2024-09-28 09:29:47, GGRNA.v2 : RefSeq release 225 (Jul, 2024)
LOCUS NM_001290303 3725 bp mRNA linear ROD 05-JUN-2024 DEFINITION Mus musculus nrde-2 necessary for RNA interference, domain containing (Nrde2), transcript variant 1, mRNA. ACCESSION NM_001290303 XM_006515732 VERSION NM_001290303.1 KEYWORDS RefSeq; RefSeq Select. 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 3725) 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 3725) 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 3725) 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, CN706272.1, BM933283.1, CK619854.1, DN174402.1, CN710548.1, BG067060.2 and AW989733.1. On Mar 12, 2014 this sequence version replaced XM_006515732.1. Transcript Variant: This variant (1) represents the longer transcript and encodes the longer 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. CCDS Note: The exon combination of this CCDS representation is inferred due to a lack of full-length transcript support for this gene. It is supported by tiled partial transcript alignments. ##Evidence-Data-START## Transcript exon combination :: SRR1660825.104847.1, SRR1660821.2909.1 [ECO:0000332] RNAseq introns :: single sample supports all introns SAMN01164139 [ECO:0000348] ##Evidence-Data-END## ##RefSeq-Attributes-START## RefSeq Select criteria :: based on conservation, expression, longest protein ##RefSeq-Attributes-END## COMPLETENESS: full length. PRIMARY REFSEQ_SPAN PRIMARY_IDENTIFIER PRIMARY_SPAN COMP 1-35 AC166349.4 130706-130740 c 36-615 CD546085.1 3-582 616-966 CN706272.1 246-596 967-1082 AC166349.4 114826-114941 c 1083-1271 AC166349.4 113197-113385 c 1272-1501 BM933283.1 1-230 1502-1622 AC166349.4 111092-111212 c 1623-1627 AC166349.4 108861-108865 c 1628-2246 CK619854.1 1-619 2247-2651 DN174402.1 242-646 2652-2971 CN710548.1 167-486 2972-3516 BG067060.2 207-751 c 3517-3725 AW989733.1 203-411 FEATURES Location/Qualifiers source 1..3725 /organism="Mus musculus" /mol_type="mRNA" /strain="C57BL/6" /db_xref="taxon:10090" /chromosome="12" /map="12" gene 1..3725 /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..3569 /gene="Nrde2" /gene_synonym="6720454P05Rik" /note="isoform a is encoded by transcript variant 1; UPF0614 protein C14orf102 homolog; protein NRDE2 homolog; nuclear exosome regulator NRDE2" /codon_start=1 /product="nuclear exosome regulator NRDE2 isoform a" /protein_id="NP_001277232.1" /db_xref="CCDS:CCDS70414.1" /db_xref="GeneID:217827" /db_xref="MGI:MGI:2670969" /translation="
MALFPAFADVSEASGDGAFRKELDWLSNPSFRVGNLTSLSRQTEEVTALASEGSPPPRYSFIRSPLKSELSGESNTSEKLAQTSRKKKKEKKKRRKHQHHRKTKRRHEQLSSSGSESDTEAGKDRASRSIRDDQKEAEKPCQGSNAAAAVAAAAGHRSIWLEDIHDLTDVFRTDKKPDPANWEYKSLYRGDIARYKRKGDSCLGINPKKQCISWEGASAAKKHSHRHLERYFTKKNVGLMRTEGIAVCSNPEPASSEPVTFIPVKDSAEAATPVTSWLNPLGIYDQSTTQWLQGQGPAEQESKQPDSQQDRENAALKARVEEFNRRVRENPWDTQLWMAFVAFQDEVMRSPGIYALGEGEQEKHRKSLKLLLEKKLAVLERAIESNPGSVELKLAKLQLCSEFWEPSALAKEWQKLLFLHPNNTSLWQRYLSFCQSQFGTFSVSKLHSLYGKCLSTLSAVKDGSMLSHPVLPGTEEAMFGLFLQQCHFLRQAGHSEKVISLFQAMVDFTFFKPDSVKELPTKVQVEFFEPFWDSGEPRVGEKGARGWRAWMHQQERGGWVLITPDEDDEEPEEEDQEIKDKTLPRWQIWLAVERSRDQRHWRPWRPDKTKKQTEEDCEDPERQVLFDDIGQSLIRLSSPDLQFQLIQAFLQFLGVPSGFLPPASCLYLAMDESSIFESELYDEKPLTYFNPSFSGISCVGSMEQLGRPRWTKGHNREGEEFVRNVFHLVLPLLAGKQKSQLSLSWLRYEIAKVIWCLHTKKKRLKSQGKSCKKLAKNLLKEPENRNNFCLWKQYAHLEWLLGNTEDARKVFDTALSMAGSSELKDRELCELSLLYAELEMELSPDSRGATTGRAVHILTRLTESSPYGPYTGQVSSTQVLKARKAYELALQDCLGQSCASSPAPAEALDCLGSLVRCFMLFQYLTVGIDAAVQIYGRVFAKLKGSARLEDPGPEDSTSSQSLTNVLEAVSMMHTSLLRFHMNVCVYPLAPLRETLSDALKLYPGNQVLWRAYVQIQNKSHSANKTRRFFDTVTRSAKHLEPWLFAIEAEKLRKKLVESVQRVGGREVHATIPETGLTHRIRALFENAIRSDKGNQCPLLWRMYLNFLVSLGNKERSKGVFYKALQSCPWAKVLYMDAMEYFPDELQEILDVMTEKELRVRLPLEELELLLED"
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 186..482 /gene="Nrde2" /gene_synonym="6720454P05Rik" /note="propagated from UniProtKB/Swiss-Prot (Q80XC6.3); Region: Disordered. /evidence=ECO:0000256|SAM:MobiDB-lite" misc_feature 561..875 /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 561..848 /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(561..584,591..596,606..611,615..617,621..665, 672..680,684..692,714..722,732..737,741..746,753..773, 798..809,819..848) /gene="Nrde2" /gene_synonym="6720454P05Rik" /note="MTR4 binding site [polypeptide binding]; other site" /db_xref="CDD:412062" misc_feature 924..989 /gene="Nrde2" /gene_synonym="6720454P05Rik" /note="propagated from UniProtKB/Swiss-Prot (Q80XC6.3); Region: Disordered. /evidence=ECO:0000256|SAM:MobiDB-lite" misc_feature 990..1088 /gene="Nrde2" /gene_synonym="6720454P05Rik" /note="propagated from UniProtKB/Swiss-Prot (Q80XC6.3); Region: HAT 1" misc_feature 1014..2012 /gene="Nrde2" /gene_synonym="6720454P05Rik" /note="necessary for RNA interference; Region: NRDE-2; pfam08424" /db_xref="CDD:462472" misc_feature 1260..1358 /gene="Nrde2" /gene_synonym="6720454P05Rik" /note="propagated from UniProtKB/Swiss-Prot (Q80XC6.3); Region: HAT 2" misc_feature 2346..2450 /gene="Nrde2" /gene_synonym="6720454P05Rik" /note="propagated from UniProtKB/Swiss-Prot (Q80XC6.3); Region: HAT 3" misc_feature 3006..3104 /gene="Nrde2" /gene_synonym="6720454P05Rik" /note="propagated from UniProtKB/Swiss-Prot (Q80XC6.3); Region: HAT 4" misc_feature 3273..3377 /gene="Nrde2" /gene_synonym="6720454P05Rik" /note="propagated from UniProtKB/Swiss-Prot (Q80XC6.3); Region: HAT 5" exon 115..238 /gene="Nrde2" /gene_synonym="6720454P05Rik" /inference="alignment:Splign:2.1.0" exon 239..472 /gene="Nrde2" /gene_synonym="6720454P05Rik" /inference="alignment:Splign:2.1.0" exon 473..631 /gene="Nrde2" /gene_synonym="6720454P05Rik" /inference="alignment:Splign:2.1.0" exon 632..1082 /gene="Nrde2" /gene_synonym="6720454P05Rik" /inference="alignment:Splign:2.1.0" exon 1083..1488 /gene="Nrde2" /gene_synonym="6720454P05Rik" /inference="alignment:Splign:2.1.0" exon 1489..1622 /gene="Nrde2" /gene_synonym="6720454P05Rik" /inference="alignment:Splign:2.1.0" exon 1623..1743 /gene="Nrde2" /gene_synonym="6720454P05Rik" /inference="alignment:Splign:2.1.0" exon 1744..1919 /gene="Nrde2" /gene_synonym="6720454P05Rik" /inference="alignment:Splign:2.1.0" exon 1920..2306 /gene="Nrde2" /gene_synonym="6720454P05Rik" /inference="alignment:Splign:2.1.0" exon 2307..3232 /gene="Nrde2" /gene_synonym="6720454P05Rik" /inference="alignment:Splign:2.1.0" exon 3233..3371 /gene="Nrde2" /gene_synonym="6720454P05Rik" /inference="alignment:Splign:2.1.0" exon 3372..3443 /gene="Nrde2" /gene_synonym="6720454P05Rik" /inference="alignment:Splign:2.1.0" exon 3444..3725 /gene="Nrde2" /gene_synonym="6720454P05Rik" /inference="alignment:Splign:2.1.0" regulatory 3704..3709 /regulatory_class="polyA_signal_sequence" /gene="Nrde2" /gene_synonym="6720454P05Rik" /note="hexamer: GATAAA" polyA_site 3723 /gene="Nrde2" /gene_synonym="6720454P05Rik" /note="major polyA site" ORIGIN
ctccagacggcgccatttctgaggcaggagtggtagtgcggcctgtgatcatggcgctgttcccggcttttgcggacgtaagtgaggcctccggtgatggggcattcaggaaagagttagattggctgagcaacccaagctttcgtgttggaaatctaacttctctgagccgacaaactgaagaggtcacagcccttgcttctgaagggtcaccaccgccaaggtactcttttatcaggagtcctctgaagtcagagctctcaggtgagagcaacactagcgagaagctcgcacagacaagcaggaagaagaagaaggagaaaaagaagagacggaagcatcagcaccacaggaaaaccaagaggaggcacgagcagttgagcagcagcggctctgagtcagacacagaggctgggaaggacagggcttcccggagcatcagggacgaccagaaggaagccgagaaaccctgtcagggaagcaatgcggctgctgctgttgctgctgctgctggacatcggtccatttggctggaagatattcacgatctgaccgacgtcttcaggactgataagaagccagatcctgccaactgggagtataaatctctgtatcgtggggatatagcaaggtacaagaggaagggagactcctgcctgggtatcaatcctaagaaacagtgtatatcttgggaaggggcttctgcagcaaagaagcactcacacaggcacctggagcgctattttaccaagaagaatgtggggttaatgagaacagagggcattgctgtgtgcagtaaccccgagcctgcctcctccgagcccgtcacattcatcccagtgaaggactctgctgaggcagctactcctgttacatcatggctgaatcctctggggatttatgatcagtctaccacacagtggttacaaggacagggtccagcagagcaagagtcaaagcagccggactcgcaacaggacagggagaatgctgctctcaaggccagagtggaagagtttaacagaagggttcgggagaatccttgggacacgcaactatggatggcgtttgtggctttccaggacgaggtcatgaggagtcctggcatctatgcccttggggaaggagaacaggagaagcacaggaagtccctgaagctcctcctggagaagaagctggctgtgctggagcgggccatcgagagcaacccaggcagcgtggagctgaagcttgccaagctgcagctgtgctcagagttctgggagcccagtgcgctggccaaggagtggcagaagctcctcttcctgcaccccaacaacacaagcctgtggcagcgctatctctccttttgccagagccagtttggtaccttttctgtgtccaaactccacagtctgtatggcaagtgcttgagtaccttgtctgctgttaaagatggcagcatgctatcccaccctgtgttgccgggcaccgaggaggccatgtttgggctctttcttcagcagtgccactttctacggcaggctggccactcagagaaggtcatctctttgttccaggccatggttgacttcaccttcttcaagcctgacagtgtgaaagagctgcctactaaagtacaggtggaattctttgagcccttctgggacagcggagaaccacgcgttggggagaagggagcccgaggctggcgggcgtggatgcaccaacaggagcgaggtggctgggtgctcatcaccccagatgaggatgacgaggagcccgaagaggaggaccaggagataaaagacaagaccctgccccggtggcagatctggcttgctgttgagcgttctcgagaccagaggcactggcgtccctggcgccctgataagaccaagaagcaaacggaggaagactgtgaggaccctgagagacaggtgctgtttgatgacattgggcaatctttgatcagactttccagcccagaccttcagttccagctcatccaggcctttctgcagttcctgggcgtgccttccggcttcctgcccccagcctcctgcctttacctggccatggacgagagcagcatctttgagagtgaactttatgatgaaaagcccctgacttacttcaacccttccttttcgggcattagctgtgtcggctccatggaacagttgggtcgccctcgctggaccaaaggtcacaaccgagagggcgaggagtttgtccgcaatgtcttccacctggtgctgcctttgctcgcaggcaagcagaagtcccagctcagcctctcctggttacggtacgagattgcaaaggtcatttggtgtctacacactaaaaagaagcgattgaagtctcagggaaagagctgcaaaaaactagccaagaatctcctcaaggagccagaaaaccgcaacaacttctgcctctggaagcagtatgcacacctggagtggttgctcggtaacacagaggatgccagaaaagtgttcgacacagcactcagcatggcaggcagcagcgagctgaaggaccgtgaactctgcgagctcagtctgctctatgccgagctggagatggaactgtcgccggactcgagaggagccaccacaggccgagcggtccacatattaacacggctgacggagagcagtccctacgggccctacacggggcaggtctcgtccacccaggtgctgaaagctcggaaggcttacgagctcgcgctgcaggactgcctgggccagagctgtgcctccagcccagctcctgcagaggccttggactgcctgggtagcttggtccgatgctttatgctcttccagtatttgactgtgggcattgatgctgctgtgcagatatacggaagggtgtttgccaagctgaagggctctgctcgcttagaagacccagggccagaggacagcaccagctcccagagtttgaccaatgtgctcgaggctgtcagcatgatgcacacaagcctgctgcgattccacatgaacgtttgtgtttaccctctggctccactccgagagaccctctccgatgctttaaagctgtatccgggcaaccaggttctttggagggcttatgtacagattcagaataagtcccacagtgctaacaagaccagaaggttctttgacacagttactaggtctgccaaacatttggagccttggctatttgcaatcgaagctgagaagctgaggaaaaagctagtggaatctgttcagagggtaggaggcagagaggtccatgcaacaatccccgagactggccttacgcatcgcatcagagctttgtttgaaaatgcgattcggagcgacaagggcaaccagtgtcccctactgtggaggatgtatttgaattttttggtttccttaggaaacaaagaaagaagcaaaggcgtgttctacaaggccctccagagctgtccttgggcaaaggtgctatacatggacgccatggagtatttcccagacgagctgcaggagatcctggacgtgatgaccgagaaggagctccgtgtgcgcctgccccttgaggagctggagctgctgctggaggattagtgtgcagccaggcctgggccagcctgcagagcccaaagccgcagctgtgcaggctccactgtcctgctggggttggacgtattgacttacatattatatatgtgatctctatgtacaagtggagtcgtgccagtgataaaccttttgtggttgaca
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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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