AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene060279

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene060279.t1 MTR_5g005130 100.000 56 0 0 1 56 1 56 9.62e-38 119
MS.gene060279.t1 MTR_3g115330 100.000 56 0 0 1 56 1 56 9.62e-38 119
MS.gene060279.t1 MTR_1g106755 100.000 56 0 0 1 56 1 56 9.62e-38 119
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene060279.t1 AT4G33865 92.857 56 4 0 1 56 1 56 6.55e-34 109
MS.gene060279.t1 AT3G44010 92.857 56 4 0 1 56 1 56 6.55e-34 109
MS.gene060279.t1 AT3G43980 92.857 56 4 0 1 56 1 56 6.55e-34 109
MS.gene060279.t1 AT3G44010 92.857 56 4 0 1 56 1 56 6.55e-34 109

Find 25 sgRNAs with CRISPR-Local

Find 46 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CACAGCAATGCCAAGGAAAT+TGG 0.216340 1.2:-79538536 MS.gene060279:CDS
CAAGGAAATTGGCTTCATTA+AGG 0.276234 1.2:-79538525 MS.gene060279:intron
CATGGATTGATAAGGAAGTA+TGG 0.378864 1.2:-79538584 MS.gene060279:CDS
CCATGGGACACTCAAATGTT+TGG 0.382308 1.2:-79539240 MS.gene060279:CDS
GAACCAGGACCATAGGTCTT+GGG 0.410602 1.2:+79539208 None:intergenic
CTTAATGAAGCCAATTTCCT+TGG 0.421882 1.2:+79538526 None:intergenic
AGCATTGCCTGCAGCACATA+AGG 0.453112 1.2:+79538561 None:intergenic
GGAACCAGGACCATAGGTCT+TGG 0.464100 1.2:+79539207 None:intergenic
ATGGTCCTGGTTCCCGCACT+TGG 0.475887 1.2:-79539198 MS.gene060279:intron
CACCCCAAGACCTATGGTCC+TGG 0.491604 1.2:-79539211 MS.gene060279:CDS
AACTCTCACCCCAAGACCTA+TGG 0.505813 1.2:-79539217 MS.gene060279:CDS
GGAATTCACATGGATTGATA+AGG 0.515737 1.2:-79538592 MS.gene060279:CDS
ATATACCAAGTGCGGGAACC+AGG 0.531737 1.2:+79539193 None:intergenic
AGTATGGCCTTATGTGCTGC+AGG 0.540472 1.2:-79538568 MS.gene060279:CDS
CCAAACATTTGAGTGTCCCA+TGG 0.543494 1.2:+79539240 None:intergenic
TAACTTGTAGCCGTGTGTGC+GGG 0.573381 1.2:-79538613 MS.gene060279:intron
CATGTGAATTCCCGCACACA+CGG 0.574250 1.2:+79538603 None:intergenic
AAGAATGAATATACCAAGTG+CGG 0.579658 1.2:+79539185 None:intergenic
AGTGCGGGAACCAGGACCAT+AGG 0.585453 1.2:+79539201 None:intergenic
CAATTTCCTTGGCATTGCTG+TGG 0.593734 1.2:+79538537 None:intergenic
AACCAGGACCATAGGTCTTG+GGG 0.597207 1.2:+79539209 None:intergenic
CGTGTGTGCGGGAATTCACA+TGG 0.601988 1.2:-79538602 MS.gene060279:CDS
AGAATGAATATACCAAGTGC+GGG 0.603783 1.2:+79539186 None:intergenic
ATGCTTCCACAGCAATGCCA+AGG 0.620494 1.2:-79538543 MS.gene060279:CDS
ATAACTTGTAGCCGTGTGTG+CGG 0.665136 1.2:-79538614 MS.gene060279:intron

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! TGTTATTGATAATATGTTTT+GGG - chr1.2:79538701-79538720 MS.gene060279:intron 15.0%
!! AAACCTAAATGAATTGAAAA+AGG + chr1.2:79538530-79538549 None:intergenic 20.0%
!! GCAAGATAAATAAAAACAAA+TGG + chr1.2:79539230-79539249 None:intergenic 20.0%
!! TAATTAAGATTTGATTCAGA+TGG - chr1.2:79538783-79538802 MS.gene060279:intron 20.0%
!! TTATGTTATTGCTATCATAT+CGG - chr1.2:79538888-79538907 MS.gene060279:intron 20.0%
!!! ATTTAGGTTTCTAGTATTTT+GGG - chr1.2:79538540-79538559 MS.gene060279:CDS 20.0%
!!! GTGTTATTGATAATATGTTT+TGG - chr1.2:79538700-79538719 MS.gene060279:intron 20.0%
!!! GTTATTGATAATATGTTTTG+GGG - chr1.2:79538702-79538721 MS.gene060279:intron 20.0%
!!! TAACCTTTTTCAATTCATTT+AGG - chr1.2:79538524-79538543 MS.gene060279:intron 20.0%
!!! TTGGGGATTTTTATTTTTTT+GGG - chr1.2:79538719-79538738 MS.gene060279:intron 20.0%
!!! TTTGGGGATTTTTATTTTTT+TGG - chr1.2:79538718-79538737 MS.gene060279:intron 20.0%
! CAAAATGTAAACTTTAACAG+CGG + chr1.2:79538575-79538594 None:intergenic 25.0%
! GATATGATAGCAATAACATA+AGG + chr1.2:79538889-79538908 None:intergenic 25.0%
! GATTCAAAATTCAAGAAAGA+GGG + chr1.2:79538600-79538619 None:intergenic 25.0%
! TTTGAACATATGTAGTTTAG+TGG - chr1.2:79538859-79538878 MS.gene060279:intron 25.0%
!! TAATGGTTTTCTATTGCTTT+GGG - chr1.2:79538646-79538665 MS.gene060279:intron 25.0%
!!! CATTTAGGTTTCTAGTATTT+TGG - chr1.2:79538539-79538558 MS.gene060279:CDS 25.0%
AAGAATGAATATACCAAGTG+CGG + chr1.2:79538488-79538507 None:intergenic 30.0%
CGATTCAAAATTCAAGAAAG+AGG + chr1.2:79538601-79538620 None:intergenic 30.0%
! CTAATGGTTTTCTATTGCTT+TGG - chr1.2:79538645-79538664 MS.gene060279:intron 30.0%
!! GTGTTGTTTCTATGTTCTAA+TGG - chr1.2:79538629-79538648 MS.gene060279:intron 30.0%
AGAATGAATATACCAAGTGC+GGG + chr1.2:79538487-79538506 None:intergenic 35.0%
CTTAATGAAGCCAATTTCCT+TGG + chr1.2:79539147-79539166 None:intergenic 35.0%
! CAAGGAAATTGGCTTCATTA+AGG - chr1.2:79539145-79539164 MS.gene060279:intron 35.0%
! CATGGATTGATAAGGAAGTA+TGG - chr1.2:79539086-79539105 MS.gene060279:intron 35.0%
! GGAATTCACATGGATTGATA+AGG - chr1.2:79539078-79539097 MS.gene060279:intron 35.0%
TGCTATCATATCGGTACTAG+AGG - chr1.2:79538897-79538916 MS.gene060279:intron 40.0%
!! TCTATTGCTTTGGGTTGTAC+TGG - chr1.2:79538655-79538674 MS.gene060279:intron 40.0%
CAATTTCCTTGGCATTGCTG+TGG + chr1.2:79539136-79539155 None:intergenic 45.0%
CACAGCAATGCCAAGGAAAT+TGG - chr1.2:79539134-79539153 MS.gene060279:intron 45.0%
! ATAACTTGTAGCCGTGTGTG+CGG - chr1.2:79539056-79539075 MS.gene060279:intron 45.0%
!! TGCTTTGGGTTGTACTGGTA+TGG - chr1.2:79538660-79538679 MS.gene060279:intron 45.0%
AACCAGGACCATAGGTCTTG+GGG + chr1.2:79538464-79538483 None:intergenic 50.0%
AACTCTCACCCCAAGACCTA+TGG - chr1.2:79538453-79538472 MS.gene060279:intron 50.0%
AGCATTGCCTGCAGCACATA+AGG + chr1.2:79539112-79539131 None:intergenic 50.0%
ATATACCAAGTGCGGGAACC+AGG + chr1.2:79538480-79538499 None:intergenic 50.0%
ATGCTTCCACAGCAATGCCA+AGG - chr1.2:79539127-79539146 MS.gene060279:intron 50.0%
CATGTGAATTCCCGCACACA+CGG + chr1.2:79539070-79539089 None:intergenic 50.0%
GAACCAGGACCATAGGTCTT+GGG + chr1.2:79538465-79538484 None:intergenic 50.0%
! TAACTTGTAGCCGTGTGTGC+GGG - chr1.2:79539057-79539076 MS.gene060279:intron 50.0%
!! AGTATGGCCTTATGTGCTGC+AGG - chr1.2:79539102-79539121 MS.gene060279:intron 50.0%
CGTGTGTGCGGGAATTCACA+TGG - chr1.2:79539068-79539087 MS.gene060279:intron 55.0%
GGAACCAGGACCATAGGTCT+TGG + chr1.2:79538466-79538485 None:intergenic 55.0%
AGTGCGGGAACCAGGACCAT+AGG + chr1.2:79538472-79538491 None:intergenic 60.0%
ATGGTCCTGGTTCCCGCACT+TGG - chr1.2:79538472-79538491 MS.gene060279:intron 60.0%
CACCCCAAGACCTATGGTCC+TGG - chr1.2:79538459-79538478 MS.gene060279:intron 60.0%


Chromosome Type Strat End Strand Name
chr1.2 gene 79538432 79539260 79538432 ID=MS.gene060279
chr1.2 mRNA 79538432 79539260 79538432 ID=MS.gene060279.t1;Parent=MS.gene060279
chr1.2 exon 79539199 79539260 79539199 ID=MS.gene060279.t1.exon1;Parent=MS.gene060279.t1
chr1.2 CDS 79539199 79539260 79539199 ID=cds.MS.gene060279.t1;Parent=MS.gene060279.t1
chr1.2 exon 79538526 79538625 79538526 ID=MS.gene060279.t1.exon2;Parent=MS.gene060279.t1
chr1.2 CDS 79538526 79538625 79538526 ID=cds.MS.gene060279.t1;Parent=MS.gene060279.t1
chr1.2 exon 79538432 79538440 79538432 ID=MS.gene060279.t1.exon3;Parent=MS.gene060279.t1
chr1.2 CDS 79538432 79538440 79538432 ID=cds.MS.gene060279.t1;Parent=MS.gene060279.t1
Gene Sequence

>MS.gene060279

ATGGGACACTCAAATGTTTGGAACTCTCACCCCAAGACCTATGGTCCTGGTTCCCGCACTTGGTATATTCATTCTTCAATCTTCGATTCACATAACCTTTTTCAATTCATTTAGGTTTCTAGTATTTTGGGTTTTATTTTCCGCTGTTAAAGTTTACATTTTGATCCCTCTTTCTTGAATTTTGAATCGTTTGACTAGTGTTGTTTCTATGTTCTAATGGTTTTCTATTGCTTTGGGTTGTACTGGTATGGTTTGAGATTGATGAATAGTGTTATTGATAATATGTTTTGGGGATTTTTATTTTTTTGGGTCAGCTTTGATATCAGCTTATGTTATAGCTAAGCAGTGAACTAATTAAGATTTGATTCAGATGGCTTAAGTTGATTATTAATTTCGTTCAATGTTGTTTTGTTCTCGTTGTTGATGATTTGAACATATGTAGTTTAGTGGAAAACCTTATGTTATTGCTATCATATCGGTACTAGAGGAACACTGAACAGTAATTTTTGAATAATAGTGTATATTATACACATTCTCACAGTTCTGTAGAATAATTGATGTTGTATTGCAGATCTGTTGTTTTTTAATTTAGAATTGTCTTGCTGATTGTGATTCATTTTGTGTATAACTTGTAGCCGTGTGTGCGGGAATTCACATGGATTGATAAGGAAGTATGGCCTTATGTGCTGCAGGCAATGCTTCCACAGCAATGCCAAGGAAATTGGCTTCATTAAGGTAAACTTTTGATTGTGTTGATCTCAGATACAATCATTTAAAATGTCTGTATGTGTAACACCATTTGTTTTTATTTATCTTGCAGTACCGTTGA
Protein sequence

>MS.gene060279.t1

MGHSNVWNSHPKTYGPGSRTCRVCGNSHGLIRKYGLMCCRQCFHSNAKEIGFIKYR