MVKLAIGSIGDSLSGASVKSYLAEFIATLLFVFAGVGSAIAYGQLTADAA
LDPAGLVAIAIAHAFALFVGVSMAANISGGHLNPAVTLGLAVGGNITIIT
GLFYWIAQLLGSTAACFLLKFVTAGKAIPTHAVVSGMGAAEGVVFEIIIT
FALVYTVYATAADPKKGSLGTIAPIAIGFIVGANILAAGPFSGGSMNPAR
SFGPAVASGDFSGHWVYWAGPLIGGALAGLVYGDVFIGSYEALPASEDYA
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| Relationships |
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| The polypeptide, DCAR_004963, derives from mRNA, DCAR_004963. |
Analysis Date: 2021-12-09
Analysis Name: DCAR peptide blastp to SwissProt and TrEMBL without DCAR
Total hits: 20
Match: P93706 ((Root specific {ECO:0000313|EMBL:BAA19129.1}))
HSP 1 Score: 433.721 bits (1114), Expect = 1.405e-153
Identity = 227/250 (90.80%), Postives = 235/250 (94.00%), Query Frame = 0
Query: 1 MVKLAIGSIGDSLSGASVKSYLAEFIATLLFVFAGVGSAIAYGQLTADAALDPAGLVAIAIAHAFALFVGVSMAANISGGHLNPAVTLGLAVGGNITIITGLFYWIAQLLGSTAACFLLKFVTAGKAIPTHAVVSGMGAAEGVVFEIIITFALVYTVYATAADPKKGSLGTIAPIAIGFIVGANILAAGPFSGGSMNPARSFGPAVASGDFSGHWVYWAGPLIGGALAGLVYGDVFIGSYEALPASEDYA 250
MVKLAIGS+GDS S S+KSYLAEFIATLLFVFAGVGSAIAYG LTADAALDPAGLVAIAIAHAFALFVGVSMAANISGGHLNPAVTLGLA+GGNITIITGLFYWIAQ LGST ACFLLKFVTAGKAIPTH V +G+GAAEGVVFEI+ITFALVYTVYATAADPKKGSLGTIAPIAIGFIVGANILAAGPFSGGSMNPARSFGPAVAS DFSGHW+YW GPLIGG LAGLVYGDVFIGSY P +EDYA
Sbjct: 1 MVKLAIGSVGDSFSAVSLKSYLAEFIATLLFVFAGVGSAIAYGHLTADAALDPAGLVAIAIAHAFALFVGVSMAANISGGHLNPAVTLGLAIGGNITIITGLFYWIAQCLGSTVACFLLKFVTAGKAIPTHGVGAGLGAAEGVVFEIVITFALVYTVYATAADPKKGSLGTIAPIAIGFIVGANILAAGPFSGGSMNPARSFGPAVASFDFSGHWIYWVGPLIGGGLAGLVYGDVFIGSYA--PIAEDYA 248
Match: A0A103XJM0 ((Aquaporin-like protein {ECO:0000313|EMBL:KVH91956.1}))
HSP 1 Score: 431.409 bits (1108), Expect = 1.199e-152
Identity = 222/250 (88.80%), Postives = 231/250 (92.40%), Query Frame = 0
Query: 1 MVKLAIGSIGDSLSGASVKSYLAEFIATLLFVFAGVGSAIAYGQLTADAALDPAGLVAIAIAHAFALFVGVSMAANISGGHLNPAVTLGLAVGGNITIITGLFYWIAQLLGSTAACFLLKFVTAGKAIPTHAVVSGMGAAEGVVFEIIITFALVYTVYATAADPKKGSLGTIAPIAIGFIVGANILAAGPFSGGSMNPARSFGPAVASGDFSGHWVYWAGPLIGGALAGLVYGDVFIGSYEALPASEDYA 250
MVKLAIGSIGDSLS S+KSYLAEFIATLLFVFAGVGSAIAYG+LT DAALDPAGLVAIAIAHAFALFVGVSMAANISGGHLNPAVT GLA+GGNITIITGLFYWIAQLLGS ACFLL+FVT G A+PTH V GM +GVV EIIITFALVYTVYATAADPKKGSLGTIAPIAIGFIVGANILAAGPFSGGSMNPARSFGPAV SGDFS +W+YW GPLIGG LAGL+YGDVFIGSYEALPASEDYA
Sbjct: 1 MVKLAIGSIGDSLSVGSIKSYLAEFIATLLFVFAGVGSAIAYGKLTKDAALDPAGLVAIAIAHAFALFVGVSMAANISGGHLNPAVTFGLAIGGNITIITGLFYWIAQLLGSIVACFLLQFVTGGLAVPTHGVADGMNGLQGVVMEIIITFALVYTVYATAADPKKGSLGTIAPIAIGFIVGANILAAGPFSGGSMNPARSFGPAVVSGDFSQNWIYWVGPLIGGGLAGLIYGDVFIGSYEALPASEDYA 250
Match: A0A2J6JUE5 ((Uncharacterized protein {ECO:0000313|EMBL:PLY66433.1}))
HSP 1 Score: 427.943 bits (1099), Expect = 2.978e-151
Identity = 219/250 (87.60%), Postives = 230/250 (92.00%), Query Frame = 0
Query: 1 MVKLAIGSIGDSLSGASVKSYLAEFIATLLFVFAGVGSAIAYGQLTADAALDPAGLVAIAIAHAFALFVGVSMAANISGGHLNPAVTLGLAVGGNITIITGLFYWIAQLLGSTAACFLLKFVTAGKAIPTHAVVSGMGAAEGVVFEIIITFALVYTVYATAADPKKGSLGTIAPIAIGFIVGANILAAGPFSGGSMNPARSFGPAVASGDFSGHWVYWAGPLIGGALAGLVYGDVFIGSYEALPASEDYA 250
MVKLAIGSIGDS S SVKSYLAEFIATLLFVFAGVGSAIAYG+LTADAALDPAGLVA+AIAHAFALFVGVS+AANISGGHLNPAVT GLA+GGNITIITGLFYWIAQLLGS ACFLL+FVT G A+PTH V SGM + +GVVFEIIITFALVYTVYATAADPKKGSLGTIAPIAIGFIVGANILAAG FSGGSMNPARSFGPAV SGDFS +W+YW GPLIGG LAG +YGDVFIGSYE LP SEDYA
Sbjct: 1 MVKLAIGSIGDSFSAVSVKSYLAEFIATLLFVFAGVGSAIAYGKLTADAALDPAGLVAVAIAHAFALFVGVSIAANISGGHLNPAVTFGLAIGGNITIITGLFYWIAQLLGSIVACFLLQFVTGGLAVPTHGVASGMSSIQGVVFEIIITFALVYTVYATAADPKKGSLGTIAPIAIGFIVGANILAAGAFSGGSMNPARSFGPAVVSGDFSQNWIYWVGPLIGGGLAGFIYGDVFIGSYETLPTSEDYA 250
Match: A0A6S7NPP1 ((Uncharacterized protein {ECO:0000313|EMBL:CAB4103226.1}))
HSP 1 Score: 427.557 bits (1098), Expect = 3.708e-151
Identity = 219/250 (87.60%), Postives = 230/250 (92.00%), Query Frame = 0
Query: 1 MVKLAIGSIGDSLSGASVKSYLAEFIATLLFVFAGVGSAIAYGQLTADAALDPAGLVAIAIAHAFALFVGVSMAANISGGHLNPAVTLGLAVGGNITIITGLFYWIAQLLGSTAACFLLKFVTAGKAIPTHAVVSGMGAAEGVVFEIIITFALVYTVYATAADPKKGSLGTIAPIAIGFIVGANILAAGPFSGGSMNPARSFGPAVASGDFSGHWVYWAGPLIGGALAGLVYGDVFIGSYEALPASEDYA 250
MVKL IGSIGDS S SVKSYLAEFIATLLFVFAGVGSAIAYG+LTADAALDPAGLVA+AIAHAFALFVGVS+AANISGGHLNPAVT GLA+GGNITIITGLFYWIAQLLGS ACFLL+FVT G A+PTH V SGM + +GVVFEIIITFALVYTVYATAADPKKGSLGTIAPIAIGFIVGANILAAG FSGGSMNPARSFGPAV SGDFS +W+YW GPLIGG LAGL+YGDVFIGSYE LP SEDYA
Sbjct: 1 MVKLTIGSIGDSFSAGSVKSYLAEFIATLLFVFAGVGSAIAYGKLTADAALDPAGLVAVAIAHAFALFVGVSIAANISGGHLNPAVTFGLAIGGNITIITGLFYWIAQLLGSIVACFLLQFVTGGLAVPTHGVASGMSSIQGVVFEIIITFALVYTVYATAADPKKGSLGTIAPIAIGFIVGANILAAGAFSGGSMNPARSFGPAVVSGDFSQNWIYWVGPLIGGGLAGLIYGDVFIGSYETLPTSEDYA 250
Match: A0A6S7NN39 ((Uncharacterized protein {ECO:0000313|EMBL:CAB4103227.1}))
HSP 1 Score: 426.787 bits (1096), Expect = 8.531e-151
Identity = 220/250 (88.00%), Postives = 231/250 (92.40%), Query Frame = 0
Query: 1 MVKLAIGSIGDSLSGASVKSYLAEFIATLLFVFAGVGSAIAYGQLTADAALDPAGLVAIAIAHAFALFVGVSMAANISGGHLNPAVTLGLAVGGNITIITGLFYWIAQLLGSTAACFLLKFVTAGKAIPTHAVVSGMGAAEGVVFEIIITFALVYTVYATAADPKKGSLGTIAPIAIGFIVGANILAAGPFSGGSMNPARSFGPAVASGDFSGHWVYWAGPLIGGALAGLVYGDVFIGSYEALPASEDYA 250
MVKL IGSIGDS S SVKSYLAEFIATLLFVFAGVGSAIAYG+LTADAALDPAGLVA+AIAHAFALFVGVS+AANISGGHLNPAVT GLA+GGNITIITGLFYWIAQLLGS ACFLL+FVT G A+PTH V SGM + +GVVFEIIITFALVYTVYATAADPKKGSLGTIAPIAIGFIVGANILAAG FSGGSMNPARSFGPAV SGDFS +W+YW GPLIGG LAGL+YGDVFIGSYEALPAS DYA
Sbjct: 1 MVKLTIGSIGDSFSAGSVKSYLAEFIATLLFVFAGVGSAIAYGKLTADAALDPAGLVAVAIAHAFALFVGVSIAANISGGHLNPAVTFGLAIGGNITIITGLFYWIAQLLGSIVACFLLQFVTGGLAVPTHGVASGMSSIQGVVFEIIITFALVYTVYATAADPKKGSLGTIAPIAIGFIVGANILAAGAFSGGSMNPARSFGPAVVSGDFSQNWIYWVGPLIGGGLAGLIYGDVFIGSYEALPASGDYA 250
Match: A0A2J6JUF0 ((Uncharacterized protein {ECO:0000313|EMBL:PLY66434.1}))
HSP 1 Score: 426.787 bits (1096), Expect = 9.416e-151
Identity = 220/250 (88.00%), Postives = 231/250 (92.40%), Query Frame = 0
Query: 1 MVKLAIGSIGDSLSGASVKSYLAEFIATLLFVFAGVGSAIAYGQLTADAALDPAGLVAIAIAHAFALFVGVSMAANISGGHLNPAVTLGLAVGGNITIITGLFYWIAQLLGSTAACFLLKFVTAGKAIPTHAVVSGMGAAEGVVFEIIITFALVYTVYATAADPKKGSLGTIAPIAIGFIVGANILAAGPFSGGSMNPARSFGPAVASGDFSGHWVYWAGPLIGGALAGLVYGDVFIGSYEALPASEDYA 250
MVKL IGSIGDS S SVKSYLAEFIATLLFVFAGVGSAIAYG+LTADAALDPAGLVA+AIAHAFALFVGVS+AANISGGHLNPAVT GLA+GGNITIITGLFYWIAQLLGS ACFLL+FVT G A+PTH V SGM + +GVVFEIIITFALVYTVYATAADPKKGSLGTIAPIAIGFIVGANILAAG FSGGSMNPARSFGPAV SGDFS +W+YW GPLIGG LAGL+YGDVFIGSYEALPAS DYA
Sbjct: 1 MVKLTIGSIGDSFSAGSVKSYLAEFIATLLFVFAGVGSAIAYGKLTADAALDPAGLVAVAIAHAFALFVGVSIAANISGGHLNPAVTFGLAIGGNITIITGLFYWIAQLLGSVVACFLLQFVTGGLAVPTHGVASGMSSIQGVVFEIIITFALVYTVYATAADPKKGSLGTIAPIAIGFIVGANILAAGAFSGGSMNPARSFGPAVVSGDFSQNWIYWVGPLIGGGLAGLIYGDVFIGSYEALPASGDYA 250
Match: A0A200QA86 ((Major intrinsic protein {ECO:0000313|EMBL:OVA07375.1}))
HSP 1 Score: 426.402 bits (1095), Expect = 1.086e-150
Identity = 219/250 (87.60%), Postives = 234/250 (93.60%), Query Frame = 0
Query: 1 MVKLAIGSIGDSLSGASVKSYLAEFIATLLFVFAGVGSAIAYGQLTADAALDPAGLVAIAIAHAFALFVGVSMAANISGGHLNPAVTLGLAVGGNITIITGLFYWIAQLLGSTAACFLLKFVTAGKAIPTHAVVSGMGAAEGVVFEIIITFALVYTVYATAADPKKGSLGTIAPIAIGFIVGANILAAGPFSGGSMNPARSFGPAVASGDFSGHWVYWAGPLIGGALAGLVYGDVFIGSYEALPASEDYA 250
MVKLAIGSIGDSLS S+K+YLAEFI+TLLFVFAGVGSAIAY +LT+DA+LDPAGLVAIA+AHAFALFVGVSMAANISGGHLNPAVT GLA+GGNITIITG+FYW+AQLLGS AACFLLKFVT GKAIPTH V +GM GVV EI+ITFALVYTVYATAADPKKGSLGTIAPIAIGFIVGANILAAGPFSGGSMNPARSFGPAVASGDF+G+W+YW GPLIGG LAGLVYGDVFIGSY ALPASEDYA
Sbjct: 1 MVKLAIGSIGDSLSVGSLKAYLAEFISTLLFVFAGVGSAIAYSKLTSDASLDPAGLVAIAVAHAFALFVGVSMAANISGGHLNPAVTFGLAIGGNITIITGIFYWVAQLLGSIAACFLLKFVTNGKAIPTHGVAAGMTDFGGVVMEIVITFALVYTVYATAADPKKGSLGTIAPIAIGFIVGANILAAGPFSGGSMNPARSFGPAVASGDFTGNWIYWVGPLIGGGLAGLVYGDVFIGSYSALPASEDYA 250
Match: A0A2J6KTA0 ((Uncharacterized protein {ECO:0000313|EMBL:PLY78294.1}))
HSP 1 Score: 425.246 bits (1092), Expect = 3.359e-150
Identity = 219/250 (87.60%), Postives = 230/250 (92.00%), Query Frame = 0
Query: 1 MVKLAIGSIGDSLSGASVKSYLAEFIATLLFVFAGVGSAIAYGQLTADAALDPAGLVAIAIAHAFALFVGVSMAANISGGHLNPAVTLGLAVGGNITIITGLFYWIAQLLGSTAACFLLKFVTAGKAIPTHAVVSGMGAAEGVVFEIIITFALVYTVYATAADPKKGSLGTIAPIAIGFIVGANILAAGPFSGGSMNPARSFGPAVASGDFSGHWVYWAGPLIGGALAGLVYGDVFIGSYEALPASEDYA 250
MVKL IGSIGDS S SVKSYLAEFIATLLFVFAGVGSAIAYG+LTADAALDPAGLVA+AIAHAFALFVGVS+AANISGGHLNPAVT GLA+GGNITIITGLFYWIAQLLGS ACFLL+FVT G A+PTH V SGM + +GVVFEIIITFALVYTVYATAADPKKGSLGTIAPIAIGFIVGANILAAG FSGGSMNPARSFGPAV SGDFS +W+YW GPLIGG LAGL+YGDVFIGSYEALP S DYA
Sbjct: 1 MVKLTIGSIGDSFSAGSVKSYLAEFIATLLFVFAGVGSAIAYGKLTADAALDPAGLVAVAIAHAFALFVGVSIAANISGGHLNPAVTFGLAIGGNITIITGLFYWIAQLLGSIVACFLLQFVTGGLAVPTHGVASGMSSIQGVVFEIIITFALVYTVYATAADPKKGSLGTIAPIAIGFIVGANILAAGAFSGGSMNPARSFGPAVVSGDFSQNWIYWVGPLIGGGLAGLIYGDVFIGSYEALPTSGDYA 250
Match: A0A6S7NNX7 ((Uncharacterized protein {ECO:0000313|EMBL:CAB4103228.1}))
HSP 1 Score: 426.787 bits (1096), Expect = 4.160e-150
Identity = 217/250 (86.80%), Postives = 229/250 (91.60%), Query Frame = 0
Query: 1 MVKLAIGSIGDSLSGASVKSYLAEFIATLLFVFAGVGSAIAYGQLTADAALDPAGLVAIAIAHAFALFVGVSMAANISGGHLNPAVTLGLAVGGNITIITGLFYWIAQLLGSTAACFLLKFVTAGKAIPTHAVVSGMGAAEGVVFEIIITFALVYTVYATAADPKKGSLGTIAPIAIGFIVGANILAAGPFSGGSMNPARSFGPAVASGDFSGHWVYWAGPLIGGALAGLVYGDVFIGSYEALPASEDYA 250
MVKL IGSIGDS S SVKSYLAEFIATLLFVFAGVGSAIAYG+LTADAALDPAGLVA+AIAHAFALFVGVS+AANISGGHLNPAVT GLA+GGNITIITGLFYWIAQLLGS ACFLL+FVT G A+PTH V SGM + +GVVFEIIITFALVYTVYATAADPKKGSLGTIAPIAIGFIVGANILAAG FSGGSMNPARSFGPAV SGDFS +W+YW GPLIGG LAG +YGDVFIGSY+ LP SEDYA
Sbjct: 48 MVKLTIGSIGDSFSAVSVKSYLAEFIATLLFVFAGVGSAIAYGKLTADAALDPAGLVAVAIAHAFALFVGVSIAANISGGHLNPAVTFGLAIGGNITIITGLFYWIAQLLGSIVACFLLQFVTGGLAVPTHGVASGMSSIQGVVFEIIITFALVYTVYATAADPKKGSLGTIAPIAIGFIVGANILAAGAFSGGSMNPARSFGPAVVSGDFSQNWIYWVGPLIGGGLAGFIYGDVFIGSYDTLPTSEDYA 297
Match: Q39956 ((Aquaporin {ECO:0000313|EMBL:CAA65187.1}) (Putative major intrinsic protein, Aquaporin-like protein {ECO:0000313|EMBL:OTG02826.1}))
HSP 1 Score: 417.927 bits (1073), Expect = 2.211e-147
Identity = 214/250 (85.60%), Postives = 225/250 (90.00%), Query Frame = 0
Query: 1 MVKLAIGSIGDSLSGASVKSYLAEFIATLLFVFAGVGSAIAYGQLTADAALDPAGLVAIAIAHAFALFVGVSMAANISGGHLNPAVTLGLAVGGNITIITGLFYWIAQLLGSTAACFLLKFVTAGKAIPTHAVVSGMGAAEGVVFEIIITFALVYTVYATAADPKKGSLGTIAPIAIGFIVGANILAAGPFSGGSMNPARSFGPAVASGDFSGHWVYWAGPLIGGALAGLVYGDVFIGSYEALPASEDYA 250
MVKLAIGSIGDSLS S+KSYLAEFIATLLFVFAGVGSAIAYG+LT DAALDPAGLVAIAIAHAFALFVGVSMAANISGGHLNPAVT GLA+GGNITIITGLFYWIAQ LGS ACFLL+FVT G A+PTH V GM +GVV EIIITFALVYTVYATA DPKKGSLGTIAP+AIGFIVGANILAAGPFSGGSMNPARSFGPAV SGDFS +W+YW GPLIGG LAG ++GDVFIGSYE LP S DYA
Sbjct: 1 MVKLAIGSIGDSLSAGSIKSYLAEFIATLLFVFAGVGSAIAYGKLTTDAALDPAGLVAIAIAHAFALFVGVSMAANISGGHLNPAVTFGLAIGGNITIITGLFYWIAQCLGSIVACFLLQFVTGGLAVPTHGVADGMNGVQGVVMEIIITFALVYTVYATAVDPKKGSLGTIAPMAIGFIVGANILAAGPFSGGSMNPARSFGPAVVSGDFSQNWIYWVGPLIGGGLAGFIFGDVFIGSYETLPDSGDYA 250
| Match Name | Stats | Description |
|---|---|---|
| P93706 | E-Value: 1.405e-153, PID: 90.80 | (Root specific {ECO:0000313|EMBL:BAA19129.1})[more] |
| A0A103XJM0 | E-Value: 1.199e-152, PID: 88.80 | (Aquaporin-like protein {ECO:0000313|EMBL:KVH91956... [more] |
| A0A2J6JUE5 | E-Value: 2.978e-151, PID: 87.60 | (Uncharacterized protein {ECO:0000313|EMBL:PLY6643... [more] |
| A0A6S7NPP1 | E-Value: 3.708e-151, PID: 87.60 | (Uncharacterized protein {ECO:0000313|EMBL:CAB4103... [more] |
| A0A6S7NN39 | E-Value: 8.531e-151, PID: 88.00 | (Uncharacterized protein {ECO:0000313|EMBL:CAB4103... [more] |
| A0A2J6JUF0 | E-Value: 9.416e-151, PID: 88.00 | (Uncharacterized protein {ECO:0000313|EMBL:PLY6643... [more] |
| A0A200QA86 | E-Value: 1.086e-150, PID: 87.60 | (Major intrinsic protein {ECO:0000313|EMBL:OVA0737... [more] |
| A0A2J6KTA0 | E-Value: 3.359e-150, PID: 87.60 | (Uncharacterized protein {ECO:0000313|EMBL:PLY7829... [more] |
| A0A6S7NNX7 | E-Value: 4.160e-150, PID: 86.80 | (Uncharacterized protein {ECO:0000313|EMBL:CAB4103... [more] |
| Q39956 | E-Value: 2.211e-147, PID: 85.60 | (Aquaporin {ECO:0000313|EMBL:CAA65187.1}) (Putativ... [more] |
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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. |