AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene006904

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene006904.t1 MTR_4g084110 98.065 155 3 0 1 155 1 155 1.30e-112 316
MS.gene006904.t1 MTR_5g014260 66.418 134 45 0 22 155 33 166 2.85e-66 199
MS.gene006904.t1 MTR_5g014260 69.892 93 28 0 22 114 33 125 1.32e-43 141
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene006904.t1 AT2G35120 78.205 156 33 1 1 155 1 156 2.69e-88 254
MS.gene006904.t1 AT1G32470 58.084 167 57 2 1 155 1 166 7.88e-63 191
MS.gene006904.t1 AT2G35370 65.441 136 47 0 20 155 30 165 1.81e-62 189

Find 34 sgRNAs with CRISPR-Local

Find 96 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GACATCAACTCTCCTGTTTC+AGG 0.209182 4.2:-25835991 MS.gene006904:CDS
TTCACTGCCGTTCCCACTTC+TGG 0.241034 4.2:+25836060 None:intergenic
AACTCAAGCCCCTATGAAAA+TGG 0.268193 4.2:-25835799 MS.gene006904:CDS
AGATGGCTTGCAGGCAGTTA+TGG 0.326829 4.2:-25837513 MS.gene006904:CDS
TGATCATGCCCAAGATCATT+TGG 0.340864 4.2:-25836106 MS.gene006904:CDS
GTGAAACAAGGAGATGGTTT+TGG 0.366878 4.2:-25836042 MS.gene006904:CDS
ATCTTCTTCTTCACAGAACT+TGG 0.368009 4.2:+25835708 None:intergenic
CAACATCACCCAAATGATCT+TGG 0.387609 4.2:+25836097 None:intergenic
GATGGCTTGCAGGCAGTTAT+GGG 0.405390 4.2:-25837512 MS.gene006904:CDS
TGGCGAACTTGACAAATTGA+TGG 0.434808 4.2:-25835746 MS.gene006904:CDS
GCTCAGCAACTCTCCTGCTT+TGG 0.435121 4.2:-25835944 MS.gene006904:intron
CCTGAGGTATGATGCGGCTC+TGG 0.441316 4.2:+25837486 None:intergenic
GATCATGCCCAAGATCATTT+GGG 0.482133 4.2:-25836105 MS.gene006904:CDS
GCAATAAAACTCACCAAAGC+AGG 0.490891 4.2:+25835931 None:intergenic
CATGAATGGGTGAAAGTTGA+CGG 0.492157 4.2:-25836153 MS.gene006904:CDS
AACATCACCCAAATGATCTT+GGG 0.497081 4.2:+25836098 None:intergenic
CCAGAGCCGCATCATACCTC+AGG 0.521213 4.2:-25837486 MS.gene006904:CDS
AGTATGCTGATTCTCATGAA+TGG 0.523325 4.2:-25836167 MS.gene006904:CDS
CAAGCCCCTATGAAAATGGA+TGG 0.537218 4.2:-25835795 MS.gene006904:CDS
GTATGCTGATTCTCATGAAT+GGG 0.551627 4.2:-25836166 MS.gene006904:CDS
GACGGAAAATCTGCAACCAT+TGG 0.558598 4.2:-25836135 MS.gene006904:CDS
TCGGCAAGACTATCAATGAC+TGG 0.570070 4.2:+25835684 None:intergenic
TTTCACAGAACCTTCTCTAA+CGG 0.580128 4.2:-25837454 MS.gene006904:intron
TGAATGAATACCGTTAGAGA+AGG 0.619094 4.2:+25837444 None:intergenic
TGGTGCAGTTGAAAGTGTGA+AGG 0.619953 4.2:-25836022 MS.gene006904:CDS
TGAATTGCCAGAAGTGGGAA+CGG 0.630383 4.2:-25836067 MS.gene006904:CDS
GTGGGAACGGCAGTGAAACA+AGG 0.631106 4.2:-25836054 MS.gene006904:CDS
ACGGCAGTGAAACAAGGAGA+TGG 0.634473 4.2:-25836048 MS.gene006904:CDS
GGCATGATCAGTTATGCCAA+TGG 0.640158 4.2:+25836119 None:intergenic
GTATGTTGAATTGCCAGAAG+TGG 0.646780 4.2:-25836073 MS.gene006904:CDS
TGTGAAAGACAGAGATCCTG+AGG 0.655630 4.2:+25837470 None:intergenic
TATGTTGAATTGCCAGAAGT+GGG 0.663199 4.2:-25836072 MS.gene006904:CDS
AGAGATCCTGAGGTATGATG+CGG 0.690860 4.2:+25837480 None:intergenic
AAAGTTGAGATGAGTGACAG+TGG 0.702478 4.2:-25835766 MS.gene006904:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! ATAAAAGTTAATTATGAATA+AGG + chr4.2:25837301-25837320 None:intergenic 10.0%
!! TAATAATAAAATAAAAAGCG+AGG + chr4.2:25835868-25835887 None:intergenic 15.0%
!! TTAAAATTCAATATGCAAAT+TGG + chr4.2:25836768-25836787 None:intergenic 15.0%
!! TTGTTAACAAAAAAACAAAA+TGG + chr4.2:25836101-25836120 None:intergenic 15.0%
!!! AAAATTTATAATTTGTAGGA+TGG - chr4.2:25836722-25836741 MS.gene006904:intron 15.0%
!!! AACCAAAATTTATAATTTGT+AGG - chr4.2:25836718-25836737 MS.gene006904:intron 15.0%
!!! AGATTTTATTGAGATATTAA+CGG + chr4.2:25836570-25836589 None:intergenic 15.0%
!!! ATCCTACAAATTATAAATTT+TGG + chr4.2:25836723-25836742 None:intergenic 15.0%
!!! TTTTAATATCTTGAAAGTTT+TGG - chr4.2:25836782-25836801 MS.gene006904:intron 15.0%
!! AAAAATGTAACAAACAACAT+AGG + chr4.2:25836199-25836218 None:intergenic 20.0%
!! AGATCAAGTTCAAAATAAAT+TGG + chr4.2:25835969-25835988 None:intergenic 20.0%
!! ATATGTAAGTAACATATACT+AGG - chr4.2:25836120-25836139 MS.gene006904:CDS 20.0%
!!! AAATGTTTGAATAGCTTTAT+AGG + chr4.2:25836469-25836488 None:intergenic 20.0%
!!! ATTTTGTTCTAACTATTATC+TGG - chr4.2:25836602-25836621 MS.gene006904:intron 20.0%
! ATAACTCAGTCAAAAGAAAT+TGG + chr4.2:25836433-25836452 None:intergenic 25.0%
! CTTACAAATGAACAATGATA+TGG + chr4.2:25836681-25836700 None:intergenic 25.0%
! TAAAACTTAAAGTGAACGAT+GGG - chr4.2:25836650-25836669 MS.gene006904:intron 25.0%
! TAGGAAAACATAAAAACACT+TGG + chr4.2:25837370-25837389 None:intergenic 25.0%
! TATTATCTGGTACATCATAT+TGG - chr4.2:25836615-25836634 MS.gene006904:intron 25.0%
! TCAAGTTCAAAATAAATTGG+AGG + chr4.2:25835966-25835985 None:intergenic 25.0%
! TTAAAACTTAAAGTGAACGA+TGG - chr4.2:25836649-25836668 MS.gene006904:intron 25.0%
!! AATTATCCATCCATTTTCAT+AGG + chr4.2:25837421-25837440 None:intergenic 25.0%
!! AGAATATTCCATTTCCATTT+TGG + chr4.2:25836153-25836172 None:intergenic 25.0%
!! ATTATCCATCCATTTTCATA+GGG + chr4.2:25837420-25837439 None:intergenic 25.0%
!! TAACGGTTTAATTGATTTCA+AGG + chr4.2:25836553-25836572 None:intergenic 25.0%
!! TTTTAGTGAATAGTGACAAA+AGG - chr4.2:25836069-25836088 MS.gene006904:CDS 25.0%
!!! AAGTTCGTTTTTGCTTTTAA+AGG - chr4.2:25836318-25836337 MS.gene006904:intron 25.0%
!!! GAATAGCTTTATAGGTAAAT+TGG + chr4.2:25836461-25836480 None:intergenic 25.0%
AATAATCCAAATTACTCTCG+AGG - chr4.2:25836492-25836511 MS.gene006904:intron 30.0%
AATTGAAAGAATAGATCGTC+CGG + chr4.2:25836051-25836070 None:intergenic 30.0%
ATTGCCTTTATATACGTTAG+TGG - chr4.2:25835906-25835925 MS.gene006904:intron 30.0%
CAATTGAACAAGTAGCATAT+TGG - chr4.2:25836918-25836937 MS.gene006904:intron 30.0%
GCTAAATTCCAAAATGGAAA+TGG - chr4.2:25836142-25836161 MS.gene006904:CDS 30.0%
GTGCATATTTCGAAATTAAG+TGG - chr4.2:25836276-25836295 MS.gene006904:intron 30.0%
TACTAGGCTAAATTCCAAAA+TGG - chr4.2:25836136-25836155 MS.gene006904:CDS 30.0%
TTGCCTTTATATACGTTAGT+GGG - chr4.2:25835907-25835926 MS.gene006904:intron 30.0%
! ATTGAAACCAACATTTTGCA+AGG - chr4.2:25836968-25836987 MS.gene006904:intron 30.0%
! CAATATGCTACTTGTTCAAT+TGG + chr4.2:25836920-25836939 None:intergenic 30.0%
! TTATCCATCCATTTTCATAG+GGG + chr4.2:25837419-25837438 None:intergenic 30.0%
! TTTTGAACTTGATCTGTATG+TGG - chr4.2:25835974-25835993 MS.gene006904:CDS 30.0%
!! AATTTAGCTTGTTAGCACTT+TGG - chr4.2:25836355-25836374 MS.gene006904:intron 30.0%
!! ATTTAGCTTGTTAGCACTTT+GGG - chr4.2:25836356-25836375 MS.gene006904:intron 30.0%
!! TAACAAACTGTTGGTTTGTT+TGG - chr4.2:25836385-25836404 MS.gene006904:intron 30.0%
!! TTTCCTATTTTTCTTCGTGT+AGG - chr4.2:25837383-25837402 MS.gene006904:intron 30.0%
AACATCACCCAAATGATCTT+GGG + chr4.2:25837112-25837131 None:intergenic 35.0%
AAGATCCAGATTCCAGATAT+TGG + chr4.2:25835842-25835861 None:intergenic 35.0%
ACATGATAATCATCATCTGC+AGG - chr4.2:25836841-25836860 MS.gene006904:intron 35.0%
ATAAATTGGAGGTGACTGAA+TGG + chr4.2:25835955-25835974 None:intergenic 35.0%
ATCTTCTTCTTCACAGAACT+TGG + chr4.2:25837502-25837521 None:intergenic 35.0%
ATGTTTCCTCGAGAGTAATT+TGG + chr4.2:25836501-25836520 None:intergenic 35.0%
CATACAACCTTGCAAAATGT+TGG + chr4.2:25836978-25836997 None:intergenic 35.0%
CATGTTGTTGATCCAATATC+TGG - chr4.2:25835827-25835846 MS.gene006904:intron 35.0%
CTTCCCACTAACGTATATAA+AGG + chr4.2:25835913-25835932 None:intergenic 35.0%
CTTTATATACGTTAGTGGGA+AGG - chr4.2:25835911-25835930 MS.gene006904:intron 35.0%
TATGTTGAATTGCCAGAAGT+GGG - chr4.2:25837135-25837154 MS.gene006904:intron 35.0%
TGAATGAATACCGTTAGAGA+AGG + chr4.2:25835766-25835785 None:intergenic 35.0%
TGACCTACACGAAGAAAAAT+AGG + chr4.2:25837389-25837408 None:intergenic 35.0%
TTTCACAGAACCTTCTCTAA+CGG - chr4.2:25835753-25835772 MS.gene006904:CDS 35.0%
! CGGTTTAATTGATTTCAAGG+AGG + chr4.2:25836550-25836569 None:intergenic 35.0%
! TTGATCCAATATCTGGAATC+TGG - chr4.2:25835834-25835853 MS.gene006904:intron 35.0%
!! AGTATGCTGATTCTCATGAA+TGG - chr4.2:25837040-25837059 MS.gene006904:intron 35.0%
!! GTATGCTGATTCTCATGAAT+GGG - chr4.2:25837041-25837060 MS.gene006904:intron 35.0%
!! TCAATCACTTTTCCTGAAAC+AGG + chr4.2:25837231-25837250 None:intergenic 35.0%
!! TTTAGCTTGTTAGCACTTTG+GGG - chr4.2:25836357-25836376 MS.gene006904:intron 35.0%
AAAGTTGAGATGAGTGACAG+TGG - chr4.2:25837441-25837460 MS.gene006904:intron 40.0%
AACTCAAGCCCCTATGAAAA+TGG - chr4.2:25837408-25837427 MS.gene006904:intron 40.0%
CAACATCACCCAAATGATCT+TGG + chr4.2:25837113-25837132 None:intergenic 40.0%
CATGAATGGGTGAAAGTTGA+CGG - chr4.2:25837054-25837073 MS.gene006904:intron 40.0%
GATCATGCCCAAGATCATTT+GGG - chr4.2:25837102-25837121 MS.gene006904:intron 40.0%
GCAATAAAACTCACCAAAGC+AGG + chr4.2:25837279-25837298 None:intergenic 40.0%
GGGGGAAAATAACAAACTGT+TGG - chr4.2:25836376-25836395 MS.gene006904:intron 40.0%
GTATGTTGAATTGCCAGAAG+TGG - chr4.2:25837134-25837153 MS.gene006904:intron 40.0%
TGAATGGTGTAGTGCACTTT+CGG + chr4.2:25835939-25835958 None:intergenic 40.0%
TGATCATGCCCAAGATCATT+TGG - chr4.2:25837101-25837120 MS.gene006904:intron 40.0%
TGGCGAACTTGACAAATTGA+TGG - chr4.2:25837461-25837480 MS.gene006904:CDS 40.0%
! GTGAAACAAGGAGATGGTTT+TGG - chr4.2:25837165-25837184 MS.gene006904:intron 40.0%
!! CACCAAAAGTTGATATACGG+CGG + chr4.2:25836028-25836047 None:intergenic 40.0%
!! CGGCACCAAAAGTTGATATA+CGG + chr4.2:25836031-25836050 None:intergenic 40.0%
!! CGTATATCAACTTTTGGTGC+CGG - chr4.2:25836029-25836048 MS.gene006904:CDS 40.0%
!! TTAGCTTGTTAGCACTTTGG+GGG - chr4.2:25836358-25836377 MS.gene006904:intron 40.0%
AGAGATCCTGAGGTATGATG+CGG + chr4.2:25835730-25835749 None:intergenic 45.0%
CAAGCCCCTATGAAAATGGA+TGG - chr4.2:25837412-25837431 MS.gene006904:intron 45.0%
CAGATGAGAAGACAGAGACT+CGG + chr4.2:25836815-25836834 None:intergenic 45.0%
GACATCAACTCTCCTGTTTC+AGG - chr4.2:25837216-25837235 MS.gene006904:intron 45.0%
GACGGAAAATCTGCAACCAT+TGG - chr4.2:25837072-25837091 MS.gene006904:intron 45.0%
GGCATGATCAGTTATGCCAA+TGG + chr4.2:25837091-25837110 None:intergenic 45.0%
TGAATTGCCAGAAGTGGGAA+CGG - chr4.2:25837140-25837159 MS.gene006904:intron 45.0%
TGTGAAAGACAGAGATCCTG+AGG + chr4.2:25835740-25835759 None:intergenic 45.0%
! GTCCGCCGTATATCAACTTT+TGG - chr4.2:25836023-25836042 MS.gene006904:CDS 45.0%
! TGGTGCAGTTGAAAGTGTGA+AGG - chr4.2:25837185-25837204 MS.gene006904:intron 45.0%
ACGGCAGTGAAACAAGGAGA+TGG - chr4.2:25837159-25837178 MS.gene006904:intron 50.0%
GCTCAGCAACTCTCCTGCTT+TGG - chr4.2:25837263-25837282 MS.gene006904:intron 55.0%
GTGGGAACGGCAGTGAAACA+AGG - chr4.2:25837153-25837172 MS.gene006904:intron 55.0%
TTCACTGCCGTTCCCACTTC+TGG + chr4.2:25837150-25837169 None:intergenic 55.0%
CCAGAGCCGCATCATACCTC+AGG - chr4.2:25835721-25835740 MS.gene006904:CDS 60.0%
CCTGAGGTATGATGCGGCTC+TGG + chr4.2:25835724-25835743 None:intergenic 60.0%


Chromosome Type Strat End Strand Name
chr4.2 gene 25835696 25837533 25835696 ID=MS.gene006904
chr4.2 mRNA 25835696 25837533 25835696 ID=MS.gene006904.t1;Parent=MS.gene006904
chr4.2 exon 25837455 25837533 25837455 ID=MS.gene006904.t1.exon1;Parent=MS.gene006904.t1
chr4.2 CDS 25837455 25837533 25837455 ID=cds.MS.gene006904.t1;Parent=MS.gene006904.t1
chr4.2 exon 25835945 25836204 25835945 ID=MS.gene006904.t1.exon2;Parent=MS.gene006904.t1
chr4.2 CDS 25835945 25836204 25835945 ID=cds.MS.gene006904.t1;Parent=MS.gene006904.t1
chr4.2 exon 25835696 25835824 25835696 ID=MS.gene006904.t1.exon3;Parent=MS.gene006904.t1
chr4.2 CDS 25835696 25835824 25835696 ID=cds.MS.gene006904.t1;Parent=MS.gene006904.t1
Gene Sequence

>MS.gene006904

ATGGCTTGCAGGCAGTTATGGGCATCCAGAGCCGCATCATACCTCAGGATCTCTGTCTTTCACAGAACCTTCTCTAACGGTATTCATTCATTCTTCTCTCTTTCTTTGATCTGTTAATTTTATTTCATGTGCATGTTGTTGATCCAATATCTGGAATCTGGATCTTGATCCTCGCTTTTTATTTTATTATTATTATTATTATGTTAATTTATTGCCTTTATATACGTTAGTGGGAAGGATCCGAAAGTGCACTACACCATTCAGTCACCTCCAATTTATTTTGAACTTGATCTGTATGTGGTTCGTATTTTGATTAGCTTAATCTGTGTCCGCCGTATATCAACTTTTGGTGCCGGACGATCTATTCTTTCAATTTTAGTGAATAGTGACAAAAGGAAGAGACCATTTTGTTTTTTTGTTAACAATATGTAAGTAACATATACTAGGCTAAATTCCAAAATGGAAATGGAATATTCTTTCATCTGAATCGTTATTTTGTACCTATGTTGTTTGTTACATTTTTAATATTTATGCTTTAATACTATCACTTTACAAAGAAAGACTTTTTCATTCTTTTTTAGTGCATATTTCGAAATTAAGTGGAGAATCACTTTTGAGTGTTAAGTTCGTTTTTGCTTTTAAAGGTGAATTTTTCAACAAATTTAGCTTGTTAGCACTTTGGGGGAAAATAACAAACTGTTGGTTTGTTTGGCTAAAATACATTTTAGACACAGCCAATTTCTTTTGACTGAGTTATATGCACCAATTTACCTATAAAGCTATTCAAACATTTCTTAATAATCCAAATTACTCTCGAGGAAACATTACTCATTGTTTTTCAAAGTCATTTTCCTCCTTGAAATCAATTAAACCGTTAATATCTCAATAAAATCTTTTAGTTGCTTAATTTTGTTCTAACTATTATCTGGTACATCATATTGGAGCTTAATGTGTTAAAACTTAAAGTGAACGATGGGATAATCCATATCATTGTTCATTTGTAAGCATTTTCGAAAAGAATTAACCAAAATTTATAATTTGTAGGATGGAATGAAAACTCAAAATATCTCCAATTTGCATATTGAATTTTAATATCTTGAAAGTTTTGGTGATTTTCCGAGTCTCTGTCTTCTCATCTGCAGACTACATGATAATCATCATCTGCAGGCTACATGATAATCATCATCTGCAGGCTACTTGATAATCATAAGTGTGAAATATCCAATTGAACAAGTAGCATATTGGAGATGATTTTTTGTTGTTGTTATTGTTATTGAAACCAACATTTTGCAAGGTTGTATGCATAATGAATTCAAATTGTCAATACAGTTCTGAACAATCTGAAGTATGCTGATTCTCATGAATGGGTGAAAGTTGACGGAAAATCTGCAACCATTGGCATAACTGATCATGCCCAAGATCATTTGGGTGATGTTGTGTATGTTGAATTGCCAGAAGTGGGAACGGCAGTGAAACAAGGAGATGGTTTTGGTGCAGTTGAAAGTGTGAAGGCAACTAGTGACATCAACTCTCCTGTTTCAGGAAAAGTGATTGAAGTTAATGAAGAGCTCAGCAACTCTCCTGCTTTGGTGAGTTTTATTGCCTTATTCATAATTAACTTTTATGATAGAATATGTGTGCTGAAGAATCACAACATTCATTTTTTATCTGCCAAGTGTTTTTATGTTTTCCTATTTTTCTTCGTGTAGGTCAACTCAAGCCCCTATGAAAATGGATGGATAATTAAAGTTGAGATGAGTGACAGTGGCGAACTTGACAAATTGATGGATTCAGAAAAGTATACCAAGTTCTGTGAAGAAGAAGATTCCAGTCATTGA
Protein sequence

>MS.gene006904.t1

MACRQLWASRAASYLRISVFHRTFSNVLNNLKYADSHEWVKVDGKSATIGITDHAQDHLGDVVYVELPEVGTAVKQGDGFGAVESVKATSDINSPVSGKVIEVNEELSNSPALVNSSPYENGWIIKVEMSDSGELDKLMDSEKYTKFCEEEDSSH