IK Gene
protein-coding GIFtS: 55
GCID: GC05P140028
|
|
IK cytokine, down-regulator of HLA II
| |
Aliases
for IK gene
(According to
1HGNC,
2Entrez Gene,
3UniProtKB/Swiss-Prot,
4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc,
7Ensembl,
8DME,
9miRBase,
and/or 10fRNAdb)
About This Section
|
| Aliases |
|---|
| IK Cytokine, Down-Regulator Of HLA II1 2 | | Prer Protein2 | | RED2 3 5 | | Protein Red2 | | Cytokine IK2 3 | | RD Element2 | | IK Factor2 3 | | RER3 | | CSA22 | | Protein RER3 | | Chondrosarcoma-Associated Protein 22 | | |
| External Ids: | HGNC: 59581 | Entrez Gene: 35502 | Ensembl: ENSG000001131417 | OMIM: 6005495 | UniProtKB: Q131233 |
|---|
|
Export aliases for IK gene to outside databasesPrevious GC identifers: GC05P139843 GC05P140610 GC05P140009 GC05P140055 GC05P139992 GC05P139993 GC05P140007 GC05P135173
Summaries
for IK 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 IK:
The protein encoded by this gene was identified by its RED repeat, a stretch of repeated arginine, glutamic acid andaspartic acid residues. The protein localizes to discrete dots within the nucleus, excluding the nucleolus. Itsfunction is unknown. This gene maps to chromosome 5; however, a pseudogene may exist on chromosome 2. (provided byRefSeq, Jul 2008)
UniProtKB/Swiss-Prot: RED_HUMAN, Q13123Function: May bind to chromatin
Gene Wiki entry for IK
|
Genomic Views
for IK 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_000005.9 NC_018916.1 NT_029289.11
Regulatory elements:
 SABiosciences Regulatory transcription factor binding sites in the IK gene promoter:
CREB deltaCREB c-Jun
Other transcription factors
Search SABiosciences Chromatin IP Primers for IK
Epigenetics:
| | QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays in human, mouse, rat IK |
Genomic Location:
Genomic View: UCSC Golden Path with GeneCards custom track
Entrez Gene cytogenetic band: 5q31.3 Ensembl cytogenetic band: 5q31.3 HGNC cytogenetic band: 5q31.3IK Gene in genomic location: bands according to Ensembl, locations according to
 (and/or Entrez Gene and/or Ensembl if different)
GeneLoc information about chromosome 5 GeneLoc Exon Structure GeneLoc location for GC05P140028: view genomic region
(about GC identifiers)
Start:
|
140,026,643 bp from pter |
End:
|
140,042,065 bp from pter |
Size:
|
15,423 bases |
Orientation:
|
plus strand |
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Proteins
for IK 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: RED_HUMAN, Q13123 (See
protein sequence)Recommended Name: Protein Red Size: 557 amino acids; 65602 Da
Subcellular location: Nucleus
Developmental stage: Expressed at similar levels in fetal and adult tissues
Caution: Was originally (PubMed:7970704) thought to be the IK factor, a cytokine involved in the negative regulatorypathway of constitutive MHC class II antigens expression
Secondary accessions: Q6IPD8Explore the universe of human proteins at neXtProt for IK: NX_Q13123
Post-translational modifications:
View modification sites using PhosphoSitePlus2View neXtProt modification sites for NX_Q13123
IK Protein expression data from MOPED and PaxDb: About this image 
REFSEQ proteins: NP_006074.2
ENSEMBL proteins: ENSP00000425564 ENSP00000396301 ENSP00000421930 ENSP00000424622 ENSP00000422641 ENSP00000426764
Human Recombinant Protein Products:
Gene Ontology (GO): 3 cellular component terms (GO ID links to tree view): About this table
IK for ontologies About GeneDecksing
IK Antibody Products:
Assay Products for IK: |
Protein
Domains /
Families
for IK gene(According to InterPro, ProtoNet,
UniProtKB, and/or BLOCKS,
Sets of similar genes according to GeneDecks)
About This Section
|
IK for domains About GeneDecksing
2 InterPro domains/families:Graphical View of Domain Structure for InterPro Entry Q13123ProtoNet protein and cluster: Q13123 1 Blocks protein family: IPB012492 RED-like
UniProtKB/Swiss-Prot: RED_HUMAN, Q13123Similarity: Belongs to the RED family |
Function
for IK 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: RED_HUMAN, Q13123Function: May bind to chromatin Genatlas biochemistry entry for IK:cytokine IK (19kDa) downregulating HLA class II expression on the cell surface
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 IK (see all 3)
OriGene untagged cDNA clones in CMV expression vector in human, mouse, rat for IK
OriGene custom cloning services – gene synthesis, subcloning, mutagenesis,
variant library, vector shuttling 
| |  | GenScript: all cDNA clones in your preferred vector: IK (NM_001197) | |  | Browse Sino Biological Human cDNA Clones | |  | DNA2.0 Custom Codon Optimized Gene
Synthesis Service for IK | |  | Vector BioLabs ready-to-use adenovirus/AAV for human, mouse, rat IK |
In Situ Assay
Products: |
 | Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for IK |
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:0005515 | protein binding |
IPI | -- |
IK for ontologies About GeneDecksing
8 GenomeRNAi human phenotypes for IK:
|
Pathways & Interactions
for IK 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 IK
STRING Interaction
Network Preview (showing 5 interactants - click image to see 24)
5/586 Interacting proteins for IK (Q131231, 2, 3 ENSP000003963014) via UniProtKB, MINT, STRING, and/or I2D (see all 586)About this table
Gene Ontology (GO): 2 biological process terms (GO ID links to tree view): About this table
IK for ontologies About GeneDecksing
|
Drugs & Compounds
for IK 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 IK
Search CenterWatch for drugs/clinical trials and news about IK / RED
|
Transcripts
for IK 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 IK gene: NM_006083.3 Unigene Cluster for IK: IK cytokine, down-regulator of HLA II Hs.421245 [show with all ESTs]Unigene Representative Sequence: AK22592411 Ensembl transcripts including schematic representations, and UCSC links where relevant: ENST00000513256 ENST00000417647(uc011czk.1 uc003lgq.3 uc021yen.1)
ENST00000503332 ENST00000507593 ENST00000508301 ENST00000523672 ENST00000502899
ENST00000512827 ENST00000515015 ENST00000515592 ENST00000518969
Clone
Products: | | OriGene Myc/DDK tagged cDNA clones in CMV expression vector in human, mouse, rat for IK (see all 3)
OriGene untagged cDNA clones in CMV expression vector in human, mouse, rat for IK
OriGene custom cloning services – gene synthesis, subcloning, mutagenesis,
variant library, vector shuttling
| | | GenScript: all cDNA clones in your preferred vector: IK (NM_001197) | | | DNA2.0 Custom Codon Optimized Gene
Synthesis Service for IK | | | Vector BioLabs ready-to-use adenovirus/AAV for human, mouse, rat IK |
Additional cDNA sequence: AF182645.1 AJ005579.1 AK225924.1 AK293626.1 AK308730.1 AK312363.1 AL050296.1 AY007094.1 BC013005.2 BC051295.1 BC071964.1 S74221.1 24/32 DOTS entries (see all 32): DT.418420 DT.40248441 DT.92459896 DT.100845637 DT.100845634 DT.95170073 DT.121031617 DT.100059633 DT.95170088 DT.120833500 DT.120833425 DT.120833416 DT.120833479 DT.95170072 DT.100043123 DT.100845635 DT.120833460 DT.120833503 DT.121031572 DT.319462 DT.100839133 DT.100845629 DT.100059632 DT.120833409 24/295 AceView cDNA sequences (see all 295): BM667779 BM806610 AA235321 BQ102505 CK299491 CA434844 BQ019101 CA442072 BU741196 BM726920 AA953244 AA436395 AW238950 BC071964 AI831143 CA434842 AA531032 BG940194 BU677068 BX102908 BQ000956 BM989324 BU680989 BU615396
GeneLoc Exon Structure
|
Expression
for IK 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
| IK expression in normal human tissues (normalized intensities)
See probesets specificity/sensitivity at GeneAnnot
About this imageBioGPS
CGAP TAG: GCTGTGGATA
About this image
See IK Protein Expression from SPIRE MOPED and PaxDB
Genevestigator expression for IK
SOURCE GeneReport for Unigene cluster: Hs.421245
UniProtKB/Swiss-Prot: RED_HUMAN, Q13123Tissue specificity: Ubiquitous
SABiosciences Expression via Pathway-Focused PCR Array including IK:
Primer
Products: | | OriGene genome-wide validated SYBR primer pairs in human, mouse, rat for IK
Browse OriGene validated miRNA SYBR primer pairs
| | | SABiosciences RT2 qPCR Primer Assay in human, mouse, rat IK | | | QIAGEN QuantiTect SYBR Green Assays in human, mouse, rat IK | | | QIAGEN QuantiFast Probe-based Assays in human, mouse, rat IK | In Situ
Assay Products: |
| Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for IK |
Orthologs
for IK 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 IK gene from 9/29 species (see all 29) About this table
ENSEMBL Gene Tree for IK (if available)
TreeFam Gene Tree for IK (if available) |
Paralogs
for IK gene(Paralogs according to
1HomoloGene,
2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
About This Section
| Paralogs for IK gene
18/51 SIMAP similar genes for IK using alignment to 7 protein entries: RED_HUMAN (see all proteins)
(see all similar genes):DKFZp564B112 CSA2 CALCOCO2 CSPP1 SLC24A1 C14orf105
CCL28 ANKRD55 TAF2 ARL6IP5 C11orf80 EIF3G
EIF3K TMX3 SMYD4 ZNF559 FRG1 KIAA0101
IK for paralogs About GeneDecksing
1 Pseudogenes.org Pseudogene for IK
PGOHUM00000240052
|
Genomic Variants
for IK 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 5 pos | Sequence | # | AA
Chg | Type | More | # | Allele
freq | Pop | Total
sample | More |
|---|
HapMap Linkage Disequilibrium report for IK (140026643 - 140042065 bp)
Structural Variations (Copy Number Variations, Insertions/Deletions, Inversions)
Database of Genomic Variants (DGV) variations for IK: -- | SABiosciences Cancer Mutation PCR Assays |
| | QIAGEN SeqTarget long-range PCR primers in human, mouse, rat for resequencing IK |
|
Disorders
/ Diseases
for IK 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
|
IK for disorders About GeneDecksing
OMIM gene information: 600549
OMIM disorders: --
16  diseases for IK: About MalaCardschondrosarcoma papillary thyroid carcinoma hypertensive encephalopathy fanconi's anemia
folliculitis cutaneous t cell lymphoma thyroid carcinoma hepatitis b
anemia thyroiditis cardiomyopathy hepatitis
pneumonia hypertension carcinoma malaria
1 disease from the University of Copenhagen DISEASES database for IK:Central sleep apnea Human Genome Epidemiology (HuGE) Navigator: IK (115 documents)
Export disorders for IK gene to outside databases
|
Publications
for IK 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 IK gene, integrated from 9 sources (see all 38):
(articles sorted by number of sources associating them with IK) | |  | Utopia: connect your pdf to the dynamic
world of online information |
- A new cytokine (IK) down-regulating HLA class II: monoclonal antibodies, cloning and chromosome localization. (PubMed id 7970704)1, 2, 3, 9 Krief P.... Azzarone B. (1994)
- Isolation, sequencing and expression of RED, a novel human gene encoding an acidic-basic dipeptide repeat. (PubMed id 10216252)1, 2 Assier E.... Rich T. (1999)
- Implication of a new molecule IK in CD34+ hematopoietic progenitor cell proliferation and differentiation. (PubMed id 9160666)1, 9 Cao L.X....Krief P. (1997)
- A census of human soluble protein complexes. (PubMed id 22939629)1 Havugimana P.C....Emili A. (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)
- RED, a spindle pole-associated protein, is required fo r kinetochore localization of MAD1, mitotic progression, and activation of the s pindle assembly checkpoint. (PubMed id 22351768)1 Yeh P.C....Juang Y.L. (2012)
- The proteomic analysis of endogenous FAT10 substrates identifies p62/SQSTM1 as a substrate of FAT10ylation. (PubMed id 22797925)1 Aichem A....Groettrup M. (2012)
- Global landscape of HIV-human protein complexes. (PubMed id 22190034)1 Jager S....Krogan N.J. (2012)
- Functional proteomics establishes the interaction of S IRT7 with chromatin remodeling complexes and expands its role in regulation of R NA polymerase I transcription. (PubMed id 22586326)1 Tsai Y.C....Cristea I.M. (2012)
- Initial characterization of the human central proteome. (PubMed id 21269460)2 Burkard T.R.... Colinge J. (2011)
|
External Searches for IK gene
(in PubMed,
OMIM, and NCBI Bookshelf)
About This Section
|
|
Genome Databases showing IK gene
(According to
Entrez Gene,
HGNC,
AceView,
euGenes,
Ensembl,
miRBase,
ECgene,
Kegg,
and/or
H-InvDB)
About This Section
|
|
Other Databases showing IK gene
(According to HUGE)
About This Section
| -- |
Specialized Databases showing IK 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 IK | Pharmacogenomics, SNPs, Pathways |
|
| | |
About This Section
| Patent Information for IK gene:
Search GeneIP for patents involving IK
GeneCards and IP:
Japan Patent Office Licenses GeneCards European Patent Office Licenses GeneCards Improving the IP Search
|
Products
for IK 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
|
 | |
 | |
 |
| | |  | OriGene Antibodies for IK | | Browse OriGene shRNA RFPs | | | OriGene 29mer shRNA kits in GFP-retroviral vector in human, mouse, rat for IK | | OriGene genome-wide validated SYBR primer pairs in human, mouse, rat for IK | | | OriGene Protein Over-expression Lysate for IK | | Browse OriGene Fluorogenic Cell Assay Kits | | | Browse OriGene siRNAs | | OriGene 3'-UTR Clone for IK | | | OriGene untagged cDNA clones in CMV expression vector in human, mouse, rat for IK | | OriGene Myc/DDK tagged cDNA clones in CMV expression vector in human, mouse, rat for IK | | | Browse OriGene GFP tagged cDNA clones in CMV expression vector | | Browse OriGene MicroRNA Expression Plasmids | | | Browse OriGene basic RS shRNAs | | Browse OriGene validated miRNA SYBR primer pairs | | | Browse OriGene full length recombinant human proteins expressed in human HEK293 cells | | OriGene custom cloning services - gene synthesis, subcloning, mutagenesis,
variant library, vector shuttling | | | OriGene Custom Antibody Services for IK | | OriGene Custom Protein Services for IK | | | OriGene Custom Immunoassay Development | | |
| |
 |
 |
| | | QIAGEN Custom miScript Target Protector blocks miRNA-binding site of in human, mouse, rat IK | | | QIAGEN SeqTarget long-range PCR primers in human, mouse, rat for resequencing IK | | | QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays in human, mouse, rat IK | | | QIAGEN FlexiTube/FlexiPlate siRNA for gene silencing in human, mouse, rat IK | | | QIAGEN QuantiFast Probe-based Assays in human, mouse, rat IK | | | QIAGEN QuantiTect SYBR Green Assays in human, mouse, rat IK |
| |
 |  |  |  | |
| | | | Search Tocris compounds for IK |
| |  |  |  |  | | | | |
 |
 |
 |
 | | | IK Proteins, Antibodies, CLIAs, and ELISAs |
| | | | | Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for IK |
|  |  |  | | | | ThermoFisher Antibodies for IK |
| | | Vector BioLabs ready-to-use adenovirus/AAV for human, mouse, rat IK |
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