LOCUS       NM_204104               1973 bp    mRNA    linear   VRT 08-APR-2024
DEFINITION  Gallus gallus retina and anterior neural fold homeobox 2 (RAX2),
            mRNA.
ACCESSION   NM_204104 XM_428732
VERSION     NM_204104.3
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 1973)
  AUTHORS   Tang,H., Finn,R.D. and Thomas,P.D.
  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   2  (bases 1 to 1973)
  AUTHORS   Burge,S., Kelly,E., Lonsdale,D., Mutowo-Muellenet,P., McAnulla,C.,
            Mitchell,A., Sangrador-Vegas,A., Yong,S.Y., 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   3  (bases 1 to 1973)
  AUTHORS   Chen,C.M. and Cepko,C.L.
  TITLE     The chicken RaxL gene plays a role in the initiation of
            photoreceptor differentiation
  JOURNAL   Development 129 (23), 5363-5375 (2002)
   PUBMED   12403708
REFERENCE   4  (bases 1 to 1973)
  AUTHORS   Ohuchi,H., Tomonari,S., Itoh,H., Mikawa,T. and Noji,S.
  TITLE     Identification of chick rax/rx genes with overlapping patterns of
            expression during early eye and brain development
  JOURNAL   Mech Dev 85 (1-2), 193-195 (1999)
   PUBMED   10415362
COMMENT     VALIDATED REFSEQ: This record has undergone validation or
            preliminary review. The reference sequence was derived from
            JAENSK010000374.1.
            
            On Nov 24, 2021 this sequence version replaced NM_204104.2.
            
            Sequence Note: The RefSeq transcript and protein were derived from
            genomic sequence to make the sequence consistent with the reference
            genome assembly. The genomic coordinates used for the transcript
            record were based on alignments.
            
            ##Evidence-Data-START##
            Transcript exon combination :: AF420601.1, SRR13267662.11140.1
                                           [ECO:0000332]
            RNAseq introns              :: single sample supports all introns
                                           SAMEA103992290, SAMEA3109051
                                           [ECO:0000348]
            ##Evidence-Data-END##
PRIMARY     REFSEQ_SPAN         PRIMARY_IDENTIFIER PRIMARY_SPAN        COMP
            1-329               JAENSK010000374.1  929214-929542
            330-356             JAENSK010000374.1  930136-930162
            357-607             JAENSK010000374.1  930982-931232
            608-1973            JAENSK010000374.1  932661-934026
FEATURES             Location/Qualifiers
     source          1..1973
                     /organism="Gallus gallus"
                     /mol_type="mRNA"
                     /db_xref="taxon:9031"
                     /chromosome="28"
                     /map="28"
     gene            1..1973
                     /gene="RAX2"
                     /gene_synonym="cRax1; cRaxL; RAX; RAX1; RAXL; Rx-like;
                     RX1; RX2"
                     /note="retina and anterior neural fold homeobox 2"
                     /db_xref="CGNC:48945"
                     /db_xref="GeneID:373893"
     exon            1..329
                     /gene="RAX2"
                     /gene_synonym="cRax1; cRaxL; RAX; RAX1; RAXL; Rx-like;
                     RX1; RX2"
                     /inference="alignment:Splign:2.1.0"
     exon            330..356
                     /gene="RAX2"
                     /gene_synonym="cRax1; cRaxL; RAX; RAX1; RAXL; Rx-like;
                     RX1; RX2"
                     /inference="alignment:Splign:2.1.0"
     misc_feature    347..349
                     /gene="RAX2"
                     /gene_synonym="cRax1; cRaxL; RAX; RAX1; RAXL; Rx-like;
                     RX1; RX2"
                     /note="upstream in-frame stop codon"
     exon            357..607
                     /gene="RAX2"
                     /gene_synonym="cRax1; cRaxL; RAX; RAX1; RAXL; Rx-like;
                     RX1; RX2"
                     /inference="alignment:Splign:2.1.0"
     CDS             365..1051
                     /gene="RAX2"
                     /gene_synonym="cRax1; cRaxL; RAX; RAX1; RAXL; Rx-like;
                     RX1; RX2"
                     /note="retinal homeobox protein Rx1"
                     /codon_start=1
                     /product="retinal homeobox protein Rx2"
                     /protein_id="NP_989435.2"
                     /db_xref="CGNC:48945"
                     /db_xref="GeneID:373893"
                     /translation="

MFLNKCEGDLGELRKPGDSEGTPPAAAEEEQPKKKHRRNRTTFTTYQLHELERAFEKSHYPDVYSREELAMKVNLPEVRVQVWFQNRRAKWRRQEKMEASSMKLHDTPMLSFNRPPMTANVGPMSNSLPLDPWLTSPISSATPVHSIPGFMGAPQALQPPYGGHSFLNTPPGMAQGMQPMAPAPYQCGTPFVDKYPLEDVDQRSSSIASLRMKAKEHIQTIDKTWQPI"

     misc_feature    365..487
                     /gene="RAX2"
                     /gene_synonym="cRax1; cRaxL; RAX; RAX1; RAXL; Rx-like;
                     RX1; RX2"
                     /note="propagated from UniProtKB/Swiss-Prot (Q9PVY0.1);
                     Region: Disordered. /evidence=ECO:0000256|SAM:MobiDB-lite"
     misc_feature    473..643
                     /gene="RAX2"
                     /gene_synonym="cRax1; cRaxL; RAX; RAX1; RAXL; Rx-like;
                     RX1; RX2"
                     /note="Region: Homeodomain; pfam00046"
                     /db_xref="CDD:459649"
     misc_feature    <683..>916
                     /gene="RAX2"
                     /gene_synonym="cRax1; cRaxL; RAX; RAX1; RAXL; Rx-like;
                     RX1; RX2"
                     /note="endolytic peptidoglycan transglycosylase RlpA;
                     Region: PRK10672"
                     /db_xref="CDD:236733"
     misc_feature    965..1015
                     /gene="RAX2"
                     /gene_synonym="cRax1; cRaxL; RAX; RAX1; RAXL; Rx-like;
                     RX1; RX2"
                     /note="OAR motif; Region: OAR; pfam03826"
                     /db_xref="CDD:461067"
     misc_feature    977..1018
                     /gene="RAX2"
                     /gene_synonym="cRax1; cRaxL; RAX; RAX1; RAXL; Rx-like;
                     RX1; RX2"
                     /note="propagated from UniProtKB/Swiss-Prot (Q9PVY0.1);
                     Region: OAR.
                     /evidence=ECO:0000255|PROSITE-ProRule:PRU00138"
     misc_feature    995..1009
                     /gene="RAX2"
                     /gene_synonym="cRax1; cRaxL; RAX; RAX1; RAXL; Rx-like;
                     RX1; RX2"
                     /note="propagated from UniProtKB/Swiss-Prot (Q9PVY0.1);
                     Region: Nuclear localization signal.
                     /evidence=ECO:0000255"
     exon            608..1973
                     /gene="RAX2"
                     /gene_synonym="cRax1; cRaxL; RAX; RAX1; RAXL; Rx-like;
                     RX1; RX2"
                     /inference="alignment:Splign:2.1.0"
ORIGIN      

ccccggcccgcccggcgctggggggacatttagagcaattacttgtccagaaagtaactgtcaatcattcttaaaggggaaggcctccaattaataacctcgtcttaatcctttggactcatttccaatctgcggggccttggtgacatctgcaacactaaataaagattctcccgagccttagcgcggcggttctgtgacaaataagaagactagaggcaactttggctgccaagctgcaagattggtgaggttgagccgcttgtttggttcccaggagggaccggcaaagttaaatactcctggaaaagccgcgtcgggcccagcaggtgtggagctgcgcaaatgagaagcgggcaccaagatgttcctcaataagtgtgagggggacctgggcgagctgcggaagccgggggacagcgaggggacccctccagctgctgctgaggaggaacagcccaagaagaagcaccggcggaaccgcaccacgttcaccacctaccagctgcacgagctggagcgcgccttcgagaagtcccactaccccgacgtgtacagccgcgaggagctggccatgaaggtcaacctgcccgaggtccgcgtgcaggtctggttccagaaccggcgagccaagtggaggcggcaggagaagatggaggccagctccatgaagctccacgacacccccatgctgtccttcaaccggccgcccatgacggccaacgtggggcccatgagcaactccctcccgctcgacccgtggctgacatcgcccatctccagcgccaccccggtgcacagcatccccggcttcatgggagccccccaggccctgcagcccccctatggcgggcactccttcctcaacacccccccgggcatggctcagggcatgcagcccatggcccccgcgccctaccagtgcggcaccccctttgtggacaagtacccgctggaggacgtcgaccagaggagctccagtatcgcctcgctccgcatgaaagccaaggagcacattcagaccatcgacaagacctggcagcccatttgatgaacgctccccactgctccctaccccggggggtgacggcggggtgctcggcaggaccagagcagggaggtgccccccccggacgcagcaccgcggacagcggcacgggggcacccagcagccgccccggcgcggccgcgcaggacctgggggggtccctgcacccctttattattattattattgtcatcaagaagttcttttttttttttccttccttttttttttatgcacaaacagaaacgctctgttttcgtagggaacaaccggggggtgttgtcttttcagccgcgttgggtgcagtgcgggagatgggtgtatggctggtaaggagaagagtgggatgcgctgctctgctcggcgatggggaaatcccccttaacatcacccacactccacatccgcacggagacgccgccgtccccacacatgggtgaccgaatcccggcccgcgtcccgcctgcttgtcagggggaatctgctccgccgtcactccggccctaattgctctccagcggtgccggtggcacaaagctgccgtaattgccgggcggaagggggggggggctcagccccaatgggggcagcggggtcccgatgggagcagggatgggagggcgggtggtggggtgccccgccatggcgctggggatggtgtgtggttggcactgttggggcggcgcgggggcgatggcacacgtgggggcttcggggttccaaacatggaacgtgttggggcagatggggtcggttggggccaaacacggggcagagctgcacccacggctgcggtggcattggggtctcccgatgacaccatccgggctgcgcgctgaccccgtggggacccggctcctcgtccccgtcccccggctgctgctgctcgtctgcttcgttagcgataattaaacctttaacaacc

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