MEPCE methylphosphate capping enzyme [Homo sapiens (human)] - Gene

Summary

Official Symbol: MEPCEprovided by HGNC
Official Full Name: methylphosphate capping enzymeprovided by HGNC
Primary source: HGNC:HGNC:20247
See related: Ensembl:ENSG00000146834 MIM:611478; AllianceGenome:HGNC:20247
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: BCDIN3
Summary: Enables 7SK snRNA binding activity and RNA 5'-gamma-phosphate methyltransferase activity. Involved in RNA modification; positive regulation of protein localization to Cajal body; and positive regulation of snRNA transcription by RNA polymerase II. Located in nucleus. Part of 7SK snRNP. [provided by Alliance of Genome Resources, Nov 2024]
Expression: Ubiquitous expression in testis (RPKM 29.4), spleen (RPKM 17.1) and 25 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 7q22.1

Exon count:: 6

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	7	NC_000007.14 (100428790..100434118)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	7	NC_060931.1 (101668175..101674196)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	7	NC_000007.13 (100026413..100031741)

Chromosome 7 - NC_000007.14 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?

LARP3, LARP7, and MePCE are involved in the early stage of human telomerase RNA biogenesis.
Title: LARP3, LARP7, and MePCE are involved in the early stage of human telomerase RNA biogenesis.
Excessive transcription-replication conflicts are a vulnerability of BRCA1-mutant cancers.
Title: Excessive transcription-replication conflicts are a vulnerability of BRCA1-mutant cancers.
Long noncoding RNA ST8SIA6AS1 promotes the migration and invasion of hypoxiatreated hepatocellular carcinoma cells through the miR338/MEPCE axis.
Title: Long non‑coding RNA ST8SIA6‑AS1 promotes the migration and invasion of hypoxia‑treated hepatocellular carcinoma cells through the miR‑338/MEPCE axis.
HEXIM1 Diffusion in the Nucleus Is Regulated by Its Interactions with Both 7SK and P-TEFb.
Title: HEXIM1 Diffusion in the Nucleus Is Regulated by Its Interactions with Both 7SK and P-TEFb.
our results suggest that crosstalk between the histone-binding and RNA methylation activities of MePCE regulates P-TEFb activation on chromatin in a 7SK- and Brd4-independent manner.
Title: Crosstalk between the RNA Methylation and Histone-Binding Activities of MePCE Regulates P-TEFb Activation on Chromatin.
The 7SK small nuclear RNP (snRNP), composed of the 7SK small nuclear RNA (snRNA), MePCE, and Larp7, also functions as a canonical transcription factor that, in collaboration with the little elongation complex (LEC) comprising ELL, Ice1, Ice2, and ZC3H8, promotes transcription of RNAPII-specific spliceosomal snRNA and small nucleolar RNA (snoRNA) genes.
Title: The 7SK snRNP associates with the little elongation complex to promote snRNA gene expression.
Data indicate the binding of RNA-binding protein HEXIM with 7SKsnRNP complex comprising the non-coding RNA 7SK and proteins MePCE and LARP7.
Title: Intermolecular recognition of the non-coding RNA 7SK and HEXIM protein in perspective.
Capping enzyme can play a direct role in transcription by modulating displacement of nascent RNA during transcription.
Title: Human capping enzyme promotes formation of transcriptional R loops in vitro.

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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

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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Protein interactions

Protein	Gene	Interaction	Pubs
Tat	tat	A La-related protein, LARP7, is associated with P-TEFb, HEXIM1/2, MEPCE, and 7SK RNA in a large stable complex form. Knockdown of LARP7 decreases the steady-state level of 7SK, but increases free P-TEFb and enhances Tat-mediated transcription	PubMed
	tat	HIV-1 Tat forms at least two distinct P-TEFb-containing complexes. Tatcom1 is composed of P-TEFb, AF9, ENL, ELL, AFF1, AFF4, and PAF1, presenting strong CTD-kinase activity, while Tatcom2 consists of 7SK, LARP7, and MEPCE with two molecules of Tat/P-TEFb	PubMed
	tat	HIV-1 Tat complexes with LARP7, MEPCE, SART3, NPM1, PPM1G, hnRNP-F, and 7SK RNA to form a Tat-7SK RNP complex to control HIV-1 transcription	PubMed
	tat	CDK9-CycT1-AFF1 is stimulated by HIV-1 Tat and transferred as a single complex unit to BRD4 upon stress-induced disruption of AFF1-containing 7SK snRNP (HEXIM1, MEPCE, LARP7, 7SK RNA, CDK9, CycT1, and AFF1)	PubMed
	tat	HIV-1 Tat is identified to have a physical interaction with 7SK snRNA methylphosphate capping enzyme (MEPCE) in human HEK293 and/or Jurkat cell lines by using affinity tagging and purification mass spectrometry analyses	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

WIAF-1510 (e-PCR)
- UniSTS:42291

RH104102 (e-PCR)
- UniSTS:98427

STS-Z41431 (e-PCR)
- UniSTS:3013

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables 7SK snRNA binding	IDA Inferred from Direct Assay more info	PubMed
enables O-methyltransferase activity	IBA Inferred from Biological aspect of Ancestor more info
enables RNA 5'-gamma-phosphate methyltransferase activity	IDA Inferred from Direct Assay more info	PubMed
enables RNA binding	HDA more info	PubMed
enables RNA binding	IPI Inferred from Physical Interaction more info	PubMed
enables RNA methyltransferase activity	IBA Inferred from Biological aspect of Ancestor more info
enables RNA methyltransferase activity	IDA Inferred from Direct Assay more info	PubMed
enables RNA methyltransferase activity	IMP Inferred from Mutant Phenotype more info	PubMed
enables S-adenosylmethionine-dependent methyltransferase activity	IDA Inferred from Direct Assay more info	PubMed
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables snRNA binding	IBA Inferred from Biological aspect of Ancestor more info

Process	Evidence Code	Pubs
involved_in RNA methylation	IDA Inferred from Direct Assay more info	PubMed
involved_in negative regulation of transcription by RNA polymerase II	IEA Inferred from Electronic Annotation more info
involved_in positive regulation of G1/S transition of mitotic cell cycle	IEA Inferred from Electronic Annotation more info
involved_in positive regulation of protein localization to Cajal body	IDA Inferred from Direct Assay more info	PubMed
involved_in positive regulation of snRNA transcription by RNA polymerase II	IDA Inferred from Direct Assay more info	PubMed
involved_in snRNA metabolic process	IDA Inferred from Direct Assay more info	PubMed
involved_in snRNA modification	IBA Inferred from Biological aspect of Ancestor more info
involved_in snRNA modification	IDA Inferred from Direct Assay more info	PubMed

Component	Evidence Code	Pubs
part_of 7SK snRNP	IDA Inferred from Direct Assay more info	PubMed
located_in nucleus	IDA Inferred from Direct Assay more info	PubMed
part_of ribonucleoprotein complex	IDA Inferred from Direct Assay more info	PubMed

General protein information

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Preferred Names: 7SK snRNA methylphosphate capping enzyme

Names: bicoid-interacting protein 3 homolog; bin3 homolog; bin3, bicoid-interacting 3, homolog

NP_001181919.1

EC 2.1.1.-

NP_001181920.1

EC 2.1.1.-

NP_001181921.1

EC 2.1.1.-

NP_001350415.1

EC 2.1.1.-

NP_062552.2

EC 2.1.1.-

XP_054214631.1

EC 2.1.1.-

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_001194990.2 → NP_001181919.1 7SK snRNA methylphosphate capping enzyme isoform B

See identical proteins and their annotated locations for NP_001181919.1

Status: VALIDATED

Description

Transcript Variant: This variant (2) differs in the 5' UTR, lacks a portion of the 5' coding region, and initiates translation at a downstream AUG, compared to variant 1. The resulting protein (isoform B) has a shorter N-terminus, compared to isoform A. Variants 2, 3 and 4 encode the same isoform (B).

Source sequence(s)

AC092849, AK055964, CB152355

Consensus CDS

CCDS55136.1

UniProtKB/Swiss-Prot

Q7L2J0

Related

ENSP00000400875.1, ENST00000414441.5

Conserved Domains (1) summary

pfam06859
Location:106 → 214

Bin3; Bicoid-interacting protein 3 (Bin3)
NM_001194991.2 → NP_001181920.1 7SK snRNA methylphosphate capping enzyme isoform B

See identical proteins and their annotated locations for NP_001181920.1

Status: VALIDATED

Description

Transcript Variant: This variant (3) differs in the 5' UTR, lacks a portion of the 5' coding region, and initiates translation at a downstream AUG, compared to variant 1. The resulting protein (isoform B) has a shorter N-terminus, compared to isoform A. Variants 2, 3 and 4 encode the same isoform (B).

Source sequence(s)

BC018935, CB152355, CD672398

Consensus CDS

CCDS55136.1

UniProtKB/Swiss-Prot

Q7L2J0

Conserved Domains (1) summary

pfam06859
Location:106 → 214

Bin3; Bicoid-interacting protein 3 (Bin3)
NM_001194992.2 → NP_001181921.1 7SK snRNA methylphosphate capping enzyme isoform B

See identical proteins and their annotated locations for NP_001181921.1

Status: VALIDATED

Description

Transcript Variant: This variant (4) differs in the 5' UTR, lacks a portion of the 5' coding region, and initiates translation at a downstream AUG, compared to variant 1. The resulting protein (isoform B) has a shorter N-terminus, compared to isoform A. Variants 2, 3 and 4 encode the same isoform (B).

Source sequence(s)

AC092849, BC018935, BP217791

Consensus CDS

CCDS55136.1

UniProtKB/Swiss-Prot

Q7L2J0

Related

ENSP00000511703.1, ENST00000497759.2

Conserved Domains (1) summary

pfam06859
Location:106 → 214

Bin3; Bicoid-interacting protein 3 (Bin3)
NM_001363486.2 → NP_001350415.1 7SK snRNA methylphosphate capping enzyme isoform B

Status: VALIDATED

Source sequence(s)

AC092849, AK055964, HY017414

Consensus CDS

CCDS55136.1

Related

ENSP00000511704.1, ENST00000479201.2

Conserved Domains (1) summary

pfam06859
Location:106 → 214

Bin3; Bicoid-interacting protein 3 (Bin3)
NM_019606.6 → NP_062552.2 7SK snRNA methylphosphate capping enzyme isoform A

See identical proteins and their annotated locations for NP_062552.2

Status: VALIDATED

Description

Transcript Variant: This variant (1) represents the longest transcript and encodes the longer isoform (A).

Source sequence(s)

BC016396, BC018935

Consensus CDS

CCDS5693.1

UniProtKB/Swiss-Prot

B3KP86, D6W5V7, Q7L2J0, Q9NPD4

UniProtKB/TrEMBL

A8K5Q1

Related

ENSP00000308546.2, ENST00000310512.4

Conserved Domains (2) summary

cd02440
Location:446 → 616

AdoMet_MTases; S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy). ...

pfam06859
Location:575 → 683

Bin3; Bicoid-interacting protein 3 (Bin3)