LOCUS KHJ47246.1 840 aa PRT CON 17-DEC-2014
DEFINITION Trichuris suis ABC transporter transmembrane region protein.
ACCESSION KN538379-2
PROTEIN_ID KHJ47246.1
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JOURNAL Unpublished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_02106"
/inference="protein motif:HMMPfam:IPR001140"
/inference="protein motif:HMMPfam:IPR003439"
/note="KEGG: phu:Phum_PHUM351610 1.2e-182 multidrug
resistance protein, putative"
/db_xref="InterPro:IPR001140"
/db_xref="InterPro:IPR003439"
intron_pos 12:0 (1/10)
intron_pos 138:0 (2/10)
intron_pos 194:0 (3/10)
intron_pos 253:1 (4/10)
intron_pos 267:2 (5/10)
intron_pos 567:2 (6/10)
intron_pos 614:0 (7/10)
intron_pos 648:0 (8/10)
intron_pos 749:0 (9/10)
intron_pos 804:2 (10/10)
BEGIN
1 MRKLEGSVAV QGTISYVPQQ AWILNATVRD NILFTKPNRP NFYTQVVKAC SLDVDIEEMS
61 EKSDTEIGEK VCCNQLLLFV QLFFDIYFRV SYKYSNKILI QKISLVEKIF FLSKECPAVF
121 AVSILAAFPA LTSSFFQGIN LSGGQKQRLS IARAVYQYTD IYLFDDPLSA VDSRVGRHIF
181 DNVIGRKGLL KDKTRVFVTH ALAFLKDVDL IVIMDQGRIK KVGTPSQLLT EWDGLSEFLE
241 EKNDNAEEPK LSDEESGDEN AEMLRSRRNT VTSVSSSKSS KLDARNSLRE SNAIANGPAK
301 SHENEWNIKR KRLIEEETAE TGRVKAHVYK LYVQSIGFLS SFVVFILYMV SGGLSVGSSI
361 WLAEWSEDSV CSAKNRSDCV QTDTRIGVYA ALGIGQALFV FAAALLMMLC MVASSANLHE
421 RLLHNLLRVP MSFYETTPLG RVLNRIGKDI DVVDNTLPAA VRTWMNCLVQ IIATLVIIAM
481 NMKAFAAAII PLAIFYYAVQ RFYVSSSRQL KRMESVSRSP IYSLFQEVIQ GAVSIRAYRA
541 QKHFRDMFDK HVDANQMTYY PMIVSNRFRW LAVRLEFIGN LLVFLAAIFA VYNREEGILS
601 AGMVGLAVTY ALSITQTLNW VVRMTSDLET NIVSVERIVE YMNVPTEADW TTEYRPPHNW
661 PSMGRVEFDR YAMRYRPGLD LVLKGISFVA HGGEKVGIVG RTGAGKSSIT LALFRIVEPV
721 EGSIVIDSVD IGLIGLHDLR SRISIIPQEP VLFCGSIRMN IDPTGQKNDD EIWTALEHAH
781 LKSFISTLPD KLDHEVVEGG ENLRLLVLSN GQVVDNDSPA NLLTRLDGEF YAMAKEANIV
//