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Protein

E3 ubiquitin-protein ligase RNF38

Gene

RNF38

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

Functioni

Acts as an E3 ubiquitin-protein ligase able to ubiquitinate p53/TP53 which promotes its relocalization to discrete foci associated with PML nuclear bodies. Exhibits preference for UBE2D2 as a E2 enzyme.1 Publication

Pathwayi: protein ubiquitination

This protein is involved in the pathway protein ubiquitination, which is part of Protein modification.
View all proteins of this organism that are known to be involved in the pathway protein ubiquitination and in Protein modification.

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Zinc fingeri463 – 504RING-typePROSITE-ProRule annotationAdd BLAST42

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Ligase

Keywords - Biological processi

Ubl conjugation pathway

Keywords - Ligandi

Metal-binding, Zinc

Enzyme and pathway databases

UniPathwayiUPA00143.

Names & Taxonomyi

Protein namesi
Recommended name:
E3 ubiquitin-protein ligase RNF38 (EC:6.3.2.-)
Alternative name(s):
RING finger protein 38
Gene namesi
Name:RNF38
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
Proteomesi
  • UP000005640 Componenti: Chromosome 9

Organism-specific databases

HGNCiHGNC:18052. RNF38.

Subcellular locationi

GO - Cellular componenti

  • cytoplasm Source: GO_Central
  • nucleoplasm Source: GO_Central
  • nucleus Source: FlyBase
  • sperm flagellum Source: Ensembl
Complete GO annotation...

Keywords - Cellular componenti

Nucleus

Pathology & Biotechi

Organism-specific databases

OpenTargetsiENSG00000137075.
PharmGKBiPA34438.

Polymorphism and mutation databases

BioMutaiRNF38.
DMDMi56749664.

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00000560781 – 515E3 ubiquitin-protein ligase RNF38Add BLAST515

Proteomic databases

PaxDbiQ9H0F5.
PeptideAtlasiQ9H0F5.
PRIDEiQ9H0F5.

PTM databases

iPTMnetiQ9H0F5.
PhosphoSitePlusiQ9H0F5.

Expressioni

Tissue specificityi

Widely expressed with highest levels in testis.1 Publication

Gene expression databases

BgeeiENSG00000137075.
CleanExiHS_RNF38.
GenevisibleiQ9H0F5. HS.

Organism-specific databases

HPAiHPA015853.

Interactioni

Protein-protein interaction databases

BioGridi127416. 16 interactors.
IntActiQ9H0F5. 10 interactors.
MINTiMINT-4720518.
STRINGi9606.ENSP00000259605.

Structurei

Secondary structure

1515
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Helixi441 – 445Combined sources5
Beta strandi448 – 450Combined sources3
Beta strandi453 – 455Combined sources3
Beta strandi457 – 459Combined sources3
Turni464 – 467Combined sources4
Beta strandi475 – 478Combined sources4
Turni480 – 482Combined sources3
Beta strandi484 – 486Combined sources3
Helixi487 – 496Combined sources10
Turni501 – 503Combined sources3

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1X4JNMR-A445-506[»]
4V3KX-ray2.04C/F439-515[»]
4V3LX-ray1.53C439-515[»]
ProteinModelPortaliQ9H0F5.
SMRiQ9H0F5.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiQ9H0F5.

Family & Domainsi

Motif

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Motifi57 – 71Bipartite nuclear localization signal 1Add BLAST15
Motifi115 – 131Bipartite nuclear localization signal 2Add BLAST17

Compositional bias

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Compositional biasi239 – 404Pro-richAdd BLAST166

Sequence similaritiesi

Contains 1 RING-type zinc finger.PROSITE-ProRule annotation

Zinc finger

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Zinc fingeri463 – 504RING-typePROSITE-ProRule annotationAdd BLAST42

Keywords - Domaini

Zinc-finger

Phylogenomic databases

eggNOGiKOG0800. Eukaryota.
ENOG41121N2. LUCA.
GeneTreeiENSGT00730000110459.
HOGENOMiHOG000231638.
HOVERGENiHBG059283.
InParanoidiQ9H0F5.
KOiK19041.
OMAiMVDIHEQ.
OrthoDBiEOG091G09VT.
PhylomeDBiQ9H0F5.
TreeFamiTF325756.

Family and domain databases

Gene3Di3.30.40.10. 1 hit.
InterProiIPR001841. Znf_RING.
IPR013083. Znf_RING/FYVE/PHD.
[Graphical view]
PfamiPF13639. zf-RING_2. 1 hit.
[Graphical view]
SMARTiSM00184. RING. 1 hit.
[Graphical view]
PROSITEiPS50089. ZF_RING_2. 1 hit.
[Graphical view]

Sequences (5)i

Sequence statusi: Complete.

This entry describes 5 isoformsi produced by alternative splicing. AlignAdd to basket

Isoform 1 (identifier: Q9H0F5-1) [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
MACKISPGAN SASLPGHPNK VICERVRLQS LFPLLPSDQN TTVQEDAHFK
60 70 80 90 100
AFFQSEDSPS PKRQRLSHSV FDYTSASPAP SPPMRPWEMT SNRQPPSVRP
110 120 130 140 150
SQHHFSGERC NTPARNRRSP PVRRQRGRRD RLSRHNSISQ DENYHHLPYA
160 170 180 190 200
QQQAIEEPRA FHPPNVSPRL LHPAAHPPQQ NAVMVDIHDQ LHQGTVPVSY
210 220 230 240 250
TVTTVAPHGI PLCTGQHIPA CSTQQVPGCS VVFSGQHLPV CSVPPPMLQA
260 270 280 290 300
CSVQHLPVPY AAFPPLISSD PFLIHPPHLS PHHPPHLPPP GQFVPFQTQQ
310 320 330 340 350
SRSPLQRIEN EVELLGEHLP VGGFTYPPSA HPPTLPPSAP LQFLTHDPLH
360 370 380 390 400
QEVSFGVPYP PFMPRRLTGR SRYRSQQPIP PPPYHPSLLP YVLSMLPVPP
410 420 430 440 450
AVGPTFSFEL DVEDGEVENY EALLNLAERL GEAKPRGLTK ADIEQLPSYR
460 470 480 490 500
FNPNNHQSEQ TLCVVCMCDF ESRQLLRVLP CNHEFHAKCV DKWLKANRTC
510
PICRADASEV HRDSE
Length:515
Mass (Da):57,595
Last modified:December 21, 2004 - v4
Checksum:iABFE9486CA732AFA
GO
Isoform 2 (identifier: Q9H0F5-2) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     5-54: Missing.

Note: No experimental confirmation available.
Show »
Length:465
Mass (Da):52,106
Checksum:i18A919182C967BA6
GO
Isoform 3 (identifier: Q9H0F5-3) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     1-83: Missing.

Show »
Length:432
Mass (Da):48,562
Checksum:iCCC2D1396DB31D2C
GO
Isoform 4 (identifier: Q9H0F5-4) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     1-44: MACKISPGAN...LPSDQNTTVQ → MQHTCTQQKK...NLAGFQLQSP
     45-120: Missing.

Note: No experimental confirmation available.
Show »
Length:439
Mass (Da):49,265
Checksum:i76E2EFFA9FDFA02D
GO
Isoform 5 (identifier: Q9H0F5-5) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     1-183: Missing.

Note: No experimental confirmation available.
Show »
Length:332
Mass (Da):36,836
Checksum:i4A2E365DA4A094A0
GO

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti308I → K in CAB66751 (PubMed:11230166).Curated1
Sequence conflicti421E → G in BAG52726 (PubMed:14702039).Curated1

Natural variant

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Natural variantiVAR_055400206A → T.1 PublicationCorresponds to variant rs183475137dbSNPEnsembl.1

Alternative sequence

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Alternative sequenceiVSP_0538451 – 183Missing in isoform 5. 1 PublicationAdd BLAST183
Alternative sequenceiVSP_0373371 – 83Missing in isoform 3. 1 PublicationAdd BLAST83
Alternative sequenceiVSP_0538461 – 44MACKI…NTTVQ → MQHTCTQQKKVTYKHIARFS PRNRLCQADAVFNNNLAGFQ LQSP in isoform 4. 1 PublicationAdd BLAST44
Alternative sequenceiVSP_0122435 – 54Missing in isoform 2. 1 PublicationAdd BLAST50
Alternative sequenceiVSP_05384745 – 120Missing in isoform 4. 1 PublicationAdd BLAST76

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF394047 mRNA. Translation: AAM73697.1.
AL136817 mRNA. Translation: CAB66751.3.
AK024996 mRNA. Translation: BAB15050.1.
AK093480 mRNA. Translation: BAG52726.1.
AL161792, AL354935 Genomic DNA. Translation: CAO03553.1.
AL354935, AL161792 Genomic DNA. Translation: CAO03540.1.
AL354935, AL161792 Genomic DNA. Translation: CAO03541.1.
AL161792, AL354935 Genomic DNA. Translation: CAO03554.1.
CH471071 Genomic DNA. Translation: EAW58305.1.
BC033786 mRNA. Translation: AAH33786.2.
CCDSiCCDS6603.1. [Q9H0F5-1]
CCDS6604.1. [Q9H0F5-2]
RefSeqiNP_073618.3. NM_022781.4. [Q9H0F5-1]
NP_919309.1. NM_194328.2. [Q9H0F5-3]
NP_919310.1. NM_194329.2. [Q9H0F5-2]
NP_919311.1. NM_194330.2. [Q9H0F5-3]
NP_919313.1. NM_194332.2. [Q9H0F5-3]
XP_005251423.1. XM_005251366.3. [Q9H0F5-3]
XP_005251424.1. XM_005251367.3. [Q9H0F5-3]
XP_005251425.1. XM_005251368.3. [Q9H0F5-3]
XP_006716784.1. XM_006716721.3. [Q9H0F5-3]
XP_011516014.1. XM_011517712.2. [Q9H0F5-3]
XP_011516015.1. XM_011517713.2. [Q9H0F5-3]
XP_016869784.1. XM_017014295.1. [Q9H0F5-3]
UniGeneiHs.333503.

Genome annotation databases

EnsembliENST00000259605; ENSP00000259605; ENSG00000137075. [Q9H0F5-1]
ENST00000350199; ENSP00000343947; ENSG00000137075. [Q9H0F5-3]
ENST00000353739; ENSP00000335239; ENSG00000137075. [Q9H0F5-2]
ENST00000357058; ENSP00000349566; ENSG00000137075. [Q9H0F5-3]
ENST00000377877; ENSP00000367109; ENSG00000137075. [Q9H0F5-4]
ENST00000377885; ENSP00000367117; ENSG00000137075. [Q9H0F5-3]
ENST00000611646; ENSP00000483536; ENSG00000137075. [Q9H0F5-4]
GeneIDi152006.
KEGGihsa:152006.
UCSCiuc003zzh.5. human. [Q9H0F5-1]

Keywords - Coding sequence diversityi

Alternative splicing, Polymorphism

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF394047 mRNA. Translation: AAM73697.1.
AL136817 mRNA. Translation: CAB66751.3.
AK024996 mRNA. Translation: BAB15050.1.
AK093480 mRNA. Translation: BAG52726.1.
AL161792, AL354935 Genomic DNA. Translation: CAO03553.1.
AL354935, AL161792 Genomic DNA. Translation: CAO03540.1.
AL354935, AL161792 Genomic DNA. Translation: CAO03541.1.
AL161792, AL354935 Genomic DNA. Translation: CAO03554.1.
CH471071 Genomic DNA. Translation: EAW58305.1.
BC033786 mRNA. Translation: AAH33786.2.
CCDSiCCDS6603.1. [Q9H0F5-1]
CCDS6604.1. [Q9H0F5-2]
RefSeqiNP_073618.3. NM_022781.4. [Q9H0F5-1]
NP_919309.1. NM_194328.2. [Q9H0F5-3]
NP_919310.1. NM_194329.2. [Q9H0F5-2]
NP_919311.1. NM_194330.2. [Q9H0F5-3]
NP_919313.1. NM_194332.2. [Q9H0F5-3]
XP_005251423.1. XM_005251366.3. [Q9H0F5-3]
XP_005251424.1. XM_005251367.3. [Q9H0F5-3]
XP_005251425.1. XM_005251368.3. [Q9H0F5-3]
XP_006716784.1. XM_006716721.3. [Q9H0F5-3]
XP_011516014.1. XM_011517712.2. [Q9H0F5-3]
XP_011516015.1. XM_011517713.2. [Q9H0F5-3]
XP_016869784.1. XM_017014295.1. [Q9H0F5-3]
UniGeneiHs.333503.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1X4JNMR-A445-506[»]
4V3KX-ray2.04C/F439-515[»]
4V3LX-ray1.53C439-515[»]
ProteinModelPortaliQ9H0F5.
SMRiQ9H0F5.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi127416. 16 interactors.
IntActiQ9H0F5. 10 interactors.
MINTiMINT-4720518.
STRINGi9606.ENSP00000259605.

PTM databases

iPTMnetiQ9H0F5.
PhosphoSitePlusiQ9H0F5.

Polymorphism and mutation databases

BioMutaiRNF38.
DMDMi56749664.

Proteomic databases

PaxDbiQ9H0F5.
PeptideAtlasiQ9H0F5.
PRIDEiQ9H0F5.

Protocols and materials databases

DNASUi152006.
Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENST00000259605; ENSP00000259605; ENSG00000137075. [Q9H0F5-1]
ENST00000350199; ENSP00000343947; ENSG00000137075. [Q9H0F5-3]
ENST00000353739; ENSP00000335239; ENSG00000137075. [Q9H0F5-2]
ENST00000357058; ENSP00000349566; ENSG00000137075. [Q9H0F5-3]
ENST00000377877; ENSP00000367109; ENSG00000137075. [Q9H0F5-4]
ENST00000377885; ENSP00000367117; ENSG00000137075. [Q9H0F5-3]
ENST00000611646; ENSP00000483536; ENSG00000137075. [Q9H0F5-4]
GeneIDi152006.
KEGGihsa:152006.
UCSCiuc003zzh.5. human. [Q9H0F5-1]

Organism-specific databases

CTDi152006.
GeneCardsiRNF38.
HGNCiHGNC:18052. RNF38.
HPAiHPA015853.
MIMi612488. gene.
neXtProtiNX_Q9H0F5.
OpenTargetsiENSG00000137075.
PharmGKBiPA34438.
GenAtlasiSearch...

Phylogenomic databases

eggNOGiKOG0800. Eukaryota.
ENOG41121N2. LUCA.
GeneTreeiENSGT00730000110459.
HOGENOMiHOG000231638.
HOVERGENiHBG059283.
InParanoidiQ9H0F5.
KOiK19041.
OMAiMVDIHEQ.
OrthoDBiEOG091G09VT.
PhylomeDBiQ9H0F5.
TreeFamiTF325756.

Enzyme and pathway databases

UniPathwayiUPA00143.

Miscellaneous databases

ChiTaRSiRNF38. human.
EvolutionaryTraceiQ9H0F5.
GeneWikiiRNF38.
GenomeRNAii152006.
PROiQ9H0F5.
SOURCEiSearch...

Gene expression databases

BgeeiENSG00000137075.
CleanExiHS_RNF38.
GenevisibleiQ9H0F5. HS.

Family and domain databases

Gene3Di3.30.40.10. 1 hit.
InterProiIPR001841. Znf_RING.
IPR013083. Znf_RING/FYVE/PHD.
[Graphical view]
PfamiPF13639. zf-RING_2. 1 hit.
[Graphical view]
SMARTiSM00184. RING. 1 hit.
[Graphical view]
PROSITEiPS50089. ZF_RING_2. 1 hit.
[Graphical view]
ProtoNetiSearch...

Entry informationi

Entry nameiRNF38_HUMAN
AccessioniPrimary (citable) accession number: Q9H0F5
Secondary accession number(s): A6PVP9
, B1AM81, B1AM82, B3KSG4, E7EVL3, Q7LB33, Q8N0Y0, Q9H748
Entry historyi
Integrated into UniProtKB/Swiss-Prot: December 21, 2004
Last sequence update: December 21, 2004
Last modified: November 30, 2016
This is version 131 of the entry and version 4 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, Reference proteome

Documents

  1. Human chromosome 9
    Human chromosome 9: entries, gene names and cross-references to MIM
  2. Human entries with polymorphisms or disease mutations
    List of human entries with polymorphisms or disease mutations
  3. Human polymorphisms and disease mutations
    Index of human polymorphisms and disease mutations
  4. MIM cross-references
    Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot
  5. PATHWAY comments
    Index of metabolic and biosynthesis pathways
  6. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  7. 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.