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2021-10-29 03:32:57, GGRNA.v2 : RefSeq release 207 (Jul, 2021)

LOCUS       NM_001039505            2635 bp    mRNA    linear   ROD 10-FEB-2021
DEFINITION  Rattus norvegicus iroquois homeobox 2 (Irx2), mRNA.
ACCESSION   NM_001039505 XM_225077
VERSION     NM_001039505.3
KEYWORDS    RefSeq.
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 2635)
  AUTHORS   Werner S, Stamm H, Pandjaitan M, Kemming D, Brors B, Pantel K and
            Wikman H.
  TITLE     Iroquois homeobox 2 suppresses cellular motility and chemokine
            expression in breast cancer cells
  JOURNAL   BMC Cancer 15, 896 (2015)
   PUBMED   26560478
  REMARK    Publication Status: Online-Only
REFERENCE   2  (bases 1 to 2635)
  AUTHORS   Jolma A, Yan J, Whitington T, Toivonen J, Nitta KR, Rastas P,
            Morgunova E, Enge M, Taipale M, Wei G, Palin K, Vaquerizas JM,
            Vincentelli R, Luscombe NM, Hughes TR, Lemaire P, Ukkonen E,
            Kivioja T and Taipale J.
  TITLE     DNA-binding specificities of human transcription factors
  JOURNAL   Cell 152 (1-2), 327-339 (2013)
   PUBMED   23332764
REFERENCE   3  (bases 1 to 2635)
  AUTHORS   Reggiani L, Raciti D, Airik R, Kispert A and Brandli AW.
  TITLE     The prepattern transcription factor Irx3 directs nephron segment
            identity
  JOURNAL   Genes Dev 21 (18), 2358-2370 (2007)
   PUBMED   17875669
COMMENT     VALIDATED REFSEQ: This record has undergone validation or
            preliminary review. The reference sequence was derived from
            JACYVU010000009.1.
            On Feb 10, 2021 this sequence version replaced NM_001039505.2.
            
            Sequence Note: The RefSeq transcript and protein were derived from
            genomic sequence to make the sequence consistent with the reference
            genome assembly. There are no full-length rat transcripts
            supporting this RefSeq. The genomic coordinates and exon
            combination used for the transcript record were based on alignment
            to full-length mouse mRNA BC085291.1.
            
            ##Evidence-Data-START##
            RNAseq introns :: single sample supports all introns SAMEA5760383,
                              SAMEA5760389 [ECO:0000348]
            ##Evidence-Data-END##
            
            ##RefSeq-Attributes-START##
            inferred exon combination :: based on alignments, homology
            ##RefSeq-Attributes-END##
            COMPLETENESS: complete on the 3' end.
PRIMARY     REFSEQ_SPAN         PRIMARY_IDENTIFIER PRIMARY_SPAN        COMP
            1-519               JACYVU010000009.1  3398845-3399363     c
            520-925             JACYVU010000009.1  3397191-3397596     c
            926-1639            JACYVU010000009.1  3396195-3396908     c
            1640-1715           JACYVU010000009.1  3395510-3395585     c
            1716-2635           JACYVU010000009.1  3393945-3394864     c
FEATURES             Location/Qualifiers
     source          1..2635
                     /organism="Rattus norvegicus"
                     /mol_type="mRNA"
                     /strain="BN"
                     /db_xref="taxon:10116"
                     /chromosome="1"
                     /map="1p11"
     gene            1..2635
                     /gene="Irx2"
                     /note="iroquois homeobox 2"
                     /db_xref="GeneID:306657"
                     /db_xref="RGD:1309834"
     exon            1..519
                     /gene="Irx2"
                     /inference="alignment:Splign:2.1.0"
     misc_feature    142..144
                     /gene="Irx2"
                     /note="upstream in-frame stop codon"
     CDS             268..1692
                     /gene="Irx2"
                     /note="Iroquois related homeobox 2; Iroquois related
                     homeobox 5"
                     /codon_start=1
                     /product="iroquois-class homeodomain protein IRX-2"
                     /protein_id="NP_001034594.1"
                     /db_xref="GeneID:306657"
                     /db_xref="RGD:1309834"
                     /translation="
MSYPQGYLYQAPGSLALYSCPAYGASALAAPRSEELARSASGSAFSPYPGSAAFTAQAATGFGSPLQYSADAAAAAAAGFPSYMGSPYDTHTTGMTGAISYHPYGSAAYPYQLNDPAYRKNATRDATATLKAWLNEHRKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKKENKMTWAPRNKSEDEDEDEGDASRSKEENPDKAQDGTETSAEDEGISLHVDSLTDHSCSAESDGEKLPCRAGDPLCESGSECKDKFEDLEDEEDDEDECERDLVPPKPVTSSPLTGVEAPLLSPAPEAAPRGGSGGKTPLGSRTSPGAPPPASKPKLWSLAEIATSDLKQPSLGPGCGPPGLPAAAAPASSGAPPGGSPYSASPLLGRHLYYTSPFYGNYTNYGNLNAALQGQGLLRYNTAASSPGETLHAIPKAASDAGKAGSHSLESHYRPPGGGYEPKKDASEGCAVVGAGVQPYL"
     misc_feature    <610..918
                     /gene="Irx2"
                     /note="Homeodomain-containing transcription factor
                     [Transcription]; Region: COG5576"
                     /db_xref="CDD:227863"
     misc_feature    order(622..627,631..633,691..693,709..711,748..750,
                     754..759,766..771,775..783,787..792)
                     /gene="Irx2"
                     /note="DNA binding site [nucleotide binding]"
                     /db_xref="CDD:238039"
     misc_feature    order(628..630,757..759,766..771,778..780)
                     /gene="Irx2"
                     /note="specific DNA base contacts [nucleotide binding];
                     other site"
                     /db_xref="CDD:238039"
     misc_feature    664..783
                     /gene="Irx2"
                     /note="Homeobox KN domain; Region: Homeobox_KN; pfam05920"
                     /db_xref="CDD:283551"
     misc_feature    1240..1293
                     /gene="Irx2"
                     /note="Motif in Iroquois-class homeodomain proteins
                     (only). Unknown function; Region: IRO; smart00548"
                     /db_xref="CDD:214716"
     exon            520..925
                     /gene="Irx2"
                     /inference="alignment:Splign:2.1.0"
     exon            926..1639
                     /gene="Irx2"
                     /inference="alignment:Splign:2.1.0"
     exon            1640..1715
                     /gene="Irx2"
                     /inference="alignment:Splign:2.1.0"
     exon            1716..2635
                     /gene="Irx2"
                     /inference="alignment:Splign:2.1.0"
ORIGIN      
gagcgctccttcctcaactcctcactcctgactgcagactcccccaaatcccgaccgccggcctggcgcgcggctgcgcccaccggctccgctctgctgccgccgccgccgccccaccgatccgccagccccgcgcccagctagcgccctccagtccagcctgccccgacccacggccccggtgcgccccggccgggcgtggatggagggcgccgcgcgcgctgcccgctgctccgtgtgacgcgggccctgcgcccggcgcccaccatgtcctacccgcagggctacctgtaccaagcgcccggctcgctggcgctctactcgtgccccgcgtacggcgcgtccgcgctggcggcgccgcgcagcgaagagctggcgcgctcggcttcgggctccgcgttcagtccgtaccccggctcagcggccttcacagcgcaggcggccaccggcttcggcagcccgctgcagtactcggccgacgctgccgccgccgccgctgccggcttcccgtcctacatgggctcgccatacgacacgcacaccaccggaatgactggcgccatcagttatcacccatatggcagcgcggcctacccataccagcttaacgaccccgcgtaccgcaagaacgccacgcgggacgccactgccacactgaaagcctggctcaacgaacaccgcaagaacccgtaccccaccaagggagagaagatcatgctggccatcatcaccaagatgaccctcacgcaggtttccacctggttcgccaacgcgcgccggcgcctcaagaaggagaacaaaatgacctgggccccgaggaacaaaagcgaagacgaggacgaggacgagggagatgcttccagaagcaaggaggagaatccagacaaggcacaggacggcacagagacctccgcggaggacgaagggatcagtctacacgtcgactcgctcaccgaccactcgtgctcggcggagtcagatggggagaaattgccctgccgcgccggggatcccttgtgcgaatcgggctctgagtgtaaggacaagtttgaggacctggaggatgaggaggacgatgaagacgagtgcgagcgggatctggtgccgcccaagcccgtaacctcctcgcccctcaccggcgtggaggcacccctgctgagcccggcgcccgaagccgcgccgcgcggtggtagcggtggcaagacgcccctaggcagccggacgtcgcctggagcgccgccgcctgccagcaagcccaagctgtggtcgctggccgagatagccacgtcggacctcaagcaaccaagcttgggcccagggtgcgggcctccgggtctgcccgctgccgccgcgcctgcctcgtctggggcccctccgggaggctcgccctactctgcttcgccgctgctgggccgccacctctattacacgtcccctttctatggcaactacacaaactacgggaacttaaacgcagcgctccaaggccagggccttctgcggtacaataccgcggcctcctcaccaggcgagacactgcacgccatcccaaaggcggccagcgacgcgggcaaggcgggctcgcattcgctggagtcccactacaggcctccgggcggcggctacgagcccaagaaagatgccagtgagggctgtgcagttgttggtgcaggcgtccagccctacctataggagggccaagctcagcagtgcaagtaggtgtcacaattgctttggaaaaaaaaagtcaggaggccattctcccttcccaagctcataaatacacagatacaaaccccagatgtggaaatgcggaccacattttgtgccactgtatagaggatgcagactgcactgccaacccacagactctaaggactggacacacgttgtttgggcatatgagaactcgttggcatagtatagcttccctatgtttgtgtgacttttggaaacaatctgttttttctcaggatatcttcacttcattgccacggtatatattctataggtgtgatagaacttgctgtaaaatttatttgtaaaaaaaaatgtacacggtagaactaatgtgattgaagaacttgggtccttcagaagtggaaacaaatttgatatttatttttataatgacataaagcttctagtaatttatgcaagttgtattgcaatgaaatctaaaacttttgtaaataaattctgcctggtttttatttgaacattgctggttatacaatctctgttggttgtttaacatgaattctctactaatttatatctaaaactgtaaataaaaacagatgagcctacaagaaaatggtgttcggggctcatttttcctggagagccattctggtaggagctacagtgttgaccctggttcctgccccaaaggtgatcctagctcaccttttaagtgaagagcccagtgaaataaacttccttctcaagcttatttgaaaattgcagacctgagagagattaatgtgcaacagggaaaatacctatgctttagtttatttacaggcaaatgtgtctcgagaaagtaattcaggtttttgttctctgaatatgcaaatcccttcttagtgtaaatttctaaaacatgaaaaaaaataaaaggatatgtcacctc
//

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]