AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene062057

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene062057.t1 MTR_2g045630 89.600 125 9 1 10 134 157 277 1.19e-74 223
MS.gene062057.t1 MTR_2g045670 85.714 119 17 0 17 135 163 281 2.12e-68 207
MS.gene062057.t1 MTR_2g045700 85.714 119 17 0 17 135 153 271 5.35e-64 196
MS.gene062057.t1 MTR_1g034500 76.667 120 27 1 17 135 188 307 1.13e-55 176
MS.gene062057.t1 MTR_8g077950 45.000 80 44 0 50 129 200 279 1.83e-16 73.9
MS.gene062057.t1 MTR_8g077950 45.000 80 44 0 50 129 260 339 2.29e-16 73.9
MS.gene062057.t1 MTR_8g077950 45.000 80 44 0 50 129 258 337 2.53e-16 73.9
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene062057.t1 AT4G36730 38.750 80 49 0 50 129 220 299 3.90e-13 65.1
MS.gene062057.t1 AT4G36730 38.750 80 49 0 50 129 222 301 4.44e-13 64.7
MS.gene062057.t1 AT2G35530 39.706 68 41 0 50 117 305 372 3.55e-11 59.7

Find 17 sgRNAs with CRISPR-Local

Find 64 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
ATCTGGGATGGCTCAGAATT+TGG 0.139505 2.3:+44951357 MS.gene062057:CDS
CACTCTTAAGAATGAAAATT+TGG 0.222390 2.3:+44951875 MS.gene062057:CDS
TCTGGGATGGCTCAGAATTT+GGG 0.322428 2.3:+44951358 MS.gene062057:CDS
GCTCAGCGAGCGTTTGTGTT+AGG 0.338670 2.3:-44951899 None:intergenic
TACTTTGTAGAAAATCCATC+TGG 0.371434 2.3:+44951340 MS.gene062057:CDS
GAAGACCTCGTTAAGGAGTA+TGG 0.391285 2.3:+44952390 MS.gene062057:CDS
AAGATCAAAGATAAAGAAAC+AGG 0.437513 2.3:+44951642 MS.gene062057:CDS
AATAGATCCGCAATTGATTC+TGG 0.439062 2.3:-44952414 None:intergenic
CAATGAAAACGATTCTATTG+AGG 0.546332 2.3:+44951947 MS.gene062057:CDS
CTGGGATGGCTCAGAATTTG+GGG 0.567456 2.3:+44951359 MS.gene062057:CDS
AAATTCTGAGCCATCCCAGA+TGG 0.581446 2.3:-44951355 None:intergenic
GGAACAGGAAGACCTCGTTA+AGG 0.599969 2.3:+44952383 MS.gene062057:intron
TGTAGAAAATCCATCTGGGA+TGG 0.612430 2.3:+44951345 MS.gene062057:CDS
GAATTTGGGGACTGTCGTCA+AGG 0.620583 2.3:+44951372 MS.gene062057:CDS
ACTTTGTAGAAAATCCATCT+GGG 0.631448 2.3:+44951341 MS.gene062057:CDS
CTGGTCCATACTCCTTAACG+AGG 0.672092 2.3:-44952395 None:intergenic
GTATGGACCAGAATCAATTG+CGG 0.711023 2.3:+44952407 MS.gene062057:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! GATTAAATTTTATATAAATG+TGG + chr2.3:44950981-44951000 MS.gene062057:intron 10.0%
!! TCAAATTATAGATCAAAATA+AGG - chr2.3:44951251-44951270 None:intergenic 15.0%
!!! AATTATTTATTTTCCAAGAT+TGG + chr2.3:44952270-44952289 MS.gene062057:intron 15.0%
!!! TTTGAAATTTTTCTTTAGTA+GGG + chr2.3:44951080-44951099 MS.gene062057:intron 15.0%
!! AAAATTGAACAAGTAAGAAA+GGG - chr2.3:44951988-44952007 None:intergenic 20.0%
!! AAGATATCTAACATGATTAT+TGG + chr2.3:44951172-44951191 MS.gene062057:intron 20.0%
!! AATAGAATCGTTTACATTAA+TGG - chr2.3:44952155-44952174 None:intergenic 20.0%
!! ACAAATATTAGAAAACAAGA+TGG - chr2.3:44952074-44952093 None:intergenic 20.0%
!! CAACATTTATAAATAGGAAA+TGG + chr2.3:44951693-44951712 MS.gene062057:intron 20.0%
!! TAAAATTGAACAAGTAAGAA+AGG - chr2.3:44951989-44952008 None:intergenic 20.0%
!! TTGCTAATTTGATTGTAATT+TGG + chr2.3:44952356-44952375 MS.gene062057:intron 20.0%
!! TTTATAAATAGGAAATGGTT+TGG + chr2.3:44951698-44951717 MS.gene062057:intron 20.0%
!!! CTTTGAAATTTTTCTTTAGT+AGG + chr2.3:44951079-44951098 MS.gene062057:intron 20.0%
!!! TTTTCATAGCTAAATATGTA+TGG + chr2.3:44951459-44951478 MS.gene062057:intron 20.0%
! AAACTTAGCAACATTAAGAA+GGG - chr2.3:44951508-44951527 None:intergenic 25.0%
! AAGATCAAAGATAAAGAAAC+AGG + chr2.3:44951642-44951661 MS.gene062057:CDS 25.0%
! AATCAAATTAGCAACAATCT+TGG - chr2.3:44952350-44952369 None:intergenic 25.0%
! ACATCTTTATAAACCAATCT+TGG - chr2.3:44952286-44952305 None:intergenic 25.0%
! AGTAGGGTTATACAAAATTT+CGG + chr2.3:44951096-44951115 MS.gene062057:intron 25.0%
! CAAAAGAAATGCTACTAAAT+TGG - chr2.3:44951562-44951581 None:intergenic 25.0%
! CACTCTTAAGAATGAAAATT+TGG + chr2.3:44951875-44951894 MS.gene062057:CDS 25.0%
! CTAACTTCTTAAGATAAAAG+TGG - chr2.3:44951029-44951048 None:intergenic 25.0%
! CTAATTTGATTGTAATTTGG+TGG + chr2.3:44952359-44952378 MS.gene062057:intron 25.0%
! CTATAATTTGAATGTTCAGA+AGG + chr2.3:44951260-44951279 MS.gene062057:intron 25.0%
! GATATCTTCTTCATACTTAA+AGG - chr2.3:44951160-44951179 None:intergenic 25.0%
! GCATTGCAACATTTATAAAT+AGG + chr2.3:44951687-44951706 MS.gene062057:intron 25.0%
! GTCTAATTACATAGTTTCTT+TGG + chr2.3:44951125-44951144 MS.gene062057:intron 25.0%
! TAAACTTAGCAACATTAAGA+AGG - chr2.3:44951509-44951528 None:intergenic 25.0%
! TGATGCTCAACTAAAAAATA+TGG + chr2.3:44951417-44951436 MS.gene062057:CDS 25.0%
!! AATGGACATCTTATGATTTT+TGG - chr2.3:44952137-44952156 None:intergenic 25.0%
AAAGAAAAAGACTGTCAAAC+AGG + chr2.3:44951608-44951627 MS.gene062057:CDS 30.0%
AATTACATAGTTTCTTTGGC+AGG + chr2.3:44951129-44951148 MS.gene062057:intron 30.0%
ACTTTGTAGAAAATCCATCT+GGG + chr2.3:44951341-44951360 MS.gene062057:CDS 30.0%
CAATGAAAACGATTCTATTG+AGG + chr2.3:44951947-44951966 MS.gene062057:CDS 30.0%
CTTAAGAAGTTAGAAGACTT+AGG + chr2.3:44951036-44951055 MS.gene062057:intron 30.0%
TACTTTGTAGAAAATCCATC+TGG + chr2.3:44951340-44951359 MS.gene062057:CDS 30.0%
TATCTAACTTCTGATGTGTT+TGG + chr2.3:44951762-44951781 MS.gene062057:intron 30.0%
TCTAACATGATTATTGGTGA+TGG + chr2.3:44951178-44951197 MS.gene062057:intron 30.0%
TCTTCATATTCTTTCTGACA+AGG - chr2.3:44951837-44951856 None:intergenic 30.0%
! ATTTGATTGTAATTTGGTGG+TGG + chr2.3:44952362-44952381 MS.gene062057:intron 30.0%
! CTCAATAGAATCGTTTTCAT+TGG - chr2.3:44951949-44951968 None:intergenic 30.0%
! GGATTTTCTACAAAGTAACA+AGG - chr2.3:44951337-44951356 None:intergenic 30.0%
! TTAGTAGCATTTCTTTTGAC+AGG + chr2.3:44951564-44951583 MS.gene062057:intron 30.0%
GTCATTTAACAAGATGAACC+TGG - chr2.3:44952250-44952269 None:intergenic 35.0%
TAATTCTCCGTATTGTGTTG+TGG + chr2.3:44952306-44952325 MS.gene062057:intron 35.0%
TTGAGAACCACAACACAATA+CGG - chr2.3:44952316-44952335 None:intergenic 35.0%
! AATAGATCCGCAATTGATTC+TGG - chr2.3:44952417-44952436 None:intergenic 35.0%
AACCTGGCTACATTCATGTT+AGG - chr2.3:44952234-44952253 None:intergenic 40.0%
GGTACATACATGACCATGAT+CGG + chr2.3:44951663-44951682 MS.gene062057:intron 40.0%
GTATGGACCAGAATCAATTG+CGG + chr2.3:44952407-44952426 MS.gene062057:CDS 40.0%
TACCTAACATGAATGTAGCC+AGG + chr2.3:44952229-44952248 MS.gene062057:intron 40.0%
TGTAGAAAATCCATCTGGGA+TGG + chr2.3:44951345-44951364 MS.gene062057:CDS 40.0%
!! TTGTAATTTGGTGGTGGAAC+AGG + chr2.3:44952368-44952387 MS.gene062057:intron 40.0%
AAATTCTGAGCCATCCCAGA+TGG - chr2.3:44951358-44951377 None:intergenic 45.0%
GAAGACCTCGTTAAGGAGTA+TGG + chr2.3:44952390-44952409 MS.gene062057:CDS 45.0%
! ATCTGGGATGGCTCAGAATT+TGG + chr2.3:44951357-44951376 MS.gene062057:CDS 45.0%
! ATGTTGCAATGCACCGATCA+TGG - chr2.3:44951679-44951698 None:intergenic 45.0%
! CACATGAACTGCAGTTGATG+TGG + chr2.3:44951297-44951316 MS.gene062057:intron 45.0%
! TCTGGGATGGCTCAGAATTT+GGG + chr2.3:44951358-44951377 MS.gene062057:CDS 45.0%
CTGGGATGGCTCAGAATTTG+GGG + chr2.3:44951359-44951378 MS.gene062057:CDS 50.0%
CTGGTCCATACTCCTTAACG+AGG - chr2.3:44952398-44952417 None:intergenic 50.0%
GAATTTGGGGACTGTCGTCA+AGG + chr2.3:44951372-44951391 MS.gene062057:CDS 50.0%
GGAACAGGAAGACCTCGTTA+AGG + chr2.3:44952383-44952402 MS.gene062057:intron 50.0%
GCTCAGCGAGCGTTTGTGTT+AGG - chr2.3:44951902-44951921 None:intergenic 55.0%


Chromosome Type Strat End Strand Name
chr2.3 gene 44950944 44952455 44950944 ID=MS.gene062057
chr2.3 mRNA 44950944 44952455 44950944 ID=MS.gene062057.t1;Parent=MS.gene062057
chr2.3 exon 44950944 44950969 44950944 ID=MS.gene062057.t1.exon1;Parent=MS.gene062057.t1
chr2.3 CDS 44950944 44950969 44950944 ID=cds.MS.gene062057.t1;Parent=MS.gene062057.t1
chr2.3 exon 44951327 44951438 44951327 ID=MS.gene062057.t1.exon2;Parent=MS.gene062057.t1
chr2.3 CDS 44951327 44951438 44951327 ID=cds.MS.gene062057.t1;Parent=MS.gene062057.t1
chr2.3 exon 44951586 44951663 44951586 ID=MS.gene062057.t1.exon3;Parent=MS.gene062057.t1
chr2.3 CDS 44951586 44951663 44951586 ID=cds.MS.gene062057.t1;Parent=MS.gene062057.t1
chr2.3 exon 44951843 44951968 44951843 ID=MS.gene062057.t1.exon4;Parent=MS.gene062057.t1
chr2.3 CDS 44951843 44951968 44951843 ID=cds.MS.gene062057.t1;Parent=MS.gene062057.t1
chr2.3 exon 44952390 44952455 44952390 ID=MS.gene062057.t1.exon5;Parent=MS.gene062057.t1
chr2.3 CDS 44952390 44952455 44952390 ID=cds.MS.gene062057.t1;Parent=MS.gene062057.t1
Gene Sequence

>MS.gene062057

ATGGAGATCAAGATGATAGTAACAATGTATGTTTATTGATTAAATTTTATATAAATGTGGTTGATGAATGTAATGTGTTCTGCCACTTTTATCTTAAGAAGTTAGAAGACTTAGGAAATGAATAGTTTATTAAAGCTTTGAAATTTTTCTTTAGTAGGGTTATACAAAATTTCGGCAAAATGTCTAATTACATAGTTTCTTTGGCAGGATTCTCCTTTAAGTATGAAGAAGATATCTAACATGATTATTGGTGATGGTAAGATTATTGATTTTTCTTTTGATTATTTTATAATAAGACTTCATGCCTTATTTTGATCTATAATTTGAATGTTCAGAAGGTGACTAATACGAAACACATGAACTGCAGTTGATGTGGCTAACAGTCTCGCACCTTGTTACTTTGTAGAAAATCCATCTGGGATGGCTCAGAATTTGGGGACTGTCGTCAAGGAATCAGACACTGACATTGATGTTGATGCTCAACTAAAAAATATGGTATTATAAAGTTTTATGTGTTTTCATAGCTAAATATGTATGGTAAATACACTTCAGAAAGTAAATCCCTTCTTAATGTTGCTAAGTTTAGTTGCATTTCTTGCACAATGTCTAGCATTTCCAATTTAGTAGCATTTCTTTTGACAGGAAGTTGATGAAATAAGAAAAGAAAGAAAAAGACTGTCAAACAGGAAATCAGCTCAAAGATCAAAGATAAAGAAACAGGTACATACATGACCATGATCGGTGCATTGCAACATTTATAAATAGGAAATGGTTTGGTTACATATGATTAAAATGTAAAAAGAAAAAGATGATCTGATTATCTAACTTCTGATGTGTTTGGTTGATAATCTTTTTAACTTGTATTTCATTTGATGTTATCATTATTTGTGCCTTGTCAGAAAGAATATGAAGAGCAATGTCAAAAGATAAACACTCTTAAGAATGAAAATTTGGTCCTAACACAAACGCTCGCTGAGCTTACAGAGAAATGTCTCGAGCTCACCAATGAAAACGATTCTATTGAGGTCAATCATTTTAACTCCCTTTCTTACTTGTTCAATTTTATATCATTCAATAAACAAGATACTTGTTTGATTTGAGAAATATTTTTTTCAATTAAAAAAATTCCATCTTGTTTTCTAATATTTGTATGAGAAACAATTAAATAAACTAAGAAGATTCTTATGAATCCAAAAATCATAAGATGTCCATTAATGTAAACGATTCTATTGATCTCTCTTTGTAACAAACTTTCTAATAAACTAGTGCAACAAATAATCTAAGTTACCTAACATGAATGTAGCCAGGTTCATCTTGTTAAATGACAATTATTTATTTTCCAAGATTGGTTTATAAAGATGTTAATTCTCCGTATTGTGTTGTGGTTCTCAATGCTCTATTTTCCAAGATTGTTGCTAATTTGATTGTAATTTGGTGGTGGAACAGGAAGACCTCGTTAAGGAGTATGGACCAGAATCAATTGCGGATCTATTGCATATGAATCCTACTTGA
Protein sequence

>MS.gene062057.t1

MEIKMIVTILAPCYFVENPSGMAQNLGTVVKESDTDIDVDAQLKNMEVDEIRKERKRLSNRKSAQRSKIKKQKEYEEQCQKINTLKNENLVLTQTLAELTEKCLELTNENDSIEEDLVKEYGPESIADLLHMNPT