LOCUS       KHJ47555.1               134 aa    PRT              CON 17-DEC-2014
DEFINITION  Trichuris suis hypothetical protein protein.
ACCESSION   KN538379-311
PROTEIN_ID  KHJ47555.1
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  JOURNAL   Unpublished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_02415"
BEGIN
        1 MMNRKYSGGA LFESSLKLEA VGGLVPRCLV TVSNGKFNML VRNLFDHELC VPKKILLGKI
       61 SPLCRDICSL EETRTASKEN DVELKAILWK LTTETAEESL DEKQKSSLFE LLWSFRDVFA
      121 ANKRDLGQAR CSSS
//