AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1023180


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1023180 MtrunA17_Chr7g0240411 92.405 79 6 0 1 79 1 79 5.24e-49 149
Msa1023180 MtrunA17_Chr4g0008691 62.963 81 28 2 1 79 1 81 2.30e-32 107
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 38 sgRNAs with CRISPR-Local

Find 117 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
ATTACCTTGGTTTGAAATTA+AGG 0.129246 7_1:-50526929 None:intergenic
GAGTTCGATATTATGTTAAA+TGG 0.198013 7_1:-50527739 None:intergenic
CACTTTGATTTACAAAATTA+TGG 0.210495 7_1:+50527642 Msa1023180:three_prime_UTR
TTCTCTAAACTTTGATATAT+AGG 0.300426 7_1:-50527222 None:intergenic
ATGAGAACATGAGGCTTGTT+TGG 0.314452 7_1:-50526841 None:intergenic
ATGAATTGTTACACAATTCA+TGG 0.321299 7_1:+50527672 Msa1023180:three_prime_UTR
CTAAAGAGTTTAGAAGGATA+AGG 0.353995 7_1:+50527508 Msa1023180:three_prime_UTR
CTTGAACCTCTCTAACTTTG+AGG 0.354710 7_1:+50526760 Msa1023180:five_prime_UTR
AGTTGACTAAAGAGTTTAGA+AGG 0.373568 7_1:+50527502 Msa1023180:three_prime_UTR
GAGTTGGGAGATATATAAAA+AGG 0.385399 7_1:-50526720 None:intergenic
TTTGTGTCTGCTAGTGCTAA+TGG 0.389664 7_1:+50527274 Msa1023180:three_prime_UTR
GAGGTACTTGCACTAGTACT+TGG 0.403825 7_1:+50527114 Msa1023180:CDS
CTTTAGTCAACTTTAGTTGA+AGG 0.419390 7_1:-50527491 None:intergenic
TAAAGAGTTTAGAAGGATAA+GGG 0.425247 7_1:+50527509 Msa1023180:three_prime_UTR
ATGAATTGTGTAACAATTCA+TGG 0.427262 7_1:-50527670 None:intergenic
AAGGATAAGGGATGGATATC+CGG 0.440238 7_1:+50527521 Msa1023180:three_prime_UTR
TTTGGTTTGAAACAAGTCAA+TGG 0.446404 7_1:+50527341 Msa1023180:three_prime_UTR
TGCAAATGTTGTGATGGAAT+TGG 0.452852 7_1:+50527092 Msa1023180:CDS
TTGGTTTGAAACAAGTCAAT+GGG 0.459688 7_1:+50527342 Msa1023180:three_prime_UTR
TTAGAGAGGTTCAAGAGCTA+TGG 0.483018 7_1:-50526752 None:intergenic
TTGTGTCTGCTAGTGCTAAT+GGG 0.495526 7_1:+50527275 Msa1023180:three_prime_UTR
GCTATGGAGCACTGATGAGT+TGG 0.497002 7_1:-50526736 None:intergenic
CTATGGAGCACTGATGAGTT+GGG 0.500776 7_1:-50526735 None:intergenic
GTCCTTGCTTCTATAAGTGA+TGG 0.503145 7_1:-50526901 None:intergenic
AGGATAGGAAACTTGTAGGA+TGG 0.515633 7_1:-50526700 None:intergenic
GGATAGGAAACTTGTAGGAT+GGG 0.533450 7_1:-50526699 None:intergenic
GTTGTTTGCAAATGTTGTGA+TGG 0.534057 7_1:+50527086 Msa1023180:CDS
AATAACTAGTGTGATTTCCA+AGG 0.557652 7_1:-50527167 None:intergenic
GAGTTTAGAAGGATAAGGGA+TGG 0.574430 7_1:+50527513 Msa1023180:three_prime_UTR
CTTTCCTTAATTTCAAACCA+AGG 0.576150 7_1:+50526925 Msa1023180:CDS
ATAGGAAACTTGTAGGATGG+GGG 0.578714 7_1:-50526697 None:intergenic
AACCATCACTTATAGAAGCA+AGG 0.587548 7_1:+50526899 Msa1023180:CDS
ATAACTTAAAGTGTTCACCT+TGG 0.595348 7_1:+50527150 Msa1023180:CDS
ATGAAACCTCAAAGTTAGAG+AGG 0.596758 7_1:-50526766 None:intergenic
AAATGTTGTGATGGAATTGG+AGG 0.597103 7_1:+50527095 Msa1023180:CDS
ATTAGTAATATGAGAACATG+AGG 0.602881 7_1:-50526850 None:intergenic
GATAGGAAACTTGTAGGATG+GGG 0.605112 7_1:-50526698 None:intergenic
AACAAGTTGCAATAGACATG+TGG 0.663724 7_1:-50527391 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! ATTATTATAATTAATTACCT+TGG - chr7_1:50526945-50526964 None:intergenic 10.0%
!! ATTATTATAATTAATTACCT+TGG - chr7_1:50526945-50526964 None:intergenic 10.0%
!! AAATAAAAAATTAGATCTAG+TGG - chr7_1:50527009-50527028 None:intergenic 15.0%
!!! TTATTTTGTTATGTATTTTC+AGG + chr7_1:50527035-50527054 Msa1023180:intron 15.0%
!!! TATTTTGTTATGTATTTTCA+GGG + chr7_1:50527036-50527055 Msa1023180:intron 15.0%
!!! TGTGTAATTTTATTTTGTTT+TGG + chr7_1:50527566-50527585 Msa1023180:three_prime_UTR 15.0%
!!! GTGTAATTTTATTTTGTTTT+GGG + chr7_1:50527567-50527586 Msa1023180:three_prime_UTR 15.0%
!! AAATAAAAAATTAGATCTAG+TGG - chr7_1:50527009-50527028 None:intergenic 15.0%
!!! TTATTTTGTTATGTATTTTC+AGG + chr7_1:50527035-50527054 Msa1023180:intron 15.0%
!!! TATTTTGTTATGTATTTTCA+GGG + chr7_1:50527036-50527055 Msa1023180:intron 15.0%
!!! TGTGTAATTTTATTTTGTTT+TGG + chr7_1:50527566-50527585 Msa1023180:three_prime_UTR 15.0%
!!! GTGTAATTTTATTTTGTTTT+GGG + chr7_1:50527567-50527586 Msa1023180:three_prime_UTR 15.0%
!! ATATAAAAACATCAATCATG+TGG + chr7_1:50526652-50526671 Msa1023180:five_prime_UTR 20.0%
!!! AGTTATTTTTGTGATTTTTC+TGG + chr7_1:50527183-50527202 Msa1023180:exon 20.0%
!! TTCTCTAAACTTTGATATAT+AGG - chr7_1:50527225-50527244 None:intergenic 20.0%
!!! ATGATTTTTCATTGATGATA+AGG + chr7_1:50527457-50527476 Msa1023180:three_prime_UTR 20.0%
!!! TGATTTTTCATTGATGATAA+GGG + chr7_1:50527458-50527477 Msa1023180:three_prime_UTR 20.0%
!!! CACTTTGATTTACAAAATTA+TGG + chr7_1:50527642-50527661 Msa1023180:three_prime_UTR 20.0%
!!! ATGAAGCATATTTTAACTTT+TGG + chr7_1:50527702-50527721 Msa1023180:three_prime_UTR 20.0%
!!! TGAAGCATATTTTAACTTTT+GGG + chr7_1:50527703-50527722 Msa1023180:three_prime_UTR 20.0%
!! ATATAAAAACATCAATCATG+TGG + chr7_1:50526652-50526671 Msa1023180:five_prime_UTR 20.0%
!!! AGTTATTTTTGTGATTTTTC+TGG + chr7_1:50527183-50527202 Msa1023180:exon 20.0%
!! TTCTCTAAACTTTGATATAT+AGG - chr7_1:50527225-50527244 None:intergenic 20.0%
!!! ATGATTTTTCATTGATGATA+AGG + chr7_1:50527457-50527476 Msa1023180:three_prime_UTR 20.0%
!!! TGATTTTTCATTGATGATAA+GGG + chr7_1:50527458-50527477 Msa1023180:three_prime_UTR 20.0%
!!! CACTTTGATTTACAAAATTA+TGG + chr7_1:50527642-50527661 Msa1023180:three_prime_UTR 20.0%
!!! ATGAAGCATATTTTAACTTT+TGG + chr7_1:50527702-50527721 Msa1023180:three_prime_UTR 20.0%
!!! TGAAGCATATTTTAACTTTT+GGG + chr7_1:50527703-50527722 Msa1023180:three_prime_UTR 20.0%
! ATTAGTAATATGAGAACATG+AGG - chr7_1:50526853-50526872 None:intergenic 25.0%
!! ATTACCTTGGTTTGAAATTA+AGG - chr7_1:50526932-50526951 None:intergenic 25.0%
!!! TATATGTGTCCATAGTTTTT+TGG + chr7_1:50527323-50527342 Msa1023180:three_prime_UTR 25.0%
! TGTTTCAAACCAAAAAACTA+TGG - chr7_1:50527335-50527354 None:intergenic 25.0%
! TAAAGAGTTTAGAAGGATAA+GGG + chr7_1:50527509-50527528 Msa1023180:three_prime_UTR 25.0%
! ATGAATTGTGTAACAATTCA+TGG - chr7_1:50527673-50527692 None:intergenic 25.0%
! ATGAATTGTTACACAATTCA+TGG + chr7_1:50527672-50527691 Msa1023180:three_prime_UTR 25.0%
! GAGTTCGATATTATGTTAAA+TGG - chr7_1:50527742-50527761 None:intergenic 25.0%
! ATTAGTAATATGAGAACATG+AGG - chr7_1:50526853-50526872 None:intergenic 25.0%
!! ATTACCTTGGTTTGAAATTA+AGG - chr7_1:50526932-50526951 None:intergenic 25.0%
!!! TATATGTGTCCATAGTTTTT+TGG + chr7_1:50527323-50527342 Msa1023180:three_prime_UTR 25.0%
! TGTTTCAAACCAAAAAACTA+TGG - chr7_1:50527335-50527354 None:intergenic 25.0%
! TAAAGAGTTTAGAAGGATAA+GGG + chr7_1:50527509-50527528 Msa1023180:three_prime_UTR 25.0%
! ATGAATTGTGTAACAATTCA+TGG - chr7_1:50527673-50527692 None:intergenic 25.0%
! ATGAATTGTTACACAATTCA+TGG + chr7_1:50527672-50527691 Msa1023180:three_prime_UTR 25.0%
! GAGTTCGATATTATGTTAAA+TGG - chr7_1:50527742-50527761 None:intergenic 25.0%
AAAAAGGATAGGAAACTTGT+AGG - chr7_1:50526707-50526726 None:intergenic 30.0%
GGGAGATATATAAAAAGGAT+AGG - chr7_1:50526718-50526737 None:intergenic 30.0%
GAGTTGGGAGATATATAAAA+AGG - chr7_1:50526723-50526742 None:intergenic 30.0%
CTTTCCTTAATTTCAAACCA+AGG + chr7_1:50526925-50526944 Msa1023180:CDS 30.0%
! TCAAAGATTTTTGCAACACT+TGG + chr7_1:50527062-50527081 Msa1023180:CDS 30.0%
! ATAACTTAAAGTGTTCACCT+TGG + chr7_1:50527150-50527169 Msa1023180:CDS 30.0%
AATAACTAGTGTGATTTCCA+AGG - chr7_1:50527170-50527189 None:intergenic 30.0%
!! TTTGGTTTGAAACAAGTCAA+TGG + chr7_1:50527341-50527360 Msa1023180:three_prime_UTR 30.0%
! TTGGTTTGAAACAAGTCAAT+GGG + chr7_1:50527342-50527361 Msa1023180:three_prime_UTR 30.0%
CTTTAGTCAACTTTAGTTGA+AGG - chr7_1:50527494-50527513 None:intergenic 30.0%
AGTTGACTAAAGAGTTTAGA+AGG + chr7_1:50527502-50527521 Msa1023180:three_prime_UTR 30.0%
CTAAAGAGTTTAGAAGGATA+AGG + chr7_1:50527508-50527527 Msa1023180:three_prime_UTR 30.0%
AAAAAGGATAGGAAACTTGT+AGG - chr7_1:50526707-50526726 None:intergenic 30.0%
GGGAGATATATAAAAAGGAT+AGG - chr7_1:50526718-50526737 None:intergenic 30.0%
GAGTTGGGAGATATATAAAA+AGG - chr7_1:50526723-50526742 None:intergenic 30.0%
CTTTCCTTAATTTCAAACCA+AGG + chr7_1:50526925-50526944 Msa1023180:CDS 30.0%
! TCAAAGATTTTTGCAACACT+TGG + chr7_1:50527062-50527081 Msa1023180:CDS 30.0%
! ATAACTTAAAGTGTTCACCT+TGG + chr7_1:50527150-50527169 Msa1023180:CDS 30.0%
AATAACTAGTGTGATTTCCA+AGG - chr7_1:50527170-50527189 None:intergenic 30.0%
!! TTTGGTTTGAAACAAGTCAA+TGG + chr7_1:50527341-50527360 Msa1023180:three_prime_UTR 30.0%
! TTGGTTTGAAACAAGTCAAT+GGG + chr7_1:50527342-50527361 Msa1023180:three_prime_UTR 30.0%
CTTTAGTCAACTTTAGTTGA+AGG - chr7_1:50527494-50527513 None:intergenic 30.0%
AGTTGACTAAAGAGTTTAGA+AGG + chr7_1:50527502-50527521 Msa1023180:three_prime_UTR 30.0%
CTAAAGAGTTTAGAAGGATA+AGG + chr7_1:50527508-50527527 Msa1023180:three_prime_UTR 30.0%
ATGAAACCTCAAAGTTAGAG+AGG - chr7_1:50526769-50526788 None:intergenic 35.0%
AACCATCACTTATAGAAGCA+AGG + chr7_1:50526899-50526918 Msa1023180:CDS 35.0%
AATTAGATCTAGTGGAAGAG+AGG - chr7_1:50527001-50527020 None:intergenic 35.0%
GTTGTTTGCAAATGTTGTGA+TGG + chr7_1:50527086-50527105 Msa1023180:CDS 35.0%
! TGCAAATGTTGTGATGGAAT+TGG + chr7_1:50527092-50527111 Msa1023180:CDS 35.0%
! AAATGTTGTGATGGAATTGG+AGG + chr7_1:50527095-50527114 Msa1023180:CDS 35.0%
AACAAGTTGCAATAGACATG+TGG - chr7_1:50527394-50527413 None:intergenic 35.0%
! AGCATCTTTTGAGCTAAAAC+CGG - chr7_1:50527543-50527562 None:intergenic 35.0%
ATGAAACCTCAAAGTTAGAG+AGG - chr7_1:50526769-50526788 None:intergenic 35.0%
AACCATCACTTATAGAAGCA+AGG + chr7_1:50526899-50526918 Msa1023180:CDS 35.0%
AATTAGATCTAGTGGAAGAG+AGG - chr7_1:50527001-50527020 None:intergenic 35.0%
GTTGTTTGCAAATGTTGTGA+TGG + chr7_1:50527086-50527105 Msa1023180:CDS 35.0%
! TGCAAATGTTGTGATGGAAT+TGG + chr7_1:50527092-50527111 Msa1023180:CDS 35.0%
! AAATGTTGTGATGGAATTGG+AGG + chr7_1:50527095-50527114 Msa1023180:CDS 35.0%
AACAAGTTGCAATAGACATG+TGG - chr7_1:50527394-50527413 None:intergenic 35.0%
! AGCATCTTTTGAGCTAAAAC+CGG - chr7_1:50527543-50527562 None:intergenic 35.0%
ATAGGAAACTTGTAGGATGG+GGG - chr7_1:50526700-50526719 None:intergenic 40.0%
GATAGGAAACTTGTAGGATG+GGG - chr7_1:50526701-50526720 None:intergenic 40.0%
GGATAGGAAACTTGTAGGAT+GGG - chr7_1:50526702-50526721 None:intergenic 40.0%
AGGATAGGAAACTTGTAGGA+TGG - chr7_1:50526703-50526722 None:intergenic 40.0%
TTAGAGAGGTTCAAGAGCTA+TGG - chr7_1:50526755-50526774 None:intergenic 40.0%
CTTGAACCTCTCTAACTTTG+AGG + chr7_1:50526760-50526779 Msa1023180:five_prime_UTR 40.0%
! ATGAGAACATGAGGCTTGTT+TGG - chr7_1:50526844-50526863 None:intergenic 40.0%
GTCCTTGCTTCTATAAGTGA+TGG - chr7_1:50526904-50526923 None:intergenic 40.0%
TTTGTGTCTGCTAGTGCTAA+TGG + chr7_1:50527274-50527293 Msa1023180:three_prime_UTR 40.0%
TTGTGTCTGCTAGTGCTAAT+GGG + chr7_1:50527275-50527294 Msa1023180:three_prime_UTR 40.0%
GAGTTTAGAAGGATAAGGGA+TGG + chr7_1:50527513-50527532 Msa1023180:three_prime_UTR 40.0%
AAGGATAAGGGATGGATATC+CGG + chr7_1:50527521-50527540 Msa1023180:three_prime_UTR 40.0%
ATAGGAAACTTGTAGGATGG+GGG - chr7_1:50526700-50526719 None:intergenic 40.0%
GATAGGAAACTTGTAGGATG+GGG - chr7_1:50526701-50526720 None:intergenic 40.0%
GGATAGGAAACTTGTAGGAT+GGG - chr7_1:50526702-50526721 None:intergenic 40.0%
AGGATAGGAAACTTGTAGGA+TGG - chr7_1:50526703-50526722 None:intergenic 40.0%
TTAGAGAGGTTCAAGAGCTA+TGG - chr7_1:50526755-50526774 None:intergenic 40.0%
CTTGAACCTCTCTAACTTTG+AGG + chr7_1:50526760-50526779 Msa1023180:five_prime_UTR 40.0%
! ATGAGAACATGAGGCTTGTT+TGG - chr7_1:50526844-50526863 None:intergenic 40.0%
GTCCTTGCTTCTATAAGTGA+TGG - chr7_1:50526904-50526923 None:intergenic 40.0%
TTTGTGTCTGCTAGTGCTAA+TGG + chr7_1:50527274-50527293 Msa1023180:three_prime_UTR 40.0%
TTGTGTCTGCTAGTGCTAAT+GGG + chr7_1:50527275-50527294 Msa1023180:three_prime_UTR 40.0%
GAGTTTAGAAGGATAAGGGA+TGG + chr7_1:50527513-50527532 Msa1023180:three_prime_UTR 40.0%
AAGGATAAGGGATGGATATC+CGG + chr7_1:50527521-50527540 Msa1023180:three_prime_UTR 40.0%
!! CTATGGAGCACTGATGAGTT+GGG - chr7_1:50526738-50526757 None:intergenic 45.0%
! GAGGTACTTGCACTAGTACT+TGG + chr7_1:50527114-50527133 Msa1023180:CDS 45.0%
!! CTATGGAGCACTGATGAGTT+GGG - chr7_1:50526738-50526757 None:intergenic 45.0%
! GAGGTACTTGCACTAGTACT+TGG + chr7_1:50527114-50527133 Msa1023180:CDS 45.0%
!!! ATGTTTTTATATTATTAATT+AGG - chr7_1:50526644-50526663 None:intergenic 5.0%
!! GCTATGGAGCACTGATGAGT+TGG - chr7_1:50526739-50526758 None:intergenic 50.0%
!! GCTATGGAGCACTGATGAGT+TGG - chr7_1:50526739-50526758 None:intergenic 50.0%
GTAGGATGGGGGATGCTGCT+TGG - chr7_1:50526689-50526708 None:intergenic 60.0%
GTAGGATGGGGGATGCTGCT+TGG - chr7_1:50526689-50526708 None:intergenic 60.0%
Chromosome Type Strat End Strand Name
chr7_1 gene 50526644 50527793 50526644 ID=Msa1023180;Name=Msa1023180
chr7_1 mRNA 50526644 50527793 50526644 ID=Msa1023180-mRNA-1;Parent=Msa1023180;Name=Msa1023180-mRNA-1;_AED=0.04;_eAED=0.04;_QI=191|1|1|1|1|1|2|609|79
chr7_1 exon 50526644 50526946 50526644 ID=Msa1023180-mRNA-1:exon:9906;Parent=Msa1023180-mRNA-1
chr7_1 exon 50527057 50527793 50527057 ID=Msa1023180-mRNA-1:exon:9907;Parent=Msa1023180-mRNA-1
chr7_1 five_prime_UTR 50526644 50526834 50526644 ID=Msa1023180-mRNA-1:five_prime_utr;Parent=Msa1023180-mRNA-1
chr7_1 CDS 50526835 50526946 50526835 ID=Msa1023180-mRNA-1:cds;Parent=Msa1023180-mRNA-1
chr7_1 CDS 50527057 50527184 50527057 ID=Msa1023180-mRNA-1:cds;Parent=Msa1023180-mRNA-1
chr7_1 three_prime_UTR 50527185 50527793 50527185 ID=Msa1023180-mRNA-1:three_prime_utr;Parent=Msa1023180-mRNA-1
Gene Sequence

>Msa1023180

ATGAGTCCAAACAAGCCTCATGTTCTCATATTACTAATCATCATGCTTGTTTCAGTTTCTAATAAACCATCACTTATAGAAGCAAGGACACTTTCCTTAATTTCAAACCAAGGGTACTCAAAGATTTTTGCAACACTTGGAGTTGTTTGCAAATGTTGTGATGGAATTGGAGGTACTTGCACTAGTACTTGGACACAATCTTGTAATAACTTAAAGTGTTCACCTTGGAAATCACACTAG

Protein sequence

>Msa1023180

MSPNKPHVLILLIIMLVSVSNKPSLIEARTLSLISNQGYSKIFATLGVVCKCCDGIGGTCTSTWTQSCNNLKCSPWKSH*