Related articles in PubMed
The draft genome of the parasitic nematode Trichinella spiralis.
Mitreva M, Jasmer DP, Zarlenga DS, Wang Z, Abubucker S, Martin J, Taylor CM, Yin Y, Fulton L, Minx P, Yang SP, Warren WC, Fulton RS, Bhonagiri V, Zhang X, Hallsworth-Pepin K, Clifton SW, McCarter JP, Appleton J, Mardis ER, Wilson RK
Nature genetics43(3)228-35(2011 Mar)
GeneRIFs: Gene References Into Functions What's a GeneRIF?
The following Tsp_02039 gene cDNA ORF clone sequences were retrieved from the NCBI Reference Sequence Database (RefSeq). These sequences represent the protein coding region of the Tsp_02039 cDNA ORF which is encoded by the open reading frame (ORF) sequence. ORF sequences can be delivered in our standard vector, pcDNA3.1+/C-(K)DYK or the vector of your choice as an expression/transfection-ready ORF clone. Not the clone you want? Click here to find your clone.
| CloneID |
OTr122488 |
| Clone ID Related Accession (Same CDS sequence) |
XM_003377792.1
|
| Accession Version |
XM_003377792.1 Latest version! |
Documents for ORF clone product in default vector |
| Sequence Information |
ORF Nucleotide Sequence (Length: 2409bp)
Protein sequence
SNP |
| Vector |
pcDNA3.1+/C-(K)DYK or customized vector |
 User Manual |
| Clone information |
Clone Map |
MSDS |
| Tag on pcDNA3.1+/C-(K)DYK |
C terminal DYKDDDDK tags |
| ORF Insert Method |
CloneEZ™ Seamless cloning technology |
| Insert Structure |
linear |
| Update Date |
2011-06-30 |
| Organism |
Trichinella spiralis |
| Product |
hypothetical protein |
| Comment |
Comment: PROVISIONAL REFSEQ: This record has not yet been subject to final NCBI review. This record is derived from an annotated genomic sequence (NW_003526943). Trichinella spiralis is a roundworm that cause most of the human trichinella infections and deaths around the world. Its pathogenicity is higher than that of other trichinella species due to the higher number of newborn larvae produced by the females and for the stronger immune reaction induced in humans. The life cycle of the parasite begins when a person or an animal eats contaminated meat containing larvae. T. spiralis is a basal nematode with a well-defined phylogenetic position near the root of the phylum Nematoda. The genome size estimate based on flow sorted nuclei stained with PI (Spencer Johnston, Texas A&M University) is 1C = 71.3 +/1 1.2 Mb. The strain being sequenced (ISS 195) was obtained from the laboratory of Judith Appleton (Cornell University) and has been maintained in rats since 1970. Worm isolation and DNA extraction was performed by Dante Zarlenga (USDA)
This assembly consists of plasmid, fosmid and BAC end sequences. The data were assembled using the assembly engine, PCAP (Xiaoqiu Huang et. al. 2006). Our goal is to explore this WGS draft sequence of T. spiralis in several ways: i) to provide a better understanding of evolutionary biology by identifying gene loss or gain across the phylum Nematoda and clarify evolution of genome architecture (synteny, operons); ii) help identify RNA genes and regulatory regions; and iii) better define proteins involved in nematode parasitism that impact health and disease and are relevant to both host-parasite relationships and basic biological processes..
We masked the repeats by using RECON (Bao and Eddy, 2002) and RepeatMasker (A.F.A. Smit, R. Hubley & P. Green RepeatMasker at http://repeatmasker.org). Then the Ribosomal RNA genes were identified using RNAmmer ((http://www.cbs.dtu.dk/cgi-bin/nph-sw_request?rnammer ). Transfer RNA genes 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). Protein-coding genes were predicted using a combination of ab initio programs (Snap, Korf, 2004 and Fgenesh, Softberry, Corp) and an inhouse evidence based program Eannot (Eannot Ding et al., 2004) which uses mRNA, EST and protein alignment information from same species or cross-species to aid in gene structure determination. A consensus gene set from the above prediction algorithms will be generated, using a logical, hierarchical approach. Gene product naming was determined by BER (JCVI: http://ber.sourceforge.net ).
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 T. spiralis genome project contact Makedonka Mitreva [email protected] (Washington University School of Medicine). The National Human Genome Research Institute (NHGRI) of the National Institutes of Health (NIH) provided funds for this project.
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1
61
121
181
241
301
361
421
481
541
601
661
721
781
841
901
961
1021
1081
1141
1201
1261
1321
1381
1441
1501
1561
1621
1681
1741
1801
1861
1921
1981
2041
2101
2161
2221
2281
2341
2401
| ATGCTTTCAG AGTTGATAAT AAGTTTTACT TTGCTGGTCA ACGCTGGAGC AGTATTAAAT
TTCAAATTTC GATCAGCGGA AGATAACTTT TCTGTAGAAG AAGGTTATAG AAGTTTTGGT
AATAATAATA ATTTTTCTTT TATTCCATTC ATCGTTCAAT TTTCTTCAGA TTTTTTTCCC
ATTGATAAAA TGTTACCGTT CGATTTTACC AATCAACTCG ACCAGTGTCG TGTGGAGTTG
GATCGATTGA ACGTGGACGC GTCGGCATTG GACACCGAAA TCCGGTCGTT GTTGGCCGCC
AGTTCGCAAC GGGCTCGCGA ACTGGCCGGT CCACTGGTCC GGGTCGAAGG GGAAATTGCC
GCCGCCGAAT CCGACTTTCG CCAACTGGCC AACGTGTTCA CGTCCAACTG GACACTGGCC
AACGGAATCG GCGCCCGAGT GCGTCGGCTG GACACAGCGA AAATTCGTGT CGTCGACTGC
ATGCAGTTGG TCGACGACGC GCTCGATTCG CGCCTCTGCG TCGACGGTGT CCAGTCGTCG
TTGGCCGCCG GCCAGTACGA CCGAGCCGCC GACCAGTTGC GCCGATTTTT GGGCGTCGAC
GCCGCCGTTC GCCGGCTGGC CAGTGGCGAC GGCGCTCACG ACCCGACGTC GTTGATGCTC
GACGCCAGAG ATCGTCTGCG GACAATTTTG GTCGACGAAT TCGACCGGGC CGACCGGCGA
GACGACAACG CGTCGGTCGA ACGTTTTTTC AAATTGTTCC CGTTGATCGG CGAACACGAG
CTCGGCTTGG CCGAATTTGG CGCCCAGTTG ACGCGCCGAT TGACCGACTT GGTCCAGCGC
AGTCTGACTG TAGTGGACGA CAGTGGTCAG CCGCCGTTCG TCGACGCTTT ACGACTTTTG
CTCGACTGGC TCGTTCGACT GATCGACGCC CAACAGCCGA TCGTCGACTC TTGCTACGGA
CCGGGCAAGT TGTTCGTCTT GTGGCGTCTG TTGCAGGCCC AATGCGACGT CGAAGCGGGA
CGCATTTTGG ACAACTTTTT CGACCACAGG CAATTTTACA AAAAACTCAG TCTAGCCGAA
AATTGTCTCA AACAGTCGGC TGCCAGTCGA ACGACCGTCG TTGATCCGCT CGATTTGGAC
GCTTTGCTCA GTGAAATAAC TTTGATCCGG ACATTTGTTC GTCGTAAAGT GAGTATTGGA
ATTGGTAAAA TGCCAGACGA AACAGCGAAG CAAAAAGAAG AAAAACAACG CTTGGAGGAA
AAATTCCAAA CCCATCTTTC CAATTGTGTG TTGAATTGTC GCATGCAAGA ACTGCTCGGC
CAGTACGTGG CAATTGAAGA GTACTACATG CGAGAGTCGA TATTGAAGGC GATTCGGCTC
GAATGCCGCG AATCCGGCAC GTTGCTTTCC AGCGTTGTGG ACGATTGTTT TTTCATAATT
AGCAAAAGTG TCCGTCGGGC ATTGGCGACG TCGGATGTCG ACTGCATCTG CGCGATGTTG
AACCATGCTT GCGCGTTGCT GGAAACCCAT CATTTGGCCC ATTTGAAAAG TCGACTCAAA
CTTGGCTATC CTTCATCTGT CAGTGTTGAA TGTGTGGAAA AGTTGAAGAA TCGACTGAAG
GACGACTTTC GAAATGTTCT ACTCCAACTG AACGACGTTG ACCAGCAGAA GCTGGACAGC
TGTTTGGGGC AGTTGGACGA GACGGCGAAC AAATTCCACT CGGCGTTGTC CGACGCCGTT
GACCAACTTG TTCGAACATC CTTCAAGCCA CGCCTACGCT TGGCGGTCGA TGGCTTTTTC
AACGACACGC ACGCGCCCAG TGAGTTGGAG TTTGTGGAAT TGGAATCGCG CGGCTTGTTT
GTAGAAAATA TCATCGGATG TTTGCAGCTG CTGTTGGAAG ATTTGAGACA GTCACTTGGA
GAACGACCGT TGGCCATGGT GCATGCGACG ACGGCGTCGT TGACCGCGGA CTTGTTGGAA
AAGGCTACAC TGAAGGGAAC GTACAACCGC CTGGGCGGGC TTTTGCTCGA CAAGCAGATC
CGCAAACTAG CCGGATACTG GACGCAGTTT GCCGGTTGGA GCACCAGGCA ACGCTTCTCA
AAATTGGACC AAATTGTTTC CCTGTTGAAC GTGGATTCGG TAGCCGATGC GCAAAATTAT
TGTCAATCCG AAAGTGTCAC TTGGTTATTG AACTTGGCCG AAATTCGACA AGTGCTTGCT
TTGAGAATCG ATCTGCCCGG CAACGAGATA CAAATACAAA AAGATGTTTT TTATCTGCTG
AAATTTGGAC AGATTATGTA CAGTTTTTAC CATCGAAGAG TTGCTCGAGT AAGATGGATA
AAGGCAGATA GGTGGCTATA TAGCATTCAG AGAGGTTTGC TTGTTGGAAC TCTTTGGCTC
GTAGACTAA |
The stop codons will be deleted if pcDNA3.1+/C-(K)DYK vector is selected.
| RefSeq |
XP_003377840.1 |
| CDS | 1..2409 |
| Translation | |
Target ORF information:
| RefSeq Version | XM_003377792.1 |
| Organism | Trichinella spiralis |
| Definition | Trichinella spiralis hypothetical protein (Tsp_02039) mRNA, complete cds. |
Target ORF information:
| Epitope | DYKDDDDK |
| Bacterial selection | AMPR |
| Mammalian selection | NeoR |
| Vector | pcDNA3.1+/C-(K)DYK |
|
 XM_003377792.1 |
ORF Insert Sequence:
1
61
121
181
241
301
361
421
481
541
601
661
721
781
841
901
961
1021
1081
1141
1201
1261
1321
1381
1441
1501
1561
1621
1681
1741
1801
1861
1921
1981
2041
2101
2161
2221
2281
2341
2401
| ATGCTTTCAG AGTTGATAAT AAGTTTTACT TTGCTGGTCA ACGCTGGAGC AGTATTAAAT
TTCAAATTTC GATCAGCGGA AGATAACTTT TCTGTAGAAG AAGGTTATAG AAGTTTTGGT
AATAATAATA ATTTTTCTTT TATTCCATTC ATCGTTCAAT TTTCTTCAGA TTTTTTTCCC
ATTGATAAAA TGTTACCGTT CGATTTTACC AATCAACTCG ACCAGTGTCG TGTGGAGTTG
GATCGATTGA ACGTGGACGC GTCGGCATTG GACACCGAAA TCCGGTCGTT GTTGGCCGCC
AGTTCGCAAC GGGCTCGCGA ACTGGCCGGT CCACTGGTCC GGGTCGAAGG GGAAATTGCC
GCCGCCGAAT CCGACTTTCG CCAACTGGCC AACGTGTTCA CGTCCAACTG GACACTGGCC
AACGGAATCG GCGCCCGAGT GCGTCGGCTG GACACAGCGA AAATTCGTGT CGTCGACTGC
ATGCAGTTGG TCGACGACGC GCTCGATTCG CGCCTCTGCG TCGACGGTGT CCAGTCGTCG
TTGGCCGCCG GCCAGTACGA CCGAGCCGCC GACCAGTTGC GCCGATTTTT GGGCGTCGAC
GCCGCCGTTC GCCGGCTGGC CAGTGGCGAC GGCGCTCACG ACCCGACGTC GTTGATGCTC
GACGCCAGAG ATCGTCTGCG GACAATTTTG GTCGACGAAT TCGACCGGGC CGACCGGCGA
GACGACAACG CGTCGGTCGA ACGTTTTTTC AAATTGTTCC CGTTGATCGG CGAACACGAG
CTCGGCTTGG CCGAATTTGG CGCCCAGTTG ACGCGCCGAT TGACCGACTT GGTCCAGCGC
AGTCTGACTG TAGTGGACGA CAGTGGTCAG CCGCCGTTCG TCGACGCTTT ACGACTTTTG
CTCGACTGGC TCGTTCGACT GATCGACGCC CAACAGCCGA TCGTCGACTC TTGCTACGGA
CCGGGCAAGT TGTTCGTCTT GTGGCGTCTG TTGCAGGCCC AATGCGACGT CGAAGCGGGA
CGCATTTTGG ACAACTTTTT CGACCACAGG CAATTTTACA AAAAACTCAG TCTAGCCGAA
AATTGTCTCA AACAGTCGGC TGCCAGTCGA ACGACCGTCG TTGATCCGCT CGATTTGGAC
GCTTTGCTCA GTGAAATAAC TTTGATCCGG ACATTTGTTC GTCGTAAAGT GAGTATTGGA
ATTGGTAAAA TGCCAGACGA AACAGCGAAG CAAAAAGAAG AAAAACAACG CTTGGAGGAA
AAATTCCAAA CCCATCTTTC CAATTGTGTG TTGAATTGTC GCATGCAAGA ACTGCTCGGC
CAGTACGTGG CAATTGAAGA GTACTACATG CGAGAGTCGA TATTGAAGGC GATTCGGCTC
GAATGCCGCG AATCCGGCAC GTTGCTTTCC AGCGTTGTGG ACGATTGTTT TTTCATAATT
AGCAAAAGTG TCCGTCGGGC ATTGGCGACG TCGGATGTCG ACTGCATCTG CGCGATGTTG
AACCATGCTT GCGCGTTGCT GGAAACCCAT CATTTGGCCC ATTTGAAAAG TCGACTCAAA
CTTGGCTATC CTTCATCTGT CAGTGTTGAA TGTGTGGAAA AGTTGAAGAA TCGACTGAAG
GACGACTTTC GAAATGTTCT ACTCCAACTG AACGACGTTG ACCAGCAGAA GCTGGACAGC
TGTTTGGGGC AGTTGGACGA GACGGCGAAC AAATTCCACT CGGCGTTGTC CGACGCCGTT
GACCAACTTG TTCGAACATC CTTCAAGCCA CGCCTACGCT TGGCGGTCGA TGGCTTTTTC
AACGACACGC ACGCGCCCAG TGAGTTGGAG TTTGTGGAAT TGGAATCGCG CGGCTTGTTT
GTAGAAAATA TCATCGGATG TTTGCAGCTG CTGTTGGAAG ATTTGAGACA GTCACTTGGA
GAACGACCGT TGGCCATGGT GCATGCGACG ACGGCGTCGT TGACCGCGGA CTTGTTGGAA
AAGGCTACAC TGAAGGGAAC GTACAACCGC CTGGGCGGGC TTTTGCTCGA CAAGCAGATC
CGCAAACTAG CCGGATACTG GACGCAGTTT GCCGGTTGGA GCACCAGGCA ACGCTTCTCA
AAATTGGACC AAATTGTTTC CCTGTTGAAC GTGGATTCGG TAGCCGATGC GCAAAATTAT
TGTCAATCCG AAAGTGTCAC TTGGTTATTG AACTTGGCCG AAATTCGACA AGTGCTTGCT
TTGAGAATCG ATCTGCCCGG CAACGAGATA CAAATACAAA AAGATGTTTT TTATCTGCTG
AAATTTGGAC AGATTATGTA CAGTTTTTAC CATCGAAGAG TTGCTCGAGT AAGATGGATA
AAGGCAGATA GGTGGCTATA TAGCATTCAG AGAGGTTTGC TTGTTGGAAC TCTTTGGCTC
GTAGACTAA |
The stop codons will be deleted if pcDNA3.1+/C-(K)DYK vector is selected.
 |
The draft genome of the parasitic nematode Trichinella spiralis.
Nature genetics43(3)228-35(2011 Mar)
Mitreva M,Jasmer DP,Zarlenga DS,Wang Z,Abubucker S,Martin J,Taylor CM,Yin Y,Fulton L,Minx P,Yang SP,Warren WC,Fulton RS,Bhonagiri V,Zhang X,Hallsworth-Pepin K,Clifton SW,McCarter JP,Appleton J,Mardis ER,Wilson RK |
