LOCUS KHJ47415.1 1106 aa PRT CON 17-DEC-2014 DEFINITION Trichuris suis receptor L domain protein protein. ACCESSION KN538379-171 PROTEIN_ID KHJ47415.1 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 REFERENCE 1 (bases 1 to 2343098) AUTHORS Mitreva,M. TITLE Draft genome of Trichuris suis JOURNAL Unpublished REFERENCE 2 (bases 1 to 2343098) AUTHORS Mitreva,M., Pepin,K.H., Abubucker,S., Martin,J., Minx,P., Warren,C., Palsikar,V.B., Zhang,X., Rosa,B.A. and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_02275" /inference="protein motif:HMMPfam:IPR000494" /inference="protein motif:HMMPfam:IPR001245" /inference="protein motif:HMMPfam:IPR006211" /note="KEGG: phu:Phum_PHUM581050 4.0e-228 Epidermal growth factor receptor precursor, putative" /db_xref="InterPro:IPR000494" /db_xref="InterPro:IPR001245" /db_xref="InterPro:IPR006211" intron_pos 30:0 (1/23) intron_pos 77:1 (2/23) intron_pos 113:1 (3/23) intron_pos 156:2 (4/23) intron_pos 207:2 (5/23) intron_pos 275:1 (6/23) intron_pos 319:2 (7/23) intron_pos 342:0 (8/23) intron_pos 387:2 (9/23) intron_pos 416:0 (10/23) intron_pos 455:0 (11/23) intron_pos 500:2 (12/23) intron_pos 550:0 (13/23) intron_pos 578:2 (14/23) intron_pos 662:0 (15/23) intron_pos 756:0 (16/23) intron_pos 808:0 (17/23) intron_pos 833:1 (18/23) intron_pos 882:1 (19/23) intron_pos 915:0 (20/23) intron_pos 968:0 (21/23) intron_pos 1005:1 (22/23) intron_pos 1054:1 (23/23) BEGIN 1 MCFGEYNPQY CCHAECAAGC HGPSDRDCYG CRAMRDDGRC VDKCPTPELY DPVTTQYIKN 61 PNGKYAFNRE CVTVCPSHMV IYKDGCVSRC PEGYFAEVGS NVCEPCQGVC PKTCIIEHHV 121 SSFNIKDFIG CTKVDGFIEI RKDTFEYGAL FLANDSFVRY DPMSEDQLEA LSSVQQVTHY 181 VLIQSERLKS LSFLRNLEKI EGRKLFESSY ALYITHSFSM QYLGTVSLRS ILNGDVYIAS 241 NYDLCYIHNI PWSKRIISVG HSSRVRSNRK ADICELEGKV CDPSCDHSQG CWGPGPEMCF 301 DCMHWRLGNS CVDECNADGL YRAAPKQCAY CHVECMKCTG AGPRNCTECK HVSLDGECVL 361 SCPKYTHYEN ILTRKCEKCH QNCYGYGCTG PGNFVGPGGC KRCKYGVLDE ESQTITRCLQ 421 ELSAEKPCSH DADLENYYWT VPLSRKIQMS VALAVCIKCH PVCRRCYGFG TDYAHYGCEC 481 LKYSLRESSN STTCVLECPR NTFTATPLQD DAAGECIPCD PQCNSCTGPE STDCLECLHY 541 KDFIAESDKF NCTSSCPEQR PFVSQDRLCT DVDIMMEKHK KSQVIIGVVV AALVSLCILF 601 FICLLFIRPK ASLLAHFKEP NPKLEIVAAV TPNLARLLLI RDFELNRGGV LGYGAFGTVY 661 KGIWTPEKEK VKIPVAIKVL HEANASAQQE TLEEARIMAS MSHPHLVQLI GVCVGQQMML 721 VTPLMPLGNL LDYVQNNRSK IGSAALICWC TQIADGMSYL EEHRLVHRDL AARNVLVQKP 781 YHIRITDFGL AKLLEYGENE VKIFEGKMPI KWLALECIKY RRYTHKSDIW AFGITLWELF 841 TFGDKPYKDV PLHQIPQLLE NGERLSQPKT ATLDMYMIMI RCWMVDADAR PTFKELKDIF 901 VKMAKDPGRY LVVEGDALLR LPNYTPQDQR DMIRQLIDDP EVVDPDEYFS AAPSSSPPVS 961 PTTLRKPLIE DREARASCCN QRHTSAVSQR YASDPLKNMP GLNTSKFSDS PTLTTDVENY 1021 LIPDSQQASQ GLSPCDDGVF MVYGGPGELP CCTGGHAYYN EFSKPNTGIC LENLEYMQGS 1081 LSEQDYHNCV PKNLQMSDIV QNETVV //