GGRNA ver.2 Home | Help | Advanced search    Previous release (v1)

2024-03-29 19:11:07, GGRNA.v2 : RefSeq release 222 (Jan, 2024)

LOCUS       NM_001173469            1834 bp    mRNA    linear   ROD 20-MAR-2023
DEFINITION  Rattus norvegicus homeo box D9 (Hoxd9), mRNA.
ACCESSION   NM_001173469 XM_002726192
VERSION     NM_001173469.2
KEYWORDS    RefSeq; RefSeq Select.
SOURCE      Rattus norvegicus (Norway rat)
  ORGANISM  Rattus norvegicus
            Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
            Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha;
            Muroidea; Muridae; Murinae; Rattus.
REFERENCE   1  (bases 1 to 1834)
  AUTHORS   Hong Q, Li XD, Xie P and Du SX.
  TITLE     All-trans-retinoic acid suppresses rat embryo hindlimb bud
            mesenchymal chondrogenesis by modulating HoxD9 expression
  JOURNAL   Bioengineered 12 (1), 3900-3911 (2021)
   PUBMED   34288810
  REMARK    GeneRIF: All-trans-retinoic acid suppresses rat embryo hindlimb bud
            mesenchymal chondrogenesis by modulating HoxD9 expression.
REFERENCE   2  (bases 1 to 1834)
  AUTHORS   Raines AM, Adam M, Magella B, Meyer SE, Grimes HL, Dey SK and
            Potter SS.
  TITLE     Recombineering-based dissection of flanking and paralogous Hox gene
            functions in mouse reproductive tracts
  JOURNAL   Development 140 (14), 2942-2952 (2013)
   PUBMED   23760953
REFERENCE   3  (bases 1 to 1834)
  AUTHORS   McIntyre DC, Rakshit S, Yallowitz AR, Loken L, Jeannotte L,
            Capecchi MR and Wellik DM.
  TITLE     Hox patterning of the vertebrate rib cage
  JOURNAL   Development 134 (16), 2981-2989 (2007)
   PUBMED   17626057
REFERENCE   4  (bases 1 to 1834)
  AUTHORS   de la Cruz CC, Der-Avakian A, Spyropoulos DD, Tieu DD and Carpenter
            EM.
  TITLE     Targeted disruption of Hoxd9 and Hoxd10 alters locomotor behavior,
            vertebral identity, and peripheral nervous system development
  JOURNAL   Dev Biol 216 (2), 595-610 (1999)
   PUBMED   10642795
REFERENCE   5  (bases 1 to 1834)
  AUTHORS   Chen F and Capecchi MR.
  TITLE     Paralogous mouse Hox genes, Hoxa9, Hoxb9, and Hoxd9, function
            together to control development of the mammary gland in response to
            pregnancy
  JOURNAL   Proc Natl Acad Sci U S A 96 (2), 541-546 (1999)
   PUBMED   9892669
REFERENCE   6  (bases 1 to 1834)
  AUTHORS   Fromental-Ramain C, Warot X, Lakkaraju S, Favier B, Haack H,
            Birling C, Dierich A, Doll e P and Chambon P.
  TITLE     Specific and redundant functions of the paralogous Hoxa-9 and
            Hoxd-9 genes in forelimb and axial skeleton patterning
  JOURNAL   Development 122 (2), 461-472 (1996)
   PUBMED   8625797
REFERENCE   7  (bases 1 to 1834)
  AUTHORS   Zappavigna V, Renucci A, Izpisua-Belmonte JC, Urier G, Peschle C
            and Duboule D.
  TITLE     HOX4 genes encode transcription factors with potential auto- and
            cross-regulatory capacities
  JOURNAL   EMBO J 10 (13), 4177-4187 (1991)
   PUBMED   1756725
REFERENCE   8  (bases 1 to 1834)
  AUTHORS   Oliver G, Sidell N, Fiske W, Heinzmann C, Mohandas T, Sparkes RS
            and De Robertis EM.
  TITLE     Complementary homeo protein gradients in developing limb buds
  JOURNAL   Genes Dev 3 (5), 641-650 (1989)
   PUBMED   2568311
COMMENT     PROVISIONAL REFSEQ: This record has not yet been subject to final
            NCBI review. The reference sequence was derived from
            JACYVU010000115.1.
            
            On Nov 27, 2020 this sequence version replaced NM_001173469.1.
            
            ##Evidence-Data-START##
            Transcript exon combination :: BC169092.1, FM043112.1 [ECO:0000332]
            RNAseq introns              :: single sample supports all introns
                                           SAMEA5756307, SAMEA5760383
                                           [ECO:0000348]
            ##Evidence-Data-END##
            
            ##RefSeq-Attributes-START##
            RefSeq Select criteria :: based on single protein-coding transcript
            ##RefSeq-Attributes-END##
PRIMARY     REFSEQ_SPAN         PRIMARY_IDENTIFIER PRIMARY_SPAN        COMP
            1-859               JACYVU010000115.1  53057396-53058254
            860-1834            JACYVU010000115.1  53058602-53059576
FEATURES             Location/Qualifiers
     source          1..1834
                     /organism="Rattus norvegicus"
                     /mol_type="mRNA"
                     /strain="BN"
                     /db_xref="taxon:10116"
                     /chromosome="3"
                     /map="3q23"
     gene            1..1834
                     /gene="Hoxd9"
                     /note="homeo box D9"
                     /db_xref="GeneID:688999"
                     /db_xref="RGD:1582908"
     exon            1..859
                     /gene="Hoxd9"
                     /inference="alignment:Splign:2.1.0"
     CDS             70..1101
                     /gene="Hoxd9"
                     /note="homeobox Hox-D9"
                     /codon_start=1
                     /product="homeobox protein Hox-D9"
                     /protein_id="NP_001166940.1"
                     /db_xref="GeneID:688999"
                     /db_xref="RGD:1582908"
                     /translation="
MSSSGTLSNYYVDSLIGHEGDEVFAARFGPPGPGTQGRPAGVADGPAAAAEFASCSFAPKSSVFSASWSAVAAQPPAAATMSGLYHPYVSPPPLAAAEPGRYVRSWMEPLPGFPGGAGGGGGSGGGGGGGSGGPGPVPSPGGPANGRHYGIKPETGAAPAPSAASTSSSTSSSSSSKRTECSAARESQGSGGPEFPCNSFLRDKAAAAAAAAAGNGPGVGIGTGPGTGGSSEPSACSDHPSPGCPLKEEEKQPPQPPQQQLDPNNPAANWIHARSTRKKRCPYTKYQTLELEKEFLFNMYLTRDRRYEVARILNLTERQVKIWFQNRRMKMKKMSKEKCPKGD"
     misc_feature    70..>534
                     /gene="Hoxd9"
                     /note="Hox9 activation region; Region: Hox9_act;
                     pfam04617"
                     /db_xref="CDD:428038"
     misc_feature    406..657
                     /gene="Hoxd9"
                     /note="propagated from UniProtKB/Swiss-Prot (B5DFK3.1);
                     Region: Disordered. /evidence=ECO:0000256|SAM:MobiDB-lite"
     misc_feature    727..870
                     /gene="Hoxd9"
                     /note="propagated from UniProtKB/Swiss-Prot (B5DFK3.1);
                     Region: Disordered. /evidence=ECO:0000256|SAM:MobiDB-lite"
     misc_feature    895..1053
                     /gene="Hoxd9"
                     /note="Homeodomain; Region: HOX; smart00389"
                     /db_xref="CDD:197696"
     misc_feature    order(904..906,913..915,1033..1035,1042..1047)
                     /gene="Hoxd9"
                     /note="specific DNA base contacts [nucleotide binding];
                     other site"
                     /db_xref="CDD:238039"
     exon            860..1834
                     /gene="Hoxd9"
                     /inference="alignment:Splign:2.1.0"
ORIGIN      
cgggcgccggcgaggagccgctcggcggtgggcagtgtaaccttgggtgggagcgcgcggtgcctcaacatgtcgtccagtggcaccctcagcaactactacgtggactcgctcataggccatgagggcgacgaggtgttcgccgcgcgctttgggccaccggggccggggacacagggtcggcccgcaggtgtggccgatggcccggccgccgccgccgagttcgcctcgtgtagttttgcccccaaatcgtccgtgttctccgcctcgtggtccgcggtggccgcccagcccccggcggcggcgacgatgagcggcctgtaccacccgtacgtgtccccgccgcccctggccgccgccgagccgggccgctacgtacgctcctggatggagccgctgcccggcttccccggcggcgcgggcggtggcggtggcagtggtggcggcggtggcggaggtagcggaggcccgggtcccgttcccagccccggcggtccagccaacgggcgccactacgggattaagcctgaaaccggagcagccccggccccctctgcagcctccacttcctcctccacctcctcgtcctcctcctccaaaaggactgagtgctccgcggcccgcgagtcccaggggagcggcggcccagaattcccgtgcaactcgttcctgcgggacaaggcggcagcggcggcggcggcggcggcagggaacgggcccggggtgggaatcgggaccgggcctgggacgggaggctcgtccgagccctcagcttgcagcgatcacccgagcccgggctgcccgctgaaggaggaggagaagcagccgccgcagccgccgcagcagcaacttgacccaaacaaccctgcagcgaactggatccacgctcgctccacccggaaaaagcgctgtccctacaccaaataccagacgctagagctggagaaggaattcctcttcaacatgtacctcacccgggaccggcgctacgaggtggccaggattctgaaccttacagagagacaagtcaaaatctggttccagaaccgtaggatgaaaatgaaaaagatgagcaaggagaaatgtcctaaaggagactgacccagtgcgggtcaggcctgcagcgctcaaaaggcagcgggttttggttttttgttgttgattgttttctttgtgggtgcttgattcagaaactctgcagcgattcggacattcttcttttttttttaggtagaagtgactgtgtggttggtctctgtgagttatttgggggacgctgtatttgctcgcatatgtattggagaatccaagtggctttggagtcttgtcctatctcactccctccctttcccactcccttggttccttaggaaatgctttattttgtgagtgcacgcaggcttgatggagccctatcctgtgtaaatgttcctcatgtttctggaaagtgctgtagtgtagtctcaccccatccagcctcccaaacagggccaactatctaattccgagaatctgaaagaagagaaagactgtggacacacaccccctcccccaaaaaacccagctcagctgcaggaaaacccctatcctcagggagcccgcggactgacttccagagaggcctaccaagaagccctgggccctgggacacgaggttggggtggggttgaggagaggcttagtccttggagcacggggaagctactttctccccaggagggctgggctccctggggcggcctcgggaggtggccctccatattcctgcctgaggaccagttgtaaatgttaccgcttcctacaaataaatgctgatctgaacaaatggagccca
//

by @meso_cacase at DBCLS
This page is licensed under a Creative Commons Attribution 4.0 International License (CC BY 4.0).

If you use GGRNA in your work, please cite:
Naito Y, Bono H. (2012)
GGRNA: an ultrafast, transcript-oriented search engine for genes and transcripts.
Nucleic Acids Res., 40, W592-W596. [Full Text]