RNF170 Gene
protein-coding GIFtS: 49
GCID: GC08M042705
|
|
ring finger protein 170
| |
Aliases
for RNF170 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 1701 2 3 | | Putative LAG1-Interacting Protein2 3 | | DKFZP564A0221 | | SNAX12 | | E3 Ubiquitin-Protein Ligase RNF1702 | | EC 6.3.2.-3 |
Export aliases for RNF170 gene to outside databasesPrevious GC identifers: GC08M042824 GC08M041227 |
Summaries
for RNF170 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 RNF170:
This gene encodes a RING domain-containing protein that resides in the endoplasmic reticulum (ER) membrane. Thisprotein functions as an E3 ubiquitin ligase and mediates ubiquitination and processing of inositol 1,4,5-trisphosphate(IP3) receptors via the ER-associated protein degradation pathway. It is recruited to the activated IP3 receptors bythe ERLIN1/ERLIN2 complex to which it is constitutively bound. Mutations in this gene are associated with autosomaldominant sensory ataxia. Alternatively spliced transcript variants have been found for this gene. (provided by RefSeq,Jun 2012)
UniProtKB/Swiss-Prot: RN170_HUMAN, Q96K19Function: E3 ubiquitin-protein ligase that plays an essential role in stimulus-induced inositol 1,4,5-trisphosphatereceptor type 1 (ITPR1) ubiquitination and degradation via the endoplasmic reticulum-associated degradation (ERAD)pathway. Also involved in ITPR1 turnover in resting cells
|
Genomic Views
for RNF170 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_000008.10 NC_018919.1 NT_167187.1
Regulatory elements:
 SABiosciences Regulatory transcription factor binding sites in the RNF170 gene promoter:
STAT5B STAT1 STAT4 STAT1beta STAT6 STAT5A STAT1alpha PPAR-alpha STAT2 STAT3
Other transcription factors
Search SABiosciences Chromatin IP Primers for RNF170
Epigenetics:
| | QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays in human, mouse, rat RNF170 |
Genomic Location:
Genomic View: UCSC Golden Path with GeneCards custom track
Entrez Gene cytogenetic band: 8p11.21 Ensembl cytogenetic band: 8p11.21 HGNC cytogenetic band: 8p11.21RNF170 Gene in genomic location: bands according to Ensembl, locations according to
 (and/or Entrez Gene and/or Ensembl if different)
GeneLoc information about chromosome 8 GeneLoc Exon Structure GeneLoc location for GC08M042705: view genomic region
(about GC identifiers)
Start:
|
42,704,780 bp from pter |
End:
|
42,752,433 bp from pter |
Size:
|
47,654 bases |
Orientation:
|
minus strand |
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Proteins
for RNF170 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: RN170_HUMAN, Q96K19 (See
protein sequence)Recommended Name: E3 ubiquitin-protein ligase RNF170 Size: 258 amino acids; 29815 Da
Subunit: Constitutively associated with the ERLIN1/ERLIN 2 complex. Interacts with activated ITPR1
Subcellular location: Endoplasmic reticulum membrane; Multi-pass membrane protein (By similarity)
Sequence caution: Sequence=AAH39461.1; Type=Erroneous initiation; Note=Translation N-terminally shortened;Sequence=AAH44566.1; Type=Erroneous initiation; Note=Translation N-terminally shortened;
Secondary accessions: D3DSY6 E9PIL4 Q7Z483 Q86YC0 Q8IXR7 Q8N2B5 Q8N5G9 Q8NG30 Q9H0V6Alternative splicing: 6 isoforms: Q96K19-1 Q96K19-2 Q96K19-3 Q96K19-4 Q96K19-5 Q96K19-6 (No experimental confirmation available)Explore the universe of human proteins at neXtProt for RNF170: NX_Q96K19
Post-translational modifications:
View modification sites using PhosphoSitePlus2View neXtProt modification sites for NX_Q96K19
RNF170 Protein expression data from MOPED and PaxDb: About this image 
REFSEQ proteins (4 alternative transcripts):
NP_001153695.1 NP_001153696.1 NP_001153697.1 NP_112216.3
ENSEMBL proteins: ENSP00000326138 ENSP00000434797 ENSP00000240159 ENSP00000435782 ENSP00000436416 ENSP00000437146 ENSP00000445725 ENSP00000325969
Human Recombinant Protein Products:
Gene Ontology (GO): 2 cellular component terms (GO ID links to tree view): About this table | GO ID | Qualified GO term | Evidence | PubMed IDs |
|---|
| GO:0005789 | endoplasmic reticulum membrane |
IEA | -- | | GO:0016021 | integral to membrane |
IEA | -- |
RNF170 for ontologies About GeneDecksing
RNF170 Antibody Products:
Assay Products for RNF170: |
Protein
Domains /
Families
for RNF170 gene(According to InterPro, ProtoNet,
UniProtKB, and/or BLOCKS,
Sets of similar genes according to GeneDecks)
About This Section
|
RNF170 for domains About GeneDecksing
4 InterPro domains/families:Graphical View of Domain Structure for InterPro Entry Q96K19ProtoNet protein and cluster: Q96K19 1 Blocks protein family: IPB001841 Zn-finger
UniProtKB/Swiss-Prot: RN170_HUMAN, Q96K19Similarity: Contains 1 RING-type zinc finger |
Function
for RNF170 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
|
Function Summary:
UniProtKB/Swiss-Prot: RN170_HUMAN, Q96K19Function: E3 ubiquitin-protein ligase that plays an essential role in stimulus-induced inositol 1,4,5-trisphosphatereceptor type 1 (ITPR1) ubiquitination and degradation via the endoplasmic reticulum-associated degradation (ERAD)pathway. Also involved in ITPR1 turnover in resting cellsEnzyme Number (IUBMB): EC 6.3.2.-1
Clone
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OriGene untagged cDNA clones in CMV expression vector in human, mouse, rat for RNF170 (see all 5)
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Synthesis Service for RNF170 | |  | Vector BioLabs ready-to-use adenovirus/AAV for human, mouse, rat RNF170 |
In Situ Assay
Products: |
 | Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for RNF170 |
Gene Ontology (GO): 2 molecular function terms (GO ID links to tree view): About this table | GO ID | Qualified GO term | Evidence | PubMed IDs |
|---|
| GO:0008270 | zinc ion binding |
IEA | -- | | GO:0016874 | ligase activity |
IEA | -- |
RNF170 for ontologies About GeneDecksing
3 GenomeRNAi human phenotypes for RNF170:
|
Pathways & Interactions
for RNF170 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
|
UniProtKB/Swiss-Prot: RN170_HUMAN, Q96K19Pathway: Protein modification; protein ubiquitinationInteractions:
Search SABiosciences Gene Network CentralTM Interacting Genes and Proteins Networks for RNF170
STRING Interaction
Network Preview (showing 3 interactants - click image to see more details)
5/6 Interacting proteins for RNF170 (Q96K193 ENSP000002401594) via UniProtKB, MINT, STRING, and/or I2D (see all 6) About this table
Gene Ontology (GO): 1 biological process term (GO ID links to tree view): About this table | GO ID | Qualified GO term | Evidence | PubMed IDs |
|---|
| GO:0016567 | protein ubiquitination |
IEA | -- |
RNF170 for ontologies About GeneDecksing
|
Drugs & Compounds
for RNF170 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 RNF170
Search CenterWatch for drugs/clinical trials and news about RNF170 / RN170
|
Transcripts
for RNF170 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 RNF170 gene (4 alternative transcripts): NM_001160223.1 NM_001160224.1 NM_001160225.1 NM_030954.3 Unigene Cluster for RNF170: Ring finger protein 170 Hs.491626 [show with all ESTs]Unigene Representative Sequence: NM_0011602239 Ensembl transcripts including schematic representations, and UCSC links where relevant: ENST00000319104(uc011lcx.2) ENST00000527424 ENST00000240159 ENST00000526349
ENST00000528318(uc003xpq.4) ENST00000531440 ENST00000524954 ENST00000534961(uc010lxp.3 uc003xpo.3 uc003xpm.3 uc003xpp.3)
ENST00000319073(uc003xpn.3)
Clone
Products: | | OriGene Myc/DDK tagged cDNA clones in CMV expression vector in human, mouse, rat for RNF170 (see all 5)
OriGene untagged cDNA clones in CMV expression vector in human, mouse, rat for RNF170 (see all 5)
OriGene custom cloning services – gene synthesis, subcloning, mutagenesis,
variant library, vector shuttling
| | | GenScript: all cDNA clones in your preferred vector (see all 4): RNF170 (NM_030954) | | | DNA2.0 Custom Codon Optimized Gene
Synthesis Service for RNF170 | | | Vector BioLabs ready-to-use adenovirus/AAV for human, mouse, rat RNF170 |
Additional cDNA sequence: AF209504.1 AK027748.1 AK090864.1 AK225086.1 AK225568.1 AL136620.1 BC032393.1 BC039461.1 BC058289.1 NR_027668.1 NR_027669.1 12 DOTS entries: DT.100785896 DT.211764 DT.424810 DT.101958837 DT.100785891 DT.100785893 DT.91705503 DT.95161168 DT.100026051 DT.100785892 DT.91705507 DT.92014543 24/124 AceView cDNA sequences (see all 124): BG109210 AK090864 CA423416 AI658891 AX746655 AI088240 AA747394 CF529399 AA349453 BE905842 CF530018 BU684703 BG054666 BM126157 AA731169 AI801728 AA648420 BM459392 NM_030954 M85820 AI702320 BU608543 CR610418 AK027748
GeneLoc Exon Structure
4 Alternative Splicing Database (ASD) splice patterns (SP) for RNF170 About this scheme
| ExUns: | 1a | · | 1b | ^ | 2 | ^ | 3 | ^ | 4 | ^ | 5 | ^ | 6 | ^ | 7a | · | 7b | ^ | 8 | ^ | 9 |
|---|
|
| SP1: | | | | | | | | | | | | | | | | | | | | | | | |
| SP2: | | | | | - | | | | | | | | | | | | | | | | | | |
| SP3: | | | | | - | | | | | | | | - | | | | | | | | | | |
| SP4: | | | | | - | | | | | | | | | | - | | - | | - | | | |
ECgene alternative splicing isoforms for RNF170
|
Expression
for RNF170 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
| RNF170 expression in normal human tissues (normalized intensities)
See probesets specificity/sensitivity at GeneAnnot
About this imageBioGPS
CGAP TAG: TTTGAAGTTC
About this image
See RNF170 Protein Expression from SPIRE MOPED and PaxDB
Genevestigator expression for RNF170
SOURCE GeneReport for Unigene cluster: Hs.491626
UniProtKB/Swiss-Prot: RN170_HUMAN, Q96K19Tissue specificity: Expressed in the spinal chord
SABiosciences Expression via Pathway-Focused PCR Array including RNF170:
Primer
Products: | | OriGene genome-wide validated SYBR primer pairs in human, mouse, rat for RNF170
Browse OriGene validated miRNA SYBR primer pairs
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Assay Products: |
| Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for RNF170 |
Orthologs
for RNF170 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 RNF170 gene from 8/20 species (see all 20) About this table
ENSEMBL Gene Tree for RNF170 (if available)
TreeFam Gene Tree for RNF170 (if available) |
Paralogs
for RNF170 gene(Paralogs according to
1HomoloGene,
2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
About This Section
| -- |
Genomic Variants
for RNF170 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 8 pos | Sequence | # | AA
Chg | Type | More | # | Allele
freq | Pop | Total
sample | More |
|---|
HapMap Linkage Disequilibrium report for RNF170 (42704780 - 42752433 bp)
Structural Variations (Copy Number Variations, Insertions/Deletions, Inversions)
Database of Genomic Variants (DGV): 2 variations for RNF170
2 Indels: 41081 100329
Human Gene Mutation Database (HGMD): RNF170
| SABiosciences Cancer Mutation PCR Assays |
| | QIAGEN SeqTarget long-range PCR primers in human, mouse, rat for resequencing RNF170 |
|
Disorders
/ Diseases
for RNF170 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
|
RNF170 for disorders About GeneDecksing
OMIM gene information: 614649
OMIM disorders: --
UniProtKB/Swiss-Prot: RN170_HUMAN, Q96K19
Defects in RNF170 are the cause of ataxia, sensory, type 1, autosomal dominant (SNAX1) [MIM:608984]. A raredisease characterized by progressive ataxia caused by degeneration of the posterior columns of the spinal cord.Affected individuals have a reduced ability to feel pain, temperature and vibration, particularly in the hands andfeet. Their most prominent feature is an ataxic gait resulting from a severe loss of proprioception. Thus, patientsrely on visual cues for maintaining proper body posture, such that they are unable to remain upright if their eyes areclosed (Romberg sign)
1  disease for RNF170: About MalaCardsataxia
Human Genome Epidemiology (HuGE) Navigator: RNF170 (1 document)
Export disorders for RNF170 gene to outside databases
|
Publications
for RNF170 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 RNF170 gene, integrated from 9 sources (see all 12):
(articles sorted by number of sources associating them with RNF170) | |  | Utopia: connect your pdf to the dynamic
world of online information |
- Towards a catalog of human genes and proteins: sequencing and analysis of 500 novel complete protein coding human cDNAs. (PubMed id 11230166)1, 2, 3 Wiemann S.... Poustka A. (2001)
- A mutation in the RNF170 gene causes autosomal domina nt sensory ataxia. (PubMed id 21115467)1, 2 Valdmanis P.N....Rouleau G.A. (2011)
- RNF170 protein, an endoplasmic reticulum membrane ubi quitin ligase, mediates inositol 1,4,5-trisphosphate receptor ubiquitination an d degradation. (PubMed id 21610068)1, 2 Lu J.P....Wojcikiewicz R.J. (2011)
- 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)
- Complete sequencing and characterization of 21,243 full-length human cDNAs. (PubMed id 14702039)1, 2 Ota T.... Sugano S. (2004)
- Initial characterization of the human central proteome. (PubMed id 21269460)2 Burkard T.R.... Colinge J. (2011)
- A proteome-wide, quantitative survey of in vivo ubiqui tylation sites reveals widespread regulatory roles. (PubMed id 21890473)1 Wagner S.A....Choudhary C. (2011)
- A comprehensive framework of E2-RING E3 interactions of the human ubiquitin-proteasome system. (PubMed id 19690564)1 van Wijk S.J....Timmers H.T. (2009)
- Diversification of transcriptional modulation: large-scale identification and characterization of putative alternative promoters of human genes. (PubMed id 16344560)1 Kimura K.... Sugano S. (2006)
- DNA sequence and analysis of human chromosome 8. (PubMed id 16421571)2 Nusbaum C....Lander E.S. (2006)
|
External Searches for RNF170 gene
(in PubMed,
OMIM, and NCBI Bookshelf)
About This Section
|
|
Genome Databases showing RNF170 gene
(According to
Entrez Gene,
HGNC,
AceView,
euGenes,
Ensembl,
miRBase,
ECgene,
Kegg,
and/or
H-InvDB)
About This Section
|
|
Other Databases showing RNF170 gene
(According to HUGE)
About This Section
| -- |
Specialized Databases showing RNF170 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 RNF170 | Pharmacogenomics, SNPs, Pathways |
|
| | |
About This Section
| Patent Information for RNF170 gene:
Search GeneIP for patents involving RNF170
GeneCards and IP:
Japan Patent Office Licenses GeneCards European Patent Office Licenses GeneCards Improving the IP Search
|
Products
for RNF170 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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| | | | | Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for RNF170 |
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