AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene53530

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene53530.t1 MTR_1g045040 86.555 119 16 0 1 119 1 119 8.62e-67 198
MS.gene53530.t1 MTR_1g089830 75.833 120 22 2 1 119 1 114 6.28e-61 183
MS.gene53530.t1 MTR_8g089170 37.324 142 63 3 6 122 7 147 6.72e-20 80.1
MS.gene53530.t1 MTR_8g089130 34.266 143 68 3 6 122 7 149 4.10e-18 75.5
MS.gene53530.t1 MTR_8g039350 70.732 41 12 0 4 44 15 55 8.06e-17 69.7
MS.gene53530.t1 MTR_5g013370 50.000 54 26 1 3 56 12 64 4.42e-11 58.9
MS.gene53530.t1 MTR_5g013370 50.000 54 26 1 3 56 12 64 6.65e-11 58.5
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 19 sgRNAs with CRISPR-Local

Find 49 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
AACAAAAGCTTCAAAGTCTA+TGG 0.184389 1.2:+27891836 MS.gene53530:CDS
CGCTTGTGGACTACATTTCA+AGG 0.405648 1.2:+27891193 MS.gene53530:CDS
TGGAGTTTGGTTTGAAAGCT+CGG 0.432563 1.2:-27891306 None:intergenic
CCACAAGCGTTACATAGTAT+TGG 0.448818 1.2:-27891179 None:intergenic
GAAACTAAACTTTGGCGTAA+AGG 0.456777 1.2:+27891143 MS.gene53530:CDS
ATCAGACCTTGACGTTGAAA+AGG 0.465983 1.2:+27891268 MS.gene53530:CDS
GGACTACATTTCAAGGCTAA+AGG 0.474721 1.2:+27891200 MS.gene53530:CDS
TGTATACCAAGCAATGAGAT+AGG 0.479877 1.2:+27891925 MS.gene53530:CDS
CATAGTATTGGCTTCTCATA+CGG 0.490978 1.2:-27891167 None:intergenic
ATCGATTGTGAAGAATCAAA+TGG 0.491491 1.2:+27891804 MS.gene53530:CDS
GGAGTTTGGTTTGAAAGCTC+GGG 0.497343 1.2:-27891305 None:intergenic
CTTTGGAAGATAGTTATCAA+TGG 0.499183 1.2:-27891225 None:intergenic
ATTTGATTCTTCACAATCGA+TGG 0.523804 1.2:-27891802 None:intergenic
TCCAAGCCTATCTCATTGCT+TGG 0.532760 1.2:-27891931 None:intergenic
ACCAAGCAATGAGATAGGCT+TGG 0.538476 1.2:+27891930 MS.gene53530:CDS
ACAAAAGCTTCAAAGTCTAT+GGG 0.556384 1.2:+27891837 MS.gene53530:CDS
GAGCTTTCAAACCAAACTCC+AGG 0.591419 1.2:+27891308 MS.gene53530:CDS
CCAATACTATGTAACGCTTG+TGG 0.608782 1.2:+27891179 MS.gene53530:CDS
GATTGTGAAGAATCAAATGG+AGG 0.680011 1.2:+27891807 MS.gene53530:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! AATTTTAATTTTTTGTAGAA+AGG + chr1.2:27891776-27891795 MS.gene53530:intron 10.0%
!! AAATAGATGATATAAAATGG+AGG - chr1.2:27891411-27891430 None:intergenic 20.0%
!! AAATATATGCTATTAAAGTG+TGG - chr1.2:27891691-27891710 None:intergenic 20.0%
!! AACACTACTATTTATATATG+AGG + chr1.2:27891454-27891473 MS.gene53530:intron 20.0%
!! AATAGATGATATAAAATGGA+GGG - chr1.2:27891410-27891429 None:intergenic 20.0%
!! GGAAAATAGATGATATAAAA+TGG - chr1.2:27891414-27891433 None:intergenic 20.0%
!! TTAGATCAATGCATTATTAA+AGG - chr1.2:27891435-27891454 None:intergenic 20.0%
!!! TATTGCATTTTTTTATTACC+TGG - chr1.2:27891329-27891348 None:intergenic 20.0%
!!! TTTGAATGAATTGTATTGAT+GGG + chr1.2:27891548-27891567 MS.gene53530:intron 20.0%
!!! TTTTGAATGAATTGTATTGA+TGG + chr1.2:27891547-27891566 MS.gene53530:intron 20.0%
! ATTGACAATGAAAGGAATTA+GGG - chr1.2:27891494-27891513 None:intergenic 25.0%
! GATATAAGATTGAGATTGAT+TGG - chr1.2:27891669-27891688 None:intergenic 25.0%
! TATCCATAAATGTATGAATG+TGG - chr1.2:27891597-27891616 None:intergenic 25.0%
! TATTGACAATGAAAGGAATT+AGG - chr1.2:27891495-27891514 None:intergenic 25.0%
! TTATATGTATACATCGTACA+CGG - chr1.2:27891756-27891775 None:intergenic 25.0%
!! TTGAATGAATTGTATTGATG+GGG + chr1.2:27891549-27891568 MS.gene53530:intron 25.0%
!! TTTTGACAGAAACTAAACTT+TGG + chr1.2:27891135-27891154 MS.gene53530:CDS 25.0%
!!! TTTTTTTATTACCTGGAGTT+TGG - chr1.2:27891322-27891341 None:intergenic 25.0%
AAATACAACAAGAGATTGGT+TGG + chr1.2:27891632-27891651 MS.gene53530:intron 30.0%
AACAAAAGCTTCAAAGTCTA+TGG + chr1.2:27891836-27891855 MS.gene53530:CDS 30.0%
ACAAAAGCTTCAAAGTCTAT+GGG + chr1.2:27891837-27891856 MS.gene53530:CDS 30.0%
ACTCCACATTCATACATTTA+TGG + chr1.2:27891591-27891610 MS.gene53530:intron 30.0%
ATCGATTGTGAAGAATCAAA+TGG + chr1.2:27891804-27891823 MS.gene53530:CDS 30.0%
ATGCAAATACAACAAGAGAT+TGG + chr1.2:27891628-27891647 MS.gene53530:intron 30.0%
ATGCTCTTATTGACAATGAA+AGG - chr1.2:27891502-27891521 None:intergenic 30.0%
ATTTGATTCTTCACAATCGA+TGG - chr1.2:27891805-27891824 None:intergenic 30.0%
! CTTTGGAAGATAGTTATCAA+TGG - chr1.2:27891228-27891247 None:intergenic 30.0%
!! GTCTGATAACTGATTTTGTT+GGG - chr1.2:27891255-27891274 None:intergenic 30.0%
GAAACTAAACTTTGGCGTAA+AGG + chr1.2:27891143-27891162 MS.gene53530:CDS 35.0%
GATTGTGAAGAATCAAATGG+AGG + chr1.2:27891807-27891826 MS.gene53530:CDS 35.0%
TGTATACCAAGCAATGAGAT+AGG + chr1.2:27891925-27891944 MS.gene53530:CDS 35.0%
! GAATTGTATTGATGGGGATT+AGG + chr1.2:27891555-27891574 MS.gene53530:intron 35.0%
! TGATTTTGTTGGGATGTCTT+TGG - chr1.2:27891245-27891264 None:intergenic 35.0%
!! CATAGTATTGGCTTCTCATA+CGG - chr1.2:27891170-27891189 None:intergenic 35.0%
!! GGTCTGATAACTGATTTTGT+TGG - chr1.2:27891256-27891275 None:intergenic 35.0%
AGCATTCATTTGCGTAGACA+CGG + chr1.2:27891517-27891536 MS.gene53530:intron 40.0%
ATCAGACCTTGACGTTGAAA+AGG + chr1.2:27891268-27891287 MS.gene53530:CDS 40.0%
ATTTGCGTAGACACGGTATT+AGG + chr1.2:27891524-27891543 MS.gene53530:intron 40.0%
CCAATACTATGTAACGCTTG+TGG + chr1.2:27891179-27891198 MS.gene53530:CDS 40.0%
CCACAAGCGTTACATAGTAT+TGG - chr1.2:27891182-27891201 None:intergenic 40.0%
GGACTACATTTCAAGGCTAA+AGG + chr1.2:27891200-27891219 MS.gene53530:CDS 40.0%
TCGTACACGGTACATATCAA+TGG - chr1.2:27891743-27891762 None:intergenic 40.0%
! CAGATTCCTTTTCAACGTCA+AGG - chr1.2:27891277-27891296 None:intergenic 40.0%
!! TGGAGTTTGGTTTGAAAGCT+CGG - chr1.2:27891309-27891328 None:intergenic 40.0%
ACCAAGCAATGAGATAGGCT+TGG + chr1.2:27891930-27891949 MS.gene53530:CDS 45.0%
GAGCTTTCAAACCAAACTCC+AGG + chr1.2:27891308-27891327 MS.gene53530:CDS 45.0%
TCCAAGCCTATCTCATTGCT+TGG - chr1.2:27891934-27891953 None:intergenic 45.0%
! CGCTTGTGGACTACATTTCA+AGG + chr1.2:27891193-27891212 MS.gene53530:CDS 45.0%
!! GGAGTTTGGTTTGAAAGCTC+GGG - chr1.2:27891308-27891327 None:intergenic 45.0%


Chromosome Type Strat End Strand Name
chr1.2 gene 27891131 27891966 27891131 ID=MS.gene53530
chr1.2 mRNA 27891131 27891966 27891131 ID=MS.gene53530.t1;Parent=MS.gene53530
chr1.2 exon 27891131 27891329 27891131 ID=MS.gene53530.t1.exon1;Parent=MS.gene53530.t1
chr1.2 CDS 27891131 27891329 27891131 ID=cds.MS.gene53530.t1;Parent=MS.gene53530.t1
chr1.2 exon 27891794 27891966 27891794 ID=MS.gene53530.t1.exon2;Parent=MS.gene53530.t1
chr1.2 CDS 27891794 27891966 27891794 ID=cds.MS.gene53530.t1;Parent=MS.gene53530.t1
Gene Sequence

>MS.gene53530

ATGGTTTTGACAGAAACTAAACTTTGGCGTAAAGGACCGTATGAGAAGCCAATACTATGTAACGCTTGTGGACTACATTTCAAGGCTAAAGGAACCATTGATAACTATCTTCCAAAGACATCCCAACAAAATCAGTTATCAGACCTTGACGTTGAAAAGGAATCTGAAAGTGATCCCGAGCTTTCAAACCAAACTCCAGGTAATAAAAAAATGCAATAAGTTAATTAACTATTCACTCGATTTTTCAACAAATGTAAAGCACAATTTATACAATTTCCCTCCATTTTATATCATCTATTTTCCTTTAATAATGCATTGATCTAAACACTACTATTTATATATGAGGTGTAACATTATCAACCCTAATTCCTTTCATTGTCAATAAGAGCATTCATTTGCGTAGACACGGTATTAGGTTTTGAATGAATTGTATTGATGGGGATTAGGTGACATACATACAACTCCACATTCATACATTTATGGATATATTTGTGCTAATGCAAATACAACAAGAGATTGGTTGGTATATGATTGACCAATCAATCTCAATCTTATATCCACACTTTAATAGCATATATTTTTTTTCAAATAATACATATAAATGATTATCCATTGATATGTACCGTGTACGATGTATACATATAAAATTTTAATTTTTTGTAGAAAGGACACCATCGATTGTGAAGAATCAAATGGAGGAGTTTCAACAAAAGCTTCAAAGTCTATGGGAATCTGAGAAAGAATCAAATGAATCATCTGCAGACAATATTTTGTTGTTTGATAATATGAACAACTGTATACCAAGCAATGAGATAGGCTTGGATGCACTCTACTGA
Protein sequence

>MS.gene53530.t1

MVLTETKLWRKGPYEKPILCNACGLHFKAKGTIDNYLPKTSQQNQLSDLDVEKESESDPELSNQTPERTPSIVKNQMEEFQQKLQSLWESEKESNESSADNILLFDNMNNCIPSNEIGLDALY