ELL2 elongation factor for RNA polymerase II 2 [Homo sapiens (human)] - Gene

Summary

Official Symbol: ELL2provided by HGNC
Official Full Name: elongation factor for RNA polymerase II 2provided by HGNC
Primary source: HGNC:HGNC:17064
See related: Ensembl:ENSG00000118985 MIM:601874; AllianceGenome:HGNC:17064
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: MRCCAT1
Summary: Predicted to enable cis-regulatory region sequence-specific DNA binding activity. Involved in snRNA transcription by RNA polymerase II. Located in nucleoplasm. Part of transcription elongation factor complex. [provided by Alliance of Genome Resources, Jan 2025]
Expression: Ubiquitous expression in esophagus (RPKM 18.5), salivary gland (RPKM 14.3) and 25 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 5q15

Exon count:: 14

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	5	NC_000005.10 (95885098..95961851, complement)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	5	NC_060929.1 (96386338..96463172, complement)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	5	NC_000005.9 (95220802..95297555, complement)

Chromosome 5 - NC_000005.10 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: Tissue-specific circular RNA induction during human fetal development
Description: 35 human fetal samples from 6 tissues (3 - 7 replicates per tissue) collected between 10 and 20 weeks gestational time were sequenced using Illumina TruSeq Stranded Total RNA
BioProject: PRJNA270632
Publication: PMID 26076956
Analysis date: Mon Apr 2 22:54:59 2018

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Characterizing the Interaction between the HTLV-1 Transactivator Tax-1 with Transcription Elongation Factor ELL2 and Its Impact on Viral Transactivation.
Title: Characterizing the Interaction between the HTLV-1 Transactivator Tax-1 with Transcription Elongation Factor ELL2 and Its Impact on Viral Transactivation.
Allosteric transcription stimulation by RNA polymerase II super elongation complex.
Title: Allosteric transcription stimulation by RNA polymerase II super elongation complex.
MRCCAT1 is upregulated in glioma, predicting poor outcome for patients. MRCCAT1 promotes glioma cell proliferation and migration by activating p38-MAPK signaling.
Title: Upregulation of long noncoding RNA MRCCAT1 predicts poor prognosis and functions as an oncogene in glioma.
ELL2 protein was downregulated in prostate cancer specimens and was up-regulated by androgens in prostate cancer cell lines LNCaP and C4-2. ELL2 knockdown enhanced prostate cancer cell proliferation and motility.
Title: Regulation of ELL2 stability and polyubiquitination by EAF2 in prostate cancer cells.
Study in CD138+ plasma cells from 1630 multiple myeloma (MM) patients show that the MM risk allele at 5q15 lowers ELL2 expression in these cells, but not in peripheral blood or other tissues.
Title: The multiple myeloma risk allele at 5q15 lowers ELL2 expression and increases ribosomal gene expression.
Study reports the 2.0-A resolution crystal structure of the human ELL2 C-terminal domain bound to its 50-residue binding site on AFF4, the ELLBow. The ELLBow consists of an N-terminal helix followed by an extended hairpin and occupies most of the concave surface of ELL2. This surface is important for the ability of ELL2 to promote HIV-1 Tat-mediated proviral transcription.
Title: Structural basis for ELL2 and AFF4 activation of HIV-1 proviral transcription.
Knockdown of RNA polymerase II elongation factor ELL2 (ELL2) sensitized prostate cancer cells to DNA damage and overexpression of ELL2 protected prostate cancer cells from DNA damage.
Title: ELL2 regulates DNA non-homologous end joining (NHEJ) repair in prostate cancer cells.
expression is consistent with inherited genetic variation contributing to arrest of plasma cell development, facilitating multiple myeloma clonal expansion.
Title: Genetic Predisposition to Multiple Myeloma at 5q15 Is Mediated by an ELL2 Enhancer Polymorphism.
Results provide the first evidence that ELL2 is a direct target of miR-299 and increased ELL2 expression and down-regulation of miR-299 are associated with GBM progression and poor prognosis in patients.
Title: Up-regulated microRNA-299 corrected with poor prognosis of glioblastoma multiforme patients by targeting ELL2.
Selective expression of the transcription elongation factor ELL3 in B cells prior to ELL2 drives proliferation and survival
Title: Selective expression of the transcription elongation factor ELL3 in B cells prior to ELL2 drives proliferation and survival.

Submit: New GeneRIF Correction See all GeneRIFs (17)

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

EBI GWAS Catalog

Description
Discovery and fine mapping of serum protein loci through transethnic meta-analysis. EBI GWAS Catalog EBI GWAS CatalogPubMed
Loci associated with N-glycosylation of human immunoglobulin G show pleiotropy with autoimmune diseases and haematological cancers. 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)

HIV-1 interactions

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Replication interactions

Interaction	Pubs
HIV-1 replication requires ELL2, AFF4 and AFF1 for transcriptional elongation as shown through CRISPR/Cas genome editing	PubMed

Protein interactions

Protein	Gene	Interaction	Pubs
Tat	tat	Binding of isolated AFF1(1-308) CBS to CDK9/CycT1 prevents HIV-1 Tat from activating HIV transcription and assembling complete SECs (AFF1, AFF4, ELL2, and ENL). The AFF1(1-308) M60A/L61A mutant shows no suppression of Tat transactivation	PubMed
	tat	HIV-1 Tat increases the amount of ELL2 bound to P-TEFb without affecting the AFF4-P-TEFb binding. CDK9 is required for the Tat-induced ELL2 accumulation and Tat interaction with ELL2	PubMed
	tat	Brd4 inhibits HIV-1 Tat-human super elongation complex (components AFF4, ELL2, CycT1, and CDK9) by competing with HIV-1 Tat for binding to P-TEFb on HIV-1 promoter	PubMed

Go to the HIV-1, Human Interaction Database

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

RH69404 (e-PCR)
- UniSTS:92460

STS-H56561 (e-PCR)
- UniSTS:28722

RH46186 (e-PCR)
- UniSTS:50513

Cda1ba12 (e-PCR)
- UniSTS:69469

RH69314 (e-PCR)
- UniSTS:15457

SGC32614 (e-PCR)
- UniSTS:26212

ELL2_3553 (e-PCR)
- UniSTS:462181

SHGC-54510 (e-PCR)
- UniSTS:80249

G36675 (e-PCR)
- UniSTS:2688

RH93840 (e-PCR)
- UniSTS:91812

WI-11385 (e-PCR)
- UniSTS:39603

RH80608 (e-PCR)
- UniSTS:92865

G54567 (e-PCR)
- UniSTS:117705

G19765 (e-PCR)
- UniSTS:50149

A001X44 (e-PCR)
- UniSTS:50150

RH47475 (e-PCR)
- UniSTS:2279

RH79988 (e-PCR)
- UniSTS:92399

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables cis-regulatory region sequence-specific DNA binding	IBA Inferred from Biological aspect of Ancestor more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed

Process	Evidence Code	Pubs
involved_in positive regulation of transcription elongation by RNA polymerase II	IBA Inferred from Biological aspect of Ancestor more info
involved_in snRNA transcription by RNA polymerase II	IBA Inferred from Biological aspect of Ancestor more info
involved_in snRNA transcription by RNA polymerase II	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in transcription elongation by RNA polymerase II	IEA Inferred from Electronic Annotation more info

Component	Evidence Code	Pubs
located_in nucleoplasm	IDA Inferred from Direct Assay more info
located_in nucleoplasm	TAS Traceable Author Statement more info
part_of transcription elongation factor complex	IBA Inferred from Biological aspect of Ancestor more info
part_of transcription elongation factor complex	IDA Inferred from Direct Assay more info	PubMed

General protein information

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Preferred Names: RNA polymerase II elongation factor ELL2

Names: ELL-related RNA polymerase II, elongation factor; elongation factor RNA for polymerase II 2; elongation factor, RNA polymerase II, 2; metastatic renal cell carcinoma-associated transcript 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_012081.6 → NP_036213.2 RNA polymerase II elongation factor ELL2

See identical proteins and their annotated locations for NP_036213.2

Status: VALIDATED

Source sequence(s)

AB209343, AV652801, BC028412, BC151238, BX538289

Consensus CDS

CCDS4080.1

UniProtKB/Swiss-Prot

B4DNK7, O00472

UniProtKB/TrEMBL

Q59FW6

Related

ENSP00000237853.4, ENST00000237853.9

Conserved Domains (2) summary

pfam07303
Location:532 → 633

Occludin_ELL; Occludin homology domain

pfam10390
Location:11 → 291

ELL; RNA polymerase II elongation factor ELL

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_000005.10 Reference GRCh38.p14 Primary Assembly

Range

95885098..95961851 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_017009240.3 → XP_016864729.1 RNA polymerase II elongation factor ELL2 isoform X3

UniProtKB/TrEMBL

Q59FW6

Conserved Domains (3) summary

pfam01690
Location:252 → 484

PLRV_ORF5; Potato leaf roll virus readthrough protein

pfam07303
Location:403 → 500

Occludin_ELL; Occludin homology domain

pfam10390
Location:1 → 157

ELL; RNA polymerase II elongation factor ELL
XM_047416959.1 → XP_047272915.1 RNA polymerase II elongation factor ELL2 isoform X2

UniProtKB/TrEMBL

Q59FW6
XM_047416960.1 → XP_047272916.1 RNA polymerase II elongation factor ELL2 isoform X3

UniProtKB/TrEMBL

Q59FW6
XM_017009239.2 → XP_016864728.1 RNA polymerase II elongation factor ELL2 isoform X1

Alternate T2T-CHM13v2.0

Genomic

NC_060929.1 Alternate T2T-CHM13v2.0

Range

96386338..96463172 complement

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_054352099.1 → XP_054208074.1 RNA polymerase II elongation factor ELL2 isoform X3

UniProtKB/TrEMBL

Q59FW6
XM_054352098.1 → XP_054208073.1 RNA polymerase II elongation factor ELL2 isoform X2

UniProtKB/TrEMBL

Q59FW6
XM_054352100.1 → XP_054208075.1 RNA polymerase II elongation factor ELL2 isoform X3

UniProtKB/TrEMBL

Q59FW6
XM_054352097.1 → XP_054208072.1 RNA polymerase II elongation factor ELL2 isoform X1