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H1FNT Gene

protein-coding   GIFtS: 38
GCID: GC12P048722

H1 Histone Family, Member N, Testis-Specific

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(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, 10fRNAdb, 12H-InvDB, 13NCBI, 14NONCODE, and/or 15RNAdb)
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Aliases
H1 Histone Family, Member N, Testis-Specific1 2
Haploid Germ Cell-Specific Nuclear Protein 12 3
Histone H1t22 3
HANP12 3
H1T22
Testis-Specific H1 Histone2

External Ids:    HGNC: 248931   Entrez Gene: 3415672   Ensembl: ENSG000001871667   UniProtKB: Q75WM63   

Export aliases for H1FNT gene to outside databases

Previous GC identifers: GC12P047012 GC12P045755


(According to Entrez Gene, GeneCards, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
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GeneCards Summary for H1FNT Gene:
H1FNT (H1 histone family, member N, testis-specific) is a protein-coding gene.

UniProtKB/Swiss-Prot: H1FNT_HUMAN, Q75WM6
Function: Essential for normal spermatogenesis and male fertility. Required for proper cell restructuring and DNA
condensation during the elongation phase of spermiogenesis. Involved in the histone-protamine transition of sperm
chromatin and the subsequent production of functional sperm. Binds both double-stranded and single-stranded DNA,
ATP and protamine-1 (By similarity)




(According to GeneLoc and/or HGNC, and/or
Entrez Gene (NCBI build 37),
and/or miRBase,
Genomic Views according to UCSC (hg19) and Ensembl (release 75), Regulatory elements and Epigenetics data according to QIAGEN, and/or SwitchGear Genomics)
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RefSeq DNA sequence at NCBI GenBank:
NC_000012.11  NC_018923.2  NT_029419.13  
Regulatory elements:
   Regulatory transcription factor binding sites in the H1FNT gene promoter:
         GR   GR-beta   NF-kappaB   C/EBPalpha   E47   HEN1   NF-kappaB2   GR-alpha   NF-kappaB1   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidH1FNT promoter sequence
   Search Chromatin IP Primers for H1FNT

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat H1FNT


Genomic Location:
Genomic View: UCSC Golden Path with GeneCards custom track

Entrez Gene cytogenetic band: 12q13.11   Ensembl cytogenetic band:  12q13.11   HGNC cytogenetic band: 12q13.11

H1FNT Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
H1FNT gene location

GeneLoc information about chromosome 12         GeneLoc Exon Structure

GeneLoc location for GC12P048722:  view genomic region     (about GC identifiers)

Start:
48,722,763 bp from pter      End:
48,724,062 bp from pter
Size:
1,300 bases      Orientation:
plus strand

(According to 1UniProtKB, HORDE, 2neXtProt, Ensembl, and/or Reactome, Modification sites according to PhosphoSitePlus, Specific Peptides from DME, RefSeq according to NCBI, PDB rendering according to OCA and/or Proteopedia, Recombinant Proteins from EMD Millipore, R&D Systems, GenScript, Enzo Life Sciences, OriGene, Novus Biologicals, Sino Biological, ProSpec, Cloud-Clone Corp., and/or eBioscience,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, Cloud-Clone Corp., and/or eBioscience, Antibodies by EMD Millipore, R&D Systems, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, LSBio, Abcam, Cloud-Clone Corp, and/or others.)
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UniProtKB/Swiss-Prot: H1FNT_HUMAN, Q75WM6 (See protein sequence)
Recommended Name: Testis-specific H1 histone  
Size: 255 amino acids; 28116 Da
Caution: It is uncertain whether Met-1 or Met-22 is the initiator
Sequence caution: Sequence=BAD13382.2; Type=Erroneous initiation;
Secondary accessions: Q147U8 Q5GKZ5 Q7Z694

Explore the universe of human proteins at neXtProt for H1FNT: NX_Q75WM6

Explore proteomics data for H1FNT at MOPED


See H1FNT Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

REFSEQ proteins: NP_861453.1  
ENSEMBL proteins: 
 ENSP00000334805  

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(According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
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HGNC Gene Families:
RIH: Histones / Replication-independent

ProtoNet protein and cluster: Q75WM6

UniProtKB/Swiss-Prot: H1FNT_HUMAN, Q75WM6
Similarity: Belongs to the histone H1/H5 family


(According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013, inGenious Targeting Laboratory, genOway,
transcription factor targeting from QIAGEN and/or HOMER, miRNA Gene Targets from miRTarBase, shRNA from OriGene, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, SwitchGear Genomics, Gene Editing from DNA2.0, Clones from OriGene, GenScript, Sino Biological, DNA2.0, Vector BioLabs and/or Addgene, Cell Lines from GenScript, ESI BIO, In Situ Hybridization Assays from Advanced Cell Diagnostics, Flow cytometry from eBioscience, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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Molecular Function:

     UniProtKB/Swiss-Prot Summary: H1FNT_HUMAN, Q75WM6
Function: Essential for normal spermatogenesis and male fertility. Required for proper cell restructuring and DNA
condensation during the elongation phase of spermiogenesis. Involved in the histone-protamine transition of sperm
chromatin and the subsequent production of functional sperm. Binds both double-stranded and single-stranded DNA,
ATP and protamine-1 (By similarity)

     Gene Ontology (GO): 2 molecular function terms:    About this table

GO IDQualified GO termEvidencePubMed IDs
GO:0003677DNA binding IEA--
GO:0005524ATP binding IEA--
     
Find genes that share ontologies with H1FNT           About GenesLikeMe


Phenotypes:
     1 MGI mutant phenotype (inferred from 2 alleles(MGI details for H1fnt):
 reproductive system 

Find genes that share phenotypes with H1FNT           About GenesLikeMe

Animal Models:
     MGI mouse knock-outs for H1FNT: H1fnttm1Idvd H1fnttm1Yoni

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(According to UniProtKB, COMPARTMENTS Subcellular localization database, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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Subcellular locations from UniProtKB/Swiss-Prot
H1FNT_HUMAN, Q75WM6: Nucleus (By similarity). Chromosome (By similarity). Note=In round and elongating
spermatids, specifically localizes to a chromatin domain at the apical pole (By similarity)
Subcellular locations from COMPARTMENTS: 

CompartmentConfidence
nucleus4

Gene Ontology (GO): 2 cellular component terms:    About this table

GO IDQualified GO termEvidencePubMed IDs
GO:0000790nuclear chromatin ISS15710904
GO:0005634nucleus ----

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(SuperPaths according to PathCards, Pathways according to R&D Systems, Cell Signaling Technology, KEGG, PharmGKB, BioSystems, Sino Biological, Reactome, Tocris Bioscience, GeneGo (Thomson Reuters), QIAGEN, and/or UniProtKB, Sets of similar genes according to GeneDecks, Interaction Networks according to QIAGEN, and/or STRING, Interactions according to 1UniProtKB, 2MINT, 3I2D, and/or 4STRING, with links to IntAct and Ensembl, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene).
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    Custom Pathway & Disease-focused RT2 Profiler PCR Arrays for H1FNT
Interactions:

    Search GeneGlobe Interaction Network for H1FNT

Gene Ontology (GO): 4 biological process terms:    About this table

GO IDQualified GO termEvidencePubMed IDs
GO:0007275multicellular organismal development IEA--
GO:0007290spermatid nucleus elongation ISS15710904
GO:0030261chromosome condensation IEA--
GO:0035092sperm chromatin condensation ISS15710904

Find genes that share ontologies with H1FNT           About GenesLikeMe



(Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience, ApexBio, HMDB, BitterDB, and/or Novoseek, Ligands according to IUPHAR, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB)
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   Browse drugs & compounds from Enzo Life Sciences
  Browse compounds at ApexBio 

Browse Tocris compounds for H1FNT



(Secondary structures according to fRNAdb,
GenBank/EMBL/DDBJ Accessions according to
Unigene (Build 236 Homo sapiens; Apr 25 2013) or GenBank,
RefSeq according to Entrez Gene,
DOTS (version 10), and/or AceView, transcript ids from Ensembl with links to UCSC,
exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
siRNAs from OriGene, QIAGEN, shRNA from OriGene, microRNA from QIAGEN, SwitchGear Genomics,
Tagged/untagged cDNA clones from OriGene, GenScript, DNA2.0, Vector BioLabs, and/or Addgene, Primers from OriGene, and/or QIAGEN, Flow cytometry from eBioscience )
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REFSEQ mRNAs for H1FNT gene: 
NM_181788.1  

Unigene Cluster for H1FNT:

H1 histone family, member N, testis-specific
Hs.155833  [show with all ESTs]
Unigene Representative Sequence: AY302593
1 Ensembl transcript including schematic representation, and UCSC links where relevant:
ENST00000335017(uc001rrm.3)
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Additional mRNA sequence: 

AB121028.2 AY302593.1 BC118635.1 BC119787.1 

1 DOTS entry:

DT.40227313 

17 AceView cDNA sequences:

BE466599 AI624717 AY302593 AI650408 AI808336 BF431650 AI990167 NM_181788 
AI671196 BE502688 AW013835 BI825819 AI142283 AW665295 BX335317 AB121028 
AA903784 

GeneLoc Exon Structure


(RNA expression data according to H-InvDB, NONCODE, miRBase, and RNAdb, Expression images according to data from BioGPS, Illumina Human BodyMap, and CGAP SAGE, Sets of similar genes according to GeneDecks, in vivo and in vitro expression data from LifeMap Discovery™, Protein expression images according to data from SPIRE 1MOPED, 2PaxDb, and 3MaxQB, plus additional links to SOURCE, and/or BioGPS, and/or UniProtKB,
PCR Arrays from QIAGEN, Primers from OriGene, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
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H1FNT expression in normal human tissues (normalized intensities)
See probesets specificity/sensitivity at GeneAnnot
About this imageBioGPS <intensity>2/3
CGAP TAG: GCTGAGGCGC
H1FNT Expression
About this image

H1FNT Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

H1FNT Protein Expression

SOURCE GeneReport for Unigene cluster: Hs.155833

UniProtKB/Swiss-Prot: H1FNT_HUMAN, Q75WM6
Tissue specificity: Testis-specific

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In Situ
Assay Products:
 

 
Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for H1FNT

(Orthologs according to 1,2HomoloGene (2older version, for species not in 1newer version), 3euGenes, 4SGD , 5MGI Mar 06 2013, with possible further links to Flybase and/or WormBase, and/or 6Ensembl pan taxonomic compara , Gene Trees according to Ensembl and TreeFam)
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This gene was present in the common ancestor of human and mouse.

Orthologs for H1FNT gene from Selected species (see all 4)    About this table
Organism Taxonomic
classification
Gene Description Human
Similarity
Orthology
Type
Details
mouse
(Mus musculus)
Mammalia H1fnt5 H1 histone family, member N, testis-specific   --   15 (54.26 cM) 98255982 


ENSEMBL Gene Tree for H1FNT (if available)
TreeFam Gene Tree for H1FNT (if available)

(Paralogs according to 1HomoloGene,
2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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(SNPs/Variants according to the 1NCBI SNP Database, 2Ensembl, 3PupaSUITE, 4UniProtKB, and DNA2.0, Linkage Disequilibrium by HapMap, Structural Variations(CNVs/InDels/Inversions) from the Database of Genomic Variants, Mutations from the Human Gene Mutation Database (HGMD), the Human Cytochrome P450 Allele Nomenclature Database, and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers, Cancer Mutation PCR Arrays and Assays, and Copy Number PCR Arrays from QIAGEN)
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Selected SNPs for H1FNT (see all 105)    About this table                                 

Genomic DataTranscription Related DataAllele Frequencies
SNP IDValidClinical
significance
Chr 12 posSequence#AA
Chg
TypeMore#Allele
freq
PopTotal
sample
More
----------
rs774195731,2
F--48720810(+) TCTAGC/TCCTAT 1 -- us2k11Minor allele frequency- T:0.04NA 120
rs751340251,2
C,F--48720827(+) ACCTAT/CGAATT 1 -- us2k11Minor allele frequency- C:0.03NA 120
rs777127631,2
C,F--48720884(+) AAGAAG/ACACTG 1 -- us2k11Minor allele frequency- A:0.13NA 120
rs1396629591,2
--48720989(+) TGGCCA/GACATG 1 -- us2k10--------
rs1138846351,2
C,F--48721144(+) GAAACC/TCCATC 1 -- us2k12Minor allele frequency- T:0.04WA 120
rs777044761,2
C,F--48721177(+) GCTGGG/ACATGG 1 -- us2k12Minor allele frequency- A:0.08WA 120
rs1831540231,2
--48721186(+) GGTAGA/CAGGAA 1 -- us2k10--------
rs79681161,2
C--48721250(+) gaggcA/Ggaggt 1 -- us2k10--------
rs24090031,2
C,F,A,H--48721276(+) ttgcaC/Tcactg 1 -- us2k14Minor allele frequency- T:0.50NA 8
rs1120580431,2
C,F--48721282(+) CACTGC/TACTCC 1 -- us2k11Minor allele frequency- T:0.50NA 2

HapMap Linkage Disequilibrium report for H1FNT (48722763 - 48724062 bp)

Structural Variations
     Database of Genomic Variants (DGV) 7 variations for H1FNT:    About this table    
Variant IDTypeSubtypePubMed ID
nsv437752CNV Loss16327808
nsv826362CNV Gain20364138
esv34439CNV Gain17911159
nsv832402CNV Gain17160897
nsv8971CNV Gain+Loss18304495
dgv509e1CNV Complex17122850
dgv510e1CNV Complex17122850

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(in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
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(in PubMed. Associations of this gene to articles via 1Entrez Gene, 2UniProtKB/Swiss-Prot, 3HGNC, 4GAD, 5PharmGKB, 6HMDB, 7DrugBank, 8UniProtKB/TrEMBL, 9 Novoseek, and/or 10fRNAdb)
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PubMed articles for H1FNT gene integrated from 10 sources:
(articles sorted by number of sources associating them with H1FNT)
    Utopia: connect your pdf to the dynamic
world of online information

  1. Polar nuclear localization of H1T2, a histone H1 variant, required for spermatid elongation and DNA condensation during spermiogenesis. (PubMed id 15710904)1, 2, 3 Martianov I.... Davidson I. (Proc. Natl. Acad. Sci. U.S.A. 2005)
  2. Expression profiles and single-nucleotide polymorphism analysis of human HANP1/H1T2 encoding a histone H1-like protein. (PubMed id 16533358)1, 2, 9 Tanaka H.... Nishimune Y. (Int. J. Androl. 2006)
  3. The finished DNA sequence of human chromosome 12. (PubMed id 16541075)2 Scherer S.E.... Gibbs R.A. (Nature 2006)
  4. HANP1/H1T2, a novel histone H1-like protein involved in nuclear formation and sperm fertility. (PubMed id 16055721)1 Tanaka H....Nishimune Y. (Mol. Cell. Biol. 2005)
  5. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PubMed id 15489334)2 Gerhard D.S.... Malek J. (Genome Res. 2004)
  6. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. (PubMed id 12477932)1 Strausberg R.L....Marra M.A. (Proc. Natl. Acad. Sci. U.S.A. 2002)
  7. (PubMed id )2 
  8. mRNA levels of the differentiation-associated linker histone variant H1 zero in mitotically active and postmitotic senescent human diploid fibroblast cell populations. (PubMed id 11672986)9 Tsapali D.S....Sourlingas T.G. (Exp. Gerontol. 2001)

(in PubMed, OMIM, and NCBI Bookshelf)
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 ANDOR
Aliases
Free Text  

  Query String
PubMed
OMIM
NCBI Bookshelf
  (Note: In FireFox, select the above section and copy using Ctrl-C)

(According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
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Entrez Gene: 341567 HGNC: 24893 AceView: LOC341567 Ensembl:ENSG00000187166 euGenes: HUgn341567
ECgene: H1FNT H-InvDB: H1FNT

(According to HUGE)
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(According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL, and/or others, e.g. Wikipedia and GeneReviews, via UniProtKB/Swiss-Prot)
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NameDescription
PharmGKB entry for H1FNT Pharmacogenomics, SNPs, Pathways

(Patent information from GeneIP,
Licensable technologies from WIS Yeda, Salk, Tufts,
IP news from LifeMap Sciences, Inc.)
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Patent Information for H1FNT gene:
Search GeneIP for patents involving H1FNT

GeneCards and IP:
Japan Patent Office Licenses GeneCards     European Patent Office Licenses GeneCards     Improving the IP Search



(Antibodies, recombinant proteins, and assays from EMD Millipore, R&D Systems, OriGene, QIAGEN, GenScript, Cell Signaling Technology, Novus Biologicals, Sino Biological, Enzo Life Sciences, Abcam, ProSpec, Cloud-Clone Corp., Thermo Fisher Scientific, LSBio, eBioscience, and/or others, Gene Editing from DNA2.0. Clones from OriGene, GenScript, Sino Biological, DNA2.0, SwitchGear Genomics, Vector BioLabs, Addgene, Cell lines from GenScript, and ESI BIO, Flow cytometery from eBioscience, PCR Arrays from QIAGEN, Drugs and/or compounds from EMD Millipore, Tocris Bioscience, Enzo Life Sciences, and/or ApexBio, In Situ Hybridization Assays from
Advanced Cell Diagnostics, Animal models from inGenious Targeting Laboratory, genOway)
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GeneCards Homepage - Last full update: 7 May 2014 - Incrementals: 9 May 2014 , 2 Jun 2014 , 26 Jun 2014 , 30 Jun 2014 , 21 Aug 2014 , 8 Sep 2014

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