2024-09-28 11:21:51, GGRNA.v2 : RefSeq release 225 (Jul, 2024)
LOCUS NM_001168257 1339 bp mRNA linear ROD 04-JUN-2024 DEFINITION Mus musculus transmembrane protein 40 (Tmem40), transcript variant 3, mRNA. ACCESSION NM_001168257 VERSION NM_001168257.1 KEYWORDS RefSeq. SOURCE Mus musculus (house mouse) ORGANISM Mus musculus Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus. REFERENCE 1 (bases 1 to 1339) AUTHORS Carninci,P., Waki,K., Shiraki,T., Konno,H., Shibata,K., Itoh,M., Aizawa,K., Arakawa,T., Ishii,Y., Sasaki,D., Bono,H., Kondo,S., Sugahara,Y., Saito,R., Osato,N., Fukuda,S., Sato,K., Watahiki,A., Hirozane-Kishikawa,T., Nakamura,M., Shibata,Y., Yasunishi,A., Kikuchi,N., Yoshiki,A., Kusakabe,M., Gustincich,S., Beisel,K., Pavan,W., Aidinis,V., Nakagawara,A., Held,W.A., Iwata,H., Kono,T., Nakauchi,H., Lyons,P., Wells,C., Hume,D.A., Fagiolini,M., Hensch,T.K., Brinkmeier,M., Camper,S., Hirota,J., Mombaerts,P., Muramatsu,M., Okazaki,Y., Kawai,J. and Hayashizaki,Y. TITLE Targeting a complex transcriptome: the construction of the mouse full-length cDNA encyclopedia JOURNAL Genome Res 13 (6B), 1273-1289 (2003) PUBMED 12819125 REFERENCE 2 (bases 1 to 1339) AUTHORS Thut,C.J., Rountree,R.B., Hwa,M. and Kingsley,D.M. TITLE A large-scale in situ screen provides molecular evidence for the induction of eye anterior segment structures by the developing lens JOURNAL Dev Biol 231 (1), 63-76 (2001) PUBMED 11180952 COMMENT VALIDATED REFSEQ: This record has undergone validation or preliminary review. The reference sequence was derived from BY279100.1, CV561368.1 and AC109169.13. Transcript Variant: This variant (3) lacks an alternate in-frame exon compared to variant 1. The resulting isoform (b) has the same N- and C-termini but is shorter compared to isoform a. Sequence Note: This RefSeq record was created from transcript and genomic sequence data to make the sequence consistent with the reference genome assembly. The genomic coordinates used for the transcript record were based on transcript alignments. ##Evidence-Data-START## Transcript exon combination :: CV561368.1 [ECO:0000332] RNAseq introns :: single sample supports all introns SAMN01164143 [ECO:0000348] ##Evidence-Data-END## COMPLETENESS: complete on the 3' end. PRIMARY REFSEQ_SPAN PRIMARY_IDENTIFIER PRIMARY_SPAN COMP 1-70 BY279100.1 1-70 71-899 CV561368.1 13-841 900-1339 AC109169.13 135332-135771 FEATURES Location/Qualifiers source 1..1339 /organism="Mus musculus" /mol_type="mRNA" /strain="C57BL/6" /db_xref="taxon:10090" /chromosome="6" /map="6 53.68 cM" gene 1..1339 /gene="Tmem40" /gene_synonym="9030407H20Rik" /note="transmembrane protein 40" /db_xref="GeneID:94346" /db_xref="MGI:MGI:2137870" exon 1..194 /gene="Tmem40" /gene_synonym="9030407H20Rik" /inference="alignment:Splign:2.1.0" misc_feature 101..103 /gene="Tmem40" /gene_synonym="9030407H20Rik" /note="upstream in-frame stop codon" exon 195..272 /gene="Tmem40" /gene_synonym="9030407H20Rik" /inference="alignment:Splign:2.1.0" CDS 203..805 /gene="Tmem40" /gene_synonym="9030407H20Rik" /note="isoform b is encoded by transcript variant 3" /codon_start=1 /product="transmembrane protein 40 isoform b" /protein_id="NP_001161729.1" /db_xref="CCDS:CCDS51879.1" /db_xref="GeneID:94346" /db_xref="MGI:MGI:2137870" /translation="
MEASGSSSQSQDSGGVHRETEDHYQETELHKHHGKARERYKRDKSSSSSSSSSSSSSSSSSSSSSSSGADHGELEVLKDELQLCGGAAGEMVPTGESGLRRRGSGSAEGEVEASQLRRLNIKKDDEFFHFVLLCFAIGALLVCYHYYADWFMSLGVGLLTFASLETIGIYFGLVYRIHSVLQGFIPLLQKFRLPGFRRTN"
misc_feature 440..799 /gene="Tmem40" /gene_synonym="9030407H20Rik" /note="Transmembrane protein 40 family; Region: TMEM40; pfam15817" /db_xref="CDD:464892" exon 273..404 /gene="Tmem40" /gene_synonym="9030407H20Rik" /inference="alignment:Splign:2.1.0" exon 405..458 /gene="Tmem40" /gene_synonym="9030407H20Rik" /inference="alignment:Splign:2.1.0" exon 459..494 /gene="Tmem40" /gene_synonym="9030407H20Rik" /inference="alignment:Splign:2.1.0" exon 495..527 /gene="Tmem40" /gene_synonym="9030407H20Rik" /inference="alignment:Splign:2.1.0" exon 528..575 /gene="Tmem40" /gene_synonym="9030407H20Rik" /inference="alignment:Splign:2.1.0" exon 576..647 /gene="Tmem40" /gene_synonym="9030407H20Rik" /inference="alignment:Splign:2.1.0" exon 648..722 /gene="Tmem40" /gene_synonym="9030407H20Rik" /inference="alignment:Splign:2.1.0" exon 723..785 /gene="Tmem40" /gene_synonym="9030407H20Rik" /inference="alignment:Splign:2.1.0" exon 786..1339 /gene="Tmem40" /gene_synonym="9030407H20Rik" /inference="alignment:Splign:2.1.0" regulatory 917..922 /regulatory_class="polyA_signal_sequence" /gene="Tmem40" /gene_synonym="9030407H20Rik" /note="hexamer: AATAAA" polyA_site 943 /gene="Tmem40" /gene_synonym="9030407H20Rik" /note="major polyA site" ORIGIN
ttcgctgctgtgaatagacaagggaatggctattcagcactttcagagagtggccggtggacacagaaactatctgcccaccacgagctgacagaggatctgactcctcctatcaactctgcagcgagggcaagagcaagcagaaagcaggccagaggcatggactgacatctcaccaagagaaaggaaaggagggaaagtcatggaggcttcaggatcttcttcccagtctcaagacagtggtggagtccacagggaaacggaagatcactaccaagagacagagctccacaagcatcatgggaaggcccgggagcgatataagagagacaagtcttcctcttcatcctcatcctcgtcatcttcttcctcctcttcctcctcatcttcttcctcctcctcaggtgccgaccatggggaactggaagtgctaaaggacgagcttcagctctgcggaggtgctgctggggaaatggtgcctactggggagtcaggactccgaaggagaggttccggctcagcggagggagaagtggaggcctctcagttaagaagactgaacataaagaaggatgatgagtttttccattttgtccttctctgctttgccatcggagccttgctggtgtgttaccactactatgcagactggttcatgtccctcggggtcggcctgctcacctttgcttctctcgagaccattggcatctatttcgggctcgtgtaccggatccacagcgtgcttcagggcttcatccccctccttcagaagttccggctgccagggttcaggagaactaactgagatcactgcctgacagcagctgagccagtccccaatgtgaccactgtaaccactgccatgcctgagcccagaagacagaacgacgcgctggaagacaccagaaggccacacaataaagagctctttccttccacgtgatctgagtgtcggcaccagtgggcaggctcttgctctgcagattaacacgcagtctccgtggggaagagaagaggggatagcgtcgggtcagcacggaggagctgggatgccattgctcataggtcaacatgaatcctgggttctgcaggctggcatctgcgggcctgggtctctctggtgtcctcaggccatgcccaggagctcacagttcctgcagagccttcttgggacagccattctgaggcagggagctaccaggctgggttcccaggggaacttgttgcaggtaagacgctggggaccaaagctgcggacccatcatagctgaccaaccctgttgcccttggactcctaaaatccaaataaattttctgttccttgtgcttaaaaaaaaaa
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Creative Commons Attribution 4.0 International License (CC BY 4.0).
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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