atrx ATRX chromatin remodeler [Danio rerio (zebrafish)] - Gene

Summary

Official Symbol: atrxprovided by ZNC
Official Full Name: ATRX chromatin remodelerprovided by ZNC
Primary source: ZFIN:ZDB-GENE-030912-11
See related: Ensembl:ENSDARG00000042236 AllianceGenome:ZFIN:ZDB-GENE-030912-11
Gene type: protein coding
RefSeq status: VALIDATED
Organism: Danio rerio
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Actinopterygii; Neopterygii; Teleostei; Ostariophysi; Cypriniformes; Danionidae; Danioninae; Danio
Also known as: atrxl; zgc:66223; wu:fb26e12; wu:fb52h08; wu:fb72g09; wu:fb94e07
Summary: Predicted to enable several functions, including ATP binding activity; DNA helicase activity; and metal ion binding activity. Predicted to act upstream of or within DNA repair. Predicted to be located in chromosome, telomeric region and nucleus. Used to study alpha thalassemia-X-linked intellectual disability syndrome. Human ortholog(s) of this gene implicated in X-linked mental retardation-hypotonic facies syndrome-1; alpha thalassemia-X-linked intellectual disability syndrome; alpha-thalassemia myelodysplasia syndrome; high grade glioma; and lung small cell carcinoma. Orthologous to human ATRX (ATRX chromatin remodeler). [provided by Alliance of Genome Resources, Apr 2022]
Orthologs: human mouse all
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Genomic context

Location:: chromosome: 14

Exon count:: 36

Annotation release	Status	Assembly	Chr	Location
106	current	GRCz11 (GCF_000002035.6)	14	NC_007125.7 (10656492..10736965)
105	previous assembly	GRCz10 (GCF_000002035.5)	14	NC_007125.6 (10350961..10430945)

Chromosome 14 - NC_007125.7 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

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Expression

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See details

Project title: Sequencing the Zebrafish transcriptome from a range of tissues and developmental stages Sequencing the Zebrafish transcriptome from a range of tissues and developmental stages
Description: Sequencing the Zebrafish transcriptome from a range of tissues and developmental stages
BioProject: PRJEB1986
Analysis date: Fri Dec 8 19:48:10 2017

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

In p53/nf1-deficiencies, neither peripheral nerve sheath tumors nor gliomas showed accelerated onset in atrx+/- fish, but these fish developed various tumors that were not observed in their atrx+/+ siblings, including epithelioid sarcoma, angiosarcoma, undifferentiated pleomorphic sarcoma and rare types of carcinoma.
Title: Loss of atrx cooperates with p53-deficiency to promote the development of sarcomas and other malignancies.

Submit: New GeneRIF Correction

General gene information

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Markers

fb36e03.x1 (e-PCR)
- UniSTS:190477

fb36e03.x1 (e-PCR)
- UniSTS:190478

fc57h01.y1 (e-PCR)
- UniSTS:194105

fb26e12 (e-PCR)
- UniSTS:189001

fb13d02.x1 (e-PCR)
- UniSTS:202895

AI444378 (e-PCR)
- UniSTS:206566

fk38a05.y1 (e-PCR)
- UniSTS:200940

Gene Ontology Provided by ZFIN

Function	Evidence Code	Pubs
enables ATP binding	IEA Inferred from Electronic Annotation more info
enables ATP-dependent chromatin remodeler activity	IEA Inferred from Electronic Annotation more info
enables DNA binding	IEA Inferred from Electronic Annotation more info
enables chromatin DNA binding	IBA Inferred from Biological aspect of Ancestor more info
enables hydrolase activity	IEA Inferred from Electronic Annotation more info
enables metal ion binding	IEA Inferred from Electronic Annotation more info
enables methylated histone binding	IBA Inferred from Biological aspect of Ancestor more info
enables nucleotide binding	IEA Inferred from Electronic Annotation more info

Process	Evidence Code	Pubs
acts_upstream_of_or_within DNA damage response	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within DNA repair	IEA Inferred from Electronic Annotation more info
involved_in chromatin remodeling	IBA Inferred from Biological aspect of Ancestor more info
involved_in negative regulation of macromolecule biosynthetic process	IEA Inferred from Electronic Annotation more info
involved_in replication fork processing	IBA Inferred from Biological aspect of Ancestor more info

Component	Evidence Code	Pubs
located_in chromosome	IEA Inferred from Electronic Annotation more info
located_in chromosome, telomeric region	IEA Inferred from Electronic Annotation more info
is_active_in nucleus	IBA Inferred from Biological aspect of Ancestor more info
located_in nucleus	IEA Inferred from Electronic Annotation more info
part_of pericentric heterochromatin	IBA Inferred from Biological aspect of Ancestor more info

General protein information

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Preferred Names: transcriptional regulator ATRX

NP_956947.2

EC 3.6.4.12

XP_021336651.1

EC 3.6.4.12

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_200653.2 → NP_956947.2 transcriptional regulator ATRX

Status: VALIDATED

Source sequence(s)

CR855117, CR931764

UniProtKB/TrEMBL

A0A8M1PD71, E7F4M2

Related

ENSDARP00000105895.5, ENSDART00000127594.5

Conserved Domains (4) summary

cd00046
Location:1142 → 1304

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.

cd00079
Location:1562 → 1706

HELICc; Helicase superfamily c-terminal domain; associated with DEXDc-, DEAD-, and DEAH-box proteins, yeast initiation factor 4A, Ski2p, and Hepatitis C virus NS3 helicases; this domain is found in a wide variety of helicases and helicase related proteins; may ...

cd11726
Location:118 → 221

ADDz_ATRX; ADDz domain found in ATRX (alpha-thalassemia/mental retardation, X-linked)

pfam00176
Location:1117 → 1443

SNF2_N; SNF2 family N-terminal domain

RefSeqs of Annotated Genomes: Danio rerio Annotation Release 106 details...

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

Reference GRCz11 Primary Assembly

Genomic

NC_007125.7 Reference GRCz11 Primary Assembly

Range

10656492..10736965

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_021480976.1 → XP_021336651.1 transcriptional regulator ATRX isoform X1

UniProtKB/TrEMBL

A0A8M9QKH6

Conserved Domains (4) summary

cd00079
Location:1602 → 1746

HELICc; Helicase superfamily c-terminal domain; associated with DEXDc-, DEAD-, and DEAH-box proteins, yeast initiation factor 4A, Ski2p, and Hepatitis C virus NS3 helicases; this domain is found in a wide variety of helicases and helicase related proteins; may ...

cd11726
Location:158 → 261

ADDz_ATRX; ADDz domain found in ATRX (alpha-thalassemia/mental retardation, X-linked)

pfam00176
Location:1157 → 1483

SNF2_N; SNF2 family N-terminal domain

cl26511
Location:594 → 1151

Neuromodulin_N; Gap junction protein N-terminal region