam00271
Location:383 → 500

Helicase_C; Helicase conserved C-terminal domain

pfam00567
Location:904 → 1013

TUDOR; Tudor domain
XM_011536397.3 → XP_011534699.1 ATP-dependent RNA helicase TDRD9 isoform X3

Conserved Domains (6) summary

cd04508
Location:914 → 961

TUDOR; Tudor domains are found in many eukaryotic organisms and have been implicated in protein-protein interactions in which methylated protein substrates bind to these domains. For example, the Tudor domain of Survival of Motor Neuron (SMN) binds to ...

smart00847
Location:553 → 630

HA2; Helicase associated domain (HA2) Add an annotation

COG1643
Location:132 → 681

HrpA; HrpA-like RNA helicase [Translation, ribosomal structure and biogenesis]

cd00046
Location:149 → 290

DEXDc; DEAD-like helicases superfamily. A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.

pfam00271
Location:383 → 465

Helicase_C; Helicase conserved C-terminal domain

pfam00567
Location:869 → 978

TUDOR; Tudor domain
XM_047430910.1 → XP_047286866.1 ATP-dependent RNA helicase TDRD9 isoform X8
XM_011536400.3 → XP_011534702.1 ATP-dependent RNA helicase TDRD9 isoform X7

Conserved Domains (5) summary

cd04508
Location:862 → 909

TUDOR; Tudor domains are found in many eukaryotic organisms and have been implicated in protein-protein interactions in which methylated protein substrates bind to these domains. For example, the Tudor domain of Survival of Motor Neuron (SMN) binds to ...

smart00847
Location:501 → 578

HA2; Helicase associated domain (HA2) Add an annotation

COG1643
Location:132 → 629

HrpA; HrpA-like RNA helicase [Translation, ribosomal structure and biogenesis]

cd00046
Location:149 → 290

DEXDc; DEAD-like helicases superfamily. A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.

pfam00567
Location:817 → 926

TUDOR; Tudor domain
XM_006720020.4 → XP_006720083.1 ATP-dependent RNA helicase TDRD9 isoform X2

Conserved Domains (6) summary

cd04508
Location:922 → 969

TUDOR; Tudor domains are found in many eukaryotic organisms and have been implicated in protein-protein interactions in which methylated protein substrates bind to these domains. For example, the Tudor domain of Survival of Motor Neuron (SMN) binds to ...

smart00847
Location:561 → 638

HA2; Helicase associated domain (HA2) Add an annotation

COG1643
Location:132 → 689

HrpA; HrpA-like RNA helicase [Translation, ribosomal structure and biogenesis]

cd00046
Location:149 → 263

DEXDc; DEAD-like helicases superfamily. A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.

pfam00271
Location:356 → 473

Helicase_C; Helicase conserved C-terminal domain

pfam00567
Location:877 → 986

TUDOR; Tudor domain
XM_047430909.1 → XP_047286865.1 ATP-dependent RNA helicase TDRD9 isoform X6
XM_047430912.1 → XP_047286868.1 ATP-dependent RNA helicase TDRD9 isoform X10
XM_011536398.4 → XP_011534700.1 ATP-dependent RNA helicase TDRD9 isoform X4

Conserved Domains (6) summary

cd04508
Location:911 → 958

TUDOR; Tudor domains are found in many eukaryotic organisms and have been implicated in protein-protein interactions in which methylated protein substrates bind to these domains. For example, the Tudor domain of Survival of Motor Neuron (SMN) binds to ...

smart00847
Location:550 → 627

HA2; Helicase associated domain (HA2) Add an annotation

COG1643
Location:94 → 678

HrpA; HrpA-like RNA helicase [Translation, ribosomal structure and biogenesis]

cd00046
Location:111 → 252

DEXDc; DEAD-like helicases superfamily. A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.

pfam00271
Location:345 → 462

Helicase_C; Helicase conserved C-terminal domain

pfam00567
Location:866 → 975

TUDOR; Tudor domain
XM_047430911.1 → XP_047286867.1 ATP-dependent RNA helicase TDRD9 isoform X9
XM_011536402.3 → XP_011534704.1 ATP-dependent RNA helicase TDRD9 isoform X11

UniProtKB/TrEMBL

H0YJJ2

Conserved Domains (4) summary

cd04508
Location:587 → 634

TUDOR; Tudor domains are found in many eukaryotic organisms and have been implicated in protein-protein interactions in which methylated protein substrates bind to these domains. For example, the Tudor domain of Survival of Motor Neuron (SMN) binds to ...

smart00847
Location:226 → 303

HA2; Helicase associated domain (HA2) Add an annotation

pfam00271
Location:21 → 138

Helicase_C; Helicase conserved C-terminal domain

pfam00567
Location:542 → 651

TUDOR; Tudor domain