LOCUS KHJ47354.1 472 aa PRT CON 17-DEC-2014 DEFINITION Trichuris suis peptidyl-prolyl cis-trans isomerase, cyclophilin- type protein. ACCESSION KN538379-110 PROTEIN_ID KHJ47354.1 SOURCE Trichuris suis (pig whipworm) ORGANISM Trichuris suis Eukaryota; Metazoa; Ecdysozoa; Nematoda; Enoplea; Dorylaimia; Trichinellida; Trichuridae; Trichuris. REFERENCE 1 (bases 1 to 2343098) AUTHORS Mitreva,M. TITLE Draft genome of Trichuris suis JOURNAL Unpublished REFERENCE 2 (bases 1 to 2343098) AUTHORS Mitreva,M., Pepin,K.H., Abubucker,S., Martin,J., Minx,P., Warren,C., Palsikar,V.B., Zhang,X., Rosa,B.A. and Wilson,R.K. TITLE Direct Submission JOURNAL Submitted (27-JAN-2014) The Genome Institute, Washington University School of Medicine, 4444 Forest Park, St. Louis, MO 63108, USA COMMENT Trichuris suis contaminated a dirt lot located at the USDA, Agricultural Research Service, Beltsville Agricultural Research Center, Animal Parasitic Disease Laboratory in Beltsville, MD since the early 1960s. Adult worms were isolated for passage from pigs placed on the lot and naturally infected. The T. suis adults were manually removed from the cecum and proximal colon tissue and cultured in vitro to release fertilized eggs that were removed after 24-48 hours and embryonated to an infective stage (Hill et al., Experimental Parasitology 77, 170-178, 1993). The strain has been actively passed in pigs one to two times per year since that time and characterized for pathogenesis in pigs (Mansfield and Urban, Veterinary Immunology and Immunopathology 50, 1-17, 1996). This strain of T. suis has also been used therapeutically in human subjects with inflammatory bowel disease (Trichuris suis therapy in Crohn's disease. Summers RW, Elliott DE, Urban JF Jr, Thompson R, Weinstock JV. Gut. 2005 Jan;54(1):87-90. The Genome Institute collaborators that provided material for the genome/transcriptome sequencing are: USDA - Urban, Jr., J.F., Hill, D. E. and Michigan State University - Mansfield L.S. The repeat library was generated using Repeatmodeler (A. Smit, R. Hubley http://www.systemsbiology.org/). The Ribosomal RNA genes were identified using RNAmmer ((http://www.cbs.dtu.dk/cgi-bin/nph-sw_request?rnammer ) and transfer RNA's were identified with tRNAscan-SE (Lowe and Eddy, 1997). Non-coding RNAs, such as microRNAs, were identified by sequence homology search of the Rfam database (http://selab.janelia.org/software.html). Repeats and predicted RNA's were then masked using RepeatMasker (A. Smit, R. Hubley & P. Green http://repeatmasker.org). Protein-coding genes were predicted using a combination of ab initio programs Snap (I. Korf, 2004), Fgenesh (Softberry, Corp) and Augustus (M. Stanke, et. Al 2008) and the annotation pipeline tool Maker (M. Yandell et. al., 2007) which aligns mRNA, EST and protein information from same species or cross-species to aid in gene structure determination and modifications. A consensus gene set from the above prediction algorithms was generated, using a logical, hierarchical approach developed at the Genome institute. Gene product naming was determined by BER (JCVI: http://ber.sourceforge.net). Our goal is to explore this WGS draft sequence of Trichuris suis to better define proteins involved in nematode parasitism that impact health and disease and are relevant to both host-parasite relationships and basic biological processes. For information regarding this assembly or project, or any other GSC genome project, please visit our Genome Groups web page (http://genome.wustl.edu/genome_group_index.cgi) and email the designated contact person. For specific questions regarding the Trichuris suis genome project contact Makedonka Mitreva (mmitreva@genome.wustl.edu) at Washington University School of Medicine. The National Human Genome Research Institute (NHGRI) of the National Institutes of Health (NIH) provided funds for this project. ##Genome-Assembly-Data-START## Finishing Goal :: High-Quality Draft Current Finishing Status :: High-Quality Draft Assembly Method :: ALLPATHS_LG v. 2012-11-02 Assembly Name :: T_suis_1.0.allpaths Genome Coverage :: 392x Sequencing Technology :: Illumina ##Genome-Assembly-Data-END## FEATURES Qualifiers source /organism="Trichuris suis" /mol_type="genomic DNA" /submitter_seqid="T_suis-1.0_Cont4" /isolation_source="cecum and proximal colon of infected animals which were naturally infected" /host="Sus scrofa (pig)" /db_xref="taxon:68888" /chromosome="Unknown" /dev_stage="adult" /country="USA: Beltsville, MD" protein /locus_tag="D918_02214" /inference="protein motif:HMMPfam:IPR002130" /note="KEGG: mdo:100018740 1.7e-94 similar to SDCCAG10; K12737 peptidyl-prolyl cis-trans isomerase SDCCAG10" /db_xref="InterPro:IPR002130" intron_pos 15:0 (1/11) intron_pos 85:0 (2/11) intron_pos 134:0 (3/11) intron_pos 167:0 (4/11) intron_pos 198:2 (5/11) intron_pos 222:0 (6/11) intron_pos 260:0 (7/11) intron_pos 318:2 (8/11) intron_pos 346:1 (9/11) intron_pos 381:0 (10/11) intron_pos 419:2 (11/11) BEGIN 1 MSEVCINEPA TNGKVCLKTT VGDIEIELWS KECPKACRNF VTLCITGYYN NTIFHRVEPG 61 FIVQGGDPTG TGCGGESAFG EPFKDEFHSR LRFSRRGLVA MASAGKRHTN GSQFFFTLGR 121 TPELQNKHTI FGKVNKATLV NMLRLEECQV DKQSRPLYPE KILSCKVISN PFNDIVLPSV 181 AVASKAIEEK PKKEVKQRNL ALLSFGDEAK EEEEALEVVN KKLFLRGKSA HDVIPDNRRL 241 SSKPVLSARE LNRVRGDLEA AMYAGNESEK KKLDDAISNR LRLLTGAKSK LEEDVASDGE 301 DLEDLLNEKE REQKKARLEK VKEEYRALRK ELVRGSDVGG GDDDSNKKIL KPAVAEYMAE 361 RNKYKNVSAA ARGTTDRERE TLKILEKFQS RLKAANQVVI ERSKKPDDND KDDGPVEAWM 421 THKFVAPVLE PEVKGSRPQD KDMFKIEDMR VSTAAAEMAT TSKVEKRGVS DS //