Human Gene KIAA1549 (ENST00000422774.2_11) from GENCODE V47lift37

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Description: KIAA1549, transcript variant 2 (from RefSeq NM_001164665.2)
Gencode Transcript: ENST00000422774.2_11
Gencode Gene: ENSG00000122778.10_12
Transcript (Including UTRs)
Position: hg19 chr7:138,516,126-138,666,135 Size: 150,010 Total Exon Count: 20 Strand: -
Coding Region
Position: hg19 chr7:138,522,651-138,666,015 Size: 143,365 Coding Exon Count: 20

Page Index	Sequence and Links	UniProtKB Comments	Primers	MalaCards	CTD
Gene Alleles	RNA-Seq Expression	Microarray Expression	RNA Structure	Protein Structure	Other Species
GO Annotations	mRNA Descriptions	Pathways	Other Names	GeneReviews	Model Information
Methods

Data last updated at UCSC: 2024-08-22 23:36:26

Sequence and Links to Tools and Databases

Genomic Sequence (chr7:138,516,126-138,666,135)			mRNA (may differ from genome)		Protein (1950 aa)
Gene Sorter	Genome Browser	Other Species FASTA	VisiGene	Gene interactions	Table Schema
AlphaFold	BioGPS	Ensembl	Entrez Gene	ExonPrimer	GeneCards
HGNC	Malacards	MGI	OMIM	PubMed	Reactome
UniProtKB	BioGrid CRISPR DB

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;

Primer design for this transcript

Primer3Plus can design qPCR Primers that straddle exon-exon-junctions, which amplify only cDNA, not genomic DNA.
Click here to load the transcript sequence and exon structure into Primer3Plus

Exonprimer can design one pair of Sanger sequencing primers around every exon, located in non-genic sequence.
Click here to open Exonprimer with this transcript

To design primers for a non-coding sequence, zoom to a region of interest and select from the drop-down menu: View > In External Tools > Primer3

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 D004958 Estradiol D024483 Vitamin K 3

Common Gene Haplotype Alleles


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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


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mRNA Secondary Structure of 3' and 5' UTRs

Region	Fold Energy	Bases	Energy/Base	Display As
5' UTR	-70.60	120	-0.588	Picture	PostScript	Text
3' UTR	-1928.40	6525	-0.296	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


Front	Top	Side

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.

Mouse	Rat	Zebrafish	D. melanogaster	C. elegans	S. cerevisiae
No ortholog	No ortholog	No ortholog	No ortholog	No ortholog	No ortholog
Gene Details	Gene Details
Gene Sorter	Gene Sorter
	RGD

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, ENST00000422774.1, K1549_HUMAN, KIAA1549 , NM_001164665, Q5BJD6, Q8IY15, Q9H0M3, Q9HCM3, uc319scd.1, uc319scd.2 UCSC ID: ENST00000422774.2_11 RefSeq Accession: NM_001164665.2 Protein: Q9HCM3 (aka K1549_HUMAN)

GeneReviews for This Gene


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

Gene Model Information


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Methods, Credits, and Use Restrictions


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