LOCUS       NM_013629               3342 bp    mRNA    linear   ROD 09-FEB-2025
DEFINITION  Mus musculus putative homeodomain transcription factor 1 (Phtf1),
            transcript variant 1, mRNA.
ACCESSION   NM_013629
VERSION     NM_013629.2
KEYWORDS    RefSeq; RefSeq Select.
SOURCE      Mus musculus (house mouse)
  ORGANISM  Mus musculus
            Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
            Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha;
            Muroidea; Muridae; Murinae; Mus; Mus.
REFERENCE   1  (bases 1 to 3342)
  AUTHORS   Adams,D.J., Barlas,B., McIntyre,R.E., Salguero,I., van der
            Weyden,L., Barros,A., Vicente,J.R., Karimpour,N., Haider,A.,
            Ranzani,M., Turner,G., Thompson,N.A., Harle,V., Olvera-Leon,R.,
            Robles-Espinoza,C.D., Speak,A.O., Geisler,N., Weninger,W.J.,
            Geyer,S.H., Hewinson,J., Karp,N.A., Fu,B., Yang,F., Kozik,Z.,
            Choudhary,J., Yu,L., van Ruiten,M.S., Rowland,B.D., Lelliott,C.J.,
            Del Castillo Velasco-Herrera,M., Verstraten,R., Bruckner,L.,
            Henssen,A.G., Rooimans,M.A., de Lange,J., Mohun,T.J., Arends,M.J.,
            Kentistou,K.A., Coelho,P.A., Zhao,Y., Zecchini,H., Perry,J.R.B.,
            Jackson,S.P. and Balmus,G.
  CONSRTM   Sanger Mouse Genetics Project
  TITLE     Genetic determinants of micronucleus formation in vivo
  JOURNAL   Nature 627 (8002), 130-136 (2024)
   PUBMED   38355793
REFERENCE   2  (bases 1 to 3342)
  AUTHORS   He,Y., Chen,Q., Dai,J., Cui,Y., Zhang,C., Wen,X., Li,J., Xiao,Y.,
            Peng,X., Liu,M., Shen,B., Sha,J., Hu,Z., Li,J. and Shu,W.
  TITLE     Single-cell RNA-Seq reveals a highly coordinated transcriptional
            program in mouse germ cells during primordial follicle formation
  JOURNAL   Aging Cell 20 (7), e13424 (2021)
   PUBMED   34174788
REFERENCE   3  (bases 1 to 3342)
  AUTHORS   Dickinson,M.E., Flenniken,A.M., Ji,X., Teboul,L., Wong,M.D.,
            White,J.K., Meehan,T.F., Weninger,W.J., Westerberg,H., Adissu,H.,
            Baker,C.N., Bower,L., Brown,J.M., Caddle,L.B., Chiani,F., Clary,D.,
            Cleak,J., Daly,M.J., Denegre,J.M., Doe,B., Dolan,M.E., Edie,S.M.,
            Fuchs,H., Gailus-Durner,V., Galli,A., Gambadoro,A., Gallegos,J.,
            Guo,S., Horner,N.R., Hsu,C.W., Johnson,S.J., Kalaga,S., Keith,L.C.,
            Lanoue,L., Lawson,T.N., Lek,M., Mark,M., Marschall,S., Mason,J.,
            McElwee,M.L., Newbigging,S., Nutter,L.M., Peterson,K.A.,
            Ramirez-Solis,R., Rowland,D.J., Ryder,E., Samocha,K.E.,
            Seavitt,J.R., Selloum,M., Szoke-Kovacs,Z., Tamura,M., Trainor,A.G.,
            Tudose,I., Wakana,S., Warren,J., Wendling,O., West,D.B., Wong,L.,
            Yoshiki,A., MacArthur,D.G., Tocchini-Valentini,G.P., Gao,X.,
            Flicek,P., Bradley,A., Skarnes,W.C., Justice,M.J., Parkinson,H.E.,
            Moore,M., Wells,S., Braun,R.E., Svenson,K.L., de Angelis,M.H.,
            Herault,Y., Mohun,T., Mallon,A.M., Henkelman,R.M., Brown,S.D.,
            Adams,D.J., Lloyd,K.C., McKerlie,C., Beaudet,A.L., Bucan,M. and
            Murray,S.A.
  CONSRTM   International Mouse Phenotyping Consortium; Jackson Laboratory;
            Infrastructure Nationale PHENOMIN, Institut Clinique de la Souris
            (ICS); Charles River Laboratories; MRC Harwell; Toronto Centre for
            Phenogenomics; Wellcome Trust Sanger Institute; RIKEN BioResource
            Center
  TITLE     High-throughput discovery of novel developmental phenotypes
  JOURNAL   Nature 537 (7621), 508-514 (2016)
   PUBMED   27626380
  REMARK    Erratum:[Nature. 2017 Nov 16;551(7680):398. doi:
            10.1038/nature24643.. PMID: 29144450]
REFERENCE   4  (bases 1 to 3342)
  AUTHORS   Thompson,C.L., Ng,L., Menon,V., Martinez,S., Lee,C.K.,
            Glattfelder,K., Sunkin,S.M., Henry,A., Lau,C., Dang,C.,
            Garcia-Lopez,R., Martinez-Ferre,A., Pombero,A., Rubenstein,J.L.R.,
            Wakeman,W.B., Hohmann,J., Dee,N., Sodt,A.J., Young,R., Smith,K.,
            Nguyen,T.N., Kidney,J., Kuan,L., Jeromin,A., Kaykas,A., Miller,J.,
            Page,D., Orta,G., Bernard,A., Riley,Z., Smith,S., Wohnoutka,P.,
            Hawrylycz,M.J., Puelles,L. and Jones,A.R.
  TITLE     A high-resolution spatiotemporal atlas of gene expression of the
            developing mouse brain
  JOURNAL   Neuron 83 (2), 309-323 (2014)
   PUBMED   24952961
REFERENCE   5  (bases 1 to 3342)
  AUTHORS   Koscielny,G., Yaikhom,G., Iyer,V., Meehan,T.F., Morgan,H.,
            Atienza-Herrero,J., Blake,A., Chen,C.K., Easty,R., Di Fenza,A.,
            Fiegel,T., Grifiths,M., Horne,A., Karp,N.A., Kurbatova,N.,
            Mason,J.C., Matthews,P., Oakley,D.J., Qazi,A., Regnart,J.,
            Retha,A., Santos,L.A., Sneddon,D.J., Warren,J., Westerberg,H.,
            Wilson,R.J., Melvin,D.G., Smedley,D., Brown,S.D., Flicek,P.,
            Skarnes,W.C., Mallon,A.M. and Parkinson,H.
  TITLE     The International Mouse Phenotyping Consortium Web Portal, a
            unified point of access for knockout mice and related phenotyping
            data
  JOURNAL   Nucleic Acids Res 42 (Database issue), D802-D809 (2014)
   PUBMED   24194600
REFERENCE   6  (bases 1 to 3342)
  AUTHORS   Yokoyama,S., Ito,Y., Ueno-Kudoh,H., Shimizu,H., Uchibe,K.,
            Albini,S., Mitsuoka,K., Miyaki,S., Kiso,M., Nagai,A., Hikata,T.,
            Osada,T., Fukuda,N., Yamashita,S., Harada,D., Mezzano,V., Kasai,M.,
            Puri,P.L., Hayashizaki,Y., Okado,H., Hashimoto,M. and Asahara,H.
  TITLE     A systems approach reveals that the myogenesis genome network is
            regulated by the transcriptional repressor RP58
  JOURNAL   Dev Cell 17 (6), 836-848 (2009)
   PUBMED   20059953
REFERENCE   7  (bases 1 to 3342)
  AUTHORS   Oyhenart,J., Benichou,S. and Raich,N.
  TITLE     Putative homeodomain transcription factor 1 interacts with the
            feminization factor homolog fem1b in male germ cells
  JOURNAL   Biol Reprod 72 (4), 780-787 (2005)
   PUBMED   15601915
  REMARK    GeneRIF: neither FEM1B nor PHTF1 are directly implicated in
            apoptosis in testis tissue
REFERENCE   8  (bases 1 to 3342)
  AUTHORS   Blackshaw,S., Harpavat,S., Trimarchi,J., Cai,L., Huang,H.,
            Kuo,W.P., Weber,G., Lee,K., Fraioli,R.E., Cho,S.H., Yung,R.,
            Asch,E., Ohno-Machado,L., Wong,W.H. and Cepko,C.L.
  TITLE     Genomic analysis of mouse retinal development
  JOURNAL   PLoS Biol 2 (9), E247 (2004)
   PUBMED   15226823
REFERENCE   9  (bases 1 to 3342)
  AUTHORS   Manuel,A., Beaupain,D., Romeo,P.H. and Raich,N.
  TITLE     Molecular characterization of a novel gene family (PHTF) conserved
            from Drosophila to mammals
  JOURNAL   Genomics 64 (2), 216-220 (2000)
   PUBMED   10729229
REFERENCE   10 (bases 1 to 3342)
  AUTHORS   Raich,N., Mattei,M.G., Romeo,P.H. and Beaupain,D.
  TITLE     PHTF, a novel atypical homeobox gene on chromosome 1p13, is
            evolutionarily conserved
  JOURNAL   Genomics 59 (1), 108-109 (1999)
   PUBMED   10395808
COMMENT     VALIDATED REFSEQ: This record has undergone validation or
            preliminary review. The reference sequence was derived from
            AC162922.4, AK019146.1, BU053202.1, CO041244.1 and BE948000.1.
            
            On Jul 21, 2009 this sequence version replaced NM_013629.1.
            
            Transcript Variant: This variant (1) represents the longest
            transcript and encodes the longest isoform (a). Variants 1 and 2
            both encode the same isoform.
            
            Sequence Note: This RefSeq record was created from transcript and
            genomic sequence data to make the sequence consistent with the
            reference genome assembly. The genomic coordinates used for the
            transcript record were based on transcript alignments.
            
            Publication Note:  This RefSeq record includes a subset of the
            publications that are available for this gene. Please see the Gene
            record to access additional publications.
            
            ##Evidence-Data-START##
            Transcript exon combination :: AJ242864.1, BC021147.1 [ECO:0000332]
            RNAseq introns              :: single sample supports all introns
                                           SAMN00849381, SAMN00849382
                                           [ECO:0000348]
            ##Evidence-Data-END##
            
            ##RefSeq-Attributes-START##
            RefSeq Select criteria :: based on conservation, expression,
                                      longest protein
            ##RefSeq-Attributes-END##
            COMPLETENESS: complete on the 3' end.
PRIMARY     REFSEQ_SPAN         PRIMARY_IDENTIFIER PRIMARY_SPAN        COMP
            1-257               AC162922.4         158581-158837
            258-2049            AK019146.1         162-1953
            2050-2688           BU053202.1         50-688
            2689-3326           CO041244.1         16-653              c
            3327-3342           BE948000.1         1-16                c
FEATURES             Location/Qualifiers
     source          1..3342
                     /organism="Mus musculus"
                     /mol_type="mRNA"
                     /strain="C57BL/6"
                     /db_xref="taxon:10090"
                     /chromosome="3"
                     /map="3 45.52 cM"
     gene            1..3342
                     /gene="Phtf1"
                     /gene_synonym="Phft; Phtf"
                     /note="putative homeodomain transcription factor 1"
                     /db_xref="GeneID:18685"
                     /db_xref="MGI:MGI:1332671"
     exon            1..530
                     /gene="Phtf1"
                     /gene_synonym="Phft; Phtf"
                     /inference="alignment:Splign:2.1.0"
     exon            531..606
                     /gene="Phtf1"
                     /gene_synonym="Phft; Phtf"
                     /inference="alignment:Splign:2.1.0"
     CDS             562..2847
                     /gene="Phtf1"
                     /gene_synonym="Phft; Phtf"
                     /note="isoform a is encoded by transcript variant 1;
                     protein PHTF1"
                     /codon_start=1
                     /product="protein PHTF1 isoform a"
                     /protein_id="NP_038657.2"
                     /db_xref="CCDS:CCDS17698.1"
                     /db_xref="GeneID:18685"
                     /db_xref="MGI:MGI:1332671"
                     /translation="MASNERDAISWYQKKIGAYDQQIWEKSIEQTQIKGFKNKPKKMG
                     HIKPDLIDVDLIRGSTFAKAKPEIPWTSLTRKGLVRVVFFPLFSSWWIQVTSLRIFVW
                     LLLLYLMQVTAVVLYLLMPIVSASEVLGPLCLMLLMGTVHCQIVSTQITRPSGNNGNR
                     RRRKLRKTVNGDGSRDNGNNSPDKVRAVETLESASSVGGFWGTLFGNRIKRVKLVSNK
                     GTETDNDSGCFHPILKKRQGRPEIRMWQAREKAKVSDGEKCRREAYRRLGNGISDDLS
                     SEEDGEARTQMILLRRSVEGASSDNGYEVKNRRSILSRHLNSQVKKTTRWCHIVRDSD
                     SLAESEFESAVFSQGSRSGMSGGSRSLNLSRRDSESTRHDSETEDMLWDDLLHGPECR
                     SSVTSDSEGAHVNTIHSGTKRDPKEDVFQQNHLFWLQNSSPASERVSAIIWEGNECKK
                     MDMSVLEISGIIMSRVNAYEQGVGYQMLGNAVTVGLALFPFLYRLFREKSFDQLKSIS
                     AEEVLTLFCGAPPVTPVVILSIINFIERLCLTWMFFFMMCVAERTYKQRFLFAKLFSH
                     ITSARKARKYEIPHFRLKKVENIKIWLSLRSYLKRRGPQRSVDVVVSSVFLLTLSIAF
                     ICCAQVLQGHKTFLNDAYNWEFLIWETALLLFLLRLASLGSETNKKYSNVSILLTEQI
                     NLYLKMEKKPNKKEQLTLVNNVLKLSTKLLKELDTPFRLYGLTMNPLIYNITRVVILS
                     AVSGVISDLLGFNIRLWKIKS"
     exon            607..663
                     /gene="Phtf1"
                     /gene_synonym="Phft; Phtf"
                     /inference="alignment:Splign:2.1.0"
     exon            664..733
                     /gene="Phtf1"
                     /gene_synonym="Phft; Phtf"
                     /inference="alignment:Splign:2.1.0"
     exon            734..892
                     /gene="Phtf1"
                     /gene_synonym="Phft; Phtf"
                     /inference="alignment:Splign:2.1.0"
     exon            893..1049
                     /gene="Phtf1"
                     /gene_synonym="Phft; Phtf"
                     /inference="alignment:Splign:2.1.0"
     exon            1050..1184
                     /gene="Phtf1"
                     /gene_synonym="Phft; Phtf"
                     /inference="alignment:Splign:2.1.0"
     exon            1185..1344
                     /gene="Phtf1"
                     /gene_synonym="Phft; Phtf"
                     /inference="alignment:Splign:2.1.0"
     exon            1345..1518
                     /gene="Phtf1"
                     /gene_synonym="Phft; Phtf"
                     /inference="alignment:Splign:2.1.0"
     exon            1519..1605
                     /gene="Phtf1"
                     /gene_synonym="Phft; Phtf"
                     /inference="alignment:Splign:2.1.0"
     exon            1606..1827
                     /gene="Phtf1"
                     /gene_synonym="Phft; Phtf"
                     /inference="alignment:Splign:2.1.0"
     exon            1828..1956
                     /gene="Phtf1"
                     /gene_synonym="Phft; Phtf"
                     /inference="alignment:Splign:2.1.0"
     exon            1957..2229
                     /gene="Phtf1"
                     /gene_synonym="Phft; Phtf"
                     /inference="alignment:Splign:2.1.0"
     exon            2230..2361
                     /gene="Phtf1"
                     /gene_synonym="Phft; Phtf"
                     /inference="alignment:Splign:2.1.0"
     exon            2362..2448
                     /gene="Phtf1"
                     /gene_synonym="Phft; Phtf"
                     /inference="alignment:Splign:2.1.0"
     exon            2449..2604
                     /gene="Phtf1"
                     /gene_synonym="Phft; Phtf"
                     /inference="alignment:Splign:2.1.0"
     exon            2605..2700
                     /gene="Phtf1"
                     /gene_synonym="Phft; Phtf"
                     /inference="alignment:Splign:2.1.0"
     exon            2701..2826
                     /gene="Phtf1"
                     /gene_synonym="Phft; Phtf"
                     /inference="alignment:Splign:2.1.0"
     exon            2827..3329
                     /gene="Phtf1"
                     /gene_synonym="Phft; Phtf"
                     /inference="alignment:Splign:2.1.0"
     regulatory      3307..3312
                     /regulatory_class="polyA_signal_sequence"
                     /gene="Phtf1"
                     /gene_synonym="Phft; Phtf"
                     /note="hexamer: AATAAA"
     polyA_site      3329
                     /gene="Phtf1"
                     /gene_synonym="Phft; Phtf"
                     /note="major polyA site"
ORIGIN      
        1 gttacacgcg aggcggctgt cggcttcttc ctccgggcag ccagagcggc gggaaggcgg
       61 ccgggggcgg agccggaagg cggaagcggc cgatcgcatc gagagcttgt ggagctgcgg
      121 cccgtccctc acggaggacg cgcgccgttg ctccggcccg gggccgtctg ctggcttcca
      181 gccgggcacc cagcccttgc gggtgccgag gtggctggcg aaggcaccct tcccgcttcc
      241 ttctgctcat tccccagttg gctcctggct tctcccatgg cctgttctgt ggccgcctag
      301 gtcgggcgtc tgtggctgca ggctgcgctc ctcccggcgc aggacgctgg gctgcctccg
      361 gggcagggct ggccgccgcg gtctccatgg taacggccag gcggacggcc gggcctctgg
      421 gggaagatgc ggcctgccgg gcccgccgcc tcgcccccgg cctctcggtc cggcgggggt
      481 cactgagcag cgggggcccg gccggcagcc tgcctggcag cgggcaccag tgagatccca
      541 tttctctggc tggagacaca gatggcctca aatgagagag atgctatatc atggtatcag
      601 aagaagattg gagcatatga tcagcagata tgggaaaagt caatcgaaca gactcagatt
      661 aagggtttca aaaacaaacc aaaaaaaatg ggccatataa aaccagactt gattgatgtt
      721 gacttaatca gaggctcaac atttgccaaa gccaagcctg agattccatg gacctcgctc
      781 actcggaagg ggcttgttcg agtggtgttt ttcccgttgt tcagcagctg gtggattcag
      841 gttacctctc tcagaatctt tgtttggttg ctgctacttt acctcatgca agtcacagcg
      901 gttgtgttgt atctcctgat gcctattgtg agcgccagtg aagtgcttgg acccttgtgc
      961 cttatgctac tcatgggaac tgtccactgt cagattgtgt cgactcagat aacaaggccg
     1021 tcaggaaaca atggaaatcg gagaagaaga aaattacgaa aaactgtaaa tggtgatggg
     1081 agccgagaca atggaaataa ctcccctgat aaagtcagag cagtagaaac tctggagtct
     1141 gcatccagtg ttggtggttt ttgggggact ctctttggca acaggattaa aagggtgaaa
     1201 ttagtatcta acaaaggtac tgaaactgac aatgactcag gctgtttcca tcctatcctt
     1261 aagaagagac agggtcgacc cgagatcaga atgtggcaag caagagagaa agcgaaggtt
     1321 tcggatggag aaaagtgccg tagggaggct tataggcgtt tgggtaatgg aatttcagac
     1381 gatctgtcaa gtgaggagga tggtgaagca cggacacaga tgatattatt gcgtaggagt
     1441 gtggaagggg cgtcaagtga caatggttat gaagttaaga atagaaggtc aatactttca
     1501 aggcacctaa attctcaggt aaagaaaacc acaaggtggt gtcatattgt tcgggattca
     1561 gatagtctgg ctgaatcaga gtttgaatca gcagtcttca gccagggttc tagatctggt
     1621 atgagtggtg gctctcggag ccttaacttg tcaagaagag actcagaaag cacccgacat
     1681 gactccgaga ctgaggatat gttatgggat gaccttctcc atggtccaga gtgccggtca
     1741 tctgtcacca gtgacagtga gggggctcat gtaaatacca ttcattcagg gaccaaacgt
     1801 gaccccaaag aagatgtttt tcagcagaac catttattct ggcttcagaa ttcaagtcct
     1861 gcctctgagc gagttagtgc gataatctgg gaaggaaacg agtgcaaaaa gatggacatg
     1921 tctgtgttgg agataagcgg catcatcatg agcagggtca atgcatacga gcaaggtgtt
     1981 ggctatcaga tgctggggaa tgcagtcacc gttggcttag cacttttccc atttttatat
     2041 cgacttttcc gagagaagag ctttgaccaa ctaaagtcca tctcagcaga ggaggttctg
     2101 accctcttct gtggtgcgcc acccgtcaca cctgttgtta ttttgtctat aattaatttt
     2161 attgaaagat tgtgtcttac gtggatgttt tttttcatga tgtgtgtggc agagagaaca
     2221 tataagcaga gatttttatt tgcaaaactc ttcagccata ttacttctgc caggaaggcc
     2281 aggaaatatg aaatacctca tttcagactt aaaaaggtgg agaacattaa aatatggtta
     2341 tccctgcgct cctatctaaa gaggcggggt ccacagcgct cagtggacgt ggttgtgtcc
     2401 tccgtcttct tactgacact ttcaattgct ttcatttgtt gtgcacaggt tcttcaaggt
     2461 cacaagacat tcctgaatga tgcttacaac tgggagttct tgatctggga aacagcattg
     2521 ctgctgtttt tgcttcgcct ggcctcactg gggtcagaaa ccaacaagaa gtacagcaat
     2581 gtttccatcc tgctcactga acagattaat ttatatctta aaatggaaaa aaagccaaat
     2641 aagaaagaac agctcacgct agtgaataat gtattgaagc tgtccacaaa gctgttaaag
     2701 gagctggaca caccatttag actctatgga ctgaccatga accccttaat ctacaacatc
     2761 acaagagtag tcatcctttc tgctgtctct ggagttataa gcgaccttct aggattcaac
     2821 ataagactgt ggaaaattaa gtcctgagct gagatgtgtg cctggactct gctggctggt
     2881 gtcactgctc ccccactgag gacaaagatg gcccacagaa accagtggcc ccacctgcag
     2941 gctcacatgc atcagtctct ccactcagcc ccgtctaacg aatggagctt cggcacctcc
     3001 tttccccggg gcctgtgtta aaaacctgca ctttcatggt tctcaagcaa cgtgaatagt
     3061 cagcaaacta aagcctgcct cacaaagact cggactattc ctgagtcagg acatttatcc
     3121 tggagcctcc agtactgtgc tagttatact tactgtaaat agtctcttgg gtaaccatgg
     3181 taggtgcccg aagcatgacg caactgtctc ttattggaaa tatttaaatg cattactttt
     3241 ctactatagt ctatggattg gggacttctc tatcagaagg agagaaacta ttttaggttg
     3301 aatccaaata aaagaacttt actagagaaa aaaaaaaaaa aa
//
