RNF38 Gene
protein-coding GIFtS: 49
GCID: GC09M036336
|
|
ring finger protein 38
| |
Aliases
for RNF38 gene
(According to
1HGNC,
2Entrez Gene,
3UniProtKB/Swiss-Prot,
4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc,
7Ensembl,
8DME,
9miRBase,
and/or 10fRNAdb)
About This Section
|
| Aliases |
|---|
| Ring Finger Protein 381 2 |
Export aliases for RNF38 gene to outside databasesPrevious GC identifers: GC09M036648 GC09M036505 GC09M036326 GC09M036289 |
Summaries
for RNF38 gene(According to Entrez Gene,
Tocris Bioscience,
Wikipedia's
Gene Wiki,
PharmGKB,
UniProtKB/Swiss-Prot,
and/or
UniProtKB/TrEMBL)
About This Section
|
Entrez Gene summary for RNF38:
This gene encodes a protein with a coiled-coil motif and a RING-H2 motif (C3H2C2) at its carboxy-terminus. The RINGmotif is a zinc-binding domain found in a large set of proteins playing roles in diverse cellular processes includingoncogenesis, development, signal transduction, and apoptosis. Multiple transcript variants encoding different isoformshave been found for this gene. (provided by RefSeq, Dec 2008)
Gene Wiki entry for RNF38
|
Genomic Views
for RNF38 gene
(According to
GeneLoc and/or
HGNC, and/or
Entrez Gene (NCBI build 37),
and/or miRBase,
Genomic Views according to
UCSC (hg19) and
Ensembl (release 69),
Regulatory elements and Epigenetics data according to
QIAGEN,
SABiosciences, and/or
SwitchGear Genomics)
About This Section
| RefSeq DNA sequence:- NC_000009.11 NC_018920.1 NT_008413.18
Regulatory elements:
 SABiosciences Regulatory transcription factor binding sites in the RNF38 gene promoter:
Nkx3-1 v2 Nkx3-1 FOXO4 Nkx3-1 v1
Other transcription factors
Search SABiosciences Chromatin IP Primers for RNF38
Epigenetics:
| | QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays in human, mouse, rat RNF38 |
Genomic Location:
Genomic View: UCSC Golden Path with GeneCards custom track
Entrez Gene cytogenetic band: 9p13 Ensembl cytogenetic band: 9p13.2 HGNC cytogenetic band: 9pRNF38 Gene in genomic location: bands according to Ensembl, locations according to
 (and/or Entrez Gene and/or Ensembl if different)
GeneLoc information about chromosome 9 GeneLoc Exon Structure GeneLoc location for GC09M036336: view genomic region
(about GC identifiers)
Start:
|
36,336,393 bp from pter |
End:
|
36,487,545 bp from pter |
Size:
|
151,153 bases |
Orientation:
|
minus strand |
|
Proteins
for RNF38 gene
(According to
1UniProtKB,
HORDE,
neXtProt,
Ensembl,
and/or Reactome,
Modification sites according to 2PhosphoSitePlus,
Specific Peptides from DME,
Protein expression images according to data from SPIRE MOPED and PaxDb,
RefSeq according to NCBI,
PDB rendering according to OCA and/or Proteopedia,
Recombinant Proteins
from
EMD Millipore,
R&D Systems,
GenScript,
Enzo Life Sciences,
OriGene,
Novus Biologicals,
Sino Biological,
ProSpec, and/or
Uscn,
Biochemical Assays by
EMD Millipore,
R&D Systems,
OriGene,
GenScript,
Cell Signaling Technology,
Enzo Life Sciences, and/or
Uscn,
Ontologies according to Gene
Ontology Consortium 01 Mar 2013 and
Entrez Gene,
Antibodies by
EMD Millipore,
R&D Systems,
GenScript,
Cell Signaling Technology,
OriGene,
Novus Biologicals,
Thermo Fisher Scientific,
Abcam, and/or
Uscn)
About This Section
|
UniProtKB/Swiss-Prot: RNF38_HUMAN, Q9H0F5 (See
protein sequence)Recommended Name: RING finger protein 38 Size: 515 amino acids; 57595 Da
1 PDB 3D structure from  and Proteopedia  for RNF38:1X4J (3D)
Secondary accessions: A6PVP9 B1AM82 Q7LB33 Q8N0Y0Alternative splicing: 3 isoforms: Q9H0F5-1 Q9H0F5-2 Q9H0F5-3 (No experimental confirmation available)Explore the universe of human proteins at neXtProt for RNF38: NX_Q9H0F5
Post-translational modifications:
View modification sites using PhosphoSitePlus2View neXtProt modification sites for NX_Q9H0F5
RNF38 Protein expression data from MOPED and PaxDb: About this image 
REFSEQ proteins (5 alternative transcripts):
NP_073618.3 NP_919309.1 NP_919310.1 NP_919311.1 NP_919313.1
ENSEMBL proteins: ENSP00000259605 ENSP00000335239 ENSP00000367101 ENSP00000367117 ENSP00000349566 ENSP00000343947 ENSP00000367109
Human Recombinant Protein Products:
RNF38 Antibody Products:
Assay Products for RNF38: |
Protein
Domains /
Families
for RNF38 gene(According to InterPro, ProtoNet,
UniProtKB, and/or BLOCKS,
Sets of similar genes according to GeneDecks)
About This Section
|
RNF38 for domains About GeneDecksing
2 InterPro domains/families:Graphical View of Domain Structure for InterPro Entry Q9H0F5ProtoNet protein and cluster: Q9H0F5 1 Blocks protein family: IPB001841 Zn-finger
UniProtKB/Swiss-Prot: RNF38_HUMAN, Q9H0F5Similarity: Contains 1 RING-type zinc finger |
Function
for RNF38 gene
(According to 1UniProtKB,
Genatlas,
LifeMap Discovery™,
IUBMB, and/or
2DME,
Human phenotypes from GenomeRNAi,
Animal models from MGI Mar 06 2013,
bound targets from SABiosciences,
miRNA Gene Targets from miRTarBase
shRNA from
OriGene,
RNAi from
EMD Millipore,
siRNAs from
OriGene,
QIAGEN,
microRNA from QIAGEN,
Gene Editing from DNA2.0,
Clones from EMD Millipore,
OriGene,
SwitchGear Genomics,
GenScript,
Sino Biological,
DNA2.0,
and Vector BioLabs,
Cell Lines from GenScript,
LifeMap BioReagents,
In Situ Hybridization Assays from Advanced Cell Diagnostics,
Ontologies according to Gene Ontology Consortium 01 Mar 2013 via
Entrez Gene.)
About This Section
|
Clone
Products: |  | Browse Clones for the Expression of Recombinant Proteins Available from EMD Millipore | |  | OriGene Myc/DDK tagged cDNA clones in CMV expression vector in human, mouse, rat for RNF38 (see all 8)
OriGene untagged cDNA clones in CMV expression vector in human, mouse, rat for RNF38 (see all 6)
OriGene custom cloning services – gene synthesis, subcloning, mutagenesis,
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In Situ Assay
Products: |
 | Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for RNF38 |
Gene Ontology (GO): 1 molecular function term (GO ID links to tree view): About this table | GO ID | Qualified GO term | Evidence | PubMed IDs |
|---|
| GO:0008270 | zinc ion binding |
IEA | -- |
RNF38 for ontologies About GeneDecksing
1 GenomeRNAi human phenotype for RNF38:
|
Pathways & Interactions
for RNF38 gene
(Pathways according to
EMD Millipore,
R&D Systems,
Cell Signaling Technology,
KEGG,
PharmGKB,
BioSystems,
Reactome,
Tocris Bioscience,
GeneGo (Thomson Reuters),
QIAGEN,
and/or UniProtKB,
Sets of similar genes according to GeneDecks,
Interaction Networks according to
SABiosciences,
and/or STRING,
Interactions according to 1UniProtKB,
2MINT,
3I2D, and/or
4STRING,
with links to IntAct and
Ensembl,
Ontologies according to Gene Ontology Consortium 01 Mar 2013 via
Entrez Gene).
About This Section
|
Interactions:
Search SABiosciences Gene Network CentralTM Interacting Genes and Proteins Networks for RNF38
STRING Interaction
Network Preview (showing 5 interactants - click image to see 13)
5/13 Interacting proteins for RNF38 (Q9H0F53 ENSP000002596054) via UniProtKB, MINT, STRING, and/or I2D (see all 13)About this table
|
Drugs & Compounds
for RNF38 gene(Chemical Compounds according to UniProtKB, Enzo Life Sciences,
EMD Millipore, Tocris Bioscience
HMDB,
BitterDB, and/or
Novoseek, and Drugs according to
DrugBank,
Enzo Life Sciences, and/or
PharmGKB, with drugs/clinical trials/news
search links to CenterWatch)
About This Section
|
 Browse Tocris compounds for RNF38
Search CenterWatch for drugs/clinical trials and news about RNF38
|
Transcripts
for RNF38 gene(Secondary structures according to
fRNAdb,
GenBank/EMBL/DDBJ Accessions according to
Unigene
(Build 235 Homo sapiens; Mar 10 2013) or GenBank,
RefSeq according to Entrez Gene,
DOTS (version 10), and/or
AceView,
transcript ids from Ensembl
with links to UCSC,
exon structure from GeneLoc,
alternative splicing isoforms according to ASD and/or
ECgene,
RNAi Products from
EMD Millipore,
siRNAs from
OriGene,
QIAGEN,
shRNA from
OriGene,
microRNA from QIAGEN,
Tagged/untagged cDNA clones from
OriGene,
SwitchGear Genomics,
GenScript,
DNA2.0,
Vector BioLabs,
Primers from
OriGene,
SABiosciences, and/or
QIAGEN
)
About This Section
|
REFSEQ mRNAs for RNF38 gene (6 alternative transcripts): NM_022781.4 NM_194328.2 NM_194329.2 NM_194330.2 NM_194332.2 NM_194331.1 Unigene Cluster for RNF38: Ring finger protein 38 Hs.333503 [show with all ESTs]Unigene Representative Sequence: NM_19432810 Ensembl transcripts including schematic representations, and UCSC links where relevant: ENST00000259605(uc003zzh.3) ENST00000353739(uc003zzi.3) ENST00000377870
ENST00000491349 ENST00000484621 ENST00000488058 ENST00000377885(uc003zzm.3)
ENST00000357058(uc003zzj.3) ENST00000350199(uc003zzk.3 uc003zzl.3)
ENST00000377877
Clone
Products: | | OriGene Myc/DDK tagged cDNA clones in CMV expression vector in human, mouse, rat for RNF38 (see all 8)
OriGene untagged cDNA clones in CMV expression vector in human, mouse, rat for RNF38 (see all 6)
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Additional cDNA sequence: AK025466.1 AK093480.1 AK097653.1 AL136817.1 BC033786.1 23 DOTS entries: DT.100797959 DT.95292790 DT.101983162 DT.100024468 DT.121209582 DT.314651 DT.92465935 DT.100797958 DT.100873711 DT.100024469 DT.70104522 DT.100024470 DT.91950066 DT.97790373 DT.92465958 DT.121209626 DT.121209627 DT.121209644 DT.121209659 DT.95190237 DT.95190258 DT.99961867 DT.92027800 24/244 AceView cDNA sequences (see all 244): AA485216 NM_194329 NM_022781 AI291934 CA435761 AI435322 Z45376 AA890083 R19716 AI362301 BQ921356 AI493807 AK024996 CD723699 Z41092 CD723723 T08778 AF394047 BQ029085 AA719190 BM670981 BI520161 AI499421 AI126596
GeneLoc Exon Structure
5/15 Alternative Splicing Database (ASD) splice patterns (SP) for RNF38 (see all 15) About this scheme
| ExUns: | 1a | · | 1b | ^ | 2a | · | 2b | ^ | 3a | · | 3b | ^ | 4a | · | 4b | ^ | 5a | · | 5b | ^ | 6 | ^ | 7a | · | 7b | ^ | 8a | · | 8b | ^ | 9 | ^ | 10a | · | 10b | · | 10c | ^ | 11a | · | 11b | · | 11c | · | 11d | · | 11e | ^ | 12 | ^ | 13 | ^ |
|---|
|
| SP1: | | | | | | | | | | | | | - | | - | | - | | - | | - | | | | | | | | | | - | | | | | | | | | | | | | | | | | | | | | | |
| SP2: | | | | | | | | | | | | | - | | - | | - | | - | | - | | - | | - | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
| SP3: | | | | | | | | | | | | | | | | | | | | | - | | - | | - | | | | | | - | | | | | | | | | | | | | | | | | | | | | | |
| SP4: | | | | | - | | - | | - | | - | | - | | - | | - | | - | | - | | | | | | | | | | - | | | | | | | | | | | | | | | | | | | | | | |
| SP5: | | | | | | | | | - | | - | | - | | - | | - | | - | | - | | | | | | | | | | - | | | | | | | | | | | | | | | | | | | | | |
| ExUns: | 14 | ^ | 15 | ^ | 16 | ^ | 17 | ^ | 18 | ^ | 19a | · | 19b | · | 19c |
|---|
|
| SP1: | | | | | - | | | | | | | | | | | | |
| SP2: | | | | | - | | | | | | | | | | | | |
| SP3: | | | | | - | | | | | | | | | | | | |
| SP4: | | | | | | | | | | | | | | | | | |
| SP5: | | | | | | | | | | | | | | | | |
ECgene alternative splicing isoforms for RNF38
|
Expression
for RNF38 gene
(RNA expression data according to
H-InvDB,
NONCODE,
miRBase, and
RNAdb,
Expression images according to data from
BioGPS,
Illumina Human BodyMap, and
CGAP
SAGE,
Sets of similar genes according to GeneDecks,
in vivo and in vitro expression data from LifeMap Discovery™,
plus additional links to
Genevestigator, and/or
SOURCE, and/or
BioGPS, and/or
UniProtKB,
PCR Arrays from
SABiosciences,
Primers from
OriGene,
SABiosciences, and/or
QIAGEN,
In Situ Hybridization Assays from Advanced Cell Diagnostics)
About This Section
| RNF38 expression in normal human tissues (normalized intensities)
See probesets specificity/sensitivity at GeneAnnot
About this imageBioGPS
CGAP TAG: AATTGTCATC
About this image
See RNF38 Protein Expression from SPIRE MOPED and PaxDB
Genevestigator expression for RNF38
SOURCE GeneReport for Unigene cluster: Hs.333503
UniProtKB/Swiss-Prot: RNF38_HUMAN, Q9H0F5Tissue specificity: Widely expressed with highest levels in testis
SABiosciences Expression via Pathway-Focused PCR Array including RNF38:
Primer
Products: | | OriGene genome-wide validated SYBR primer pairs in human, mouse, rat for RNF38
Browse OriGene validated miRNA SYBR primer pairs
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Assay Products: |
| Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for RNF38 |
Orthologs
for RNF38 gene
(Orthologs according to
1,2HomoloGene (2older version, for species not in 1newer version),
3euGenes,
4SGD
,
5MGI Mar 06 2013,
with possible further links to
Flybase
and/or
WormBase,
and/or
6Ensembl pan taxonomic compara ,
Gene Trees according to Ensembl and
TreeFam)
About This Section
|
This gene was present in the common ancestor of eukaryotes.
Orthologs for RNF38 gene from 7/22 species (see all 22) About this table
ENSEMBL Gene Tree for RNF38 (if available)
TreeFam Gene Tree for RNF38 (if available) |
Paralogs
for RNF38 gene(Paralogs according to
1HomoloGene,
2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
About This Section
| Paralogs for RNF38 gene
- RNF62 RNF112 RNF1652 RLIM2 RNF442 RNF1112
1 SIMAP similar gene for RNF38 using alignment to 2 protein entries: RNF38_HUMAN (see all proteins):RNF44
RNF38 for paralogs About GeneDecksing
|
Genomic Variants
for RNF38 gene(SNPs/Variants according to the
1NCBI SNP Database,
2Ensembl,
3PupaSUITE,
UniProtKB, and
DNA2.0,
Linkage Disequilibrium by HapMap,
Structural Variations(CNVs/InDels/Inversions) from the Database of Genomic Variants, Mutations from the Human Gene
Mutation Database (HGMD) and the Locus Specific Mutation
Databases (LSDB), Blood group antigen gene mutations by BGMUT,
Resequencing Primers from QIAGEN,
Cancer Mutation PCR Arrays and Assays and Copy Number PCR Arrays from SABiosciences)
About This Section
|
| Genomic Data | Transcription Related Data | Allele Frequencies | | SNP ID | Valid | Clinical
significance | Chr 9 pos | Sequence | # | AA
Chg | Type | More | # | Allele
freq | Pop | Total
sample | More |
|---|
HapMap Linkage Disequilibrium report for RNF38 (36336393 - 36487545 bp)
Structural Variations (Copy Number Variations, Insertions/Deletions, Inversions)
Database of Genomic Variants (DGV): 17 variations for RNF38
5 CNVs: 36950 43344 65385 100634 47924
11 Indels: 95959 82940 95958 82938 82942 95956 11342 82941 95957 82939 82937
1 Inversion: 37330
Human Gene Mutation Database (HGMD): RNF38
| SABiosciences Cancer Mutation PCR Assays |
| | QIAGEN SeqTarget long-range PCR primers in human, mouse, rat for resequencing RNF38 |
|
Disorders
/ Diseases
for RNF38 gene
(in which this Gene is Involved, According to MalaCards,
OMIM, UniProtKB,
the University of Copenhagen DISEASES
database,
Genatlas, GeneTests,
GAD,
HuGE Navigator,
and/or TGDB.)
About This Section
|
RNF38 for disorders About GeneDecksing
OMIM gene information: 612488
OMIM disorders: --
2  diseases for RNF38: About MalaCardshepatocellular carcinoma carcinoma
Export disorders for RNF38 gene to outside databases
|
Publications
for RNF38 gene (in
PubMed.
Associations of this gene to articles via
1Entrez Gene,
2UniProtKB/Swiss-Prot,
3HGNC,
4GAD,
5PharmGKB,
6HMDB,
7DrugBank,
8UniProtKB/TrEMBL,
9 Novoseek, and/or
10fRNAdb)
About This Section
|
PubMed articles for RNF38 gene, integrated from 9 sources (see all 19):
(articles sorted by number of sources associating them with RNF38) | |  | Utopia: connect your pdf to the dynamic
world of online information |
- DNA sequence and analysis of human chromosome 9. (PubMed id 15164053)1, 2 Humphray S.J.... Dunham I. (2004)
- The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PubMed id 15489334)1, 2 Gerhard D.S....Malek J. (2004)
- Cloning and characterization of a novel human gene RNF38 encoding a conserved putative protein with a RING finger domain. (PubMed id 12074600)1, 2 Eisenberg I....Mitrani-Rosenbaum S. (2002)
- Towards a catalog of human genes and proteins: sequencing and analysis of 500 novel complete protein coding human cDNAs. (PubMed id 11230166)1, 2 Wiemann S.... Poustka A. (2001)
- Systematic analysis of dimeric E3-RING interactions re veals increased combinatorial complexity in human ubiquitination networks. (PubMed id 22493164)1 Woodsmith J....Sanderson C.M. (2012)
- Methods for quantification of in vivo changes in prote in ubiquitination following proteasome and deubiquitinase inhibition. (PubMed id 22505724)1 Udeshi N.D....Carr S.A. (2012)
- Systematic and quantitative assessment of the ubiquiti n-modified proteome. (PubMed id 21906983)1 Kim W....Gygi S.P. (2011)
- A genome-scale protein interaction profile of Drosoph ila p53 uncovers additional nodes of the human p53 network. (PubMed id 20308539)1 Lunardi A....Collavin L. (2010)
- Analysis of the human E2 ubiquitin conjugating enzyme protein interaction network. (PubMed id 19549727)1 Markson G....Sanderson C.M. (2009)
- Ubiquitin-mediated proteolysis of HuR by heat shock. (PubMed id 19322201)1 Abdelmohsen K....Gorospe M. (2009)
|
External Searches for RNF38 gene
(in PubMed,
OMIM, and NCBI Bookshelf)
About This Section
|
|
Genome Databases showing RNF38 gene
(According to
Entrez Gene,
HGNC,
AceView,
euGenes,
Ensembl,
miRBase,
ECgene,
Kegg,
and/or
H-InvDB)
About This Section
|
|
Other Databases showing RNF38 gene
(According to HUGE)
About This Section
| -- |
Specialized Databases showing RNF38 gene(According to PharmGKB,
ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL,
Wikipedia and/or GeneReviews via UniProtKB/Swiss-Prot)
About This Section
|
| Name | Description |
| PharmGKB entry for RNF38 | Pharmacogenomics, SNPs, Pathways |
|
| | |
About This Section
| Patent Information for RNF38 gene:
Search GeneIP for patents involving RNF38
GeneCards and IP:
Japan Patent Office Licenses GeneCards European Patent Office Licenses GeneCards Improving the IP Search
|
Products
for RNF38 gene(Antibodies, recombinant proteins, and assays from EMD Millipore, R&D Systems, OriGene, QIAGEN, GenScript, Cell Signaling Technology, SABiosciences, Novus Biologicals, Sino Biological, Enzo Life Sciences, Abcam, ProSpec, Uscn, Thermo Fisher Scientific, Gene Editing from DNA2.0, Clones from EMD Millipore, OriGene, GenScript, Sino Biological, DNA2.0, SwitchGear Genomics, Vector BioLabs, Cell lines from GenScript and LifeMap BioReagents, PCR Arrays from SABiosciences, Drugs and/or compounds from EMD Millipore, Tocris Bioscience, and/or
Enzo Life Sciences),
In Situ Hybridization Assays from
Advanced Cell Diagnostics
About This Section
|
 | |
 | |
 |
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| |
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| | | | | Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for RNF38 |
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| | | Vector BioLabs ready-to-use adenovirus/AAV for human, mouse, rat RNF38 |
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