LOCUS KHJ47266.1 2365 aa PRT CON 17-DEC-2014
DEFINITION Trichuris suis hypothetical protein protein.
ACCESSION KN538379-22
PROTEIN_ID KHJ47266.1
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JOURNAL Unpublished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_02126"
/inference="protein motif:HMMPfam:IPR001747"
/inference="protein motif:HMMPfam:IPR015255"
/db_xref="InterPro:IPR001747"
/db_xref="InterPro:IPR015255"
intron_pos 19:1 (1/28)
intron_pos 35:1 (2/28)
intron_pos 92:0 (3/28)
intron_pos 164:0 (4/28)
intron_pos 213:0 (5/28)
intron_pos 278:1 (6/28)
intron_pos 423:1 (7/28)
intron_pos 473:0 (8/28)
intron_pos 524:0 (9/28)
intron_pos 572:1 (10/28)
intron_pos 715:0 (11/28)
intron_pos 771:0 (12/28)
intron_pos 894:2 (13/28)
intron_pos 982:0 (14/28)
intron_pos 1053:0 (15/28)
intron_pos 1102:1 (16/28)
intron_pos 1208:0 (17/28)
intron_pos 1333:0 (18/28)
intron_pos 1466:0 (19/28)
intron_pos 1529:2 (20/28)
intron_pos 1762:2 (21/28)
intron_pos 1941:0 (22/28)
intron_pos 1985:2 (23/28)
intron_pos 2095:2 (24/28)
intron_pos 2196:1 (25/28)
intron_pos 2259:0 (26/28)
intron_pos 2310:2 (27/28)
intron_pos 2359:0 (28/28)
BEGIN
1 MKSHLASFVL FLFLCLHQEV YCKTHGDACF AECSGKNDKF HFDRGYRYAY DWHLKTKVAY
61 NGTDRSPEVL TYNLNGKVHL YAMAPCEFTM KIISAEQTGG GTAQLDLEVL EKYTTQFSFD
121 NGAIRSICPD PVEPIWSVNI KRGILSAFQN LYEETALESE VEEADVSGLC PTSYRGKASG
181 SDLLVTKTKY LNSCRNRGHG SFGRMVPYKS RSNYQNVPLF SGQQRCTQEI RNKILHRASC
241 EESNTFAPAY TDARGGLFVY AEMELSYRDS AAETVPAEQR NHQPLYFDYS DQEREMSSDA
301 VSKMEALLPK FCAASSEVVR DTPDLFSELV HCLTRVTRTD IEAVWNRVEK QHECDAQLNY
361 IADGLSACGS PSCVSFIIDH LSQRQQTEDQ KKRWLDSLIF IDNPTLDVIS SLTPLIKKSE
421 KEELFRLSNV IHKYCAHDSH CASHREIIQA LDALSGHLTH GCNPRSPEDF DKMLFALRAA
481 GNIDVPSTGL QNQLKCLSDK TAADELRLAA VQSVRRLPCH PSANTHLFAL LNDQSESVEI
541 RISAFMVLMK CPTDSMVDRI LALLKTETSM QVASFIWSYL NSIIKGNSPS QEHLRHLLMF
601 KTLEPKVDRD ARKFSKFSQF STYSTHGNMG LDVEKSLIFS PDEYIPRQAL LNLTMHIYGQ
661 SVNFLEIGAR TVGLDSLVEH LFGPDGYFTN PEGHYFKEPI SAHSNPSIRT LTDKFQRHMK
721 TKENFDLAVY ARIFGDDVFH YSGREMDAKH FVRESATIEN LMRQLAKERH FEKKRNVVFA
781 DWKYTMPTVG GLPLQFDLNG VASVNVALTG KLDVKDLLKG KTDVDIKTNV RGSVAARTAA
841 VVSILPGKSS FGMSIKTRFF ANRAVELAAL LKGGKSLHLK FLLPKEEMDL LRIESETFVV
901 RGDTWAPLYP PDASGHLTHA CSNKELNEWL GFKVCYSQRL PEKLISPQAL LTGPTLFRLN
961 LKNNVHGQQA YEMTVTWKMT PEEKRVHVKA EHSDYTADFV YYPKGELLME VKSDKRPMNL
1021 RINAEYTHEK KLANFTFSGD KGQIFSGHAY LKRKVASPLE SSVEFDLLIS AHHERKLLLH
1081 YDYNHKYPQA GRQTRSLGKR YGSRRRRDNS DEEAYLLNLN FESPWRNLHL NGKLNASPHV
1141 SLMALTADYQ RGTKDDTAKL KAEYRRSVQG EHAFIVLASS LEFTKHPERR TEFSLKASNM
1201 SNSLSVEAHL TSGERTMSFV GNAKKDPANG IYSAEGKIGG NVLSEHLLSG TYQNKLPNLF
1261 KFGARVQGPN IGEAAYDVKY TKKNERLTRV EIESKAQYGK KTLDFVSTVS EIEPKIYDVA
1321 AELKSPERNY IMIKGKAMAR IHSTKKFNCS LNSILRILDQ PDLTLVKSIQ RDGFNIYIDS
1381 ILSDAASELY HGTFKTASKD AGVYDGHLSF KSKVGKPMDL VVDSHWTPTD NGHVSILKMR
1441 NMDHEIFKTE LIIPKSFKQK FNQIKLQIIS NWRNAHKHLI MDYSLTRSDV ITHSLDLEGK
1501 LMDHNHYLNV KLIKAKVNQL TVKLGKGGSV NLQIHSNYSV QQSPTKDGYN TVLTTALTSN
1561 LGGQSCSWTG NLTFEKHPKG HLAHAEVKSA ENKNARFAFL YGSRMDVGER FRKTDFLVHV
1621 KLHGLQFEVK DEFWRQMQKQ NFSNKLTVTW NKNSLVNSDQ RFTNDFHICL SPFAVSTSTE
1681 FGSGHSSMLH SSVLFGVRPE HFDASIKLDL ANKSVLHFNG MYRLRGRHEV FEGMLASQMG
1741 NSYNLGVHLS RDRTLYGTFS AELTFGDRNV IKINRRKETN SEGNHVERLS FEQHSKGELV
1801 RYLTTVVEIQ KQTQLQKFEI AFKVGGIDYS AHGEYSTKDK SGRIQIKKTK EGTALTDGKF
1861 TEQAPNEYAT VLTGGQLVGE VDIKINTHAD KQMLKIDVRH VDSPFTLEAE SHWQAQRASI
1921 RILVIQRDSQ GKETSKSGFA FSVQTPKTHS ITIDCEFLRS NGDILIHLSY VNERPALLNF
1981 KFLINPARPS REQWSGLSFV HRLESSEKRS LKISLIDPKI ADNVYLTTNW QLSGDCRLLK
2041 PQSCRISVDS EASYSSDKNR LIKATFNFNR ENAADGVWAV DAGIQNAFTN LDFHCYHTYK
2101 FRKCKNSDLW CERQVEWVIR RLDEQGQAKR YELSYNEHRG QSAQLKAKCN EGEWVLQVHK
2161 EEQGYKVNIL RDGAFKYTLA CTYVREEKLA KCQVENPYTI LLHGYAQLVT NEWFTGSVWH
2221 SKTNGERIND IDVSSKIEAN DILTTRVYIR PDIKSSVKSW LDGIDARSKL NEYLSGISRT
2281 SGLLKKLMII ADDQVVQLAS TREQWQKEFS QLVNDHADAV RELTRVRQAA RSWLKGASME
2341 LYEIFIGMGR RFVEATKHIY LLIAM
//