The protein encoded by this gene was identified by its RED repeat, a stretch of repeated arginine, glutamic acid and aspartic acid residues. The protein localizes to discrete dots within the nucleus, excluding the nucleolus. Its function is unknown. This gene maps to chromosome 5; however, a pseudogene may exist on chromosome 2. [provided by RefSeq, Jul 2008] See more...

Aliases for IK Gene

Aliases for IK Gene

  • IK Cytokine 2 3 5
  • IK Cytokine, Down-Regulator Of HLA II 2 3
  • Cytokine IK 3 4
  • Protein Red 3 4
  • IK Factor 3 4
  • RED 3 4
  • RER 3 4
  • Chondrosarcoma-Associated Protein 2 3
  • Prer Protein 3
  • Protein RER 4
  • RD Element 3
  • CSA2 3

External Ids for IK Gene

Previous GeneCards Identifiers for IK Gene

  • GC05P139843
  • GC05P140610
  • GC05P140009
  • GC05P140055
  • GC05P139992
  • GC05P139993
  • GC05P140007
  • GC05P140028
  • GC05P135173
  • GC05P141198
  • GC05P141473
  • GC05P142383
  • GC05P142489
  • GC05P142599
  • GC05P141579
  • GC05P141687
  • GC05P141789
  • GC05P141881
  • GC05P141989
  • GC05P142092
  • GC05P142198
  • GC05P142300

Summaries for IK Gene

Entrez Gene Summary for IK Gene

  • The protein encoded by this gene was identified by its RED repeat, a stretch of repeated arginine, glutamic acid and aspartic acid residues. The protein localizes to discrete dots within the nucleus, excluding the nucleolus. Its function is unknown. This gene maps to chromosome 5; however, a pseudogene may exist on chromosome 2. [provided by RefSeq, Jul 2008]

GeneCards Summary for IK Gene

IK (IK Cytokine) is a Protein Coding gene. Diseases associated with IK include Radial Neuropathy and Influenza. Gene Ontology (GO) annotations related to this gene include identical protein binding. An important paralog of this gene is WDR55.

UniProtKB/Swiss-Prot Summary for IK Gene

  • Involved in pre-mRNA splicing as a component of the spliceosome (PubMed:28781166). Auxiliary spliceosomal protein that regulates selection of alternative splice sites in a small set of target pre-mRNA species (Probable). Required for normal mitotic cell cycle progression (PubMed:22351768, PubMed:24252166). Recruits MAD1L1 and MAD2L1 to kinetochores, and is required to trigger the spindle assembly checkpoint (PubMed:22351768). Required for normal accumulation of SMU1 (PubMed:24945353).
  • (Microbial infection) Required, together with SMU1, for normal splicing of influenza A virus NS1 pre-mRNA, which is required for the production of the exportin NS2 and for the production of influenza A virus particles. Not required for the production of VSV virus particles.

Gene Wiki entry for IK Gene

Additional gene information for IK Gene

No data available for CIViC Summary , Tocris Summary , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for IK Gene

Genomics for IK Gene

GeneHancer (GH) Regulatory Elements for IK Gene

Promoters and enhancers for IK Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH05J140646 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE CraniofacialAtlas 500.7 +0.7 743 2.8 FOXK2 ZBTB40 ZNF217 EP300 SIN3A NRF1 TCF12 POLR2G SP1 GTF2E2 MIR3655 IK NDUFA2 RF00017-4951 lnc-NDUFA2-1 piR-50576 SRA1 ENSG00000228737 EIF4EBP3 CD14
GH05J140112 Promoter/Enhancer 2 UCNEbase Ensembl ENCODE CraniofacialAtlas 19.4 -532.4 -532372 5 CTCF SIN3A NRF1 USF1 POLR2G BCLAF1 GTF2E2 PHF8 ZFX ZNF10 MALINC1 piR-52459 HARS2 ANKHD1 TMCO6 IK WDR55 APBB3 piR-39974 PURA
GH05J140106 Promoter/Enhancer 1.7 Ensembl ENCODE CraniofacialAtlas 20.8 -538.4 -538421 4.7 HNRNPK ZNF217 EP300 CTCF ZSCAN5C NRF1 POLR2G GTF2E2 PHF8 ZFX PURA lnc-IGIP-1 HARS2 IK UBE2D2 APBB3 ANKHD1 TMCO6 piR-30317 MALINC1
GH05J140611 Promoter/Enhancer 1.5 FANTOM5 Ensembl ENCODE 22.4 -35.2 -35227 1.5 GTF2E2 PHB2 AFF1 TARDBP HES1 RUNX1 CTBP1 MYC HDAC3 NCOR1 CD14 TMCO6 APBB3 ANKHD1 IK WDR55 HARS2 SLC35A4 EIF4EBP3 NDUFA2
GH05J139633 Promoter/Enhancer 2.7 EPDnew FANTOM5 Ensembl ENCODE CraniofacialAtlas dbSUPER 9.8 -993.6 -993629 40.2 RXRA EP300 FOXK2 HNRNPK ZBTB40 ZNF217 CTCF ZSCAN5C SIN3A NRF1 CXXC5 ANKHD1 TMCO6 APBB3 STING1 IK PSD2 DNAJC18 ENSG00000253404 MZB1
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around IK on UCSC Golden Path with GeneCards custom track

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for IK

Top Transcription factor binding sites by QIAGEN in the IK gene promoter:
  • c-Jun
  • CREB
  • deltaCREB

Genomic Locations for IK Gene

Genomic Locations for IK Gene
chr5:140,647,058-140,662,480
(GRCh38/hg38)
Size:
15,423 bases
Orientation:
Plus strand
chr5:140,026,643-140,042,065
(GRCh37/hg19)
Size:
15,423 bases
Orientation:
Plus strand

Genomic View for IK Gene

Genes around IK on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
IK Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for IK Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for IK Gene

Proteins for IK Gene

  • Protein details for IK Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q13123-RED_HUMAN
    Recommended name:
    Protein Red
    Protein Accession:
    Q13123
    Secondary Accessions:
    • Q6IPD8

    Protein attributes for IK Gene

    Size:
    557 amino acids
    Molecular mass:
    65602 Da
    Quaternary structure:
    • (Microbial infection) Identified in a complex with SMU1 and influenza A virus RNA polymerase subunits PB1 and PB2. Directly interacts with SMU1 and with influenza A virus RNA polymerase subunits PB1 and PB2.
    • Component of the spliceosome B complex (PubMed:22365833, PubMed:28781166). Interacts with SMU1 (PubMed:22365833, PubMed:24945353). Interacts with MAD1L1 (PubMed:22351768). May interact with DHX15 (PubMed:24252166).

    Three dimensional structures from OCA and Proteopedia for IK Gene

neXtProt entry for IK Gene

Post-translational modifications for IK Gene

  • Ubiquitination at Lys164, Lys173, and Lys260
  • Modification sites at PhosphoSitePlus

Other Protein References for IK Gene

No data available for DME Specific Peptides for IK Gene

Domains & Families for IK Gene

Gene Families for IK Gene

Protein Domains for IK Gene

Blocks:
  • RED-like, C-terminal
InterPro:
ProtoNet:

Suggested Antigen Peptide Sequences for IK Gene

GenScript: Design optimal peptide antigens:
  • IK cytokine, down-regulator of HLA II (Q95HA6_HUMAN)
  • Chondrosarcoma-associated protein 2 (Q9UK43_HUMAN)
  • Protein RER (RED_HUMAN)

Graphical View of Domain Structure for InterPro Entry

Q13123

UniProtKB/Swiss-Prot:

RED_HUMAN :
  • Belongs to the RED family.
Family:
  • Belongs to the RED family.
genes like me logo Genes that share domains with IK: view

Function for IK Gene

Molecular function for IK Gene

UniProtKB/Swiss-Prot Function:
Involved in pre-mRNA splicing as a component of the spliceosome (PubMed:28781166). Auxiliary spliceosomal protein that regulates selection of alternative splice sites in a small set of target pre-mRNA species (Probable). Required for normal mitotic cell cycle progression (PubMed:22351768, PubMed:24252166). Recruits MAD1L1 and MAD2L1 to kinetochores, and is required to trigger the spindle assembly checkpoint (PubMed:22351768). Required for normal accumulation of SMU1 (PubMed:24945353).
UniProtKB/Swiss-Prot Function:
(Microbial infection) Required, together with SMU1, for normal splicing of influenza A virus NS1 pre-mRNA, which is required for the production of the exportin NS2 and for the production of influenza A virus particles. Not required for the production of VSV virus particles.
UniProtKB/Swiss-Prot Induction:
Up-regulated during mitosis (at protein level).
GENATLAS Biochemistry:
cytokine IK (19kDa) downregulating HLA class II expression on the cell surface

Phenotypes From GWAS Catalog for IK Gene

Gene Ontology (GO) - Molecular Function for IK Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005515 protein binding IPI 22190034
GO:0042802 identical protein binding IPI 22365833
genes like me logo Genes that share ontologies with IK: view
genes like me logo Genes that share phenotypes with IK: view

Animal Model Products

CRISPR Products

miRNA for IK Gene

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for IK

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for IK Gene

Localization for IK Gene

Subcellular locations from UniProtKB/Swiss-Prot for IK Gene

Nucleus. Nucleus, nucleoplasm. Chromosome. Cytoplasm, cytoskeleton, spindle pole. Note=Predominantly present throughout the nucleoplasm during prometaphase, metaphase and anaphase. Is also detected in nuclear foci that are not identical with Cajal bodies. Starts to accumulate at chromosomes during telophase, and is nearly exclusively associated with chromosomes in newly divided cells (PubMed:24252166). Colocalizes with MAD1L1 at mitotic spindle poles during metaphase and anaphase (PubMed:22351768). {ECO:0000269 PubMed:24252166}.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for IK gene
Compartment Confidence
nucleus 5
cytoskeleton 3
cytosol 2
plasma membrane 1
extracellular 1
mitochondrion 1
endoplasmic reticulum 1
endosome 1
lysosome 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Nuclear speckles (4)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for IK Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000228 colocalizes_with nuclear chromosome IMP 24252166
GO:0000922 spindle pole IEA --
GO:0005634 nucleus IEA,IDA 28781166
GO:0005654 nucleoplasm IDA,IEA 24252166
GO:0005681 spliceosomal complex IEA --
genes like me logo Genes that share ontologies with IK: view

Pathways & Interactions for IK Gene

PathCards logo

SuperPathways for IK Gene

No Data Available

Gene Ontology (GO) - Biological Process for IK Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000278 mitotic cell cycle IMP 24252166
GO:0000398 mRNA splicing, via spliceosome IDA 28781166
GO:0006397 mRNA processing IEA --
GO:0007094 mitotic spindle assembly checkpoint IEA,IMP 22351768
GO:0008380 RNA splicing IEA --
genes like me logo Genes that share ontologies with IK: view

No data available for Pathways by source and SIGNOR curated interactions for IK Gene

Drugs & Compounds for IK Gene

No Compound Related Data Available

Transcripts for IK Gene

mRNA/cDNA for IK Gene

1 REFSEQ mRNAs :
13 NCBI additional mRNA sequence :
11 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for IK

Alternative Splicing Database (ASD) splice patterns (SP) for IK Gene

No ASD Table

Relevant External Links for IK Gene

GeneLoc Exon Structure for
IK

Expression for IK Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for IK Gene

Protein differential expression in normal tissues from HIPED for IK Gene

This gene is overexpressed in Adrenal (14.1), Peripheral blood mononuclear cells (13.0), and Blymphocyte (6.1).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for IK Gene



Protein tissue co-expression partners for IK Gene

- Elite partner

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for IK

SOURCE GeneReport for Unigene cluster for IK Gene:

Hs.421245

mRNA Expression by UniProt/SwissProt for IK Gene:

Q13123-RED_HUMAN
Tissue specificity: Ubiquitous.

Evidence on tissue expression from TISSUES for IK Gene

  • Lung(4.7)
  • Nervous system(4.7)
  • Liver(4.5)
  • Skin(3.4)
  • Eye(2.9)
  • Intestine(2.5)
  • Heart(2.4)
  • Muscle(2.4)
  • Spleen(2.4)
  • Blood(2.2)
  • Kidney(2.2)
genes like me logo Genes that share expression patterns with IK: view

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , mRNA differential expression in normal tissues and Phenotype-based relationships between genes and organs from Gene ORGANizer for IK Gene

Orthologs for IK Gene

This gene was present in the common ancestor of animals.

Orthologs for IK Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia IK 30
  • 99.76 (n)
platypus
(Ornithorhynchus anatinus)
Mammalia IK 31
  • 92 (a)
OneToOne
cow
(Bos Taurus)
Mammalia IK 31 30
  • 91.83 (n)
OneToOne
dog
(Canis familiaris)
Mammalia IK 30
  • 91.65 (n)
mouse
(Mus musculus)
Mammalia Ik 17 31 30
  • 90.84 (n)
rat
(Rattus norvegicus)
Mammalia Ik 30
  • 90.31 (n)
chicken
(Gallus gallus)
Aves IK 31 30
  • 83.91 (n)
OneToOne
lizard
(Anolis carolinensis)
Reptilia IK 31
  • 51 (a)
OneToOne
African clawed frog
(Xenopus laevis)
Amphibia Xl.24451 30
tropical clawed frog
(Silurana tropicalis)
Amphibia Str.11062 30
zebrafish
(Danio rerio)
Actinopterygii ik 31 30
  • 75.56 (n)
OneToOne
wufb54c03 30
rainbow trout
(Oncorhynchus mykiss)
Actinopterygii Omy.755 30
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP004738 30
  • 58.55 (n)
fruit fly
(Drosophila melanogaster)
Insecta beag 30
  • 57.77 (n)
CG18005 31 32
  • 46 (a)
OneToOne
worm
(Caenorhabditis elegans)
Secernentea smu-2 31
  • 35 (a)
OneToOne
sea squirt
(Ciona savignyi)
Ascidiacea CSA.10369 31
  • 52 (a)
OneToOne
Species where no ortholog for IK was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • oppossum (Monodelphis domestica)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)

Evolution for IK Gene

ENSEMBL:
Gene Tree for IK (if available)
TreeFam:
Gene Tree for IK (if available)
Aminode:
Evolutionary constrained regions (ECRs) for IK: view image

Paralogs for IK Gene

Paralogs for IK Gene

Pseudogenes.org Pseudogenes for IK Gene

genes like me logo Genes that share paralogs with IK: view

Variants for IK Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for IK Gene

SNP ID Clinical significance and condition Chr 05 pos Variation AA Info Type
724585 Benign: not provided 140,648,481(+) C/T SYNONYMOUS_VARIANT
772873 Benign: not provided 140,662,219(+) C/T INTRON_VARIANT

Additional dbSNP identifiers (rs#s) for IK Gene

Variation tolerance for IK Gene

Residual Variation Intolerance Score: 29% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 1.33; 26.31% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for IK Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
IK

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot and Structural Variations from Database of Genomic Variants (DGV) for IK Gene

Disorders for IK Gene

MalaCards: The human disease database

(7) MalaCards diseases for IK Gene - From: DISEASES and GeneCards

Disorder Aliases PubMed IDs
radial neuropathy
influenza
  • flu
white piedra
  • tinea blanca
chronic rhinitis
  • rhinitis - chronic
coffin-siris syndrome 1
  • css1
- elite association - COSMIC cancer census association via MalaCards
Search IK in MalaCards View complete list of genes associated with diseases

Additional Disease Information for IK

Genetic Association Database
(GAD)
Human Genome Epidemiology Navigator
(HuGE)
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
genes like me logo Genes that share disorders with IK: view

No data available for UniProtKB/Swiss-Prot and Genatlas for IK Gene

Publications for IK Gene

  1. A new cytokine (IK) down-regulating HLA class II: monoclonal antibodies, cloning and chromosome localization. (PMID: 7970704) Krief P … Azzarone B (Oncogene 1994) 2 3 4 23 54
  2. Cryo-EM Structure of a Pre-catalytic Human Spliceosome Primed for Activation. (PMID: 28781166) Bertram K … Stark H (Cell 2017) 3 4 54
  3. Recruitment of RED-SMU1 complex by Influenza A Virus RNA polymerase to control Viral mRNA splicing. (PMID: 24945353) Fournier G … Naffakh N (PLoS pathogens 2014) 3 4 54
  4. Nuclear protein IK undergoes dynamic subcellular translocation and forms unique nuclear bodies during the cell cycle. (PMID: 24252166) Hu L … Dai W (Biomarker research 2013) 3 4 54
  5. Dynamic protein-protein interaction wiring of the human spliceosome. (PMID: 22365833) Hegele A … Stelzl U (Molecular cell 2012) 3 4 54

Products for IK Gene

  • Signalway ELISA kits for IK
  • Signalway Proteins for IK

Sources for IK Gene