Human Gene TRIP13 (ENST00000166345.8_4) from GENCODE V47lift37

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Description: thyroid hormone receptor interactor 13, transcript variant 1 (from RefSeq NM_004237.4)
Gencode Transcript: ENST00000166345.8_4
Gencode Gene: ENSG00000071539.14_12
Transcript (Including UTRs)
Position: hg19 chr5:892,999-918,235 Size: 25,237 Total Exon Count: 13 Strand: +
Coding Region
Position: hg19 chr5:893,114-917,218 Size: 24,105 Coding Exon Count: 13

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	Other Names	Model Information	Methods

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

Sequence and Links to Tools and Databases

Genomic Sequence (chr5:892,999-918,235)			mRNA (may differ from genome)		Protein (432 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	UniProtKB
Wikipedia	BioGrid CRISPR DB

Comments and Description Text from UniProtKB


	ID: PCH2_HUMAN DESCRIPTION: RecName: Full=Pachytene checkpoint protein 2 homolog; AltName: Full=Human papillomavirus type 16 E1 protein-binding protein; Short=16E1-BP; Short=HPV16 E1 protein-binding protein; AltName: Full=Thyroid hormone receptor interactor 13; AltName: Full=Thyroid receptor-interacting protein 13; Short=TR-interacting protein 13; Short=TRIP-13; FUNCTION: Plays a key role in chromosome recombination and chromosome structure development during meiosis. Required at early steps in meiotic recombination that leads to non-crossovers pathways. Also needed for efficient completion of homologous synapsis by influencing crossover distribution along the chromosomes affecting both crossovers and non-crossovers pathways. Also required for development of higher-order chromosome structures and is needed for synaptonemal-complex formation. In males, required for efficient synapsis of the sex chromosomes and for sex body formation. Promotes early steps of the DNA double- strand breaks (DSBs) repair process upstream of the assembly of RAD51 complexes. Required for depletion of HORMAD1 and HORMAD2 from synapsed chromosomes (By similarity). SUBUNIT: Specifically interacts with the ligand binding domain of the thyroid receptor (TR). This interaction does not require the presence of thyroid hormone for its interaction. Interacts with HPV16 E1. INTERACTION: Q969Q4:ARL11; NbExp=3; IntAct=EBI-358993, EBI-751892; Q9H0W9:C11orf54; NbExp=3; IntAct=EBI-358993, EBI-740204; Q9BWC7:COMT; NbExp=3; IntAct=EBI-358993, EBI-743305; O95865:DDAH2; NbExp=3; IntAct=EBI-358993, EBI-749139; Q8IVS8:GLYCTK; NbExp=3; IntAct=EBI-358993, EBI-748515; Q9BSH5:HDHD3; NbExp=3; IntAct=EBI-358993, EBI-745201; Q6P9B6:KIAA1609; NbExp=3; IntAct=EBI-358993, EBI-746504; Q14847:LASP1; NbExp=3; IntAct=EBI-358993, EBI-742828; Q96JB6:LOXL4; NbExp=3; IntAct=EBI-358993, EBI-749562; Q15013:MAD2L1BP; NbExp=5; IntAct=EBI-358993, EBI-712181; Q9GZT8:NIF3L1; NbExp=3; IntAct=EBI-358993, EBI-740897; O60260:PARK2; NbExp=3; IntAct=EBI-358993, EBI-716346; P67775:PPP2CA; NbExp=3; IntAct=EBI-358993, EBI-712311; Q96HA8:WDYHV1; NbExp=3; IntAct=EBI-358993, EBI-741158; SIMILARITY: Belongs to the AAA ATPase family. PCH2 subfamily. SEQUENCE CAUTION: Sequence=AAC41732.1; Type=Frameshift; Positions=1, 5;

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: TRIP13 Diseases sorted by gene-association score: mosaic variegated aneuploidy syndrome 3* (900) * = Manually curated disease association

Comparative Toxicogenomics Database (CTD)


	The following chemicals interact with this gene D000082 Acetaminophen D013749 Tetrachlorodibenzodioxin C006780 bisphenol A C006253 pirinixic acid C028474 1,4-bis(2-(3,5-dichloropyridyloxy))benzene C029497 2,3-bis(3'-hydroxybenzyl)butyrolactone C063002 2,3-dimethoxy-1,4-naphthoquinone C532162 2-(1H-indazol-4-yl)-6-(4-methanesulfonylpiperazin-1-ylmethyl)-4-morpholin-4-ylthieno(3,2-d)pyrimidine C027576 4-hydroxy-2-nonenal D015123 7,8-Dihydro-7,8-dihydroxybenzo(a)pyrene 9,10-oxide more ... click here to view the complete list

Common Gene Haplotype Alleles


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RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)


	Highest median expression: 26.24 RPKM in Testis Total median expression: 71.19 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	-62.20	115	-0.541	Picture	PostScript	Text
3' UTR	-223.80	1017	-0.220	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
IPR003593 - AAA+_ATPase
IPR003959 - ATPase_AAA_core
IPR003960 - ATPase_AAA_CS
IPR001270 - Chaprnin_ClpA/B

Pfam Domains:
PF00004 - ATPase family associated with various cellular activities (AAA)
PF13401 - AAA domain

SCOP Domains:
52540 - P-loop containing nucleoside triphosphate hydrolases
53795 - PEP carboxykinase-like

ModBase Predicted Comparative 3D Structure on Q15645


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	Genome Browser	Genome Browser
Gene Details	Gene Details		Gene Details	Gene Details	Gene Details
Gene Sorter	Gene Sorter		Gene Sorter	Gene Sorter	Gene Sorter
	RGD	Ensembl		WormBase	SGD
				Protein Sequence	Protein Sequence
				Alignment	Alignment

Gene Ontology (GO) Annotations with Structured Vocabulary


	Molecular Function: GO:0000166 nucleotide binding GO:0003712 transcription cofactor activity GO:0005515 protein binding GO:0005524 ATP binding GO:0042802 identical protein binding Biological Process: GO:0001556 oocyte maturation GO:0006302 double-strand break repair GO:0006366 transcription from RNA polymerase II promoter GO:0007094 mitotic spindle assembly checkpoint GO:0007130 synaptonemal complex assembly GO:0007131 reciprocal meiotic recombination GO:0007141 male meiosis I GO:0007144 female meiosis I GO:0007283 spermatogenesis GO:0007286 spermatid development GO:0030154 cell differentiation GO:0048477 oogenesis GO:0051321 meiotic cell cycle Cellular Component: GO:0001673 male germ cell nucleus GO:0005634 nucleus

Descriptions from all associated GenBank mRNAs


	BC000404 - Homo sapiens thyroid hormone receptor interactor 13, mRNA (cDNA clone MGC:8565 IMAGE:2822981), complete cds. BC019294 - Homo sapiens thyroid hormone receptor interactor 13, mRNA (cDNA clone MGC:4108 IMAGE:2822981), complete cds. U96131 - Homo sapiens HPV16 E1 protein binding protein mRNA, complete cds. JD020997 - Sequence 2021 from Patent EP1572962. JD020734 - Sequence 1758 from Patent EP1572962. AK310376 - Homo sapiens cDNA, FLJ17418. JD337337 - Sequence 318361 from Patent EP1572962. JD381644 - Sequence 362668 from Patent EP1572962. JD485604 - Sequence 466628 from Patent EP1572962. AB527502 - Synthetic construct DNA, clone: pF1KB7979, Homo sapiens TRIP13 gene for thyroid hormone receptor interactor 13, without stop codon, in Flexi system. EU446745 - Synthetic construct Homo sapiens clone IMAGE:100070036; IMAGE:100011954; FLH258241.01L thyroid hormone receptor interactor 13 (TRIP13) gene, encodes complete protein. CU674196 - Synthetic construct Homo sapiens gateway clone IMAGE:100018276 5' read TRIP13 mRNA. KJ892743 - Synthetic construct Homo sapiens clone ccsbBroadEn_02137 TRIP13 gene, encodes complete protein. CR456744 - Homo sapiens full open reading frame cDNA clone RZPDo834B0611D for gene TRIP13, thyroid hormone receptor interactor 13; complete cds, incl. stopcodon. L40384 - Homo sapiens thyroid receptor interactor (TRIP13) mRNA, partial cds. KY966275 - Homo sapiens cell line 93T449 SH3TC1/TRIP13 fusion mRNA, partial sequence. KY966296 - Homo sapiens cell line 94T778 SH3TC1/TRIP13 fusion mRNA, partial sequence. JD042726 - Sequence 23750 from Patent EP1572962. JD431494 - Sequence 412518 from Patent EP1572962. JD491111 - Sequence 472135 from Patent EP1572962. JD058446 - Sequence 39470 from Patent EP1572962. JD507232 - Sequence 488256 from Patent EP1572962. JD361543 - Sequence 342567 from Patent EP1572962. JD328456 - Sequence 309480 from Patent EP1572962. JD034218 - Sequence 15242 from Patent EP1572962. JD021314 - Sequence 2338 from Patent EP1572962. JD374481 - Sequence 355505 from Patent EP1572962. JD189956 - Sequence 170980 from Patent EP1572962. JD029402 - Sequence 10426 from Patent EP1572962. JD274507 - Sequence 255531 from Patent EP1572962. JD103150 - Sequence 84174 from Patent EP1572962. JD378825 - Sequence 359849 from Patent EP1572962. JD187785 - Sequence 168809 from Patent EP1572962. JD554219 - Sequence 535243 from Patent EP1572962. JD554220 - Sequence 535244 from Patent EP1572962. JD111594 - Sequence 92618 from Patent EP1572962. JD058451 - Sequence 39475 from Patent EP1572962. JD298366 - Sequence 279390 from Patent EP1572962.

Other Names for This Gene


	Alternate Gene Symbols: C9K0T3, D3DTC0, ENST00000166345.1, ENST00000166345.2, ENST00000166345.3, ENST00000166345.4, ENST00000166345.5, ENST00000166345.6, ENST00000166345.7, NM_004237, O15324, PCH2, PCH2_HUMAN, Q15645, uc317cdi.1, uc317cdi.2 UCSC ID: ENST00000166345.8_4 RefSeq Accession: NM_004237.4 Protein: Q15645 (aka PCH2_HUMAN)

Gene Model Information


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Methods, Credits, and Use Restrictions


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