2024-09-28 11:18:48, GGRNA.v2 : RefSeq release 225 (Jul, 2024)
LOCUS NM_183155 3710 bp mRNA linear ROD 03-JUN-2024 DEFINITION Mus musculus nrde-2 necessary for RNA interference, domain containing (Nrde2), transcript variant 2, mRNA. ACCESSION NM_183155 XM_484171 XM_912077 VERSION NM_183155.3 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 3710) AUTHORS Flemr,M., Schwaiger,M., Hess,D., Iesmantavicius,V., Ahel,J., Tuck,A.C., Mohn,F. and Buhler,M. TITLE Mouse nuclear RNAi-defective 2 promotes splicing of weak 5' splice sites JOURNAL RNA 29 (8), 1140-1165 (2023) PUBMED 37137667 REMARK GeneRIF: Mouse nuclear RNAi-defective 2 promotes splicing of weak 5' splice sites. REFERENCE 2 (bases 1 to 3710) AUTHORS Sharov,A.A., Piao,Y., Matoba,R., Dudekula,D.B., Qian,Y., VanBuren,V., Falco,G., Martin,P.R., Stagg,C.A., Bassey,U.C., Wang,Y., Carter,M.G., Hamatani,T., Aiba,K., Akutsu,H., Sharova,L., Tanaka,T.S., Kimber,W.L., Yoshikawa,T., Jaradat,S.A., Pantano,S., Nagaraja,R., Boheler,K.R., Taub,D., Hodes,R.J., Longo,D.L., Schlessinger,D., Keller,J., Klotz,E., Kelsoe,G., Umezawa,A., Vescovi,A.L., Rossant,J., Kunath,T., Hogan,B.L., Curci,A., D'Urso,M., Kelso,J., Hide,W. and Ko,M.S. TITLE Transcriptome analysis of mouse stem cells and early embryos JOURNAL PLoS Biol 1 (3), E74 (2003) PUBMED 14691545 REFERENCE 3 (bases 1 to 3710) AUTHORS Piao,Y., Ko,N.T., Lim,M.K. and Ko,M.S. TITLE Construction of long-transcript enriched cDNA libraries from submicrogram amounts of total RNAs by a universal PCR amplification method JOURNAL Genome Res 11 (9), 1553-1558 (2001) PUBMED 11544199 COMMENT VALIDATED REFSEQ: This record has undergone validation or preliminary review. The reference sequence was derived from AC166349.4, CD546085.1, BU055364.1, CN706272.1, BM933283.1, CK619854.1, DN174402.1, CN710548.1, BG067060.2 and AW989733.1. On Mar 12, 2014 this sequence version replaced NM_183155.2. Transcript Variant: This variant (2) uses an alternate in-frame splice site in the 5' coding region, compared to variant 1, resulting in an isoform (b) that is shorter than isoform a. The exon combination of this variant is inferred based on tiled partial transcript alignments. 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 :: SRR7652917.760103.1, ERR3363658.1574652.1 [ECO:0000332] RNAseq introns :: single sample supports all introns SAMN01164139 [ECO:0000348] ##Evidence-Data-END## COMPLETENESS: full length. PRIMARY REFSEQ_SPAN PRIMARY_IDENTIFIER PRIMARY_SPAN COMP 1-35 AC166349.4 130706-130740 c 36-165 CD546085.1 3-132 166-258 BU055364.1 74-166 259-600 CD546085.1 241-582 601-951 CN706272.1 246-596 952-1067 AC166349.4 114826-114941 c 1068-1256 AC166349.4 113197-113385 c 1257-1486 BM933283.1 1-230 1487-1607 AC166349.4 111092-111212 c 1608-1612 AC166349.4 108861-108865 c 1613-2231 CK619854.1 1-619 2232-2636 DN174402.1 242-646 2637-2956 CN710548.1 167-486 2957-3501 BG067060.2 207-751 c 3502-3710 AW989733.1 203-411 FEATURES Location/Qualifiers source 1..3710 /organism="Mus musculus" /mol_type="mRNA" /strain="C57BL/6" /db_xref="taxon:10090" /chromosome="12" /map="12" gene 1..3710 /gene="Nrde2" /gene_synonym="6720454P05Rik" /note="nrde-2 necessary for RNA interference, domain containing" /db_xref="GeneID:217827" /db_xref="MGI:MGI:2670969" exon 1..114 /gene="Nrde2" /gene_synonym="6720454P05Rik" /inference="alignment:Splign:2.1.0" CDS 51..3554 /gene="Nrde2" /gene_synonym="6720454P05Rik" /note="isoform b is encoded by transcript variant 2; UPF0614 protein C14orf102 homolog; protein NRDE2 homolog; nuclear exosome regulator NRDE2" /codon_start=1 /product="nuclear exosome regulator NRDE2 isoform b" /protein_id="NP_898978.2" /db_xref="GeneID:217827" /db_xref="MGI:MGI:2670969" /translation="
MALFPAFADVSEASGDGAFRKELDWLSNPSFRVGNLTSLSRQTEEVTALASEGSPPPRSPLKSELSGESNTSEKLAQTSRKKKKEKKKRRKHQHHRKTKRRHEQLSSSGSESDTEAGKDRASRSIRDDQKEAEKPCQGSNAAAAVAAAAGHRSIWLEDIHDLTDVFRTDKKPDPANWEYKSLYRGDIARYKRKGDSCLGINPKKQCISWEGASAAKKHSHRHLERYFTKKNVGLMRTEGIAVCSNPEPASSEPVTFIPVKDSAEAATPVTSWLNPLGIYDQSTTQWLQGQGPAEQESKQPDSQQDRENAALKARVEEFNRRVRENPWDTQLWMAFVAFQDEVMRSPGIYALGEGEQEKHRKSLKLLLEKKLAVLERAIESNPGSVELKLAKLQLCSEFWEPSALAKEWQKLLFLHPNNTSLWQRYLSFCQSQFGTFSVSKLHSLYGKCLSTLSAVKDGSMLSHPVLPGTEEAMFGLFLQQCHFLRQAGHSEKVISLFQAMVDFTFFKPDSVKELPTKVQVEFFEPFWDSGEPRVGEKGARGWRAWMHQQERGGWVLITPDEDDEEPEEEDQEIKDKTLPRWQIWLAVERSRDQRHWRPWRPDKTKKQTEEDCEDPERQVLFDDIGQSLIRLSSPDLQFQLIQAFLQFLGVPSGFLPPASCLYLAMDESSIFESELYDEKPLTYFNPSFSGISCVGSMEQLGRPRWTKGHNREGEEFVRNVFHLVLPLLAGKQKSQLSLSWLRYEIAKVIWCLHTKKKRLKSQGKSCKKLAKNLLKEPENRNNFCLWKQYAHLEWLLGNTEDARKVFDTALSMAGSSELKDRELCELSLLYAELEMELSPDSRGATTGRAVHILTRLTESSPYGPYTGQVSSTQVLKARKAYELALQDCLGQSCASSPAPAEALDCLGSLVRCFMLFQYLTVGIDAAVQIYGRVFAKLKGSARLEDPGPEDSTSSQSLTNVLEAVSMMHTSLLRFHMNVCVYPLAPLRETLSDALKLYPGNQVLWRAYVQIQNKSHSANKTRRFFDTVTRSAKHLEPWLFAIEAEKLRKKLVESVQRVGGREVHATIPETGLTHRIRALFENAIRSDKGNQCPLLWRMYLNFLVSLGNKERSKGVFYKALQSCPWAKVLYMDAMEYFPDELQEILDVMTEKELRVRLPLEELELLLED"
misc_feature 54..56 /gene="Nrde2" /gene_synonym="6720454P05Rik" /note="N-acetylalanine. /evidence=ECO:0000250|UniProtKB:Q9H7Z3; propagated from UniProtKB/Swiss-Prot (Q80XC6.3); acetylation site" misc_feature 546..860 /gene="Nrde2" /gene_synonym="6720454P05Rik" /note="propagated from UniProtKB/Swiss-Prot (Q80XC6.3); Region: MID/MTR4-interacting domain. /evidence=ECO:0000250|UniProtKB:Q9H7Z3" misc_feature 546..833 /gene="Nrde2" /gene_synonym="6720454P05Rik" /note="MTR4-interacting domain (MID) found in nuclear exosome regulator NRDE2 and similar proteins; Region: NRDE2_MID; cd22200" /db_xref="CDD:412062" misc_feature order(546..569,576..581,591..596,600..602,606..650, 657..665,669..677,699..707,717..722,726..731,738..758, 783..794,804..833) /gene="Nrde2" /gene_synonym="6720454P05Rik" /note="MTR4 binding site [polypeptide binding]; other site" /db_xref="CDD:412062" misc_feature 909..974 /gene="Nrde2" /gene_synonym="6720454P05Rik" /note="propagated from UniProtKB/Swiss-Prot (Q80XC6.3); Region: Disordered. /evidence=ECO:0000256|SAM:MobiDB-lite" misc_feature 975..1073 /gene="Nrde2" /gene_synonym="6720454P05Rik" /note="propagated from UniProtKB/Swiss-Prot (Q80XC6.3); Region: HAT 1" misc_feature 999..1997 /gene="Nrde2" /gene_synonym="6720454P05Rik" /note="necessary for RNA interference; Region: NRDE-2; pfam08424" /db_xref="CDD:462472" misc_feature 1245..1343 /gene="Nrde2" /gene_synonym="6720454P05Rik" /note="propagated from UniProtKB/Swiss-Prot (Q80XC6.3); Region: HAT 2" misc_feature 2331..2435 /gene="Nrde2" /gene_synonym="6720454P05Rik" /note="propagated from UniProtKB/Swiss-Prot (Q80XC6.3); Region: HAT 3" misc_feature 2991..3089 /gene="Nrde2" /gene_synonym="6720454P05Rik" /note="propagated from UniProtKB/Swiss-Prot (Q80XC6.3); Region: HAT 4" misc_feature 3258..3362 /gene="Nrde2" /gene_synonym="6720454P05Rik" /note="propagated from UniProtKB/Swiss-Prot (Q80XC6.3); Region: HAT 5" exon 115..223 /gene="Nrde2" /gene_synonym="6720454P05Rik" /inference="alignment:Splign:2.1.0" exon 224..457 /gene="Nrde2" /gene_synonym="6720454P05Rik" /inference="alignment:Splign:2.1.0" exon 458..616 /gene="Nrde2" /gene_synonym="6720454P05Rik" /inference="alignment:Splign:2.1.0" exon 617..1067 /gene="Nrde2" /gene_synonym="6720454P05Rik" /inference="alignment:Splign:2.1.0" exon 1068..1473 /gene="Nrde2" /gene_synonym="6720454P05Rik" /inference="alignment:Splign:2.1.0" exon 1474..1607 /gene="Nrde2" /gene_synonym="6720454P05Rik" /inference="alignment:Splign:2.1.0" exon 1608..1728 /gene="Nrde2" /gene_synonym="6720454P05Rik" /inference="alignment:Splign:2.1.0" exon 1729..1904 /gene="Nrde2" /gene_synonym="6720454P05Rik" /inference="alignment:Splign:2.1.0" exon 1905..2291 /gene="Nrde2" /gene_synonym="6720454P05Rik" /inference="alignment:Splign:2.1.0" exon 2292..3217 /gene="Nrde2" /gene_synonym="6720454P05Rik" /inference="alignment:Splign:2.1.0" exon 3218..3356 /gene="Nrde2" /gene_synonym="6720454P05Rik" /inference="alignment:Splign:2.1.0" exon 3357..3428 /gene="Nrde2" /gene_synonym="6720454P05Rik" /inference="alignment:Splign:2.1.0" exon 3429..3710 /gene="Nrde2" /gene_synonym="6720454P05Rik" /inference="alignment:Splign:2.1.0" regulatory 3689..3694 /regulatory_class="polyA_signal_sequence" /gene="Nrde2" /gene_synonym="6720454P05Rik" /note="hexamer: GATAAA" polyA_site 3708 /gene="Nrde2" /gene_synonym="6720454P05Rik" /note="major polyA site" ORIGIN
ctccagacggcgccatttctgaggcaggagtggtagtgcggcctgtgatcatggcgctgttcccggcttttgcggacgtaagtgaggcctccggtgatggggcattcaggaaagagttagattggctgagcaacccaagctttcgtgttggaaatctaacttctctgagccgacaaactgaagaggtcacagcccttgcttctgaagggtcaccaccgccaaggagtcctctgaagtcagagctctcaggtgagagcaacactagcgagaagctcgcacagacaagcaggaagaagaagaaggagaaaaagaagagacggaagcatcagcaccacaggaaaaccaagaggaggcacgagcagttgagcagcagcggctctgagtcagacacagaggctgggaaggacagggcttcccggagcatcagggacgaccagaaggaagccgagaaaccctgtcagggaagcaatgcggctgctgctgttgctgctgctgctggacatcggtccatttggctggaagatattcacgatctgaccgacgtcttcaggactgataagaagccagatcctgccaactgggagtataaatctctgtatcgtggggatatagcaaggtacaagaggaagggagactcctgcctgggtatcaatcctaagaaacagtgtatatcttgggaaggggcttctgcagcaaagaagcactcacacaggcacctggagcgctattttaccaagaagaatgtggggttaatgagaacagagggcattgctgtgtgcagtaaccccgagcctgcctcctccgagcccgtcacattcatcccagtgaaggactctgctgaggcagctactcctgttacatcatggctgaatcctctggggatttatgatcagtctaccacacagtggttacaaggacagggtccagcagagcaagagtcaaagcagccggactcgcaacaggacagggagaatgctgctctcaaggccagagtggaagagtttaacagaagggttcgggagaatccttgggacacgcaactatggatggcgtttgtggctttccaggacgaggtcatgaggagtcctggcatctatgcccttggggaaggagaacaggagaagcacaggaagtccctgaagctcctcctggagaagaagctggctgtgctggagcgggccatcgagagcaacccaggcagcgtggagctgaagcttgccaagctgcagctgtgctcagagttctgggagcccagtgcgctggccaaggagtggcagaagctcctcttcctgcaccccaacaacacaagcctgtggcagcgctatctctccttttgccagagccagtttggtaccttttctgtgtccaaactccacagtctgtatggcaagtgcttgagtaccttgtctgctgttaaagatggcagcatgctatcccaccctgtgttgccgggcaccgaggaggccatgtttgggctctttcttcagcagtgccactttctacggcaggctggccactcagagaaggtcatctctttgttccaggccatggttgacttcaccttcttcaagcctgacagtgtgaaagagctgcctactaaagtacaggtggaattctttgagcccttctgggacagcggagaaccacgcgttggggagaagggagcccgaggctggcgggcgtggatgcaccaacaggagcgaggtggctgggtgctcatcaccccagatgaggatgacgaggagcccgaagaggaggaccaggagataaaagacaagaccctgccccggtggcagatctggcttgctgttgagcgttctcgagaccagaggcactggcgtccctggcgccctgataagaccaagaagcaaacggaggaagactgtgaggaccctgagagacaggtgctgtttgatgacattgggcaatctttgatcagactttccagcccagaccttcagttccagctcatccaggcctttctgcagttcctgggcgtgccttccggcttcctgcccccagcctcctgcctttacctggccatggacgagagcagcatctttgagagtgaactttatgatgaaaagcccctgacttacttcaacccttccttttcgggcattagctgtgtcggctccatggaacagttgggtcgccctcgctggaccaaaggtcacaaccgagagggcgaggagtttgtccgcaatgtcttccacctggtgctgcctttgctcgcaggcaagcagaagtcccagctcagcctctcctggttacggtacgagattgcaaaggtcatttggtgtctacacactaaaaagaagcgattgaagtctcagggaaagagctgcaaaaaactagccaagaatctcctcaaggagccagaaaaccgcaacaacttctgcctctggaagcagtatgcacacctggagtggttgctcggtaacacagaggatgccagaaaagtgttcgacacagcactcagcatggcaggcagcagcgagctgaaggaccgtgaactctgcgagctcagtctgctctatgccgagctggagatggaactgtcgccggactcgagaggagccaccacaggccgagcggtccacatattaacacggctgacggagagcagtccctacgggccctacacggggcaggtctcgtccacccaggtgctgaaagctcggaaggcttacgagctcgcgctgcaggactgcctgggccagagctgtgcctccagcccagctcctgcagaggccttggactgcctgggtagcttggtccgatgctttatgctcttccagtatttgactgtgggcattgatgctgctgtgcagatatacggaagggtgtttgccaagctgaagggctctgctcgcttagaagacccagggccagaggacagcaccagctcccagagtttgaccaatgtgctcgaggctgtcagcatgatgcacacaagcctgctgcgattccacatgaacgtttgtgtttaccctctggctccactccgagagaccctctccgatgctttaaagctgtatccgggcaaccaggttctttggagggcttatgtacagattcagaataagtcccacagtgctaacaagaccagaaggttctttgacacagttactaggtctgccaaacatttggagccttggctatttgcaatcgaagctgagaagctgaggaaaaagctagtggaatctgttcagagggtaggaggcagagaggtccatgcaacaatccccgagactggccttacgcatcgcatcagagctttgtttgaaaatgcgattcggagcgacaagggcaaccagtgtcccctactgtggaggatgtatttgaattttttggtttccttaggaaacaaagaaagaagcaaaggcgtgttctacaaggccctccagagctgtccttgggcaaaggtgctatacatggacgccatggagtatttcccagacgagctgcaggagatcctggacgtgatgaccgagaaggagctccgtgtgcgcctgccccttgaggagctggagctgctgctggaggattagtgtgcagccaggcctgggccagcctgcagagcccaaagccgcagctgtgcaggctccactgtcctgctggggttggacgtattgacttacatattatatatgtgatctctatgtacaagtggagtcgtgccagtgataaaccttttgtggttgaca
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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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