Human Gene IK (uc003lgq.3) Description and Page Index
  Description: Homo sapiens IK cytokine, down-regulator of HLA II (IK), mRNA.
RefSeq Summary (NM_006083): 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]. Publication Note: This RefSeq record includes a subset of the publications that are available for this gene. Please see the Gene record to access additional publications. ##Evidence-Data-START## Transcript exon combination :: SRR3476690.680642.1, SRR3476690.957447.1 [ECO:0000332] RNAseq introns :: single sample supports all introns SAMEA1965299, SAMEA1966682 [ECO:0000348] ##Evidence-Data-END## ##RefSeq-Attributes-START## MANE Ensembl match :: ENST00000417647.7/ ENSP00000396301.2 RefSeq Select criteria :: based on single protein-coding transcript ##RefSeq-Attributes-END##
Transcript (Including UTRs)
   Position: hg19 chr5:140,027,384-140,042,065 Size: 14,682 Total Exon Count: 20 Strand: +
Coding Region
   Position: hg19 chr5:140,027,494-140,041,914 Size: 14,421 Coding Exon Count: 20 

Page IndexSequence and LinksUniProtKB CommentsGenetic AssociationsCTDGene Alleles
RNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther SpeciesGO Annotations
mRNA DescriptionsOther NamesModel InformationMethods
Data last updated: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr5:140,027,384-140,042,065)mRNA (may differ from genome)Protein (557 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
BioGPSCGAPEnsemblEntrez GeneExonPrimerGeneCards
GeneNetworkH-INVHGNCHPRDLynxMGI
neXtProtOMIMPubMedStanford SOURCEUniProtKBWikipedia

-  Comments and Description Text from UniProtKB
  ID: RED_HUMAN
DESCRIPTION: RecName: Full=Protein Red; AltName: Full=Cytokine IK; AltName: Full=IK factor; AltName: Full=Protein RER;
FUNCTION: May bind to chromatin.
INTERACTION: P04618:rev (xeno); NbExp=3; IntAct=EBI-713456, EBI-6164309;
SUBCELLULAR LOCATION: Nucleus.
TISSUE SPECIFICITY: Ubiquitous.
DEVELOPMENTAL STAGE: Expressed at similar levels in fetal and adult tissues.
PTM: Phosphorylated upon DNA damage, probably by ATM or ATR.
SIMILARITY: Belongs to the RED family.
CAUTION: Was originally (PubMed:7970704) thought to be the IK factor, a cytokine involved in the negative regulatory pathway of constitutive MHC class II antigens expression.

-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): IK
CDC HuGE Published Literature: IK

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene           more ... click here to view the complete list

+  Common Gene Haplotype Alleles
  Press "+" in the title bar above to open this section.

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 104.03 RPKM in Testis
Total median expression: 2381.26 RPKM



View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
  Press "+" in the title bar above to open this section.

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -32.90110-0.299 Picture PostScript Text
3' UTR -23.40151-0.155 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  InterPro Domains: Graphical view of domain structure
IPR012492 - RED_C
IPR012916 - RED_N

Pfam Domains:
PF07807 - RED-like protein C-terminal region
PF07808 - RED-like protein N-terminal region

ModBase Predicted Comparative 3D Structure on Q13123
FrontTopSide
The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
No orthologGenome BrowserGenome BrowserNo orthologNo orthologNo ortholog
 Gene Details    
 Gene Sorter    
 RGDEnsembl   
 Protein SequenceProtein Sequence   
 AlignmentAlignment   

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0005515 protein binding
GO:0042802 identical protein binding

Biological Process:
GO:0000278 mitotic cell cycle
GO:0000398 mRNA splicing, via spliceosome
GO:0006397 mRNA processing
GO:0007094 mitotic spindle assembly checkpoint
GO:0008380 RNA splicing
GO:0016032 viral process
GO:0034501 protein localization to kinetochore

Cellular Component:
GO:0000922 spindle pole
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:0005681 spliceosomal complex
GO:0005694 chromosome
GO:0005737 cytoplasm
GO:0005856 cytoskeleton
GO:0016607 nuclear speck
GO:0071005 U2-type precatalytic spliceosome
GO:0000228 nuclear chromosome
GO:0097431 mitotic spindle pole


-  Descriptions from all associated GenBank mRNAs
  AF182645 - Homo sapiens chondrosarcoma-associated protein 2 (CSA2) mRNA, complete cds.
JD139622 - Sequence 120646 from Patent EP1572962.
AK225924 - Homo sapiens mRNA for RED protein variant, clone: FCC118A06.
AK312363 - Homo sapiens cDNA, FLJ92684, highly similar to Homo sapiens IK cytokine, down-regulator of HLA II (IK), mRNA.
AL050296 - Homo sapiens mRNA; cDNA DKFZp564B112 (from clone DKFZp564B112).
AK293626 - Homo sapiens cDNA FLJ53904 complete cds, highly similar to Protein Red.
BC051295 - Homo sapiens IK cytokine, down-regulator of HLA II, mRNA (cDNA clone IMAGE:3635553).
HZ480287 - JP 2015535430-A/793: TERMINALLY MODIFIED RNA.
HZ790218 - JP 2016504050-A/1963: SIGNAL-SENSOR POLYNUCLEOTIDES FOR THE ALTERATION OF CELLULAR PHENOTYPES.
JC512950 - Sequence 3203 from Patent WO2014113089.
LF160390 - JP 2016513950-A/456: Oligomers with improved off-target profile.
LQ070538 - Sequence 862 from Patent EP2964234.
HZ409117 - JP 2015528002-A/1714: CHIRAL CONTROL.
LG052451 - KR 1020150036642-A/1717: CHIRAL CONTROL.
BC013005 - Homo sapiens IK cytokine, down-regulator of HLA II, mRNA (cDNA clone MGC:3980 IMAGE:3030079), complete cds.
BC071964 - Homo sapiens IK cytokine, down-regulator of HLA II, mRNA (cDNA clone MGC:88657 IMAGE:6461871), complete cds.
AK308730 - Homo sapiens cDNA, FLJ98771.
AY007094 - Homo sapiens clone TCCCIA00142 mRNA sequence.
CU687202 - Synthetic construct Homo sapiens gateway clone IMAGE:100023141 5' read IK mRNA.
AB591032 - Synthetic construct DNA, clone: pFN21AE1980, Homo sapiens IK gene for IK cytokine, down-regulator of HLA II, without stop codon, in Flexi system.
AJ005579 - Homo sapiens mRNA for Prer protein.
A25270 - Human IFN-gamma antagonist cytokine cDNA.
S74221 - IK=IK factor [human, leukemic cells K562, chronic myeloid leukemia patient, mRNA, 756 nt].
JD396722 - Sequence 377746 from Patent EP1572962.
JD087376 - Sequence 68400 from Patent EP1572962.
AK097968 - Homo sapiens cDNA FLJ40649 fis, clone THYMU2018028, moderately similar to RED PROTEIN.
JD362080 - Sequence 343104 from Patent EP1572962.
JD085306 - Sequence 66330 from Patent EP1572962.
JD558165 - Sequence 539189 from Patent EP1572962.
MA644039 - JP 2017113010-A/1963: SIGNAL-SENSOR POLYNUCLEOTIDES FOR THE ALTERATION OF CELLULAR PHENOTYPES.
MA731923 - JP 2017140048-A/793: TERMINALLY MODIFIED RNA.
MA801092 - JP 2018183181-A/1963: SIGNAL-SENSOR POLYNUCLEOTIDES FOR THE ALTERATION OF CELLULAR PHENOTYPES.

-  Other Names for This Gene
  Alternate Gene Symbols: NM_006083, NP_006074, Q13123, Q6IPD8, RED, RED_HUMAN, RER
UCSC ID: uc003lgq.3
RefSeq Accession: NM_006083
Protein: Q13123 (aka RED_HUMAN)
CCDS: CCDS47280.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_006083.3
exon count: 20CDS single in 3' UTR: no RNA size: 1955
ORF size: 1674CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 3548.00frame shift in genome: no % Coverage: 98.98
has start codon: yes stop codon in genome: no # of Alignments: 1
has end codon: yes retained intron: no # AT/AC introns 0
selenocysteine: no end bleed into intron: 0# strange splices: 1
Click here for a detailed description of the fields of the table above.

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.