Q3UA06 (PCH2_MOUSE) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
Pachytene checkpoint protein 2 homolog

Alternative name(s):
Thyroid hormone receptor interactor 13
Thyroid receptor-interacting protein 13
Short name=TR-interacting protein 13
Short name=TRIP-13

Gene names

Name:	Trip13
Synonyms:	Pch2

Organism

Mus musculus (Mouse) [Reference proteome]

Taxonomic identifier

10090 [NCBI]

Taxonomic lineage

cellular organisms › Eukaryota › Opisthokonta › Metazoa › Eumetazoa › Bilateria › Deuterostomia › Chordata › Craniata › Vertebrata › Gnathostomata › Teleostomi › Euteleostomi › Sarcopterygii › Tetrapoda › Amniota › Mammalia › Theria › Eutheria › Euarchontoglires › Glires › Rodentia › Sciurognathi › Muroidea › Muridae › Murinae › Mus › Mus

Protein attributes

Sequence length	432 AA.
Sequence status	Complete.
Protein existence	Evidence at transcript level

General annotation (Comments)

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. Ref.5 Ref.6 Ref.7
Subunit structure	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 By similarity.
Tissue specificity	Widely expressed, including in testis. Ref.7
Disruption phenotype	Mice develop normally without obvious somatic defects but males and females are sterile due to meiotic disruption in meiocytes. Homozygous mutants display small gonads and females have few or no follicles, due to oocyte elimination between pachynema and dictyate. Mutant testes display reduced populated tubules and spermatogenesis is mainly arrested at spermatocyte stages of epithelial stage IV, corresponding to pachynema. Different phenotypes are observed in the different knockout experiments tested. In Trip13(RRB047) mutant mice, also named Trip13(mod) allele for moderate, the number of crossovers are not affected and meiocytes undergo homologous chromosome synapsis despide the presence of unrepaired DSBs in pachynema. Using a more severe mutant allele, named Trip13(sev) for severe, additional defects are observed: the numbers of crossovers and chiasmata are reduced in the absence of TRIP13, and their distribution along the chromosomes is altered (Ref.7). Autosomal bivalents in meiocytes frequently display pericentric synaptic forks and other defects (Ref.7). Recombination defects are evident very early in meiotic prophase, soon after DSB formation (Ref.7). These results suggest that the absence of defects in the number of crossovers observed in Trip13(RRB047) mutant is due to the use of a weak hypomorphic mutant allele. Ref.5 Ref.7
Sequence similarities	Belongs to the AAA ATPase family. PCH2 subfamily.

Ontologies

Keywords
Biological process	Differentiation Meiosis Oogenesis Spermatogenesis
Coding sequence diversity	Alternative splicing
Ligand	ATP-binding Nucleotide-binding
Technical term	Complete proteome Reference proteome
Gene Ontology (GO)
Biological_process	double-strand break repair Inferred from mutant phenotype Ref.7. Source: UniProtKB female meiosis I Inferred from mutant phenotype Ref.5. Source: MGI male meiosis I Inferred from mutant phenotype Ref.5. Source: MGI oocyte maturation Inferred from mutant phenotype Ref.5. Source: MGI pachytene Inferred from mutant phenotype Ref.5. Source: MGI reciprocal meiotic recombination Inferred from mutant phenotype Ref.7. Source: UniProtKB spermatid development Inferred from mutant phenotype Ref.5. Source: MGI synaptonemal complex assembly Inferred from mutant phenotype Ref.7. Source: UniProtKB
Cellular_component	male germ cell nucleus Inferred from direct assay Ref.5. Source: MGI
Molecular_function	ATP binding Inferred from electronic annotation. Source: UniProtKB-KW nucleoside-triphosphatase activity Inferred from electronic annotation. Source: InterPro
Complete GO annotation...

Alternative products

This entry describes 2 isoforms produced by alternative splicing. [Align] [Select]

Isoform 1 (identifier: Q3UA06-1)

This isoform has been chosen as the 'canonical' sequence. All positional information in this entry refers to it. This is also the sequence that appears in the downloadable versions of the entry.

Isoform 2 (identifier: Q3UA06-2)

The sequence of this isoform differs from the canonical sequence as follows:
     1-231: Missing.

Note: No experimental confirmation available.

Sequence annotation (Features)

	Feature key	Position(s)	Length	Description	Graphical view	Feature identifier
Molecule processing
	Chain	1 – 432	432	Pachytene checkpoint protein 2 homolog		PRO_0000084783
Regions
	Nucleotide binding	179 – 186	8	ATP Potential
Natural variations
	Alternative sequence	1 – 231	231	Missing in isoform 2.		VSP_041559
Experimental info
	Sequence conflict	148	1	H → R in BAB26861. Ref.1
	Sequence conflict	274	1	I → F in BAB26861. Ref.1
	Sequence conflict	409	1	G → S in BAE25076. Ref.1

Sequences

	Sequence		Length	Mass (Da)
	Isoform 1 [UniParc]. Last modified October 11, 2005. Version 1. Checksum: 4427E94AF4D733DB	FASTA	432	48,377
	10 20 30 40 50 60 MDEAVGDLKQ ALPCVAESPA VHVEVLQRSG STAKKEDIKS SVYRLLNRHN IVFGDYVWTE 70 80 90 100 110 120 FDDPFLSRNV QSVSIVDTEL KAKDPQPIDL SACTIALHIF QLNEEGPSSE NLDEETENII 130 140 150 160 170 180 AASHWVLPAA EFHGLWDSLV YDVEVKSHLL DYVMTTVLFS DKNVDSNLIT WNRVVLLHGP 190 200 210 220 230 240 PGTGKTSLCK ALAQKLTIRL SSRYRYGQLI EINSHSLFSK WFSESGKLVT KMFQKIQDLI 250 260 270 280 290 300 DDKEALVFVL IDEVESLTAA RNACRAGAEP SDAIRVVNAV LTQIDQIKRH SNVVILTTSN 310 320 330 340 350 360 ITEKIDVAFV DRADIKQYIG PPSAAAIFKI YLSCLEELMK CQIIYPRQQL LTLRELEMIG 370 380 390 400 410 420 FIENNVSKLS LLLSEISRKS EGLSGRVLRK LPFLAHALYI QAPSVTIEGF LQALSLAVDK 430 QFEEKKKLSA YV
	Isoform 2 [UniParc]. Checksum: 29169AB648C9963C	FASTA	201	22,508
	10 20 30 40 50 60 MFQKIQDLID DKEALVFVLI DEVESLTAAR NACRAGAEPS DAIRVVNAVL TQIDQIKRHS 70 80 90 100 110 120 NVVILTTSNI TEKIDVAFVD RADIKQYIGP PSAAAIFKIY LSCLEELMKC QIIYPRQQLL 130 140 150 160 170 180 TLRELEMIGF IENNVSKLSL LLSEISRKSE GLSGRVLRKL PFLAHALYIQ APSVTIEGFL 190 200 QALSLAVDKQ FEEKKKLSAY V

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"The transcriptional landscape of the mammalian genome." Carninci P., Kasukawa T., Katayama S., Gough J., Frith M.C., Maeda N., Oyama R., Ravasi T., Lenhard B., Wells C., Kodzius R., Shimokawa K., Bajic V.B., Brenner S.E., Batalov S., Forrest A.R., Zavolan M., Davis M.J. , Wilming L.G., Aidinis V., Allen J.E., Ambesi-Impiombato A., Apweiler R., Aturaliya R.N., Bailey T.L., Bansal M., Baxter L., Beisel K.W., Bersano T., Bono H., Chalk A.M., Chiu K.P., Choudhary V., Christoffels A., Clutterbuck D.R., Crowe M.L., Dalla E., Dalrymple B.P., de Bono B., Della Gatta G., di Bernardo D., Down T., Engstrom P., Fagiolini M., Faulkner G., Fletcher C.F., Fukushima T., Furuno M., Futaki S., Gariboldi M., Georgii-Hemming P., Gingeras T.R., Gojobori T., Green R.E., Gustincich S., Harbers M., Hayashi Y., Hensch T.K., Hirokawa N., Hill D., Huminiecki L., Iacono M., Ikeo K., Iwama A., Ishikawa T., Jakt M., Kanapin A., Katoh M., Kawasawa Y., Kelso J., Kitamura H., Kitano H., Kollias G., Krishnan S.P., Kruger A., Kummerfeld S.K., Kurochkin I.V., Lareau L.F., Lazarevic D., Lipovich L., Liu J., Liuni S., McWilliam S., Madan Babu M., Madera M., Marchionni L., Matsuda H., Matsuzawa S., Miki H., Mignone F., Miyake S., Morris K., Mottagui-Tabar S., Mulder N., Nakano N., Nakauchi H., Ng P., Nilsson R., Nishiguchi S., Nishikawa S., Nori F., Ohara O., Okazaki Y., Orlando V., Pang K.C., Pavan W.J., Pavesi G., Pesole G., Petrovsky N., Piazza S., Reed J., Reid J.F., Ring B.Z., Ringwald M., Rost B., Ruan Y., Salzberg S.L., Sandelin A., Schneider C., Schoenbach C., Sekiguchi K., Semple C.A., Seno S., Sessa L., Sheng Y., Shibata Y., Shimada H., Shimada K., Silva D., Sinclair B., Sperling S., Stupka E., Sugiura K., Sultana R., Takenaka Y., Taki K., Tammoja K., Tan S.L., Tang S., Taylor M.S., Tegner J., Teichmann S.A., Ueda H.R., van Nimwegen E., Verardo R., Wei C.L., Yagi K., Yamanishi H., Zabarovsky E., Zhu S., Zimmer A., Hide W., Bult C., Grimmond S.M., Teasdale R.D., Liu E.T., Brusic V., Quackenbush J., Wahlestedt C., Mattick J.S., Hume D.A., Kai C., Sasaki D., Tomaru Y., Fukuda S., Kanamori-Katayama M., Suzuki M., Aoki J., Arakawa T., Iida J., Imamura K., Itoh M., Kato T., Kawaji H., Kawagashira N., Kawashima T., Kojima M., Kondo S., Konno H., Nakano K., Ninomiya N., Nishio T., Okada M., Plessy C., Shibata K., Shiraki T., Suzuki S., Tagami M., Waki K., Watahiki A., Okamura-Oho Y., Suzuki H., Kawai J., Hayashizaki Y. Science 309:1559-1563(2005) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 1). Strain: C57BL/6J. Tissue: Bone marrow, Heart and Stomach.
[2]	"Lineage-specific biology revealed by a finished genome assembly of the mouse." Church D.M., Goodstadt L., Hillier L.W., Zody M.C., Goldstein S., She X., Bult C.J., Agarwala R., Cherry J.L., DiCuccio M., Hlavina W., Kapustin Y., Meric P., Maglott D., Birtle Z., Marques A.C., Graves T., Zhou S. , Teague B., Potamousis K., Churas C., Place M., Herschleb J., Runnheim R., Forrest D., Amos-Landgraf J., Schwartz D.C., Cheng Z., Lindblad-Toh K., Eichler E.E., Ponting C.P. PLoS Biol. 7:E1000112-E1000112(2009) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: C57BL/6J.
[3]	Mural R.J., Adams M.D., Myers E.W., Smith H.O., Venter J.C. Submitted (JUL-2005) to the EMBL/GenBank/DDBJ databases Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
[4]	"The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC)." The MGC Project Team Genome Res. 14:2121-2127(2004) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORMS 1 AND 2). Strain: FVB/N.
[5]	"Mouse pachytene checkpoint 2 (trip13) is required for completing meiotic recombination but not synapsis." Li X.C., Schimenti J.C. PLoS Genet. 3:E130-E130(2007) [PubMed] [Europe PMC] [Abstract] Cited for: FUNCTION, DISRUPTION PHENOTYPE.
[6]	"Mouse HORMAD1 and HORMAD2, two conserved meiotic chromosomal proteins, are depleted from synapsed chromosome axes with the help of TRIP13 AAA-ATPase." Wojtasz L., Daniel K., Roig I., Bolcun-Filas E., Xu H., Boonsanay V., Eckmann C.R., Cooke H.J., Jasin M., Keeney S., McKay M.J., Toth A. PLoS Genet. 5:E1000702-E1000702(2009) [PubMed] [Europe PMC] [Abstract] Cited for: FUNCTION.
[7]	"Mouse TRIP13/PCH2 is required for recombination and normal higher-order chromosome structure during meiosis." Roig I., Dowdle J.A., Toth A., de Rooij D.G., Jasin M., Keeney S. PLoS Genet. 6:E1001062-E1001062(2010) [PubMed] [Europe PMC] [Abstract] Cited for: FUNCTION, TISSUE SPECIFICITY, DISRUPTION PHENOTYPE.
+	Additional computationally mapped references.

Cross-references

Sequence databases
EMBL GenBank DDBJ	AK010336 mRNA. Translation: BAB26861.1. AK142463 mRNA. Translation: BAE25076.1. AK146877 mRNA. Translation: BAE27499.1. AK151568 mRNA. Translation: BAE30510.1. CT010471 Genomic DNA. No translation available. CH466563 Genomic DNA. Translation: EDL37076.1. BC023834 mRNA. Translation: AAH23834.1. BC126946 mRNA. Translation: AAI26947.1.
IPI	IPI00318000. IPI01019210.
RefSeq	NP_081458.1. NM_027182.2.
UniGene	Mm.275095.
3D structure databases
ProteinModelPortal	Q3UA06.
SMR	Q3UA06. Positions 110-426.
ModBase	Search...
Protein-protein interaction databases
IntAct	Q3UA06. 6 interactions.
MINT	MINT-218773.
PTM databases
PhosphoSite	Q3UA06.
Proteomic databases
PaxDb	Q3UA06.
PRIDE	Q3UA06.
Protocols and materials databases
StructuralBiologyKnowledgebase	Search...
Genome annotation databases
Ensembl	ENSMUST00000022053; ENSMUSP00000022053; ENSMUSG00000021569.
GeneID	69716.
KEGG	mmu:69716.
Organism-specific databases
CTD	9319.
MGI	MGI:1916966. Trip13.
Phylogenomic databases
eggNOG	COG0464.
GeneTree	ENSGT00390000017432.
HOGENOM	HOG000234557.
HOVERGEN	HBG052830.
InParanoid	Q05CL4.
OMA	TEKIDMA.
OrthoDB	EOG4STS4K.
Gene expression databases
Bgee	Q3UA06.
CleanEx	MM_TRIP13.
Genevestigator	Q3UA06.
GermOnline	ENSMUSG00000021569. Mus musculus.
Family and domain databases
InterPro	IPR003593. AAA+_ATPase. IPR003959. ATPase_AAA_core. IPR003960. ATPase_AAA_CS. IPR001270. Chaprnin_ClpA/B. [Graphical view]
Pfam	PF00004. AAA. 1 hit. [Graphical view]
PRINTS	PR00300. CLPPROTEASEA.
SMART	SM00382. AAA. 1 hit. [Graphical view]
PROSITE	PS00674. AAA. 1 hit. [Graphical view]
ProtoNet	Search...
Other
NextBio	330162.
SOURCE	Search...

Entry information

Entry name

PCH2_MOUSE

Accession

Primary (citable) accession number: Q3UA06
Secondary accession number(s): A0JNT8 , Q05CL4, Q3UQG6, Q9CWW8

Entry history

Integrated into UniProtKB/Swiss-Prot:	January 10, 2006
Last sequence update:	October 11, 2005
Last modified:	May 1, 2013
This is version 64 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Chordata Protein Annotation Program