AHCTF1 AT-hook containing transcription factor 1 [Homo sapiens (human)] - Gene

Summary

Official Symbol: AHCTF1provided by HGNC
Official Full Name: AT-hook containing transcription factor 1provided by HGNC
Primary source: HGNC:HGNC:24618
See related: Ensembl:ENSG00000153207 MIM:610853; AllianceGenome:HGNC:24618
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: ELYS; MST108; TMBS62; MSTP108
Summary: Predicted to enable DNA binding activity. Involved in nuclear pore complex assembly and regulation of cytokinesis. Located in chromosome; nuclear body; and nuclear envelope. Part of nuclear envelope. [provided by Alliance of Genome Resources, Nov 2024]
Expression: Broad expression in testis (RPKM 25.0), bone marrow (RPKM 11.9) and 25 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 1q44

Exon count:: 38

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	1	NC_000001.11 (246839098..246931948, complement)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	1	NC_060925.1 (246270496..246363018, complement)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	1	NC_000001.10 (247002400..247095250, complement)

Chromosome 1 - NC_000001.11 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: HPA RNA-seq normal tissues 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?

Phosphorylation of ELYS promotes its interaction with VAPB at decondensing chromosomes during mitosis.
Title: Phosphorylation of ELYS promotes its interaction with VAPB at decondensing chromosomes during mitosis.
Canonical WNT signaling-dependent gating of MYC requires a noncanonical CTCF function at a distal binding site.
Title: Canonical WNT signaling-dependent gating of MYC requires a noncanonical CTCF function at a distal binding site.
we identify ELYS as a novel positive effector of mammalian nuclear size and propose that nuclear size is sensitive to NPC density and nuclear import capacity.
Title: The nucleoporin ELYS regulates nuclear size by controlling NPC number and nuclear import capacity.
AHCTF1 regulates the super-enhancer-mediated gene gating process.The cancer-cell-specific gating of MYC is regulated by AHCTF1, which connects nucleoporins to the oncogenic super-enhancer via beta-catenin.
Title: WNT signaling and AHCTF1 promote oncogenic MYC expression through super-enhancer-mediated gene gating.
These observations point to a new mechanism regulating the localization of LBR, which is governed by an ELYS-mediated phosphorylation network.
Title: ELYS regulates the localization of LBR by modulating its phosphorylation state.
ELYS/Mel28 plays a role in NE subdomain formation in late mitosis
Title: The nucleoporin ELYS/Mel28 regulates nuclear envelope subdomain formation in HeLa cells.
Results suggets that ELYS is an unexpected member of the nuclear pore and kinetochore that functions in both pore assembly at the nucleus and faithful cell division.
Title: ELYS is a dual nucleoporin/kinetochore protein required for nuclear pore assembly and proper cell division.

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Phenotypes

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Review eQTL and phenotype association data in this region using PheGenI

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

HIV-1 interactions

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Replication interactions

Interaction	Pubs
Knockdown of AT hook containing transcription factor 1 (AHCTF1) by siRNA inhibits the early stages of HIV-1 replication in 293T cells infected with VSV-G pseudotyped HIV-1	PubMed

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Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

RH120984 (e-PCR)
- UniSTS:133741

RH26330 (e-PCR)
- UniSTS:84426

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables DNA binding	IEA Inferred from Electronic Annotation more info

Process	Evidence Code	Pubs
involved_in cell division	IEA Inferred from Electronic Annotation more info
involved_in mRNA transport	IEA Inferred from Electronic Annotation more info
involved_in nuclear pore complex assembly	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in nucleocytoplasmic transport	NAS Non-traceable Author Statement more info	PubMed
involved_in protein transport	IEA Inferred from Electronic Annotation more info
involved_in regulation of cytokinesis	IMP Inferred from Mutant Phenotype more info	PubMed

Component	Evidence Code	Pubs
located_in chromatin	IDA Inferred from Direct Assay more info	PubMed
located_in cytosol	TAS Traceable Author Statement more info
located_in extracellular exosome	HDA more info	PubMed
colocalizes_with kinetochore	IDA Inferred from Direct Assay more info	PubMed
located_in nuclear body	IDA Inferred from Direct Assay more info
located_in nuclear envelope	IDA Inferred from Direct Assay more info	PubMed
located_in nuclear matrix	IEA Inferred from Electronic Annotation more info
located_in nuclear membrane	IDA Inferred from Direct Assay more info
part_of nuclear pore	IDA Inferred from Direct Assay more info	PubMed
part_of nuclear pore	NAS Non-traceable Author Statement more info	PubMed
part_of nuclear pore outer ring	IDA Inferred from Direct Assay more info	PubMed
located_in nucleoplasm	IDA Inferred from Direct Assay more info
located_in nucleus	IDA Inferred from Direct Assay more info	PubMed

General protein information

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Preferred Names: protein ELYS

Names: ELYS transcription factor-like protein TMBS62; embryonic large molecule derived from yolk sac; putative AT-hook-containing transcription factor 1

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_001323342.2 → NP_001310271.1 protein ELYS isoform 2

Status: VALIDATED

Source sequence(s)

AC113174

Consensus CDS

CCDS91190.1

UniProtKB/Swiss-Prot

A6NGM0, A8MSG9, A8MZ86, Q7Z4E3, Q8IZA4, Q8WYP5, Q96EH9, Q9Y4Q6

Related

ENSP00000497061.2, ENST00000648844.2

Conserved Domains (4) summary

pfam09528
Location:1637 → 2003

Ehrlichia_rpt; Ehrlichia tandem repeat (Ehrlichia_rpt)

pfam13934
Location:722 → 947

ELYS; Nuclear pore complex assembly

pfam16687
Location:2 → 489

ELYS-bb; beta-propeller of ELYS nucleoporin

sd00039
Location:223 → 259

7WD40; WD40 repeat [structural motif]
NM_001323343.2 → NP_001310272.1 protein ELYS isoform 3

Status: VALIDATED

Source sequence(s)

AC113174
NM_001410950.1 → NP_001397879.1 protein ELYS isoform 4

Status: VALIDATED

Source sequence(s)

AC113174

Consensus CDS

CCDS91191.1

Related

ENSP00000355464.1, ENST00000366508.5
NM_015446.5 → NP_056261.4 protein ELYS isoform 1

Status: VALIDATED

Source sequence(s)

AB059277, AC113174, BC012307

Consensus CDS

CCDS1629.2

UniProtKB/Swiss-Prot

Q8WYP5

Related

ENSP00000355465.1, ENST00000326225.3

Conserved Domains (4) summary

pfam09528
Location:1646 → 2012

Ehrlichia_rpt; Ehrlichia tandem repeat (Ehrlichia_rpt)

pfam13934
Location:731 → 956

ELYS; Nuclear pore complex assembly

pfam16687
Location:11 → 498

ELYS-bb; beta-propeller of ELYS nucleoporin

sd00039
Location:232 → 268

7WD40; WD40 repeat [structural motif]

RNA

NR_136586.2 RNA Sequence

Status: VALIDATED

Source sequence(s)

AC113174

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_000001.11 Reference GRCh38.p14 Primary Assembly

Range

246839098..246931948 complement

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_011544157.4 → XP_011542459.3 protein ELYS isoform X2
XM_011544156.3 → XP_011542458.3 protein ELYS isoform X1
XM_047417231.1 → XP_047273187.1 protein ELYS isoform X3
XM_047417232.1 → XP_047273188.1 protein ELYS isoform X4

Alternate T2T-CHM13v2.0

Genomic

NC_060925.1 Alternate T2T-CHM13v2.0

Range

246270496..246363018 complement

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_054335862.1 → XP_054191837.1 protein ELYS isoform X2
XM_054335861.1 → XP_054191836.1 protein ELYS isoform X1
XM_054335863.1 → XP_054191838.1 protein ELYS isoform X3
XM_054335864.1 → XP_054191839.1 protein ELYS isoform X4

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

NM_175865.1: Suppressed sequence

Description

NM_175865.1: This RefSeq was removed because currently there is insufficient support for the transcript and the protein.