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O75940

- SPF30_HUMAN

UniProt

O75940 - SPF30_HUMAN

Protein

Survival of motor neuron-related-splicing factor 30

Gene

SMNDC1

Organism
Homo sapiens (Human)
Status
Reviewed - Annotation score: 5 out of 5- Experimental evidence at protein leveli
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    • History
      Entry version 136 (01 Oct 2014)
      Sequence version 1 (01 Nov 1998)
      Previous versions | rss
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    Functioni

    Necessary for spliceosome assembly. Overexpression causes apoptosis.3 Publications

    GO - Molecular functioni

    1. poly(A) RNA binding Source: UniProtKB
    2. protein binding Source: IntAct

    GO - Biological processi

    1. apoptotic process Source: ProtInc
    2. mRNA processing Source: ProtInc
    3. RNA splicing Source: ProtInc
    4. RNA splicing, via transesterification reactions Source: UniProtKB

    Keywords - Biological processi

    Apoptosis, mRNA processing, mRNA splicing

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Survival of motor neuron-related-splicing factor 30
    Alternative name(s):
    30 kDa splicing factor SMNrp
    SMN-related protein
    Survival motor neuron domain-containing protein 1
    Gene namesi
    Name:SMNDC1
    Synonyms:SMNR, SPF30
    OrganismiHomo sapiens (Human)
    Taxonomic identifieri9606 [NCBI]
    Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
    ProteomesiUP000005640: Chromosome 10

    Organism-specific databases

    HGNCiHGNC:16900. SMNDC1.

    Subcellular locationi

    Nucleus speckle. NucleusCajal body
    Note: Detected in nuclear speckles containing snRNP and in Cajal (coiled) bodies.

    GO - Cellular componenti

    1. Cajal body Source: UniProtKB-SubCell
    2. cytoplasm Source: HPA
    3. intermediate filament cytoskeleton Source: HPA
    4. nuclear speck Source: UniProtKB-SubCell
    5. nucleus Source: HPA
    6. spliceosomal complex Source: ProtInc

    Keywords - Cellular componenti

    Nucleus, Spliceosome

    Pathology & Biotechi

    Organism-specific databases

    PharmGKBiPA134990780.

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 238238Survival of motor neuron-related-splicing factor 30PRO_0000218908Add
    BLAST

    Amino acid modifications

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Modified residuei201 – 2011Phosphoserine4 Publications
    Modified residuei219 – 2191N6-acetyllysine1 Publication

    Keywords - PTMi

    Acetylation, Phosphoprotein

    Proteomic databases

    MaxQBiO75940.
    PaxDbiO75940.
    PeptideAtlasiO75940.
    PRIDEiO75940.

    PTM databases

    PhosphoSiteiO75940.

    Expressioni

    Tissue specificityi

    Detected at intermediate levels in skeletal muscle, and at low levels in heart and pancreas.1 Publication

    Gene expression databases

    BgeeiO75940.
    CleanExiHS_SMNDC1.
    GenevestigatoriO75940.

    Organism-specific databases

    HPAiHPA050508.

    Interactioni

    Subunit structurei

    Associates with spliceosomes. Associates with U4/U5/U6 tri-snRNP and with U2 snRNP.1 Publication

    Binary interactionsi

    WithEntry#Exp.IntActNotes
    KPNB1Q149742EBI-1052641,EBI-286758
    PRPF3O433952EBI-1052641,EBI-744322

    Protein-protein interaction databases

    BioGridi115574. 24 interactions.
    IntActiO75940. 4 interactions.
    MINTiMINT-4527315.
    STRINGi9606.ENSP00000358605.

    Structurei

    Secondary structure

    1
    238
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Beta strandi78 – 825
    Turni84 – 863
    Beta strandi87 – 9812
    Turni99 – 1024
    Beta strandi103 – 1086
    Turni109 – 1124
    Beta strandi113 – 1186
    Helixi119 – 1213

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    4A4FNMR-A65-128[»]
    4A4HNMR-A65-128[»]
    ProteinModelPortaliO75940.
    SMRiO75940. Positions 65-128.
    ModBaseiSearch...
    MobiDBiSearch...

    Family & Domainsi

    Domains and Repeats

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Domaini72 – 13261TudorPROSITE-ProRule annotationAdd
    BLAST

    Motif

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Motifi142 – 16019Nuclear localization signalSequence AnalysisAdd
    BLAST

    Domaini

    The Tudor domain mediates association with dimethylarginines, which are common in snRNP proteins.

    Sequence similaritiesi

    Belongs to the SMN family.Curated
    Contains 1 Tudor domain.PROSITE-ProRule annotation

    Phylogenomic databases

    eggNOGiNOG251685.
    HOGENOMiHOG000007521.
    HOVERGENiHBG057021.
    InParanoidiO75940.
    KOiK12839.
    OMAiNNKAYSK.
    OrthoDBiEOG7K6PVX.
    PhylomeDBiO75940.
    TreeFamiTF315413.

    Family and domain databases

    InterProiIPR010304. Survival_motor_neuron.
    IPR002999. Tudor.
    [Graphical view]
    PfamiPF06003. SMN. 1 hit.
    [Graphical view]
    SMARTiSM00333. TUDOR. 1 hit.
    [Graphical view]
    PROSITEiPS50304. TUDOR. 1 hit.
    [Graphical view]

    Sequencei

    Sequence statusi: Complete.

    O75940-1 [UniParc]FASTAAdd to Basket

    « Hide

    MSEDLAKQLA SYKAQLQQVE AALSGNGENE DLLKLKKDLQ EVIELTKDLL    50
    STQPSETLAS SDSFASTQPT HSWKVGDKCM AVWSEDGQCY EAEIEEIDEE 100
    NGTAAITFAG YGNAEVTPLL NLKPVEEGRK AKEDSGNKPM SKKEMIAQQR 150
    EYKKKKALKK AQRIKELEQE REDQKVKWQQ FNNRAYSKNK KGQVKRSIFA 200
    SPESVTGKVG VGTCGIADKP MTQYQDTSKY NVRHLMPQ 238
    Length:238
    Mass (Da):26,711
    Last modified:November 1, 1998 - v1
    Checksum:i7F60852AD4D1F53A
    GO

    Experimental Info

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Sequence conflicti174 – 1741Q → R in BAG36724. (PubMed:14702039)Curated

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    AF083385 mRNA. Translation: AAC64086.1.
    AF107463 mRNA. Translation: AAC84148.1.
    AK314013 mRNA. Translation: BAG36724.1.
    AL360182 Genomic DNA. Translation: CAI15482.1.
    CH471066 Genomic DNA. Translation: EAW49561.1.
    CH471066 Genomic DNA. Translation: EAW49562.1.
    CH471066 Genomic DNA. Translation: EAW49564.1.
    BC011234 mRNA. Translation: AAH11234.1.
    CCDSiCCDS7565.1.
    RefSeqiNP_005862.1. NM_005871.3.
    UniGeneiHs.632093.

    Genome annotation databases

    EnsembliENST00000369592; ENSP00000358605; ENSG00000119953.
    ENST00000369603; ENSP00000358616; ENSG00000119953.
    GeneIDi10285.
    KEGGihsa:10285.
    UCSCiuc001kzc.4. human.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    AF083385 mRNA. Translation: AAC64086.1 .
    AF107463 mRNA. Translation: AAC84148.1 .
    AK314013 mRNA. Translation: BAG36724.1 .
    AL360182 Genomic DNA. Translation: CAI15482.1 .
    CH471066 Genomic DNA. Translation: EAW49561.1 .
    CH471066 Genomic DNA. Translation: EAW49562.1 .
    CH471066 Genomic DNA. Translation: EAW49564.1 .
    BC011234 mRNA. Translation: AAH11234.1 .
    CCDSi CCDS7565.1.
    RefSeqi NP_005862.1. NM_005871.3.
    UniGenei Hs.632093.

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    Entry Method Resolution (Å) Chain Positions PDBsum
    4A4F NMR - A 65-128 [» ]
    4A4H NMR - A 65-128 [» ]
    ProteinModelPortali O75940.
    SMRi O75940. Positions 65-128.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    BioGridi 115574. 24 interactions.
    IntActi O75940. 4 interactions.
    MINTi MINT-4527315.
    STRINGi 9606.ENSP00000358605.

    PTM databases

    PhosphoSitei O75940.

    Proteomic databases

    MaxQBi O75940.
    PaxDbi O75940.
    PeptideAtlasi O75940.
    PRIDEi O75940.

    Protocols and materials databases

    DNASUi 10285.
    Structural Biology Knowledgebase Search...

    Genome annotation databases

    Ensembli ENST00000369592 ; ENSP00000358605 ; ENSG00000119953 .
    ENST00000369603 ; ENSP00000358616 ; ENSG00000119953 .
    GeneIDi 10285.
    KEGGi hsa:10285.
    UCSCi uc001kzc.4. human.

    Organism-specific databases

    CTDi 10285.
    GeneCardsi GC10M112042.
    GeneReviewsi SMNDC1.
    HGNCi HGNC:16900. SMNDC1.
    HPAi HPA050508.
    MIMi 603519. gene.
    neXtProti NX_O75940.
    PharmGKBi PA134990780.
    GenAtlasi Search...

    Phylogenomic databases

    eggNOGi NOG251685.
    HOGENOMi HOG000007521.
    HOVERGENi HBG057021.
    InParanoidi O75940.
    KOi K12839.
    OMAi NNKAYSK.
    OrthoDBi EOG7K6PVX.
    PhylomeDBi O75940.
    TreeFami TF315413.

    Miscellaneous databases

    ChiTaRSi SMNDC1. human.
    GeneWikii Survival_motor_neuron_domain_containing_1.
    GenomeRNAii 10285.
    NextBioi 38968.
    PROi O75940.
    SOURCEi Search...

    Gene expression databases

    Bgeei O75940.
    CleanExi HS_SMNDC1.
    Genevestigatori O75940.

    Family and domain databases

    InterProi IPR010304. Survival_motor_neuron.
    IPR002999. Tudor.
    [Graphical view ]
    Pfami PF06003. SMN. 1 hit.
    [Graphical view ]
    SMARTi SM00333. TUDOR. 1 hit.
    [Graphical view ]
    PROSITEi PS50304. TUDOR. 1 hit.
    [Graphical view ]
    ProtoNeti Search...

    Publicationsi

    1. "Mass spectrometry and EST-database searching allows characterization of the multi-protein spliceosome complex."
      Neubauer G., King A., Rappsilber J., Calvio C., Watson M., Ajuh P., Sleeman J., Lamond A.I., Mann M.
      Nat. Genet. 20:46-50(1998) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [MRNA], PARTIAL PROTEIN SEQUENCE, IDENTIFICATION BY MASS SPECTROMETRY, INTERACTION WITH THE SPLICEOSOME.
    2. "Isolating and cloning HSP cDNA."
      Chen J.H., Luo W.Q., Zhou Y., Huang X.W., Yuan J.G., Qiang B.Q.
      Submitted (NOV-1998) to the EMBL/GenBank/DDBJ databases
      Cited for: NUCLEOTIDE SEQUENCE [MRNA].
    3. "Complete sequencing and characterization of 21,243 full-length human cDNAs."
      Ota T., Suzuki Y., Nishikawa T., Otsuki T., Sugiyama T., Irie R., Wakamatsu A., Hayashi K., Sato H., Nagai K., Kimura K., Makita H., Sekine M., Obayashi M., Nishi T., Shibahara T., Tanaka T., Ishii S.
      , Yamamoto J., Saito K., Kawai Y., Isono Y., Nakamura Y., Nagahari K., Murakami K., Yasuda T., Iwayanagi T., Wagatsuma M., Shiratori A., Sudo H., Hosoiri T., Kaku Y., Kodaira H., Kondo H., Sugawara M., Takahashi M., Kanda K., Yokoi T., Furuya T., Kikkawa E., Omura Y., Abe K., Kamihara K., Katsuta N., Sato K., Tanikawa M., Yamazaki M., Ninomiya K., Ishibashi T., Yamashita H., Murakawa K., Fujimori K., Tanai H., Kimata M., Watanabe M., Hiraoka S., Chiba Y., Ishida S., Ono Y., Takiguchi S., Watanabe S., Yosida M., Hotuta T., Kusano J., Kanehori K., Takahashi-Fujii A., Hara H., Tanase T.-O., Nomura Y., Togiya S., Komai F., Hara R., Takeuchi K., Arita M., Imose N., Musashino K., Yuuki H., Oshima A., Sasaki N., Aotsuka S., Yoshikawa Y., Matsunawa H., Ichihara T., Shiohata N., Sano S., Moriya S., Momiyama H., Satoh N., Takami S., Terashima Y., Suzuki O., Nakagawa S., Senoh A., Mizoguchi H., Goto Y., Shimizu F., Wakebe H., Hishigaki H., Watanabe T., Sugiyama A., Takemoto M., Kawakami B., Yamazaki M., Watanabe K., Kumagai A., Itakura S., Fukuzumi Y., Fujimori Y., Komiyama M., Tashiro H., Tanigami A., Fujiwara T., Ono T., Yamada K., Fujii Y., Ozaki K., Hirao M., Ohmori Y., Kawabata A., Hikiji T., Kobatake N., Inagaki H., Ikema Y., Okamoto S., Okitani R., Kawakami T., Noguchi S., Itoh T., Shigeta K., Senba T., Matsumura K., Nakajima Y., Mizuno T., Morinaga M., Sasaki M., Togashi T., Oyama M., Hata H., Watanabe M., Komatsu T., Mizushima-Sugano J., Satoh T., Shirai Y., Takahashi Y., Nakagawa K., Okumura K., Nagase T., Nomura N., Kikuchi H., Masuho Y., Yamashita R., Nakai K., Yada T., Nakamura Y., Ohara O., Isogai T., Sugano S.
      Nat. Genet. 36:40-45(2004) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
      Tissue: Testis.
    4. "The DNA sequence and comparative analysis of human chromosome 10."
      Deloukas P., Earthrowl M.E., Grafham D.V., Rubenfield M., French L., Steward C.A., Sims S.K., Jones M.C., Searle S., Scott C., Howe K., Hunt S.E., Andrews T.D., Gilbert J.G.R., Swarbreck D., Ashurst J.L., Taylor A., Battles J.
      , Bird C.P., Ainscough R., Almeida J.P., Ashwell R.I.S., Ambrose K.D., Babbage A.K., Bagguley C.L., Bailey J., Banerjee R., Bates K., Beasley H., Bray-Allen S., Brown A.J., Brown J.Y., Burford D.C., Burrill W., Burton J., Cahill P., Camire D., Carter N.P., Chapman J.C., Clark S.Y., Clarke G., Clee C.M., Clegg S., Corby N., Coulson A., Dhami P., Dutta I., Dunn M., Faulkner L., Frankish A., Frankland J.A., Garner P., Garnett J., Gribble S., Griffiths C., Grocock R., Gustafson E., Hammond S., Harley J.L., Hart E., Heath P.D., Ho T.P., Hopkins B., Horne J., Howden P.J., Huckle E., Hynds C., Johnson C., Johnson D., Kana A., Kay M., Kimberley A.M., Kershaw J.K., Kokkinaki M., Laird G.K., Lawlor S., Lee H.M., Leongamornlert D.A., Laird G., Lloyd C., Lloyd D.M., Loveland J., Lovell J., McLaren S., McLay K.E., McMurray A., Mashreghi-Mohammadi M., Matthews L., Milne S., Nickerson T., Nguyen M., Overton-Larty E., Palmer S.A., Pearce A.V., Peck A.I., Pelan S., Phillimore B., Porter K., Rice C.M., Rogosin A., Ross M.T., Sarafidou T., Sehra H.K., Shownkeen R., Skuce C.D., Smith M., Standring L., Sycamore N., Tester J., Thorpe A., Torcasso W., Tracey A., Tromans A., Tsolas J., Wall M., Walsh J., Wang H., Weinstock K., West A.P., Willey D.L., Whitehead S.L., Wilming L., Wray P.W., Young L., Chen Y., Lovering R.C., Moschonas N.K., Siebert R., Fechtel K., Bentley D., Durbin R.M., Hubbard T., Doucette-Stamm L., Beck S., Smith D.R., Rogers J.
      Nature 429:375-381(2004) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    5. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    6. "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].
      Tissue: Brain.
    7. "Characterization of a gene encoding survival motor neuron (SMN)-related protein, a constituent of the spliceosome complex."
      Talbot K., Miguel-Aliaga I., Mohaghegh P., Ponting C.P., Davies K.E.
      Hum. Mol. Genet. 7:2149-2156(1998) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION, TISSUE SPECIFICITY, SUBCELLULAR LOCATION.
    8. "SMNrp is an essential pre-mRNA splicing factor required for the formation of the mature spliceosome."
      Meister G., Hannus S., Ploettner O., Baars T., Hartmann E., Fakan S., Laggerbauer B., Fischer U.
      EMBO J. 20:2304-2314(2001) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION, INTERACTION WITH THE SPLICEOSOME; U2 SNRNP AND U4/U5/U6 TRI-SNRNP.
    9. "SPF30 is an essential human splicing factor required for assembly of the U4/U5/U6 tri-small nuclear ribonucleoprotein into the spliceosome."
      Rappsilber J., Ajuh P., Lamond A.I., Mann M.
      J. Biol. Chem. 276:31142-31150(2001) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION, SUBCELLULAR LOCATION, INTERACTION WITH THE SPLICEOSOME; WITH U2 SNRNP AND WITH U4/U5/U6 TRI-SNRNP.
    10. "A probability-based approach for high-throughput protein phosphorylation analysis and site localization."
      Beausoleil S.A., Villen J., Gerber S.A., Rush J., Gygi S.P.
      Nat. Biotechnol. 24:1285-1292(2006) [PubMed] [Europe PMC] [Abstract]
      Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-201, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
      Tissue: Cervix carcinoma.
    11. Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-201, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
      Tissue: Cervix carcinoma.
    12. "Quantitative phosphoproteomic analysis of T cell receptor signaling reveals system-wide modulation of protein-protein interactions."
      Mayya V., Lundgren D.H., Hwang S.-I., Rezaul K., Wu L., Eng J.K., Rodionov V., Han D.K.
      Sci. Signal. 2:RA46-RA46(2009) [PubMed] [Europe PMC] [Abstract]
      Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-201, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
      Tissue: Leukemic T-cell.
    13. "Lysine acetylation targets protein complexes and co-regulates major cellular functions."
      Choudhary C., Kumar C., Gnad F., Nielsen M.L., Rehman M., Walther T.C., Olsen J.V., Mann M.
      Science 325:834-840(2009) [PubMed] [Europe PMC] [Abstract]
      Cited for: ACETYLATION [LARGE SCALE ANALYSIS] AT LYS-219, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
    14. "Quantitative phosphoproteomics reveals widespread full phosphorylation site occupancy during mitosis."
      Olsen J.V., Vermeulen M., Santamaria A., Kumar C., Miller M.L., Jensen L.J., Gnad F., Cox J., Jensen T.S., Nigg E.A., Brunak S., Mann M.
      Sci. Signal. 3:RA3-RA3(2010) [PubMed] [Europe PMC] [Abstract]
      Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-201, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
      Tissue: Cervix carcinoma.
    15. Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
    16. "Structural basis for dimethylarginine recognition by the Tudor domains of human SMN and SPF30 proteins."
      Tripsianes K., Madl T., Machyna M., Fessas D., Englbrecht C., Fischer U., Neugebauer K.M., Sattler M.
      Nat. Struct. Mol. Biol. 18:1414-1420(2011) [PubMed] [Europe PMC] [Abstract]
      Cited for: STRUCTURE BY NMR OF 65-128 IN COMPLEX WITH DIMETHYLATED ARGININE.

    Entry informationi

    Entry nameiSPF30_HUMAN
    AccessioniPrimary (citable) accession number: O75940
    Secondary accession number(s): B2RA27, D3DRB1, Q5T3K6
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: September 26, 2003
    Last sequence update: November 1, 1998
    Last modified: October 1, 2014
    This is version 136 of the entry and version 1 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programChordata Protein Annotation Program
    DisclaimerAny medical or genetic information present in this entry is provided for research, educational and informational purposes only. It is not in any way intended to be used as a substitute for professional medical advice, diagnosis, treatment or care.

    Miscellaneousi

    Keywords - Technical termi

    3D-structure, Complete proteome, Direct protein sequencing, Reference proteome

    Documents

    1. Human chromosome 10
      Human chromosome 10: entries, gene names and cross-references to MIM
    2. MIM cross-references
      Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot
    3. PDB cross-references
      Index of Protein Data Bank (PDB) cross-references
    4. SIMILARITY comments
      Index of protein domains and families

    External Data

    Dasty 3