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PHTF2 putative homeodomain transcription factor 2 [ Homo sapiens (human) ]

Gene ID: 57157, updated on 2-Nov-2024

Summary

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Official Symbol
PHTF2provided by HGNC
Official Full Name
putative homeodomain transcription factor 2provided by HGNC
Primary source
HGNC:HGNC:13411
See related
Ensembl:ENSG00000006576 MIM:616785; AllianceGenome:HGNC:13411
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
Summary
Located in endoplasmic reticulum. [provided by Alliance of Genome Resources, Nov 2024]
Expression
Ubiquitous expression in lymph node (RPKM 6.3), appendix (RPKM 5.5) and 25 other tissues See more
Orthologs
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Genomic context

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See PHTF2 in Genome Data Viewer
Location:
7q11.23-q21.11
Exon count:
21
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 7 NC_000007.14 (77798773..77957504)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 7 NC_060931.1 (79050700..79209413)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 7 NC_000007.13 (77428090..77586821)

Chromosome 7 - NC_000007.14Genomic Context describing neighboring genes Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:77324871-77325766 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:77325767-77326662 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18329 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:77393580-77394080 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26208 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18330 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26209 Neighboring gene H3K27ac hESC enhancer GRCh37_chr7:77464234-77464734 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18331 Neighboring gene round spermatid basic protein 1 like Neighboring gene Alu-mediated CDKN1A/p21 transcriptional regulator Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr7:77501601-77502172 Neighboring gene uncharacterized LOC124901682 Neighboring gene transmembrane protein 60 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr7:77619182-77620381 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr7:77635196-77635696 Neighboring gene H3K27ac hESC enhancer GRCh37_chr7:77648359-77648860 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18332 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18333 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:77677051-77677551 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr7:77703601-77704220 Neighboring gene DDX3 interacting lncRNA 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:77763787-77764288 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:77764289-77764788 Neighboring gene uncharacterized LOC124901684 Neighboring gene membrane associated guanylate kinase, WW and PDZ domain containing 2

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • 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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Related articles in PubMed

  1. Molecular characterization of a novel gene family (PHTF) conserved from Drosophila to mammals. Manuel A, et al. Genomics, 2000 Mar 1. PMID 10729229
  2. GWAS of dental caries patterns in the permanent dentition. Shaffer JR, et al. J Dent Res, 2013 Jan. PMID 23064961, Free PMC Article
  3. New loci associated with kidney function and chronic kidney disease. Köttgen A, et al. Nat Genet, 2010 May. PMID 20383146, Free PMC Article
  4. Systematic subcellular localization of novel proteins identified by large-scale cDNA sequencing. Simpson JC, et al. EMBO Rep, 2000 Sep. PMID 11256614, Free PMC Article
  5. The LIFEdb database in 2006. Mehrle A, et al. Nucleic Acids Res, 2006 Jan 1. PMID 16381901, Free PMC Article

See all (22) citations in PubMed

GeneRIFs: Gene References Into Functions

Phenotypes

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Review eQTL and phenotype association data in this region using PheGenI

EBI GWAS Catalog

Description
GWAS of dental caries patterns in the permanent dentition.
EBI GWAS Catalog
New loci associated with kidney function and chronic kidney disease.
EBI GWAS Catalog
Novel genetic loci identified for the pathophysiology of childhood obesity in the Hispanic population.
EBI GWAS Catalog

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Clone Names

  • FLJ33324, MGC86999, DKFZp564F013

Gene Ontology Provided by GOA

Component Evidence Code Pubs
located_in endoplasmic reticulum IDA
Inferred from Direct Assay
more info
  
located_in membrane IEA
Inferred from Electronic Annotation
more info
  

General protein information

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Preferred Names
protein PHTF2

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)

  1. NM_001127357.2 → NP_001120829.1  protein PHTF2 isoform 1

    See identical proteins and their annotated locations for NP_001120829.1

    Status: VALIDATED

    Source sequence(s)
    AC073520, AL136883, BC022419, BC127093, CB051673
    Consensus CDS
    CCDS47621.1
    UniProtKB/Swiss-Prot
    Q8N3S3
    Conserved Domains (1) summary
    pfam12129
    Location:5 → 158
    Phtf-FEM1B_bdg; Male germ-cell putative homeodomain transcription factor

  2. NM_001127358.2 → NP_001120830.1  protein PHTF2 isoform 2

    See identical proteins and their annotated locations for NP_001120830.1

    Status: VALIDATED

    Source sequence(s)
    AC004955, AK225854, AL136883, BP321440, CB051673
    Consensus CDS
    CCDS47622.1
    UniProtKB/Swiss-Prot
    Q8N3S3
    Related
    ENSP00000307699.8, ENST00000307305.12
    Conserved Domains (1) summary
    pfam12129
    Location:5 → 152
    Phtf-FEM1B_bdg; Male germ-cell putative homeodomain transcription factor

  3. NM_001127359.2 → NP_001120831.1  protein PHTF2 isoform 3

    See identical proteins and their annotated locations for NP_001120831.1

    Status: VALIDATED

    Source sequence(s)
    AC004990, AC073520, BC022419, BE880432, BP395569
    Consensus CDS
    CCDS47623.1
    UniProtKB/Swiss-Prot
    Q8N3S3
    Related
    ENSP00000387355.1, ENST00000450574.5
    Conserved Domains (1) summary
    pfam12129
    Location:5 → 156
    Phtf-FEM1B_bdg; Male germ-cell putative homeodomain transcription factor

  4. NM_001127360.2 → NP_001120832.1  protein PHTF2 isoform 4

    Status: VALIDATED

    Source sequence(s)
    AC004955, AC004990, BC022419, BC067742, BE880432, BP321440, BP395569
    Consensus CDS
    CCDS47624.1
    UniProtKB/Swiss-Prot
    Q8N3S3
    Related
    ENSP00000408035.2, ENST00000415251.6
    Conserved Domains (1) summary
    pfam12129
    Location:5 → 152
    Phtf-FEM1B_bdg; Male germ-cell putative homeodomain transcription factor

  5. NM_001366081.1 → NP_001353010.1  protein PHTF2 isoform 5

    Status: VALIDATED

    Source sequence(s)
    AC004955, AC004990, AL136883
    Consensus CDS
    CCDS94133.1
    Related
    ENSP00000275575.7, ENST00000275575.11
    Conserved Domains (1) summary
    pfam12129
    Location:5 → 152
    Phtf-FEM1B_bdg; Male germ-cell putative homeodomain transcription factor

  6. NM_001366082.2 → NP_001353011.1  protein PHTF2 isoform 6

    Status: VALIDATED

    Source sequence(s)
    AC004955, AK090643, BQ014377
    Consensus CDS
    CCDS94134.1
    Related
    ENSP00000403620.1, ENST00000424760.5
    Conserved Domains (1) summary
    pfam12129
    Location:5 → 152
    Phtf-FEM1B_bdg; Male germ-cell putative homeodomain transcription factor

  7. NM_001366083.1 → NP_001353012.1  protein PHTF2 isoform 7

    Status: VALIDATED

    Source sequence(s)
    AC004955, AC004990, AC073520
    Conserved Domains (1) summary
    pfam12129
    Location:5 → 152
    Phtf-FEM1B_bdg; Male germ-cell putative homeodomain transcription factor

  8. NM_001366084.1 → NP_001353013.1  protein PHTF2 isoform 8

    Status: VALIDATED

    Source sequence(s)
    AC004955, AC004990, AC073520
    Conserved Domains (1) summary
    pfam12129
    Location:5 → 152
    Phtf-FEM1B_bdg; Male germ-cell putative homeodomain transcription factor

  9. NM_001366085.2 → NP_001353014.1  protein PHTF2 isoform 9

    Status: VALIDATED

    Source sequence(s)
    AC004955, AC004990, AC073520
    Conserved Domains (1) summary
    pfam12129
    Location:5 → 152
    Phtf-FEM1B_bdg; Male germ-cell putative homeodomain transcription factor

  10. NM_001366086.1 → NP_001353015.1  protein PHTF2 isoform 2

    Status: VALIDATED

    Source sequence(s)
    AC004955, AC004990, AC073520
    Consensus CDS
    CCDS47622.1
    Conserved Domains (1) summary
    pfam12129
    Location:5 → 152
    Phtf-FEM1B_bdg; Male germ-cell putative homeodomain transcription factor

  11. NM_001366087.1 → NP_001353016.1  protein PHTF2 isoform 8

    Status: VALIDATED

    Source sequence(s)
    AC004955, AC004990, AC073520
    Conserved Domains (1) summary
    pfam12129
    Location:5 → 152
    Phtf-FEM1B_bdg; Male germ-cell putative homeodomain transcription factor

  12. NM_001366088.2 → NP_001353017.1  protein PHTF2 isoform 6

    Status: VALIDATED

    Source sequence(s)
    AC004955, AC004990, AC073520
    Consensus CDS
    CCDS94134.1
    Conserved Domains (1) summary
    pfam12129
    Location:5 → 152
    Phtf-FEM1B_bdg; Male germ-cell putative homeodomain transcription factor

  13. NM_001366089.1 → NP_001353018.1  protein PHTF2 isoform 10

    Status: VALIDATED

    Source sequence(s)
    AC004990, AC073520
    Consensus CDS
    CCDS94132.1
    UniProtKB/Swiss-Prot
    A0JP04, A0JP05, A4D1C2, B3KQZ2, E9PEE3, G5E9H7, Q6NW35, Q8N3S3, Q8TBW4, Q9H099
    Related
    ENSP00000248550.7, ENST00000248550.7
    Conserved Domains (1) summary
    pfam12129
    Location:5 → 190
    Phtf-FEM1B_bdg; Male germ-cell putative homeodomain transcription factor

  14. NM_001395270.1 → NP_001382199.1  protein PHTF2 isoform 11

    Status: VALIDATED

    Source sequence(s)
    AC004955, AC004990, AC073520
    Conserved Domains (1) summary
    pfam12129
    Location:5 → 154
    Phtf-FEM1B_bdg; Male germ-cell putative homeodomain transcription factor

  15. NM_001395271.1 → NP_001382200.1  protein PHTF2 isoform 12

    Status: VALIDATED

    Source sequence(s)
    AC004955, AC004990, AC073520
    Conserved Domains (1) summary
    pfam12129
    Location:5 → 158
    Phtf-FEM1B_bdg; Male germ-cell putative homeodomain transcription factor

  16. NM_001395272.1 → NP_001382201.1  protein PHTF2 isoform 1

    Status: VALIDATED

    Source sequence(s)
    AC004955, AC004990, AC073520
    Consensus CDS
    CCDS47621.1
    Related
    ENSP00000403042.2, ENST00000422959.8
    Conserved Domains (1) summary
    pfam12129
    Location:5 → 158
    Phtf-FEM1B_bdg; Male germ-cell putative homeodomain transcription factor

  17. NM_020432.5 → NP_065165.3  protein PHTF2 isoform 2

    See identical proteins and their annotated locations for NP_065165.3

    Status: VALIDATED

    Source sequence(s)
    AC073520, AL136883, BC022419, BC127094, CB051673
    Consensus CDS
    CCDS47622.1
    UniProtKB/Swiss-Prot
    Q8N3S3
    Conserved Domains (1) summary
    pfam12129
    Location:5 → 152
    Phtf-FEM1B_bdg; Male germ-cell putative homeodomain transcription factor

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

  1. NC_000007.14 Reference GRCh38.p14 Primary Assembly

    Range
    77798773..77957504
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011516422.4 → XP_011514724.1  protein PHTF2 isoform X2

    Conserved Domains (1) summary
    pfam12129
    Location:5 → 156
    Phtf-FEM1B_bdg; Male germ-cell putative homeodomain transcription factor

  2. XM_011516423.4 → XP_011514725.1  protein PHTF2 isoform X4

    Conserved Domains (1) summary
    pfam12129
    Location:5 → 156
    Phtf-FEM1B_bdg; Male germ-cell putative homeodomain transcription factor

  3. XM_047420638.1 → XP_047276594.1  protein PHTF2 isoform X3

  4. XM_047420640.1 → XP_047276596.1  protein PHTF2 isoform X5

  5. XM_005250509.5 → XP_005250566.1  protein PHTF2 isoform X1

    See identical proteins and their annotated locations for XP_005250566.1

    UniProtKB/Swiss-Prot
    Q8N3S3
    Conserved Domains (1) summary
    pfam12129
    Location:5 → 158
    Phtf-FEM1B_bdg; Male germ-cell putative homeodomain transcription factor

  6. XM_047420639.1 → XP_047276595.1  protein PHTF2 isoform X3

  7. XM_011516424.3 → XP_011514726.1  protein PHTF2 isoform X6

    Conserved Domains (1) summary
    pfam12129
    Location:1 → 15
    Phtf-FEM1B_bdg; Male germ-cell putative homeodomain transcription factor

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060931.1 Alternate T2T-CHM13v2.0

    Range
    79050700..79209413
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054358687.1 → XP_054214662.1  protein PHTF2 isoform X2

  2. XM_054358690.1 → XP_054214665.1  protein PHTF2 isoform X4

  3. XM_054358688.1 → XP_054214663.1  protein PHTF2 isoform X3

  4. XM_054358691.1 → XP_054214666.1  protein PHTF2 isoform X5

  5. XM_054358686.1 → XP_054214661.1  protein PHTF2 isoform X1

  6. XM_054358689.1 → XP_054214664.1  protein PHTF2 isoform X3

  7. XM_054358692.1 → XP_054214667.1  protein PHTF2 isoform X6

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q8N3S3.2 GenPept UniProtKB/Swiss-Prot:Q8N3S3

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