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

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

Summary

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
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Genomic context

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

Expression

  • 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

Variation

Alleles

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

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

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
 

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_001163467.1NP_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:5149
    Phtf-FEM1B_bdg; Male germ-cell putative homeodomain transcription factor
  2. NM_001163468.1NP_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:596
    Phtf-FEM1B_bdg; Male germ-cell putative homeodomain transcription factor
  3. NM_001163469.1NP_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:5149
    Phtf-FEM1B_bdg; Male germ-cell putative homeodomain transcription factor
  4. NM_013629.2NP_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:5149
    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_006501126.4XP_006501189.1  protein PHTF1 isoform X2

    See identical proteins and their annotated locations for XP_006501189.1

    Conserved Domains (1) summary
    pfam12129
    Location:5151
    Phtf-FEM1B_bdg; Male germ-cell putative homeodomain transcription factor
  2. XM_030252459.2XP_030108319.1  protein PHTF1 isoform X12

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

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

    Conserved Domains (1) summary
    pfam12129
    Location:232
    Phtf-FEM1B_bdg; Male germ-cell putative homeodomain transcription factor
  5. XM_036162929.1XP_036018822.1  protein PHTF1 isoform X1

    Conserved Domains (1) summary
    pfam12129
    Location:5132
    Phtf-FEM1B_bdg; Male germ-cell putative homeodomain transcription factor
  6. XM_036162931.1XP_036018824.1  protein PHTF1 isoform X4

    Conserved Domains (1) summary
    pfam12129
    Location:579
    Phtf-FEM1B_bdg; Male germ-cell putative homeodomain transcription factor
  7. XM_036162934.1XP_036018827.1  protein PHTF1 isoform X10

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

    Conserved Domains (1) summary
    pfam12129
    Location:232
    Phtf-FEM1B_bdg; Male germ-cell putative homeodomain transcription factor
  9. XM_030252457.1XP_030108317.1  protein PHTF1 isoform X6

    Conserved Domains (1) summary
    pfam12129
    Location:232
    Phtf-FEM1B_bdg; Male germ-cell putative homeodomain transcription factor
  10. XM_017319484.2XP_017174973.1  protein PHTF1 isoform X9

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

    Conserved Domains (1) summary
    pfam12129
    Location:598
    Phtf-FEM1B_bdg; Male germ-cell putative homeodomain transcription factor
  12. XM_036162930.1XP_036018823.1  protein PHTF1 isoform X3

    Conserved Domains (1) summary
    pfam12129
    Location:5132
    Phtf-FEM1B_bdg; Male germ-cell putative homeodomain transcription factor
  13. XM_017319483.1XP_017174972.1  protein PHTF1 isoform X12

RNA

  1. XR_004941294.1 RNA Sequence