LOCUS ABJB010539798 4643 bp DNA linear INV 29-FEB-2008 DEFINITION Ixodes scapularis strain Wikel colony gcontig_1108379684480, whole genome shotgun sequence. ACCESSION ABJB010539798 ABJB010000000 VERSION ABJB010539798.1 DBLINK BioProject: PRJNA16232 BioSample: SAMN03004382 KEYWORDS WGS. SOURCE Ixodes scapularis (black-legged tick) ORGANISM Ixodes scapularis Eukaryota; Metazoa; Ecdysozoa; Arthropoda; Chelicerata; Arachnida; Acari; Parasitiformes; Ixodida; Ixodoidea; Ixodidae; Ixodinae; Ixodes. REFERENCE 1 (bases 1 to 4643) AUTHORS Ayllon,N., Villar,M., Galindo,R.C., Kocan,K.M., Sima,R., Lopez,J.A., Vazquez,J., Alberdi,P., Cabezas-Cruz,A., Kopacek,P. and de la Fuente,J. TITLE Systems Biology of Tissue-Specific Response to Anaplasma phagocytophilum Reveals Differentiated Apoptosis in the Tick Vector Ixodes scapularis JOURNAL PLoS Genet. 11 (3), E1005120 (2015) PUBMED 25815810 REMARK Publication Status: Online-Only REFERENCE 2 (bases 1 to 4643) AUTHORS Nene,V. CONSRTM Ixodes scapularis Genome Project TITLE Direct Submission JOURNAL Submitted (11-DEC-2007) J. Craig Venter Institute, 9704 Medical Center Drive, Rockville, MD 20850, USA REFERENCE 3 (bases 1 to 4643) AUTHORS Nene,V. CONSRTM Ixodes scapularis Genome Project TITLE Direct Submission JOURNAL Submitted (21-FEB-2008) J. Craig Venter Institute, 9704 Medical Center Drive, Rockville, MD 20850, USA COMMENT This Wikel tick colony was established in 1996 using field collected ticks from New York, Oklahoma and a Lyme Disease endemic area of Connecticut. This colony has been continuously in-bred since establishment and has not been supplemented with field collected material. The colony is known to be a competent vector of various Borrelia and Babesia isolates. Genomic DNA was prepared from embryonated eggs. The genome of Ixodes scapularis Wikel strain has been sequenced to approximately 6x coverage in a joint effort by the Broad Institute and The J. Craig Venter Institute (JCVI) and funded by the National Institute of Allergy and Infectious Diseases, National Institutes of Health. Assembly was performed at JCVI and consists of 369,492 scaffolds built from 570,637 contigs with an estimated 3.8x coverage of the assembly. The other 570958 contigs in the 01 version of this project represent degenerate contigs that were not incorporated into scaffolds. The first public assembly is deposited as JCVI_ISG_i3_1.0 and has the VectorBase Designation IscaW1. Additional information about the Ixodes scapularis sequencing project and assembly can be found at http://iscapularis.vectorbase.org/ and http://msc.jcvi.org/i_scapularis/. The annotation for this assembly was produced in a joint effort between JCVI and VectorBase with support from The Broad Institute of Harvard/MIT. A total of 18,385 scaffolds were annotated, containing 20,486 protein coding genes, and 4,439 non-coding RNA genes. Computational annotation methods were optimized with respect to training data sets resulting in a high confidence set of predicted gene models making extensive use of protein and/or EST supporting evidence. Long-term curation of the sequence and subsequent annotation updates will be the responsibility of VectorBase at http://www.vectorbase.org. Assembly name: JCVI_ISG_i3_1.0 Genome coverage: 3.8x on assembled contigs; 6x based on an estimated genome size of 2.1 Gbp. Annotation was added to the scaffolds in December 2008. The VEuPathDB Bioinformatics Resource Center (www.veupathdb.org) is responsible for the assembled genome sequence and its annotation as of March 2022. Annotation and related data can be viewed and updated at http://veupathdb.org and inquiries can be sent to help@veupathdb.org. ##Genome-Assembly-Data-START## Assembly Method :: unknown v. before 2008 Assembly Name :: JCVI_ISG_i3_1.0 Genome Coverage :: 6x Sequencing Technology :: Sanger ##Genome-Assembly-Data-END## FEATURES Location/Qualifiers source 1..4643 /organism="Ixodes scapularis" /mol_type="genomic DNA" /strain="Wikel colony" /db_xref="taxon:6945" /dev_stage="embryonated eggs" BASE COUNT 1250 a 1031 c 1063 g 1299 t ORIGIN 1 ttctttcttc tgtctaacat cttccaacga cttcttatgt gagtcggtca tcgaggcttc 61 gtaagtatac taacaaatgt aatgcaaggt caaagtcatg aattctcggt agcattgtta 121 acatattgtc atccccctgt cttgtcttca gtggatggag gttggagtgg ctggaacagc 181 tggcaggagt gcgaccaggt tggcaaagac ccaatgggag accgctgcct gtgccgctcc 241 agagcgtgcg acagcccagc gccgctcaac ggtgggaagc cctgcgaggg atcttcactg 301 gaagtcacca actgcacacg tgagtccctt cctagaacca gaaacctcga aatatgtgtg 361 tgtttcgcag agtgtcatcc atcctctgga tatgctcttg gactcccagg attcctgtca 421 ctatgcagct ccctcctagt aactcagaca cagtgattga ggaagcctct tctggctttc 481 actgtgcatg gagaagcctc tatgcaccct caaagcaaac acagtcttca gcatctggtc 541 actttcatat atgtgttggt acatgctgca ttgtagagag cattttaaaa cctttaaagc 601 aagattgtta atgccaaaga caaaatgtgt acgcactttt ctcctctgat cacatgcatt 661 cttgcaaatg ccgcactcgt taagactgca gtctgccgaa cagatttcca atcaactcgc 721 tcctccaaaa agtcccgttt gagcagccta ctgctgttgg catgggcggg cgatggagag 781 cattagttta cacatagcaa tcttaatagt gttgagaccg tagaattggg gcctcgagtt 841 atccaaaatc gttttgtgct cactaatgta ctatcgtcga gcccttcgag ccatgttcac 901 ccgaatacag tgaattatcc tttatatgaa acgtatatat ttcttacaaa aatgcatgta 961 atatttttat aaaaaaaaaa caagtcggct acactgagct cgatcagaat gtgcagaccc 1021 tcaaaaatgc tcaaacacct gttccatttt caaaaaggga gaaaaaaaaa ctcgcaagga 1081 gcaacaccaa acgaaaagag tggggacagg gaaacataga cagaaaaaga gagaaagatg 1141 caatgaaaaa acaaggtcaa gatatgcggt tcgaataatc caatgcaggt ttcccaccat 1201 tttatttttc tttcctgcac aatcggtagc ccttgttatt ctgaggtttg tttcctttcc 1261 tcctcgccaa gtgatttccg cctagaggcc aagatcagtg tgtgcgtcgt ctgcttcatt 1321 cgttggtagc tttaattttt gtttgacttt tatgtgctaa cccccttctc gtggaaatgg 1381 caaccatttt cctcctctaa caatgtggaa gtaccttgtg acgtggaaca cagtaaaggg 1441 gcacaaactt ccgcccattc gtggctggat gggaggcggc tggcacccac atgtgccatc 1501 agggggtacc caatgggaaa ggactctcta gctccccaag tggtggcaca agtggcgctt 1561 tcatttgtgc gaagtgtgcg gtgcgattct gtgcgggtct gctagtttca tttgaagtct 1621 caagccagaa gaaagaaatt gcatctcttt caagaacatg cttgacatag tgcagactat 1681 ggttctaaca cagacagatg agcacacata gagacgggca ctttgggatc acccctgatc 1741 ggcgtgcctt tcacagagca tcctaaacag atcaaagata aaacactttc catttttttc 1801 gctctagtct gggtgcttca atctcgtgta catccccaca gaatgaacag tcgtggaagc 1861 ctttgactat tttatctacg tattagcccg catagagttt cataccaata ttaatgtgaa 1921 agcattatat gccccattac gcgaaaatcc ggcgtcggcg tgattgagcg atgggaccaa 1981 aaagaaccca cagcgcaaag agtaaaaaca tgtcaaaaat gctctgattg acgtcgaatt 2041 tttcagggag gttcttgtaa acaaagtaaa ttaatggctt tgaaaataga attcggtaca 2101 tttctgtctg ggttggaatc gatcccgggc ctccggggta cgagacgagc atccttcccc 2161 gacaccacga cggttccatg gttctggctg actagaggtg cgcctggtgc gtgggtcatg 2221 tacaagtgat tttgatctgg tgtcctgacg tatattgcgc atgacaaacg gtgcattgtt 2281 gtgttcagat gtgtttggtg ccaggcagac gcatactatg atgagtccac ttggcagcga 2341 caaggcacac atttgccatg atcataccac tctgcgagtt gggcgttggg tttggcgtag 2401 atggcaactc ctgccgcagt gtttcctggt ctgtgtgcac tgcttacgaa gtggtacccc 2461 gggatctctc tgctgtcgtt cggattcata cacgtttttt tgaggcacag aatggacgct 2521 tcgttgaggt tgatgttttg ggctacgtct tctttgtgtt ttggcaggga cacaaagaaa 2581 catcaatcta aaacatttcg tcagagggac tatattgctt tcggattccc acatgtaagc 2641 agtcttaagt gtctctgccg aattttatgt tttccagatc aacctttctt tttttgtttc 2701 gctgtccaca gaaggactta ttaatgagtg tactgtacac ccaacatcaa aattttgtat 2761 tgcaaatatg tggctttgaa ttttgttata tgcgggtttc tatgtagcaa actacctgac 2821 agattgaatt aattgtgcgt cccacggagt ttgctataaa tgggagggca tgagttgcgc 2881 ttcatttcag gttgaagtca aatgagttgt gcttcttttc aggttgaagt caatttatac 2941 tcgtgtaaat cttctacaac ctgggacttc ccaaaaccat tacatctaat catcaaacgt 3001 ctggtgctgc ttacccctat ggtttgcacg attaagtctg gcgaaactac ccagaaaaaa 3061 aatttctgca aaaaacattc attgtgaaaa atgccatatt tacatccacc aacatctgag 3121 agttttcaca gaaagtttaa tttgttacac agcatagtta tttttttata aattattttc 3181 ggtccaccaa tgctaaagaa aaggtgtaca aagttcaagc actttgtaca cgtttttctt 3241 aattcaggtt tttgacagca aatcccacct taatataact cgtttcagta tgaaagtttc 3301 gagaaactta atttttgcag cttgtatgtc tgaattttat ggagtttgtt attataaact 3361 tagattttgc attttcatgt tcctttatta tgaaaaattg taatttgcaa aacctaataa 3421 acatcagaaa aaaaaattac ataaattttt ttacctagaa aatgtgcatt ttctgatatt 3481 tcttttcata gcaacctgca acaggtattc cagcatgcat tccaccacaa aaatatctga 3541 ttatcaacac catttctcaa cgatagattc attgagtaga ttccatgttc tgggggtata 3601 ggacctcagc aaattaattc aaagggctga aactttgcat gccctctttt tatatggcta 3661 caaacagcac ctgcaaatat cacgccgatt gagtaggcgg ctcaaaagtt gacattccca 3721 ggtagtgtcc ccccttaatg tttgtttact tcactgactg ctttgctgtc tcagagaggt 3781 cccaggatcg aaaaagacca ggcaggtttt ttcaacggca cgccagttgc ctacaataga 3841 gggtgcaggt tgtgctccat ttcaggtggg agtaaattta gtctcgcata aaagagttga 3901 actgtgcaac tcaatccgtg tgccgtctcc caaccttcag tgtggtgttg cccccaacag 3961 agaatgggca atggacagag tggtctgcct ggtcggcctg ctcccagagc tgcggcatag 4021 cagtcaagtc ccgccgcagg acgtgcagca accccaagcc caagcacgga ggccgagtct 4081 gcctggggcc cgagcaggag cagatctact gcagctccaa cccaccctgt cccggtaggc 4141 acactcttca tactgtaggg cccaatcttt ttcgctcaat ggaatgcaac ggtggtggga 4201 caaggcatgg aaagtatgct cgtctgttcc agcaggctag tttttagtta aaaagagcgg 4261 agtgaaagaa cttggagggt ggggtgtgtg ggttggggga gggggaagag aggaagataa 4321 tgctgcaggg attctcaaac tgggttccgt gagctggtct catgggtacc acaaacaacg 4381 aaaatgaaac ccctccctcc cccccccccc cttagtcgta ggctacacgg caggatcgtg 4441 caaagcgccc ttatatcact ttgtactgac attgcaattg attgatatgg tggggatata 4501 tgacaagcaa cacaagaaaa attgcctacg attgtgcttg tgttacttct tggtcagcaa 4561 atatggaggg aggaggggag gagggggggg cgggcggggc tttaaagacc gaccaacgaa 4621 accatttccg caaggtagga aaa //