AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0779820


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0779820 MtrunA17_Chr5g0444551 96.622 148 5 0 1 148 1 148 9.84e-102 288
Msa0779820 MtrunA17_Chr5g0444571 95.745 94 4 0 1 94 1 94 1.30e-58 177
Msa0779820 MtrunA17_Chr4g0024941 48.227 141 73 0 1 141 1 141 5.13e-44 144
Msa0779820 MtrunA17_Chr2g0288831 50.000 144 71 1 1 143 1 144 7.45e-43 141
Msa0779820 MtrunA17_Chr2g0322421 46.512 129 68 1 1 128 1 129 4.76e-31 110
Msa0779820 MtrunA17_Chr7g0235621 39.695 131 78 1 1 130 1 131 1.39e-28 104
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0779820 AT5G42570.1 50.355 141 70 0 1 141 1 141 2.22e-44 145
Msa0779820 AT1G11905.1 49.645 141 71 0 1 141 1 141 1.56e-42 140
Msa0779820 AT3G20450.1 45.736 129 69 1 1 128 5 133 3.22e-36 122
Msa0779820 AT1G11905.2 43.262 141 79 1 1 141 1 140 1.15e-32 115
Msa0779820 AT5G48660.1 42.188 128 73 1 1 127 1 128 1.01e-28 105
Msa0779820 AT3G07190.1 43.750 128 71 1 1 127 1 128 4.03e-28 103
Msa0779820 AT5G48660.2 48.077 52 27 0 76 127 1 52 3.11e-11 58.2

Find 32 sgRNAs with CRISPR-Local

Find 105 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CAACATCCATTGAACGTTTA+TGG 0.094726 5_2:-61167987 None:intergenic
ACCACTGTATTTGTTGTATT+TGG 0.123258 5_2:+61167937 Msa0779820:CDS
TCCTCTATCTCTCTTCTCTT+TGG 0.214919 5_2:-61168582 None:intergenic
ACAGGTTTCTCTCTATTCTT+TGG 0.261214 5_2:+61168462 Msa0779820:intron
TTCTCGATTTGGGAGTTTCT+TGG 0.274478 5_2:-61168733 None:intergenic
TTGATATGCAATTCTCGATT+TGG 0.291370 5_2:-61168744 None:intergenic
TCTCTTAGAAGCATCTCTTA+TGG 0.322946 5_2:+61168050 Msa0779820:CDS
AAATCCAATAGGAAAATTAA+TGG 0.328146 5_2:+61167855 Msa0779820:CDS
AGAGGAAACTGAGAAGAAAA+AGG 0.332303 5_2:+61168599 Msa0779820:CDS
TACAAAATAAGAGTTTGATT+TGG 0.335189 5_2:+61167708 Msa0779820:five_prime_UTR
TGATATGCAATTCTCGATTT+GGG 0.354851 5_2:-61168743 None:intergenic
CTCTTAGAAGCATCTCTTAT+GGG 0.365951 5_2:+61168051 Msa0779820:CDS
GTACACATACAGACATGTTT+AGG 0.407202 5_2:-61168660 None:intergenic
TCTATCTCTCTTCTCTTTGG+AGG 0.415834 5_2:-61168579 None:intergenic
TCCAACAGAGGAGGTTCTAA+TGG 0.420935 5_2:+61168020 Msa0779820:CDS
AAAATAAGAGTTTGATTTGG+AGG 0.430028 5_2:+61167711 Msa0779820:five_prime_UTR
CAAAATCCATAAACGTTCAA+TGG 0.441548 5_2:+61167981 Msa0779820:CDS
TCCAAAGAGAAGAGAGATAG+AGG 0.454256 5_2:+61168581 Msa0779820:CDS
GACCCCTTCCACGCTTCAAA+AGG 0.463134 5_2:-61167891 None:intergenic
GCCATTAGAACCTCCTCTGT+TGG 0.483298 5_2:-61168021 None:intergenic
TACTTGAATGTTGGTTTCGA+TGG 0.490667 5_2:-61167756 None:intergenic
CATAAACGTTCAATGGATGT+TGG 0.531550 5_2:+61167988 Msa0779820:CDS
TTGTAGAACTACTTGAATGT+TGG 0.532246 5_2:-61167765 None:intergenic
TCTTTGGATTGATGATCGAT+AGG 0.543666 5_2:+61168478 Msa0779820:CDS
ACGTTCAATGGATGTTGGCA+TGG 0.548399 5_2:+61167993 Msa0779820:CDS
AATAGGAAAATTAATGGTGA+AGG 0.568358 5_2:+61167861 Msa0779820:CDS
TTTGAGTATCGTATATATGG+TGG 0.571975 5_2:-61167962 None:intergenic
TTAAAGAGATCACTTCATTG+AGG 0.591642 5_2:+61168514 Msa0779820:CDS
CACTTCATTGAGGAAGAATG+TGG 0.608657 5_2:+61168524 Msa0779820:CDS
CATGGTTAATCCAACAGAGG+AGG 0.638279 5_2:+61168011 Msa0779820:CDS
GCCAAATACAACAAATACAG+TGG 0.645246 5_2:-61167938 None:intergenic
TGGCATGGTTAATCCAACAG+AGG 0.731698 5_2:+61168008 Msa0779820:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! TAAAATATTATATTATCTAC+TGG + chr5_2:61168849-61168868 Msa0779820:three_prime_UTR 10.0%
!!! TAATTTAGATTGTTTTTCAA+AGG + chr5_2:61168190-61168209 Msa0779820:intron 15.0%
!!! TAAAAAAACGTTTGATAATA+TGG - chr5_2:61168780-61168799 None:intergenic 15.0%
!!! TAATTTAGATTGTTTTTCAA+AGG + chr5_2:61168190-61168209 Msa0779820:intron 15.0%
!!! TAAAAAAACGTTTGATAATA+TGG - chr5_2:61168780-61168799 None:intergenic 15.0%
!! TACAAAATAAGAGTTTGATT+TGG + chr5_2:61167708-61167727 Msa0779820:five_prime_UTR 20.0%
!! AAATCCAATAGGAAAATTAA+TGG + chr5_2:61167855-61167874 Msa0779820:CDS 20.0%
!!! GCTATTGTTTTTATGATTAA+TGG - chr5_2:61167916-61167935 None:intergenic 20.0%
!!! CTAGTATTGAAAGAAAAATA+AGG - chr5_2:61168097-61168116 None:intergenic 20.0%
!! ATTAAAACTAAGACATCAAA+TGG + chr5_2:61168343-61168362 Msa0779820:intron 20.0%
!! TTTCCATATCCTATAAAATA+CGG + chr5_2:61168430-61168449 Msa0779820:intron 20.0%
!! GAAGAAAAAGGATAATTAAA+TGG + chr5_2:61168611-61168630 Msa0779820:exon 20.0%
!! TACAAAATAAGAGTTTGATT+TGG + chr5_2:61167708-61167727 Msa0779820:five_prime_UTR 20.0%
!! AAATCCAATAGGAAAATTAA+TGG + chr5_2:61167855-61167874 Msa0779820:CDS 20.0%
!!! GCTATTGTTTTTATGATTAA+TGG - chr5_2:61167916-61167935 None:intergenic 20.0%
!!! CTAGTATTGAAAGAAAAATA+AGG - chr5_2:61168097-61168116 None:intergenic 20.0%
!! ATTAAAACTAAGACATCAAA+TGG + chr5_2:61168343-61168362 Msa0779820:intron 20.0%
!! TTTCCATATCCTATAAAATA+CGG + chr5_2:61168430-61168449 Msa0779820:intron 20.0%
!! GAAGAAAAAGGATAATTAAA+TGG + chr5_2:61168611-61168630 Msa0779820:exon 20.0%
!!! AAAATAAGAGTTTGATTTGG+AGG + chr5_2:61167711-61167730 Msa0779820:five_prime_UTR 25.0%
!! TTCACCATTAATTTTCCTAT+TGG - chr5_2:61167862-61167881 None:intergenic 25.0%
! AATAGGAAAATTAATGGTGA+AGG + chr5_2:61167861-61167880 Msa0779820:CDS 25.0%
!!! GATTTTGAGTATCGTATATA+TGG - chr5_2:61167968-61167987 None:intergenic 25.0%
! ACATAAAGATGCATTTATCA+TGG + chr5_2:61168137-61168156 Msa0779820:intron 25.0%
!!! TTGCATGAATATGTCATTTT+AGG - chr5_2:61168314-61168333 None:intergenic 25.0%
! TTCCATATCCTATAAAATAC+GGG + chr5_2:61168431-61168450 Msa0779820:intron 25.0%
!!! AAAATAAGAGTTTGATTTGG+AGG + chr5_2:61167711-61167730 Msa0779820:five_prime_UTR 25.0%
!! TTCACCATTAATTTTCCTAT+TGG - chr5_2:61167862-61167881 None:intergenic 25.0%
! AATAGGAAAATTAATGGTGA+AGG + chr5_2:61167861-61167880 Msa0779820:CDS 25.0%
!!! GATTTTGAGTATCGTATATA+TGG - chr5_2:61167968-61167987 None:intergenic 25.0%
! ACATAAAGATGCATTTATCA+TGG + chr5_2:61168137-61168156 Msa0779820:intron 25.0%
!!! TTGCATGAATATGTCATTTT+AGG - chr5_2:61168314-61168333 None:intergenic 25.0%
! TTCCATATCCTATAAAATAC+GGG + chr5_2:61168431-61168450 Msa0779820:intron 25.0%
TTGTAGAACTACTTGAATGT+TGG - chr5_2:61167768-61167787 None:intergenic 30.0%
! CTATCTTTTGCAAATCCAAT+AGG + chr5_2:61167844-61167863 Msa0779820:CDS 30.0%
!! ACCACTGTATTTGTTGTATT+TGG + chr5_2:61167937-61167956 Msa0779820:CDS 30.0%
! TTTGAGTATCGTATATATGG+TGG - chr5_2:61167965-61167984 None:intergenic 30.0%
CAAAATCCATAAACGTTCAA+TGG + chr5_2:61167981-61168000 Msa0779820:CDS 30.0%
! TTCCCGTATTTTATAGGATA+TGG - chr5_2:61168436-61168455 None:intergenic 30.0%
! GCAATATTCCCGTATTTTAT+AGG - chr5_2:61168442-61168461 None:intergenic 30.0%
TTAAAGAGATCACTTCATTG+AGG + chr5_2:61168514-61168533 Msa0779820:CDS 30.0%
TGATATGCAATTCTCGATTT+GGG - chr5_2:61168746-61168765 None:intergenic 30.0%
TTGATATGCAATTCTCGATT+TGG - chr5_2:61168747-61168766 None:intergenic 30.0%
TTGTAGAACTACTTGAATGT+TGG - chr5_2:61167768-61167787 None:intergenic 30.0%
! CTATCTTTTGCAAATCCAAT+AGG + chr5_2:61167844-61167863 Msa0779820:CDS 30.0%
!! ACCACTGTATTTGTTGTATT+TGG + chr5_2:61167937-61167956 Msa0779820:CDS 30.0%
! TTTGAGTATCGTATATATGG+TGG - chr5_2:61167965-61167984 None:intergenic 30.0%
CAAAATCCATAAACGTTCAA+TGG + chr5_2:61167981-61168000 Msa0779820:CDS 30.0%
! TTCCCGTATTTTATAGGATA+TGG - chr5_2:61168436-61168455 None:intergenic 30.0%
! GCAATATTCCCGTATTTTAT+AGG - chr5_2:61168442-61168461 None:intergenic 30.0%
TTAAAGAGATCACTTCATTG+AGG + chr5_2:61168514-61168533 Msa0779820:CDS 30.0%
TGATATGCAATTCTCGATTT+GGG - chr5_2:61168746-61168765 None:intergenic 30.0%
TTGATATGCAATTCTCGATT+TGG - chr5_2:61168747-61168766 None:intergenic 30.0%
!! TACTTGAATGTTGGTTTCGA+TGG - chr5_2:61167759-61167778 None:intergenic 35.0%
GCCAAATACAACAAATACAG+TGG - chr5_2:61167941-61167960 None:intergenic 35.0%
CAACATCCATTGAACGTTTA+TGG - chr5_2:61167990-61168009 None:intergenic 35.0%
CATAAACGTTCAATGGATGT+TGG + chr5_2:61167988-61168007 Msa0779820:CDS 35.0%
!! TCTCTTAGAAGCATCTCTTA+TGG + chr5_2:61168050-61168069 Msa0779820:CDS 35.0%
!! CTCTTAGAAGCATCTCTTAT+GGG + chr5_2:61168051-61168070 Msa0779820:CDS 35.0%
AAAATACGGGAATATTGCAC+AGG + chr5_2:61168444-61168463 Msa0779820:intron 35.0%
ACAGGTTTCTCTCTATTCTT+TGG + chr5_2:61168462-61168481 Msa0779820:intron 35.0%
! TCTTTGGATTGATGATCGAT+AGG + chr5_2:61168478-61168497 Msa0779820:CDS 35.0%
AGAGGAAACTGAGAAGAAAA+AGG + chr5_2:61168599-61168618 Msa0779820:CDS 35.0%
GTACACATACAGACATGTTT+AGG - chr5_2:61168663-61168682 None:intergenic 35.0%
!! TACTTGAATGTTGGTTTCGA+TGG - chr5_2:61167759-61167778 None:intergenic 35.0%
GCCAAATACAACAAATACAG+TGG - chr5_2:61167941-61167960 None:intergenic 35.0%
CAACATCCATTGAACGTTTA+TGG - chr5_2:61167990-61168009 None:intergenic 35.0%
CATAAACGTTCAATGGATGT+TGG + chr5_2:61167988-61168007 Msa0779820:CDS 35.0%
!! TCTCTTAGAAGCATCTCTTA+TGG + chr5_2:61168050-61168069 Msa0779820:CDS 35.0%
!! CTCTTAGAAGCATCTCTTAT+GGG + chr5_2:61168051-61168070 Msa0779820:CDS 35.0%
AAAATACGGGAATATTGCAC+AGG + chr5_2:61168444-61168463 Msa0779820:intron 35.0%
ACAGGTTTCTCTCTATTCTT+TGG + chr5_2:61168462-61168481 Msa0779820:intron 35.0%
! TCTTTGGATTGATGATCGAT+AGG + chr5_2:61168478-61168497 Msa0779820:CDS 35.0%
AGAGGAAACTGAGAAGAAAA+AGG + chr5_2:61168599-61168618 Msa0779820:CDS 35.0%
GTACACATACAGACATGTTT+AGG - chr5_2:61168663-61168682 None:intergenic 35.0%
CACTTCATTGAGGAAGAATG+TGG + chr5_2:61168524-61168543 Msa0779820:CDS 40.0%
TCTATCTCTCTTCTCTTTGG+AGG - chr5_2:61168582-61168601 None:intergenic 40.0%
TCCAAAGAGAAGAGAGATAG+AGG + chr5_2:61168581-61168600 Msa0779820:CDS 40.0%
TCCTCTATCTCTCTTCTCTT+TGG - chr5_2:61168585-61168604 None:intergenic 40.0%
!! TTCTCGATTTGGGAGTTTCT+TGG - chr5_2:61168736-61168755 None:intergenic 40.0%
CACTTCATTGAGGAAGAATG+TGG + chr5_2:61168524-61168543 Msa0779820:CDS 40.0%
TCTATCTCTCTTCTCTTTGG+AGG - chr5_2:61168582-61168601 None:intergenic 40.0%
TCCAAAGAGAAGAGAGATAG+AGG + chr5_2:61168581-61168600 Msa0779820:CDS 40.0%
TCCTCTATCTCTCTTCTCTT+TGG - chr5_2:61168585-61168604 None:intergenic 40.0%
!! TTCTCGATTTGGGAGTTTCT+TGG - chr5_2:61168736-61168755 None:intergenic 40.0%
!!! GTGTTAGACCTTTTGAAGCG+TGG + chr5_2:61167883-61167902 Msa0779820:CDS 45.0%
!!! TAGACCTTTTGAAGCGTGGA+AGG + chr5_2:61167887-61167906 Msa0779820:CDS 45.0%
!!! AGACCTTTTGAAGCGTGGAA+GGG + chr5_2:61167888-61167907 Msa0779820:CDS 45.0%
ACGTTCAATGGATGTTGGCA+TGG + chr5_2:61167993-61168012 Msa0779820:CDS 45.0%
TGGCATGGTTAATCCAACAG+AGG + chr5_2:61168008-61168027 Msa0779820:CDS 45.0%
CATGGTTAATCCAACAGAGG+AGG + chr5_2:61168011-61168030 Msa0779820:CDS 45.0%
! TCCAACAGAGGAGGTTCTAA+TGG + chr5_2:61168020-61168039 Msa0779820:CDS 45.0%
!!! GTGTTAGACCTTTTGAAGCG+TGG + chr5_2:61167883-61167902 Msa0779820:CDS 45.0%
!!! TAGACCTTTTGAAGCGTGGA+AGG + chr5_2:61167887-61167906 Msa0779820:CDS 45.0%
!!! AGACCTTTTGAAGCGTGGAA+GGG + chr5_2:61167888-61167907 Msa0779820:CDS 45.0%
ACGTTCAATGGATGTTGGCA+TGG + chr5_2:61167993-61168012 Msa0779820:CDS 45.0%
TGGCATGGTTAATCCAACAG+AGG + chr5_2:61168008-61168027 Msa0779820:CDS 45.0%
CATGGTTAATCCAACAGAGG+AGG + chr5_2:61168011-61168030 Msa0779820:CDS 45.0%
! TCCAACAGAGGAGGTTCTAA+TGG + chr5_2:61168020-61168039 Msa0779820:CDS 45.0%
!!! GACCTTTTGAAGCGTGGAAG+GGG + chr5_2:61167889-61167908 Msa0779820:CDS 50.0%
GCCATTAGAACCTCCTCTGT+TGG - chr5_2:61168024-61168043 None:intergenic 50.0%
!!! GACCTTTTGAAGCGTGGAAG+GGG + chr5_2:61167889-61167908 Msa0779820:CDS 50.0%
GCCATTAGAACCTCCTCTGT+TGG - chr5_2:61168024-61168043 None:intergenic 50.0%
GACCCCTTCCACGCTTCAAA+AGG - chr5_2:61167894-61167913 None:intergenic 55.0%
GACCCCTTCCACGCTTCAAA+AGG - chr5_2:61167894-61167913 None:intergenic 55.0%
Chromosome Type Strat End Strand Name
chr5_2 gene 61167706 61168869 61167706 ID=Msa0779820;Name=Msa0779820
chr5_2 mRNA 61167706 61168869 61167706 ID=Msa0779820-mRNA-1;Parent=Msa0779820;Name=Msa0779820-mRNA-1;_AED=0.03;_eAED=0.03;_QI=84|1|1|1|1|1|2|240|148
chr5_2 exon 61167706 61168072 61167706 ID=Msa0779820-mRNA-1:exon:18010;Parent=Msa0779820-mRNA-1
chr5_2 exon 61168466 61168869 61168466 ID=Msa0779820-mRNA-1:exon:18011;Parent=Msa0779820-mRNA-1
chr5_2 five_prime_UTR 61167706 61167789 61167706 ID=Msa0779820-mRNA-1:five_prime_utr;Parent=Msa0779820-mRNA-1
chr5_2 CDS 61167790 61168072 61167790 ID=Msa0779820-mRNA-1:cds;Parent=Msa0779820-mRNA-1
chr5_2 CDS 61168466 61168629 61168466 ID=Msa0779820-mRNA-1:cds;Parent=Msa0779820-mRNA-1
chr5_2 three_prime_UTR 61168630 61168869 61168630 ID=Msa0779820-mRNA-1:three_prime_utr;Parent=Msa0779820-mRNA-1
Gene Sequence

>Msa0779820

ATGTTACAACTTTTATTTGCACTTTTGTCAATAGAATTAACAGTAATTCTAATACTATCTTTTGCAAATCCAATAGGAAAATTAATGGTGAAGGTGTTAGACCTTTTGAAGCGTGGAAGGGGTCCATTAATCATAAAAACAATAGCAACCACTGTATTTGTTGTATTTGGCTCCACCATATATACGATACTCAAAATCCATAAACGTTCAATGGATGTTGGCATGGTTAATCCAACAGAGGAGGTTCTAATGGCACATCATCTCTTAGAAGCATCTCTTATGGGTTTCTCTCTATTCTTTGGATTGATGATCGATAGGCAACACTACTATATTAAAGAGATCACTTCATTGAGGAAGAATGTGGAAAAATCAAAGAAACAAAGCTACAATCATGAACCTCCAAAGAGAAGAGAGATAGAGGAAACTGAGAAGAAAAAGGATAATTAA

Protein sequence

>Msa0779820

MLQLLFALLSIELTVILILSFANPIGKLMVKVLDLLKRGRGPLIIKTIATTVFVVFGSTIYTILKIHKRSMDVGMVNPTEEVLMAHHLLEASLMGFSLFFGLMIDRQHYYIKEITSLRKNVEKSKKQSYNHEPPKRREIEETEKKKDN*