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Protein

Survival of motor neuron-related-splicing factor 30

Gene

SMNDC1

Organism
Homo sapiens (Human)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Necessary for spliceosome assembly. Overexpression causes apoptosis.3 Publications

GO - Molecular functioni

  1. poly(A) RNA binding Source: UniProtKB

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
  5. spliceosomal complex assembly Source: GO_Central
Complete GO annotation...

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. nucleoplasm Source: HPA
  6. nucleus Source: HPA
  7. spliceosomal complex Source: ProtInc
Complete GO annotation...

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.

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. 25 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 – 825Combined sources
Turni84 – 863Combined sources
Beta strandi87 – 9812Combined sources
Turni99 – 1024Combined sources
Beta strandi103 – 1086Combined sources
Turni109 – 1124Combined sources
Beta strandi113 – 1186Combined sources
Helixi119 – 1213Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
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.
GeneTreeiENSGT00730000111118.
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

        10         20         30         40         50
MSEDLAKQLA SYKAQLQQVE AALSGNGENE DLLKLKKDLQ EVIELTKDLL
60 70 80 90 100
STQPSETLAS SDSFASTQPT HSWKVGDKCM AVWSEDGQCY EAEIEEIDEE
110 120 130 140 150
NGTAAITFAG YGNAEVTPLL NLKPVEEGRK AKEDSGNKPM SKKEMIAQQR
160 170 180 190 200
EYKKKKALKK AQRIKELEQE REDQKVKWQQ FNNRAYSKNK KGQVKRSIFA
210 220 230
SPESVTGKVG VGTCGIADKP MTQYQDTSKY NVRHLMPQ
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:
EMBLi
GenBanki
DDBJi
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:
EMBLi
GenBanki
DDBJi
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.

3D structure databases

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

Protein-protein interaction databases

BioGridi115574. 25 interactions.
IntActiO75940. 4 interactions.
MINTiMINT-4527315.
STRINGi9606.ENSP00000358605.

PTM databases

PhosphoSiteiO75940.

Proteomic databases

MaxQBiO75940.
PaxDbiO75940.
PeptideAtlasiO75940.
PRIDEiO75940.

Protocols and materials databases

DNASUi10285.
Structural Biology KnowledgebaseSearch...

Genome annotation databases

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

Organism-specific databases

CTDi10285.
GeneCardsiGC10M112042.
GeneReviewsiSMNDC1.
HGNCiHGNC:16900. SMNDC1.
MIMi603519. gene.
neXtProtiNX_O75940.
PharmGKBiPA134990780.
GenAtlasiSearch...

Phylogenomic databases

eggNOGiNOG251685.
GeneTreeiENSGT00730000111118.
HOGENOMiHOG000007521.
HOVERGENiHBG057021.
InParanoidiO75940.
KOiK12839.
OMAiNNKAYSK.
OrthoDBiEOG7K6PVX.
PhylomeDBiO75940.
TreeFamiTF315413.

Miscellaneous databases

ChiTaRSiSMNDC1. human.
GeneWikiiSurvival_motor_neuron_domain_containing_1.
GenomeRNAii10285.
NextBioi38968.
PROiO75940.
SOURCEiSearch...

Gene expression databases

BgeeiO75940.
CleanExiHS_SMNDC1.
GenevestigatoriO75940.

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]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  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: March 4, 2015
This is version 141 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

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 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.