AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene37567


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene37567.t1 MTR_5g089030 96.907 97 3 0 1 97 24 120 4.76e-64 189
MS.gene37567.t1 MTR_5g089030 96.907 97 3 0 1 97 17 113 6.23e-64 189
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene37567.t1 AT5G12240 51.316 76 34 3 23 96 40 114 2.88e-16 68.6

Find 17 sgRNAs with CRISPR-Local

Find 82 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CCAAACTAACAGATTCATTT+TGG 0.150883 5.2:+75600020 MS.gene37567:intron
TTTAGATGTTGCTCGAAAAT+TGG 0.248254 5.2:+75601352 MS.gene37567:CDS
AAAGTCAGAGGCTGCTAAAA+AGG 0.332380 5.2:+75600051 MS.gene37567:CDS
AGATCCAGGTGTTAATTGTC+TGG 0.439476 5.2:-75599696 None:intergenic
TTAACACCTGGATCTGGATC+TGG 0.464092 5.2:+75599704 MS.gene37567:CDS
AGACAATTAACACCTGGATC+TGG 0.479178 5.2:+75599698 MS.gene37567:CDS
GCAGATCCAGATCCAGATCC+AGG 0.505288 5.2:-75599710 None:intergenic
TGCATGGAATGAAAAGGATA+AGG 0.508203 5.2:+75599837 MS.gene37567:CDS
TATCACTGCAGCTAAATGAA+TGG 0.519982 5.2:+75599809 MS.gene37567:intron
ATCTGGATCTGCACAGGAAG+AGG 0.529978 5.2:+75599721 MS.gene37567:CDS
ATCTGGATCTGGATCTGCAC+AGG 0.538020 5.2:+75599715 MS.gene37567:CDS
GCATGATGCATGGAATGAAA+AGG 0.553411 5.2:+75599831 MS.gene37567:CDS
TTGGAACAAGCTAAAGTCAG+AGG 0.617833 5.2:+75600039 MS.gene37567:CDS
ACAGGTTGGTACAGAAGAAG+CGG 0.620709 5.2:+75600921 MS.gene37567:intron
TAAATGAATGGCATGATGCA+TGG 0.637004 5.2:+75599821 MS.gene37567:CDS
TCATCCAGACAATTAACACC+TGG 0.646730 5.2:+75599692 MS.gene37567:CDS
AATCAAGGAATCAACAAACA+TGG 0.667146 5.2:+75599868 MS.gene37567:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! ATATAAATGAATAAAATTGA+TGG + chr5.2:75601229-75601248 MS.gene37567:intron 10.0%
!! TTGTTCTTAATTATTAAAAA+TGG + chr5.2:75600133-75600152 MS.gene37567:intron 10.0%
!!! ATTTTTAATAATTAAGAACA+AGG - chr5.2:75600134-75600153 None:intergenic 10.0%
!!! TAAAACAATAAAAGAATTTT+TGG - chr5.2:75601306-75601325 None:intergenic 10.0%
!!! TTTTATTCATTTATATTTTC+TGG - chr5.2:75601225-75601244 None:intergenic 10.0%
!!! TTTTATTGTTTTATTTCTTT+AGG + chr5.2:75601313-75601332 MS.gene37567:intron 10.0%
!! ATAGCAACATTATAAATTAT+AGG + chr5.2:75600226-75600245 MS.gene37567:intron 15.0%
!!! AAATGAACATTTTGTTTTTT+AGG + chr5.2:75601096-75601115 MS.gene37567:intron 15.0%
!!! AATGAACATTTTGTTTTTTA+GGG + chr5.2:75601097-75601116 MS.gene37567:intron 15.0%
!!! GTTTAAATGATTATCATTTT+GGG + chr5.2:75600989-75601008 MS.gene37567:intron 15.0%
!! AAAATCAAAGTAATTCAAAC+TGG - chr5.2:75600375-75600394 None:intergenic 20.0%
!! AAATCAAAGTAATTCAAACT+GGG - chr5.2:75600374-75600393 None:intergenic 20.0%
!! ATAATTAAGAACAAGGATAA+TGG - chr5.2:75600127-75600146 None:intergenic 20.0%
!! ATTTATAGAAAGTAGTTTCT+TGG + chr5.2:75601051-75601070 MS.gene37567:intron 20.0%
!! TTGAAAGTTTCATTTAATGA+TGG + chr5.2:75600575-75600594 MS.gene37567:intron 20.0%
!!! ATGAACATTTTGTTTTTTAG+GGG + chr5.2:75601098-75601117 MS.gene37567:intron 20.0%
!!! CGTTTAAATGATTATCATTT+TGG + chr5.2:75600988-75601007 MS.gene37567:intron 20.0%
!!! TTATATTTTCTGGAATTTCA+TGG - chr5.2:75601215-75601234 None:intergenic 20.0%
!!! TTCTTTCATAGAAAGTATTA+TGG + chr5.2:75601014-75601033 MS.gene37567:intron 20.0%
! AACATAGCACATGTTTATAT+TGG + chr5.2:75600156-75600175 MS.gene37567:intron 25.0%
! ATGTAAGGAAAAAGTAAACA+AGG - chr5.2:75600196-75600215 None:intergenic 25.0%
! ATTGGTTATAATGTTTCAAC+AGG + chr5.2:75600903-75600922 MS.gene37567:intron 25.0%
! TGTAAGGAAAAAGTAAACAA+GGG - chr5.2:75600195-75600214 None:intergenic 25.0%
!! AAAATGAATCTGTTAGTTTG+GGG - chr5.2:75600021-75600040 None:intergenic 25.0%
!! AAAGAAGTCTTTCATTGATT+AGG + chr5.2:75601129-75601148 MS.gene37567:intron 25.0%
!! ATTTTGTTACAACAATCAAC+TGG + chr5.2:75599957-75599976 MS.gene37567:intron 25.0%
!! CAAAATGAATCTGTTAGTTT+GGG - chr5.2:75600022-75600041 None:intergenic 25.0%
!! GATGTATTTGTTGAACAATA+AGG - chr5.2:75599906-75599925 None:intergenic 25.0%
!! TAATCAGCTTCAAACTTTTA+AGG - chr5.2:75600258-75600277 None:intergenic 25.0%
!!! GTTGATGATTTTGTAAAGAT+AGG + chr5.2:75600606-75600625 MS.gene37567:intron 25.0%
AAAGTAATTCAAACTGGGTT+TGG - chr5.2:75600369-75600388 None:intergenic 30.0%
AAATTGTCACACGCATAAAT+AGG + chr5.2:75600741-75600760 MS.gene37567:intron 30.0%
AATCAAGGAATCAACAAACA+TGG + chr5.2:75599868-75599887 MS.gene37567:CDS 30.0%
AATTGTCACACGCATAAATA+GGG + chr5.2:75600742-75600761 MS.gene37567:intron 30.0%
ATAAAAATTCTTGTCCCATC+TGG + chr5.2:75600463-75600482 MS.gene37567:intron 30.0%
ATTTATGCGTGTGACAATTT+AGG - chr5.2:75600741-75600760 None:intergenic 30.0%
CCAAAATGAATCTGTTAGTT+TGG - chr5.2:75600023-75600042 None:intergenic 30.0%
GCTATAGAGATTGAAATGTA+AGG - chr5.2:75600211-75600230 None:intergenic 30.0%
GTATGCATGTAAAAATAAGC+AGG - chr5.2:75600090-75600109 None:intergenic 30.0%
GTTATAATGTTTCAACAGGT+TGG + chr5.2:75600907-75600926 MS.gene37567:intron 30.0%
TCTCTTTATCATGTTTGTGA+AGG + chr5.2:75600705-75600724 MS.gene37567:intron 30.0%
TTTAGATGTTGCTCGAAAAT+TGG + chr5.2:75601352-75601371 MS.gene37567:CDS 30.0%
! CCAAACTAACAGATTCATTT+TGG + chr5.2:75600020-75600039 MS.gene37567:intron 30.0%
!! GATAAGGATTTTGAGAATCA+AGG + chr5.2:75599853-75599872 MS.gene37567:CDS 30.0%
!!! ATTTTTTTCACATGCCAGAT+GGG - chr5.2:75600480-75600499 None:intergenic 30.0%
AGGGATAAAAGATAAGTGAG+AGG + chr5.2:75600761-75600780 MS.gene37567:intron 35.0%
GGATAAAAGATAAGTGAGAG+GGG + chr5.2:75600763-75600782 MS.gene37567:intron 35.0%
GGGATAAAAGATAAGTGAGA+GGG + chr5.2:75600762-75600781 MS.gene37567:intron 35.0%
TAAATGAATGGCATGATGCA+TGG + chr5.2:75599821-75599840 MS.gene37567:CDS 35.0%
TATCACTGCAGCTAAATGAA+TGG + chr5.2:75599809-75599828 MS.gene37567:intron 35.0%
TGCATGGAATGAAAAGGATA+AGG + chr5.2:75599837-75599856 MS.gene37567:CDS 35.0%
!!! CATTTTTTTCACATGCCAGA+TGG - chr5.2:75600481-75600500 None:intergenic 35.0%
AAAGTCAGAGGCTGCTAAAA+AGG + chr5.2:75600051-75600070 MS.gene37567:CDS 40.0%
AGACAATTAACACCTGGATC+TGG + chr5.2:75599698-75599717 MS.gene37567:CDS 40.0%
AGATCCAGGTGTTAATTGTC+TGG - chr5.2:75599699-75599718 None:intergenic 40.0%
GCATGATGCATGGAATGAAA+AGG + chr5.2:75599831-75599850 MS.gene37567:CDS 40.0%
TAGAATGACACTACGCTCAT+TGG + chr5.2:75600885-75600904 MS.gene37567:intron 40.0%
TCATCCAGACAATTAACACC+TGG + chr5.2:75599692-75599711 MS.gene37567:CDS 40.0%
TTGGAACAAGCTAAAGTCAG+AGG + chr5.2:75600039-75600058 MS.gene37567:CDS 40.0%
! AGAAGCGGAAAGATTTTGCA+AGG + chr5.2:75600936-75600955 MS.gene37567:CDS 40.0%
! ATAGGCGAGATTGTTGTTGT+AGG + chr5.2:75600624-75600643 MS.gene37567:intron 40.0%
! CTAGGGTGTTATAACTGTGA+TGG + chr5.2:75600801-75600820 MS.gene37567:intron 40.0%
AAACCAAGTCTACTGGTCAC+TGG - chr5.2:75600545-75600564 None:intergenic 45.0%
TGCATGCAAACCAAGTCTAC+TGG - chr5.2:75600552-75600571 None:intergenic 45.0%
TGGTTCCAAAGGAAGGACTA+AGG - chr5.2:75600525-75600544 None:intergenic 45.0%
TTAACACCTGGATCTGGATC+TGG + chr5.2:75599704-75599723 MS.gene37567:CDS 45.0%
TTCCAAAGGAAGGACTAAGG+AGG - chr5.2:75600522-75600541 None:intergenic 45.0%
!! ACAGGTTGGTACAGAAGAAG+CGG + chr5.2:75600921-75600940 MS.gene37567:intron 45.0%
AAGGAAGGACTAAGGAGGCA+AGG - chr5.2:75600517-75600536 None:intergenic 50.0%
ATCTGGATCTGCACAGGAAG+AGG + chr5.2:75599721-75599740 MS.gene37567:CDS 50.0%
ATCTGGATCTGGATCTGCAC+AGG + chr5.2:75599715-75599734 MS.gene37567:CDS 50.0%
GAACCAGTGACCAGTAGACT+TGG + chr5.2:75600539-75600558 MS.gene37567:intron 50.0%
GGTACATGTGTGTTGGGCTA+GGG + chr5.2:75600784-75600803 MS.gene37567:intron 50.0%
TGCACAGGAAGAGGTAGTTG+TGG + chr5.2:75599730-75599749 MS.gene37567:intron 50.0%
TGCCTCCTTAGTCCTTCCTT+TGG + chr5.2:75600517-75600536 MS.gene37567:intron 50.0%
! CTGTGATGGTGATGTTGCAG+AGG + chr5.2:75600815-75600834 MS.gene37567:intron 50.0%
! GAGAGGGGTACATGTGTGTT+GGG + chr5.2:75600778-75600797 MS.gene37567:intron 50.0%
! TGAGAGGGGTACATGTGTGT+TGG + chr5.2:75600777-75600796 MS.gene37567:intron 50.0%
!! CTACTGGTCACTGGTTCCAA+AGG - chr5.2:75600536-75600555 None:intergenic 50.0%
!! TGGTCACTGGTTCCAAAGGA+AGG - chr5.2:75600532-75600551 None:intergenic 50.0%
GCAGATCCAGATCCAGATCC+AGG - chr5.2:75599713-75599732 None:intergenic 55.0%
GGGTACATGTGTGTTGGGCT+AGG + chr5.2:75600783-75600802 MS.gene37567:intron 55.0%


Chromosome Type Strat End Strand Name
chr5.2 gene 75599674 75601388 75599674 ID=MS.gene37567
chr5.2 mRNA 75599674 75601388 75599674 ID=MS.gene37567.t1;Parent=MS.gene37567
chr5.2 exon 75599674 75599742 75599674 ID=MS.gene37567.t1.exon1;Parent=MS.gene37567.t1
chr5.2 CDS 75599674 75599742 75599674 ID=cds.MS.gene37567.t1;Parent=MS.gene37567.t1
chr5.2 exon 75599820 75599889 75599820 ID=MS.gene37567.t1.exon2;Parent=MS.gene37567.t1
chr5.2 CDS 75599820 75599889 75599820 ID=cds.MS.gene37567.t1;Parent=MS.gene37567.t1
chr5.2 exon 75600032 75600072 75600032 ID=MS.gene37567.t1.exon3;Parent=MS.gene37567.t1
chr5.2 CDS 75600032 75600072 75600032 ID=cds.MS.gene37567.t1;Parent=MS.gene37567.t1
chr5.2 exon 75600925 75600984 75600925 ID=MS.gene37567.t1.exon4;Parent=MS.gene37567.t1
chr5.2 CDS 75600925 75600984 75600925 ID=cds.MS.gene37567.t1;Parent=MS.gene37567.t1
chr5.2 exon 75601335 75601388 75601335 ID=MS.gene37567.t1.exon5;Parent=MS.gene37567.t1
chr5.2 CDS 75601335 75601388 75601335 ID=cds.MS.gene37567.t1;Parent=MS.gene37567.t1
Gene Sequence

>MS.gene37567

GAAGAATCATCATCATCATCATCCAGACAATTAACACCTGGATCTGGATCTGGATCTGCACAGGAAGAGGTAGTTGTGGTGAAATTGCTGTGTGTATTGATGTCTGTGTAAACATATAATGCTGTCTAACAAACTTATCACTGCAGCTAAATGAATGGCATGATGCATGGAATGAAAAGGATAAGGATTTTGAGAATCAAGGAATCAACAAACATGGTATCACATATAACCTTATTGTTCAACAAATACATCAAAATTCACGAGTTTCTGAGCAATATTGTTAATTTTGTTACAACAATCAACTGGACTGTGTTTTGTAAATTAATGATTTGCTTATGTGCATTCCCCAAACTAACAGATTCATTTTGGAACAAGCTAAAGTCAGAGGCTGCTAAAAAGGTTTTTTAAATTCTCCTGCTTATTTTTACATGCATACTGATTTTTGTGCTACCATTATCCTTGTTCTTAATTATTAAAAATGGAACATAGCACATGTTTATATTGGAAATTTTCTTGTGCCCTTGTTTACTTTTTCCTTACATTTCAATCTCTATAGCAACATTATAAATTATAGGCTTTAACCTTAAAAGTTTGAAGCTGATTATATGAGCTTTTAACTGAAACTAATTGCAATGCTAGATAGATTCTCTTTATATTCAATTCTAAAGCTTTTTTTTTTCTCAACAACACTTCCAAACCCAGTTTGAATTACTTTGATTTTCATTTATGCATTAGTTAAACTTAAATATTATATTCTTAATTGATTAAACACAAACTCTGTCTTTCTATATAAAAATTCTTGTCCCATCTGGCATGTGAAAAAAATGTAGACTCTTGCATCCTTGCCTCCTTAGTCCTTCCTTTGGAACCAGTGACCAGTAGACTTGGTTTGCATGCATAATTGAAAGTTTCATTTAATGATGGACATTTATGTTGATGATTTTGTAAAGATAGGCGAGATTGTTGTTGTAGGAGAAAAGCATTTTTGTCTATCACTTATATGCATGAACATTCTTTAGTTGTCTTCTTTTTCTCTTTATCATGTTTGTGAAGGTATAATTAAACCTAAATTGTCACACGCATAAATAGGGATAAAAGATAAGTGAGAGGGGTACATGTGTGTTGGGCTAGGGTGTTATAACTGTGATGGTGATGTTGCAGAGGATTTATGTCATTTATATGTCATTGTTAAATTAGCTATCAAGAAGACTTAGAATGACACTACGCTCATTGGTTATAATGTTTCAACAGGTTGGTACAGAAGAAGCGGAAAGATTTTGCAAGGCGTTTCAACAAATTCATAAGAGACTAGTACGTTTAAATGATTATCATTTTGGGCATTCTTTCATAGAAAGTATTATGGAAGACTTTTTATTTATTTATAGAAAGTAGTTTCTTGGAAAGCATATTTATTTTCATCGAAAATGAACATTTTGTTTTTTAGGGGTCTTCTTGAAAGAAGTCTTTCATTGATTAGGAAAATAATTTTTTGAACTGCATATTTGCAACAAATATAGAAAATAATATATTTATTTTCTCCATGAAATTCCAGAAAATATAAATGAATAAAATTGATGGCTCATTAAATCAATTGAAACTGAGTTTATGTTGCTATTATATCGTGTTTAACCAAAAATTCTTTTATTGTTTTATTTCTTTAGGTCAATGAAGAGTTAAGTTTAGATGTTGCTCGAAAATTGGTAAACTCATCCTAA

Protein sequence

>MS.gene37567.t1

EESSSSSSRQLTPGSGSGSAQEELNEWHDAWNEKDKDFENQGINKHDSFWNKLKSEAAKKVGTEEAERFCKAFQQIHKRLVNEELSLDVARKLVNSS