PCIF1 phosphorylated CTD interacting factor 1 [Homo sapiens (human)] - Gene

Summary

Official Symbol: PCIF1provided by HGNC
Official Full Name: phosphorylated CTD interacting factor 1provided by HGNC
Primary source: HGNC:HGNC:16200
See related: Ensembl:ENSG00000100982 MIM:618626; AllianceGenome:HGNC:16200
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: CAPAM; MT-A70; hCAPAM; hPCIF1; C20orf67; PPP1R121
Summary: Enables RNA polymerase II C-terminal domain phosphoserine binding activity; S-adenosyl-L-methionine binding activity; and mRNA (2'-O-methyladenosine-N6-)-methyltransferase activity. Involved in mRNA methylation; negative regulation of translation; and positive regulation of translation. Located in intercellular bridge; microtubule cytoskeleton; and nucleoplasm. [provided by Alliance of Genome Resources, Apr 2022]
Expression: Ubiquitous expression in ovary (RPKM 21.7), thyroid (RPKM 17.5) and 25 other tissues See more
Orthologs: mouse all
NEW: Try the new Gene table
Try the new Transcript table

Genomic context

Location:: 20q13.12

Exon count:: 18

Annotation release	Status	Assembly	Chr	Location
RS_2023_10	current	GRCh38.p14 (GCF_000001405.40)	20	NC_000020.11 (45934683..45948020)
RS_2023_10	current	T2T-CHM13v2.0 (GCF_009914755.1)	20	NC_060944.1 (47670740..47684073)
105.20220307	previous assembly	GRCh37.p13 (GCF_000001405.25)	20	NC_000020.10 (44563322..44576659)

Chromosome 20 - NC_000020.11 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

Go to the top of the page Help

Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

Go to the top of the page Help

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

Go to the top of the page Help

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

m6Am methyltransferase PCIF1 negatively regulates ciliation by inhibiting BICD2 expression.
Title: m6Am methyltransferase PCIF1 negatively regulates ciliation by inhibiting BICD2 expression.
The CTBP2-PCIF1 complex regulates m6Am modification of mRNA in head and neck squamous cell carcinoma.
Title: The CTBP2-PCIF1 complex regulates m6Am modification of mRNA in head and neck squamous cell carcinoma.
Role of PCIF1-mediated 5'-cap N6-methyladeonsine mRNA methylation in colorectal cancer and anti-PD-1 immunotherapy.
Title: Role of PCIF1-mediated 5'-cap N6-methyladeonsine mRNA methylation in colorectal cancer and anti-PD-1 immunotherapy.
Effects of the m6Am methyltransferase PCIF1 on cell proliferation and survival in gliomas.
Title: Effects of the m6Am methyltransferase PCIF1 on cell proliferation and survival in gliomas.
Enzymatic characterization of mRNA cap adenosine-N6 methyltransferase PCIF1 activity on uncapped RNAs.
Title: Enzymatic characterization of mRNA cap adenosine-N6 methyltransferase PCIF1 activity on uncapped RNAs.
The comprehensive interactomes of human adenosine RNA methyltransferases and demethylases reveal distinct functional and regulatory features.
Title: The comprehensive interactomes of human adenosine RNA methyltransferases and demethylases reveal distinct functional and regulatory features.
Methylation of viral mRNA cap structures by PCIF1 attenuates the antiviral activity of interferon-beta.
Title: Methylation of viral mRNA cap structures by PCIF1 attenuates the antiviral activity of interferon-β.
HIV reprograms host m(6)Am RNA methylome by viral Vpr protein-mediated degradation of PCIF1.
Title: HIV reprograms host m(6)Am RNA methylome by viral Vpr protein-mediated degradation of PCIF1.
Enzymatic characterization of three human RNA adenosine methyltransferases reveals diverse substrate affinities and reaction optima.
Title: Enzymatic characterization of three human RNA adenosine methyltransferases reveals diverse substrate affinities and reaction optima.
PCIF1 depletion leads to loss of m6Am RNA modification from the transcriptional-start-sites of mRNAs
Title: Atlas of quantitative single-base-resolution N(6)-methyl-adenine methylomes.

Submit: New GeneRIF Correction See all GeneRIFs (17)

Phenotypes

Go to the top of the page Help

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
Common variants at 30 loci contribute to polygenic dyslipidemia. EBI GWAS Catalog EBI GWAS CatalogPubMed

Variation

Go to the top of the page Help

See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Interactions

Go to the top of the page Help

Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

Go to the top of the page Help

Markers

STS-Z40713 (e-PCR)
- UniSTS:41011

SHGC-78139 (e-PCR)
- UniSTS:96056

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables RNA polymerase II C-terminal domain binding	IDA Inferred from Direct Assay more info	PubMed
enables RNA polymerase II C-terminal domain phosphoserine binding	IDA Inferred from Direct Assay more info	PubMed
enables S-adenosyl-L-methionine binding	IDA Inferred from Direct Assay more info	PubMed
enables mRNA (2'-O-methyladenosine-N6-)-methyltransferase activity	IDA Inferred from Direct Assay more info	PubMed

Process	Evidence Code	Pubs
involved_in mRNA processing	IDA Inferred from Direct Assay more info	PubMed
involved_in methylation	IEA Inferred from Electronic Annotation more info
involved_in negative regulation of translation	IDA Inferred from Direct Assay more info	PubMed
involved_in positive regulation of translation	IMP Inferred from Mutant Phenotype more info	PubMed
NOT involved_in regulation of translation	IDA Inferred from Direct Assay more info	PubMed

Component	Evidence Code	Pubs
located_in intercellular bridge	IDA Inferred from Direct Assay more info
located_in microtubule cytoskeleton	IDA Inferred from Direct Assay more info
located_in nucleoplasm	IDA Inferred from Direct Assay more info
is_active_in nucleus	IBA Inferred from Biological aspect of Ancestor more info
located_in nucleus	IDA Inferred from Direct Assay more info	PubMed

General protein information

Go to the top of the page Help

Preferred Names: mRNA (2'-O-methyladenosine-N(6)-)-methyltransferase

Names: PDX-1 C terminus-interacting factor 1; PDX1 C-terminal inhibiting factor 1; cap-specific adenosine methyltransferase; protein phosphatase 1, regulatory subunit 121

NP_071387.1

EC 2.1.1.62

XP_011527282.1

EC 2.1.1.62

XP_011527283.1

EC 2.1.1.62

XP_016883502.1

EC 2.1.1.62

XP_047296324.1

EC 2.1.1.62

XP_054179797.1

EC 2.1.1.62

XP_054179798.1

EC 2.1.1.62

XP_054179799.1

EC 2.1.1.62

XP_054179800.1

EC 2.1.1.62

NCBI Reference Sequences (RefSeq)

Go to the top of the page Help

NEW Try the new Transcript table

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_022104.4 → NP_071387.1 mRNA (2'-O-methyladenosine-N(6)-)-methyltransferase

See identical proteins and their annotated locations for NP_071387.1

Status: VALIDATED

Source sequence(s)

BC013365, BQ684226

Consensus CDS

CCDS13388.1

UniProtKB/Swiss-Prot

E1P5P1, Q54AB9, Q9H4Z3, Q9NT85

UniProtKB/TrEMBL

B7Z5U5

Related

ENSP00000361486.3, ENST00000372409.8

Conserved Domains (2) summary

cd00201
Location:47 → 77

WW; Two conserved tryptophans domain; also known as the WWP or rsp5 domain; around 40 amino acids; functions as an interaction module in a diverse set of signalling proteins; binds specific proline-rich sequences but at low affinities compared to other ...

pfam12237
Location:446 → 616

PCIF1_WW; Phosphorylated CTD interacting factor 1 WW domain

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

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

Reference GRCh38.p14 Primary Assembly

Genomic

NC_000020.11 Reference GRCh38.p14 Primary Assembly

Range

45934683..45948020

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_011528980.4 → XP_011527282.1 mRNA (2'-O-methyladenosine-N(6)-)-methyltransferase isoform X1

See identical proteins and their annotated locations for XP_011527282.1

UniProtKB/Swiss-Prot

E1P5P1, Q54AB9, Q9H4Z3, Q9NT85

UniProtKB/TrEMBL

B7Z5U5

Conserved Domains (2) summary

cd00201
Location:47 → 77

WW; Two conserved tryptophans domain; also known as the WWP or rsp5 domain; around 40 amino acids; functions as an interaction module in a diverse set of signalling proteins; binds specific proline-rich sequences but at low affinities compared to other ...

pfam12237
Location:446 → 616

PCIF1_WW; Phosphorylated CTD interacting factor 1 WW domain
XM_017028013.3 → XP_016883502.1 mRNA (2'-O-methyladenosine-N(6)-)-methyltransferase isoform X1

UniProtKB/Swiss-Prot

E1P5P1, Q54AB9, Q9H4Z3, Q9NT85

UniProtKB/TrEMBL

B7Z5U5

Conserved Domains (2) summary

cd00201
Location:47 → 77

WW; Two conserved tryptophans domain; also known as the WWP or rsp5 domain; around 40 amino acids; functions as an interaction module in a diverse set of signalling proteins; binds specific proline-rich sequences but at low affinities compared to other ...

pfam12237
Location:446 → 616

PCIF1_WW; Phosphorylated CTD interacting factor 1 WW domain
XM_011528981.4 → XP_011527283.1 mRNA (2'-O-methyladenosine-N(6)-)-methyltransferase isoform X1

See identical proteins and their annotated locations for XP_011527283.1

UniProtKB/Swiss-Prot

E1P5P1, Q54AB9, Q9H4Z3, Q9NT85

UniProtKB/TrEMBL

B7Z5U5

Conserved Domains (2) summary

cd00201
Location:47 → 77

WW; Two conserved tryptophans domain; also known as the WWP or rsp5 domain; around 40 amino acids; functions as an interaction module in a diverse set of signalling proteins; binds specific proline-rich sequences but at low affinities compared to other ...

pfam12237
Location:446 → 616

PCIF1_WW; Phosphorylated CTD interacting factor 1 WW domain
XM_047440368.1 → XP_047296324.1 mRNA (2'-O-methyladenosine-N(6)-)-methyltransferase isoform X2

RNA

XR_936605.3 RNA Sequence

Alternate T2T-CHM13v2.0

Genomic

NC_060944.1 Alternate T2T-CHM13v2.0

Range

47670740..47684073

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_054323822.1 → XP_054179797.1 mRNA (2'-O-methyladenosine-N(6)-)-methyltransferase isoform X1

UniProtKB/Swiss-Prot

E1P5P1, Q54AB9, Q9H4Z3, Q9NT85
XM_054323824.1 → XP_054179799.1 mRNA (2'-O-methyladenosine-N(6)-)-methyltransferase isoform X1

UniProtKB/Swiss-Prot

E1P5P1, Q54AB9, Q9H4Z3, Q9NT85
XM_054323823.1 → XP_054179798.1 mRNA (2'-O-methyladenosine-N(6)-)-methyltransferase isoform X1

UniProtKB/Swiss-Prot

E1P5P1, Q54AB9, Q9H4Z3, Q9NT85
XM_054323825.1 → XP_054179800.1 mRNA (2'-O-methyladenosine-N(6)-)-methyltransferase isoform X2