LOCUS       NM_001080549            4261 bp    mRNA    linear   ROD 30-JUL-2024
DEFINITION  Mus musculus highly divergent homeobox (Hdx), transcript variant 1,
            mRNA.
ACCESSION   NM_001080549 XM_142098 XM_909280 XM_973136 XM_986566 XM_987853
            XM_987887
VERSION     NM_001080549.2
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 4261)
  AUTHORS   Memic,F., Knoflach,V., Morarach,K., Sadler,R., Laranjeira,C.,
            Hjerling-Leffler,J., Sundstrom,E., Pachnis,V. and Marklund,U.
  TITLE     Transcription and Signaling Regulators in Developing Neuronal
            Subtypes of Mouse and Human Enteric Nervous System
  JOURNAL   Gastroenterology 154 (3), 624-636 (2018)
   PUBMED   29031500
REFERENCE   2  (bases 1 to 4261)
  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   3  (bases 1 to 4261)
  AUTHORS   Cox,B.J., Vollmer,M., Tamplin,O., Lu,M., Biechele,S.,
            Gertsenstein,M., van Campenhout,C., Floss,T., Kuhn,R., Wurst,W.,
            Lickert,H. and Rossant,J.
  TITLE     Phenotypic annotation of the mouse X chromosome
  JOURNAL   Genome Res 20 (8), 1154-1164 (2010)
   PUBMED   20548051
COMMENT     VALIDATED REFSEQ: This record has undergone validation or
            preliminary review. The reference sequence was derived from
            CJ060144.1, BC116300.1 and AK083436.1.
            
            On Feb 10, 2007 this sequence version replaced NM_001080549.1.
            
            Transcript Variant: This variant (1) represents the longer
            transcript and encodes the longer isoform (1).
            
            ##Evidence-Data-START##
            Transcript exon combination :: BC116300.1, SRR14777535.709870.1
                                           [ECO:0000332]
            RNAseq introns              :: mixed sample support SAMN00849381,
                                           SAMN00849382 [ECO:0006172]
            ##Evidence-Data-END##
            
            ##RefSeq-Attributes-START##
            RefSeq Select criteria :: based on conservation, expression,
                                      longest protein
            ##RefSeq-Attributes-END##
PRIMARY     REFSEQ_SPAN         PRIMARY_IDENTIFIER PRIMARY_SPAN        COMP
            1-57                CJ060144.1         2-58
            58-2800             BC116300.1         1-2743
            2801-4261           AK083436.1         2642-4102
FEATURES             Location/Qualifiers
     source          1..4261
                     /organism="Mus musculus"
                     /mol_type="mRNA"
                     /strain="C57BL/6"
                     /db_xref="taxon:10090"
                     /chromosome="X"
                     /map="X 48.29 cM"
     gene            1..4261
                     /gene="Hdx"
                     /gene_synonym="D030011N01Rik; Gm380"
                     /note="highly divergent homeobox"
                     /db_xref="GeneID:245596"
                     /db_xref="MGI:MGI:2685226"
     exon            1..113
                     /gene="Hdx"
                     /gene_synonym="D030011N01Rik; Gm380"
                     /inference="alignment:Splign:2.1.0"
     CDS             114..2192
                     /gene="Hdx"
                     /gene_synonym="D030011N01Rik; Gm380"
                     /note="isoform 1 is encoded by transcript variant 1"
                     /codon_start=1
                     /product="highly divergent homeobox isoform 1"
                     /protein_id="NP_001074018.1"
                     /db_xref="CCDS:CCDS41105.1"
                     /db_xref="GeneID:245596"
                     /db_xref="MGI:MGI:2685226"
                     /translation="MNLRSVFTVEQQRILQRYYENGMTNQSKNCFQLILQCAQETKLD
                     FSVVRTWVGNKRRKMSSKSCESGAAGTVSGTSLAAPDITVRNVVNIARPSSQQSSWTS
                     ANNDVIVTGIYSPVSSSSKQGTTKHTNTQITEAHKIPIQKAANKNDTELQLHIPVQRQ
                     VAHCKNASVLLGEKTIILSRQTSVLNAGNSVYNHTKKSYGSSPVQASEMTVPQKPSVC
                     QRPCKIEPVGIQRSYKPEHAGLASHNLCGQKPTIRDPCCRTQNLEIREVFSLAVSDYP
                     QRILGGNSTQKPASAEGTCLSIAMETGDAEDEYAREEELASMGAQITSYSRFYESGNS
                     LRAENQSTNLPGPGRNLPNSQMVNIRDLSDNVLYQTRDYHLTPRTSLHTASSTMYSNT
                     NPSRSNFSPHFVSSNQLRLSQNQNNYQISGNLSVPWITGCSRKRALQDRTQFSDRDLA
                     TLKKYWDNGMTSLGSVCREKIEAVAIELNVDCEIVRTWIGNRRRKYRLMGIEVPPPRG
                     GPADFSEQPESGSLSALTPGEEAGPEVGEDNDRNDEVSICLSEASSQEESNELIPNET
                     RAHKDEEHQAVSADNVKIEIIDDEESDMISNSEVEQENSLLDYKNEEVRFIENELEIQ
                     KQKYFKLQSFVRNLILAMKADDKDQQQALLSDLPPELEEMDCSHASPDPDDTSLSVSS
                     LSEKNASDSL"
     exon            114..260
                     /gene="Hdx"
                     /gene_synonym="D030011N01Rik; Gm380"
                     /inference="alignment:Splign:2.1.0"
     exon            261..1370
                     /gene="Hdx"
                     /gene_synonym="D030011N01Rik; Gm380"
                     /inference="alignment:Splign:2.1.0"
     exon            1371..1424
                     /gene="Hdx"
                     /gene_synonym="D030011N01Rik; Gm380"
                     /inference="alignment:Splign:2.1.0"
     exon            1425..1571
                     /gene="Hdx"
                     /gene_synonym="D030011N01Rik; Gm380"
                     /inference="alignment:Splign:2.1.0"
     exon            1572..1779
                     /gene="Hdx"
                     /gene_synonym="D030011N01Rik; Gm380"
                     /inference="alignment:Splign:2.1.0"
     exon            1780..1859
                     /gene="Hdx"
                     /gene_synonym="D030011N01Rik; Gm380"
                     /inference="alignment:Splign:2.1.0"
     exon            1860..1943
                     /gene="Hdx"
                     /gene_synonym="D030011N01Rik; Gm380"
                     /inference="alignment:Splign:2.1.0"
     exon            1944..2066
                     /gene="Hdx"
                     /gene_synonym="D030011N01Rik; Gm380"
                     /inference="alignment:Splign:2.1.0"
     exon            2067..4261
                     /gene="Hdx"
                     /gene_synonym="D030011N01Rik; Gm380"
                     /inference="alignment:Splign:2.1.0"
     regulatory      2351..2356
                     /regulatory_class="polyA_signal_sequence"
                     /gene="Hdx"
                     /gene_synonym="D030011N01Rik; Gm380"
                     /note="hexamer: AATAAA"
     polyA_site      2370
                     /gene="Hdx"
                     /gene_synonym="D030011N01Rik; Gm380"
                     /note="major polyA site"
     regulatory      2852..2857
                     /regulatory_class="polyA_signal_sequence"
                     /gene="Hdx"
                     /gene_synonym="D030011N01Rik; Gm380"
                     /note="hexamer: CATAAA"
     polyA_site      2878
                     /gene="Hdx"
                     /gene_synonym="D030011N01Rik; Gm380"
     regulatory      3437..3442
                     /regulatory_class="polyA_signal_sequence"
                     /gene="Hdx"
                     /gene_synonym="D030011N01Rik; Gm380"
                     /note="hexamer: ATTAAA"
     polyA_site      3461
                     /gene="Hdx"
                     /gene_synonym="D030011N01Rik; Gm380"
ORIGIN      
        1 attgtctgag gcggcagtgg agacccagga aaaaatcttg cggactccgc ctgctctggc
       61 cctggtctca tcttggaacc tctgatctct ttcgtgaccg caccacgccc gagatgaatc
      121 tacgttctgt atttactgta gagcaacaaa ggattttaca gcgttattat gaaaatggaa
      181 tgacaaatca aagtaaaaat tgctttcagc tcatattaca gtgtgcacag gagactaagc
      241 tggacttcag tgtagtcagg acgtgggttg gcaataagcg aagaaaaatg agtagtaaaa
      301 gctgtgaatc aggagcagca ggaactgtgt ctggtacctc attggcagcg ccagacatta
      361 cagtcagaaa tgtggttaat attgcccgcc cttcaagcca gcaatcttct tggacttctg
      421 ccaataatga tgtcattgta actggtatat acagtccagt aagctcatca agtaagcaag
      481 gcactacaaa gcatacaaat acacaaatta cagaagcaca taaaattcct attcagaagg
      541 cagccaataa aaatgacact gaattacaat tgcacattcc tgttcaaaga caagtagcgc
      601 actgtaagaa tgcttctgtg ctcctagggg aaaagacaat tattttgtca agacagacaa
      661 gtgtactaaa tgctggaaac tcagtgtaca atcacacaaa gaaaagctat ggaagttctc
      721 cggtgcaagc ttcagaaatg acagtacctc aaaagccatc tgtgtgccag cgaccttgca
      781 aaattgaacc agttgggatt caaaggtcat ataaacctga acatgcaggt ctggcatcac
      841 ataacttatg tgggcaaaag ccaaccatta gagacccttg ctgtagaaca caaaacttgg
      901 aaattcgtga agtgttttca ttggcagtca gtgattaccc tcagagaatt ctgggaggaa
      961 atagcacaca gaagccggcc tcagcagaag gaacttgttt gtccattgca atggagactg
     1021 gagacgcaga ggatgaatat gccagagaag aagaactggc atcaatggga gcacaaataa
     1081 caagctactc aaggttttat gaaagtggca attcccttcg agctgagaac caaagtacaa
     1141 atttgcctgg accaggaaga aacctgccaa attcacaaat ggtgaatatt agagatttgt
     1201 cagacaatgt actgtatcag actagagact accatttgac accacggacc tcattgcata
     1261 cagcatctag tactatgtac agtaatacta atccatcacg gagtaatttt tctccacatt
     1321 ttgtatcatc aaaccaactg aggttatcac aaaaccaaaa caattaccag atttcaggaa
     1381 acctttctgt gccttggatt acagggtgtt ctaggaaaag agcactacag gaccgcactc
     1441 aattcagtga ccgagacttg gctactctta agaagtactg ggacaatggt atgaccagcc
     1501 tgggctctgt atgtagagag aagattgaag ctgttgcaat tgaattaaat gtcgactgtg
     1561 aaatagttcg gacttggatt gggaatcgaa gaagaaaata ccgtttaatg ggaattgaag
     1621 ttccacctcc aagaggaggc cctgctgatt tctctgagca gcctgagtct ggttctttgt
     1681 ctgcactcac accaggagag gaagctgggc ctgaagtagg agaggataat gacagaaatg
     1741 atgaagtgtc catctgtttg tccgaagcaa gctctcaaga ggagtccaat gaacttatcc
     1801 caaatgagac cagggcacat aaggatgaag agcaccaggc agtatctgca gataatgtga
     1861 aaatagaaat tatcgatgat gaagaaagtg acatgataag caattctgag gtagaacaag
     1921 aaaattctct cctggattac aagaatgaag aagtcagatt tattgaaaat gagctagaga
     1981 ttcaaaagca aaaatacttt aagctccagt cttttgttag aaacctgatt ctcgctatga
     2041 aagctgatga taaagaccag cagcaggcac tgctgtcaga tttacctcca gaattagaag
     2101 agatggattg cagtcatgcc tcgccggatc ctgatgatac ctcactcagt gtgtcttctt
     2161 tatcagagaa aaatgcctca gacagcttgt gattgggagt gggggatatg atctagtctg
     2221 ttgattgcct aacaggtgtg catttcaaga taactgtact gtttcccaaa cagtcttcaa
     2281 ctggaaaaac acattgttaa agcaaacata tgctgtgaag gaatgacaag atatagtggc
     2341 tacaatacaa aataaaaagc atgtacaata cttgaaatgg tttgttttta aaacttatat
     2401 aaaatcctag gaaattgtat ttaattttga ccaactccac tatgaaatct attatatctg
     2461 atttctgaaa gatttttttg cttattcttt aagaagaatc ttaattttat ccagaaatat
     2521 agaaaataag catatcacaa cattactaag ttggttagtt ttattttgta gccattacat
     2581 ctttcttcct acttcatttt cttatcattc atatacattt ttactcagga aagtgggcta
     2641 aaaatttaca acaggcctaa tcatatattt aacctggatg aatcctggga tttatttttc
     2701 aattccgatg agaatttgac ctaagataat gattgaaaat tgaagcactt actaggacgt
     2761 aattgtaagt tattggtact cctgacactg gggagaggga aaaatcctct gaaaagtaga
     2821 atcattgtca aaatgtcaaa acatttaagt acataaaaac tgtacttttt aaaaaacact
     2881 tttaatctca attcttgtat acaataagtg ataagtattg atgattaata ttctaccata
     2941 tagtaaattt atataattga gtcagacaaa atattgcaca aatacttcaa gtttatcaac
     3001 attttcataa tacttttcat atcttaaaat ttgtgaaaca ggaaatcaaa gtatggtact
     3061 ggtatctgtt tgtttttatt taattctaga catacaactt tgccacaaag tttacctcat
     3121 ttccatatga ggcctgcaca aagccaacaa taatgtcaaa aaaataatta tatataatac
     3181 tttgattgta aatcaaagtc ctctggatct cttggatgct attctatgaa tacacaccta
     3241 aaatgagcat ggtacccagt tgttactatt agtaggtacc aaatggcagc acactgtaga
     3301 catctttttg catcttccct tctggaatac cagatggtat tactaaggtc tgtctataga
     3361 tggaaaaata ctagtttctg cctaaactca caatgtcata tatttgtaac taggttgtgt
     3421 ggaactatat tacacgatta aattattatc tattcctgaa agatgcatga agcatctaga
     3481 taactgtttc aattatcaag tttcagatat gtttaagttt cttaactaca gctattctga
     3541 tctcagaatt tactgatacc aatttatgat tccagaaagg cccttattaa tccctctagc
     3601 tcagaaatgt cctttctcat tactatatac aagtaaagtt cactgatgac cattcagttc
     3661 atcaaatgtt tgattttaca ctgttgccac acaacctcta tggcttcctt gtcagcagaa
     3721 atatttcagt agtcagctaa tcatgtcctt tagctgaaag tcatgtggtt ctttgcaaac
     3781 aacttctggt agtccttgct gacaaaccaa attccattca gggaaaagac cactgagcca
     3841 cagaagctca aacatctaga ttaagctctt cagtcacata aatttctcca taaaataaga
     3901 gtcctcccta catacaacaa atacagaaac cctgattatt ttattatatg gaggattaag
     3961 acaaattttc ctgtagccca atctggcctc atatttccaa tatagctgag gatggctttg
     4021 agtcctgctg ttcctgcctt tgtttcccaa atgcctggat ggcagatgtg ccccaccaca
     4081 cctaggttcc gtttgtttga gtaggaaccc atttctggtc tcaagtctct ctgtgatctt
     4141 ctttagtacc attgagtttc tctttaaact gcttcagttt aagacacttc ctagttggtt
     4201 ttcattacag aacaaatgaa aacaacaaaa aattattttc acatcttaga aatgtgttac
     4261 t
//
