AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1263930

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1263930 MtrunA17_Chr4g0074501 96.581 117 4 0 1 117 1 117 3.06e-81 233
Msa1263930 MtrunA17_Chr2g0287961 70.192 104 30 1 1 104 1 103 4.77e-51 157
Msa1263930 MtrunA17_Chr0c30g0494111 97.368 76 2 0 42 117 1 76 1.07e-50 155
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1263930 AT5G19190.1 48.113 106 43 5 1 99 1 101 1.76e-19 78.6
Msa1263930 AT3G06070.1 48.315 89 40 5 1 84 1 88 9.28e-16 68.9

Find 42 sgRNAs with CRISPR-Local

Find 122 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GCAAATTTCACTCTTAATTA+TGG 0.136487 8_2:-67308557 Msa1263930:CDS
ATTCCTCAACCATTATTTAT+AGG 0.264588 8_2:+67307813 None:intergenic
ATTATTATTAGTCTTATTAT+AGG 0.268857 8_2:-67307667 Msa1263930:three_prime_UTR
TCATCGTCCACACTCTCTTC+AGG 0.320482 8_2:-67308509 Msa1263930:intron
TCTATAGAATTATTCATATC+TGG 0.338746 8_2:+67307744 None:intergenic
TATAATAAGACTAATAATAA+TGG 0.349468 8_2:+67307669 None:intergenic
AATACGATTATACACAAATA+TGG 0.354840 8_2:-67308629 Msa1263930:exon
TCTATAGATGGTTAATTTCA+AGG 0.387240 8_2:-67307729 Msa1263930:three_prime_UTR
AACTATAAATAGAATATACT+TGG 0.397089 8_2:-67308670 Msa1263930:five_prime_UTR
GATATGAATAATTCTATAGA+TGG 0.427177 8_2:-67307741 Msa1263930:three_prime_UTR
GGTTACAGAATAAACCTTGC+AGG 0.434621 8_2:+67307637 None:intergenic
TTGGTTGTGTTGTTGACTGT+GGG 0.440738 8_2:+67307931 None:intergenic
CCAAGAAGGAAGCACAGAAA+AGG 0.442519 8_2:-67307912 Msa1263930:CDS
AAATTACCTGTACGAGCAAA+TGG 0.461900 8_2:-67307991 Msa1263930:CDS
TATAATCGTATTCTCTACTT+TGG 0.466919 8_2:+67308640 None:intergenic
AAATTATGCGGTTCTGAAGA+AGG 0.467127 8_2:+67307790 None:intergenic
TCAAGGATTTATATATACAT+AGG 0.469022 8_2:-67307712 Msa1263930:three_prime_UTR
AAAACTTTCCCACACGGTGA+TGG 0.477259 8_2:+67307615 None:intergenic
TCAAAGCCATTTGCTCGTAC+AGG 0.480966 8_2:+67307985 None:intergenic
AAACCTATAAATAATGGTTG+AGG 0.481405 8_2:-67307816 Msa1263930:exon
CTTGGTTGTGTTGTTGACTG+TGG 0.483790 8_2:+67307930 None:intergenic
AATTTGACTGTGGAGGAGGA+TGG 0.488195 8_2:+67308009 None:intergenic
AAACTTTCCCACACGGTGAT+GGG 0.490691 8_2:+67307616 None:intergenic
AGGTAATTTGACTGTGGAGG+AGG 0.498056 8_2:+67308005 None:intergenic
AGTCAACAACACAACCAAGA+AGG 0.507607 8_2:-67307926 Msa1263930:CDS
TACATAGGTCATTATGTACA+TGG 0.516976 8_2:-67307697 Msa1263930:three_prime_UTR
TTATTAGTCTTATTATAGGA+AGG 0.518907 8_2:-67307663 Msa1263930:three_prime_UTR
TGTGGACGATGAGAAGTAAG+AGG 0.521453 8_2:+67308520 None:intergenic
GTCTCAAGATACAACAATAA+CGG 0.540371 8_2:-67307856 Msa1263930:CDS
TATTAGTCTTATTATAGGAA+GGG 0.551351 8_2:-67307662 Msa1263930:three_prime_UTR
CTTTGAGAAGACAAAGCAAA+GGG 0.576411 8_2:-67307968 Msa1263930:CDS
AGAAGACAAAGCAAAGGGAC+AGG 0.577461 8_2:-67307963 Msa1263930:CDS
TTCTGTAACCCATCACCGTG+TGG 0.585512 8_2:-67307624 Msa1263930:three_prime_UTR
TTATAGGAAGGGTCCCTGCA+AGG 0.598310 8_2:-67307651 Msa1263930:three_prime_UTR
TACAGGTAATTTGACTGTGG+AGG 0.614404 8_2:+67308002 None:intergenic
TCTGTAACCCATCACCGTGT+GGG 0.614764 8_2:-67307623 Msa1263930:three_prime_UTR
GCTTTGAGAAGACAAAGCAA+AGG 0.646564 8_2:-67307969 Msa1263930:CDS
ACATAGGTCATTATGTACAT+GGG 0.655302 8_2:-67307696 Msa1263930:three_prime_UTR
GTTACAGAATAAACCTTGCA+GGG 0.675715 8_2:+67307638 None:intergenic
ACGATTATACACAAATATGG+AGG 0.680249 8_2:-67308626 Msa1263930:exon
ATGATCAGTAGAAAATTATG+CGG 0.699599 8_2:+67307778 None:intergenic
TCGTACAGGTAATTTGACTG+TGG 0.729368 8_2:+67307999 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AAATAATTTCCAATAATTAA+TGG - chr8_2:67308170-67308189 Msa1263930:intron 10.0%
!! TATAATAAGACTAATAATAA+TGG + chr8_2:67308669-67308688 None:intergenic 10.0%
!!! ATTATTATTAGTCTTATTAT+AGG - chr8_2:67308668-67308687 Msa1263930:five_prime_UTR 10.0%
!! AAATAATTTCCAATAATTAA+TGG - chr8_2:67308170-67308189 Msa1263930:intron 10.0%
!! TATAATAAGACTAATAATAA+TGG + chr8_2:67308669-67308688 None:intergenic 10.0%
!!! ATTATTATTAGTCTTATTAT+AGG - chr8_2:67308668-67308687 Msa1263930:five_prime_UTR 10.0%
!! AACTATAAATAGAATATACT+TGG - chr8_2:67307665-67307684 Msa1263930:three_prime_UTR 15.0%
!!! ATATATTATTCATGAGTTTT+GGG + chr8_2:67308029-67308048 None:intergenic 15.0%
!!! TATATATTATTCATGAGTTT+TGG + chr8_2:67308030-67308049 None:intergenic 15.0%
!!! TCTTTTAAACCTATAAATAA+TGG - chr8_2:67308513-67308532 Msa1263930:CDS 15.0%
!! AACTATAAATAGAATATACT+TGG - chr8_2:67307665-67307684 Msa1263930:three_prime_UTR 15.0%
!!! ATATATTATTCATGAGTTTT+GGG + chr8_2:67308029-67308048 None:intergenic 15.0%
!!! TATATATTATTCATGAGTTT+TGG + chr8_2:67308030-67308049 None:intergenic 15.0%
!!! TCTTTTAAACCTATAAATAA+TGG - chr8_2:67308513-67308532 Msa1263930:CDS 15.0%
!! AATACGATTATACACAAATA+TGG - chr8_2:67307706-67307725 Msa1263930:three_prime_UTR 20.0%
!! TTATTTAGTGTGAATATATG+CGG + chr8_2:67308156-67308175 None:intergenic 20.0%
!! TCCAATAATTAATGGAATTA+TGG - chr8_2:67308178-67308197 Msa1263930:intron 20.0%
!! TCCATAATTCCATTAATTAT+TGG + chr8_2:67308182-67308201 None:intergenic 20.0%
!! TCTATAGAATTATTCATATC+TGG + chr8_2:67308594-67308613 None:intergenic 20.0%
!! GATATGAATAATTCTATAGA+TGG - chr8_2:67308594-67308613 Msa1263930:CDS 20.0%
!! TCAAGGATTTATATATACAT+AGG - chr8_2:67308623-67308642 Msa1263930:exon 20.0%
!!! TTATTAGTCTTATTATAGGA+AGG - chr8_2:67308672-67308691 Msa1263930:five_prime_UTR 20.0%
!!! TATTAGTCTTATTATAGGAA+GGG - chr8_2:67308673-67308692 Msa1263930:five_prime_UTR 20.0%
!! AATACGATTATACACAAATA+TGG - chr8_2:67307706-67307725 Msa1263930:three_prime_UTR 20.0%
!! TTATTTAGTGTGAATATATG+CGG + chr8_2:67308156-67308175 None:intergenic 20.0%
!! TCCAATAATTAATGGAATTA+TGG - chr8_2:67308178-67308197 Msa1263930:intron 20.0%
!! TCCATAATTCCATTAATTAT+TGG + chr8_2:67308182-67308201 None:intergenic 20.0%
!! TCTATAGAATTATTCATATC+TGG + chr8_2:67308594-67308613 None:intergenic 20.0%
!! GATATGAATAATTCTATAGA+TGG - chr8_2:67308594-67308613 Msa1263930:CDS 20.0%
!! TCAAGGATTTATATATACAT+AGG - chr8_2:67308623-67308642 Msa1263930:exon 20.0%
!!! TTATTAGTCTTATTATAGGA+AGG - chr8_2:67308672-67308691 Msa1263930:five_prime_UTR 20.0%
!!! TATTAGTCTTATTATAGGAA+GGG - chr8_2:67308673-67308692 Msa1263930:five_prime_UTR 20.0%
! TATAATCGTATTCTCTACTT+TGG + chr8_2:67307698-67307717 None:intergenic 25.0%
! GCAAATTTCACTCTTAATTA+TGG - chr8_2:67307778-67307797 Msa1263930:three_prime_UTR 25.0%
! ACGTTAAATACATGATTATG+TGG + chr8_2:67307879-67307898 None:intergenic 25.0%
! TTTAACGTAGTTACACAATT+TGG - chr8_2:67307891-67307910 Msa1263930:CDS 25.0%
!! TTGAGTCTAAAATACAAAGT+TGG - chr8_2:67307952-67307971 Msa1263930:CDS 25.0%
! AAAATACAAAGTTGGAATTG+TGG - chr8_2:67307960-67307979 Msa1263930:CDS 25.0%
! TATTTAGTGTGAATATATGC+GGG + chr8_2:67308155-67308174 None:intergenic 25.0%
! AAACCTATAAATAATGGTTG+AGG - chr8_2:67308519-67308538 Msa1263930:CDS 25.0%
! ATTCCTCAACCATTATTTAT+AGG + chr8_2:67308525-67308544 None:intergenic 25.0%
! ATGATCAGTAGAAAATTATG+CGG + chr8_2:67308560-67308579 None:intergenic 25.0%
! TCTATAGATGGTTAATTTCA+AGG - chr8_2:67308606-67308625 Msa1263930:CDS 25.0%
! TATAATCGTATTCTCTACTT+TGG + chr8_2:67307698-67307717 None:intergenic 25.0%
! GCAAATTTCACTCTTAATTA+TGG - chr8_2:67307778-67307797 Msa1263930:three_prime_UTR 25.0%
! ACGTTAAATACATGATTATG+TGG + chr8_2:67307879-67307898 None:intergenic 25.0%
! TTTAACGTAGTTACACAATT+TGG - chr8_2:67307891-67307910 Msa1263930:CDS 25.0%
!! TTGAGTCTAAAATACAAAGT+TGG - chr8_2:67307952-67307971 Msa1263930:CDS 25.0%
! AAAATACAAAGTTGGAATTG+TGG - chr8_2:67307960-67307979 Msa1263930:CDS 25.0%
! TATTTAGTGTGAATATATGC+GGG + chr8_2:67308155-67308174 None:intergenic 25.0%
! AAACCTATAAATAATGGTTG+AGG - chr8_2:67308519-67308538 Msa1263930:CDS 25.0%
! ATTCCTCAACCATTATTTAT+AGG + chr8_2:67308525-67308544 None:intergenic 25.0%
! ATGATCAGTAGAAAATTATG+CGG + chr8_2:67308560-67308579 None:intergenic 25.0%
! TCTATAGATGGTTAATTTCA+AGG - chr8_2:67308606-67308625 Msa1263930:CDS 25.0%
ACGATTATACACAAATATGG+AGG - chr8_2:67307709-67307728 Msa1263930:three_prime_UTR 30.0%
! ACAAATTTTCAGTCTTTCTC+TGG - chr8_2:67308297-67308316 Msa1263930:intron 30.0%
GTCTCAAGATACAACAATAA+CGG - chr8_2:67308479-67308498 Msa1263930:intron 30.0%
TACATAGGTCATTATGTACA+TGG - chr8_2:67308638-67308657 Msa1263930:five_prime_UTR 30.0%
ACATAGGTCATTATGTACAT+GGG - chr8_2:67308639-67308658 Msa1263930:five_prime_UTR 30.0%
TAGATAAAAACTTTCCCACA+CGG + chr8_2:67308729-67308748 None:intergenic 30.0%
ACGATTATACACAAATATGG+AGG - chr8_2:67307709-67307728 Msa1263930:three_prime_UTR 30.0%
! ACAAATTTTCAGTCTTTCTC+TGG - chr8_2:67308297-67308316 Msa1263930:intron 30.0%
GTCTCAAGATACAACAATAA+CGG - chr8_2:67308479-67308498 Msa1263930:intron 30.0%
TACATAGGTCATTATGTACA+TGG - chr8_2:67308638-67308657 Msa1263930:five_prime_UTR 30.0%
ACATAGGTCATTATGTACAT+GGG - chr8_2:67308639-67308658 Msa1263930:five_prime_UTR 30.0%
TAGATAAAAACTTTCCCACA+CGG + chr8_2:67308729-67308748 None:intergenic 30.0%
TGTATTCACATTTAGACCGT+CGG + chr8_2:67308122-67308141 None:intergenic 35.0%
AAATTACCTGTACGAGCAAA+TGG - chr8_2:67308344-67308363 Msa1263930:intron 35.0%
! CTTTGAGAAGACAAAGCAAA+GGG - chr8_2:67308367-67308386 Msa1263930:intron 35.0%
!! AAATTATGCGGTTCTGAAGA+AGG + chr8_2:67308548-67308567 None:intergenic 35.0%
GTTACAGAATAAACCTTGCA+GGG + chr8_2:67308700-67308719 None:intergenic 35.0%
TGTATTCACATTTAGACCGT+CGG + chr8_2:67308122-67308141 None:intergenic 35.0%
AAATTACCTGTACGAGCAAA+TGG - chr8_2:67308344-67308363 Msa1263930:intron 35.0%
! CTTTGAGAAGACAAAGCAAA+GGG - chr8_2:67308367-67308386 Msa1263930:intron 35.0%
!! AAATTATGCGGTTCTGAAGA+AGG + chr8_2:67308548-67308567 None:intergenic 35.0%
GTTACAGAATAAACCTTGCA+GGG + chr8_2:67308700-67308719 None:intergenic 35.0%
TGAAAAACCTGAAGAGAGTG+TGG + chr8_2:67307836-67307855 None:intergenic 40.0%
! TTTGGGACAACAATGTCTAG+TGG + chr8_2:67308012-67308031 None:intergenic 40.0%
ATTGTCTGATCTTGATCCGA+CGG - chr8_2:67308103-67308122 Msa1263930:intron 40.0%
TACAGGTAATTTGACTGTGG+AGG + chr8_2:67308336-67308355 None:intergenic 40.0%
TCGTACAGGTAATTTGACTG+TGG + chr8_2:67308339-67308358 None:intergenic 40.0%
!! GCTTTGAGAAGACAAAGCAA+AGG - chr8_2:67308366-67308385 Msa1263930:intron 40.0%
! TTGGTTGTGTTGTTGACTGT+GGG + chr8_2:67308407-67308426 None:intergenic 40.0%
AGTCAACAACACAACCAAGA+AGG - chr8_2:67308409-67308428 Msa1263930:intron 40.0%
GGTTACAGAATAAACCTTGC+AGG + chr8_2:67308701-67308720 None:intergenic 40.0%
TGAAAAACCTGAAGAGAGTG+TGG + chr8_2:67307836-67307855 None:intergenic 40.0%
! TTTGGGACAACAATGTCTAG+TGG + chr8_2:67308012-67308031 None:intergenic 40.0%
ATTGTCTGATCTTGATCCGA+CGG - chr8_2:67308103-67308122 Msa1263930:intron 40.0%
TACAGGTAATTTGACTGTGG+AGG + chr8_2:67308336-67308355 None:intergenic 40.0%
TCGTACAGGTAATTTGACTG+TGG + chr8_2:67308339-67308358 None:intergenic 40.0%
!! GCTTTGAGAAGACAAAGCAA+AGG - chr8_2:67308366-67308385 Msa1263930:intron 40.0%
! TTGGTTGTGTTGTTGACTGT+GGG + chr8_2:67308407-67308426 None:intergenic 40.0%
AGTCAACAACACAACCAAGA+AGG - chr8_2:67308409-67308428 Msa1263930:intron 40.0%
GGTTACAGAATAAACCTTGC+AGG + chr8_2:67308701-67308720 None:intergenic 40.0%
TGTGGACGATGAGAAGTAAG+AGG + chr8_2:67307818-67307837 None:intergenic 45.0%
AATTTGACTGTGGAGGAGGA+TGG + chr8_2:67308329-67308348 None:intergenic 45.0%
AGGTAATTTGACTGTGGAGG+AGG + chr8_2:67308333-67308352 None:intergenic 45.0%
TCAAAGCCATTTGCTCGTAC+AGG + chr8_2:67308353-67308372 None:intergenic 45.0%
AGAAGACAAAGCAAAGGGAC+AGG - chr8_2:67308372-67308391 Msa1263930:intron 45.0%
! CTTGGTTGTGTTGTTGACTG+TGG + chr8_2:67308408-67308427 None:intergenic 45.0%
! CCTTTTCTGTGCTTCCTTCT+TGG + chr8_2:67308426-67308445 None:intergenic 45.0%
! CCAAGAAGGAAGCACAGAAA+AGG - chr8_2:67308423-67308442 Msa1263930:intron 45.0%
AAACTTTCCCACACGGTGAT+GGG + chr8_2:67308722-67308741 None:intergenic 45.0%
AAAACTTTCCCACACGGTGA+TGG + chr8_2:67308723-67308742 None:intergenic 45.0%
TGTGGACGATGAGAAGTAAG+AGG + chr8_2:67307818-67307837 None:intergenic 45.0%
AATTTGACTGTGGAGGAGGA+TGG + chr8_2:67308329-67308348 None:intergenic 45.0%
AGGTAATTTGACTGTGGAGG+AGG + chr8_2:67308333-67308352 None:intergenic 45.0%
TCAAAGCCATTTGCTCGTAC+AGG + chr8_2:67308353-67308372 None:intergenic 45.0%
AGAAGACAAAGCAAAGGGAC+AGG - chr8_2:67308372-67308391 Msa1263930:intron 45.0%
! CTTGGTTGTGTTGTTGACTG+TGG + chr8_2:67308408-67308427 None:intergenic 45.0%
! CCTTTTCTGTGCTTCCTTCT+TGG + chr8_2:67308426-67308445 None:intergenic 45.0%
! CCAAGAAGGAAGCACAGAAA+AGG - chr8_2:67308423-67308442 Msa1263930:intron 45.0%
AAACTTTCCCACACGGTGAT+GGG + chr8_2:67308722-67308741 None:intergenic 45.0%
AAAACTTTCCCACACGGTGA+TGG + chr8_2:67308723-67308742 None:intergenic 45.0%
TCATCGTCCACACTCTCTTC+AGG - chr8_2:67307826-67307845 Msa1263930:CDS 50.0%
TTATAGGAAGGGTCCCTGCA+AGG - chr8_2:67308684-67308703 Msa1263930:five_prime_UTR 50.0%
TTCTGTAACCCATCACCGTG+TGG - chr8_2:67308711-67308730 Msa1263930:five_prime_UTR 50.0%
TCTGTAACCCATCACCGTGT+GGG - chr8_2:67308712-67308731 Msa1263930:five_prime_UTR 50.0%
TCATCGTCCACACTCTCTTC+AGG - chr8_2:67307826-67307845 Msa1263930:CDS 50.0%
TTATAGGAAGGGTCCCTGCA+AGG - chr8_2:67308684-67308703 Msa1263930:five_prime_UTR 50.0%
TTCTGTAACCCATCACCGTG+TGG - chr8_2:67308711-67308730 Msa1263930:five_prime_UTR 50.0%
TCTGTAACCCATCACCGTGT+GGG - chr8_2:67308712-67308731 Msa1263930:five_prime_UTR 50.0%
Chromosome Type Strat End Strand Name
chr8_2 gene 67307600 67308757 67307600 ID=Msa1263930;Name=Msa1263930
chr8_2 mRNA 67307600 67308757 67307600 ID=Msa1263930-mRNA-1;Parent=Msa1263930;Name=Msa1263930-mRNA-1;_AED=0.01;_eAED=0.01;_QI=125|1|1|1|1|1|2|218|117
chr8_2 exon 67307600 67308048 67307600 ID=Msa1263930-mRNA-1:exon:22104;Parent=Msa1263930-mRNA-1
chr8_2 exon 67308510 67308757 67308510 ID=Msa1263930-mRNA-1:exon:22103;Parent=Msa1263930-mRNA-1
chr8_2 five_prime_UTR 67308633 67308757 67308633 ID=Msa1263930-mRNA-1:five_prime_utr;Parent=Msa1263930-mRNA-1
chr8_2 CDS 67308510 67308632 67308510 ID=Msa1263930-mRNA-1:cds;Parent=Msa1263930-mRNA-1
chr8_2 CDS 67307818 67308048 67307818 ID=Msa1263930-mRNA-1:cds;Parent=Msa1263930-mRNA-1
chr8_2 three_prime_UTR 67307600 67307817 67307600 ID=Msa1263930-mRNA-1:three_prime_utr;Parent=Msa1263930-mRNA-1
Gene Sequence

>Msa1263930

ATGGAGGTTGCTGTTGAACTTGAAGATGATTTATATTTTGCAGACTTAAGCAAGCAAATTTCACTCTTAATTATGGATGAAGATGAAGATCCTCTTACTTCTCATCGTCCACACTCTCTTCAGTCTTTCTCTGGAGCAATCCATCCTCCTCCACAGTCAAATTACCTGTACGAGCAAATGGCTTTGAGAAGACAAAGCAAAGGGACAGGTGTGTTTATCCCACAGTCAACAACACAACCAAGAAGGAAGCACAGAAAAGGAAGATCTTCTTCATATGCAAAATGTCAAAAACAGTCTCAAGATACAACAATAACGGTTTCTCAAAATTCTTTTAAACCTATAAATAATGGTTGA
Protein sequence

>Msa1263930

MEVAVELEDDLYFADLSKQISLLIMDEDEDPLTSHRPHSLQSFSGAIHPPPQSNYLYEQMALRRQSKGTGVFIPQSTTQPRRKHRKGRSSSYAKCQKQSQDTTITVSQNSFKPINNG*