ID   HXD4_MOUSE              Reviewed;         250 AA.
AC   P10628; A2ASN3; P97451; Q3UXL6;
DT   01-JUL-1989, integrated into UniProtKB/Swiss-Prot.
DT   05-SEP-2006, sequence version 3.
DT   24-JAN-2024, entry version 191.
DE   RecName: Full=Homeobox protein Hox-D4;
DE   AltName: Full=Homeobox protein Hox-4.2;
DE   AltName: Full=Homeobox protein Hox-5.1;
GN   Name=Hoxd4; Synonyms=Hox-4.2, Hoxd-4;
OS   Mus musculus (Mouse).
OC   Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia;
OC   Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae;
OC   Murinae; Mus; Mus.
OX   NCBI_TaxID=10090;
RN   [1]
RP   NUCLEOTIDE SEQUENCE [MRNA].
RX   PubMed=2898782; DOI=10.1073/pnas.85.13.4760;
RA   Featherstone M.S., Baron A., Gaunt S.J., Mattei M.-G., Duboule D.;
RT   "Hox-5.1 defines a homeobox-containing gene locus on mouse chromosome 2.";
RL   Proc. Natl. Acad. Sci. U.S.A. 85:4760-4764(1988).
RN   [2]
RP   SEQUENCE REVISION.
RX   PubMed=7907418; DOI=10.1093/nar/22.3.376;
RA   Rambaldi I., Kovacs E.N., Featherstone M.S.;
RT   "A proline-rich transcriptional activation domain in murine HOXD-4
RT   (HOX-4.2).";
RL   Nucleic Acids Res. 22:376-382(1994).
RN   [3]
RP   NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC   STRAIN=129/Sv;
RX   PubMed=9360992; DOI=10.1074/jbc.272.46.29151;
RA   Folberg A., Kovacs E.N., Featherstone M.S.;
RT   "Characterization and retinoic acid responsiveness of the murine Hoxd4
RT   transcription unit.";
RL   J. Biol. Chem. 272:29151-29157(1997).
RN   [4]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RC   STRAIN=C57BL/6J; TISSUE=Muellerian duct;
RX   PubMed=16141072; DOI=10.1126/science.1112014;
RA   Carninci P., Kasukawa T., Katayama S., Gough J., Frith M.C., Maeda N.,
RA   Oyama R., Ravasi T., Lenhard B., Wells C., Kodzius R., Shimokawa K.,
RA   Bajic V.B., Brenner S.E., Batalov S., Forrest A.R., Zavolan M., Davis M.J.,
RA   Wilming L.G., Aidinis V., Allen J.E., Ambesi-Impiombato A., Apweiler R.,
RA   Aturaliya R.N., Bailey T.L., Bansal M., Baxter L., Beisel K.W., Bersano T.,
RA   Bono H., Chalk A.M., Chiu K.P., Choudhary V., Christoffels A.,
RA   Clutterbuck D.R., Crowe M.L., Dalla E., Dalrymple B.P., de Bono B.,
RA   Della Gatta G., di Bernardo D., Down T., Engstrom P., Fagiolini M.,
RA   Faulkner G., Fletcher C.F., Fukushima T., Furuno M., Futaki S.,
RA   Gariboldi M., Georgii-Hemming P., Gingeras T.R., Gojobori T., Green R.E.,
RA   Gustincich S., Harbers M., Hayashi Y., Hensch T.K., Hirokawa N., Hill D.,
RA   Huminiecki L., Iacono M., Ikeo K., Iwama A., Ishikawa T., Jakt M.,
RA   Kanapin A., Katoh M., Kawasawa Y., Kelso J., Kitamura H., Kitano H.,
RA   Kollias G., Krishnan S.P., Kruger A., Kummerfeld S.K., Kurochkin I.V.,
RA   Lareau L.F., Lazarevic D., Lipovich L., Liu J., Liuni S., McWilliam S.,
RA   Madan Babu M., Madera M., Marchionni L., Matsuda H., Matsuzawa S., Miki H.,
RA   Mignone F., Miyake S., Morris K., Mottagui-Tabar S., Mulder N., Nakano N.,
RA   Nakauchi H., Ng P., Nilsson R., Nishiguchi S., Nishikawa S., Nori F.,
RA   Ohara O., Okazaki Y., Orlando V., Pang K.C., Pavan W.J., Pavesi G.,
RA   Pesole G., Petrovsky N., Piazza S., Reed J., Reid J.F., Ring B.Z.,
RA   Ringwald M., Rost B., Ruan Y., Salzberg S.L., Sandelin A., Schneider C.,
RA   Schoenbach C., Sekiguchi K., Semple C.A., Seno S., Sessa L., Sheng Y.,
RA   Shibata Y., Shimada H., Shimada K., Silva D., Sinclair B., Sperling S.,
RA   Stupka E., Sugiura K., Sultana R., Takenaka Y., Taki K., Tammoja K.,
RA   Tan S.L., Tang S., Taylor M.S., Tegner J., Teichmann S.A., Ueda H.R.,
RA   van Nimwegen E., Verardo R., Wei C.L., Yagi K., Yamanishi H.,
RA   Zabarovsky E., Zhu S., Zimmer A., Hide W., Bult C., Grimmond S.M.,
RA   Teasdale R.D., Liu E.T., Brusic V., Quackenbush J., Wahlestedt C.,
RA   Mattick J.S., Hume D.A., Kai C., Sasaki D., Tomaru Y., Fukuda S.,
RA   Kanamori-Katayama M., Suzuki M., Aoki J., Arakawa T., Iida J., Imamura K.,
RA   Itoh M., Kato T., Kawaji H., Kawagashira N., Kawashima T., Kojima M.,
RA   Kondo S., Konno H., Nakano K., Ninomiya N., Nishio T., Okada M., Plessy C.,
RA   Shibata K., Shiraki T., Suzuki S., Tagami M., Waki K., Watahiki A.,
RA   Okamura-Oho Y., Suzuki H., Kawai J., Hayashizaki Y.;
RT   "The transcriptional landscape of the mammalian genome.";
RL   Science 309:1559-1563(2005).
RN   [5]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=C57BL/6J;
RX   PubMed=19468303; DOI=10.1371/journal.pbio.1000112;
RA   Church D.M., Goodstadt L., Hillier L.W., Zody M.C., Goldstein S., She X.,
RA   Bult C.J., Agarwala R., Cherry J.L., DiCuccio M., Hlavina W., Kapustin Y.,
RA   Meric P., Maglott D., Birtle Z., Marques A.C., Graves T., Zhou S.,
RA   Teague B., Potamousis K., Churas C., Place M., Herschleb J., Runnheim R.,
RA   Forrest D., Amos-Landgraf J., Schwartz D.C., Cheng Z., Lindblad-Toh K.,
RA   Eichler E.E., Ponting C.P.;
RT   "Lineage-specific biology revealed by a finished genome assembly of the
RT   mouse.";
RL   PLoS Biol. 7:E1000112-E1000112(2009).
RN   [6]
RP   NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 175-198.
RX   PubMed=1348361; DOI=10.1073/pnas.89.7.2883;
RA   Nazarali A., Kim Y., Nirenberg M.;
RT   "Hox-1.11 and Hox-4.9 homeobox genes.";
RL   Proc. Natl. Acad. Sci. U.S.A. 89:2883-2887(1992).
RN   [7]
RP   INTERACTION WITH PBX1.
RX   PubMed=7791786; DOI=10.1128/mcb.15.7.3786;
RA   Lu Q., Knoepfler P.S., Scheele J., Wright D.D., Kamps M.P.;
RT   "Both Pbx1 and E2A-Pbx1 bind the DNA motif ATCAATCAA cooperatively with the
RT   products of multiple murine Hox genes, some of which are themselves
RT   oncogenes.";
RL   Mol. Cell. Biol. 15:3786-3795(1995).
CC   -!- FUNCTION: Sequence-specific transcription factor which is part of a
CC       developmental regulatory system that provides cells with specific
CC       positional identities on the anterior-posterior axis.
CC   -!- SUBUNIT: Forms a DNA-binding heterodimer with transcription factor
CC       PBX1. {ECO:0000269|PubMed:7791786}.
CC   -!- SUBCELLULAR LOCATION: Nucleus.
CC   -!- SIMILARITY: Belongs to the Antp homeobox family. Deformed subfamily.
CC       {ECO:0000305}.
CC   -!- SEQUENCE CAUTION:
CC       Sequence=AAA20072.1; Type=Erroneous initiation; Evidence={ECO:0000305};
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DR   EMBL; J03770; AAA20072.1; ALT_INIT; mRNA.
DR   EMBL; U77364; AAB41222.1; -; Genomic_DNA.
DR   EMBL; AK135479; BAE22547.1; -; mRNA.
DR   EMBL; AL928644; -; NOT_ANNOTATED_CDS; Genomic_DNA.
DR   EMBL; M87804; AAA37851.1; -; Genomic_DNA.
DR   CCDS; CCDS16145.1; -.
DR   PIR; A36170; A36170.
DR   PIR; E42694; E42694.
DR   RefSeq; NP_034599.2; NM_010469.2.
DR   AlphaFoldDB; P10628; -.
DR   SMR; P10628; -.
DR   BioGRID; 200397; 3.
DR   IntAct; P10628; 3.
DR   STRING; 10090.ENSMUSP00000047949; -.
DR   PhosphoSitePlus; P10628; -.
DR   MaxQB; P10628; -.
DR   PaxDb; 10090-ENSMUSP00000047949; -.
DR   ProteomicsDB; 267181; -.
DR   DNASU; 15436; -.
DR   Ensembl; ENSMUST00000047904.4; ENSMUSP00000047949.4; ENSMUSG00000101174.9.
DR   Ensembl; ENSMUST00000111980.4; ENSMUSP00000107611.2; ENSMUSG00000101174.9.
DR   GeneID; 15436; -.
DR   KEGG; mmu:15436; -.
DR   UCSC; uc008kef.1; mouse.
DR   AGR; MGI:96208; -.
DR   CTD; 3233; -.
DR   MGI; MGI:96208; Hoxd4.
DR   VEuPathDB; HostDB:ENSMUSG00000101174; -.
DR   eggNOG; KOG0489; Eukaryota.
DR   GeneTree; ENSGT00940000157270; -.
DR   HOGENOM; CLU_061398_0_0_1; -.
DR   InParanoid; P10628; -.
DR   OMA; QGVYPRS; -.
DR   PhylomeDB; P10628; -.
DR   TreeFam; TF352857; -.
DR   BioGRID-ORCS; 15436; 1 hit in 72 CRISPR screens.
DR   ChiTaRS; Hoxd4; mouse.
DR   PRO; PR:P10628; -.
DR   Proteomes; UP000000589; Chromosome 2.
DR   RNAct; P10628; Protein.
DR   Bgee; ENSMUSG00000101174; Expressed in vertebra cartilage element and 105 other cell types or tissues.
DR   GO; GO:0030054; C:cell junction; ISO:MGI.
DR   GO; GO:0005654; C:nucleoplasm; ISO:MGI.
DR   GO; GO:0001228; F:DNA-binding transcription activator activity, RNA polymerase II-specific; ISO:MGI.
DR   GO; GO:0000981; F:DNA-binding transcription factor activity, RNA polymerase II-specific; IBA:GO_Central.
DR   GO; GO:0000978; F:RNA polymerase II cis-regulatory region sequence-specific DNA binding; IBA:GO_Central.
DR   GO; GO:0000977; F:RNA polymerase II transcription regulatory region sequence-specific DNA binding; ISO:MGI.
DR   GO; GO:1990837; F:sequence-specific double-stranded DNA binding; ISO:MGI.
DR   GO; GO:0009952; P:anterior/posterior pattern specification; IMP:MGI.
DR   GO; GO:0048704; P:embryonic skeletal system morphogenesis; IMP:MGI.
DR   GO; GO:0045944; P:positive regulation of transcription by RNA polymerase II; ISO:MGI.
DR   GO; GO:0048863; P:stem cell differentiation; IDA:MGI.
DR   CDD; cd00086; homeodomain; 1.
DR   Gene3D; 1.10.10.60; Homeodomain-like; 1.
DR   InterPro; IPR009057; Homeobox-like_sf.
DR   InterPro; IPR017995; Homeobox_antennapedia.
DR   InterPro; IPR001827; Homeobox_Antennapedia_CS.
DR   InterPro; IPR017970; Homeobox_CS.
DR   InterPro; IPR001356; Homeobox_dom.
DR   InterPro; IPR020479; Homeobox_metazoa.
DR   PANTHER; PTHR45771:SF5; HOMEOBOX PROTEIN HOX-D4; 1.
DR   PANTHER; PTHR45771; HOMEOTIC PROTEIN DEFORMED; 1.
DR   Pfam; PF00046; Homeodomain; 1.
DR   PRINTS; PR00025; ANTENNAPEDIA.
DR   PRINTS; PR00024; HOMEOBOX.
DR   SMART; SM00389; HOX; 1.
DR   SUPFAM; SSF46689; Homeodomain-like; 1.
DR   PROSITE; PS00032; ANTENNAPEDIA; 1.
DR   PROSITE; PS00027; HOMEOBOX_1; 1.
DR   PROSITE; PS50071; HOMEOBOX_2; 1.
DR   Genevisible; P10628; MM.
PE   1: Evidence at protein level;
KW   Developmental protein; DNA-binding; Homeobox; Nucleus; Reference proteome;
KW   Transcription; Transcription regulation.
FT   CHAIN           1..250
FT                   /note="Homeobox protein Hox-D4"
FT                   /id="PRO_0000200211"
FT   DNA_BIND        152..211
FT                   /note="Homeobox"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU00108"
FT   REGION          31..126
FT                   /note="Disordered"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   REGION          210..250
FT                   /note="Disordered"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   MOTIF           131..136
FT                   /note="Antp-type hexapeptide"
FT   COMPBIAS        217..234
FT                   /note="Polar residues"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   CONFLICT        95
FT                   /note="R -> P (in Ref. 1 and 3)"
FT                   /evidence="ECO:0000305"
FT   CONFLICT        143
FT                   /note="V -> A (in Ref. 1; AAA20072)"
FT                   /evidence="ECO:0000305"
SQ   SEQUENCE   250 AA;  27371 MW;  2B20A00BAD1B8757 CRC64;
     MAMSSYMVNS KYVDPKFPPC EEYLQGGYLG EQGADYYGSG AQGADFQPSG LYPRPDFGEQ
     PFGGGGPGPG SALPARGHGQ EPSGPGSHYG APGERCPAPP PAPLPGARAC SQPTGPKQPP
     PGTALKQPAV VYPWMKKVHV NSVNPNYTGG EPKRSRTAYT RQQVLELEKE FHFNRYLTRR
     RRIEIAHTLC LSERQIKIWF QNRRMKWKKD HKLPNTKGRS SSSSSCSSSA APGQHLQPMA
     KDHHTDLTTL
//