AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene52970


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene52970.t1 MTR_1g075720 99.248 133 1 0 1 133 1 133 2.34e-90 258
MS.gene52970.t1 MTR_4g120770 95.489 133 6 0 1 133 1 133 4.44e-89 254
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene52970.t1 AT2G20450 84.962 133 20 0 1 133 1 133 7.52e-77 224
MS.gene52970.t1 AT4G27090 85.385 130 19 0 1 130 1 130 6.52e-76 221

Find 41 sgRNAs with CRISPR-Local

Find 97 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TGAACCTATCAAAATCATTA+AGG 0.237759 1.1:-56661519 None:intergenic
TTGACGAGATCCTTCTTCTT+AGG 0.250131 1.1:-56661281 None:intergenic
GATTATGTTGGCCAAGATTA+AGG 0.263288 1.1:+56661543 MS.gene52970:CDS
GTCAACTATGGTCCAGATTA+TGG 0.285686 1.1:+56661034 MS.gene52970:CDS
GAAAATGGGTTACCCTAGTT+TGG 0.329740 1.1:-56661087 None:intergenic
GAAAGTCTCTTGAAATTGAT+TGG 0.345301 1.1:-56661224 None:intergenic
TATCAATCTTGATATCAGTT+AGG 0.362900 1.1:-56661247 None:intergenic
AAAGTCTCTTGAAATTGATT+GGG 0.365242 1.1:-56661223 None:intergenic
ACAACGAGCTTGCCATAATC+TGG 0.375981 1.1:-56661046 None:intergenic
CTAAAATTATACCTTAATCT+TGG 0.381940 1.1:-56661554 None:intergenic
TCTTGTTGATGCACCTGATA+TGG 0.389997 1.1:+56661193 MS.gene52970:CDS
ATTGGGGCTCTCTCCATATC+AGG 0.404038 1.1:-56661206 None:intergenic
TGCAGAGGGCTGGTGTTGTT+AGG 0.431787 1.1:+56662448 MS.gene52970:intron
TTGATGTTATCGACCAAACT+AGG 0.433748 1.1:+56661074 MS.gene52970:CDS
GAACCTATCAAAATCATTAA+GGG 0.440003 1.1:-56661518 None:intergenic
AACAATCAATTTCCTTCCCC+AGG 0.448020 1.1:-56661479 None:intergenic
ATCAATCTTGATATCAGTTA+GGG 0.462600 1.1:-56661246 None:intergenic
AGAGTTGCACTTGTCAACTA+TGG 0.467898 1.1:+56661022 MS.gene52970:CDS
GCTGAGGAAGACCGCAGCTT+AGG 0.479614 1.1:+56662485 MS.gene52970:CDS
TTTCAATTTGTGCAGAGGGC+TGG 0.483986 1.1:+56662438 MS.gene52970:intron
GAAGGATCTCGTCAAGGCTA+TGG 0.488672 1.1:+56661289 MS.gene52970:CDS
GGAAATTGATTGTTAAGAAG+AGG 0.493248 1.1:+56661488 MS.gene52970:CDS
TTCAAGAGGTTTGTTGAGAT+CGG 0.494020 1.1:+56660998 MS.gene52970:CDS
CAAGAGAGTTCCTAAGAAGA+AGG 0.504705 1.1:+56661271 MS.gene52970:CDS
ACAAGTGGGAGAAGAGCTCC+TGG 0.539704 1.1:+56661461 MS.gene52970:CDS
AATTGATTGTTAAGAAGAGG+AGG 0.539799 1.1:+56661491 MS.gene52970:CDS
TGATAGGTTCAAGATTATGT+TGG 0.542816 1.1:+56661531 MS.gene52970:CDS
TGATAGATGTGAAGAACAAG+TGG 0.562094 1.1:+56661446 MS.gene52970:intron
ATCTCAACAAACCTCTTGAA+CGG 0.571035 1.1:-56660995 None:intergenic
AAGTCTCTTGAAATTGATTG+GGG 0.581289 1.1:-56661222 None:intergenic
GGGAGAAGAGCTCCTGGGGA+AGG 0.586483 1.1:+56661467 MS.gene52970:CDS
GTCAAGGCTATGGAAGCTGC+AGG 0.587422 1.1:+56661299 MS.gene52970:CDS
ATTGATTGTTAAGAAGAGGA+GGG 0.602431 1.1:+56661492 MS.gene52970:CDS
TGATGTTATCGACCAAACTA+GGG 0.607546 1.1:+56661075 MS.gene52970:CDS
GGCAAGAACTTGCTAAGCTG+AGG 0.613930 1.1:+56662469 MS.gene52970:CDS
AAGTGGGAGAAGAGCTCCTG+GGG 0.619297 1.1:+56661463 MS.gene52970:CDS
TCTTTGTTAAGCCGTTCAAG+AGG 0.622760 1.1:+56660984 MS.gene52970:intron
GATAGATGTGAAGAACAAGT+GGG 0.623335 1.1:+56661447 MS.gene52970:intron
TAAGAAGAAGGATCTCGTCA+AGG 0.637349 1.1:+56661283 MS.gene52970:CDS
CAAGTGGGAGAAGAGCTCCT+GGG 0.641380 1.1:+56661462 MS.gene52970:CDS
ATGAAGTAATGCCTAAGCTG+CGG 0.676586 1.1:-56662496 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! ACAAAAATAAATATATAGAT+AGG - chr1.1:56661340-56661359 None:intergenic 10.0%
!!! AATTTTATGATAAAAGATTA+AGG - chr1.1:56662206-56662225 None:intergenic 10.0%
!!! ATTTTATGATAAAAGATTAA+GGG - chr1.1:56662205-56662224 None:intergenic 10.0%
!!! TAATCTTTTATCATAAAATT+TGG + chr1.1:56662206-56662225 MS.gene52970:intron 10.0%
!! AAAGATTGGAAATTTGAAAA+TGG - chr1.1:56661105-56661124 None:intergenic 20.0%
!! AAGATTGGAAATTTGAAAAT+GGG - chr1.1:56661104-56661123 None:intergenic 20.0%
!! ATTAGAGAAAGATTAAGAAA+TGG - chr1.1:56660952-56660971 None:intergenic 20.0%
!! CTAAAATTATACCTTAATCT+TGG - chr1.1:56661557-56661576 None:intergenic 20.0%
!! TTAAGTTATTTATCCAAACA+AGG - chr1.1:56661708-56661727 None:intergenic 20.0%
!! TTTATGTATTATTCATGGAT+TGG - chr1.1:56662136-56662155 None:intergenic 20.0%
!!! AAGCTTTTATGTATTATTCA+TGG - chr1.1:56662086-56662105 None:intergenic 20.0%
!!! ATTGTATTTCTATAAGCTTT+AGG + chr1.1:56661933-56661952 MS.gene52970:intron 20.0%
!!! GAAATTGGATTTTAATTTTG+TGG + chr1.1:56661403-56661422 MS.gene52970:intron 20.0%
!!! GATTTTAATTTTGTGGTAAT+TGG + chr1.1:56661410-56661429 MS.gene52970:intron 20.0%
!!! TGTGAAATGATTTTAAGTTA+GGG + chr1.1:56661598-56661617 MS.gene52970:intron 20.0%
!!! TTGTATTTCTATAAGCTTTA+GGG + chr1.1:56661934-56661953 MS.gene52970:intron 20.0%
!!! TTGTGAAATGATTTTAAGTT+AGG + chr1.1:56661597-56661616 MS.gene52970:intron 20.0%
! AAAGTCTCTTGAAATTGATT+GGG - chr1.1:56661226-56661245 None:intergenic 25.0%
! ATCAATCTTGATATCAGTTA+GGG - chr1.1:56661249-56661268 None:intergenic 25.0%
! CAAGTTTGTCTATGAAAAAA+CGG - chr1.1:56662057-56662076 None:intergenic 25.0%
! GAACCTATCAAAATCATTAA+GGG - chr1.1:56661521-56661540 None:intergenic 25.0%
! GGTTATTATATAAGCTGTTA+TGG + chr1.1:56661873-56661892 MS.gene52970:intron 25.0%
! TAAAATAAGCTAATCCAAAC+AGG + chr1.1:56662322-56662341 MS.gene52970:intron 25.0%
! TAAATTTCAATTTGTGCAGA+GGG + chr1.1:56662434-56662453 MS.gene52970:intron 25.0%
! TATCAATCTTGATATCAGTT+AGG - chr1.1:56661250-56661269 None:intergenic 25.0%
! TGAACCTATCAAAATCATTA+AGG - chr1.1:56661522-56661541 None:intergenic 25.0%
! TTAAATTTCAATTTGTGCAG+AGG + chr1.1:56662433-56662452 MS.gene52970:intron 25.0%
!! TTGCATTTTATAGTGTAAGT+GGG + chr1.1:56661729-56661748 MS.gene52970:intron 25.0%
!! TTTGCATTTTATAGTGTAAG+TGG + chr1.1:56661728-56661747 MS.gene52970:intron 25.0%
!!! TAGCTTTTGTTTGTTGAAAT+TGG + chr1.1:56661388-56661407 MS.gene52970:intron 25.0%
!!! TTTTGAGAAATTACGCAAAT+GGG - chr1.1:56661145-56661164 None:intergenic 25.0%
!!! TTTTTGAGAAATTACGCAAA+TGG - chr1.1:56661146-56661165 None:intergenic 25.0%
AAGTCTCTTGAAATTGATTG+GGG - chr1.1:56661225-56661244 None:intergenic 30.0%
AATTGATTGTTAAGAAGAGG+AGG + chr1.1:56661491-56661510 MS.gene52970:CDS 30.0%
ATGGAGATACAATGTTTGTT+AGG - chr1.1:56662031-56662050 None:intergenic 30.0%
ATTGATTGTTAAGAAGAGGA+GGG + chr1.1:56661492-56661511 MS.gene52970:CDS 30.0%
GAAAGTCTCTTGAAATTGAT+TGG - chr1.1:56661227-56661246 None:intergenic 30.0%
GGAAATTGATTGTTAAGAAG+AGG + chr1.1:56661488-56661507 MS.gene52970:CDS 30.0%
GGATGAAAATGGAAAAAGAT+TGG - chr1.1:56661119-56661138 None:intergenic 30.0%
TAAAAGATTAAGGGTCTGTT+TGG - chr1.1:56662196-56662215 None:intergenic 30.0%
TGATAGGTTCAAGATTATGT+TGG + chr1.1:56661531-56661550 MS.gene52970:CDS 30.0%
TTGTGAAATGCTCTTAAGTT+GGG + chr1.1:56661682-56661701 MS.gene52970:intron 30.0%
! TGCATTTTATAGTGTAAGTG+GGG + chr1.1:56661730-56661749 MS.gene52970:intron 30.0%
! TGGAGATACAATGTTTGTTA+GGG - chr1.1:56662030-56662049 None:intergenic 30.0%
!! TTGTTTTTCAACTTGTGTCT+AGG + chr1.1:56662373-56662392 MS.gene52970:intron 30.0%
!!! TTGTGATTTGTTTGTTTTGC+AGG + chr1.1:56661169-56661188 MS.gene52970:intron 30.0%
AAACCCTACATACTCAACTA+AGG - chr1.1:56662349-56662368 None:intergenic 35.0%
AACCCTACATACTCAACTAA+GGG - chr1.1:56662348-56662367 None:intergenic 35.0%
ATCTCAACAAACCTCTTGAA+CGG - chr1.1:56660998-56661017 None:intergenic 35.0%
GATAGATGTGAAGAACAAGT+GGG + chr1.1:56661447-56661466 MS.gene52970:intron 35.0%
GATTATGTTGGCCAAGATTA+AGG + chr1.1:56661543-56661562 MS.gene52970:CDS 35.0%
GTCTATGAAAAAACGGCTTA+TGG - chr1.1:56662050-56662069 None:intergenic 35.0%
GTTGTGAAATGCTCTTAAGT+TGG + chr1.1:56661681-56661700 MS.gene52970:intron 35.0%
TGATAGATGTGAAGAACAAG+TGG + chr1.1:56661446-56661465 MS.gene52970:intron 35.0%
TGATGTTATCGACCAAACTA+GGG + chr1.1:56661075-56661094 MS.gene52970:CDS 35.0%
TTCTCATAACCCAATTCAAG+CGG - chr1.1:56661961-56661980 None:intergenic 35.0%
TTGATGTTATCGACCAAACT+AGG + chr1.1:56661074-56661093 MS.gene52970:CDS 35.0%
! ATTAAGTTGTCTATCCAAGC+AGG - chr1.1:56661625-56661644 None:intergenic 35.0%
! CAGACAGTCTTACATGATTT+TGG + chr1.1:56662287-56662306 MS.gene52970:intron 35.0%
! TTAAGTTGTCTATCCAAGCA+GGG - chr1.1:56661624-56661643 None:intergenic 35.0%
!! CTGCCCTTAATGATTTTGAT+AGG + chr1.1:56661515-56661534 MS.gene52970:CDS 35.0%
!! TTCAAGAGGTTTGTTGAGAT+CGG + chr1.1:56660998-56661017 MS.gene52970:CDS 35.0%
!!! TTTGGATTGGCTTCTTTTTG+AGG - chr1.1:56662178-56662197 None:intergenic 35.0%
AACAATCAATTTCCTTCCCC+AGG - chr1.1:56661482-56661501 None:intergenic 40.0%
AGAGTTGCACTTGTCAACTA+TGG + chr1.1:56661022-56661041 MS.gene52970:CDS 40.0%
CAAGAGAGTTCCTAAGAAGA+AGG + chr1.1:56661271-56661290 MS.gene52970:CDS 40.0%
GATTAAGGGTCTGTTTGGAT+TGG - chr1.1:56662191-56662210 None:intergenic 40.0%
GTCAACTATGGTCCAGATTA+TGG + chr1.1:56661034-56661053 MS.gene52970:CDS 40.0%
TAAGAAGAAGGATCTCGTCA+AGG + chr1.1:56661283-56661302 MS.gene52970:CDS 40.0%
TCTCATAACCCAATTCAAGC+GGG - chr1.1:56661960-56661979 None:intergenic 40.0%
TCTTGTTGATGCACCTGATA+TGG + chr1.1:56661193-56661212 MS.gene52970:CDS 40.0%
TCTTTGTTAAGCCGTTCAAG+AGG + chr1.1:56660984-56661003 MS.gene52970:intron 40.0%
TGTCTGTGAGTACTTATGTG+TGG - chr1.1:56662273-56662292 None:intergenic 40.0%
TTGACGAGATCCTTCTTCTT+AGG - chr1.1:56661284-56661303 None:intergenic 40.0%
TTTGCAGCTTGTAGTTCAAG+TGG + chr1.1:56661644-56661663 MS.gene52970:intron 40.0%
! AGAAATTACGCAAATGGGCT+AGG - chr1.1:56661140-56661159 None:intergenic 40.0%
!! CAAATGGGCTAGGATGAAAA+TGG - chr1.1:56661130-56661149 None:intergenic 40.0%
!! GAAAATGGGTTACCCTAGTT+TGG - chr1.1:56661090-56661109 None:intergenic 40.0%
!!! CATGGATTGGCTTCTTTTTG+AGG - chr1.1:56662123-56662142 None:intergenic 40.0%
ACAACGAGCTTGCCATAATC+TGG - chr1.1:56661049-56661068 None:intergenic 45.0%
AGGCCCTTAGTTGAGTATGT+AGG + chr1.1:56662342-56662361 MS.gene52970:intron 45.0%
GGCCCTTAGTTGAGTATGTA+GGG + chr1.1:56662343-56662362 MS.gene52970:intron 45.0%
TACTCAACTAAGGGCCTGTT+TGG - chr1.1:56662339-56662358 None:intergenic 45.0%
TTTCAATTTGTGCAGAGGGC+TGG + chr1.1:56662438-56662457 MS.gene52970:intron 45.0%
!! CTCTTAAGTTGGGCCTTGTT+TGG + chr1.1:56661692-56661711 MS.gene52970:intron 45.0%
!!! TTTTAAGTTAGGGCCCTGCT+TGG + chr1.1:56661608-56661627 MS.gene52970:intron 45.0%
ATTGGGGCTCTCTCCATATC+AGG - chr1.1:56661209-56661228 None:intergenic 50.0%
GAAGGATCTCGTCAAGGCTA+TGG + chr1.1:56661289-56661308 MS.gene52970:CDS 50.0%
!! CTTTAGGGCCCGCTTGAATT+GGG + chr1.1:56661949-56661968 MS.gene52970:intron 50.0%
!! GGCAAGAACTTGCTAAGCTG+AGG + chr1.1:56662469-56662488 MS.gene52970:CDS 50.0%
AAGTGGGAGAAGAGCTCCTG+GGG + chr1.1:56661463-56661482 MS.gene52970:CDS 55.0%
ACAAGTGGGAGAAGAGCTCC+TGG + chr1.1:56661461-56661480 MS.gene52970:CDS 55.0%
CAAGTGGGAGAAGAGCTCCT+GGG + chr1.1:56661462-56661481 MS.gene52970:CDS 55.0%
GTCAAGGCTATGGAAGCTGC+AGG + chr1.1:56661299-56661318 MS.gene52970:CDS 55.0%
!! GCTTTAGGGCCCGCTTGAAT+TGG + chr1.1:56661948-56661967 MS.gene52970:intron 55.0%
!! TGCAGAGGGCTGGTGTTGTT+AGG + chr1.1:56662448-56662467 MS.gene52970:intron 55.0%
GGGAGAAGAGCTCCTGGGGA+AGG + chr1.1:56661467-56661486 MS.gene52970:CDS 65.0%


Chromosome Type Strat End Strand Name
chr1.1 gene 56660910 56662506 56660910 ID=MS.gene52970
chr1.1 mRNA 56660910 56662506 56660910 ID=MS.gene52970.t1;Parent=MS.gene52970
chr1.1 exon 56660910 56660912 56660910 ID=MS.gene52970.t1.exon1;Parent=MS.gene52970.t1
chr1.1 CDS 56660910 56660912 56660910 ID=cds.MS.gene52970.t1;Parent=MS.gene52970.t1
chr1.1 exon 56660995 56661096 56660995 ID=MS.gene52970.t1.exon2;Parent=MS.gene52970.t1
chr1.1 CDS 56660995 56661096 56660995 ID=cds.MS.gene52970.t1;Parent=MS.gene52970.t1
chr1.1 exon 56661191 56661320 56661191 ID=MS.gene52970.t1.exon3;Parent=MS.gene52970.t1
chr1.1 CDS 56661191 56661320 56661191 ID=cds.MS.gene52970.t1;Parent=MS.gene52970.t1
chr1.1 exon 56661452 56661564 56661452 ID=MS.gene52970.t1.exon4;Parent=MS.gene52970.t1
chr1.1 CDS 56661452 56661564 56661452 ID=cds.MS.gene52970.t1;Parent=MS.gene52970.t1
chr1.1 exon 56662453 56662506 56662453 ID=MS.gene52970.t1.exon5;Parent=MS.gene52970.t1
chr1.1 CDS 56662453 56662506 56662453 ID=cds.MS.gene52970.t1;Parent=MS.gene52970.t1
Gene Sequence

>MS.gene52970

ATGGTGAATCACATTTCTCTGTTCATCTTTGTCTCAATTCCATTTCTTAATCTTTCTCTAATCTCACTGTGTGTTCTTTGTTAAGCCGTTCAAGAGGTTTGTTGAGATCGGAAGAGTTGCACTTGTCAACTATGGTCCAGATTATGGCAAGCTCGTTGTTATCGTTGATGTTATCGACCAAACTAGGGTAACCCATTTTCAAATTTCCAATCTTTTTCCATTTTCATCCTAGCCCATTTGCGTAATTTCTCAAAAATGTTTGTGATTTGTTTGTTTTGCAGGCTCTTGTTGATGCACCTGATATGGAGAGAGCCCCAATCAATTTCAAGAGACTTTCCCTAACTGATATCAAGATTGATATCAAGAGAGTTCCTAAGAAGAAGGATCTCGTCAAGGCTATGGAAGCTGCAGGTAGATTTTCTATTAACCTATCTATATATTTATTTTTGTTTTTTTTGATGTTTTCTTTAGTTGTTTTTAGCTTTTGTTTGTTGAAATTGGATTTTAATTTTGTGGTAATTGGTTTTGTTTGAATTTGATAGATGTGAAGAACAAGTGGGAGAAGAGCTCCTGGGGAAGGAAATTGATTGTTAAGAAGAGGAGGGCTGCCCTTAATGATTTTGATAGGTTCAAGATTATGTTGGCCAAGATTAAGGTATAATTTTAGTTGCTGTTTTTTGTTTTCTGTTGTGAAATGATTTTAAGTTAGGGCCCTGCTTGGATAGACAACTTAATTTGCAGCTTGTAGTTCAAGTGGCTATTATAGAAGCTGTTGTGAAATGCTCTTAAGTTGGGCCTTGTTTGGATAAATAACTTAATTTGCATTTTATAGTGTAAGTGGGGTTATTATATATAATTTGCAGCTTGTAGTTCAAGTGGCTATTATAGAAGCTGTTGTGAAATGCTCTTAAGTTGGGCCTTGTTTGGATAAATAACTTAATTTGCATTTTATAGTGTAAGTGGGGTTATTATATAAGCTGTTATGGATGAACTGTTTCTGTTGCACAAGATAAGATGAATCAAATTGTATTTCTATAAGCTTTAGGGCCCGCTTGAATTGGGTTATGAGAAGTAGCTTATGTAAATAAATAAGCTCTTATGTTAATTCATAAGTTCTCCCTAACAAACATTGTATCTCCATAAGCCGTTTTTTCATAGACAAACTTGACAAGCTCATGAATAATACATAAAAGCTTATTTATTTGAATAACCTCAAAAAGAAGCCAATCCATGAATAATACATAAAAGCTTATTTATTTGAATAACCTCAAAAAGAAGCCAATCCAAACAGACCCTTAATCTTTTATCATAAAATTTGGAGAACTTATCAAATGAACTGTTAAAACAACTTTTGAACATGCCACACATAAGTACTCACAGACAGTCTTACATGATTTTGGCTGTTTATAAGCTAAAATAAGCTAATCCAAACAGGCCCTTAGTTGAGTATGTAGGGTTTGATTTTGTTTTTCAACTTGTGTCTAGGTTGTATTAATTCTGATTCTGATGTTGTATTGATGTTCTTAAATTTCAATTTGTGCAGAGGGCTGGTGTTGTTAGGCAAGAACTTGCTAAGCTGAGGAAGACCGCAGCTTAG

Protein sequence

>MS.gene52970.t1

MPFKRFVEIGRVALVNYGPDYGKLVVIVDVIDQTRALVDAPDMERAPINFKRLSLTDIKIDIKRVPKKKDLVKAMEAADVKNKWEKSSWGRKLIVKKRRAALNDFDRFKIMLAKIKRAGVVRQELAKLRKTAA