Human Gene KIAA1549 (uc011kql.2)
  Description: Homo sapiens KIAA1549 (KIAA1549), transcript variant 2, mRNA.
RefSeq Summary (NM_001164665): The protein encoded by this gene belongs to the UPF0606 family. This gene has been found to be fused to the BRAF oncogene in many cases of pilocytic astrocytoma. The fusion results from 2Mb tandem duplications at 7q34. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Oct 2012].
Transcript (Including UTRs)
   Position: hg19 chr7:138,516,127-138,666,064 Size: 149,938 Total Exon Count: 20 Strand: -
Coding Region
   Position: hg19 chr7:138,522,651-138,666,015 Size: 143,365 Coding Exon Count: 20 

Page IndexSequence and LinksUniProtKB CommentsGenetic AssociationsMalaCardsCTD
Gene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther Species
GO AnnotationsmRNA DescriptionsPathwaysOther NamesGeneReviewsModel Information
Data last updated at UCSC: 2013-06-14

-  Sequence and Links to Tools and Databases
Genomic Sequence (chr7:138,516,127-138,666,064)mRNA (may differ from genome)Protein (1950 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSCGAPEnsemblEntrez GeneExonPrimer

-  Comments and Description Text from UniProtKB
  ID: K1549_HUMAN
DESCRIPTION: RecName: Full=UPF0606 protein KIAA1549;
SUBCELLULAR LOCATION: Membrane; Multi-pass membrane protein (Potential).
DISEASE: Note=A chromosomal aberration involving KIAA1549 is found in pilocytic astrocytoma. A tandem duplication of 2 Mb at 7q34 leads to the expression of a KIAA1549-BRAF fusion protein with a constitutive kinase activity and inducing cell transformation.
SIMILARITY: Belongs to the UPF0606 family.
SEQUENCE CAUTION: Sequence=AAH38232.1; Type=Erroneous initiation; Note=Translation N-terminally shortened;

-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): KIAA1549
CDC HuGE Published Literature: KIAA1549
Positive Disease Associations: Electrocardiography , Stroke
Related Studies:
  1. Electrocardiography
    Daniel Levy et al. BMC medical genetics 2007, Framingham Heart Study 100K Project: genome-wide associations for blood pressure and arterial stiffness., BMC medical genetics. [PubMed 17903302]
    These results of genome-wide association testing for blood pressure and arterial stiffness phenotypes in an unselected community-based sample of adults may aid in the identification of the genetic basis of hypertension and arterial disease, help identify high risk individuals, and guide novel therapies for hypertension. Additional studies are needed to replicate any associations identified in these analyses.
  2. Stroke
    , , . [PubMed 0]

-  MalaCards Disease Associations
  MalaCards Gene Search: KIAA1549
Diseases sorted by gene-association score: pilocytic astrocytoma* (275), pilocytic astrocytoma of cerebellum (16), cerebellar astrocytoma (15), astrocytoma (12), childhood oligodendroglioma (11), fibrillary astrocytoma (8), pilomyxoid astrocytoma (7), childhood pilocytic astrocytoma (6), central nervous system organ benign neoplasm (5)
* = Manually curated disease association

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene

+  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: 2.33 RPKM in Pancreas
Total median expression: 37.06 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 -24.4049-0.498 Picture PostScript Text
3' UTR -2026.126524-0.311 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
IPR024606 - DUF3827

Pfam Domains:
PF12877 - Domain of unknown function (DUF3827)

ModBase Predicted Comparative 3D Structure on Q9HCM3
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 orthologNo orthologNo orthologNo orthologNo orthologNo ortholog
Gene Details     
Gene Sorter     

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0000981 RNA polymerase II transcription factor activity, sequence-specific DNA binding

Biological Process:
GO:0006357 regulation of transcription from RNA polymerase II promoter

Cellular Component:
GO:0005886 plasma membrane
GO:0016020 membrane
GO:0016021 integral component of membrane

-  Descriptions from all associated GenBank mRNAs
  AB046769 - Homo sapiens mRNA for KIAA1549 protein, partial cds.
BC091523 - Homo sapiens KIAA1549, mRNA (cDNA clone IMAGE:30512199), partial cds.
BC038232 - Homo sapiens KIAA1549, mRNA (cDNA clone IMAGE:5741123), partial cds.
AM989470 - Homo sapiens mRNA for KIAA1549 protein short-form, v1 (KIAA1549 gene), isolated from brain.
AM989471 - Homo sapiens mRNA for KIAA1549 protein short-form, v2 (KIAA1549 gene), isolated from brain.
AM989468 - Homo sapiens mRNA for KIAA1549 protein long-form, v1 (KIAA1549 gene), isolated from brain.
AM989469 - Homo sapiens mRNA for KIAA1549 protein long-form, v2 (KIAA1549 gene), isolated from brain.
AB384617 - Synthetic construct DNA, clone: pF1KA1549, Homo sapiens KIAA1549 gene for KIAA1549 protein, complete cds, without stop codon, in Flexi system.
BC069036 - Homo sapiens hypothetical protein LOC286025, mRNA (cDNA clone IMAGE:6377843), partial cds.
AK021793 - Homo sapiens cDNA FLJ11731 fis, clone HEMBA1005411.
AK096022 - Homo sapiens cDNA FLJ38703 fis, clone KIDNE2002265.
JD366575 - Sequence 347599 from Patent EP1572962.
JD534846 - Sequence 515870 from Patent EP1572962.
JD155911 - Sequence 136935 from Patent EP1572962.
JD059740 - Sequence 40764 from Patent EP1572962.
JD405227 - Sequence 386251 from Patent EP1572962.
JD445089 - Sequence 426113 from Patent EP1572962.
JD114453 - Sequence 95477 from Patent EP1572962.
JD188988 - Sequence 170012 from Patent EP1572962.
JD334262 - Sequence 315286 from Patent EP1572962.
JD177585 - Sequence 158609 from Patent EP1572962.
JD558675 - Sequence 539699 from Patent EP1572962.
JD201397 - Sequence 182421 from Patent EP1572962.
JD039042 - Sequence 20066 from Patent EP1572962.
JD384916 - Sequence 365940 from Patent EP1572962.
JD090394 - Sequence 71418 from Patent EP1572962.
JD093277 - Sequence 74301 from Patent EP1572962.
JD277598 - Sequence 258622 from Patent EP1572962.
JD116424 - Sequence 97448 from Patent EP1572962.
JD318756 - Sequence 299780 from Patent EP1572962.
JD197661 - Sequence 178685 from Patent EP1572962.
JD089503 - Sequence 70527 from Patent EP1572962.
JD434775 - Sequence 415799 from Patent EP1572962.
JD298130 - Sequence 279154 from Patent EP1572962.
JD510287 - Sequence 491311 from Patent EP1572962.
JD455664 - Sequence 436688 from Patent EP1572962.
JD510866 - Sequence 491890 from Patent EP1572962.
JD235665 - Sequence 216689 from Patent EP1572962.
JD090275 - Sequence 71299 from Patent EP1572962.
JD378832 - Sequence 359856 from Patent EP1572962.
JD501585 - Sequence 482609 from Patent EP1572962.
JD250440 - Sequence 231464 from Patent EP1572962.
JD110581 - Sequence 91605 from Patent EP1572962.
JD449595 - Sequence 430619 from Patent EP1572962.
JD287604 - Sequence 268628 from Patent EP1572962.
JD350052 - Sequence 331076 from Patent EP1572962.
JD112992 - Sequence 94016 from Patent EP1572962.
JD250939 - Sequence 231963 from Patent EP1572962.
JD240792 - Sequence 221816 from Patent EP1572962.
JD534456 - Sequence 515480 from Patent EP1572962.
JD292423 - Sequence 273447 from Patent EP1572962.
JD183867 - Sequence 164891 from Patent EP1572962.
JD333765 - Sequence 314789 from Patent EP1572962.
JD176400 - Sequence 157424 from Patent EP1572962.
JD387822 - Sequence 368846 from Patent EP1572962.
JD455118 - Sequence 436142 from Patent EP1572962.
JD146133 - Sequence 127157 from Patent EP1572962.
JD241729 - Sequence 222753 from Patent EP1572962.
JD373615 - Sequence 354639 from Patent EP1572962.
JD118627 - Sequence 99651 from Patent EP1572962.
JD428783 - Sequence 409807 from Patent EP1572962.
JD043734 - Sequence 24758 from Patent EP1572962.
JD182426 - Sequence 163450 from Patent EP1572962.
JD290832 - Sequence 271856 from Patent EP1572962.
JD284662 - Sequence 265686 from Patent EP1572962.
DQ581892 - Homo sapiens piRNA piR-50004, complete sequence.
AL136736 - Homo sapiens mRNA; cDNA DKFZp434O0710 (from clone DKFZp434O0710).
JD538591 - Sequence 519615 from Patent EP1572962.
JD124666 - Sequence 105690 from Patent EP1572962.
JD365826 - Sequence 346850 from Patent EP1572962.
JD284360 - Sequence 265384 from Patent EP1572962.
JD110492 - Sequence 91516 from Patent EP1572962.
CR533444 - Homo sapiens full open reading frame cDNA clone RZPDo834F0916D for gene KIAA1549, KIAA1549 protein; complete cds, incl. stopcodon.
JD096596 - Sequence 77620 from Patent EP1572962.
JD166688 - Sequence 147712 from Patent EP1572962.
JD450441 - Sequence 431465 from Patent EP1572962.
JD350729 - Sequence 331753 from Patent EP1572962.
JD379191 - Sequence 360215 from Patent EP1572962.
JD510378 - Sequence 491402 from Patent EP1572962.
AM989475 - Homo sapiens mRNA for S-protein KIAA1549:BRAF 16_9 (KIAA1549:BRAF gene), isolated from brain.
AM989472 - Homo sapiens mRNA for L-protein KIAA1549:BRAF 16_9 (KIAA1549:BRAF gene), isolated from brain.
AM989476 - Homo sapiens mRNA for S-protein KIAA1549:BRAF 16_11 (KIAA1549:BRAF gene), isolated from brain.
AM989473 - Homo sapiens mRNA for L-protein KIAA1549:BRAF 16_11 (KIAA1549:BRAF gene), isolated from brain.
AM989477 - Homo sapiens mRNA for S-protein KIAA1549:BRAF 15_9 (KIAA1549:BRAF gene), isolated from brain.
AM989474 - Homo sapiens mRNA for L-protein KIAA1549:BRAF 15_9 (KIAA1549:BRAF gene), isolated from brain.

-  Biochemical and Signaling Pathways
  Reactome (by CSHL, EBI, and GO)

Protein Q9HCM3 (Reactome details) participates in the following event(s):

R-HSA-6802927 BRAF and RAF fusion mutant dimers are phosphorylated
R-HSA-6802934 p-BRAF and RAF fusion dimers bind MAP2Ks and MAPKs
R-HSA-6802932 Dissociation of BRAF/RAF fusion complex
R-HSA-6802933 p-BRAF and RAF fusion dimers phosphorylate MAP2Ks
R-HSA-6802935 MAPKs are phosphorylated downstream of BRAF and RAF fusion dimers
R-HSA-6802952 Signaling by BRAF and RAF fusions
R-HSA-6802957 Oncogenic MAPK signaling
R-HSA-5663202 Diseases of signal transduction
R-HSA-1643685 Disease

-  Other Names for This Gene
  Alternate Gene Symbols: B6HY55, B6HY56, B6HY58, B6HY60, B6HY61, B6HY62, B6HY63, B6HY64, B6HY65, B6HY66, K1549_HUMAN, NM_001164665, NP_001158137, Q5BJD6, Q8IY15, Q9H0M3, Q9HCM3
UCSC ID: uc011kql.2
RefSeq Accession: NM_001164665
Protein: Q9HCM3 (aka K1549_HUMAN)
CCDS: CCDS47723.2, CCDS56513.1

-  GeneReviews for This Gene
  GeneReviews article(s) related to gene KIAA1549:
rp-overview (Nonsyndromic Retinitis Pigmentosa Overview)

-  Gene Model Information
category: coding nonsense-mediated-decay: no RNA accession: NM_001164665.1
exon count: 20CDS single in 3' UTR: no RNA size: 12427
ORF size: 5853CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 11719.00frame shift in genome: no % Coverage: 99.99
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: 0
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.