AFF3 ALF transcription elongation factor 3 [Homo sapiens (human)] - Gene

Summary

Official Symbol: AFF3provided by HGNC
Official Full Name: ALF transcription elongation factor 3provided by HGNC
Primary source: HGNC:HGNC:6473
See related: Ensembl:ENSG00000144218 MIM:601464; AllianceGenome:HGNC:6473
Gene type: protein coding
RefSeq status: REVIEWED
Organism: Homo sapiens
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as: KINS; LAF4; MLLT2-like
Summary: This gene encodes a tissue-restricted nuclear transcriptional activator that is preferentially expressed in lymphoid tissue. Isolation of this protein initially defined a highly conserved LAF4/MLLT2 gene family of nuclear transcription factors that may function in lymphoid development and oncogenesis. In some ALL patients, this gene has been found fused to the gene for MLL. Multiple alternatively spliced transcript variants that encode different proteins have been found for this gene. [provided by RefSeq, Jul 2008]
Expression: Broad expression in prostate (RPKM 4.8), lymph node (RPKM 3.7) and 23 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 2q11.2

Exon count:: 34

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	2	NC_000002.12 (99545419..100142590, complement)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	2	NC_060926.1 (100004081..100601540, complement)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	2	NC_000002.11 (100161881..100759052, complement)

Chromosome 2 - NC_000002.12 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?

Loss of AR-regulated AFF3 contributes to prostate cancer progression and reduces ferroptosis sensitivity by downregulating ACSL4 based on single-cell sequencing analysis.
Title: Loss of AR-regulated AFF3 contributes to prostate cancer progression and reduces ferroptosis sensitivity by downregulating ACSL4 based on single-cell sequencing analysis.
Integrated mendelian randomization analyses highlight AFF3 as a novel eQTL-mediated susceptibility gene in renal cancer and its potential mechanisms.
Title: Integrated mendelian randomization analyses highlight AFF3 as a novel eQTL-mediated susceptibility gene in renal cancer and its potential mechanisms.
Variant-specific pathophysiological mechanisms of AFF3 differently influence transcriptome profiles.
Title: Variant-specific pathophysiological mechanisms of AFF3 differently influence transcriptome profiles.
Three KINSSHIP syndrome patients with mosaic and germline AFF3 variants.
Title: Three KINSSHIP syndrome patients with mosaic and germline AFF3 variants.
A novel variant in AFF3 underlying isolated syndactyly.
Title: A novel variant in AFF3 underlying isolated syndactyly.
Association of AFF3 Gene Polymorphism rs10865035 with Rheumatoid Arthritis: A Population-Based Case-Control Study on a Pakistani Cohort.
Title: Association of AFF3 Gene Polymorphism rs10865035 with Rheumatoid Arthritis: A Population-Based Case-Control Study on a Pakistani Cohort.
Variants in the degron of AFF3 are associated with intellectual disability, mesomelic dysplasia, horseshoe kidney, and epileptic encephalopathy.
Title: Variants in the degron of AFF3 are associated with intellectual disability, mesomelic dysplasia, horseshoe kidney, and epileptic encephalopathy.
AFF3 was overexpressed in tamoxifen-resistant tumors. AFF3 overexpression in breast cancer cells resulted in tamoxifen resistance, whereas RNA interference-mediated gene knockdown reversed this phenotype.
Title: AFF3 upregulation mediates tamoxifen resistance in breast cancers.
Data identified AFF3 as an interactive protein with beclin1 and suggest that AFF3 is probably a key regulator of Beclin-1.
Title: Integrating multiple omics data for the discovery of potential Beclin-1 interactions in breast cancer.
Both the AFF3 and NTM triglyceride associations were replicated among Multi-ethnic Study of Atherosclerosis study participants (P = 1.00 x 10(-7) and 8.00 x 10(-5), respectively).
Title: Genome-wide linkage and positional association analyses identify associations of novel AFF3 and NTM genes with triglycerides: the GenSalt study.

Submit: New GeneRIF Correction See all GeneRIFs (24)

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
KINSSHIP syndrome MedGen: C5543317 OMIM: 619297 GeneReviews: Not available	Compare labs

EBI GWAS Catalog

Description
Genetics of rheumatoid arthritis contributes to biology and drug discovery. EBI GWAS Catalog EBI GWAS CatalogPubMed
Genome wide association study identifies a novel putative mammographic density locus at 1q12-q21. EBI GWAS Catalog EBI GWAS CatalogPubMed
Genome-wide association study meta-analysis identifies seven new rheumatoid arthritis risk loci. EBI GWAS Catalog EBI GWAS CatalogPubMed
New susceptibility loci associated with kidney disease in type 1 diabetes. EBI GWAS Catalog EBI GWAS CatalogPubMed
Novel risk loci for rheumatoid arthritis in Han Chinese and congruence with risk variants in Europeans. EBI GWAS Catalog EBI GWAS CatalogPubMed
Robust associations of four new chromosome regions from genome-wide analyses of type 1 diabetes. 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

G32409 (e-PCR)
- UniSTS:116996

D2S1633E (e-PCR)
- UniSTS:55812

SHGC-82826 (e-PCR)
- UniSTS:173831

RH69575 (e-PCR)
- UniSTS:62471

RH121169 (e-PCR)
- UniSTS:134164

GDB:434012 (e-PCR)
- UniSTS:157204

A009U47 (e-PCR)
- UniSTS:42005

D2S1821 (e-PCR)
- UniSTS:35366

A006S04 (e-PCR)
- UniSTS:59175

D2S1992 (e-PCR)
- UniSTS:19277

G16333 (e-PCR)
- UniSTS:78926

RH121214 (e-PCR)
- UniSTS:138325

RH12868 (e-PCR)
- UniSTS:46456

D2S2744 (e-PCR)
- UniSTS:60546

G16393 (e-PCR)
- UniSTS:43908

A009C10 (e-PCR)
- UniSTS:62869

D2S2710 (e-PCR)
- UniSTS:45984

RH118653 (e-PCR)
- UniSTS:138146

WI-17152 (e-PCR)
- UniSTS:78765

RH123972 (e-PCR)
- UniSTS:136110

G32863 (e-PCR)
- UniSTS:117442

D2S1695E (e-PCR)
- UniSTS:150724

RH104445 (e-PCR)
- UniSTS:98769

RH18039 (e-PCR)
- UniSTS:49382

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables DNA-binding transcription factor activity	IEA Inferred from Electronic Annotation more info
enables double-stranded DNA binding	IEA Inferred from Electronic Annotation more info

Process	Evidence Code	Pubs
involved_in embryonic hindlimb morphogenesis	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in regulation of DNA-templated transcription	IEA Inferred from Electronic Annotation more info
involved_in regulation of gene expression	IBA Inferred from Biological aspect of Ancestor more info
involved_in response to tumor necrosis factor	IMP Inferred from Mutant Phenotype more info	PubMed

Component	Evidence Code	Pubs
located_in cytosol	IDA Inferred from Direct Assay more info
located_in nuclear body	IDA Inferred from Direct Assay more info
located_in nucleoplasm	IDA Inferred from Direct Assay more info
located_in nucleus	IDA Inferred from Direct Assay more info	PubMed
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: MLLT2-related protein; lymphoid nuclear protein 4; lymphoid nuclear protein related to AF4; protein LAF-4

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.

Genomic

NG_052835.1 RefSeqGene

Range

4994..602165

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_001025108.2 → NP_001020279.1 AF4/FMR2 family member 3 isoform 2

See identical proteins and their annotated locations for NP_001020279.1

Status: REVIEWED

Source sequence(s)

AC010736, AC018690, AC073118, AC092667, AC093373, KF456685

Consensus CDS

CCDS33258.1

UniProtKB/Swiss-Prot

P51826

UniProtKB/TrEMBL

Q8NAP7

Related

ENSP00000386834.1, ENST00000409579.5

Conserved Domains (1) summary

pfam05110
Location:48 → 1245

AF-4; AF-4 proto-oncoprotein
NM_001386135.1 → NP_001373064.1 AF4/FMR2 family member 3 isoform 1

Status: REVIEWED

Source sequence(s)

AC010736, AC018690, AC073118, AC092667, AC093373, KF456685

Consensus CDS

CCDS42723.1

UniProtKB/Swiss-Prot

B7ZM46, B9EGL9, D3DVI6, P51826, Q53RD6, Q53S47, Q53SI6, Q53TB9, Q59F27, Q8IWJ5

Related

ENSP00000500419.1, ENST00000672756.2

Conserved Domains (2) summary

pfam05110
Location:20 → 473

AF-4; AF-4 proto-oncoprotein

pfam18876
Location:965 → 1225

AF-4_C; AF-4 proto-oncoprotein C-terminal region
NM_002285.3 → NP_002276.2 AF4/FMR2 family member 3 isoform 1

See identical proteins and their annotated locations for NP_002276.2

Status: REVIEWED

Source sequence(s)

AC010736, AC018690, AC073118, AC092667, AC093373, KF456685

Consensus CDS

CCDS42723.1

UniProtKB/Swiss-Prot

B7ZM46, B9EGL9, D3DVI6, P51826, Q53RD6, Q53S47, Q53SI6, Q53TB9, Q59F27, Q8IWJ5

Related

ENSP00000317421.4, ENST00000317233.8

Conserved Domains (2) summary

pfam05110
Location:20 → 473

AF-4; AF-4 proto-oncoprotein

pfam18876
Location:965 → 1225

AF-4_C; AF-4 proto-oncoprotein C-terminal region

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

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

Reference GRCh38.p14 Primary Assembly

Genomic

NC_000002.12 Reference GRCh38.p14 Primary Assembly

Range

99545419..100142590 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_047444286.1 → XP_047300242.1 AF4/FMR2 family member 3 isoform X13
XM_047444281.1 → XP_047300237.1 AF4/FMR2 family member 3 isoform X8
XM_047444283.1 → XP_047300239.1 AF4/FMR2 family member 3 isoform X10

UniProtKB/Swiss-Prot

B7ZM46, B9EGL9, D3DVI6, P51826, Q53RD6, Q53S47, Q53SI6, Q53TB9, Q59F27, Q8IWJ5
XM_047444280.1 → XP_047300236.1 AF4/FMR2 family member 3 isoform X8
XM_047444279.1 → XP_047300235.1 AF4/FMR2 family member 3 isoform X6
XM_011511169.4 → XP_011509471.2 AF4/FMR2 family member 3 isoform X2

Conserved Domains (1) summary

pfam05110
Location:177 → 1373

AF-4; AF-4 proto-oncoprotein
XM_024452883.2 → XP_024308651.1 AF4/FMR2 family member 3 isoform X1

Conserved Domains (1) summary

pfam05110
Location:177 → 1374

AF-4; AF-4 proto-oncoprotein
XM_047444278.1 → XP_047300234.1 AF4/FMR2 family member 3 isoform X5
XM_047444277.1 → XP_047300233.1 AF4/FMR2 family member 3 isoform X4
XM_011511171.4 → XP_011509473.2 AF4/FMR2 family member 3 isoform X3

Conserved Domains (1) summary

pfam05110
Location:177 → 1358

AF-4; AF-4 proto-oncoprotein
XM_011511170.3 → XP_011509472.1 AF4/FMR2 family member 3 isoform X7

Conserved Domains (1) summary

pfam05110
Location:100 → 1297

AF-4; AF-4 proto-oncoprotein
XM_047444284.1 → XP_047300240.1 AF4/FMR2 family member 3 isoform X11
XM_047444285.1 → XP_047300241.1 AF4/FMR2 family member 3 isoform X12
XM_005263943.5 → XP_005264000.2 AF4/FMR2 family member 3 isoform X10

See identical proteins and their annotated locations for XP_005264000.2

UniProtKB/Swiss-Prot

B7ZM46, B9EGL9, D3DVI6, P51826, Q53RD6, Q53S47, Q53SI6, Q53TB9, Q59F27, Q8IWJ5

Related

ENSP00000387207.1, ENST00000409236.6

Conserved Domains (2) summary

pfam05110
Location:20 → 473

AF-4; AF-4 proto-oncoprotein

pfam18876
Location:965 → 1225

AF-4_C; AF-4 proto-oncoprotein C-terminal region
XM_047444282.1 → XP_047300238.1 AF4/FMR2 family member 3 isoform X9
XM_011511174.4 → XP_011509476.1 AF4/FMR2 family member 3 isoform X8

See identical proteins and their annotated locations for XP_011509476.1

UniProtKB/Swiss-Prot

P51826

Conserved Domains (1) summary

pfam05110
Location:48 → 1245

AF-4; AF-4 proto-oncoprotein
XM_047444287.1 → XP_047300243.1 AF4/FMR2 family member 3 isoform X13
XM_047444289.1 → XP_047300245.1 AF4/FMR2 family member 3 isoform X17
XM_017004085.3 → XP_016859574.1 AF4/FMR2 family member 3 isoform X15
XM_047444288.1 → XP_047300244.1 AF4/FMR2 family member 3 isoform X16
XM_005263945.5 → XP_005264002.1 AF4/FMR2 family member 3 isoform X14

Conserved Domains (1) summary

pfam05110
Location:24 → 889

AF-4; AF-4 proto-oncoprotein
XM_047444290.1 → XP_047300246.1 AF4/FMR2 family member 3 isoform X20
XM_017004087.3 → XP_016859576.1 AF4/FMR2 family member 3 isoform X21
XM_011511179.4 → XP_011509481.1 AF4/FMR2 family member 3 isoform X19

Conserved Domains (1) summary

pfam05110
Location:88 → 858

AF-4; AF-4 proto-oncoprotein
XM_011511178.4 → XP_011509480.1 AF4/FMR2 family member 3 isoform X18

Conserved Domains (1) summary

pfam05110
Location:89 → 859

AF-4; AF-4 proto-oncoprotein