AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene89959

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene89959.t1 MTR_2g084815 75.824 91 22 0 1 91 1 91 1.31e-42 143
MS.gene89959.t1 MTR_2g084815 60.294 68 18 3 82 140 209 276 2.09e-13 66.6
MS.gene89959.t1 MTR_2g084815 56.489 131 53 1 1 131 1 127 4.72e-42 141
MS.gene89959.t1 MTR_2g084815 56.489 131 53 1 1 131 1 127 1.97e-41 139
MS.gene89959.t1 MTR_2g084815 64.545 110 35 1 1 110 1 106 3.09e-41 140
MS.gene89959.t1 MTR_2g084815 57.746 71 21 3 82 143 232 302 3.50e-13 66.2
MS.gene89959.t1 MTR_4g055440 50.000 98 49 0 1 98 5 102 3.49e-26 100
MS.gene89959.t1 MTR_4g055450 43.878 98 43 1 2 99 6 91 1.46e-17 79.0
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene89959.t1 AT5G03740 41.860 86 47 2 1 86 1 83 1.40e-16 75.5
MS.gene89959.t1 AT5G22650 42.697 89 47 2 1 89 1 85 7.72e-16 73.6
MS.gene89959.t1 AT5G22650 42.697 89 47 2 1 89 1 85 7.79e-16 73.6
MS.gene89959.t1 AT3G44750 37.736 106 53 3 1 96 1 103 2.34e-13 66.2
MS.gene89959.t1 AT3G44750 37.736 106 53 3 1 96 1 103 2.42e-13 66.2

Find 39 sgRNAs with CRISPR-Local

Find 85 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CACCGTTTCCAATGGAGTTT+TGG 0.171376 4.2:-47708638 None:intergenic
GTGGTTATTTACCTCGTATT+TGG 0.275316 4.2:-47708163 MS.gene89959:CDS
GAAATAAACACTCGCAGTTT+TGG 0.276973 4.2:+47708042 None:intergenic
AGGACATTCACCTCTGAAAA+TGG 0.279756 4.2:-47706993 MS.gene89959:CDS
AGGACATTCACCTCTGAAAA+TGG 0.279756 4.2:-47707166 MS.gene89959:CDS
TAAATAACCACAGGCTCTTC+TGG 0.321440 4.2:+47708175 None:intergenic
GAAGTTTCAGCATCATTGTT+AGG 0.324985 4.2:+47707312 None:intergenic
TGGTGGCCAGAAGATTGTTT+TGG 0.336064 4.2:-47708143 MS.gene89959:CDS
TGAATTAGCTGCCGAGGTTA+AGG 0.369389 4.2:-47708395 MS.gene89959:intron
AGGTTCCCAAAACAATCTTC+TGG 0.382371 4.2:+47708137 None:intergenic
GCACTTGGCGCAGCAAATAA+AGG 0.387444 4.2:-47708202 MS.gene89959:CDS
GATGCTGAAACTTCCAAGTC+TGG 0.441612 4.2:-47707303 MS.gene89959:CDS
AAGCATACCTGCTGCAACTA+CGG 0.449498 4.2:+47707268 None:intergenic
AGCAGCTATTCACATTTCTC+AGG 0.458967 4.2:-47708332 MS.gene89959:intron
TTGTTAGATTCTGAGAAAGC+TGG 0.482257 4.2:-47707366 MS.gene89959:intron
GCAAGAGAGTCCTCCAGACT+TGG 0.490554 4.2:+47707290 None:intergenic
ACTTCACTTAGCAGCATGCT+TGG 0.492494 4.2:+47706950 None:intergenic
GTTATTTACCTCGTATTTGG+TGG 0.494314 4.2:-47708160 MS.gene89959:CDS
TGGATTGCAACAACATATGA+AGG 0.511482 4.2:-47707146 MS.gene89959:CDS
GCAATTCATGACTCTAAGAA+AGG 0.512247 4.2:-47707336 MS.gene89959:CDS
TCTCTTGCCGTAGTTGCAGC+AGG 0.513623 4.2:-47707275 MS.gene89959:intron
GCTGCTGCATCATGGGCATA+CGG 0.519271 4.2:+47708349 None:intergenic
CTGCTGCATCATGGGCATAC+GGG 0.528977 4.2:+47708350 None:intergenic
GAGTCCTCTAGGAGCATGCT+TGG 0.529371 4.2:+47707123 None:intergenic
CTTCTGCAACAGAGTCCTCT+AGG 0.537070 4.2:+47707112 None:intergenic
GTGAATAGCTGCTGCATCAT+GGG 0.548035 4.2:+47708342 None:intergenic
TTAGCTGCCGAGGTTAAGGT+TGG 0.554128 4.2:-47708391 MS.gene89959:intron
TGTGAATAGCTGCTGCATCA+TGG 0.561080 4.2:+47708341 None:intergenic
AGGTTACCCCAAAACTCCAT+TGG 0.577427 4.2:+47708630 None:intergenic
AGTTTCTCCAACCTTAACCT+CGG 0.624909 4.2:+47708384 None:intergenic
GATCTTTGAATTAGCTGCCG+AGG 0.634911 4.2:-47708401 MS.gene89959:intron
TGGATTGCAAGAACATAACA+AGG 0.641394 4.2:-47706973 MS.gene89959:CDS
AATACGAGGTAAATAACCAC+AGG 0.651072 4.2:+47708166 None:intergenic
ATATTATTAAAAGTTATCTG+AGG 0.654039 4.2:+47708097 None:intergenic
AAGGCCAAGCATGCTCCTAG+AGG 0.658563 4.2:-47707127 MS.gene89959:CDS
GCTGAAACTTCCAAGTCTGG+AGG 0.660898 4.2:-47707300 MS.gene89959:CDS
TCTGTTGCAGAAGTTGCAAG+AGG 0.682206 4.2:-47707102 MS.gene89959:intron
TCTTCTGGCCACCAAATACG+AGG 0.688955 4.2:+47708152 None:intergenic
AGGCATACCAGAAGAGCCTG+TGG 0.689406 4.2:-47708182 MS.gene89959:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! ATATATTTATTACTTTTAGA+TGG - chr4.2:47708352-47708371 MS.gene89959:CDS 10.0%
!!! TAATAGTTTAAATTTTACAT+TGG - chr4.2:47707822-47707841 MS.gene89959:intron 10.0%
!!! TATATTTATTACTTTTAGAT+GGG - chr4.2:47708353-47708372 MS.gene89959:CDS 10.0%
!!! TTTTAATAATATTCTTGAAA+AGG - chr4.2:47707494-47707513 MS.gene89959:intron 10.0%
!! AAAAATTTAAGCACAAATTA+CGG + chr4.2:47708125-47708144 None:intergenic 15.0%
!! AAAGTAATAAATATATGCTT+CGG + chr4.2:47708348-47708367 None:intergenic 15.0%
!! AAAGTAATAAATATATGCTT+TGG + chr4.2:47708348-47708367 None:intergenic 15.0%
!! AAGTAATAAATATATGCTTT+GGG + chr4.2:47708347-47708366 None:intergenic 15.0%
!! ATAATAATAAATAAGTCTCA+AGG + chr4.2:47707591-47707610 None:intergenic 15.0%
!! ATATTATTAAAAGTTATCTG+AGG + chr4.2:47707486-47707505 None:intergenic 15.0%
!!! ATCTTACAATTGTTTTTAAA+TGG - chr4.2:47707931-47707950 MS.gene89959:intron 15.0%
!! AAGTAATAAATATATGCTTC+GGG + chr4.2:47708520-47708539 None:intergenic 20.0%
!! TAAAGACAAGAAAAAAAGAA+AGG + chr4.2:47708562-47708581 None:intergenic 20.0%
!! TAATAGCTTAACATGTATAT+TGG - chr4.2:47707685-47707704 MS.gene89959:intron 20.0%
!!! ATTTGTGCTTAAATTTTTGT+AGG - chr4.2:47708127-47708146 MS.gene89959:CDS 20.0%
! ACACATTTAGATAACAGATT+AGG + chr4.2:47707791-47707810 None:intergenic 25.0%
! TCAAACAACGTTTCAATTTA+CGG + chr4.2:47708045-47708064 None:intergenic 25.0%
!! ATGTGTAACAGAAGTATATA+TGG + chr4.2:47708102-47708121 None:intergenic 25.0%
!! TCTTAACTATTGATGTGTTT+TGG - chr4.2:47707861-47707880 MS.gene89959:intron 25.0%
!! TTTTTCTTGTCTTTATTACC+AGG - chr4.2:47708567-47708586 MS.gene89959:intron 25.0%
!!! TTTTTGTTGTCTTTATTACC+AGG - chr4.2:47708394-47708413 MS.gene89959:intron 25.0%
ATGATGAAAGGAGAAATATG+AGG + chr4.2:47706973-47706992 None:intergenic 30.0%
ATGTGTAACAGAAGGATATA+TGG + chr4.2:47708173-47708192 None:intergenic 30.0%
CAAACAACGTTTCAATTTAC+GGG + chr4.2:47708044-47708063 None:intergenic 30.0%
GAAGAAAAGTAGATGATGAA+AGG + chr4.2:47706985-47707004 None:intergenic 30.0%
TATTCACATTTCTCAGGTTA+GGG - chr4.2:47707254-47707273 MS.gene89959:intron 30.0%
!! GTTATTTTATAGGTAGCACT+TGG - chr4.2:47707363-47707382 MS.gene89959:intron 30.0%
!!! TGCTGCTTTGGTTATTTTAT+AGG - chr4.2:47707353-47707372 MS.gene89959:CDS 30.0%
AATACGAGGTAAATAACCAC+AGG + chr4.2:47707417-47707436 None:intergenic 35.0%
AATTACGGATGTGTAACAGA+AGG + chr4.2:47708110-47708129 None:intergenic 35.0%
CTATTCACATTTCTCAGGTT+AGG - chr4.2:47707253-47707272 MS.gene89959:intron 35.0%
GAAGTTTCAGCATCATTGTT+AGG + chr4.2:47708271-47708290 None:intergenic 35.0%
GTGGTTATTTACCTCGTATT+TGG - chr4.2:47707417-47707436 MS.gene89959:intron 35.0%
GTTATTTACCTCGTATTTGG+TGG - chr4.2:47707420-47707439 MS.gene89959:intron 35.0%
GTTGTTTGAATGTTGCATTG+AGG - chr4.2:47708056-47708075 MS.gene89959:CDS 35.0%
TGGATTGCAACAACATATGA+AGG - chr4.2:47708434-47708453 MS.gene89959:intron 35.0%
TGGATTGCAAGAACATAACA+AGG - chr4.2:47708607-47708626 MS.gene89959:intron 35.0%
! AGGAATTTTGTCCCTGATTA+AGG + chr4.2:47707466-47707485 None:intergenic 35.0%
! GAAATAAACACTCGCAGTTT+TGG + chr4.2:47707541-47707560 None:intergenic 35.0%
! GCAATTCATGACTCTAAGAA+AGG - chr4.2:47708244-47708263 MS.gene89959:intron 35.0%
! GGTTTACTAAATTGCTGCTT+TGG - chr4.2:47707341-47707360 MS.gene89959:CDS 35.0%
! TTCTTGCAATCCATTTTCAG+AGG + chr4.2:47708600-47708619 None:intergenic 35.0%
! TTGTTAGATTCTGAGAAAGC+TGG - chr4.2:47708214-47708233 MS.gene89959:intron 35.0%
! TTGTTGCAATCCATTTTCAG+AGG + chr4.2:47708427-47708446 None:intergenic 35.0%
!! ACGTTGTGTGTTTTTGTCTA+GGG - chr4.2:47707320-47707339 MS.gene89959:CDS 35.0%
!! TACGTTGTGTGTTTTTGTCT+AGG - chr4.2:47707319-47707338 MS.gene89959:CDS 35.0%
!!! TGTTTTGGGAACCTTAATCA+GGG - chr4.2:47707452-47707471 MS.gene89959:intron 35.0%
!!! TTGTTTTGGGAACCTTAATC+AGG - chr4.2:47707451-47707470 MS.gene89959:intron 35.0%
AACGTTTCAATTTACGGGTG+GGG + chr4.2:47708039-47708058 None:intergenic 40.0%
ACAACGTTTCAATTTACGGG+TGG + chr4.2:47708041-47708060 None:intergenic 40.0%
ACTGCGAGTGTTTATTTCAG+TGG - chr4.2:47707543-47707562 MS.gene89959:intron 40.0%
AGCAGCTATTCACATTTCTC+AGG - chr4.2:47707248-47707267 MS.gene89959:intron 40.0%
AGGTTCCCAAAACAATCTTC+TGG + chr4.2:47707446-47707465 None:intergenic 40.0%
AGTTTCTCCAACCTTAACCT+CGG + chr4.2:47707199-47707218 None:intergenic 40.0%
CAACGTTTCAATTTACGGGT+GGG + chr4.2:47708040-47708059 None:intergenic 40.0%
TAAATAACCACAGGCTCTTC+TGG + chr4.2:47707408-47707427 None:intergenic 40.0%
TGTACGTACGTACGTGTATT+AGG - chr4.2:47707127-47707146 MS.gene89959:CDS 40.0%
! AGGACATTCACCTCTGAAAA+TGG - chr4.2:47708414-47708433 MS.gene89959:intron 40.0%
! ATTTTCAGAGGTGAATGTCC+TGG + chr4.2:47708415-47708434 None:intergenic 40.0%
AAGCATACCTGCTGCAACTA+CGG + chr4.2:47708315-47708334 None:intergenic 45.0%
AGTGAGGAAGAAGGTGAAAC+TGG - chr4.2:47707892-47707911 MS.gene89959:intron 45.0%
GATCTTTGAATTAGCTGCCG+AGG - chr4.2:47707179-47707198 MS.gene89959:intron 45.0%
GATGCTGAAACTTCCAAGTC+TGG - chr4.2:47708277-47708296 MS.gene89959:intron 45.0%
GTGAATAGCTGCTGCATCAT+GGG + chr4.2:47707241-47707260 None:intergenic 45.0%
TCTGTTGCAGAAGTTGCAAG+AGG - chr4.2:47708478-47708497 MS.gene89959:intron 45.0%
TGAATTAGCTGCCGAGGTTA+AGG - chr4.2:47707185-47707204 MS.gene89959:intron 45.0%
TGTGAATAGCTGCTGCATCA+TGG + chr4.2:47707242-47707261 None:intergenic 45.0%
! GGTGGCCAGAAGATTGTTTT+GGG - chr4.2:47707438-47707457 MS.gene89959:intron 45.0%
! TGGTGGCCAGAAGATTGTTT+TGG - chr4.2:47707437-47707456 MS.gene89959:intron 45.0%
CTTCTGCAACAGAGTCCTCT+AGG + chr4.2:47708471-47708490 None:intergenic 50.0%
GCACTTGGCGCAGCAAATAA+AGG - chr4.2:47707378-47707397 MS.gene89959:intron 50.0%
GCTGAAACTTCCAAGTCTGG+AGG - chr4.2:47708280-47708299 MS.gene89959:intron 50.0%
GGAAGAAGGTGAAACTGGTG+AGG - chr4.2:47707897-47707916 MS.gene89959:intron 50.0%
TCTTCTGGCCACCAAATACG+AGG + chr4.2:47707431-47707450 None:intergenic 50.0%
TTAGCTGCCGAGGTTAAGGT+TGG - chr4.2:47707189-47707208 MS.gene89959:intron 50.0%
AAGGCCAAGCATGCTCCTAG+AGG - chr4.2:47708453-47708472 MS.gene89959:intron 55.0%
ACCTTCTTCCTCACTCGTGC+AGG + chr4.2:47707887-47707906 None:intergenic 55.0%
AGGCATACCAGAAGAGCCTG+TGG - chr4.2:47707398-47707417 MS.gene89959:intron 55.0%
CTGCTGCATCATGGGCATAC+GGG + chr4.2:47707233-47707252 None:intergenic 55.0%
GCAAGAGAGTCCTCCAGACT+TGG + chr4.2:47708293-47708312 None:intergenic 55.0%
GCTGCTGCATCATGGGCATA+CGG + chr4.2:47707234-47707253 None:intergenic 55.0%
TCTCTTGCCGTAGTTGCAGC+AGG - chr4.2:47708305-47708324 MS.gene89959:intron 55.0%
! GAGTCCTCTAGGAGCATGCT+TGG + chr4.2:47708460-47708479 None:intergenic 55.0%
!!! TGTTTTGGCCTGCACGAGTG+AGG - chr4.2:47707876-47707895 MS.gene89959:intron 55.0%
GCCTGCACGAGTGAGGAAGA+AGG - chr4.2:47707883-47707902 MS.gene89959:intron 60.0%


Chromosome Type Strat End Strand Name
chr4.2 gene 47706953 47708649 47706953 ID=MS.gene89959
chr4.2 mRNA 47706953 47708649 47706953 ID=MS.gene89959.t1;Parent=MS.gene89959
chr4.2 exon 47708637 47708649 47708637 ID=MS.gene89959.t1.exon1;Parent=MS.gene89959.t1
chr4.2 CDS 47708637 47708649 47708637 ID=cds.MS.gene89959.t1;Parent=MS.gene89959.t1
chr4.2 exon 47708333 47708409 47708333 ID=MS.gene89959.t1.exon2;Parent=MS.gene89959.t1
chr4.2 CDS 47708333 47708409 47708333 ID=cds.MS.gene89959.t1;Parent=MS.gene89959.t1
chr4.2 exon 47708053 47708227 47708053 ID=MS.gene89959.t1.exon3;Parent=MS.gene89959.t1
chr4.2 CDS 47708053 47708227 47708053 ID=cds.MS.gene89959.t1;Parent=MS.gene89959.t1
chr4.2 exon 47707276 47707381 47707276 ID=MS.gene89959.t1.exon4;Parent=MS.gene89959.t1
chr4.2 CDS 47707276 47707381 47707276 ID=cds.MS.gene89959.t1;Parent=MS.gene89959.t1
chr4.2 exon 47707103 47707186 47707103 ID=MS.gene89959.t1.exon5;Parent=MS.gene89959.t1
chr4.2 CDS 47707103 47707186 47707103 ID=cds.MS.gene89959.t1;Parent=MS.gene89959.t1
chr4.2 exon 47706953 47707013 47706953 ID=MS.gene89959.t1.exon6;Parent=MS.gene89959.t1
chr4.2 CDS 47706953 47707013 47706953 ID=cds.MS.gene89959.t1;Parent=MS.gene89959.t1
Gene Sequence

>MS.gene89959

ATGGAGTTTTGGGGTAACCTCATATTTCTCCTTTCATCATCTACTTTTCTTCGCTGAATAACGATTACTTGTTTTTATCGATTTTGTTTTCGTTGATTGTTTCATTCTTAATTTATTTAATAATTTATCGTTAATCTGAAGTCTGTTATTGTTAATTTGAACTCAGAACTTGTATGTACGTACGTACGTGTATTAGGTTTTGATTCATAGTTTTCTGATGTACGTTGATCTTTGAATTAGCTGCCGAGGTTAAGGTTGGAGAAACTATCAAGATTGACCCGTATGCCCATGATGCAGCAGCTATTCACATTTCTCAGGTTAGGGTTTTGCTGCTGCTGCTGTTGATGATGATGTGTTGTTATGTACTACGTTGTGTGTTTTTGTCTAGGGTTTACTAAATTGCTGCTTTGGTTATTTTATAGGTAGCACTTGGCGCAGCAAATAAAGGCATACCAGAAGAGCCTGTGGTTATTTACCTCGTATTTGGTGGCCAGAAGATTGTTTTGGGAACCTTAATCAGGGACAAAATTCCTCAGATAACTTTTAATAATATTCTTGAAAAGGAATTTGAGCTTTCTCACAATTCCAAAACTGCGAGTGTTTATTTCAGTGGATACAAAGTTTATTATGAATATCCTTGAGACTTATTTATTATTATACAGTTTATTCATATTTTTAGTTGATATATATATTTCTAAGATAGTTTGTTAGTGTATCTACATAGTGTTGCAATAATAGCTTAACATGTATATTGGCATCATTTTAATTTTTGTTTATTTTTCTAGTCAGAAATTTAAAGTATAGTTTTTTAGAGTATAGTATAGTTTGTTGCTGTCCTAATCTGTTATCTAAATGTGTAGCTAATGTTGTAATAGTTTAAATTTTACATTGGCATCATCTTAATTTTTTCTTAACTATTGATGTGTTTTGGCCTGCACGAGTGAGGAAGAAGGTGAAACTGGTGAGGCTCTGAAATTTATCTTACAATTGTTTTTAAATGGATTCATGCTTGCATTTGCATGCATGCTGTATTGTTTATATCTTTAATCTTTCTACTATACATCTGTAAACTGTTAAATTACTCCCCACCCGTAAATTGAAACGTTGTTTGAATGTTGCATTGAGGTTTTTTGCATTATATATTCTCCATATATACTTCTGTTACACATCCGTAATTTGTGCTTAAATTTTTGTAGGTTTTTTGCATTATATATTCTCCATATATCCTTCTGTTACACATCCGTAATTTGTGCTTAAATTTTTGTTAGATTCTGAGAAAGCTGGACATACAGCAATTCATGACTCTAAGAAAGGTCCTAACAATGATGCTGAAACTTCCAAGTCTGGAGGACTCTCTTGCCGTAGTTGCAGCAGGTATGCTTTTAACAAAACCCAAAGCATATATTTATTACTTTTAGATGGGTTTAGATTTAGCTTTCTTTTTTTGTTGTCTTTATTACCAGGACATTCACCTCTGAAAATGGATTGCAACAACATATGAAGGCCAAGCATGCTCCTAGAGGACTCTGTTGCAGAAGTTGCAAGAGGTATGCTTTTAACAAAACCCGAAGCATATATTTATTACTTTTAGATGGGTTGTGATTGACCTTTCTTTTTTTCTTGTCTTTATTACCAGGACATTCACCTCTGAAAATGGATTGCAAGAACATAACAAGGCCAAGCATGCTGCTAAGTGA
Protein sequence

>MS.gene89959.t1

MEFWAAEVKVGETIKIDPYAHDAAAIHISQVALGAANKGIPEEPVVIYLVFGGQKIVLGTLIRDKIPQITFNNILEKEFELSHNSKTANSEKAGHTAIHDSKKGPNNDAETSKSGGLSCRSCSRTFTSENGLQQHMKAKHAPRGLCCRSCKRTFTSENGLQEHNKAKHAAK