Tdrd9 tudor domain containing 9 [Rattus norvegicus (Norway rat)] - Gene

Summary

Official Symbol: Tdrd9provided by RGD
Official Full Name: tudor domain containing 9provided by RGD
Primary source: RGD:1306942
See related: EnsemblRapid:ENSRNOG00000053631 AllianceGenome:RGD:1306942
Gene type: protein coding
RefSeq status: VALIDATED
Organism: Rattus norvegicus
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
Summary: Predicted to enable ATP hydrolysis activity; RNA binding activity; and helicase activity. Predicted to be involved in several processes, including male meiosis I; regulatory ncRNA-mediated gene silencing; and spermatogenesis. Predicted to act upstream of or within retrotransposon silencing. Predicted to be located in piP-body. Predicted to be active in cytoplasm and nucleus. Human ortholog(s) of this gene implicated in spermatogenic failure 30. Orthologous to human TDRD9 (tudor domain containing 9). [provided by Alliance of Genome Resources, Dec 2024]
Expression: Biased expression in Thymus (RPKM 138.2) and Testes (RPKM 85.5) See more
Orthologs: human mouse all
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Genomic context

Location:: 6q32

Exon count:: 39

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCr8 (GCF_036323735.1)	6	NC_086024.1 (136850797..136966225)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	6	NC_051341.1 (131029644..131145076)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	6	NC_005105.4 (136536636..136650481)

Chromosome 6 - NC_086024.1 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: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages
Description: 320 RNA samples isolated from 11 organs (adrenal gland, brain, heart, kidney, liver, lung, muscle, spleen, thymus, and testes or uterus) from both sexes of Fischer 344 rats across four developmental stages (2-, 6-, 21-, and 104-weeks-old)
BioProject: PRJNA238328
Publication: PMID 24510058
Analysis date: Mon Jun 6 17:44:12 2016

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

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General gene information

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Gene Ontology Provided by RGD

Function	Evidence Code	Pubs
enables ATP binding	IEA Inferred from Electronic Annotation more info
enables ATP hydrolysis activity	ISO Inferred from Sequence Orthology more info
enables ATP hydrolysis activity	ISS Inferred from Sequence or Structural Similarity more info
enables ATP-dependent H2AZ histone chaperone activity	IEA Inferred from Electronic Annotation more info
enables ATP-dependent H3-H4 histone complex chaperone activity	IEA Inferred from Electronic Annotation more info
enables DNA clamp loader activity	IEA Inferred from Electronic Annotation 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 chromatin extrusion motor activity	IEA Inferred from Electronic Annotation more info
enables cohesin loader activity	IEA Inferred from Electronic Annotation more info
enables helicase activity	IBA Inferred from Biological aspect of Ancestor more info
enables helicase activity	IEA Inferred from Electronic Annotation more info
enables nucleic acid binding	IEA Inferred from Electronic Annotation more info

Process	Evidence Code	Pubs
involved_in cell differentiation	IEA Inferred from Electronic Annotation more info
involved_in chromatin looping	IEA Inferred from Electronic Annotation more info
involved_in fertilization	ISO Inferred from Sequence Orthology more info
involved_in fertilization	ISS Inferred from Sequence or Structural Similarity more info
involved_in male meiosis I	ISO Inferred from Sequence Orthology more info
involved_in male meiosis I	ISS Inferred from Sequence or Structural Similarity more info
involved_in male meiotic nuclear division	ISO Inferred from Sequence Orthology more info
involved_in male meiotic nuclear division	ISS Inferred from Sequence or Structural Similarity more info
involved_in meiotic cell cycle	IEA Inferred from Electronic Annotation more info
involved_in piRNA processing	ISO Inferred from Sequence Orthology more info
involved_in piRNA processing	ISS Inferred from Sequence or Structural Similarity more info
involved_in regulatory ncRNA-mediated gene silencing	IEA Inferred from Electronic Annotation more info
involved_in spermatogenesis	IEA Inferred from Electronic Annotation more info
involved_in spermatogenesis	ISO Inferred from Sequence Orthology more info
involved_in spermatogenesis	ISS Inferred from Sequence or Structural Similarity more info
acts_upstream_of_or_within transposable element silencing	ISO Inferred from Sequence Orthology more info
involved_in transposable element silencing by piRNA-mediated DNA methylation	ISO Inferred from Sequence Orthology more info
involved_in transposable element silencing by piRNA-mediated DNA methylation	ISS Inferred from Sequence or Structural Similarity more info
involved_in transposable element silencing by piRNA-mediated heterochromatin formation	ISO Inferred from Sequence Orthology more info
involved_in transposable element silencing by piRNA-mediated heterochromatin formation	ISS Inferred from Sequence or Structural Similarity more info

Component	Evidence Code	Pubs
is_active_in cytoplasm	IBA Inferred from Biological aspect of Ancestor more info
located_in cytoplasm	IEA Inferred from Electronic Annotation more info
located_in cytoplasm	ISO Inferred from Sequence Orthology more info
is_active_in nucleus	IBA Inferred from Biological aspect of Ancestor more info
located_in nucleus	ISO Inferred from Sequence Orthology more info
located_in nucleus	ISS Inferred from Sequence or Structural Similarity more info
located_in piP-body	ISO Inferred from Sequence Orthology more info
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: putative ATP-dependent RNA helicase TDRD9; tudor domain-containing protein 9

NP_001406506.1

EC 3.6.4.13

XP_008763207.1

EC 3.6.4.13

XP_017450003.1

EC 3.6.4.13

XP_017450004.1

EC 3.6.4.13

XP_017450005.1

EC 3.6.4.13

XP_038969315.1

EC 3.6.4.13

XP_038969316.1

EC 3.6.4.13

XP_038969319.1

EC 3.6.4.13

XP_063117861.1

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_001419577.1 → NP_001406506.1 ATP-dependent RNA helicase TDRD9

Status: VALIDATED

Source sequence(s)

JAXUCZ010000006

UniProtKB/Swiss-Prot

Q3MHU3

UniProtKB/TrEMBL

A0A8I6AIH4

Related

ENSRNOP00000073728.1, ENSRNOT00000086594.3

RefSeqs of Annotated Genomes: GCF_036323735.1-RS_2024_02

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

Reference GRCr8

Genomic

NC_086024.1 Reference GRCr8

Range

136850797..136966225

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_017594515.3 → XP_017450004.1 ATP-dependent RNA helicase TDRD9 isoform X2

UniProtKB/TrEMBL

A0A8I6AIH4

Conserved Domains (6) summary

cd04508
Location:962 → 1009

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 ...

smart00487
Location:146 → 327

DEXDc; DEAD-like helicases superfamily

smart00847
Location:590 → 667

HA2; Helicase associated domain (HA2) Add an annotation

cd00046
Location:151 → 292

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:385 → 502

Helicase_C; Helicase conserved C-terminal domain

pfam00567
Location:924 → 1026

TUDOR; Tudor domain
XM_017594516.3 → XP_017450005.1 ATP-dependent RNA helicase TDRD9 isoform X4

UniProtKB/TrEMBL

A0A8I6AIH4

Conserved Domains (6) summary

cd04508
Location:923 → 970

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 ...

smart00487
Location:146 → 327

DEXDc; DEAD-like helicases superfamily

smart00847
Location:590 → 667

HA2; Helicase associated domain (HA2) Add an annotation

cd00046
Location:151 → 292

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:385 → 502

Helicase_C; Helicase conserved C-terminal domain

pfam00567
Location:885 → 987

TUDOR; Tudor domain
XM_017594514.3 → XP_017450003.1 ATP-dependent RNA helicase TDRD9 isoform X1

UniProtKB/TrEMBL

A0A8I6AIH4

Conserved Domains (6) summary

cd04508
Location:962 → 1009

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 ...

smart00487
Location:146 → 327

DEXDc; DEAD-like helicases superfamily

smart00847
Location:590 → 667

HA2; Helicase associated domain (HA2) Add an annotation

cd00046
Location:151 → 292

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:385 → 502

Helicase_C; Helicase conserved C-terminal domain

pfam00567
Location:924 → 1026

TUDOR; Tudor domain
XM_008764985.3 → XP_008763207.1 ATP-dependent RNA helicase TDRD9 isoform X3

See identical proteins and their annotated locations for XP_008763207.1

UniProtKB/TrEMBL

A0A8I6AIH4

Conserved Domains (6) summary

cd04508
Location:951 → 998

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 ...

smart00487
Location:146 → 327

DEXDc; DEAD-like helicases superfamily

smart00847
Location:590 → 667

HA2; Helicase associated domain (HA2) Add an annotation

cd00046
Location:151 → 292

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:385 → 502

Helicase_C; Helicase conserved C-terminal domain

pfam00567
Location:913 → 1015

TUDOR; Tudor domain
XM_063261791.1 → XP_063117861.1 ATP-dependent RNA helicase TDRD9 isoform X5

UniProtKB/TrEMBL

A0A8I6AIH4

Related

ENSRNOP00000111390.1, ENSRNOT00000171820.1
XM_039113391.2 → XP_038969319.1 ATP-dependent RNA helicase TDRD9 isoform X8

Conserved Domains (1) summary

COG1643
Location:111 → 681

HrpA; HrpA-like RNA helicase [Translation, ribosomal structure and biogenesis]
XM_039113387.1 → XP_038969315.1 ATP-dependent RNA helicase TDRD9 isoform X6

UniProtKB/TrEMBL

A0A8I6AIH4

Conserved Domains (2) summary

COG1643
Location:1 → 487

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

cd20431
Location:688 → 787

Tudor_TDRD9; Tudor domain found in Tudor domain-containing protein 9 (TDRD9) and similar proteins
XM_039113388.2 → XP_038969316.1 ATP-dependent RNA helicase TDRD9 isoform X7

Conserved Domains (2) summary

COG1643
Location:13 → 316

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

cd20431
Location:517 → 616

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

RNA

XR_010052076.1 RNA Sequence

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

NM_001035250.1: Suppressed sequence

Description

NM_001035250.1: This RefSeq was suppressed temporarily based on the calculation that the encoded protein was shorter than proteins from the putative ortholog from human: TDRD9 (GeneID:122402).