LOCUS KHJ47492.1 4892 aa PRT CON 17-DEC-2014
DEFINITION Trichuris suis hypothetical protein protein.
ACCESSION KN538379-248
PROTEIN_ID KHJ47492.1
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JOURNAL Unpublished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_02352"
/inference="protein motif:HMMPfam:IPR013098"
/note="KEGG: ecb:100053844 0. hypothetical LOC100053844;
K12567 titin"
/db_xref="InterPro:IPR013098"
intron_pos 55:0 (1/56)
intron_pos 105:0 (2/56)
intron_pos 161:1 (3/56)
intron_pos 199:1 (4/56)
intron_pos 234:1 (5/56)
intron_pos 278:2 (6/56)
intron_pos 338:1 (7/56)
intron_pos 522:2 (8/56)
intron_pos 661:0 (9/56)
intron_pos 1407:2 (10/56)
intron_pos 1449:0 (11/56)
intron_pos 1494:2 (12/56)
intron_pos 1554:1 (13/56)
intron_pos 1660:1 (14/56)
intron_pos 1766:1 (15/56)
intron_pos 1871:1 (16/56)
intron_pos 1977:1 (17/56)
intron_pos 2082:1 (18/56)
intron_pos 2188:1 (19/56)
intron_pos 2288:1 (20/56)
intron_pos 2394:1 (21/56)
intron_pos 2499:1 (22/56)
intron_pos 2605:1 (23/56)
intron_pos 2725:1 (24/56)
intron_pos 2831:1 (25/56)
intron_pos 2868:0 (26/56)
intron_pos 2936:1 (27/56)
intron_pos 2973:0 (28/56)
intron_pos 3042:1 (29/56)
intron_pos 3076:0 (30/56)
intron_pos 3203:2 (31/56)
intron_pos 3264:1 (32/56)
intron_pos 3301:2 (33/56)
intron_pos 3360:1 (34/56)
intron_pos 3396:2 (35/56)
intron_pos 3455:1 (36/56)
intron_pos 3595:2 (37/56)
intron_pos 3653:1 (38/56)
intron_pos 3689:2 (39/56)
intron_pos 3748:1 (40/56)
intron_pos 3888:2 (41/56)
intron_pos 3946:1 (42/56)
intron_pos 3982:2 (43/56)
intron_pos 4085:2 (44/56)
intron_pos 4146:1 (45/56)
intron_pos 4183:2 (46/56)
intron_pos 4286:2 (47/56)
intron_pos 4346:1 (48/56)
intron_pos 4383:2 (49/56)
intron_pos 4545:1 (50/56)
intron_pos 4639:1 (51/56)
intron_pos 4681:2 (52/56)
intron_pos 4740:1 (53/56)
intron_pos 4787:2 (54/56)
intron_pos 4846:1 (55/56)
intron_pos 4880:0 (56/56)
BEGIN
1 MIRYSITANV PTDSLQRALE LMLWIPKRAS DLNLIHNILD LPTETAKLGR LLRHEQFEVW
61 QDSLDRPKGQ LHVFLFKTKI VATEKVEPED PDEVPEFKHV FTVRLDKYDI REYLGNSNIV
121 QLVPVDASLP TYFFKATAPD NAEIVKQAWI KDVQENKETT GELPESEVEV QGDFIDFSDI
181 KSEFSEYSSV SRKSSEYGDG RDDESPPAKK PKTPPAISRS TSAQSVYSMN MESLTQTGSI
241 EMEGSSVTRT QYGFRTVHET TAKMSLKVTG NPMPVITWYK DGVLLQEDER KKFYSDDDGY
301 FALTIEPVQV EDTGRYTCVA TNEYGQARTS AFFRVVRVDR EPEQPKFLKV MRDLELHEGD
361 TATFTCEVEG WPEPEIQFYL DGQPIHISRE HNIEYDGRTV RLTVREVQPE DGGSYVLKAV
421 NGSGEVQCAA TLTVIKDLEK NKMPPYFQQQ LNDVVVVEDQ SVKFKTVCSG DPTPEVVWYI
481 NGVQLTNSDK VHMIAEDGVY ILTIDNITQH FDGELTCCAF NRLGEISCCC RITVNKADYP
541 PSFEQELRDQ VVTAGEAVKL QVVISAQPEA TVSWWFNDEQ ISEYHPSVRL SAKPQAGIYS
601 IEITKATTDM CGVIKCQASN YLGTVFSSAN LSVEEAKSAP AFRNMLQDIV ALPREYLKIH
661 VSTTGYPRPT VAWKLNGEEI KESPNVKISS SGNDYYLEIL SFTENDAGEL ECTAVNSLGI
721 ASSKCQVSTS PAKMKSNFEK DLPKSTTAEE GKPISFSVQS KQSATFSWFL NGRELHDSDS
781 GIRIMAIGDQ ESRLIIESFS ESLSGRLTCT ATSPLGVSET STDIKSTLGM KEGAGPLPPI
841 VLAEYGGRVL LKVTIESDQA EVCWRLNGEP LKNSEKVHVG RKGADFFLEI EDIDDSASGE
901 LLCEVRQGTR SDTFGTTVKV ERRALTTLLD GLKDTTVRVG DTVQFNLSLK DAKKYEVKWF
961 LNDHELVESE KVHINVYPEQ AECCLKIESI TEEFNGELKC NIMTPSGDYV SSAQLHVVPR
1021 AAPVVVKGLS DSFVQAGDTV KFSVFAENAV EGKVKWVLNG SELLPSDSVI IATEQQNECS
1081 LTLKNINPQQ SGVLECLIST PYGVSRSSAK LTVKPLPEKL MKPEFRAIMA PVVIYEGDTL
1141 ETRVVLEGEP QPEVKWYIND VPLVEDSNVE ITTEKGISKV EIKKVNFDLN GVLKCVAKNE
1201 YGEVATSTSV SIRRQIPVEF EQFLCDTTCR EGDTLKLKAV LLGQPRPEVS WYLKGKKLVQ
1261 TDKIHIYTEQ NTYVAIISDI TCDYSGEVLC KAVNEFGEAS SSAMLTVLPR GVPPDFLEWM
1321 NSISAVDGAE VVHHVKFTGE PTPTIRWFIN NQEVHNSDNF AIHTDKDVCT LTIKHFSASL
1381 VGEIICKAEN DAGEVSCTSQ MSLAPAGYIR EEVSERSELE AVALSTGEIE GSEAGTDFAV
1441 SLPDEDMEEE TSRLESSVLA PKFITKIKDT RVTVGKQAVF ECIVPGTKGV CVKWLKDNKE
1501 IELLARIRVG SHKEENLIIH RLTVDDVTKA DAGTYTCVVM NEHGQEICSA RLEVDEQWTV
1561 AQLPETVPEI VEVLHSCVVE ENEEAIMHCT VTGCPDAQVR WYKDNVQLES SKRHQMVSEA
1621 EGVFVLKIPN VTMKDAGEYK CEVFNASGVA SSTATLTVTV PTAKEPTVGE AMAPKFVEPL
1681 MVSEDAHKKV TMFTCKIYGQ PRPQVRWFKN EKMLNSSYKY EIINEEQDSY VLKIHDTTTE
1741 DNGEYRCEAF NENGIASSSV ALTMKFEQVT ESTLPESAPE FSKPLKSAVL NKGEALHLEC
1801 TVVGQPAPSI QWFKSEEELK TTETVTITSL PNGVECLDMK ETMPSDSGDY RCIATNRLGY
1861 SSSEATVAVH APEEMETAEL LESTTEFVES LHNQTVKENE TGILSCRVTG PPVTSVQWFK
1921 EDVLLESSEK YEIISEANGV FALQVHDSTA EDSGEFKCEV TTEKGSSISK AYLTVEKSSV
1981 KEEFAEEQPP EILKSLTPTS LREGESLTLE CTVTGKPRPT VQWFRNGEEI EVDESVKLET
2041 SSGGVCRLTV HNVTQKDAGE YRCIATNTCG ASWSDASVTV NVAEQAVPTS LTEAAPLFVR
2101 QLQSCTVKAN EQHILQCRVT GAPKPQVRWL KNGVELEPSA KYEIVCEDGE THILKVQNFN
2161 KDDSAVYRCE ASNEKGFAAS EANIEIQRAE VATAVPTFSE TLVSTSVVEG EPLLLECTVS
2221 GEQDSIVEWF KNGQKIEATQ NVKIESLAGG VQHLEVRNIA LSDSGVYRCV VANQLGDSST
2281 EARVTVQTHE TVEEAELCEA VPVFIEVLKS QVAKENEVAS LSCKVYGLPT AEVQWFKDGV
2341 ELKSSEKYEL ISEVSGVFLL QVHNIGKQDA GEYTCVATNK MGSVSSNAFL TVSVAEERVS
2401 ASQQMAPAFL SAITEAFPMC GEKVHLECVV TGNPPPEVHW LKNGQELLST DMMKVSSFSD
2461 GTQCLEIEHV AVKDAGDYCC VATNPLGEAS TKIAVVVQTA ETEGDFKLYG TVPQFVETLH
2521 NCDVQENETA VMKCKVIGTP LPEVRWFKEN ASLESSAKFE LTSDVDGLFL LKIHNAKEED
2581 VGEYRCEVFN CKGVASSKAQ LSVTVGETSE AVKALEAPLF VKTLTSCSLT EGEHLQLNCA
2641 VSGQPTPTIQ WFKNGEEIKA TGLVKIESLP EGILTLVVQN AHVGDSGMYR CLATNEAGEC
2701 STEATVSVQG KYFPSIIQFF PLNTACETME LEELAETAPE FVQVLHFCDV AETQEGILSC
2761 KLTGFPKPQV RWFKDGVPIQ PSEKYEMVTD DNGLVLLKVH VAGREDSGEY RCEAFNSRGV
2821 AWTEAPLNVK AAELMEYEEG EEVAPDFLEP VQACVVNKGE DAVLICRISG VPTPQVCWYK
2881 NGVPLVPDER VEITSFGDRH TLVVHNAQQE DVADYRCEAK NDAGVVWSDA TVCVLSEDYL
2941 MESVQDEVAP FFVREIQQES VNAGDRAVLT CQVSGNPTPE VHWYRDGKLL DLSKDVEIAS
3001 TSDGTVTLVI QHAKVEDQGN YRCEAVNILG SACSKAPLSV FPTEEIMEVE ESASMQFIEP
3061 LHHYMREEDT VAVFECKLKA QPVSTIVWYK DGAPILPDNF TVIESLPDGL QRLTLRCTTA
3121 SAVGHYACLA KSDITEVKTE DDLLSSSACC FSSNEIYSSV SKVPLALEFL QGLKRQCVKK
3181 GDTVTMRCQV NMKGRSKLPT VKWYKSGREL LPDKRVKMEA TMDGWFTLTV SKFEENDAGM
3241 YTCIITENSS VIKSEAPVEL TVTEAGGEFT IVKELASQTI SAGEKLELEL VTSESWDDIR
3301 WLHNNEVVLN DKRTKIEQPE ACVCRLTVAE TSPKDQGNYF VIATKGNKTV ESQAKVIVTE
3361 GKHLEITKAL EDITVPAGAE VTLEVQFNEP IDHAQWYLDS KELVSDAKVS LEQLDERILR
3421 LHLKNADKND AGVYGVVAHS GEQTTECKAN LSVQAQQFLT ITKGLDDVLV EPHKPLTLTV
3481 NVDGLPEKVE WLKDGEPLKE QANLKIEVPA NGVYRLAISD TLPDSAGLYT FRAIDETGVI
3541 ESSGTLSLMD MAEELPQKRI TKLEMVEGLM DQAVAEREPV CLRIKLNKKP KVVKWYKNGK
3601 EIIPSNRFKA EVDETGASLE ISSLLAEDSG LYEVVASDER DSVASSGKLL VTSASQLDIT
3661 RGLQDRTVMK GTELTLEIQL SKPADMATWY HGTEKLANGQ NLRLEEIDGR VYRLHVQHAD
3721 IQDAGEYRVV VKGDGEKAES KANITVKTIP NLRISKELQD VSPTLHETVI MEVLLEGLPD
3781 NVEWFKNGSK LSSVPGMRIE VGGDGWHRLI LEDVLPDSAG LYKFRASNPD GSVESSGTVI
3841 LKQPVEEKPG DAEAALTLMK GLEDQTVDLG HPISLSVKLN KRPKDIKWYS NGKEIRPSMK
3901 KKIKFDGLEA TLEVDKASED DGGIYEVVVS DENTTIRSSG NVRIAVPTAL KIISGLKPCK
3961 VTVGEPLVLS VGLEGNADLI EWLKDGVKLT NVPNYSFTCT EGLYNLQVKQ AEMGNAGEYM
4021 FIARKASDAV SSVGSVVVKS PPSEEAVEQP EKLTFVECLE DQQLQEGDEL KLKVQTNKKP
4081 MTVKWTRNGI PVTSTGGTKL VDNGDRVFEL IVENASRGDA GSYKVIIGDE HASAESVADV
4141 VVIEKAAEKP LQVLKGMADL TCDIGSKACF EVQISGKPKS YRWYKNGREV KQTPRISLKE
4201 MDGGRYCLEI EKTVTDDGGE FSFEAENDVG KVHSQALLTV QSPAARKGPA AEPLVITRPL
4261 DDQTAEEGAE ISFEAEFNRG PKEVHWYKGM DVVTGNEKVK ISSPAVNASK LHVTRVSPED
4321 SSSYRVEAID DLGNIVTSTA RLTVNASPER LEFIKPMADV QVAKGDTATL EVQVKGIPQS
4381 VKWYKNGRLL PSQGRQQEIG KGTYILKIPN ASDDDQATYK CELENQLGSI STEGTLVVLP
4441 SVEEAGEKEI GALKVLKGLA DITLYVGDDL LLEVELSSKP EEVLWFNNGH PVLARNCEVE
4501 VMPNGHAVCR CRLPNIDISC DGTFTVKARN PYGSADSSNK LTVKGKPPKI LTGLEDRRTS
4561 PGNRVVFEVE VDRKPKLVKW YKNGRLVKEN ERTVLISVDD CTYQLVLNDV DKEDVGNYLV
4621 EVSNDFGVAK SEAKLTIIEP VDEMWRSSPR IVKGLNDVEI FDGNHATFSV TVEGKPTSVR
4681 WYRNGTELTS SQRVLPTQLD GFTYKLTLRE CHKDDMGVIK VLAMNDFGSD TSEGRLIVKE
4741 VPTGRMPSGM EKAARFIIPL EDVAAEESKK AVLSCKVEGL PTPLITWFKD GKEIDKNERV
4801 TYSMDEDKVC SLSIGAISPE DEGCYAALAK NSLGQDRTEC YLTIAAPKGA EELEHGVAPE
4861 FIKPLRSKSI IEGEDLTLDA RIIGNPLPEI CW
//