2024-04-28 01:10:52, GGRNA.v2 : RefSeq release 222 (Jan, 2024)
LOCUS XM_017601557 3914 bp mRNA linear ROD 11-JUN-2023 DEFINITION PREDICTED: Rattus norvegicus discoidin domain receptor tyrosine kinase 1 (Ddr1), transcript variant X3, mRNA. ACCESSION XM_017601557 VERSION XM_017601557.2 DBLINK BioProject: PRJNA677964 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. COMMENT MODEL REFSEQ: This record is predicted by automated computational analysis. This record is derived from a genomic sequence (NC_051355.1) annotated using gene prediction method: Gnomon, supported by EST evidence. Also see: Documentation of NCBI's Annotation Process On Jan 21, 2021 this sequence version replaced XM_017601557.1. ##Genome-Annotation-Data-START## Annotation Provider :: NCBI RefSeq Annotation Status :: Updated annotation Annotation Name :: GCF_015227675.2-RS_2023_06 Annotation Pipeline :: NCBI eukaryotic genome annotation pipeline Annotation Software Version :: 10.1 Annotation Method :: Best-placed RefSeq; Gnomon; cmsearch; tRNAscan-SE Features Annotated :: Gene; mRNA; CDS; ncRNA Annotation Date :: 06/06/2023 ##Genome-Annotation-Data-END## FEATURES Location/Qualifiers source 1..3914 /organism="Rattus norvegicus" /mol_type="mRNA" /strain="BN/NHsdMcwi" /db_xref="taxon:10116" /chromosome="20" /sex="male" /tissue_type="kidney" /country="USA: Wisconsin, Milwaukee, Medical College of Wisconsin" /collection_date="2019-03-08" /collected_by="Rebecca Schilling" gene 1..3914 /gene="Ddr1" /gene_synonym="Cak; Drd1; PTK3D" /note="discoidin domain receptor tyrosine kinase 1; Derived by automated computational analysis using gene prediction method: Gnomon. Supporting evidence includes similarity to: 56 ESTs, 6 long SRA reads, 23 Proteins, and 100% coverage of the annotated genomic feature by RNAseq alignments, including 100 samples with support for all annotated introns" /db_xref="GeneID:25678" /db_xref="RGD:2252" CDS 396..3128 /gene="Ddr1" /gene_synonym="Cak; Drd1; PTK3D" /codon_start=1 /product="epithelial discoidin domain-containing receptor 1 isoform X1" /protein_id="XP_017457046.1" /db_xref="GeneID:25678" /db_xref="RGD:2252" /translation="
MGTGTLSSLLLLLLLVTIGDADMKGHFDPAKCRYALGMQDRTIPDSDISVSSSWSDSTAARHSRLESSDGDGAWCPAGPVFPKEEEYLQVDLRRLHLVALVGTQGRHAGGLGKEFSRSYRLRYSRDGRRWMDWKDRWGQEVISGNEDPGGVVLKDLGPPMVARLVRFYPRADRVMSVCLRVELYGCLWRDGLLSYTAPVGQTMQLSEMVYLNDSTYDGYTAGGLQYGGLGQLADGVVGLDDFRQSQELRVWPGYDYVGWSNHSFPSGYVEMEFEFDRLRSFQTMQVHCNNMHTLGARLPGGVECRFKRGPAMAWEGEPVRHALGGSLGDPRARAISVPLGGHVGRFLQCRFLFAGPWLLFSEISFISDVVNDSSDTFPPAPWWPPGPPPTNFSSLELEPRGQQPVAKAEGSPTAILIGCLVAIILLLLLIIALMLWRLHWRRLLSKAERRVLEEELTVHLSVPGDTILINNRPGPREPPPYQEPRPRGTPTHSAPCVPNGSALLLSNPAYRLLLATYARPPRGPGPPTPAWAKPTNTQACSGDYMEPEKPGAPLLPPPPQNSVPHYAEADIVTLQGVTGGNTYAVPALPPGAVGDGPPRVDFPRSRLRFKEKLGEGQFGEVHLCEVEDPQDLVTSDFPISVQKGHPLLVAVKILRPDATKNARNDFLKEVKIMSRLKDPNIIRLLGVCVQDDPLCMITDYMENGDLNQFLSAHQLENKVTQGLPGDRESDQGPTISYPMLLHVGAQIASGMRYLATLNFVHRDLATRNCLVGENFTIKIADFGMSRNLYAGDYYRVQGRAVLPIRWMAWECILMGKFTTASDVWAFGVTLWEVLMLCRSQPFGQLTDEQVIENAGEFFRDQGRQVYLSRPPACPQTLYELMLRCWSREPEQRPPFSQLHRFLADDALNTV"
misc_feature 567..950 /gene="Ddr1" /gene_synonym="Cak; Drd1; PTK3D" /note="Coagulation factor 5/8 C-terminal domain, discoidin domain; Cell surface-attached carbohydrate-binding domain, present in eukaryotes and assumed to have horizontally transferred to eubacterial genomes; Region: FA58C; cd00057" /db_xref="CDD:238014" misc_feature order(618..620,711..713,735..737) /gene="Ddr1" /gene_synonym="Cak; Drd1; PTK3D" /note="sugar binding site [chemical binding]; other site" /db_xref="CDD:238014" misc_feature 2196..3107 /gene="Ddr1" /gene_synonym="Cak; Drd1; PTK3D" /note="Catalytic domain of the Protein Tyrosine Kinase, Discoidin Domain Receptor 1; Region: PTKc_DDR1; cd05096" /db_xref="CDD:133227" misc_feature order(2232..2246,2256..2258,2343..2345,2349..2351, 2487..2498,2505..2510,2682..2684,2694..2699,2703..2705, 2736..2738,2790..2804,2829..2831,2934..2936) /gene="Ddr1" /gene_synonym="Cak; Drd1; PTK3D" /note="active site" /db_xref="CDD:133227" misc_feature order(2232..2237,2241..2246,2256..2258,2343..2345, 2349..2351,2487..2498,2505..2510,2694..2699,2703..2705, 2736..2738) /gene="Ddr1" /gene_synonym="Cak; Drd1; PTK3D" /note="ATP binding site [chemical binding]; other site" /db_xref="CDD:133227" misc_feature order(2682..2684,2694..2696,2790..2804,2829..2831, 2934..2936) /gene="Ddr1" /gene_synonym="Cak; Drd1; PTK3D" /note="polypeptide substrate binding site [polypeptide binding]; other site" /db_xref="CDD:133227" misc_feature 2733..2810 /gene="Ddr1" /gene_synonym="Cak; Drd1; PTK3D" /note="activation loop (A-loop); other site" /db_xref="CDD:133227" ORIGIN
gcacccaggaactccctgccagactttccagtcccaacggcttgcccctctgcactgcagggctgtatccccaagggactggtggtgatgcctcttgggttctaggctctccctctagccacccagtcagctcccctcagctgctgcttcagtgatggggtttttcagctgcctcctcttacattcctgccctagagcattgtgggagcagctggaggaggacaaagggctgggggagtctacccccaactcctcctacctcctggggtgacccagcctccctatagtttaagcctgccctcacctccaaggcaactcagtcctctcagccctgggctcttctgctaccttggagatgctgtcccctcctccataggccagagggatcaggagcgatggggacagggaccctctcatctctcctgctgctgctactcttggtgacaattggagatgctgacatgaagggacattttgacccagccaagtgccgctatgccctgggcatgcaggaccgcaccattccagacagcgatatctctgtgtccagctcctggtcggactctaccgccgcccgccacagcaggctggaaagcagtgatggagatggggcttggtgccctgcagggcctgtgttccccaaagaagaggagtacctgcaggtggaccttcgtaggctacacctggtggctctggtgggcacccagggccgccatgctgggggtctgggcaaagagttctcccgaagctaccggttgcgttactcccgagatggccgacgatggatggactggaaagacagatggggtcaggaggtgatttcgggtaacgaggatcctgggggagtggtgctgaaggatctcgggccccccatggtggcccggctggtccgtttctaccccagggctgaccgggtcatgagtgtctgtcttcgggtggagctctatggctgcctctggcgggacggactcttgtcctatacagcccccgtggggcagaccatgcaattatctgagatggtgtatctcaatgattccacttacgatggatatactgctggagggctgcagtacggtggtctgggccaactggcagacggcgtggtggggctggatgatttcaggcagagccaggagctgcgggtttggccaggctatgactatgtgggatggagcaaccatagcttccccagcggctacgtggagatggagtttgagtttgaccggctgaggtctttccagaccatgcaggtccactgtaacaacatgcacactctgggagcccgcctcccaggcggggtggaatgccggtttaaaaggggtccggccatggcctgggaaggagagcctgtacgccatgccctggggggtagccttggagaccccagagccagggccatctcggtgcccctgggtggtcacgtgggccgcttcctgcagtgcagattcctctttgcaggaccctggttactcttcagtgagatctctttcatctcggatgtggtgaacgactcgtctgacaccttcccaccagccccctggtggccgcctggcccgcctcccaccaacttcagcagcttggagctggagccccggggtcaacagcctgtggccaaggcggaggggagcccaactgccatcctcattggctgcctggtggccatcatccttctcctcctccttatcattgccctgatgctctggaggctgcactggcgccggctgctcagcaaggcagagcgccgggtgttggaggaggagctgacggttcacctctctgtccctggggacaccatcctcatcaacaaccgcccagggccccgagagccacccccttaccaggaaccccggcctcgggggactccaactcactctgcgccctgcgtccccaatggctctgcgttgctgctctccaatccggcctaccgcctccttctggccacttacgcccgtccccctcgaggcccgggcccccccacacccgcctgggccaaacccaccaacacccaggcctgcagtggggactacatggagcccgagaagccgggcgccccacttctacccccacctccccagaacagcgtcccccattacgccgaggctgacattgtcaccctgcagggcgtcacagggggcaacacctacgctgttcccgcactgcccccaggggcggttggggatgggccccccagagtggatttccctcggtcacggctccgtttcaaggagaagctcggcgagggccaatttggggaggtacatctctgtgaagtagaggaccctcaagatctggtcactagtgacttccctatcagtgtgcaaaagggacaccccttgctggtggcagtgaagatcctccggccagatgccaccaaaaatgccaggaatgacttcctgaaggaggtaaagatcatgtcacggctgaaggacccaaacatcatccggctcctgggtgtgtgtgtgcaggatgaccctctctgcatgattacagactacatggagaacggtgacctgaaccaattcctcagtgcccaccagctggagaacaaggtcactcaggggcttcctggggacagagagtctgaccaggggcccacaatcagctaccctatgctgttacacgtgggggcccagatcgcctctggcatgcgatatctggccacccttaactttgtgcatcgggacctggccacccggaactgcttggttggggaaaatttcaccatcaaaatcgccgactttggcatgagccggaatctctacgctggggattattaccgtgtacagggccgggcagtgctgcccatcaggtggatggcctgggagtgtatcctcatggggaagttcacaacagccagtgatgtgtgggccttcggagtgaccctgtgggaggtgcttatgctctgcaggtcacagcccttcgggcaactcacagacgagcaggtcatcgagaacgccggcgagttcttcagggaccagggccggcaggtatacttatccaggccacccgcctgcccgcagaccttgtatgagctgatgctccggtgttggagccgggagccggagcagcggccgcccttctcccagcttcatcggttcctggcggatgatgcactcaacacagtgtaaactaaggacctggcagccctttttcactgggagccatccaggggaagctggacactaaaaccagagaagcctatggcaccccgcccaccatctccccgacttgcccattcccaagaggcagtgtctctgcaggtgggctgggcccgcccagggaaccgaagactctgttaccagatacgtgctcccttcctgttcttcctcccacctgccaagctccacccacccagctggccctgtggttgggatcctgcctgacttcttccagctatcccctagggaaagacaggggcgaatgctgggcacacactggacaaggcccactggacaacactggttcctgggaggtgacggtaccccccagcttcttcttgtcacacactggacaccgccagaattgagggggacgagggggacaaggaaggccaaccctctacaatggtcctcagccctggcttccttctgcaccctccgcctctgacacactggacctgggggtgacccctgctgtgatcctcagtcaaacacccctccttcctacctaccaccatgttgccgctagaacttccgcaaagcctctgcgttcctgtggagtaaatattaggatggggaacagatggagcagtagcccgaggccggggggtggggatttctcttgtagctaccacattggtttttctataatcacgtggggtttgtacattttttggggggagagacacagatttttacactaatatatggacctagctcgaggcagttttaatctcctgctctaggcaggtaata
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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.
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