LOCUS KHJ47314.1 762 aa PRT CON 17-DEC-2014 DEFINITION Trichuris suis NF-X1 type zinc finger protein. ACCESSION KN538379-70 PROTEIN_ID KHJ47314.1 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 REFERENCE 1 (bases 1 to 2343098) AUTHORS Mitreva,M. TITLE Draft genome of Trichuris suis JOURNAL Unpublished REFERENCE 2 (bases 1 to 2343098) AUTHORS Mitreva,M., Pepin,K.H., Abubucker,S., Martin,J., Minx,P., Warren,C., Palsikar,V.B., Zhang,X., Rosa,B.A. and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_02174" /note="KEGG: dmo:Dmoj_GI13324 1.0e-96 GI13324 gene product from transcript GI13324-RA; K12236 transcriptional repressor NF-X1" intron_pos 147:0 (1/5) intron_pos 217:0 (2/5) intron_pos 361:0 (3/5) intron_pos 411:0 (4/5) intron_pos 647:1 (5/5) BEGIN 1 MDCAKCSTDS EGNDCNSLGG SSTCVDANEK ENLSGPSVSP WMDVAKKVGE SLSEELLDVD 61 SGCLVCLEAI DRPQAVWSCT LCYSSYHLVC IQRWAKQSID AVRQKISERS TYEDRGDEPI 121 GWCCPKCRRF YDENEYPKEY RCYCGKVQNP LDDPWNPAHS CGQKCQRQLS CGHKCLLLCH 181 SGPCPPCPIT VSVSCRCGQQ PKQPRRCAHK EWSCDLICRK LLACQVHRCT VTCHDGVCPP 241 CKELVQAPCC CGSKKEKRYC SEREWKCGTK CNRPLSCGKH FCAEVCHSGA CRPCASGELF 301 CPCGAVRIGE VNCILEISCC GGTCNALLSC AYHRCCERCH LGPCPPCRQL RLKRCRCGLK 361 EKEVQCESEF LCLSKCRKMR ACGRHVCNRR CCDSQCPPCE KLCERLLPCK VPCGREKTIK 421 PPRCALNCSF LPACDHKETL PHPCHYGKCP VCMLPCNKPL PCGHRCLAKC HTIVRVVEIP 481 TWPPSKQKFL SSRDRKPLSI ECPPCYTMVT VSCLGGHEKT EMPCHLALPY ECGRICGQTL 541 ACGNHVCQKL CHDTEHEDCE QCLERCQLIR PPGCPHTCTL ACHPAPCPPC NLTVSRRCHC 601 GLSQVYGQCS AWRQSEQEAL KKMLSCGNKC PKQLICGHQC AYNCHDGVCS DPMQCSKKVT 661 VRCPCLKRTA KVACYRRKDG LKCDDHCKGN ETELGSANAY RSMPYSTRQG SAEVLDDYCG 721 TQQAQKANVY LKLDHLNPTY AAALMGALVC AFAAVAVFLF WS //