Aff3 ALF transcription elongation factor 3 [Rattus norvegicus (Norway rat)] - Gene

Summary

Official Symbol: Aff3provided by RGD
Official Full Name: ALF transcription elongation factor 3provided by RGD
Primary source: RGD:1308527
See related: EnsemblRapid:ENSRNOG00000018830 AllianceGenome:RGD:1308527
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
Also known as: Laf4
Summary: Predicted to enable DNA-binding transcription factor activity and double-stranded DNA binding activity. Predicted to be involved in embryonic hindlimb morphogenesis; regulation of DNA-templated transcription; and response to tumor necrosis factor. Predicted to be located in cytosol and nuclear body. Predicted to be part of super elongation complex. Human ortholog(s) of this gene implicated in KINSSHIP syndrome. Orthologous to human AFF3 (ALF transcription elongation factor 3). [provided by Alliance of Genome Resources, Nov 2024]
Expression: Biased expression in Thymus (RPKM 69.2), Spleen (RPKM 44.6) and 9 other tissues See more
Orthologs: human mouse all
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Genomic context

Location:: 9q21-q22

Exon count:: 25

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCr8 (GCF_036323735.1)	9	NC_086027.1 (47894903..48352380, complement)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	9	NC_051344.1 (40399099..40856716, complement)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	9	NC_005108.4 (44837979..45291964, complement)

Chromosome 9 - NC_086027.1 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: 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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Markers

RH143740 (e-PCR)
- UniSTS:232986

D9Mgh3 (e-PCR)
- UniSTS:119616

AW532340 (e-PCR)
- UniSTS:245575

BF388174 (e-PCR)
- UniSTS:260953

D9Rat26 (e-PCR)
- UniSTS:119164

BE096992 (e-PCR)
- UniSTS:244133

BE119815 (e-PCR)
- UniSTS:249275

BI286984 (e-PCR)
- UniSTS:245468

Gene Ontology Provided by RGD

Function	Evidence Code	Pubs
enables DNA-binding transcription factor activity	ISO Inferred from Sequence Orthology more info
enables double-stranded DNA binding	ISO Inferred from Sequence Orthology more info

Process	Evidence Code	Pubs
involved_in embryonic hindlimb morphogenesis	ISO Inferred from Sequence Orthology more info
involved_in regulation of DNA-templated transcription	ISO Inferred from Sequence Orthology more info
involved_in regulation of gene expression	IBA Inferred from Biological aspect of Ancestor more info
involved_in response to tumor necrosis factor	ISO Inferred from Sequence Orthology more info

Component	Evidence Code	Pubs
located_in cytosol	IEA Inferred from Electronic Annotation more info
located_in cytosol	ISO Inferred from Sequence Orthology more info
located_in nuclear body	IEA Inferred from Electronic Annotation more info
located_in nuclear body	ISO Inferred from Sequence Orthology more info
located_in nucleoplasm	ISO Inferred from Sequence Orthology more info
located_in nucleus	ISO Inferred from Sequence Orthology more info
part_of super elongation complex	IBA Inferred from Biological aspect of Ancestor more info

General protein information

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Preferred Names: AF4/FMR2 family member 3

Names: AF4/FMR2 family, member 3; lymphoid nuclear protein related to AF4

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_001413892.1 → NP_001400821.1 AF4/FMR2 family member 3

Status: VALIDATED

Source sequence(s)

JAXUCZ010000009

Related

ENSRNOP00000072037.2, ENSRNOT00000083256.3

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_086027.1 Reference GRCr8

Range

47894903..48352380 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_039083846.2 → XP_038939774.1 AF4/FMR2 family member 3 isoform X5

UniProtKB/TrEMBL

A0A0G2K1Y7, F1M681

Conserved Domains (2) summary

pfam05110
Location:1 → 395

AF-4; AF-4 proto-oncoprotein

pfam18876
Location:898 → 1158

AF-4_C; AF-4 proto-oncoprotein C-terminal region
XM_039083844.2 → XP_038939772.1 AF4/FMR2 family member 3 isoform X2

UniProtKB/TrEMBL

A0A0G2K1Y7

Related

ENSRNOP00000106658.1, ENSRNOT00000130248.1

Conserved Domains (2) summary

pfam05110
Location:45 → 497

AF-4; AF-4 proto-oncoprotein

pfam18876
Location:1000 → 1260

AF-4_C; AF-4 proto-oncoprotein C-terminal region
XM_063267370.1 → XP_063123440.1 AF4/FMR2 family member 3 isoform X3
XM_063267371.1 → XP_063123441.1 AF4/FMR2 family member 3 isoform X4
XM_063267369.1 → XP_063123439.1 AF4/FMR2 family member 3 isoform X1