LOCUS KHJ47470.1 1140 aa PRT CON 17-DEC-2014
DEFINITION Trichuris suis hypothetical protein protein.
ACCESSION KN538379-226
PROTEIN_ID KHJ47470.1
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JOURNAL Unpublished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_02330"
/inference="protein motif:HMMPfam:IPR006935"
/inference="protein motif:HMMPfam:IPR018999"
/note="KEGG: sce:YMR080C 1.9e-237 NAM7, IFS2, MOF4,
SUP113, UPF1; ATP-dependent RNA helicase of the SFI
superfamily involved in nonsense mediated mRNA decay;
required for efficient translation termination at nonsense
codons and targeting of NMD substrates to P-bodies;
involved in telomere maintenance"
/db_xref="InterPro:IPR006935"
/db_xref="InterPro:IPR018999"
intron_pos 7:1 (1/18)
intron_pos 73:0 (2/18)
intron_pos 138:2 (3/18)
intron_pos 208:2 (4/18)
intron_pos 255:0 (5/18)
intron_pos 279:2 (6/18)
intron_pos 338:1 (7/18)
intron_pos 370:1 (8/18)
intron_pos 406:2 (9/18)
intron_pos 476:0 (10/18)
intron_pos 554:2 (11/18)
intron_pos 641:0 (12/18)
intron_pos 712:1 (13/18)
intron_pos 815:0 (14/18)
intron_pos 904:0 (15/18)
intron_pos 937:1 (16/18)
intron_pos 998:1 (17/18)
intron_pos 1088:0 (18/18)
BEGIN
1 MDCLVTKGKD CITPKMSDYD RYESCAPAST SSYDGDGRIP FIGATQDSDY DYDFTIPSQM
61 DLSQTDARVE GRASPNQAQP LDSAAVRSDR KAVKPHAAVN LPEHACRYCG IYDPKYVLNC
121 NQCKKWFCNG RLKSSAGSHI INHLVRSRHK EVTLHQEGPL GETILECYNC GCRNVFVLGF
181 VAAKSESVIV LLCRQPCAAQ TALKELNWEG GHWKPLIQDR AFLTWLVKMP SVTEQMKARQ
241 VTPLQMNRLE EFWKEKPDAT LEDIENPSID EEPQRVSIKY ESASHYQSIF SPLITLEAEY
301 DRKMKEAQTQ DNVTVRWDIG LNKKHVAFFK LTKVTEGDMK LMQGDELCLK CTFAGYTWSG
361 VGHVIKIPDS HSDTVGLEMK IGTGVPSDVT HGFSVDFVWK STSFDRMRNA LARLVTIETS
421 VSEPIYYRIL GIETEDVVMK IPLPKRFSVR GLPELNHSQV FAVRTVLQRP ISLIQGPPGT
481 GKTVTSATIV HHLAKIYSSP VLVCAPSNIA VDQLAEKIHR TGLKVVRLCA KSREAIESPV
541 SFLSLHYQIR FLHGEEELSK LLQLRDETGE LSSTDEMRFR TLRNKCERDL LRNADVVCCT
601 CVGAGDPRIA QMQFRCVLID ESTQATEPEC MVPVVNGCRQ LILVGDHCQL GPVVMCKKAA
661 RAGLNQSLFE RLVVLGIRPI RLQVQYRMHP ALSAFPSDVF YEGSLQNGVT EAERTLSGFD
721 FTWPEAHSPM FFWLSMGQEE ISGSGTSYLN RTEAANIEKL ATKFLKLGAR PDQIGIITPY
781 EGQRAFIVQY MQFAGTLNKK LYLDIEVASV DAFQGREKDF ILLSCVRSND NLGIGFLNDP
841 RRLNVALTRA RFGLIIVGNP KVLARQQLWQ NLLVFYKEHH LLVEGSLNAL KESAVQFIRT
901 NVQLNSRGSQ DVDSGNEFQS ARSRHMFSNR PMPRLPTSLP ASCRPYRPLN DPLGMIMPER
961 FTTALAASAM NIPLPINMFL PQVPAVNPMM SQQRAAMRSA AIAKAKSRWQ QGASVASPVP
1021 GGMMSDGRQI QQVRDNRPQR GSSNAMSTGH QQAAASSRMS QPFHLSQGMA PSSSNAPMSQ
1081 IASEMSQDQM MDDMLRSQLE TMMLSQDMSY TNSPMVLMQS SASDGVTAAT DKKMFNQTPE
//