AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1034280


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1034280 MtrunA17_Chr7g0257121 83.838 99 14 1 5 101 136 234 3.80e-55 171
Msa1034280 MtrunA17_Chr1g0159641 76.768 99 21 1 5 101 134 232 5.83e-50 158
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1034280 AT1G77320.1 62.963 81 28 1 18 98 150 228 5.29e-30 112
Msa1034280 AT1G77320.3 62.963 81 28 1 18 98 150 228 5.30e-30 112
Msa1034280 AT1G77320.2 62.667 75 26 1 18 92 143 215 1.01e-26 102

Find 16 sgRNAs with CRISPR-Local

Find 94 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TATATGGTTCTTCCTTTCTC+TGG 0.215900 7_1:-69713611 Msa1034280:CDS
TGATGTCTGGCAGTGGGCTT+TGG 0.347637 7_1:-69713714 Msa1034280:intron
TGTTCCTCAAGAGTCATATA+TGG 0.385478 7_1:-69713627 Msa1034280:CDS
AAGTAACTACTGGTTTCTTC+AGG 0.396829 7_1:+69713687 None:intergenic
ATATGGTTCTTCCTTTCTCT+GGG 0.421830 7_1:-69713610 Msa1034280:CDS
AACCATTCATAAGTAACTAC+TGG 0.442581 7_1:+69713677 None:intergenic
AACCAGTAGTTACTTATGAA+TGG 0.446544 7_1:-69713679 Msa1034280:CDS
CATGTAATTTACAACCTGCT+TGG 0.457894 7_1:+69713564 None:intergenic
TGAAGCTTATGTTAGTTCAC+TGG 0.469003 7_1:-69714241 Msa1034280:CDS
GGGTTAAAGATCTGTGTGAC+TGG 0.518889 7_1:-69713590 Msa1034280:CDS
TTTAGATAAGCGCAAAGAGA+TGG 0.519107 7_1:-69713482 Msa1034280:intron
CAGATCTTTAACCCAGAGAA+AGG 0.530794 7_1:+69713599 None:intergenic
CAACTGATAGAATTATCAAA+AGG 0.531168 7_1:+69713381 None:intergenic
AAACTTATTCTACAAAATGG+TGG 0.599072 7_1:-69713457 Msa1034280:CDS
TGTGTGACTGGAATCCAAGC+AGG 0.611137 7_1:-69713578 Msa1034280:intron
AGAACCATATATGACTCTTG+AGG 0.617430 7_1:+69713623 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AAAAAAAACAAAAAAAATGA+AGG + chr7_1:69713636-69713655 None:intergenic 10.0%
!! AAAAAAAACAAAAAAAATGA+AGG + chr7_1:69713636-69713655 None:intergenic 10.0%
!!! ATATTATATTGCTTCTTTTT+CGG + chr7_1:69713555-69713574 None:intergenic 15.0%
!!! ATATTATATTGCTTCTTTTT+CGG + chr7_1:69713555-69713574 None:intergenic 15.0%
!!! TGGTAATGTAAAATTAGTAA+AGG - chr7_1:69713451-69713470 Msa1034280:CDS 20.0%
!!! CTCTAAAAAAAAAACATTGT+TGG - chr7_1:69713587-69713606 Msa1034280:CDS 20.0%
!!! TTTGTTTTTTTTTTCCTTCT+TGG - chr7_1:69713644-69713663 Msa1034280:CDS 20.0%
!! AATTACATGTCTATTAGTAT+TGG - chr7_1:69714106-69714125 Msa1034280:intron 20.0%
!! GAAAAACTTATTCTACAAAA+TGG - chr7_1:69714196-69714215 Msa1034280:intron 20.0%
!!! TGGTAATGTAAAATTAGTAA+AGG - chr7_1:69713451-69713470 Msa1034280:CDS 20.0%
!!! CTCTAAAAAAAAAACATTGT+TGG - chr7_1:69713587-69713606 Msa1034280:CDS 20.0%
!!! TTTGTTTTTTTTTTCCTTCT+TGG - chr7_1:69713644-69713663 Msa1034280:CDS 20.0%
!! AATTACATGTCTATTAGTAT+TGG - chr7_1:69714106-69714125 Msa1034280:intron 20.0%
!! GAAAAACTTATTCTACAAAA+TGG - chr7_1:69714196-69714215 Msa1034280:intron 20.0%
!!! TCACTGGTTGTATTATTTTA+TGG - chr7_1:69713431-69713450 Msa1034280:CDS 25.0%
! AAACTTATTCTACAAAATGG+TGG - chr7_1:69714199-69714218 Msa1034280:intron 25.0%
!!! TCACTGGTTGTATTATTTTA+TGG - chr7_1:69713431-69713450 Msa1034280:CDS 25.0%
! AAACTTATTCTACAAAATGG+TGG - chr7_1:69714199-69714218 Msa1034280:intron 25.0%
! CTACAACAAACGTTTTTCAT+TGG - chr7_1:69713610-69713629 Msa1034280:CDS 30.0%
!!! TGCTCATATGTTTTGTTTCT+TGG - chr7_1:69713717-69713736 Msa1034280:intron 30.0%
! TGGTCTTTCTCATTTAGTTT+CGG - chr7_1:69713737-69713756 Msa1034280:intron 30.0%
TACGAAGATGAACTTATTAG+TGG + chr7_1:69713796-69713815 None:intergenic 30.0%
ATTAAAATCTCCTCAGAGAT+TGG + chr7_1:69713883-69713902 None:intergenic 30.0%
AACCAGTAGTTACTTATGAA+TGG - chr7_1:69713977-69713996 Msa1034280:intron 30.0%
AACCATTCATAAGTAACTAC+TGG + chr7_1:69713982-69714001 None:intergenic 30.0%
! CTACAACAAACGTTTTTCAT+TGG - chr7_1:69713610-69713629 Msa1034280:CDS 30.0%
!!! TGCTCATATGTTTTGTTTCT+TGG - chr7_1:69713717-69713736 Msa1034280:intron 30.0%
! TGGTCTTTCTCATTTAGTTT+CGG - chr7_1:69713737-69713756 Msa1034280:intron 30.0%
TACGAAGATGAACTTATTAG+TGG + chr7_1:69713796-69713815 None:intergenic 30.0%
ATTAAAATCTCCTCAGAGAT+TGG + chr7_1:69713883-69713902 None:intergenic 30.0%
AACCAGTAGTTACTTATGAA+TGG - chr7_1:69713977-69713996 Msa1034280:intron 30.0%
AACCATTCATAAGTAACTAC+TGG + chr7_1:69713982-69714001 None:intergenic 30.0%
TGAAGCTTATGTTAGTTCAC+TGG - chr7_1:69713415-69713434 Msa1034280:CDS 35.0%
ATTAGGGATGAAAACCAAGA+AGG + chr7_1:69713661-69713680 None:intergenic 35.0%
! TGGTTTTCATCCCTAATTGT+TGG - chr7_1:69713664-69713683 Msa1034280:CDS 35.0%
! GGTTTTCATCCCTAATTGTT+GGG - chr7_1:69713665-69713684 Msa1034280:CDS 35.0%
! GTTTTCATCCCTAATTGTTG+GGG - chr7_1:69713666-69713685 Msa1034280:CDS 35.0%
! GGTCTTTCTCATTTAGTTTC+GGG - chr7_1:69713738-69713757 Msa1034280:intron 35.0%
!! TTCTCATTTAGTTTCGGGTT+TGG - chr7_1:69713743-69713762 Msa1034280:intron 35.0%
AGATTGGATAAGTGTGGAAT+TGG + chr7_1:69713867-69713886 None:intergenic 35.0%
AATATACACCATGTGATGTC+TGG - chr7_1:69713929-69713948 Msa1034280:intron 35.0%
!! AAGTAACTACTGGTTTCTTC+AGG + chr7_1:69713972-69713991 None:intergenic 35.0%
TGTTCCTCAAGAGTCATATA+TGG - chr7_1:69714029-69714048 Msa1034280:intron 35.0%
AGAACCATATATGACTCTTG+AGG + chr7_1:69714036-69714055 None:intergenic 35.0%
TATATGGTTCTTCCTTTCTC+TGG - chr7_1:69714045-69714064 Msa1034280:intron 35.0%
ATATGGTTCTTCCTTTCTCT+GGG - chr7_1:69714046-69714065 Msa1034280:intron 35.0%
CATGTAATTTACAACCTGCT+TGG + chr7_1:69714095-69714114 None:intergenic 35.0%
TTTAGATAAGCGCAAAGAGA+TGG - chr7_1:69714174-69714193 Msa1034280:intron 35.0%
TGAAGCTTATGTTAGTTCAC+TGG - chr7_1:69713415-69713434 Msa1034280:CDS 35.0%
ATTAGGGATGAAAACCAAGA+AGG + chr7_1:69713661-69713680 None:intergenic 35.0%
! TGGTTTTCATCCCTAATTGT+TGG - chr7_1:69713664-69713683 Msa1034280:CDS 35.0%
! GGTTTTCATCCCTAATTGTT+GGG - chr7_1:69713665-69713684 Msa1034280:CDS 35.0%
! GTTTTCATCCCTAATTGTTG+GGG - chr7_1:69713666-69713685 Msa1034280:CDS 35.0%
! GGTCTTTCTCATTTAGTTTC+GGG - chr7_1:69713738-69713757 Msa1034280:intron 35.0%
!! TTCTCATTTAGTTTCGGGTT+TGG - chr7_1:69713743-69713762 Msa1034280:intron 35.0%
AGATTGGATAAGTGTGGAAT+TGG + chr7_1:69713867-69713886 None:intergenic 35.0%
AATATACACCATGTGATGTC+TGG - chr7_1:69713929-69713948 Msa1034280:intron 35.0%
!! AAGTAACTACTGGTTTCTTC+AGG + chr7_1:69713972-69713991 None:intergenic 35.0%
TGTTCCTCAAGAGTCATATA+TGG - chr7_1:69714029-69714048 Msa1034280:intron 35.0%
AGAACCATATATGACTCTTG+AGG + chr7_1:69714036-69714055 None:intergenic 35.0%
TATATGGTTCTTCCTTTCTC+TGG - chr7_1:69714045-69714064 Msa1034280:intron 35.0%
ATATGGTTCTTCCTTTCTCT+GGG - chr7_1:69714046-69714065 Msa1034280:intron 35.0%
CATGTAATTTACAACCTGCT+TGG + chr7_1:69714095-69714114 None:intergenic 35.0%
TTTAGATAAGCGCAAAGAGA+TGG - chr7_1:69714174-69714193 Msa1034280:intron 35.0%
CCACAAATCCCCAACAATTA+GGG + chr7_1:69713677-69713696 None:intergenic 40.0%
ACCACAAATCCCCAACAATT+AGG + chr7_1:69713678-69713697 None:intergenic 40.0%
TAATTGTTGGGGATTTGTGG+TGG - chr7_1:69713677-69713696 Msa1034280:CDS 40.0%
TGGTGGCTAATATGACTCTA+TGG - chr7_1:69713694-69713713 Msa1034280:CDS 40.0%
ATTAGTGGTCATCTAGATGC+AGG + chr7_1:69713781-69713800 None:intergenic 40.0%
CAGATCTTTAACCCAGAGAA+AGG + chr7_1:69714060-69714079 None:intergenic 40.0%
CCACAAATCCCCAACAATTA+GGG + chr7_1:69713677-69713696 None:intergenic 40.0%
ACCACAAATCCCCAACAATT+AGG + chr7_1:69713678-69713697 None:intergenic 40.0%
TAATTGTTGGGGATTTGTGG+TGG - chr7_1:69713677-69713696 Msa1034280:CDS 40.0%
TGGTGGCTAATATGACTCTA+TGG - chr7_1:69713694-69713713 Msa1034280:CDS 40.0%
ATTAGTGGTCATCTAGATGC+AGG + chr7_1:69713781-69713800 None:intergenic 40.0%
CAGATCTTTAACCCAGAGAA+AGG + chr7_1:69714060-69714079 None:intergenic 40.0%
CCCTAATTGTTGGGGATTTG+TGG - chr7_1:69713674-69713693 Msa1034280:CDS 45.0%
CCTCAGAGATTGGATAAGTG+TGG + chr7_1:69713873-69713892 None:intergenic 45.0%
CCACACTTATCCAATCTCTG+AGG - chr7_1:69713870-69713889 Msa1034280:intron 45.0%
GGGTTAAAGATCTGTGTGAC+TGG - chr7_1:69714066-69714085 Msa1034280:intron 45.0%
CCCTAATTGTTGGGGATTTG+TGG - chr7_1:69713674-69713693 Msa1034280:CDS 45.0%
CCTCAGAGATTGGATAAGTG+TGG + chr7_1:69713873-69713892 None:intergenic 45.0%
CCACACTTATCCAATCTCTG+AGG - chr7_1:69713870-69713889 Msa1034280:intron 45.0%
GGGTTAAAGATCTGTGTGAC+TGG - chr7_1:69714066-69714085 Msa1034280:intron 45.0%
ACCATGTGATGTCTGGCAGT+GGG - chr7_1:69713936-69713955 Msa1034280:intron 50.0%
TGTGTGACTGGAATCCAAGC+AGG - chr7_1:69714078-69714097 Msa1034280:intron 50.0%
ACCATGTGATGTCTGGCAGT+GGG - chr7_1:69713936-69713955 Msa1034280:intron 50.0%
TGTGTGACTGGAATCCAAGC+AGG - chr7_1:69714078-69714097 Msa1034280:intron 50.0%
CACCATGTGATGTCTGGCAG+TGG - chr7_1:69713935-69713954 Msa1034280:intron 55.0%
! TGATGTCTGGCAGTGGGCTT+TGG - chr7_1:69713942-69713961 Msa1034280:intron 55.0%
CACCATGTGATGTCTGGCAG+TGG - chr7_1:69713935-69713954 Msa1034280:intron 55.0%
! TGATGTCTGGCAGTGGGCTT+TGG - chr7_1:69713942-69713961 Msa1034280:intron 55.0%
GCCCACTGCCAGACATCACA+TGG + chr7_1:69713940-69713959 None:intergenic 60.0%
GCCCACTGCCAGACATCACA+TGG + chr7_1:69713940-69713959 None:intergenic 60.0%
Chromosome Type Strat End Strand Name
chr7_1 gene 69713396 69714282 69713396 ID=Msa1034280;Name=Msa1034280
chr7_1 mRNA 69713396 69714282 69713396 ID=Msa1034280-mRNA-1;Parent=Msa1034280;Name=Msa1034280-mRNA-1;_AED=0.56;_eAED=0.56;_QI=0|0.5|0.33|0.66|0.5|0.66|3|0|101
chr7_1 exon 69714226 69714282 69714226 ID=Msa1034280-mRNA-1:exon:16512;Parent=Msa1034280-mRNA-1
chr7_1 exon 69713579 69713723 69713579 ID=Msa1034280-mRNA-1:exon:16511;Parent=Msa1034280-mRNA-1
chr7_1 exon 69713396 69713499 69713396 ID=Msa1034280-mRNA-1:exon:16510;Parent=Msa1034280-mRNA-1
chr7_1 CDS 69714226 69714282 69714226 ID=Msa1034280-mRNA-1:cds;Parent=Msa1034280-mRNA-1
chr7_1 CDS 69713579 69713723 69713579 ID=Msa1034280-mRNA-1:cds;Parent=Msa1034280-mRNA-1
chr7_1 CDS 69713396 69713499 69713396 ID=Msa1034280-mRNA-1:cds;Parent=Msa1034280-mRNA-1
Gene Sequence

>Msa1034280

ATGGATTTCATTTCTGATTTGAAGCTTATGTTAGTTCACTGGTTGTATTATTTTATGTGGGCTTTGGATGTCCTGAAGAAACCAGTAGTTACTTATGAATGGTTAAAGCAATGCTCAGATGAGCATCAAGTTGTTCCTCAAGAGTCATATATGGTTCTTCCTTTCTCTGGGTTAAAGATCTGTGTGACTGGAATCCAAGCAGATAAGCGCAAAGAGATGGAAAAACTTATTCTACAAAATGGTGGAAAATACTCTGCAGAACTGACAAAGAAGTGCACACATTTGATTTCTAATATATCCTTTTGA

Protein sequence

>Msa1034280

MDFISDLKLMLVHWLYYFMWALDVLKKPVVTYEWLKQCSDEHQVVPQESYMVLPFSGLKICVTGIQADKRKEMEKLILQNGGKYSAELTKKCTHLISNISF*