MVKIAIGSLGDSFSVGSLKCYLAEFIATLLFVFAGVGSALAFSSLTNDGA
LDPPGLVAIAIAHAFALFVGVSMAANISGGHLNPAVTFGLAVGGHITVIT
GFLYWIAQLLGAAAASYLLIYVTGGKAVPIHGVGAGINAFQGVVFEIIIT
FALVYTVYATAADPKKGSLGTIAPIAIGFIVGANILAAGPFSGGSMNPAR
SFGPAVASGDFSGHWIYWVGPLIGGGLAGFVYGDIFIESYGAVAASDDYA
*
| Relationships |
|---|
| The polypeptide, DCAR_006837, derives from mRNA, DCAR_006837. |
Analysis Date: 2021-12-09
Analysis Name: DCAR peptide blastp to SwissProt and TrEMBL without DCAR
Total hits: 20
Match: A0A200QA86 ((Major intrinsic protein {ECO:0000313|EMBL:OVA07375.1}))
HSP 1 Score: 403.29 bits (1035), Expect = 1.420e-141
Identity = 206/250 (82.40%), Postives = 229/250 (91.60%), Query Frame = 0
Query: 1 MVKIAIGSLGDSFSVGSLKCYLAEFIATLLFVFAGVGSALAFSSLTNDGALDPPGLVAIAIAHAFALFVGVSMAANISGGHLNPAVTFGLAVGGHITVITGFLYWIAQLLGAAAASYLLIYVTGGKAVPIHGVGAGINAFQGVVFEIIITFALVYTVYATAADPKKGSLGTIAPIAIGFIVGANILAAGPFSGGSMNPARSFGPAVASGDFSGHWIYWVGPLIGGGLAGFVYGDIFIESYGAVAASDDYA 250
MVK+AIGS+GDS SVGSLK YLAEFI+TLLFVFAGVGSA+A+S LT+D +LDP GLVAIA+AHAFALFVGVSMAANISGGHLNPAVTFGLA+GG+IT+ITG YW+AQLLG+ AA +LL +VT GKA+P HGV AG+ F GVV EI+ITFALVYTVYATAADPKKGSLGTIAPIAIGFIVGANILAAGPFSGGSMNPARSFGPAVASGDF+G+WIYWVGPLIGGGLAG VYGD+FI SY A+ AS+DYA
Sbjct: 1 MVKLAIGSIGDSLSVGSLKAYLAEFISTLLFVFAGVGSAIAYSKLTSDASLDPAGLVAIAVAHAFALFVGVSMAANISGGHLNPAVTFGLAIGGNITIITGIFYWVAQLLGSIAACFLLKFVTNGKAIPTHGVAAGMTDFGGVVMEIVITFALVYTVYATAADPKKGSLGTIAPIAIGFIVGANILAAGPFSGGSMNPARSFGPAVASGDFTGNWIYWVGPLIGGGLAGLVYGDVFIGSYSALPASEDYA 250
Match: C8YXI4 ((Tonoplast aquaporin 2 1 {ECO:0000313|EMBL:ACV52009.1}))
HSP 1 Score: 402.134 bits (1032), Expect = 4.898e-141
Identity = 212/250 (84.80%), Postives = 227/250 (90.80%), Query Frame = 0
Query: 1 MVKIAIGSLGDSFSVGSLKCYLAEFIATLLFVFAGVGSALAFSSLTNDGALDPPGLVAIAIAHAFALFVGVSMAANISGGHLNPAVTFGLAVGGHITVITGFLYWIAQLLGAAAASYLLIYVTGGKAVPIHGVGAGINAFQGVVFEIIITFALVYTVYATAADPKKGSLGTIAPIAIGFIVGANILAAGPFSGGSMNPARSFGPAVASGDFSGHWIYWVGPLIGGGLAGFVYGDIFIESYGAVAASDDYA 250
MVKI IGSLGDSFS GSLKCYLAEF ATLLFVFAGVGSA+AF++LT D LDP GLVAIA+AHAFALFVGVS+AANISGGHLNPAVTFGLAVGG+IT+ITGF YWIAQLLGA AS+LLI+VTGGKAVP HGVGAG++A +GVVFEIIITFALVYTVYATAADPKKGSLGTIAPIAIGFIVGANILAAGPFSGGSMNPARSFGPAVASGDFSGHWI WVGPLI + YGD+FI SY AV AS+DYA
Sbjct: 1 MVKITIGSLGDSFSHGSLKCYLAEFTATLLFVFAGVGSAIAFNNLTADAGLDPAGLVAIAVAHAFALFVGVSIAANISGGHLNPAVTFGLAVGGNITLITGFFYWIAQLLGATVASFLLIFVTGGKAVPTHGVGAGLDAAEGVVFEIIITFALVYTVYATAADPKKGSLGTIAPIAIGFIVGANILAAGPFSGGSMNPARSFGPAVASGDFSGHWICWVGPLIRRKPSWVHYGDVFIGSYAAVPASEDYA 250
Match: A0A103XFK6 ((Aquaporin-like protein {ECO:0000313|EMBL:KVH89783.1}))
HSP 1 Score: 400.208 bits (1027), Expect = 3.054e-140
Identity = 208/250 (83.20%), Postives = 224/250 (89.60%), Query Frame = 0
Query: 1 MVKIAIGSLGDSFSVGSLKCYLAEFIATLLFVFAGVGSALAFSSLTNDGALDPPGLVAIAIAHAFALFVGVSMAANISGGHLNPAVTFGLAVGGHITVITGFLYWIAQLLGAAAASYLLIYVTGGKAVPIHGVGAGINAFQGVVFEIIITFALVYTVYATAADPKKGSLGTIAPIAIGFIVGANILAAGPFSGGSMNPARSFGPAVASGDFSGHWIYWVGPLIGGGLAGFVYGDIFIESYGAVAASDDYA 250
MVK+A G GDSFSVGSLK YLAEFIATLLFVFAGVGSA+A+ LT D ALDP GLVAIA+AHAFALFVGVSMAANISGGHLNPAVTFGLA+GG+IT++TG YWIAQLLGA AS+LL +VTGG AVP HGV G+NA QGVV EIIITFALVYTVYATAADPKKGSLGTIAPIAIGFIVGANILAAGPFSGGSMNPARSFGPAVASGDFS +WIYWVGPLIGGGLAG +YGD+FI SY + AS+DYA
Sbjct: 1 MVKLAFGDFGDSFSVGSLKSYLAEFIATLLFVFAGVGSAIAYGKLTADAALDPAGLVAIAVAHAFALFVGVSMAANISGGHLNPAVTFGLAIGGNITILTGLFYWIAQLLGAIVASFLLQFVTGGLAVPTHGVADGMNAIQGVVMEIIITFALVYTVYATAADPKKGSLGTIAPIAIGFIVGANILAAGPFSGGSMNPARSFGPAVASGDFSENWIYWVGPLIGGGLAGLIYGDVFIGSYAPLPASEDYA 250
Match: A0A103XJM0 ((Aquaporin-like protein {ECO:0000313|EMBL:KVH91956.1}))
HSP 1 Score: 399.438 bits (1025), Expect = 5.459e-140
Identity = 207/250 (82.80%), Postives = 224/250 (89.60%), Query Frame = 0
Query: 1 MVKIAIGSLGDSFSVGSLKCYLAEFIATLLFVFAGVGSALAFSSLTNDGALDPPGLVAIAIAHAFALFVGVSMAANISGGHLNPAVTFGLAVGGHITVITGFLYWIAQLLGAAAASYLLIYVTGGKAVPIHGVGAGINAFQGVVFEIIITFALVYTVYATAADPKKGSLGTIAPIAIGFIVGANILAAGPFSGGSMNPARSFGPAVASGDFSGHWIYWVGPLIGGGLAGFVYGDIFIESYGAVAASDDYA 250
MVK+AIGS+GDS SVGS+K YLAEFIATLLFVFAGVGSA+A+ LT D ALDP GLVAIAIAHAFALFVGVSMAANISGGHLNPAVTFGLA+GG+IT+ITG YWIAQLLG+ A +LL +VTGG AVP HGV G+N QGVV EIIITFALVYTVYATAADPKKGSLGTIAPIAIGFIVGANILAAGPFSGGSMNPARSFGPAV SGDFS +WIYWVGPLIGGGLAG +YGD+FI SY A+ AS+DYA
Sbjct: 1 MVKLAIGSIGDSLSVGSIKSYLAEFIATLLFVFAGVGSAIAYGKLTKDAALDPAGLVAIAIAHAFALFVGVSMAANISGGHLNPAVTFGLAIGGNITIITGLFYWIAQLLGSIVACFLLQFVTGGLAVPTHGVADGMNGLQGVVMEIIITFALVYTVYATAADPKKGSLGTIAPIAIGFIVGANILAAGPFSGGSMNPARSFGPAVVSGDFSQNWIYWVGPLIGGGLAGLIYGDVFIGSYEALPASEDYA 250
Match: A0A7J6WNW2 ((Aquaporin tip2-3 {ECO:0000313|EMBL:KAF5198618.1}))
HSP 1 Score: 398.667 bits (1023), Expect = 1.176e-139
Identity = 206/250 (82.40%), Postives = 228/250 (91.20%), Query Frame = 0
Query: 1 MVKIAIGSLGDSFSVGSLKCYLAEFIATLLFVFAGVGSALAFSSLTNDGALDPPGLVAIAIAHAFALFVGVSMAANISGGHLNPAVTFGLAVGGHITVITGFLYWIAQLLGAAAASYLLIYVTGGKAVPIHGVGAGINAFQGVVFEIIITFALVYTVYATAADPKKGSLGTIAPIAIGFIVGANILAAGPFSGGSMNPARSFGPAVASGDFSGHWIYWVGPLIGGGLAGFVYGDIFIESYGAVAASDDYA 250
MVK+A+GSLGDSFSVG+LK YLAEFIATLLFVFAGVGSA+AFS LT+D ALDP GLVA+A+AHAFALFVGVS+AANISGGHLNPAVTFGLA+GG+IT++TG YWIAQLLG+ A +LL +VTGG AVP HGV AG++A GVV EIIITFALVYTVYATAADPKKGSLGTIAPIAIGFIVGANILAAGPFSGGSMNPARSFGPAVASGDFS +WIYWVGPLIGGGLAG +YGD+FI SY + AS+DYA
Sbjct: 1 MVKLALGSLGDSFSVGALKAYLAEFIATLLFVFAGVGSAIAFSKLTSDAALDPAGLVAVALAHAFALFVGVSIAANISGGHLNPAVTFGLAIGGNITILTGIFYWIAQLLGSIVACFLLKFVTGGLAVPTHGVSAGVSAAGGVVMEIIITFALVYTVYATAADPKKGSLGTIAPIAIGFIVGANILAAGPFSGGSMNPARSFGPAVASGDFSQNWIYWVGPLIGGGLAGLIYGDVFIASYAPLPASEDYA 250
Match: A0A2G5E3I3 ((Uncharacterized protein {ECO:0000313|EMBL:PIA50280.1}))
HSP 1 Score: 397.897 bits (1021), Expect = 2.294e-139
Identity = 205/250 (82.00%), Postives = 226/250 (90.40%), Query Frame = 0
Query: 1 MVKIAIGSLGDSFSVGSLKCYLAEFIATLLFVFAGVGSALAFSSLTNDGALDPPGLVAIAIAHAFALFVGVSMAANISGGHLNPAVTFGLAVGGHITVITGFLYWIAQLLGAAAASYLLIYVTGGKAVPIHGVGAGINAFQGVVFEIIITFALVYTVYATAADPKKGSLGTIAPIAIGFIVGANILAAGPFSGGSMNPARSFGPAVASGDFSGHWIYWVGPLIGGGLAGFVYGDIFIESYGAVAASDDYA 250
MVK+A+GS GDSFSVGSLK YLAEFIATLLFVFAGVGSA+AFS LT D ALDP GLVA+A+AHAFALFVGVS+AANISGGHLNPAVTFGLA+GG+IT++TG YWIAQLLG+ A +LL +VTGG AVP HGV AG++A GVV EIIITFALVYTVYATAADPKKGSLGTIAPIAIGFIVGANILAAGPFSGGSMNPARSFGPAVASGDFS +WIYWVGPLIGGGLAG +YGD+FI SY + +S+DYA
Sbjct: 1 MVKLALGSFGDSFSVGSLKSYLAEFIATLLFVFAGVGSAIAFSKLTTDAALDPAGLVAVALAHAFALFVGVSIAANISGGHLNPAVTFGLAIGGNITILTGIFYWIAQLLGSIVACFLLKFVTGGLAVPTHGVSAGVSAIGGVVMEIIITFALVYTVYATAADPKKGSLGTIAPIAIGFIVGANILAAGPFSGGSMNPARSFGPAVASGDFSQNWIYWVGPLIGGGLAGLIYGDVFIASYAPLPSSEDYA 250
Match: A0A1U8A287 ((probable aquaporin TIP-type RB7-5A {ECO:0000313|RefSeq:XP_010258877.1}))
HSP 1 Score: 397.127 bits (1019), Expect = 3.840e-139
Identity = 200/250 (80.00%), Postives = 227/250 (90.80%), Query Frame = 0
Query: 1 MVKIAIGSLGDSFSVGSLKCYLAEFIATLLFVFAGVGSALAFSSLTNDGALDPPGLVAIAIAHAFALFVGVSMAANISGGHLNPAVTFGLAVGGHITVITGFLYWIAQLLGAAAASYLLIYVTGGKAVPIHGVGAGINAFQGVVFEIIITFALVYTVYATAADPKKGSLGTIAPIAIGFIVGANILAAGPFSGGSMNPARSFGPAVASGDFSGHWIYWVGPLIGGGLAGFVYGDIFIESYGAVAASDDYA 250
MVKI++GSL DSF+VGSLK YLAEFIATLLFVFAGVGSA+++S LT+D +LDPPGLVAIA+AHAFALFVGVSMAANISGGHLNPAVTFGLA+GG+ITV+TG LYW+AQLLG+ A LL +VT GK++P H V +G++A +GVV EIIITFALVYTVYATAADPKKGSLGTIAPIAIGFIVGANILAAGPFSGGSMNPARSFGPAV SGDFS +WIYWVGPLIGGGLAG +YGD+FI SY ++ S+DYA
Sbjct: 1 MVKISLGSLSDSFAVGSLKTYLAEFIATLLFVFAGVGSAISYSKLTSDASLDPPGLVAIAVAHAFALFVGVSMAANISGGHLNPAVTFGLAIGGNITVLTGILYWVAQLLGSIVACLLLHFVTNGKSIPTHSVASGMSAIEGVVMEIIITFALVYTVYATAADPKKGSLGTIAPIAIGFIVGANILAAGPFSGGSMNPARSFGPAVVSGDFSQNWIYWVGPLIGGGLAGLIYGDVFIGSYTSLPVSEDYA 250
Match: A0A251RYJ7 ((Putative major intrinsic protein, Aquaporin-like protein {ECO:0000313|EMBL:OTF91527.1}))
HSP 1 Score: 393.275 bits (1009), Expect = 1.576e-137
Identity = 204/250 (81.60%), Postives = 222/250 (88.80%), Query Frame = 0
Query: 1 MVKIAIGSLGDSFSVGSLKCYLAEFIATLLFVFAGVGSALAFSSLTNDGALDPPGLVAIAIAHAFALFVGVSMAANISGGHLNPAVTFGLAVGGHITVITGFLYWIAQLLGAAAASYLLIYVTGGKAVPIHGVGAGINAFQGVVFEIIITFALVYTVYATAADPKKGSLGTIAPIAIGFIVGANILAAGPFSGGSMNPARSFGPAVASGDFSGHWIYWVGPLIGGGLAGFVYGDIFIESYGAVAASDDYA 250
MVK+A G LGDSFS SLK YLAEFIATLLFVFAGVGSA+A+ LT D ALDP GLVAIA+AH ALFVGVSMAANISGGHLNP VTFGLA+GG+IT++TG YWIAQLLGA AAS+LL +VTGG AVP HGV G++A QGVVFEIIITFALVYTVYATAADPKKGSLGTIAP+AIGFIVGANILAAGPFSGGSMNPARSFGPAVASGDFS WIYWVGPLIGGGLAG +YGD+FI SY ++ AS+DYA
Sbjct: 1 MVKLAFGDLGDSFSATSLKSYLAEFIATLLFVFAGVGSAVAYGKLTADAALDPAGLVAIAVAHGLALFVGVSMAANISGGHLNPVVTFGLAIGGNITILTGLFYWIAQLLGATAASFLLQFVTGGLAVPTHGVADGMSAIQGVVFEIIITFALVYTVYATAADPKKGSLGTIAPLAIGFIVGANILAAGPFSGGSMNPARSFGPAVASGDFSQIWIYWVGPLIGGGLAGLIYGDVFIGSYSSLPASEDYA 250
Match: A0A446VIZ6 ((Uncharacterized protein {ECO:0000313|EMBL:VAI47845.1}))
HSP 1 Score: 392.504 bits (1007), Expect = 2.437e-137
Identity = 201/250 (80.40%), Postives = 226/250 (90.40%), Query Frame = 0
Query: 1 MVKIAIGSLGDSFSVGSLKCYLAEFIATLLFVFAGVGSALAFSSLTNDGALDPPGLVAIAIAHAFALFVGVSMAANISGGHLNPAVTFGLAVGGHITVITGFLYWIAQLLGAAAASYLLIYVTGGKAVPIHGVGAGINAFQGVVFEIIITFALVYTVYATAADPKKGSLGTIAPIAIGFIVGANILAAGPFSGGSMNPARSFGPAVASGDFSGHWIYWVGPLIGGGLAGFVYGDIFIESYGAVAASDDYA 250
MVK+A GS GDSFS S++ Y+AEFIATLLFVFAGVGSA+A+ LT+DGALDP GLVAIAIAHAFALFVGV++AANISGGHLNPAVTFGLAVGGHIT++TG YW+AQLLG+ AA +LL +VT GKA+P HGV AG+N F+GVV EI+ITFALVYTVYATAADPKKGSLGTIAPIAIGFIVGANILAAGPFSGGSMNPARSFGPAVA+G+F+G+W+YWVGPLIGGGLAGFVYGD+FI SY V A DYA
Sbjct: 1 MVKLAFGSCGDSFSATSVRAYVAEFIATLLFVFAGVGSAIAYGKLTDDGALDPAGLVAIAIAHAFALFVGVAIAANISGGHLNPAVTFGLAVGGHITILTGIFYWVAQLLGSTAACFLLKFVTHGKAIPTHGVAAGMNEFEGVVMEIVITFALVYTVYATAADPKKGSLGTIAPIAIGFIVGANILAAGPFSGGSMNPARSFGPAVAAGNFAGNWVYWVGPLIGGGLAGFVYGDVFIASYQPV-ADQDYA 249
Match: A0A453P8M8 ((Uncharacterized protein {ECO:0000313|EnsemblPlants:AET6Gv20649000.2}))
HSP 1 Score: 392.504 bits (1007), Expect = 2.437e-137
Identity = 201/250 (80.40%), Postives = 226/250 (90.40%), Query Frame = 0
Query: 1 MVKIAIGSLGDSFSVGSLKCYLAEFIATLLFVFAGVGSALAFSSLTNDGALDPPGLVAIAIAHAFALFVGVSMAANISGGHLNPAVTFGLAVGGHITVITGFLYWIAQLLGAAAASYLLIYVTGGKAVPIHGVGAGINAFQGVVFEIIITFALVYTVYATAADPKKGSLGTIAPIAIGFIVGANILAAGPFSGGSMNPARSFGPAVASGDFSGHWIYWVGPLIGGGLAGFVYGDIFIESYGAVAASDDYA 250
MVK+A GS GDSFS S++ Y+AEFIATLLFVFAGVGSA+A+ LT+DGALDP GLVAIAIAHAFALFVGV++AANISGGHLNPAVTFGLAVGGHIT++TG YW+AQLLG+ AA +LL +VT GKA+P HGV AG+N F+GVV EI+ITFALVYTVYATAADPKKGSLGTIAPIAIGFIVGANILAAGPFSGGSMNPARSFGPAVA+G+F+G+W+YWVGPLIGGGLAGFVYGD+FI SY V A DYA
Sbjct: 1 MVKLAFGSCGDSFSATSVRAYVAEFIATLLFVFAGVGSAIAYGKLTDDGALDPAGLVAIAIAHAFALFVGVAIAANISGGHLNPAVTFGLAVGGHITILTGIFYWVAQLLGSTAACFLLKFVTHGKAIPTHGVAAGMNEFEGVVMEIVITFALVYTVYATAADPKKGSLGTIAPIAIGFIVGANILAAGPFSGGSMNPARSFGPAVAAGNFAGNWVYWVGPLIGGGLAGFVYGDVFIASYQPV-ADQDYA 249
| Match Name | Stats | Description |
|---|---|---|
| A0A200QA86 | E-Value: 1.420e-141, PID: 82.40 | (Major intrinsic protein {ECO:0000313|EMBL:OVA0737... [more] |
| C8YXI4 | E-Value: 4.898e-141, PID: 84.80 | (Tonoplast aquaporin 2 1 {ECO:0000313|EMBL:ACV5200... [more] |
| A0A103XFK6 | E-Value: 3.054e-140, PID: 83.20 | (Aquaporin-like protein {ECO:0000313|EMBL:KVH89783... [more] |
| A0A103XJM0 | E-Value: 5.459e-140, PID: 82.80 | (Aquaporin-like protein {ECO:0000313|EMBL:KVH91956... [more] |
| A0A7J6WNW2 | E-Value: 1.176e-139, PID: 82.40 | (Aquaporin tip2-3 {ECO:0000313|EMBL:KAF5198618.1})[more] |
| A0A2G5E3I3 | E-Value: 2.294e-139, PID: 82.00 | (Uncharacterized protein {ECO:0000313|EMBL:PIA5028... [more] |
| A0A1U8A287 | E-Value: 3.840e-139, PID: 80.00 | (probable aquaporin TIP-type RB7-5A {ECO:0000313|R... [more] |
| A0A251RYJ7 | E-Value: 1.576e-137, PID: 81.60 | (Putative major intrinsic protein, Aquaporin-like ... [more] |
| A0A446VIZ6 | E-Value: 2.437e-137, PID: 80.40 | (Uncharacterized protein {ECO:0000313|EMBL:VAI4784... [more] |
| A0A453P8M8 | E-Value: 2.437e-137, PID: 80.40 | (Uncharacterized protein {ECO:0000313|EnsemblPlant... [more] |
Pages
back to top| Name | Description |
|---|---|
An orange, doubled-haploid, Nantes-type carrot (DH1) was used for genome sequencing. We used BAC end sequences and a newly developed linkage map with 2,075 markers to correct 135 scaffolds with one or more chimeric regions. The resulting v2.0 assembly spans 421.5 Mb and contains 4,907 scaffolds (N50 of 12.7 Mb), accounting for ∼90% of the estimated genome size of 473 Mb. The scaftig N50 of 31.2 kb is similar to those of other high-quality genome assemblies such as potato and pepper. About 86% (362 Mb) of the assembled genome is included in only 60 superscaffolds anchored to the nine pseudomolecules. The longest superscaffold spans 30.2 Mb, 85% of chromosome 4. There are a few different naming schemes for this assembly. First there is the Phytozome genome ID 388: The authors' sequences and gene predictions were also submitted to Phytozome, and can be accessed at this address: https://phytozome-next.jgi.doe.gov/info/Dcarota_v2_0 LNRQ01: These sequences were then assigned GenBank accession numbers starting at LNRQ01000001.1 which corresponds to DCARv2_Chr1, up to LNRQ01004826.1 which corresponds to an unincorporated contig, DCARv2_C10750146. These reside in bioproject PRJNA268187, which is a subproject of umbrella project PRJNA285926. Assembly GCA_001625215.1: The genome assembly was later defined an accession number GCA_001625215.1 for assembly ASM162521v1 which consists of only the 9 chromosome sequences and the plastid assembly, which have accession numbers from CM004278.1 to CM004286.1 for the chromosomes and CM004358.1 for the plastid. The mitochondrial genome was not included because it is classified as an incomplete sequence. RefSeq: The assembly was then later added to RefSeq, and there another new set of identifiers was defined from NC_030381.1 to NC_030389.1 for the chromosomes, and from NW_016089425.1 to NW_016094239.1 for unincorporated scaffolds and contigs. These reside in bioproject PRJNA326436. Note that NCBI substituted different assembled organellar genomes from different genotypes for the RefSeq records. The NCBI Sequence report lists the correspondences between the various naming methods Link to the LNRQ01000000.1 master record at NCBI Raw Reads: Link to SRA accessions used for the genome assembly This genome is available in the CarrotOmics Blast Search | |
This analysis is a blastp search of all of the DCAR V1.0 Gene Prediction polypeptide sequences against combined ExPASy SwissProt and TrEMBL databases from Nov. 17, 2021. Prior to performing the blast search, the database was filtered to remove organisms not in the Viridiplantae, and also filtered to remove these same DCAR gene predictions. | |
For gene model prediction, mobile element–related repeats were masked using RepeatMasker. De novo prediction using AUGUSTUS v2.5.5, GENSCAN v.1.1.0, and GlimmerHMM-3.0.1 was trained using model species A. thaliana and S. lycoperisum training sets. The protein sequences of S. lycoperisum, Solanum tuberosum, A. thaliana, Brassica rapa, and Oryza sativa were mapped to the carrot genome using TBLASTN (BLAST All 2.2.23) and analyzed with GeneWise version 2.2.0. Carrot ESTs were aligned to the genome using BLAT and analyzed with PASA to detect spliced gene models. RNA-seq reads from 20 DH1 libraries were aligned with TopHat 2.0.9. Transcripts were predicted by Cufflinks. All gene models produced by de novo prediction, protein homology searches, and prediction and transcript-based evidence were integrated using GLEAN v1.1. Putative gene functions were assigned using the best BLASTP match to SwissProt and TrEMBL databases. Gene motifs and domains were determined with InterProScan version 4.7 against the ProDom, PRINTS, Pfam, SMART, PANTHER, and PROSITE protein databases. GO IDs for each gene were obtained from the corresponding InterPro entries. All genes were aligned against KEGG (release 58) proteins. Data from this analysis can be viewed in JBrowse here. |