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

2024-03-29 14:37:16, GGRNA.v2 : RefSeq release 222 (Jan, 2024)

LOCUS       NM_204614               2614 bp    mRNA    linear   VRT 23-SEP-2023
DEFINITION  Gallus gallus caudal type homeobox 4B (CDX4B), mRNA.
ACCESSION   NM_204614
VERSION     NM_204614.2
KEYWORDS    RefSeq.
SOURCE      Gallus gallus (chicken)
  ORGANISM  Gallus gallus
            Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
            Archelosauria; Archosauria; Dinosauria; Saurischia; Theropoda;
            Coelurosauria; Aves; Neognathae; Galloanserae; Galliformes;
            Phasianidae; Phasianinae; Gallus.
REFERENCE   1  (bases 1 to 2614)
  AUTHORS   Joshi P, Darr AJ and Skromne I.
  TITLE     CDX4 regulates the progression of neural maturation in the spinal
            cord
  JOURNAL   Dev Biol 449 (2), 132-142 (2019)
   PUBMED   30825428
  REMARK    GeneRIF: Results show that in the spinal cord, caudal type homeobox
            4 (CDX4) is part of the gene regulatory network controlling the
            sequential and progressive transition of states from high to low
            potency during neural progenitor maturation.
REFERENCE   2  (bases 1 to 2614)
  AUTHORS   Tang H, Finn RD and Thomas PD.
  TITLE     TreeGrafter: phylogenetic tree-based annotation of proteins with
            Gene Ontology terms and other annotations
  JOURNAL   Bioinformatics 35 (3), 518-520 (2019)
   PUBMED   30032202
REFERENCE   3  (bases 1 to 2614)
  AUTHORS   Burge S, Kelly E, Lonsdale D, Mutowo-Muellenet P, McAnulla C,
            Mitchell A, Sangrador-Vegas A, Yong SY, Mulder N and Hunter S.
  TITLE     Manual GO annotation of predictive protein signatures: the InterPro
            approach to GO curation
  JOURNAL   Database (Oxford) 2012, bar068 (2012)
   PUBMED   22301074
  REMARK    Publication Status: Online-Only
REFERENCE   4  (bases 1 to 2614)
  AUTHORS   Ehrman LA and Yutzey KE.
  TITLE     Anterior expression of the caudal homologue cCdx-B activates a
            posterior genetic program in avian embryos
  JOURNAL   Dev Dyn 221 (4), 412-421 (2001)
   PUBMED   11500978
REFERENCE   5  (bases 1 to 2614)
  AUTHORS   Serrano J, Scavo L, Roth J, de la Rosa EJ and de Pablo F.
  TITLE     A novel chicken homeobox-containing gene expressed in neurulating
            embryos
  JOURNAL   Biochem Biophys Res Commun 190 (1), 270-276 (1993)
   PUBMED   7678491
COMMENT     PROVISIONAL REFSEQ: This record has not yet been subject to final
            NCBI review. The reference sequence was derived from
            JAENSK010000071.1.
            
            On Sep 23, 2021 this sequence version replaced NM_204614.1.
            
            ##Evidence-Data-START##
            Transcript exon combination :: AF353624.1, SRR13267651.22564.1
                                           [ECO:0000332]
            RNAseq introns              :: single sample supports all introns
                                           SAMEA103992290, SAMEA103992323
                                           [ECO:0000348]
            ##Evidence-Data-END##
PRIMARY     REFSEQ_SPAN         PRIMARY_IDENTIFIER PRIMARY_SPAN        COMP
            1-585               JAENSK010000071.1  12065864-12066448
            586-731             JAENSK010000071.1  12071108-12071253
            732-2614            JAENSK010000071.1  12073756-12075638
FEATURES             Location/Qualifiers
     source          1..2614
                     /organism="Gallus gallus"
                     /mol_type="mRNA"
                     /db_xref="taxon:9031"
                     /chromosome="4"
                     /map="4"
     gene            1..2614
                     /gene="CDX4B"
                     /gene_synonym="cCdx-B; CDX4; CDXB; CHOX-CAD2; ox-cad2"
                     /note="caudal type homeobox 4B"
                     /db_xref="CGNC:49264"
                     /db_xref="GeneID:395320"
     exon            1..585
                     /gene="CDX4B"
                     /gene_synonym="cCdx-B; CDX4; CDXB; CHOX-CAD2; ox-cad2"
                     /inference="alignment:Splign:2.1.0"
     misc_feature    120..122
                     /gene="CDX4B"
                     /gene_synonym="cCdx-B; CDX4; CDXB; CHOX-CAD2; ox-cad2"
                     /note="upstream in-frame stop codon"
     CDS             147..938
                     /gene="CDX4B"
                     /gene_synonym="cCdx-B; CDX4; CDXB; CHOX-CAD2; ox-cad2"
                     /note="caudal-type homeobox protein CDXB; caudal type
                     homeobox 4; caudal type homeo box transcription factor 4;
                     caudal type homeobox transcription factor 4"
                     /codon_start=1
                     /product="homeobox protein CHOX-CAD2"
                     /protein_id="NP_989945.1"
                     /db_xref="CGNC:49264"
                     /db_xref="GeneID:395320"
                     /translation="
MYVSSLLDKETSMYPGPARCSNNNLPVQNFVPAPPYSDYMGYHHVPAPDSHGQPAGAWGPHYGPQREDWNAYGPCPGPSGTAAAAQLSGSSPGQGSYSPAEYSSLHPAAPGGLPPAGTVGTQQVSPTNQRHSSYEWMRKTVPTNTTGKTRTKEKYRVVYTDHQRLELEKEFHCNRYITIRRKSELAANLGLSERQVKIWFQNRRAKERKIIKKKISQFDGSGGSVQSDSGSLSPNEITSSLFPPPHGINVLQSADIHQVIVSE"
     misc_feature    183..587
                     /gene="CDX4B"
                     /gene_synonym="cCdx-B; CDX4; CDXB; CHOX-CAD2; ox-cad2"
                     /note="Caudal like protein activation region; Region:
                     Caudal_act; pfam04731"
                     /db_xref="CDD:428094"
     misc_feature    order(606..617,621..623,672..674,690..692,729..731,
                     735..740,747..752,756..764,768..770)
                     /gene="CDX4B"
                     /gene_synonym="cCdx-B; CDX4; CDXB; CHOX-CAD2; ox-cad2"
                     /note="DNA binding site [nucleotide binding]"
                     /db_xref="CDD:238039"
     misc_feature    order(609..611,618..620,738..740,747..752,759..761)
                     /gene="CDX4B"
                     /gene_synonym="cCdx-B; CDX4; CDXB; CHOX-CAD2; ox-cad2"
                     /note="specific DNA base contacts [nucleotide binding];
                     other site"
                     /db_xref="CDD:238039"
     misc_feature    612..770
                     /gene="CDX4B"
                     /gene_synonym="cCdx-B; CDX4; CDXB; CHOX-CAD2; ox-cad2"
                     /note="Homeobox domain; Region: Homeobox; pfam00046"
                     /db_xref="CDD:425441"
     exon            586..731
                     /gene="CDX4B"
                     /gene_synonym="cCdx-B; CDX4; CDXB; CHOX-CAD2; ox-cad2"
                     /inference="alignment:Splign:2.1.0"
     exon            732..2614
                     /gene="CDX4B"
                     /gene_synonym="cCdx-B; CDX4; CDXB; CHOX-CAD2; ox-cad2"
                     /inference="alignment:Splign:2.1.0"
ORIGIN      
acagttgataataaaagaggatgaagtagaagattccaagcagtttggcactattaggaaaaaaaatcaagctactattttttaagcagcaaaagaaaatacagaagagcaagatgttgtgacaacgtttacaatctgcaagcatcatgtatgtgagctctctcttggataaagagaccagcatgtatccaggacctgcaaggtgcagcaacaacaacctgccagtgcagaactttgtgcctgctcccccctactcagactacatggggtatcaccacgtgccagctccagacagccacggacagcccgcgggagcctggggaccccactacggcccccagagggaggactggaacgcttacggcccgtgcccagggccctccggcacggctgctgccgcacagctcagcggctcctctcctgggcagggctcctacagtccagctgagtacagctccctccatcccgctgcacccggggggttacctcctgcaggcaccgttggcacacagcaggtctcacccaccaaccaaaggcacagctcttacgaatggatgaggaaaacggtgccaactaacactactggtaaaacaagaacaaaagagaagtaccgggttgtttacacagaccatcagagactagaattagagaaggaatttcactgcaacagatacattacaataaggagaaagtcagaacttgcagcaaaccttggactatctgaaagacaggtaaaaatctggttccagaatcgccgagccaaagaaagaaaaataatcaagaagaaaatctctcagtttgatggcagtgggggctcagttcagagtgactctggttcactcagccctaatgaaataacaagttccctgttcccaccaccacacggaataaatgtattacagtctgctgacatccatcaggtcatagtttcagaatgaacagtgggggaaaaagaaaaacagaaaaaaagagttgtatggattttttgtttttgtttttaactccctctattgaaaactcaattttgcaaagcaccattcttgtttaactaccttcagagtacttatttccacatagaggatctggaactattaccaaaatatttcaattaaagaaatctcagggagttcgtgctgctgctaatactcatcactcaaaatcttttgaatagaagataatttacatcagataccgaagcagaaaaagatactgctgaagattcaagcaaacctaattctagtctgctcatgtatacaaagaaaactgtcagtgaattgattatagagtaatactgcataaaatgtaagatgctggatgtatttagtttgttacattttatataattaaacagtagattttataaatattcacatttaatgtgtactgaaaattaagtcattttttgaaaacaactttttaaacacttaaacactcaagagacataacaatgttacgcctggcgacacattgcgtcccattaaataaaatgaatagtctttgtattctatgcagttctatccaagcatggcagtctcctaagcaacagatatataacaacacaccaagcctgataaaatttgttcagttgtaaaaaaaaaatgcaacaaactgtgatgtgtgttaataaataccaaatagtttgaagatgtaaatattacttgtacttccatcttcagtgaacgcatgtaataccatcgaaaaattagaggagaaatgtaatggaaatagaactgttactaccatcacactaccaaaaagcaaattaagaatttgattaatatctctacagctttctcaaataacagacatgagccaccaatttcatgtgtgacacttatttcaggttaaaaggcagactttgtatttcaaagctgttattgagcagcttagcattcactgtcacagcaagcacgtacctaatgtgtgctccagaaggagcacaaatttgggataaacatgctcacagagcggttagcttttgttactggtccacactgtcagaggagatagtatcagtatctagaaggcaactgatgagactgaaaaaagtagcaagaaaacacaaagtgctagaaaaaacctagacatttcagtagtcctacttatgggcatttcctaatatgagcttctctgctgcacagaattaagtgctccatataaaagccttcatttcattggaaaggttatcaaaaaagaaaaatagaaagtacagttatctggcatatgaaaattcatacatcactcttcatttcaacagcatcagactcctggtcttagaaataacaggtcaaattctgcttagtgtcaccatgcatagataatgcactgagcaacaacaggcagaacttgtcacagcattcattatcttgattcaatacatctgcaaactaagatttgccaattatttaaagataactctattggagtaactccataaaaataattcagtcaggaactactagaataacatttctccaaaaggcattttgtgggtcattctccaatgtatttttattaatcgcctattaatgtggttgaaataaacagacatatattaatgtaaagaaactgcaaatggaaaaacatacaaatataaatatttgtaaaaactgaa
//

by @meso_cacase at DBCLS
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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]