PRM2 protamine 2 [Homo sapiens (human)] - Gene

Summary

Official Symbol: PRM2provided by HGNC
Official Full Name: protamine 2provided by HGNC
Primary source: HGNC:HGNC:9448
See related: Ensembl:ENSG00000122304 MIM:182890; AllianceGenome:HGNC:9448
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: CT94.2
Summary: Protamines substitute for histones in the chromatin of sperm during the haploid phase of spermatogenesis, and are the major DNA-binding proteins in the nucleus of sperm in many vertebrates. They package the sperm DNA into a highly condensed complex in a volume less than 5% of a somatic cell nucleus. Many mammalian species have only one protamine (protamine 1); however, a few species, including human and mouse, have two. This gene encodes protamine 2, which is cleaved to give rise to a family of protamine 2 peptides. Alternatively spliced transcript variants have also been found for this gene. [provided by RefSeq, Sep 2015]
Expression: Restricted expression toward testis (RPKM 2357.8) See more
Orthologs: mouse all
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Genomic context

Location:: 16p13.13

Exon count:: 2

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	16	NC_000016.10 (11275639..11276480, complement)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	16	NC_060940.1 (11311859..11312700, complement)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	16	NC_000016.9 (11369496..11370337, complement)

Chromosome 16 - NC_000016.10 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: 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?

Impact of tobacco smoking in association with H2BFWT, PRM1 and PRM2 genes variants on male infertility.
Title: Impact of tobacco smoking in association with H2BFWT, PRM1 and PRM2 genes variants on male infertility.
Spermatozoa retrieval in azoospermia and expression profile of JMJD1A, TNP2, and PRM2 in a subset of the Karachi population.
Title: Spermatozoa retrieval in azoospermia and expression profile of JMJD1A, TNP2, and PRM2 in a subset of the Karachi population.
Polymorphisms of sperm protamine genes and CMA3 staining in infertile men with varicocele.
Title: Polymorphisms of sperm protamine genes and CMA3 staining in infertile men with varicocele.
Protamine 1/Protamine 2 mRNA ratio in nonobstructive azoospermic patients.
Title: Protamine 1/Protamine 2 mRNA ratio in nonobstructive azoospermic patients.
Correlation Between Protamine-2 and miRNA-122 in Sperm from Heroin-addicted Men: A Case-Control Study.
Title: Correlation Between Protamine-2 and miRNA-122 in Sperm from Heroin-addicted Men: A Case-Control Study.
Evaluation of the association between polymorphisms of PRM1 and PRM2 and the risk of male infertility: a systematic review, meta-analysis, and meta-regression.
Title: Evaluation of the association between polymorphisms of PRM1 and PRM2 and the risk of male infertility: a systematic review, meta-analysis, and meta-regression.
Tobacco smoking and its impact on the expression level of sperm nuclear protein genes: H2BFWT, TNP1, TNP2, PRM1 and PRM2.
Title: Tobacco smoking and its impact on the expression level of sperm nuclear protein genes: H2BFWT, TNP1, TNP2, PRM1 and PRM2.
Bacterial infections have significant negative effects on sperm chromatin condensation and protamine P1/P2 ratio.
Title: The effects of bacterial infection on human sperm nuclear protamine P1/P2 ratio and DNA integrity.
Protamine-1 and protamine-2 mRNA levels as well as the protamine mRNA ratio and all routine semen parameters revealed significant differences between recurrent miscarriage couples and healthy volunteers. Values of protamine-1 and protamine-2 mRNAs were significantly higher and the protamine mRNA ratio was significantly lower in couples with recurrent miscarriage.
Title: Unexplained recurrent miscarriages are associated with an aberrant sperm protamine mRNA content.
Authors examined, for the first time in a Turkish population, the association between protamine gene alleles (PRM1 c.-190C>A, PRM1 c.197G>T, and PRM2 c.248C>T), and YBX2 (c.187T>C and c.1095 + 16A>G) and male infertility.
Title: Genetic Polymorphisms in PRM1, PRM2, and YBX2 Genes are Associated with Male Factor Infertility.

Submit: New GeneRIF Correction See all GeneRIFs (33)

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
Genetic variants associated with disordered eating. EBI GWAS Catalog EBI GWAS CatalogPubMed
Genome-wide meta-analysis identifies novel multiple sclerosis susceptibility loci. 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

PMC151395P1 (e-PCR)
- UniSTS:271143

GDB:438999 (e-PCR)
- UniSTS:157286

SHGC-12339 (e-PCR)
- UniSTS:164

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables DNA binding	IEA Inferred from Electronic Annotation more info
enables cadmium ion binding	IDA Inferred from Direct Assay more info	PubMed
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables zinc ion binding	IDA Inferred from Direct Assay more info	PubMed

Process	Evidence Code	Pubs
involved_in chromosome condensation	IEA Inferred from Electronic Annotation more info
involved_in chromosome organization	TAS Traceable Author Statement more info	PubMed
involved_in nucleus organization	IBA Inferred from Biological aspect of Ancestor more info
involved_in sequestering of metal ion	EXP Inferred from Experiment more info	PubMed
involved_in spermatid development	IBA Inferred from Biological aspect of Ancestor more info
involved_in spermatogenesis	ISS Inferred from Sequence or Structural Similarity more info

Component	Evidence Code	Pubs
located_in male germ cell nucleus	IEA Inferred from Electronic Annotation more info
located_in nucleoplasm	TAS Traceable Author Statement more info	PubMed
part_of nucleosome	IEA Inferred from Electronic Annotation more info
located_in nucleus	HDA more info	PubMed
is_active_in nucleus	IBA Inferred from Biological aspect of Ancestor more info

General protein information

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Preferred Names: protamine-2

Names: cancer/testis antigen family 94, member 2; sperm histone P2; sperm protamine P2; testicular secretory protein Li 40

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_001286356.2 → NP_001273285.1 protamine-2 isoform 2

See identical proteins and their annotated locations for NP_001273285.1

Status: REVIEWED

Description

Transcript Variant: This variant (2) uses an alternate acceptor splice site at the last exon that causes a frameshift compared to variant 1. The resulting isoform (2) has a longer and distinct C-terminus compared to isoform 1.

Source sequence(s)

AC009121

Consensus CDS

CCDS66944.1

UniProtKB/Swiss-Prot

P04554

Related

ENSP00000403681.2, ENST00000435245.2
NM_001286357.2 → NP_001273286.1 protamine-2 isoform 3

Status: REVIEWED

Description

Transcript Variant: This variant (3) uses alternate donor and acceptor splice sites at the junction of exons 1 and 2 compared to variant 1. The resulting isoform (3) lacks an internal protein segment and has a shorter C-terminus compared to isoform 1.

Source sequence(s)

AC009121
NM_001286358.2 → NP_001273287.1 protamine-2 isoform 4

Status: REVIEWED

Description

Transcript Variant: This variant (4) uses an alternate acceptor splice site at the last exon that causes a frameshift compared to variant 1. The resulting isoform (4) has a longer and distinct C-terminus compared to isoform 1.

Source sequence(s)

AC009121

UniProtKB/Swiss-Prot

P04554
NM_001286359.2 → NP_001273288.1 protamine-2 isoform 5

Status: REVIEWED

Description

Transcript Variant: This variant (5) uses an alternate donor splice site at the first exon compared to variant 1. The resulting isoform (5) has a distinct C-terminus compared to isoform 1.

Source sequence(s)

AC009121

UniProtKB/Swiss-Prot

P04554
NM_002762.4 → NP_002753.2 protamine-2 isoform 1

See identical proteins and their annotated locations for NP_002753.2

Status: REVIEWED

Description

Transcript Variant: This variant (1) represents the predominant transcript and encodes the predominant isoform (1).

Source sequence(s)

AC009121

Consensus CDS

CCDS42118.1

UniProtKB/Swiss-Prot

P04554, Q6ZMM0

UniProtKB/TrEMBL

Q1LZN1

Related

ENSP00000241808.5, ENST00000241808.9

RNA

NR_104428.2 RNA Sequence

Status: REVIEWED

Description

Transcript Variant: This variant (6) is alternatively spliced at the 3' end compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).

Source sequence(s)

AC009121