LOCUS KHJ47507.1 942 aa PRT CON 17-DEC-2014 DEFINITION Trichuris suis hypothetical protein protein. ACCESSION KN538379-263 PROTEIN_ID KHJ47507.1 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 REFERENCE 1 (bases 1 to 2343098) AUTHORS Mitreva,M. TITLE Draft genome of Trichuris suis JOURNAL Unpublished REFERENCE 2 (bases 1 to 2343098) AUTHORS Mitreva,M., Pepin,K.H., Abubucker,S., Martin,J., Minx,P., Warren,C., Palsikar,V.B., Zhang,X., Rosa,B.A. and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_02367" intron_pos 10:1 (1/21) intron_pos 40:1 (2/21) intron_pos 64:1 (3/21) intron_pos 122:0 (4/21) intron_pos 191:0 (5/21) intron_pos 218:2 (6/21) intron_pos 254:2 (7/21) intron_pos 282:0 (8/21) intron_pos 321:1 (9/21) intron_pos 357:2 (10/21) intron_pos 412:0 (11/21) intron_pos 459:0 (12/21) intron_pos 514:0 (13/21) intron_pos 563:1 (14/21) intron_pos 616:2 (15/21) intron_pos 671:1 (16/21) intron_pos 696:0 (17/21) intron_pos 731:2 (18/21) intron_pos 792:2 (19/21) intron_pos 815:0 (20/21) intron_pos 861:1 (21/21) BEGIN 1 MQKDCSSTIA RTSSAQTLDS LDCTRISDEP EKRYEERISI LEFELRQANA TVKTLREHLT 61 LATSEADASQ GVSSNCVPEE YVQMQIKPHE QRVLNFLVNE YLLKNDFKIT SVTFSEEVRN 121 QDFDDWADVG LNLARPPDLL SIYRHGFANL PQSKPETRDV NLQTHLFSSH SPTSGESTLS 181 TDSFVLLNRL NAENASLLQR NQHLEEELRV IKAELEATFT AQQRDDSRSP LVIENCSSHP 241 AAADVGRQNE EVSKIRQSFY KRLSNTLPPC WPVSSELGFE KLSFLTAFTG QTAATVEVIE 301 VIGEILFSLI PKMSMRKREC ILPLVAVVII AHPKPKRREE LCAMMFDLFK HPDAEQRQAL 361 VAVCTYIASK VDSTRVETEV LVHCVQRIDS RLLEQRTMAA EVVSALIPFI SRPILSSLII 421 SILRQMTLSN NAEKVLVPVI QACSRLCCFI TVGEKFHVMN ELFLTALSST SSVVVDHARN 481 AFLSSLAIWA LEDFALLEKL VASLLCRMEC IVDFLCKKSS KSGKEQQQLN IYFDCVGSIV 541 PVLFWNVVRS NPAKDKNLEG LENNLNFQVP SECLLDDLTL YTCSSEMQRL MASFHRLIGE 601 EWHSSWPMLD FFTCSVLTPL ARLIRKVETG DRSVLRSAVH CFTRFGNFFG QGFVRNRLCP 661 LFQVEQASIA DKEDVEFTSL SLPVYTVAVL GSLIQKSDTE RLKRFLKEAI TTIAERNLPI 721 RCIVLTLLEI SGVHPEKQLI FDVMHACVAH PSWRVRRLSG AIMSALATEH NGRDVEVTIS 781 SLLLRLANDS SPDVRINTVV GLCCLASGCE SDAQVSDYAK QELSKIFSDV PGTITDVCAA 841 EMLEKIARIA PTFAIQFLDY LFLPQLYALT RRCLDARDET NATVFPALFD VYIALSCCCF 901 SPATISGYFL PGLRVLVREL DARRAKVAQS IIIEQERKVS DI //