Human Gene SUMO1 (ENST00000392246.7_7) from GENCODE V47lift37
  Description: small ubiquitin like modifier 1, transcript variant 7 (from RefSeq NR_163943.1)
Gencode Transcript: ENST00000392246.7_7
Gencode Gene: ENSG00000116030.17_9
Transcript (Including UTRs)
   Position: hg19 chr2:203,070,905-203,103,320 Size: 32,416 Total Exon Count: 5 Strand: -
Coding Region
   Position: hg19 chr2:203,071,976-203,103,174 Size: 31,199 Coding Exon Count: 5 

Page IndexSequence and LinksUniProtKB CommentsPrimersMalaCardsCTD
Gene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther Species
GO AnnotationsmRNA DescriptionsPathwaysOther NamesModel InformationMethods
Data last updated at UCSC: 2024-08-22 23:36:26

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr2:203,070,905-203,103,320)mRNA (may differ from genome)Protein (101 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
HGNCMalacardsMGIOMIMPubMedReactome
UniProtKBWikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: SUMO1_HUMAN
DESCRIPTION: RecName: Full=Small ubiquitin-related modifier 1; Short=SUMO-1; AltName: Full=GAP-modifying protein 1; Short=GMP1; AltName: Full=SMT3 homolog 3; AltName: Full=Sentrin; AltName: Full=Ubiquitin-homology domain protein PIC1; AltName: Full=Ubiquitin-like protein SMT3C; Short=Smt3C; AltName: Full=Ubiquitin-like protein UBL1; Flags: Precursor;
FUNCTION: Ubiquitin-like protein that can be covalently attached to proteins as a monomer or a lysine-linked polymer. Covalent attachment via an isopeptide bond to its substrates requires prior activation by the E1 complex SAE1-SAE2 and linkage to the E2 enzyme UBE2I, and can be promoted by E3 ligases such as PIAS1-4, RANBP2 or CBX4. This post-translational modification on lysine residues of proteins plays a crucial role in a number of cellular processes such as nuclear transport, DNA replication and repair, mitosis and signal transduction. Involved for instance in targeting RANGAP1 to the nuclear pore complex protein RANBP2. Polymeric SUMO1 chains are also susceptible to polyubiquitination which functions as a signal for proteasomal degradation of modified proteins. May also regulate a network of genes involved in palate development.
SUBUNIT: Interacts with SAE2, UBE2I, RANBP2, PIAS1 and PIAS2. Interacts with PARK2. Covalently attached to a number of proteins such as IKFZ1, PML, RANGAP1, HIPK2, SP100, p53, p73-alpha, MDM2, JUN, DNMT3B and TDG. Also interacts with HIF1A, HIPK2, HIPK3, CHD3, EXOSC9, RAD51 and RAD52. Interacts with USP25 (via ts SIM domain); the interaction weakly sumoylates USP25.
INTERACTION: P10275:AR; NbExp=7; IntAct=EBI-80140, EBI-608057; Q9UER7:DAXX; NbExp=5; IntAct=EBI-80140, EBI-77321; Q9UBC3:DNMT3B; NbExp=4; IntAct=EBI-80140, EBI-80125; Q16665:HIF1A; NbExp=2; IntAct=EBI-80140, EBI-447269; P10242:MYB; NbExp=3; IntAct=EBI-80140, EBI-298355; P29590:PML; NbExp=2; IntAct=EBI-80140, EBI-295890; P46060:RANGAP1; NbExp=3; IntAct=EBI-80140, EBI-396091; Q9Y3V2:RWDD3; NbExp=2; IntAct=EBI-80140, EBI-1549885; O43290:SART1; NbExp=2; IntAct=EBI-80140, EBI-607761; Q01826:SATB1; NbExp=2; IntAct=EBI-80140, EBI-743747;
SUBCELLULAR LOCATION: Nucleus membrane. Nucleus speckle. Cytoplasm. Note=Recruited by BCL11A into the nuclear body (By similarity).
PTM: Cleavage of precursor form by SENP1 or SENP2 is necessary for function.
PTM: Polymeric SUMO1 chains undergo polyubiquitination by RNF4.
DISEASE: Defects in SUMO1 are the cause of non-syndromic orofacial cleft type 10 (OFC10) [MIM:613705]; also called non-syndromic cleft lip with or without cleft palate 10. OFC10 is a birth defect consisting of cleft lips with or without cleft palate. Cleft lips are associated with cleft palate in two-third of cases. A cleft lip can occur on one or both sides and range in severity from a simple notch in the upper lip to a complete opening in the lip extending into the floor of the nostril and involving the upper gum. Note=A chromosomal aberation involving SUMO1 is the cause of OFC10. Translocation t(2;8)(q33.1;q24.3). The breakpoint occurred in the SUMO1 gene and resulted in haploinsufficiency confirmed by protein assays.
SIMILARITY: Belongs to the ubiquitin family. SUMO subfamily.
SIMILARITY: Contains 1 ubiquitin-like domain.
WEB RESOURCE: Name=Wikipedia; Note=SUMO protein entry; URL="http://en.wikipedia.org/wiki/SUMO_protein";

-  Primer design for this transcript
 

Primer3Plus can design qPCR Primers that straddle exon-exon-junctions, which amplify only cDNA, not genomic DNA.
Click here to load the transcript sequence and exon structure into Primer3Plus

Exonprimer can design one pair of Sanger sequencing primers around every exon, located in non-genic sequence.
Click here to open Exonprimer with this transcript

To design primers for a non-coding sequence, zoom to a region of interest and select from the drop-down menu: View > In External Tools > Primer3


-  MalaCards Disease Associations
  MalaCards Gene Search: SUMO1
Diseases sorted by gene-association score: orofacial cleft 10* (1019), lip cancer (22), neuronal intranuclear inclusion disease (18), cleft lip (9), orofacial cleft (9), cheilitis (9), tooth agenesis* (6), leukemia, acute promyelocytic, somatic (5), diabetes mellitus, insulin-dependent, 5 (4)
* = Manually curated disease association

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene           more ... click here to view the complete list

+  Common Gene Haplotype Alleles
  Press "+" in the title bar above to open this section.

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 46.72 RPKM in Cells - EBV-transformed lymphocytes
Total median expression: 1449.79 RPKM



View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
  Press "+" in the title bar above to open this section.

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -56.40146-0.386 Picture PostScript Text
3' UTR -230.601071-0.215 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  InterPro Domains: Graphical view of domain structure
IPR000626 - Ubiquitin
IPR019955 - Ubiquitin_supergroup

Pfam Domains:
PF00240 - Ubiquitin family
PF11976 - Ubiquitin-2 like Rad60 SUMO-like

SCOP Domains:
47266 - 4-helical cytokines
54236 - Ubiquitin-like

Protein Data Bank (PDB) 3-D Structure
MuPIT help
1A5R - NMR MuPIT 1TGZ - X-ray MuPIT 1WYW - X-ray MuPIT 1Y8R - X-ray MuPIT 1Z5S - X-ray MuPIT 2ASQ - NMR MuPIT 2BF8 - X-ray MuPIT 2G4D - X-ray MuPIT 2IO2 - X-ray MuPIT 2IY0 - X-ray 2IY1 - X-ray 2KQS - NMR MuPIT 2LAS - NMR MuPIT 2PE6 - X-ray MuPIT 2UYZ - X-ray MuPIT 2VRR - X-ray MuPIT 3KYC - X-ray MuPIT 3KYD - X-ray 3RZW - X-ray MuPIT 3UIP - X-ray MuPIT


ModBase Predicted Comparative 3D Structure on P63165
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The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
No orthologNo orthologNo orthologNo orthologNo orthologNo ortholog
Gene DetailsGene Details    
Gene SorterGene Sorter    
 RGD    
      
      

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0001222 transcription corepressor binding
GO:0003723 RNA binding
GO:0005515 protein binding
GO:0008022 protein C-terminus binding
GO:0008134 transcription factor binding
GO:0015459 potassium channel regulator activity
GO:0019789 SUMO transferase activity
GO:0019899 enzyme binding
GO:0030674 protein binding, bridging
GO:0031386 protein tag
GO:0031625 ubiquitin protein ligase binding
GO:0035259 glucocorticoid receptor binding
GO:0044388 small protein activating enzyme binding

Biological Process:
GO:0000122 negative regulation of transcription from RNA polymerase II promoter
GO:0006281 DNA repair
GO:0006303 double-strand break repair via nonhomologous end joining
GO:0006355 regulation of transcription, DNA-templated
GO:0016032 viral process
GO:0016925 protein sumoylation
GO:0030578 PML body organization
GO:0031334 positive regulation of protein complex assembly
GO:0031647 regulation of protein stability
GO:0032436 positive regulation of proteasomal ubiquitin-dependent protein catabolic process
GO:0032880 regulation of protein localization
GO:0034605 cellular response to heat
GO:0043392 negative regulation of DNA binding
GO:0043433 negative regulation of sequence-specific DNA binding transcription factor activity
GO:0045759 negative regulation of action potential
GO:0045892 negative regulation of transcription, DNA-templated
GO:0050821 protein stabilization
GO:0060021 palate development
GO:0060334 regulation of interferon-gamma-mediated signaling pathway
GO:0071276 cellular response to cadmium ion
GO:0086004 regulation of cardiac muscle cell contraction
GO:0090204 protein localization to nuclear pore
GO:1901896 positive regulation of calcium-transporting ATPase activity
GO:1902260 negative regulation of delayed rectifier potassium channel activity
GO:1903169 regulation of calcium ion transmembrane transport

Cellular Component:
GO:0000792 heterochromatin
GO:0001650 fibrillar center
GO:0001741 XY body
GO:0005634 nucleus
GO:0005643 nuclear pore
GO:0005654 nucleoplasm
GO:0005730 nucleolus
GO:0005737 cytoplasm
GO:0005886 plasma membrane
GO:0016020 membrane
GO:0016604 nuclear body
GO:0016605 PML body
GO:0016607 nuclear speck
GO:0030425 dendrite
GO:0031510 SUMO activating enzyme complex
GO:0031965 nuclear membrane
GO:0045202 synapse
GO:0097165 nuclear stress granule
GO:0008076 voltage-gated potassium channel complex


-  Descriptions from all associated GenBank mRNAs
  U83117 - Human sentrin mRNA, complete cds.
U61397 - Human ubiquitin-homology domain protein PIC1 mRNA, complete cds.
AB062294 - Homo sapiens OK/SW-cl.43 mRNA for ubiquitin-homology domain protein PIC1, complete cds.
BC006462 - Homo sapiens SMT3 suppressor of mif two 3 homolog 1 (S. cerevisiae), mRNA (cDNA clone MGC:2095 IMAGE:3546125), complete cds.
BC066306 - Homo sapiens SMT3 suppressor of mif two 3 homolog 1 (S. cerevisiae), mRNA (cDNA clone MGC:87116 IMAGE:4818792), complete cds.
BC053528 - Homo sapiens SMT3 suppressor of mif two 3 homolog 1 (S. cerevisiae), mRNA (cDNA clone MGC:61614 IMAGE:3452929), complete cds.
BC005899 - Homo sapiens SMT3 suppressor of mif two 3 homolog 1 (S. cerevisiae), mRNA (cDNA clone IMAGE:4047245).
U38784 - Human ubiquitin-like protein mRNA, complete cds.
JD328134 - Sequence 309158 from Patent EP1572962.
JD501686 - Sequence 482710 from Patent EP1572962.
U67122 - Human ubiquitin-related protein SUMO-1 mRNA, complete cds.
JD548973 - Sequence 529997 from Patent EP1572962.
JD333954 - Sequence 314978 from Patent EP1572962.
JD362801 - Sequence 343825 from Patent EP1572962.
JD404232 - Sequence 385256 from Patent EP1572962.
JD147811 - Sequence 128835 from Patent EP1572962.
X99586 - H.sapiens mRNA for SMT3C protein.
JD250584 - Sequence 231608 from Patent EP1572962.
BT006632 - Homo sapiens ubiquitin-like 1 (sentrin) mRNA, complete cds.
CR542147 - Homo sapiens full open reading frame cDNA clone RZPDo834G0523D for gene UBL1, ubiquitin-like 1 (sentrin); complete cds, incl. stopcodon.
U72722 - Human gap modifying protein 1 mRNA, complete cds.
DQ893210 - Synthetic construct clone IMAGE:100005840; FLH195274.01X; RZPDo839A08152D SMT3 suppressor of mif two 3 homolog 1 (S. cerevisiae) (SUMO1) gene, encodes complete protein.
AK311840 - Homo sapiens cDNA, FLJ92103, Homo sapiens ubiquitin-like 1 (sentrin) (UBL1), mRNA.
KJ892349 - Synthetic construct Homo sapiens clone ccsbBroadEn_01743 SUMO1 gene, encodes complete protein.
KJ897721 - Synthetic construct Homo sapiens clone ccsbBroadEn_07115 SUMO1 gene, encodes complete protein.
DQ896156 - Synthetic construct Homo sapiens clone IMAGE:100010616; FLH195270.01L; RZPDo839A08151D SMT3 suppressor of mif two 3 homolog 1 (S. cerevisiae) (SUMO1) gene, encodes complete protein.
AB587462 - Synthetic construct DNA, clone: pF1KB8253, Homo sapiens SUMO1 gene for SMT3 suppressor of mif two 3 homolog 1, without stop codon, in Flexi system.
CR542156 - Homo sapiens full open reading frame cDNA clone RZPDo834B0124D for gene UBL1, ubiquitin-like 1 (sentrin); complete cds, without stopcodon.
JD074312 - Sequence 55336 from Patent EP1572962.
JD561554 - Sequence 542578 from Patent EP1572962.

-  Biochemical and Signaling Pathways
  BioCarta from NCI Cancer Genome Anatomy Project
h_parkinPathway - Role of Parkin in the Ubiquitin-Proteasomal Pathway
h_pmlPathway - Regulation of transcriptional activity by PML
h_ctbp1Pathway - SUMOylation as a mechanism to modulate CtBP-dependent gene responses
h_ranbp2Pathway - Sumoylation by RanBP2 Regulates Transcriptional Repression
h_sumoPathway - Basic Mechanisms of SUMOylation

Reactome (by CSHL, EBI, and GO)

Protein P63165 (Reactome details) participates in the following event(s):

R-HSA-877281 PIAS1 binds p-STAT1 dimer
R-HSA-2990833 Conjugation of SUMO1 to UBA2:SAE1
R-HSA-2990840 SENP1,2,5 proteolytically process SUMO1
R-HSA-2997709 PIAS1,4 SUMOylates BRCA1 with SUMO1
R-HSA-2997723 PIAS4 SUMOylates TP53BP1 with SUMO1
R-HSA-3000383 UBE2I, HDAC7 SUMOylate PML with SUMO1
R-HSA-3000399 RANBP2 SUMOylates SP100 with SUMO1
R-HSA-3108212 SMC5-SMC6 Complex SUMOylates Cohesin with SUMO1
R-HSA-3232162 PIAS3 SUMOylates MITF with SUMO1
R-HSA-3234081 SUMOylation of TFAP2A with SUMO1
R-HSA-3234084 SUMOylation of TFAP2B with SUMO1
R-HSA-3234094 SUMOylation of TFAP2C with SUMO1
R-HSA-3247493 PIAS1 SUMOylates SP3 with SUMO1
R-HSA-3900047 SUMOylation of DDX17 with SUMO1
R-HSA-3968414 UBE2I (UBC9), PIAS1 SUMOylate FOXL2 with SUMO1
R-HSA-4090281 PIAS1,2-1 SUMOylate HIC1 with SUMO1
R-HSA-4551604 PIAS4 SUMOylates PARP1 with SUMO1
R-HSA-4551648 SUMOylation of TDG with SUMO1
R-HSA-4551655 CBX4 SUMOylates BMI1 in PRC1 with SUMO1
R-HSA-4551661 PIAS4 SUMOylates RNF168 with SUMO1
R-HSA-4551724 PIAS4 SUMOylates HERC2 with SUMO1
R-HSA-4551727 CBX4 SUMOylates CBX4 in PRC1 with SUMO1
R-HSA-4568846 CDKN2A (p14-ARF) SUMOylates WRN with SUMO1
R-HSA-4568848 PIAS1,2-1 SUMOylates XRCC4 with SUMO1
R-HSA-4568863 SUMOylation of RAD52 with SUMO1
R-HSA-4570467 SUMOylation of NOP58 with SUMO1
R-HSA-4570493 RANBP2 (NUP358) SUMOylates HNRNPC with SUMO1
R-HSA-4570496 SUMOylation of Histone H4 with SUMO1
R-HSA-4570528 SUMOylation of XPC with SUMO1
R-HSA-4570554 SUMOylation of MDC1 with SUMO1
R-HSA-4615872 RANBP2 SUMOylates HDAC4 with SUMO1
R-HSA-4615873 PIAS2-2 SUMOylates SUZ12 with SUMO1
R-HSA-4615889 SUMOylation of HDAC1 with SUMO1
R-HSA-4615905 PIAS1 SUMOylates SATB1 with SUMO1
R-HSA-4615910 SUMOylation of PCNA with SUMO1
R-HSA-4615933 SUMOylation of CBX5 with SUMO1
R-HSA-4616015 SUMOylation of HDAC2 with SUMO1
R-HSA-4641342 SUMOylation of TOP2A with SUMO1
R-HSA-4641345 SUMOylation of TOP2B with SUMO1
R-HSA-4641362 SUMOylation of TOP1 with SUMO1
R-HSA-5228508 RANBP2 SUMOylates PML with SUMO1
R-HSA-5228525 RANBP2 SUMOylates TOP2A with SUMO1
R-HSA-5682607 PIAS4 SUMOylates HERC2 with SUMO1 at DNA DSBs
R-HSA-8956365 ZBED1 (DREF) SUMOylates CHD3 with SUMO1
R-HSA-2993780 Transfer of SUMO1 from E1 to UBE2I (UBC9)
R-HSA-5684071 RNF4 ubiquitinates MDC1
R-HSA-5693599 Association of Ku heterodimer with ends of DNA double-strand break
R-HSA-6790454 SUMOylation of XPC
R-HSA-6790487 RNF111 ubiquitinates SUMOylated XPC
R-HSA-5682629 HERC2 facilitates UBE2N:UBE2V2 binding to RNF8
R-HSA-5682863 RNF168 binds DNA DSBs
R-HSA-5683077 RNF8 and RNF168 ubiquitinate KDM4A,B
R-HSA-5682858 RNF8 and RNF168 ubiquitinate H2AFX
R-HSA-5693566 TP53BP1 associates with H4K20Me2 at DNA DSBs
R-HSA-5683384 UIMC1 and FAM175A bind DNA DSBs
R-HSA-5683405 PPP5C dephosphorylates TP53BP1
R-HSA-5683425 ATM phosphorylates TP53BP1 at DNA DSBs
R-HSA-5693551 Phosphorylation of BRCA1-A complex at multiple sites by ATM
R-HSA-5683385 Formation of BRCA1-A complex at DNA DSBs
R-HSA-5683735 CHEK2 is recruited to DNA DSBs
R-HSA-5683801 CHEK2 phosphorylates BRCA1
R-HSA-69891 Phosphorylation and activation of CHEK2 by ATM
R-HSA-5684052 PIAS4 SUMOylates MDC1
R-HSA-5686685 RIF1 and PAX1IP bind TP53BP1 at DNA DSBs
R-HSA-5686900 TP53BP1 recruits DCLRE1C to ATM
R-HSA-5686704 Activated ATM phosphorylates DCLRE1C
R-HSA-877312 Regulation of IFNG signaling
R-HSA-3065676 SUMO is conjugated to E1 (UBA2:SAE1)
R-HSA-3065679 SUMO is proteolytically processed
R-HSA-877300 Interferon gamma signaling
R-HSA-3215018 Processing and activation of SUMO
R-HSA-3108214 SUMOylation of DNA damage response and repair proteins
R-HSA-3232118 SUMOylation of transcription factors
R-HSA-8866904 Negative regulation of activity of TFAP2 (AP-2) family transcription factors
R-HSA-3899300 SUMOylation of transcription cofactors
R-HSA-4551638 SUMOylation of chromatin organization proteins
R-HSA-4570464 SUMOylation of RNA binding proteins
R-HSA-4615885 SUMOylation of DNA replication proteins
R-HSA-5693565 Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks
R-HSA-3065678 SUMO is transferred from E1 to E2 (UBE2I, UBC9)
R-HSA-5693607 Processing of DNA double-strand break ends
R-HSA-5693571 Nonhomologous End-Joining (NHEJ)
R-HSA-913531 Interferon Signaling
R-HSA-2990846 SUMOylation
R-HSA-5696395 Formation of Incision Complex in GG-NER
R-HSA-3108232 SUMO E3 ligases SUMOylate target proteins
R-HSA-8864260 Transcriptional regulation by the AP-2 (TFAP2) family of transcription factors
R-HSA-5693606 DNA Double Strand Break Response
R-HSA-5693567 HDR through Homologous Recombination (HR) or Single Strand Annealing (SSA)
R-HSA-5693532 DNA Double-Strand Break Repair
R-HSA-1280215 Cytokine Signaling in Immune system
R-HSA-597592 Post-translational protein modification
R-HSA-5696399 Global Genome Nucleotide Excision Repair (GG-NER)
R-HSA-212436 Generic Transcription Pathway
R-HSA-5693538 Homology Directed Repair
R-HSA-73894 DNA Repair
R-HSA-168256 Immune System
R-HSA-392499 Metabolism of proteins
R-HSA-5696398 Nucleotide Excision Repair
R-HSA-73857 RNA Polymerase II Transcription
R-HSA-74160 Gene expression (Transcription)
R-HSA-69473 G2/M DNA damage checkpoint
R-HSA-69481 G2/M Checkpoints
R-HSA-69620 Cell Cycle Checkpoints
R-HSA-1640170 Cell Cycle

-  Other Names for This Gene
  Alternate Gene Symbols: A8MUS8, B2R4I5, ENST00000392246.1, ENST00000392246.2, ENST00000392246.3, ENST00000392246.4, ENST00000392246.5, ENST00000392246.6, NR_163943, OK/SW-cl.43, P55856, P63165, Q6FGG0, Q6NZ62, Q93068, SMT3C, SMT3H3, SUMO1_HUMAN, UBL1, uc318uyf.1, uc318uyf.2
UCSC ID: ENST00000392246.7_7
RefSeq Accession: NM_003352.8
Protein: P63165 (aka SUMO1_HUMAN)

-  Gene Model Information
  Click here for a detailed description of the fields of the table above.

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.