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    Phtf1 putative homeodomain transcription factor 1 [ Mus musculus (house mouse) ]

    Gene ID: 18685, updated on 30-Apr-2024

    Summary

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    Official Symbol
    Phtf1provided by MGI
    Official Full Name
    putative homeodomain transcription factor 1provided by MGI
    Primary source
    MGI:MGI:1332671
    See related
    Ensembl:ENSMUSG00000058388 AllianceGenome:MGI:1332671
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Mus musculus
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
    Also known as
    Phft; Phtf
    Summary
    Predicted to be located in cis-Golgi network and endoplasmic reticulum. Is expressed in several structures, including 1st branchial arch; alimentary system; genitourinary system; nervous system; and sensory organ. Orthologous to human PHTF1 (putative homeodomain transcription factor 1). [provided by Alliance of Genome Resources, Apr 2022]
    Expression
    Ubiquitous expression in CNS E11.5 (RPKM 9.3), testis adult (RPKM 8.9) and 28 other tissues See more
    Orthologs
    human all
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    Genomic context

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    See Phtf1 in Genome Data Viewer
    Location:
    3 F2.2; 3 45.52 cM
    Exon count:
    20
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCm39 (GCF_000001635.27) 3 NC_000069.7 (103875426..103914806)
    108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 3 NC_000069.6 (103968110..104007490)

    Chromosome 3 - NC_000069.7Genomic Context describing neighboring genes Neighboring gene STARR-positive B cell enhancer ABC_E3458 Neighboring gene CapStarr-seq enhancer MGSCv37_chr3:103663204-103663387 Neighboring gene CapStarr-seq enhancer MGSCv37_chr3:103664081-103664275 Neighboring gene STARR-positive B cell enhancer ABC_E6094 Neighboring gene STARR-positive B cell enhancer ABC_E2090 Neighboring gene protein tyrosine phosphatase, non-receptor type 22 (lymphoid) Neighboring gene STARR-seq mESC enhancer starr_08604 Neighboring gene STARR-positive B cell enhancer ABC_E9222 Neighboring gene STARR-positive B cell enhancer mm9_chr3:103718150-103718451 Neighboring gene rosbin, round spermatid basic protein 1 Neighboring gene putative homeodomain transcription factor 1, opposite strand Neighboring gene STARR-seq mESC enhancer starr_08605 Neighboring gene membrane associated guanylate kinase, WW and PDZ domain containing 3 Neighboring gene STARR-seq mESC enhancer starr_08606 Neighboring gene predicted gene, 17956 Neighboring gene STARR-positive B cell enhancer ABC_E9565 Neighboring gene predicted gene, 23077

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: Mouse ENCODE transcriptome data
    • Description: RNA profiling data sets generated by the Mouse ENCODE project.
    • BioProject: PRJNA66167
    • Publication: PMID 25409824
    • Analysis date: n/a

    Bibliography

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    Related articles in PubMed

    1. Putative homeodomain transcription factor 1 interacts with the feminization factor homolog fem1b in male germ cells. Oyhenart J, et al. Biol Reprod, 2005 Apr. PMID 15601915
    2. PHTF, a novel atypical homeobox gene on chromosome 1p13, is evolutionarily conserved. Raich N, et al. Genomics, 1999 Jul 1. PMID 10395808
    3. Molecular characterization of a novel gene family (PHTF) conserved from Drosophila to mammals. Manuel A, et al. Genomics, 2000 Mar 1. PMID 10729229
    4. Single-cell RNA-Seq reveals a highly coordinated transcriptional program in mouse germ cells during primordial follicle formation. He Y, et al. Aging Cell, 2021 Jul. PMID 34174788, Free PMC Article
    5. Voltage-dependent conformational changes of Kv1.3 channels activate cell proliferation. Cidad P, et al. J Cell Physiol, 2021 Jun. PMID 33230847

    See all (30) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. neither FEM1B nor PHTF1 are directly implicated in apoptosis in testis tissue
      Title: Putative homeodomain transcription factor 1 interacts with the feminization factor homolog fem1b in male germ cells.
    Submit: New GeneRIF Correction

    Variation

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    Alleles

    Alleles of this type are documented at Mouse Genome Informatics  (MGI)
    • Targeted (1) 

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Gene Ontology Provided by MGI

    Function Evidence Code Pubs
    enables molecular_function ND
    No biological Data available
    more info
    		  
    Process Evidence Code Pubs
    involved_in biological_process ND
    No biological Data available
    more info
    		  
    Component Evidence Code Pubs
    located_in Golgi apparatus IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in cis-Golgi network membrane ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in endoplasmic reticulum IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in endoplasmic reticulum membrane ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in membrane IEA
    Inferred from Electronic Annotation
    more info
    		  

    General protein information

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    Preferred Names
    protein PHTF1

    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_001163467.1 → NP_001156939.1  protein PHTF1 isoform a

      See identical proteins and their annotated locations for NP_001156939.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) differs in the 5' UTR compared to variant 1. Variants 1 and 2 both encode the same isoform (a).
      Source sequence(s)
      AC162922, AK019146, BE948000, BU053202, CO041244
      Consensus CDS
      CCDS17698.1
      UniProtKB/Swiss-Prot
      Q9CS51, Q9CSB9, Q9QZ09, Q9QZ14
      UniProtKB/TrEMBL
      Q5IBN5
      Related
      ENSMUSP00000113973.2, ENSMUST00000117150.8
      Conserved Domains (1) summary
      pfam12129
      Location:5 → 149
      Phtf-FEM1B_bdg; Male germ-cell putative homeodomain transcription factor

    2. NM_001163468.1 → NP_001156940.1  protein PHTF1 isoform b

      See identical proteins and their annotated locations for NP_001156940.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (3) lacks an alternate in-frame coding exon compared to variant 1. The resulting isoform (b) has the same N- and C-termini but is shorter compared to isoform a.
      Source sequence(s)
      AC162922, AK019146, BE948000, BU053202, CO041244
      Consensus CDS
      CCDS51030.1
      UniProtKB/TrEMBL
      Q8C2F6
      Related
      ENSMUSP00000058137.9, ENSMUST00000055425.15
      Conserved Domains (1) summary
      pfam12129
      Location:5 → 96
      Phtf-FEM1B_bdg; Male germ-cell putative homeodomain transcription factor

    3. NM_001163469.1 → NP_001156941.1  protein PHTF1 isoform c

      See identical proteins and their annotated locations for NP_001156941.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (4) lacks an alternate in-frame coding exon compared to variant 1. The resulting isoform (c) has the same N- and C-termini but is shorter compared to isoform a.
      Source sequence(s)
      AC162922, AK019146, BE948000, BU053202, CO041244
      Consensus CDS
      CCDS51029.1
      UniProtKB/TrEMBL
      Q80YS3
      Related
      ENSMUSP00000088184.5, ENSMUST00000090685.11
      Conserved Domains (1) summary
      pfam12129
      Location:5 → 149
      Phtf-FEM1B_bdg; Male germ-cell putative homeodomain transcription factor

    4. NM_013629.2 → NP_038657.2  protein PHTF1 isoform a

      See identical proteins and their annotated locations for NP_038657.2

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (a). Variants 1 and 2 both encode the same isoform.
      Source sequence(s)
      AC162922, AK019146, BE948000, BU053202, CO041244
      Consensus CDS
      CCDS17698.1
      UniProtKB/Swiss-Prot
      Q9CS51, Q9CSB9, Q9QZ09, Q9QZ14
      UniProtKB/TrEMBL
      Q5IBN5
      Related
      ENSMUSP00000066607.8, ENSMUST00000063717.14
      Conserved Domains (1) summary
      pfam12129
      Location:5 → 149
      Phtf-FEM1B_bdg; Male germ-cell putative homeodomain transcription factor

    RefSeqs of Annotated Genomes: GCF_000001635.27-RS_2024_02

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

    Reference GRCm39 C57BL/6J

    Genomic

    1. NC_000069.7 Reference GRCm39 C57BL/6J

      Range
      103875426..103914806
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_006501126.4 → XP_006501189.1  protein PHTF1 isoform X2

      See identical proteins and their annotated locations for XP_006501189.1

      Conserved Domains (1) summary
      pfam12129
      Location:5 → 151
      Phtf-FEM1B_bdg; Male germ-cell putative homeodomain transcription factor

    2. XM_030252459.2 → XP_030108319.1  protein PHTF1 isoform X12

    3. XM_036162935.1 → XP_036018828.1  protein PHTF1 isoform X11

    4. XM_036162933.1 → XP_036018826.1  protein PHTF1 isoform X7

      Conserved Domains (1) summary
      pfam12129
      Location:2 → 32
      Phtf-FEM1B_bdg; Male germ-cell putative homeodomain transcription factor

    5. XM_036162929.1 → XP_036018822.1  protein PHTF1 isoform X1

      Conserved Domains (1) summary
      pfam12129
      Location:5 → 132
      Phtf-FEM1B_bdg; Male germ-cell putative homeodomain transcription factor

    6. XM_036162931.1 → XP_036018824.1  protein PHTF1 isoform X4

      Conserved Domains (1) summary
      pfam12129
      Location:5 → 79
      Phtf-FEM1B_bdg; Male germ-cell putative homeodomain transcription factor

    7. XM_036162934.1 → XP_036018827.1  protein PHTF1 isoform X10

    8. XM_030252458.1 → XP_030108318.1  protein PHTF1 isoform X8

      Conserved Domains (1) summary
      pfam12129
      Location:2 → 32
      Phtf-FEM1B_bdg; Male germ-cell putative homeodomain transcription factor

    9. XM_030252457.1 → XP_030108317.1  protein PHTF1 isoform X6

      Conserved Domains (1) summary
      pfam12129
      Location:2 → 32
      Phtf-FEM1B_bdg; Male germ-cell putative homeodomain transcription factor

    10. XM_017319484.2 → XP_017174973.1  protein PHTF1 isoform X9

    11. XM_036162932.1 → XP_036018825.1  protein PHTF1 isoform X5

      Conserved Domains (1) summary
      pfam12129
      Location:5 → 98
      Phtf-FEM1B_bdg; Male germ-cell putative homeodomain transcription factor

    12. XM_036162930.1 → XP_036018823.1  protein PHTF1 isoform X3

      Conserved Domains (1) summary
      pfam12129
      Location:5 → 132
      Phtf-FEM1B_bdg; Male germ-cell putative homeodomain transcription factor

    13. XM_017319483.1 → XP_017174972.1  protein PHTF1 isoform X12

    RNA

    1. XR_004941294.1 RNA Sequence

    Nucleotide Protein Strain
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9QZ09.2 GenPept UniProtKB/Swiss-Prot:Q9QZ09

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