LOCUS       NM_001243724            1375 bp    mRNA    linear   VRT 13-OCT-2024
DEFINITION  Gallus gallus retina and anterior neural fold homeobox (RAX), mRNA.
ACCESSION   NM_001243724
VERSION     NM_001243724.2
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 1375)
  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 1375)
  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 1375)
  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 1375)
  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
REFERENCE   5  (bases 1 to 1375)
  AUTHORS   Peale,F.V. Jr., Mason,K., Hunter,A.W. and Bothwell,M.
  TITLE     Multiplex display polymerase chain reaction amplifies and resolves
            related sequences sharing a single moderately conserved domain
  JOURNAL   Anal Biochem 256 (2), 158-168 (1998)
   PUBMED   9473273
COMMENT     VALIDATED REFSEQ: This record has undergone validation or
            preliminary review. The reference sequence was derived from
            JAENSK010000086.1.
            
            On Nov 27, 2021 this sequence version replaced NM_001243724.1.
            
            ##Evidence-Data-START##
            Transcript exon combination :: AF420600.1, AB020318.1 [ECO:0000332]
            RNAseq introns              :: single sample supports all introns
                                           SAMEA103992393, SAMEA103992482
                                           [ECO:0000348]
            ##Evidence-Data-END##
            
            ##RefSeq-Attributes-START##
            CDS uses downstream in-frame AUG :: upstream AUG and CDS extension
                                                is not conserved
            ##RefSeq-Attributes-END##
PRIMARY     REFSEQ_SPAN         PRIMARY_IDENTIFIER PRIMARY_SPAN        COMP
            1-448               JAENSK010000086.1  968323-968770       c
            449-678             JAENSK010000086.1  967999-968228       c
            679-1375            JAENSK010000086.1  966918-967614       c
FEATURES             Location/Qualifiers
     source          1..1375
                     /organism="Gallus gallus"
                     /mol_type="mRNA"
                     /db_xref="taxon:9031"
                     /chromosome="Z"
                     /map="Z"
     gene            1..1375
                     /gene="RAX"
                     /gene_synonym="cRax; cRax1; cRax2; orx; RAX2; RX1; RX2"
                     /note="retina and anterior neural fold homeobox"
                     /db_xref="CGNC:62091"
                     /db_xref="GeneID:100677794"
     exon            1..448
                     /gene="RAX"
                     /gene_synonym="cRax; cRax1; cRax2; orx; RAX2; RX1; RX2"
                     /inference="alignment:Splign:2.1.0"
     misc_feature    19..21
                     /gene="RAX"
                     /gene_synonym="cRax; cRax1; cRax2; orx; RAX2; RX1; RX2"
                     /note="upstream_AUG_codon; putative N-terminal extension:
                     MPCLPPPGRSGAGPRLPCRPPPLGTPPPPRGGQPAAPRRAVPEPPAPPRAGRP"
     CDS             178..1131
                     /gene="RAX"
                     /gene_synonym="cRax; cRax1; cRax2; orx; RAX2; RX1; RX2"
                     /note="retinal homeobox protein Rx2; orthodenticle-related
                     homeobox protein"
                     /codon_start=1
                     /product="retinal homeobox protein Rx1"
                     /protein_id="NP_001230653.1"
                     /db_xref="CGNC:62091"
                     /db_xref="GeneID:100677794"
                     /translation="

MHPPGAPLAMAEGAFSLSAPAARSPGGNPSRLHSIEAILGFTKDDGLLGPFQPDGGAGSAKEAADKRGPRHCLPKGPAEPPPAEHQGRFQEPYCPGSASPELPAGDGGDGKPSDEEQPKKKHRRNRTTFTTYQLHELERAFEKSHYPDVYSREELAMKVNLPEVRVQVWFQNRRAKWRRQEKLEVSSMKLQDSPILSFSRSPQAAPVGALGGSLPLETWLGPPVPGGAALQSLPGFAAPPQGLPASYTPPPFLNSPAVTHALQPLGAMGPPPPYQCGAAFVDKFPLDEGDPRNTSIASLRMKAKEHIQSIGKPWQTI"

     misc_feature    274..297
                     /gene="RAX"
                     /gene_synonym="cRax; cRax1; cRax2; orx; RAX2; RX1; RX2"
                     /note="propagated from UniProtKB/Swiss-Prot (Q9PVX0.1);
                     Region: Octapeptide motif"
     misc_feature    307..558
                     /gene="RAX"
                     /gene_synonym="cRax; cRax1; cRax2; orx; RAX2; RX1; RX2"
                     /note="propagated from UniProtKB/Swiss-Prot (Q9PVX0.1);
                     Region: Disordered. /evidence=ECO:0000256|SAM:MobiDB-lite"
     misc_feature    544..714
                     /gene="RAX"
                     /gene_synonym="cRax; cRax1; cRax2; orx; RAX2; RX1; RX2"
                     /note="Region: Homeodomain; pfam00046"
                     /db_xref="CDD:459649"
     misc_feature    1045..1095
                     /gene="RAX"
                     /gene_synonym="cRax; cRax1; cRax2; orx; RAX2; RX1; RX2"
                     /note="OAR motif; Region: OAR; pfam03826"
                     /db_xref="CDD:461067"
     misc_feature    1057..1098
                     /gene="RAX"
                     /gene_synonym="cRax; cRax1; cRax2; orx; RAX2; RX1; RX2"
                     /note="propagated from UniProtKB/Swiss-Prot (Q9PVX0.1);
                     Region: OAR.
                     /evidence=ECO:0000255|PROSITE-ProRule:PRU00138"
     misc_feature    1075..1089
                     /gene="RAX"
                     /gene_synonym="cRax; cRax1; cRax2; orx; RAX2; RX1; RX2"
                     /note="propagated from UniProtKB/Swiss-Prot (Q9PVX0.1);
                     Region: Nuclear localization signal.
                     /evidence=ECO:0000255"
     exon            449..678
                     /gene="RAX"
                     /gene_synonym="cRax; cRax1; cRax2; orx; RAX2; RX1; RX2"
                     /inference="alignment:Splign:2.1.0"
     exon            679..1375
                     /gene="RAX"
                     /gene_synonym="cRax; cRax1; cRax2; orx; RAX2; RX1; RX2"
                     /inference="alignment:Splign:2.1.0"
ORIGIN      

gccggcggggccctggggatgccctgcctccccccgccgggccggagcggcgcggggcctcgccttccctgtcgcccaccgcccctcggcactcctcccccgccccgaggagggcagcccgccgcgccgcgccgtgccgtgccagagccgcccgcgccgccccgggccggccgccccatgcaccctcccggcgccccgctcgccatggccgagggcgctttctcgctgtcggctccggcggcgcgcagccccggggggaacccgtcgaggctgcacagcatcgaggccatcctggggttcaccaaggatgacggcctcctgggccccttccagcccgacggcggcgccggcagcgccaaggaggcggcggacaagcgggggccgcggcactgcctcccgaagggacccgcggagccgccgccggctgagcaccagggccgcttccaagagccgtactgcccgggcagcgccagccccgagctgcccgccggcgacggcggcgacgggaagccgtcggacgaggagcagcccaagaagaagcaccggcggaaccgcaccaccttcaccacctaccagctccacgagctggagcgcgccttcgagaagtcgcactaccccgacgtgtacagccgcgaggagctggccatgaaggtcaacctgcccgaggtccgcgtgcaggtgtggtttcagaaccgtcgggccaagtggcggcggcaggagaagctggaggtgagctccatgaagctgcaggactcgccgatcctctccttcagccgctccccgcaggcggccccggtgggcgcgctgggcggcagcctgccgctggagacgtggctcggtccgcccgtgcccggcggcgcggccctgcagagcctgcccggcttcgcggcccctcctcaggggctgcctgccagctacacaccaccacccttcctgaactctccggccgtgacccacgcgctgcagcccctgggagccatggggccgccgccgccctaccagtgcggggccgcctttgtggacaagttccccctggacgaaggggacccgcgcaacaccagcattgcctccttgcgtatgaaggccaaggagcacatccagtccatcggcaagccctggcagaccatctgagccccctccctgcactgggatgcggccgccgagagcgccggtgccgggaggccgtgggacgcccccgacccgctccgctgccgacatcaccgcgcgtcccgactttgtatttcgtggtcctctgaaccccctttgccgtgtgccccgcggagctggggccgggctgtagcttaggaagagctctcccactgtcccttgttggctggatgctttagtcgcaataaaagctgcagtagggcgcaga

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