AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene97402

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene97402.t1 MTR_1g060700 91.324 219 10 5 1 215 274 487 9.30e-133 382
MS.gene97402.t1 MTR_2g067000 88.636 220 20 3 1 215 79 298 7.89e-125 355
MS.gene97402.t1 MTR_8g093500 58.491 53 22 0 85 137 125 177 7.11e-13 66.2
MS.gene97402.t1 MTR_3g101810 58.491 53 22 0 85 137 182 234 2.09e-12 65.1
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene97402.t1 AT1G30670 37.273 220 119 6 3 208 48 262 5.76e-29 109
MS.gene97402.t1 AT2G34820 40.000 225 101 7 2 208 81 289 2.85e-26 102
MS.gene97402.t1 AT3G21330 60.377 53 21 0 85 137 280 332 2.01e-13 68.6
MS.gene97402.t1 AT5G01305 37.500 96 51 2 85 177 48 137 1.07e-12 64.3
MS.gene97402.t1 AT4G00120 52.830 53 25 0 85 137 123 175 2.47e-11 60.8

Find 38 sgRNAs with CRISPR-Local

Find 75 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
ATCATTATGATTGCTCAATT+TGG 0.191234 2.4:+34118642 None:intergenic
AGTTGGAATGCTTCAACTTA+TGG 0.195386 2.4:-34119579 MS.gene97402:CDS
ATCTCTGCTGTGTTCATCTT+TGG 0.238213 2.4:+34119644 None:intergenic
AATTTGGTGACAAACTCTTT+TGG 0.289383 2.4:+34118658 None:intergenic
CCTCATAGTATAGCAGCTTT+TGG 0.317037 2.4:+34119906 None:intergenic
TACAATTTCTCTTGAACAAA+TGG 0.348402 2.4:+34118703 None:intergenic
ATCAAAACCTACCATCCTTA+AGG 0.361760 2.4:-34118614 MS.gene97402:CDS
AAATAACACTATTCTTGCTT+TGG 0.365183 2.4:+34118553 None:intergenic
TCAAAGGAAGCAAAAGGGTT+AGG 0.369513 2.4:+34119812 None:intergenic
TTGATTATTTCAGGAAGAAA+AGG 0.418378 2.4:-34118767 MS.gene97402:intron
GAGCTAGGGAAGTTGGTTCC+TGG 0.426916 2.4:-34119671 MS.gene97402:CDS
CAAGCTGTTTCAGACCCTTA+AGG 0.427556 2.4:+34118599 None:intergenic
GACACAAGAGCTAGGGAAGT+TGG 0.431491 2.4:-34119678 MS.gene97402:CDS
AAAATGAAATCTTCCTCAGT+TGG 0.434948 2.4:+34119959 None:intergenic
TCAAAACCTACCATCCTTAA+GGG 0.456430 2.4:-34118613 MS.gene97402:CDS
AAGGGTCTGAAACAGCTTGT+TGG 0.460418 2.4:-34118595 MS.gene97402:CDS
CAAAGGAAGCAAAAGGGTTA+GGG 0.461232 2.4:+34119813 None:intergenic
TCTGTCTCAAAGGAAGCAAA+AGG 0.462646 2.4:+34119806 None:intergenic
TTGTGTAGATCTTCACTTGG+AGG 0.465635 2.4:+34118739 None:intergenic
AAATGAAATCTTCCTCAGTT+GGG 0.470627 2.4:+34119960 None:intergenic
GTTCAATGTGAGAAGAAAGT+TGG 0.488552 2.4:-34119764 MS.gene97402:CDS
TGTAGATCTTCACTTGGAGG+AGG 0.494574 2.4:+34118742 None:intergenic
GTGTTCATCTTTGGTCCACC+AGG 0.499817 2.4:+34119653 None:intergenic
AGAGTATCGCGGCTCGAGAA+AGG 0.514420 2.4:-34119721 MS.gene97402:CDS
ACTGAGAAGACACAAGAGCT+AGG 0.516284 2.4:-34119686 MS.gene97402:CDS
CCAAAAGCTGCTATACTATG+AGG 0.553268 2.4:-34119906 MS.gene97402:CDS
AGTTTGTGTAGATCTTCACT+TGG 0.558027 2.4:+34118736 None:intergenic
TCGCGGCTCGAGAAAGGAGA+AGG 0.564993 2.4:-34119715 MS.gene97402:CDS
GTGAGAAGAAAGTTGGTGAA+AGG 0.566992 2.4:-34119757 MS.gene97402:CDS
AAGTTTCTTCAAGCTCAAGT+TGG 0.567049 2.4:-34119596 MS.gene97402:CDS
GAGTTCAAAAGCTCTTGTTG+TGG 0.567814 2.4:+34119869 None:intergenic
ACTTATGGAAACATTTAGCA+AGG 0.569731 2.4:-34119564 MS.gene97402:intron
TTCAGACCCTTAAGGATGGT+AGG 0.578594 2.4:+34118607 None:intergenic
CTGAGAAGACACAAGAGCTA+GGG 0.585998 2.4:-34119685 MS.gene97402:CDS
CTGTCTCAAAGGAAGCAAAA+GGG 0.598011 2.4:+34119807 None:intergenic
CTAGGGAAGTTGGTTCCTGG+TGG 0.615915 2.4:-34119668 MS.gene97402:CDS
CTGTTTCAGACCCTTAAGGA+TGG 0.616344 2.4:+34118603 None:intergenic
TATCTCGTCGCAGAGTATCG+CGG 0.698927 2.4:-34119732 MS.gene97402:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! ATCTTTGTAAATATCTAAAA+TGG - chr2.4:34119172-34119191 MS.gene97402:intron 15.0%
!!! CACTATTAATTTTATTTTCT+AGG + chr2.4:34119650-34119669 None:intergenic 15.0%
!! ACTAACTAAATCTACAATAA+TGG + chr2.4:34119207-34119226 None:intergenic 20.0%
!! GAATATTTAAAAACAAAGAG+TGG + chr2.4:34119540-34119559 None:intergenic 20.0%
!! TTATTGTATAAAGTTACACT+AGG + chr2.4:34119697-34119716 None:intergenic 20.0%
!!! AATATTTTCAGAGTAAAAGT+AGG + chr2.4:34119302-34119321 None:intergenic 20.0%
!!! ATATGATCATTGATTATTTC+AGG - chr2.4:34119759-34119778 MS.gene97402:CDS 20.0%
!!! CTTTTACTCTGAAAATATTT+AGG - chr2.4:34119303-34119322 MS.gene97402:intron 20.0%
! AAACTCATCCACAAAAAAAT+TGG + chr2.4:34118694-34118713 None:intergenic 25.0%
! ATCATTATGATTGCTCAATT+TGG + chr2.4:34119896-34119915 None:intergenic 25.0%
! TACAATTTCTCTTGAACAAA+TGG + chr2.4:34119835-34119854 None:intergenic 25.0%
! TTAGGAACAACAATTGTATA+TGG - chr2.4:34119483-34119502 MS.gene97402:intron 25.0%
! TTGATTATTTCAGGAAGAAA+AGG - chr2.4:34119768-34119787 MS.gene97402:CDS 25.0%
!! TGAACAACATCAACAATTTT+TGG + chr2.4:34118756-34118775 None:intergenic 25.0%
!! TTTTATCAACATAAGACCTA+AGG + chr2.4:34119108-34119127 None:intergenic 25.0%
!!! CAATAAACAAGAGAGTATTT+AGG - chr2.4:34119465-34119484 MS.gene97402:intron 25.0%
AAAATGAAATCTTCCTCAGT+TGG + chr2.4:34118579-34118598 None:intergenic 30.0%
AAATGAAATCTTCCTCAGTT+GGG + chr2.4:34118578-34118597 None:intergenic 30.0%
ACTTATGGAAACATTTAGCA+AGG - chr2.4:34118971-34118990 MS.gene97402:intron 30.0%
TAATATCCTTCCAAGTGTTT+GGG + chr2.4:34119595-34119614 None:intergenic 30.0%
TTAATATCCTTCCAAGTGTT+TGG + chr2.4:34119596-34119615 None:intergenic 30.0%
! TATTTAGTTTCCCAAACACT+TGG - chr2.4:34119582-34119601 MS.gene97402:CDS 30.0%
!! AATTTGGTGACAAACTCTTT+TGG + chr2.4:34119880-34119899 None:intergenic 30.0%
!!! AATTTTTGGTTCTGTCTCAA+AGG + chr2.4:34118742-34118761 None:intergenic 30.0%
!!! GAACTCAACCAATTTTTTTG+TGG - chr2.4:34118683-34118702 MS.gene97402:CDS 30.0%
AAGTTTCTTCAAGCTCAAGT+TGG - chr2.4:34118939-34118958 MS.gene97402:intron 35.0%
AGTTGGAATGCTTCAACTTA+TGG - chr2.4:34118956-34118975 MS.gene97402:intron 35.0%
AGTTTGTGTAGATCTTCACT+TGG + chr2.4:34119802-34119821 None:intergenic 35.0%
ATCAAAACCTACCATCCTTA+AGG - chr2.4:34119921-34119940 MS.gene97402:CDS 35.0%
ATCAACATAAGACCTAAGGA+AGG + chr2.4:34119104-34119123 None:intergenic 35.0%
CAATTGTATATGGAATGAGC+TGG - chr2.4:34119493-34119512 MS.gene97402:intron 35.0%
CGGTTAATAAGAAGAGGAAA+TGG - chr2.4:34119441-34119460 MS.gene97402:intron 35.0%
GTTCAATGTGAGAAGAAAGT+TGG - chr2.4:34118771-34118790 MS.gene97402:intron 35.0%
TCAAAACCTACCATCCTTAA+GGG - chr2.4:34119922-34119941 MS.gene97402:CDS 35.0%
! GAATGAAATTTTCCCAACTG+AGG - chr2.4:34118563-34118582 MS.gene97402:CDS 35.0%
! TTTTCAGAGTAAAAGTAGGC+AGG + chr2.4:34119298-34119317 None:intergenic 35.0%
ATCTCTGCTGTGTTCATCTT+TGG + chr2.4:34118894-34118913 None:intergenic 40.0%
CAAAGGAAGCAAAAGGGTTA+GGG + chr2.4:34118725-34118744 None:intergenic 40.0%
CCAAAAGCTGCTATACTATG+AGG - chr2.4:34118629-34118648 MS.gene97402:CDS 40.0%
CTGTCTCAAAGGAAGCAAAA+GGG + chr2.4:34118731-34118750 None:intergenic 40.0%
GAGTTCAAAAGCTCTTGTTG+TGG + chr2.4:34118669-34118688 None:intergenic 40.0%
GGGAAACGGTTAATAAGAAG+AGG - chr2.4:34119435-34119454 MS.gene97402:intron 40.0%
TAGTTTCCCAAACACTTGGA+AGG - chr2.4:34119586-34119605 MS.gene97402:CDS 40.0%
TCAAAGGAAGCAAAAGGGTT+AGG + chr2.4:34118726-34118745 None:intergenic 40.0%
TCTGTCTCAAAGGAAGCAAA+AGG + chr2.4:34118732-34118751 None:intergenic 40.0%
TTGTGTAGATCTTCACTTGG+AGG + chr2.4:34119799-34119818 None:intergenic 40.0%
! ACTGTTTTGTGTCCTTCCTT+AGG - chr2.4:34119089-34119108 MS.gene97402:intron 40.0%
! CCTCATAGTATAGCAGCTTT+TGG + chr2.4:34118632-34118651 None:intergenic 40.0%
! TATAGCAGCTTTTGGCGTTT+TGG + chr2.4:34118624-34118643 None:intergenic 40.0%
!! GTGAGAAGAAAGTTGGTGAA+AGG - chr2.4:34118778-34118797 MS.gene97402:intron 40.0%
!! TAGGTGCTGAATCATGTCAT+GGG + chr2.4:34119631-34119650 None:intergenic 40.0%
ACTGAGAAGACACAAGAGCT+AGG - chr2.4:34118849-34118868 MS.gene97402:intron 45.0%
CTGAGAAGACACAAGAGCTA+GGG - chr2.4:34118850-34118869 MS.gene97402:intron 45.0%
CTGTTTCAGACCCTTAAGGA+TGG + chr2.4:34119935-34119954 None:intergenic 45.0%
TGAGCTGGCTATGTTCAACA+AGG - chr2.4:34119508-34119527 MS.gene97402:intron 45.0%
TGTAGATCTTCACTTGGAGG+AGG + chr2.4:34119796-34119815 None:intergenic 45.0%
TTCAGACCCTTAAGGATGGT+AGG + chr2.4:34119931-34119950 None:intergenic 45.0%
! AAGGGTCTGAAACAGCTTGT+TGG - chr2.4:34119940-34119959 MS.gene97402:CDS 45.0%
! CAAGCTGTTTCAGACCCTTA+AGG + chr2.4:34119939-34119958 None:intergenic 45.0%
!! AGCTTTTGGCGTTTTGGACA+TGG + chr2.4:34118618-34118637 None:intergenic 45.0%
!! CTAGGTGCTGAATCATGTCA+TGG + chr2.4:34119632-34119651 None:intergenic 45.0%
AGAGAGAGAGAGAGAGAGAG+AGG - chr2.4:34119345-34119364 MS.gene97402:intron 50.0%
AGAGAGAGAGAGAGAGAGAG+GGG - chr2.4:34119345-34119364 MS.gene97402:intron 50.0%
AGAGAGAGAGAGAGGGGTTA+GGG - chr2.4:34119415-34119434 MS.gene97402:intron 50.0%
AGAGAGAGGGGTTAGGGAAA+CGG - chr2.4:34119421-34119440 MS.gene97402:intron 50.0%
GACACAAGAGCTAGGGAAGT+TGG - chr2.4:34118857-34118876 MS.gene97402:intron 50.0%
GAGAGAGAGAGAGAGAGAGA+GGG - chr2.4:34119344-34119363 MS.gene97402:intron 50.0%
GTGTTCATCTTTGGTCCACC+AGG + chr2.4:34118885-34118904 None:intergenic 50.0%
!! TATCTCGTCGCAGAGTATCG+CGG - chr2.4:34118803-34118822 MS.gene97402:intron 50.0%
GAGAGAGAGAGAGAGGGGTT+AGG - chr2.4:34119414-34119433 MS.gene97402:intron 55.0%
! CTAGGGAAGTTGGTTCCTGG+TGG - chr2.4:34118867-34118886 MS.gene97402:intron 55.0%
! GAGCTAGGGAAGTTGGTTCC+TGG - chr2.4:34118864-34118883 MS.gene97402:intron 55.0%
!! AGAGTATCGCGGCTCGAGAA+AGG - chr2.4:34118814-34118833 MS.gene97402:intron 55.0%
!! GGCGTTTTGGACATGGAAGC+TGG + chr2.4:34118611-34118630 None:intergenic 55.0%
TCGCGGCTCGAGAAAGGAGA+AGG - chr2.4:34118820-34118839 MS.gene97402:intron 60.0%


Chromosome Type Strat End Strand Name
chr2.4 gene 34118561 34119996 34118561 ID=MS.gene97402
chr2.4 mRNA 34118561 34119996 34118561 ID=MS.gene97402.t1;Parent=MS.gene97402
chr2.4 exon 34119565 34119996 34119565 ID=MS.gene97402.t1.exon1;Parent=MS.gene97402.t1
chr2.4 CDS 34119565 34119996 34119565 ID=cds.MS.gene97402.t1;Parent=MS.gene97402.t1
chr2.4 exon 34118561 34118776 34118561 ID=MS.gene97402.t1.exon2;Parent=MS.gene97402.t1
chr2.4 CDS 34118561 34118776 34118561 ID=cds.MS.gene97402.t1;Parent=MS.gene97402.t1
Gene Sequence

>MS.gene97402

ATGAATGAAATTTTCCCAACTGAGGAAGATTTCATTTTCAACAACTACCAGCTTCCATGTCCAAAACGCCAAAAGCTGCTATACTATGAGGAGAAAAGAGAAGAGCCACAACAAGAGCTTTTGAACTCAACCAATTTTTTTGTGGATGAGTTTATGACTAACCCTAACCCTTTTGCTTCCTTTGAGACAGAACCAAAAATTGTTGATGTTGTTCAATGTGAGAAGAAAGTTGGTGAAAGGACTATCTCGTCGCAGAGTATCGCGGCTCGAGAAAGGAGAAGGAAGATAACTGAGAAGACACAAGAGCTAGGGAAGTTGGTTCCTGGTGGACCAAAGATGAACACAGCAGAGATGCTTCATGCTGCTGCTAATTATGTCAAGTTTCTTCAAGCTCAAGTTGGAATGCTTCAACTTATGGAAACATTTAGCAAGGTAACTCTTTTTGCTTTTTTATTGTTGCAATGTTCTTATATTATTAGAGCTCATAATTGAAGTTAATTACTTTTCTTCACTTGAGTTTCGATTTCAACTGTTTTGTGTCCTTCCTTAGGTCTTATGTTGATAAAAAAAAAATGATTATATGTCATTTTTCGTAGTGTGATTATGTATGTATCTTTGTAAATATCTAAAATGGATATTAATGCCATTATTGTAGATTTAGTTAGTTTTCTCATTTATGTGTGTAAAATAATCTATTATTGTCTCAATGTTGTCTTTTTTACATTTATTTTTTTCCTGCCTACTTTTACTCTGAAAATATTTAGGAATTGCTAAAAAAAAATTGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGGGGTTAGGGAAACGGTTAATAAGAAGAGGAAATGGTCAATAAACAAGAGAGTATTTAGGAACAACAATTGTATATGGAATGAGCTGGCTATGTTCAACAAGGAATTATCCACTCTTTGTTTTTAAATATTCATTATTTTTACTTTCTTTATTATATTTAGTTTCCCAAACACTTGGAAGGATATTAAAAAATTTATAATCCCATGACATGATTCAGCACCTAGAAAATAAAATTAATAGTGTAACATTTTTGTAAAAGCTAAATTCCTAGTGTAACTTTATACAATAAAATTAATTAATGCTTCGAATATTCATTCTCTTTTGTTTATATATATGATCATTGATTATTTCAGGAAGAAAAGGAACCTCCTCCAAGTGAAGATCTACACAAACTAGTTGTTTCTCCATTTGTTCAAGAGAAATTGTATTCAGAAGAAAAGTGCTTTGTTCCAAAAGAGTTTGTCACCAAATTGAGCAATCATAATGATGTTCAATCAAAACCTACCATCCTTAAGGGTCTGAAACAGCTTGTTGGAACTGAGATTGAGAAGAAACCAAAGCAAGAATAG
Protein sequence

>MS.gene97402.t1

MNEIFPTEEDFIFNNYQLPCPKRQKLLYYEEKREEPQQELLNSTNFFVDEFMTNPNPFASFETEPKIVDVVQCEKKVGERTISSQSIAARERRRKITEKTQELGKLVPGGPKMNTAEMLHAAANYVKFLQAQVGMLQLMETFSKEEKEPPPSEDLHKLVVSPFVQEKLYSEEKCFVPKEFVTKLSNHNDVQSKPTILKGLKQLVGTEIEKKPKQE