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Protein

Sodium channel modifier 1

Gene

Scnm1

Organism
Mus musculus (Mouse)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Plays a role in RNA splicing, possibly contributing to the recognition of non-consensus donor sites.2 Publications

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Zinc fingeri42 – 7433Matrin-typeAdd
BLAST

GO - Molecular functioni

GO - Biological processi

  • mRNA processing Source: UniProtKB-KW
  • RNA splicing Source: MGI
Complete GO annotation...

Keywords - Biological processi

mRNA processing, mRNA splicing

Keywords - Ligandi

Metal-binding, Zinc

Names & Taxonomyi

Protein namesi
Recommended name:
Sodium channel modifier 1
Gene namesi
Name:Scnm1
Synonyms:Scnm1-ps
OrganismiMus musculus (Mouse)
Taxonomic identifieri10090 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresGliresRodentiaSciurognathiMuroideaMuridaeMurinaeMusMus
Proteomesi
  • UP000000589 Componenti: Chromosome 3

Organism-specific databases

MGIiMGI:1341284. Scnm1.

Subcellular locationi

GO - Cellular componenti

  • nuclear speck Source: UniProtKB-SubCell
  • nucleolus Source: MGI
  • nucleus Source: MGI
Complete GO annotation...

Keywords - Cellular componenti

Nucleus

Pathology & Biotechi

Involvement in diseasei

Allele R187X is a disease susceptibility variant, which modifies the severity of the disease jolting mutant (medjo) caused by defects in Scn8a. It reduces the abundance of correctly spliced Scn8a transcripts below the threshold for survival thereby converting a chronic movement disorder into a lethal neurological disease.

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 229229Sodium channel modifier 1PRO_0000259636Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei182 – 1821PhosphoserineCombined sources
Modified residuei218 – 2181PhosphoserineBy similarity

Keywords - PTMi

Phosphoprotein

Proteomic databases

EPDiQ8K136.
MaxQBiQ8K136.
PRIDEiQ8K136.

PTM databases

iPTMnetiQ8K136.
PhosphoSiteiQ8K136.

Expressioni

Gene expression databases

BgeeiQ8K136.
CleanExiMM_SCNM1.

Interactioni

Subunit structurei

Interacts with LUC7L2 and SNRNP70, which suggests a role as a spliceosome component.1 Publication

GO - Molecular functioni

Structurei

3D structure databases

ProteinModelPortaliQ8K136.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni187 – 22943Required for interaction with LUC7L2Add
BLAST

Motif

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Motifi4 – 2017Bipartite nuclear localization signalSequence analysisAdd
BLAST

Sequence similaritiesi

Contains 1 matrin-type zinc finger.Curated

Zinc finger

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Zinc fingeri42 – 7433Matrin-typeAdd
BLAST

Keywords - Domaini

Zinc-finger

Phylogenomic databases

GeneTreeiENSGT00390000010811.
HOGENOMiHOG000033694.
HOVERGENiHBG093936.
InParanoidiQ8K136.
OMAiENWAELA.
OrthoDBiEOG7W6WNB.

Family and domain databases

InterProiIPR031625. SCNM1_acidic.
IPR031622. Znf-SCNM1.
[Graphical view]
PfamiPF15805. SCNM1_acidic. 1 hit.
PF15803. zf-SCNM1. 1 hit.
[Graphical view]

Sequences (2)i

Sequence statusi: Complete.

This entry describes 2 isoformsi produced by alternative splicing. AlignAdd to basket

Isoform 1 (identifier: Q8K136-1) [UniParc]FASTAAdd to basket

This isoform has been chosen as the 'canonical' sequence. All positional information in this entry refers to it. This is also the sequence that appears in the downloadable versions of the entry.

« Hide

        10         20         30         40         50
MSFKREGDDW SQLNVLKKRR VGDLLASYIP EDEALMLRDG RFACAICPHR
60 70 80 90 100
PVLDTLAMLT AHRAGKKHLS SLKLFYGKKQ TGKGTEQNPR QQNELKTESK
110 120 130 140 150
TEAPLLTQTR IITQNALHRA PHYNSCCRRK HRPEAPAPSV SSPPLPTAEV
160 170 180 190 200
QLQSAEISKE PEPRERSDAK ESAALLASAP MSPTKRRVLN HYLTLRSSGW
210 220
VPDGRGRWIK DENVEFDSDE EEPPDLPLD
Length:229
Mass (Da):25,823
Last modified:October 1, 2002 - v1
Checksum:iBFE63B0E8A3361B9
GO
Isoform 3 (identifier: Q8K136-3) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     132-196: Missing.

Note: Due to disruption of a consensus exonic splicing enhancer in allele R187X, leading to exon 6 skipping. Only found in strains C57BL/6J, C57BR/cdJ, C57L/J, C57BL/10J and C58/J.
Show »
Length:164
Mass (Da):18,780
Checksum:iA4F4F11B322E92C5
GO

Polymorphismi

Strains C57BL/6J, C57BR/cdJ, C57L/J, C57BL/10J and C58/J carry the R187X allele, in which a polymorphism generates a premature stop codon, leading to either a truncated protein or an alternatively spliced isoform 3.1 Publication

Natural variant

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Natural varianti187 – 22943Missing in allele R187X.
Add
BLAST

Alternative sequence

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Alternative sequencei132 – 19665Missing in isoform 3. CuratedVSP_021490Add
BLAST

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AK013948 mRNA. Translation: BAB29077.1.
BC028867 mRNA. Translation: AAH28867.1.
CCDSiCCDS50986.1. [Q8K136-3]
RefSeqiNP_001157045.1. NM_001163573.1. [Q8K136-3]
NP_081289.2. NM_027013.2.
UniGeneiMm.182944.

Genome annotation databases

EnsembliENSMUST00000173462; ENSMUSP00000133769; ENSMUSG00000092607. [Q8K136-3]
GeneIDi69269.
KEGGimmu:69269.
UCSCiuc012ctq.1. mouse. [Q8K136-1]
uc012ctr.1. mouse. [Q8K136-3]

Keywords - Coding sequence diversityi

Alternative splicing, Polymorphism

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AK013948 mRNA. Translation: BAB29077.1.
BC028867 mRNA. Translation: AAH28867.1.
CCDSiCCDS50986.1. [Q8K136-3]
RefSeqiNP_001157045.1. NM_001163573.1. [Q8K136-3]
NP_081289.2. NM_027013.2.
UniGeneiMm.182944.

3D structure databases

ProteinModelPortaliQ8K136.
ModBaseiSearch...
MobiDBiSearch...

PTM databases

iPTMnetiQ8K136.
PhosphoSiteiQ8K136.

Proteomic databases

EPDiQ8K136.
MaxQBiQ8K136.
PRIDEiQ8K136.

Protocols and materials databases

DNASUi69269.
Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENSMUST00000173462; ENSMUSP00000133769; ENSMUSG00000092607. [Q8K136-3]
GeneIDi69269.
KEGGimmu:69269.
UCSCiuc012ctq.1. mouse. [Q8K136-1]
uc012ctr.1. mouse. [Q8K136-3]

Organism-specific databases

CTDi79005.
MGIiMGI:1341284. Scnm1.

Phylogenomic databases

GeneTreeiENSGT00390000010811.
HOGENOMiHOG000033694.
HOVERGENiHBG093936.
InParanoidiQ8K136.
OMAiENWAELA.
OrthoDBiEOG7W6WNB.

Miscellaneous databases

PROiQ8K136.
SOURCEiSearch...

Gene expression databases

BgeeiQ8K136.
CleanExiMM_SCNM1.

Family and domain databases

InterProiIPR031625. SCNM1_acidic.
IPR031622. Znf-SCNM1.
[Graphical view]
PfamiPF15805. SCNM1_acidic. 1 hit.
PF15803. zf-SCNM1. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "Evidence for a direct role of the disease modifier SCNM1 in splicing."
    Howell V.M., Jones J.M., Bergren S.K., Li L., Billi A.C., Avenarius M.R., Meisler M.H.
    Hum. Mol. Genet. 16:2506-2516(2007) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 1), FUNCTION, SUBCELLULAR LOCATION, INTERACTION WITH LUC7L2 AND SNRNP70.
    Strain: C3Heb/FeJ.
    Tissue: Brain.
  2. "The transcriptional landscape of the mammalian genome."
    Carninci P., Kasukawa T., Katayama S., Gough J., Frith M.C., Maeda N., Oyama R., Ravasi T., Lenhard B., Wells C., Kodzius R., Shimokawa K., Bajic V.B., Brenner S.E., Batalov S., Forrest A.R., Zavolan M., Davis M.J.
    , Wilming L.G., Aidinis V., Allen J.E., Ambesi-Impiombato A., Apweiler R., Aturaliya R.N., Bailey T.L., Bansal M., Baxter L., Beisel K.W., Bersano T., Bono H., Chalk A.M., Chiu K.P., Choudhary V., Christoffels A., Clutterbuck D.R., Crowe M.L., Dalla E., Dalrymple B.P., de Bono B., Della Gatta G., di Bernardo D., Down T., Engstrom P., Fagiolini M., Faulkner G., Fletcher C.F., Fukushima T., Furuno M., Futaki S., Gariboldi M., Georgii-Hemming P., Gingeras T.R., Gojobori T., Green R.E., Gustincich S., Harbers M., Hayashi Y., Hensch T.K., Hirokawa N., Hill D., Huminiecki L., Iacono M., Ikeo K., Iwama A., Ishikawa T., Jakt M., Kanapin A., Katoh M., Kawasawa Y., Kelso J., Kitamura H., Kitano H., Kollias G., Krishnan S.P., Kruger A., Kummerfeld S.K., Kurochkin I.V., Lareau L.F., Lazarevic D., Lipovich L., Liu J., Liuni S., McWilliam S., Madan Babu M., Madera M., Marchionni L., Matsuda H., Matsuzawa S., Miki H., Mignone F., Miyake S., Morris K., Mottagui-Tabar S., Mulder N., Nakano N., Nakauchi H., Ng P., Nilsson R., Nishiguchi S., Nishikawa S., Nori F., Ohara O., Okazaki Y., Orlando V., Pang K.C., Pavan W.J., Pavesi G., Pesole G., Petrovsky N., Piazza S., Reed J., Reid J.F., Ring B.Z., Ringwald M., Rost B., Ruan Y., Salzberg S.L., Sandelin A., Schneider C., Schoenbach C., Sekiguchi K., Semple C.A., Seno S., Sessa L., Sheng Y., Shibata Y., Shimada H., Shimada K., Silva D., Sinclair B., Sperling S., Stupka E., Sugiura K., Sultana R., Takenaka Y., Taki K., Tammoja K., Tan S.L., Tang S., Taylor M.S., Tegner J., Teichmann S.A., Ueda H.R., van Nimwegen E., Verardo R., Wei C.L., Yagi K., Yamanishi H., Zabarovsky E., Zhu S., Zimmer A., Hide W., Bult C., Grimmond S.M., Teasdale R.D., Liu E.T., Brusic V., Quackenbush J., Wahlestedt C., Mattick J.S., Hume D.A., Kai C., Sasaki D., Tomaru Y., Fukuda S., Kanamori-Katayama M., Suzuki M., Aoki J., Arakawa T., Iida J., Imamura K., Itoh M., Kato T., Kawaji H., Kawagashira N., Kawashima T., Kojima M., Kondo S., Konno H., Nakano K., Ninomiya N., Nishio T., Okada M., Plessy C., Shibata K., Shiraki T., Suzuki S., Tagami M., Waki K., Watahiki A., Okamura-Oho Y., Suzuki H., Kawai J., Hayashizaki Y.
    Science 309:1559-1563(2005) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ALLELE R187X).
    Strain: C57BL/6J.
    Tissue: Head.
  3. "The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC)."
    The MGC Project Team
    Genome Res. 14:2121-2127(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 1).
    Strain: FVB/N.
    Tissue: Colon.
  4. "SCNM1, a putative RNA splicing factor that modifies disease severity in mice."
    Buchner D.A., Trudeau M., Meisler M.H.
    Science 301:967-969(2003) [PubMed] [Europe PMC] [Abstract]
    Cited for: IDENTIFICATION OF ISOFORM 3, FUNCTION, SUBCELLULAR LOCATION, POLYMORPHISM, DISEASE.
  5. "The phagosomal proteome in interferon-gamma-activated macrophages."
    Trost M., English L., Lemieux S., Courcelles M., Desjardins M., Thibault P.
    Immunity 30:143-154(2009) [PubMed] [Europe PMC] [Abstract]
    Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-182, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].

Entry informationi

Entry nameiSCNM1_MOUSE
AccessioniPrimary (citable) accession number: Q8K136
Secondary accession number(s): Q9CXV5
Entry historyi
Integrated into UniProtKB/Swiss-Prot: October 31, 2006
Last sequence update: October 1, 2002
Last modified: June 8, 2016
This is version 87 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

Complete proteome, Reference proteome

Documents

  1. MGD cross-references
    Mouse Genome Database (MGD) cross-references in UniProtKB/Swiss-Prot
  2. SIMILARITY comments
    Index of protein domains and families

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.