AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1370200


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1370200 MtrunA17_Chr4g0054501 86.842 76 10 0 38 113 12 87 7.68e-44 137
Msa1370200 MtrunA17_Chr1g0158721 75.000 60 12 1 39 98 13 69 1.66e-25 94.0
Msa1370200 MtrunA17_Chr6g0449691 78.689 61 11 1 25 85 181 239 1.68e-24 96.3
Msa1370200 MtrunA17_Chr3g0113101 55.294 85 26 1 1 85 97 169 2.07e-21 87.0
Msa1370200 MtrunA17_Chr6g0487231 69.231 39 12 0 38 76 175 213 1.30e-12 62.4
Msa1370200 MtrunA17_Chr4g0070851 56.818 44 19 0 39 82 177 220 1.93e-11 59.3
Msa1370200 MtrunA17_Chr2g0299991 51.111 45 22 0 38 82 176 220 4.42e-11 58.2
Msa1370200 MtrunA17_Chr5g0410861 62.791 43 15 1 38 80 29 70 6.42e-11 54.3
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1370200 AT5G40440.4 87.234 47 6 0 39 85 192 238 3.32e-23 93.2
Msa1370200 AT5G40440.1 87.234 47 6 0 39 85 192 238 3.32e-23 93.2
Msa1370200 AT5G40440.5 87.234 47 6 0 39 85 110 156 3.49e-23 92.8
Msa1370200 AT5G40440.6 87.234 47 6 0 39 85 174 220 4.42e-23 92.8
Msa1370200 AT5G40440.3 87.234 47 6 0 39 85 174 220 4.42e-23 92.8
Msa1370200 AT5G40440.2 87.234 47 6 0 39 85 174 220 4.42e-23 92.8
Msa1370200 AT3G55800.1 49.412 85 31 1 1 85 104 176 1.26e-18 79.7
Msa1370200 AT5G56580.1 60.000 45 18 0 40 84 179 223 1.45e-12 62.8
Msa1370200 AT4G29810.3 52.083 48 23 0 38 85 185 232 5.21e-12 61.2
Msa1370200 AT4G29810.1 53.191 47 22 0 39 85 177 223 5.69e-12 61.2
Msa1370200 AT4G29810.2 53.191 47 22 0 39 85 186 232 5.82e-12 61.2

Find 14 sgRNAs with CRISPR-Local

Find 122 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
ACACAATGTGTTAACTCTTT+TGG 0.201562 tig0019099:+187649 Msa1370200:CDS
GAGCCGAAAATTACTGATTT+TGG 0.210770 tig0019099:+188673 Msa1370200:CDS
ATTTACTTGTAAACCTCAAA+GGG 0.420841 tig0019099:+188650 Msa1370200:CDS
AGGTTTACAAGTAAATTAGC+AGG 0.487423 tig0019099:-188643 None:intergenic
AATTTACTTGTAAACCTCAA+AGG 0.501450 tig0019099:+188649 Msa1370200:CDS
CATAGAGAATTCAGTTGCAA+TGG 0.563989 tig0019099:+188708 Msa1370200:CDS
GCTCAACAAGATCCTCAATA+CGG 0.592189 tig0019099:-188973 None:intergenic
TGGGGATGAGCAGCTTGCAG+TGG 0.595661 tig0019099:+187669 Msa1370200:CDS
AGATGAGCAAGTCCGTATTG+AGG 0.604364 tig0019099:+188961 Msa1370200:CDS
GCAGCTTGCAGTGGATATGA+TGG 0.623243 tig0019099:+187678 Msa1370200:CDS
GTGAAGACAACTTCTTGTGG+TGG 0.628890 tig0019099:+187625 Msa1370200:CDS
AAAGTGAAGACAACTTCTTG+TGG 0.638471 tig0019099:+187622 Msa1370200:CDS
AAGGGTCTAAGTTATCTGCA+CGG 0.655190 tig0019099:+188589 Msa1370200:intron
TTTACTTGTAAACCTCAAAG+GGG 0.694553 tig0019099:+188651 Msa1370200:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! GTTTTTTTAATCTTTTTGAA+GGG + tig0019099:188571-188590 Msa1370200:intron 15.0%
!!! GTTTTTTTAATCTTTTTGAA+GGG + tig0019099:188571-188590 Msa1370200:intron 15.0%
!! TAATTAAACTGATTATGTAG+TGG + tig0019099:187790-187809 Msa1370200:intron 20.0%
!!! TCATAATTTGTTGTTTCATT+AGG - tig0019099:187835-187854 None:intergenic 20.0%
!! AAATTAAACAATACAACATG+TGG + tig0019099:187971-187990 Msa1370200:intron 20.0%
!! ACTCTATTAGTGATATAATT+AGG + tig0019099:188268-188287 Msa1370200:intron 20.0%
!! AACATGAAACAATTATGATT+TGG - tig0019099:188343-188362 None:intergenic 20.0%
!!! GGTTTTTTTAATCTTTTTGA+AGG + tig0019099:188570-188589 Msa1370200:intron 20.0%
!!! ATACCAAAATCAGTAATTTT+CGG - tig0019099:188679-188698 None:intergenic 20.0%
!! TAATTAAACTGATTATGTAG+TGG + tig0019099:187790-187809 Msa1370200:intron 20.0%
!!! TCATAATTTGTTGTTTCATT+AGG - tig0019099:187835-187854 None:intergenic 20.0%
!! AAATTAAACAATACAACATG+TGG + tig0019099:187971-187990 Msa1370200:intron 20.0%
!! ACTCTATTAGTGATATAATT+AGG + tig0019099:188268-188287 Msa1370200:intron 20.0%
!! AACATGAAACAATTATGATT+TGG - tig0019099:188343-188362 None:intergenic 20.0%
!!! GGTTTTTTTAATCTTTTTGA+AGG + tig0019099:188570-188589 Msa1370200:intron 20.0%
!!! ATACCAAAATCAGTAATTTT+CGG - tig0019099:188679-188698 None:intergenic 20.0%
!!! ACAAAAGTATCAGAATCTTA+CGG - tig0019099:187895-187914 None:intergenic 25.0%
!!! TTGATTTGTGTTCATATAAC+AGG + tig0019099:188043-188062 Msa1370200:intron 25.0%
! AATAGAGTCACACAAATAAA+GGG - tig0019099:188256-188275 None:intergenic 25.0%
! TAATAGAGTCACACAAATAA+AGG - tig0019099:188257-188276 None:intergenic 25.0%
! ATCATTTCCACACAAATAAA+GGG - tig0019099:188302-188321 None:intergenic 25.0%
! ATGATCTCAAACATTTAAGA+AGG + tig0019099:188317-188336 Msa1370200:intron 25.0%
! TGAAACATGGATGATAAAAT+AGG - tig0019099:188455-188474 None:intergenic 25.0%
! AATTTACTTGTAAACCTCAA+AGG + tig0019099:188649-188668 Msa1370200:CDS 25.0%
! ATTTACTTGTAAACCTCAAA+GGG + tig0019099:188650-188669 Msa1370200:CDS 25.0%
!!! ACAAAAGTATCAGAATCTTA+CGG - tig0019099:187895-187914 None:intergenic 25.0%
!!! TTGATTTGTGTTCATATAAC+AGG + tig0019099:188043-188062 Msa1370200:intron 25.0%
! AATAGAGTCACACAAATAAA+GGG - tig0019099:188256-188275 None:intergenic 25.0%
! TAATAGAGTCACACAAATAA+AGG - tig0019099:188257-188276 None:intergenic 25.0%
! ATCATTTCCACACAAATAAA+GGG - tig0019099:188302-188321 None:intergenic 25.0%
! ATGATCTCAAACATTTAAGA+AGG + tig0019099:188317-188336 Msa1370200:intron 25.0%
! TGAAACATGGATGATAAAAT+AGG - tig0019099:188455-188474 None:intergenic 25.0%
! AATTTACTTGTAAACCTCAA+AGG + tig0019099:188649-188668 Msa1370200:CDS 25.0%
! ATTTACTTGTAAACCTCAAA+GGG + tig0019099:188650-188669 Msa1370200:CDS 25.0%
! ACACAATGTGTTAACTCTTT+TGG + tig0019099:187649-187668 Msa1370200:CDS 30.0%
! CACAATGTGTTAACTCTTTT+GGG + tig0019099:187650-187669 Msa1370200:CDS 30.0%
! ACAATGTGTTAACTCTTTTG+GGG + tig0019099:187651-187670 Msa1370200:CDS 30.0%
! TACCATGCAATAGTAGTTTT+AGG + tig0019099:188120-188139 Msa1370200:intron 30.0%
! ACTTATTCATGATAGCGTTA+AGG + tig0019099:188160-188179 Msa1370200:intron 30.0%
GATCATTTCCACACAAATAA+AGG - tig0019099:188303-188322 None:intergenic 30.0%
! AATTGTTTCATGTTGACTGA+TGG + tig0019099:188349-188368 Msa1370200:intron 30.0%
ATGGATGATAAAATAGGTTC+GGG - tig0019099:188449-188468 None:intergenic 30.0%
CATGGATGATAAAATAGGTT+CGG - tig0019099:188450-188469 None:intergenic 30.0%
ATTGAGATATGCTACTAACT+TGG + tig0019099:188545-188564 Msa1370200:intron 30.0%
AGGTTTACAAGTAAATTAGC+AGG - tig0019099:188646-188665 None:intergenic 30.0%
TTTACTTGTAAACCTCAAAG+GGG + tig0019099:188651-188670 Msa1370200:CDS 30.0%
!! ACTGATTTTGGTATTAGTGT+TGG + tig0019099:188685-188704 Msa1370200:CDS 30.0%
GAAGTGCAATTTCTATCTAT+AGG - tig0019099:188938-188957 None:intergenic 30.0%
! ACACAATGTGTTAACTCTTT+TGG + tig0019099:187649-187668 Msa1370200:CDS 30.0%
! CACAATGTGTTAACTCTTTT+GGG + tig0019099:187650-187669 Msa1370200:CDS 30.0%
! ACAATGTGTTAACTCTTTTG+GGG + tig0019099:187651-187670 Msa1370200:CDS 30.0%
! TACCATGCAATAGTAGTTTT+AGG + tig0019099:188120-188139 Msa1370200:intron 30.0%
! ACTTATTCATGATAGCGTTA+AGG + tig0019099:188160-188179 Msa1370200:intron 30.0%
GATCATTTCCACACAAATAA+AGG - tig0019099:188303-188322 None:intergenic 30.0%
! AATTGTTTCATGTTGACTGA+TGG + tig0019099:188349-188368 Msa1370200:intron 30.0%
ATGGATGATAAAATAGGTTC+GGG - tig0019099:188449-188468 None:intergenic 30.0%
CATGGATGATAAAATAGGTT+CGG - tig0019099:188450-188469 None:intergenic 30.0%
ATTGAGATATGCTACTAACT+TGG + tig0019099:188545-188564 Msa1370200:intron 30.0%
AGGTTTACAAGTAAATTAGC+AGG - tig0019099:188646-188665 None:intergenic 30.0%
TTTACTTGTAAACCTCAAAG+GGG + tig0019099:188651-188670 Msa1370200:CDS 30.0%
!! ACTGATTTTGGTATTAGTGT+TGG + tig0019099:188685-188704 Msa1370200:CDS 30.0%
GAAGTGCAATTTCTATCTAT+AGG - tig0019099:188938-188957 None:intergenic 30.0%
AAAGTGAAGACAACTTCTTG+TGG + tig0019099:187622-187641 Msa1370200:CDS 35.0%
! GGCTAATAATCTTCGTTTTG+AGG + tig0019099:187699-187718 Msa1370200:CDS 35.0%
CATCAATAACTCATCTGCTT+CGG + tig0019099:187863-187882 Msa1370200:intron 35.0%
ATCAATAACTCATCTGCTTC+GGG + tig0019099:187864-187883 Msa1370200:intron 35.0%
GTCCTAAAACTACTATTGCA+TGG - tig0019099:188125-188144 None:intergenic 35.0%
! GTGATACTTTTGTGGCAATT+AGG + tig0019099:188371-188390 Msa1370200:intron 35.0%
TTTGTGGCAATTAGGAGATA+AGG + tig0019099:188379-188398 Msa1370200:intron 35.0%
AATATATGCTCCTTACACGT+AGG - tig0019099:188484-188503 None:intergenic 35.0%
AGATATGCTACTAACTTGGT+TGG + tig0019099:188549-188568 Msa1370200:intron 35.0%
!!! GAGCCGAAAATTACTGATTT+TGG + tig0019099:188673-188692 Msa1370200:CDS 35.0%
CATAGAGAATTCAGTTGCAA+TGG + tig0019099:188708-188727 Msa1370200:CDS 35.0%
AACAAAGTGTGGAAGCAAAT+CGG - tig0019099:188774-188793 None:intergenic 35.0%
AAAGTGAAGACAACTTCTTG+TGG + tig0019099:187622-187641 Msa1370200:CDS 35.0%
! GGCTAATAATCTTCGTTTTG+AGG + tig0019099:187699-187718 Msa1370200:CDS 35.0%
CATCAATAACTCATCTGCTT+CGG + tig0019099:187863-187882 Msa1370200:intron 35.0%
ATCAATAACTCATCTGCTTC+GGG + tig0019099:187864-187883 Msa1370200:intron 35.0%
GTCCTAAAACTACTATTGCA+TGG - tig0019099:188125-188144 None:intergenic 35.0%
! GTGATACTTTTGTGGCAATT+AGG + tig0019099:188371-188390 Msa1370200:intron 35.0%
TTTGTGGCAATTAGGAGATA+AGG + tig0019099:188379-188398 Msa1370200:intron 35.0%
AATATATGCTCCTTACACGT+AGG - tig0019099:188484-188503 None:intergenic 35.0%
AGATATGCTACTAACTTGGT+TGG + tig0019099:188549-188568 Msa1370200:intron 35.0%
!!! GAGCCGAAAATTACTGATTT+TGG + tig0019099:188673-188692 Msa1370200:CDS 35.0%
CATAGAGAATTCAGTTGCAA+TGG + tig0019099:188708-188727 Msa1370200:CDS 35.0%
AACAAAGTGTGGAAGCAAAT+CGG - tig0019099:188774-188793 None:intergenic 35.0%
TTCCACACAAATAAAGGGTC+TGG - tig0019099:188297-188316 None:intergenic 40.0%
!! GACTGATGGTGATACTTTTG+TGG + tig0019099:188363-188382 Msa1370200:intron 40.0%
GGAGATAAGGACATTATGTG+AGG + tig0019099:188392-188411 Msa1370200:intron 40.0%
TCTACAAGACCCTCATAACA+AGG - tig0019099:188420-188439 None:intergenic 40.0%
AAGGGTCTAAGTTATCTGCA+CGG + tig0019099:188589-188608 Msa1370200:intron 40.0%
TCAGTCAAGCAAACAAAGTG+TGG - tig0019099:188785-188804 None:intergenic 40.0%
GCTCAACAAGATCCTCAATA+CGG - tig0019099:188976-188995 None:intergenic 40.0%
TTCCACACAAATAAAGGGTC+TGG - tig0019099:188297-188316 None:intergenic 40.0%
!! GACTGATGGTGATACTTTTG+TGG + tig0019099:188363-188382 Msa1370200:intron 40.0%
GGAGATAAGGACATTATGTG+AGG + tig0019099:188392-188411 Msa1370200:intron 40.0%
TCTACAAGACCCTCATAACA+AGG - tig0019099:188420-188439 None:intergenic 40.0%
AAGGGTCTAAGTTATCTGCA+CGG + tig0019099:188589-188608 Msa1370200:intron 40.0%
TCAGTCAAGCAAACAAAGTG+TGG - tig0019099:188785-188804 None:intergenic 40.0%
GCTCAACAAGATCCTCAATA+CGG - tig0019099:188976-188995 None:intergenic 40.0%
GTGAAGACAACTTCTTGTGG+TGG + tig0019099:187625-187644 Msa1370200:CDS 45.0%
! TGATAGCGTTAAGGCGTCAA+TGG + tig0019099:188169-188188 Msa1370200:intron 45.0%
! TGCCAGACCCTTTATTTGTG+TGG + tig0019099:188292-188311 Msa1370200:intron 45.0%
! ATGTGAGGCACCTTGTTATG+AGG + tig0019099:188407-188426 Msa1370200:intron 45.0%
! TGTGAGGCACCTTGTTATGA+GGG + tig0019099:188408-188427 Msa1370200:intron 45.0%
!! ACGTAGGAGCTTCTGAAACA+TGG - tig0019099:188468-188487 None:intergenic 45.0%
TTCAGAAGCTCCTACGTGTA+AGG + tig0019099:188471-188490 Msa1370200:intron 45.0%
! TAATTTTCGGCTCCCCTTTG+AGG - tig0019099:188666-188685 None:intergenic 45.0%
AGATGAGCAAGTCCGTATTG+AGG + tig0019099:188961-188980 Msa1370200:CDS 45.0%
GTGAAGACAACTTCTTGTGG+TGG + tig0019099:187625-187644 Msa1370200:CDS 45.0%
! TGATAGCGTTAAGGCGTCAA+TGG + tig0019099:188169-188188 Msa1370200:intron 45.0%
! TGCCAGACCCTTTATTTGTG+TGG + tig0019099:188292-188311 Msa1370200:intron 45.0%
! ATGTGAGGCACCTTGTTATG+AGG + tig0019099:188407-188426 Msa1370200:intron 45.0%
! TGTGAGGCACCTTGTTATGA+GGG + tig0019099:188408-188427 Msa1370200:intron 45.0%
!! ACGTAGGAGCTTCTGAAACA+TGG - tig0019099:188468-188487 None:intergenic 45.0%
TTCAGAAGCTCCTACGTGTA+AGG + tig0019099:188471-188490 Msa1370200:intron 45.0%
! TAATTTTCGGCTCCCCTTTG+AGG - tig0019099:188666-188685 None:intergenic 45.0%
AGATGAGCAAGTCCGTATTG+AGG + tig0019099:188961-188980 Msa1370200:CDS 45.0%
GCAGCTTGCAGTGGATATGA+TGG + tig0019099:187678-187697 Msa1370200:CDS 50.0%
GCAGCTTGCAGTGGATATGA+TGG + tig0019099:187678-187697 Msa1370200:CDS 50.0%
TGGGGATGAGCAGCTTGCAG+TGG + tig0019099:187669-187688 Msa1370200:CDS 60.0%
TGGGGATGAGCAGCTTGCAG+TGG + tig0019099:187669-187688 Msa1370200:CDS 60.0%
Chromosome Type Strat End Strand Name
tig0019099 gene 187604 189028 187604 ID=Msa1370200;Name=Msa1370200
tig0019099 mRNA 187604 189028 187604 ID=Msa1370200-mRNA-1;Parent=Msa1370200;Name=Msa1370200-mRNA-1;_AED=0.27;_eAED=0.27;_QI=0|0|0|0.66|0.5|0.66|3|0|113
tig0019099 exon 187604 187720 187604 ID=Msa1370200-mRNA-1:exon:1546;Parent=Msa1370200-mRNA-1
tig0019099 exon 188592 188729 188592 ID=Msa1370200-mRNA-1:exon:1547;Parent=Msa1370200-mRNA-1
tig0019099 exon 188942 189028 188942 ID=Msa1370200-mRNA-1:exon:1548;Parent=Msa1370200-mRNA-1
tig0019099 CDS 187604 187720 187604 ID=Msa1370200-mRNA-1:cds;Parent=Msa1370200-mRNA-1
tig0019099 CDS 188592 188729 188592 ID=Msa1370200-mRNA-1:cds;Parent=Msa1370200-mRNA-1
tig0019099 CDS 188942 189028 188942 ID=Msa1370200-mRNA-1:cds;Parent=Msa1370200-mRNA-1
Gene Sequence

>Msa1370200

TTGAGAACAATTTCTTTCAAAGTGAAGACAACTTCTTGTGGTGGAACACAATGTGTTAACTCTTTTGGGGATGAGCAGCTTGCAGTGGATATGATGGCTAATAATCTTCGTTTTGAGGGTCTAAGTTATCTGCACGGAGTCAGATATTTAGTTCACAGAGACATAAAGCCTGCTAATTTACTTGTAAACCTCAAAGGGGAGCCGAAAATTACTGATTTTGGTATTAGTGTTGGCATAGAGAATTCAGTTGCAATGATAGAAATTGCACTTCAAAAGATGAGCAAGTCCGTATTGAGGATCTTGTTGAGCTGTGAGAGAACGACTAGATTATCTCATTGTTGA

Protein sequence

>Msa1370200

LRTISFKVKTTSCGGTQCVNSFGDEQLAVDMMANNLRFEGLSYLHGVRYLVHRDIKPANLLVNLKGEPKITDFGISVGIENSVAMIEIALQKMSKSVLRILLSCERTTRLSHC*