LOCUS       NM_001285825            1379 bp    mRNA    linear   ROD 27-APR-2025
DEFINITION  Mus musculus small nuclear ribonucleoprotein polypeptide A (Snrpa),
            transcript variant 3, mRNA.
ACCESSION   NM_001285825
VERSION     NM_001285825.1
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 1379)
  AUTHORS   Subramania,S., Gagne,L.M., Campagne,S., Fort,V., O'Sullivan,J.,
            Mocaer,K., Feldmuller,M., Masson,J.Y., Allain,F.H.T., Hussein,S.M.
            and Huot,M.E.
  TITLE     SAM68 interaction with U1A modulates U1 snRNP recruitment and
            regulates mTor pre-mRNA splicing
  JOURNAL   Nucleic Acids Res 47 (8), 4181-4197 (2019)
   PUBMED   30767021
  REMARK    GeneRIF: SAM68 interaction with U1A modulates U1 snRNP recruitment
            and regulates mTor pre-mRNA splicing.
REFERENCE   2  (bases 1 to 1379)
  AUTHORS   Lee,N.C., Lee,Y.M., Chen,P.W., Byrne,B.J. and Hwu,W.L.
  TITLE     Mutation-adapted U1 snRNA corrects a splicing error of the dopa
            decarboxylase gene
  JOURNAL   Hum Mol Genet 25 (23), 5142-5147 (2016)
   PUBMED   27658936
  REMARK    GeneRIF: We found that only the modified U1 snRNA (IVS-AAA) that
            completely matched both the intronic and exonic U1 binding
            sequences of the mutated DDC gene could correct splicing errors of
            either the mutated human DDC minigene or the mouse artificial
            splicing construct in vitro
REFERENCE   3  (bases 1 to 1379)
  AUTHORS   Workman,E., Veith,A. and Battle,D.J.
  TITLE     U1A regulates 3' processing of the survival motor neuron mRNA
  JOURNAL   J Biol Chem 289 (6), 3703-3712 (2014)
   PUBMED   24362020
  REMARK    GeneRIF: a new mechanism for regulating SMN levels and provides new
            insight into the roles of U1A in 3' processing of mRNAs.
REFERENCE   4  (bases 1 to 1379)
  AUTHORS   Stefan,M., Simmons,R.A., Bertera,S., Trucco,M., Esni,F., Drain,P.
            and Nicholls,R.D.
  TITLE     Global deficits in development, function, and gene expression in
            the endocrine pancreas in a deletion mouse model of Prader-Willi
            syndrome
  JOURNAL   Am J Physiol Endocrinol Metab 300 (5), E909-E922 (2011)
   PUBMED   21343540
REFERENCE   5  (bases 1 to 1379)
  AUTHORS   Evsikov,A.V., Graber,J.H., Brockman,J.M., Hampl,A., Holbrook,A.E.,
            Singh,P., Eppig,J.J., Solter,D. and Knowles,B.B.
  TITLE     Cracking the egg: molecular dynamics and evolutionary aspects of
            the transition from the fully grown oocyte to embryo
  JOURNAL   Genes Dev 20 (19), 2713-2727 (2006)
   PUBMED   17015433
REFERENCE   6  (bases 1 to 1379)
  AUTHORS   Ma,J., Gunderson,S.I. and Phillips,C.
  TITLE     Non-snRNP U1A levels decrease during mammalian B-cell
            differentiation and release the IgM secretory poly(A) site from
            repression
  JOURNAL   RNA 12 (1), 122-132 (2006)
   PUBMED   16373497
  REMARK    GeneRIF: Endogenous non-snRNP associated U1A inhibits poly(A)
            polymerase activity proportional to U1A recovered, suggesting that
            available U1A level alone is responsible for changes in its
            inhibitory effect at the secretory IgM poly (A) site.
REFERENCE   7  (bases 1 to 1379)
  AUTHORS   McKee,A.E., Minet,E., Stern,C., Riahi,S., Stiles,C.D. and
            Silver,P.A.
  TITLE     A genome-wide in situ hybridization map of RNA-binding proteins
            reveals anatomically restricted expression in the developing mouse
            brain
  JOURNAL   BMC Dev Biol 5, 14 (2005)
   PUBMED   16033648
  REMARK    Publication Status: Online-Only
REFERENCE   8  (bases 1 to 1379)
  AUTHORS   Davies,S.R., Li,J., Okazaki,K. and Sandell,L.J.
  TITLE     Tissue-restricted expression of the Cdrap/Mia gene within a
            conserved multigenic housekeeping locus
  JOURNAL   Genomics 83 (4), 667-678 (2004)
   PUBMED   15028289
REFERENCE   9  (bases 1 to 1379)
  AUTHORS   Bennett,M.M., Baron,M.A. and Craft,J.
  TITLE     Nucleotide sequence analysis of the A protein of the U1 small
            nuclear ribonucleoprotein particle: the murine protein contains a
            5' amino-terminal tag
  JOURNAL   Nucleic Acids Res 21 (18), 4404 (1993)
   PUBMED   8415008
COMMENT     VALIDATED REFSEQ: This record has undergone validation or
            preliminary review. The reference sequence was derived from
            CX206945.1, CA552113.1, DV650448.1 and AI851424.1.
            
            Transcript Variant: This variant (3) differs in the 5' UTR compared
            to variant 1. Variants 1, 2 and 3 encode the same protein.
            
            ##Evidence-Data-START##
            Transcript exon combination :: ERR3835354.310733.1,
                                           SRR7345562.1176541.1 [ECO:0000332]
            RNAseq introns              :: mixed sample support SAMN00849374,
                                           SAMN00849375 [ECO:0006172]
            ##Evidence-Data-END##
            COMPLETENESS: complete on the 3' end.
PRIMARY     REFSEQ_SPAN         PRIMARY_IDENTIFIER PRIMARY_SPAN        COMP
            1-111               CX206945.1         1-111
            112-540             CA552113.1         1-429
            541-1153            DV650448.1         160-772
            1154-1379           AI851424.1         1-226               c
FEATURES             Location/Qualifiers
     source          1..1379
                     /organism="Mus musculus"
                     /mol_type="mRNA"
                     /strain="C57BL/6"
                     /db_xref="taxon:10090"
                     /chromosome="7"
                     /map="7 15.84 cM"
     gene            1..1379
                     /gene="Snrpa"
                     /gene_synonym="C430021M15Rik; Rnu1a-1; Rnu1a1; U1-A; U1A"
                     /note="small nuclear ribonucleoprotein polypeptide A"
                     /db_xref="GeneID:53607"
                     /db_xref="MGI:MGI:1855690"
     exon            1..278
                     /gene="Snrpa"
                     /gene_synonym="C430021M15Rik; Rnu1a-1; Rnu1a1; U1-A; U1A"
                     /inference="alignment:Splign:2.1.0"
     exon            279..391
                     /gene="Snrpa"
                     /gene_synonym="C430021M15Rik; Rnu1a-1; Rnu1a1; U1-A; U1A"
                     /inference="alignment:Splign:2.1.0"
     misc_feature    286..288
                     /gene="Snrpa"
                     /gene_synonym="C430021M15Rik; Rnu1a-1; Rnu1a1; U1-A; U1A"
                     /note="upstream in-frame stop codon"
     CDS             301..1164
                     /gene="Snrpa"
                     /gene_synonym="C430021M15Rik; Rnu1a-1; Rnu1a1; U1-A; U1A"
                     /note="protein A of the U1 small nuclear RNA; U1 snRNP A"
                     /codon_start=1
                     /product="U1 small nuclear ribonucleoprotein A"
                     /protein_id="NP_001272754.1"
                     /db_xref="CCDS:CCDS21014.1"
                     /db_xref="GeneID:53607"
                     /db_xref="MGI:MGI:1855690"
                     /translation="

MATIATMPVPETRANHTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSRIMKMRGQAFVIFKEVTSATNALRSMQGFPFYDKPMRIQYAKTDSDIIAKMKGTYVERDRKREKRKPKSQETPAAKKAVQGGAAAPVVGAVQPVPGMPPMPQAPRIMHHMPGQPPYMPPPGMIPPPGLAPGQIPPGAMPPQQLMPGQMPPAQPLSENPPNHILFLTNLPEETNELMLSMLFNQFPGFKEVRLVPGRHDIAFVEFDNEVQAGAARDALQGFKITQNNAMKISFAKK"

     misc_feature    337..603
                     /gene="Snrpa"
                     /gene_synonym="C430021M15Rik; Rnu1a-1; Rnu1a1; U1-A; U1A"
                     /note="RNA recognition motif 1 (RRM1) found in vertebrate
                     U1 small nuclear ribonucleoprotein A (U1A); Region:
                     RRM1_U1A; cd12477"
                     /db_xref="CDD:409906"
     misc_feature    order(355..357,361..366,373..375,448..450,454..456,
                     460..480,484..486,556..558,565..567,571..594)
                     /gene="Snrpa"
                     /gene_synonym="C430021M15Rik; Rnu1a-1; Rnu1a1; U1-A; U1A"
                     /note="RNA binding site [nucleotide binding]; other site"
                     /db_xref="CDD:409906"
     misc_feature    496..498
                     /gene="Snrpa"
                     /gene_synonym="C430021M15Rik; Rnu1a-1; Rnu1a1; U1-A; U1A"
                     /note="N6-acetyllysine.
                     /evidence=ECO:0000250|UniProtKB:P09012; propagated from
                     UniProtKB/Swiss-Prot (Q62189.3); acetylation site"
     misc_feature    616..702
                     /gene="Snrpa"
                     /gene_synonym="C430021M15Rik; Rnu1a-1; Rnu1a1; U1-A; U1A"
                     /note="propagated from UniProtKB/Swiss-Prot (Q62189.3);
                     Region: Disordered. /evidence=ECO:0000256|SAM:MobiDB-lite"
     misc_feature    769..771
                     /gene="Snrpa"
                     /gene_synonym="C430021M15Rik; Rnu1a-1; Rnu1a1; U1-A; U1A"
                     /note="Omega-N-methylarginine.
                     /evidence=ECO:0000250|UniProtKB:P09012; propagated from
                     UniProtKB/Swiss-Prot (Q62189.3); methylation site"
     misc_feature    904..1161
                     /gene="Snrpa"
                     /gene_synonym="C430021M15Rik; Rnu1a-1; Rnu1a1; U1-A; U1A"
                     /note="RNA recognition motif 2 (RRM2) found in vertebrate
                     U1 small nuclear ribonucleoprotein A (U1 snRNP A or U1-A
                     or U1A); Region: RRM2_U1A; cd12480"
                     /db_xref="CDD:409908"
     exon            392..564
                     /gene="Snrpa"
                     /gene_synonym="C430021M15Rik; Rnu1a-1; Rnu1a1; U1-A; U1A"
                     /inference="alignment:Splign:2.1.0"
     exon            565..741
                     /gene="Snrpa"
                     /gene_synonym="C430021M15Rik; Rnu1a-1; Rnu1a1; U1-A; U1A"
                     /inference="alignment:Splign:2.1.0"
     exon            742..915
                     /gene="Snrpa"
                     /gene_synonym="C430021M15Rik; Rnu1a-1; Rnu1a1; U1-A; U1A"
                     /inference="alignment:Splign:2.1.0"
     exon            916..1004
                     /gene="Snrpa"
                     /gene_synonym="C430021M15Rik; Rnu1a-1; Rnu1a1; U1-A; U1A"
                     /inference="alignment:Splign:2.1.0"
     exon            1005..1363
                     /gene="Snrpa"
                     /gene_synonym="C430021M15Rik; Rnu1a-1; Rnu1a1; U1-A; U1A"
                     /inference="alignment:Splign:2.1.0"
     regulatory      1332..1337
                     /regulatory_class="polyA_signal_sequence"
                     /gene="Snrpa"
                     /gene_synonym="C430021M15Rik; Rnu1a-1; Rnu1a1; U1-A; U1A"
                     /note="hexamer: ATTAAA"
     polyA_site      1363
                     /gene="Snrpa"
                     /gene_synonym="C430021M15Rik; Rnu1a-1; Rnu1a1; U1-A; U1A"
                     /note="major polyA site"
ORIGIN      

gcttccgaaaggcagtcttagaatgcaccagagctctaaccatgtcccaattggccagaagctcgtgcccttctttgattggtccgttccctcgcgtccagggggcgggaccccaagtgttcctttggcagacgctgaggccgggggagagactctgaacttaccgagtttgcccgccgtgattagctcgcggaagggagaagccgttgccggggaagatagttgtgtgtctgtgcagcgtagctcggcgggcgttgtcggcgggagcgacggctcagccgtacctgaacatctcacaccatggccaccatagccaccatgccagttcccgagacccgtgccaaccacactatttatatcaacaatctcaatgagaagatcaagaaggatgagctcaagaagtccctgtatgccatcttctcccagtttggccagatcctggatatcctggtgtctcggatcatgaagatgaggggccaggccttcgtcatcttcaaggaggtcaccagcgccaccaatgccctgcgctccatgcagggcttccctttctacgacaagcccatgcgcatccagtacgcaaagactgactcggacatcattgccaagatgaagggcacctatgtggagagagatcgcaaacgagagaagaggaagcccaagagtcaggagacacctgctgccaaaaaggctgttcagggtggggcagctgcgcccgtggtgggggctgtccagcccgtaccgggcatgccaccgatgcctcaggcaccccgcatcatgcaccatatgccaggacagcctccctacatgccgccacctggcatgatcccgccaccaggcctcgctcctggccagatcccccctggggccatgcccccacagcagctcatgcctgggcagatgccgcctgcccagcctctctccgagaacccacccaatcacatcctgttcctcaccaacctgcctgaggagaccaacgagctcatgctctccatgctcttcaaccagttccctggcttcaaggaggtgcgtctggtccctgggcgccatgacatcgccttcgtggagtttgacaatgaagtgcaggctggggcagcacgagatgccctgcaaggctttaagatcacacaaaacaatgctatgaagatctcttttgccaagaagtagcgcctttccctatggagtaccccagtcccttccccccctcccttggctcagtccctgaaggtaagtcccccttagggaccttctcagagccgtgtgtgtgtggttgccacacagcattgtacccagagtctgtccccagacattgcacctggcgctgttagattgtgattaaagtgagtttttgaggtttggttttttaaaaaaaaaaaaaaaaa

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