AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0914460


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0914460 MtrunA17_Chr6g0467361 93.421 76 5 0 55 130 7 82 6.56e-50 155
Msa0914460 MtrunA17_Chr4g0067431 60.000 130 52 0 1 130 178 307 7.50e-49 159
Msa0914460 MtrunA17_Chr1g0163221 50.000 182 48 4 12 153 170 348 1.34e-46 154
Msa0914460 MtrunA17_Chr6g0467351 90.909 44 4 0 12 55 183 226 1.82e-20 84.0
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0914460 AT4G31690.1 30.097 103 71 1 27 128 136 238 1.70e-12 63.5

Find 16 sgRNAs with CRISPR-Local

Find 137 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GCTCACAATAATTTGAAATT+TGG 0.213375 6_2:+28676636 Msa0914460:CDS
CTCTCTCAATGTGTGTCTTC+TGG 0.218908 6_2:-28676027 None:intergenic
TTCTATCTTGATCAACAAAA+AGG 0.293775 6_2:-28676542 None:intergenic
ACACATTGAGAGAGATCTTT+TGG 0.323525 6_2:+28676036 Msa0914460:CDS
TAGAACATGGAATGCTGATT+TGG 0.353140 6_2:+28676560 Msa0914460:CDS
TCTAATCGACCATCTTCAAT+AGG 0.374130 6_2:-28677380 None:intergenic
TGTGTCTTCACAAATTCATT+TGG 0.382410 6_2:-28676489 None:intergenic
CATATGCACATGATGAAAGA+AGG 0.522234 6_2:+28676510 Msa0914460:CDS
TAATAGTCATGATGATATCA+AGG 0.538648 6_2:+28675931 Msa0914460:CDS
AAACAATTTGCACTAACAAG+TGG 0.561217 6_2:+28676597 Msa0914460:CDS
TGATACTTGCCTATTGAAGA+TGG 0.567074 6_2:+28677371 Msa0914460:CDS
AATTTGCACTAACAAGTGGT+TGG 0.572723 6_2:+28676601 Msa0914460:CDS
AAGGATTGTTACTTCAAAGA+GGG 0.588782 6_2:+28677348 Msa0914460:CDS
GAAGGATTGTTACTTCAAAG+AGG 0.590696 6_2:+28677347 Msa0914460:CDS
TTGTTGATCAAGATAGAACA+TGG 0.602629 6_2:+28676547 Msa0914460:CDS
GGGTTGGCTAGAATTTGTGA+AGG 0.624634 6_2:+28677329 Msa0914460:intron

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! ATAAATTACCTTTAAAATTA+GGG - chr6_2:28676750-28676769 None:intergenic 10.0%
!!! AATAAATTACCTTTAAAATT+AGG - chr6_2:28676751-28676770 None:intergenic 10.0%
!! TAAATTATATTGATAAGAAA+AGG - chr6_2:28677293-28677312 None:intergenic 10.0%
!!! ATAAATTACCTTTAAAATTA+GGG - chr6_2:28676750-28676769 None:intergenic 10.0%
!!! AATAAATTACCTTTAAAATT+AGG - chr6_2:28676751-28676770 None:intergenic 10.0%
!! TAAATTATATTGATAAGAAA+AGG - chr6_2:28677293-28677312 None:intergenic 10.0%
!! TAAAATCAATAATTCAAAAC+AGG + chr6_2:28676461-28676480 Msa0914460:intron 15.0%
!! AAAAATCATAAAATCAACAA+TGG - chr6_2:28676952-28676971 None:intergenic 15.0%
!! TAAAATCAATAATTCAAAAC+AGG + chr6_2:28676461-28676480 Msa0914460:intron 15.0%
!! AAAAATCATAAAATCAACAA+TGG - chr6_2:28676952-28676971 None:intergenic 15.0%
!!! ATTCACGTCTATATTTTTAA+GGG - chr6_2:28676213-28676232 None:intergenic 20.0%
!!! TATTCACGTCTATATTTTTA+AGG - chr6_2:28676214-28676233 None:intergenic 20.0%
!! TTTCATTATCTATTCTTTCA+TGG + chr6_2:28676257-28676276 Msa0914460:intron 20.0%
!! TTCATTATCTATTCTTTCAT+GGG + chr6_2:28676258-28676277 Msa0914460:intron 20.0%
!!! TTATTAAAGTACCTAGATTA+TGG + chr6_2:28676357-28676376 Msa0914460:intron 20.0%
!!! TGAAAATTCCCTAATTTTAA+AGG + chr6_2:28676739-28676758 Msa0914460:intron 20.0%
!!! TTTTTAAAAGTTTCACATGA+AGG + chr6_2:28677129-28677148 Msa0914460:intron 20.0%
!! AATTTCCTAATGTAGTTTAT+TGG - chr6_2:28677209-28677228 None:intergenic 20.0%
!!! AGGAAATTCATTTTAGAAAA+TGG + chr6_2:28677221-28677240 Msa0914460:intron 20.0%
!!! ATTCACGTCTATATTTTTAA+GGG - chr6_2:28676213-28676232 None:intergenic 20.0%
!!! TATTCACGTCTATATTTTTA+AGG - chr6_2:28676214-28676233 None:intergenic 20.0%
!! TTTCATTATCTATTCTTTCA+TGG + chr6_2:28676257-28676276 Msa0914460:intron 20.0%
!! TTCATTATCTATTCTTTCAT+GGG + chr6_2:28676258-28676277 Msa0914460:intron 20.0%
!!! TTATTAAAGTACCTAGATTA+TGG + chr6_2:28676357-28676376 Msa0914460:intron 20.0%
!!! TGAAAATTCCCTAATTTTAA+AGG + chr6_2:28676739-28676758 Msa0914460:intron 20.0%
!!! TTTTTAAAAGTTTCACATGA+AGG + chr6_2:28677129-28677148 Msa0914460:intron 20.0%
!! AATTTCCTAATGTAGTTTAT+TGG - chr6_2:28677209-28677228 None:intergenic 20.0%
!!! AGGAAATTCATTTTAGAAAA+TGG + chr6_2:28677221-28677240 Msa0914460:intron 20.0%
! TAATAGTCATGATGATATCA+AGG + chr6_2:28675931-28675950 Msa0914460:CDS 25.0%
! TAGTAATAGATTAACCCTAA+AGG + chr6_2:28676086-28676105 Msa0914460:intron 25.0%
! AGTAATAGATTAACCCTAAA+GGG + chr6_2:28676087-28676106 Msa0914460:intron 25.0%
!!! TAAAATTTTTGGTCCCTTTA+GGG - chr6_2:28676103-28676122 None:intergenic 25.0%
!! TAAAGGGACCAAAAATTTTA+GGG + chr6_2:28676103-28676122 Msa0914460:intron 25.0%
!!! GTCTATATTCTTTAGGTTTT+TGG - chr6_2:28676132-28676151 None:intergenic 25.0%
! ATGTTTCGTCTATATTCTTT+AGG - chr6_2:28676139-28676158 None:intergenic 25.0%
!!! TGATCACTGTTGAATTTTTT+AGG + chr6_2:28676168-28676187 Msa0914460:intron 25.0%
!!! GATCACTGTTGAATTTTTTA+GGG + chr6_2:28676169-28676188 Msa0914460:intron 25.0%
!!! ATCACTGTTGAATTTTTTAG+GGG + chr6_2:28676170-28676189 Msa0914460:intron 25.0%
! TCAATCGAATTATACCATAA+TGG + chr6_2:28676309-28676328 Msa0914460:intron 25.0%
! CAATCGAATTATACCATAAT+GGG + chr6_2:28676310-28676329 Msa0914460:intron 25.0%
! AATATAACAAAGTCCCATTA+TGG - chr6_2:28676326-28676345 None:intergenic 25.0%
! AGTTATGTATAGCATACTAA+TGG + chr6_2:28676407-28676426 Msa0914460:intron 25.0%
! TTCTATCTTGATCAACAAAA+AGG - chr6_2:28676545-28676564 None:intergenic 25.0%
!! GCTCACAATAATTTGAAATT+TGG + chr6_2:28676636-28676655 Msa0914460:CDS 25.0%
!! CAAAACTTTTGTACTCAATT+AGG + chr6_2:28676918-28676937 Msa0914460:intron 25.0%
!! TTATGAGTCTTGTATATAGA+CGG - chr6_2:28676986-28677005 None:intergenic 25.0%
! AATTATATTCCAAAATCGCA+AGG - chr6_2:28677258-28677277 None:intergenic 25.0%
! TAATAGTCATGATGATATCA+AGG + chr6_2:28675931-28675950 Msa0914460:CDS 25.0%
! TAGTAATAGATTAACCCTAA+AGG + chr6_2:28676086-28676105 Msa0914460:intron 25.0%
! AGTAATAGATTAACCCTAAA+GGG + chr6_2:28676087-28676106 Msa0914460:intron 25.0%
!!! TAAAATTTTTGGTCCCTTTA+GGG - chr6_2:28676103-28676122 None:intergenic 25.0%
!! TAAAGGGACCAAAAATTTTA+GGG + chr6_2:28676103-28676122 Msa0914460:intron 25.0%
!!! GTCTATATTCTTTAGGTTTT+TGG - chr6_2:28676132-28676151 None:intergenic 25.0%
! ATGTTTCGTCTATATTCTTT+AGG - chr6_2:28676139-28676158 None:intergenic 25.0%
!!! TGATCACTGTTGAATTTTTT+AGG + chr6_2:28676168-28676187 Msa0914460:intron 25.0%
!!! GATCACTGTTGAATTTTTTA+GGG + chr6_2:28676169-28676188 Msa0914460:intron 25.0%
!!! ATCACTGTTGAATTTTTTAG+GGG + chr6_2:28676170-28676189 Msa0914460:intron 25.0%
! TCAATCGAATTATACCATAA+TGG + chr6_2:28676309-28676328 Msa0914460:intron 25.0%
! CAATCGAATTATACCATAAT+GGG + chr6_2:28676310-28676329 Msa0914460:intron 25.0%
! AATATAACAAAGTCCCATTA+TGG - chr6_2:28676326-28676345 None:intergenic 25.0%
! AGTTATGTATAGCATACTAA+TGG + chr6_2:28676407-28676426 Msa0914460:intron 25.0%
! TTCTATCTTGATCAACAAAA+AGG - chr6_2:28676545-28676564 None:intergenic 25.0%
!! GCTCACAATAATTTGAAATT+TGG + chr6_2:28676636-28676655 Msa0914460:CDS 25.0%
!! CAAAACTTTTGTACTCAATT+AGG + chr6_2:28676918-28676937 Msa0914460:intron 25.0%
!! TTATGAGTCTTGTATATAGA+CGG - chr6_2:28676986-28677005 None:intergenic 25.0%
! AATTATATTCCAAAATCGCA+AGG - chr6_2:28677258-28677277 None:intergenic 25.0%
!!! CTAAAATTTTTGGTCCCTTT+AGG - chr6_2:28676104-28676123 None:intergenic 30.0%
! CTAAAGGGACCAAAAATTTT+AGG + chr6_2:28676102-28676121 Msa0914460:intron 30.0%
! AAAGGGACCAAAAATTTTAG+GGG + chr6_2:28676104-28676123 Msa0914460:intron 30.0%
!!! TCACTGTTGAATTTTTTAGG+GGG + chr6_2:28676171-28676190 Msa0914460:intron 30.0%
CCAATCAAAATCCATAATCT+AGG - chr6_2:28676371-28676390 None:intergenic 30.0%
!! CCTAGATTATGGATTTTGAT+TGG + chr6_2:28676368-28676387 Msa0914460:intron 30.0%
TGTGTCTTCACAAATTCATT+TGG - chr6_2:28676492-28676511 None:intergenic 30.0%
TTGTTGATCAAGATAGAACA+TGG + chr6_2:28676547-28676566 Msa0914460:CDS 30.0%
AAACAATTTGCACTAACAAG+TGG + chr6_2:28676597-28676616 Msa0914460:CDS 30.0%
! AACTTTTGTACTCAATTAGG+TGG + chr6_2:28676921-28676940 Msa0914460:intron 30.0%
TCGATAAAAAGATGCTTGAT+AGG - chr6_2:28677061-28677080 None:intergenic 30.0%
GTCTACCAATAAACTACATT+AGG + chr6_2:28677201-28677220 Msa0914460:intron 30.0%
! AAGGATTGTTACTTCAAAGA+GGG + chr6_2:28677348-28677367 Msa0914460:CDS 30.0%
!!! CTAAAATTTTTGGTCCCTTT+AGG - chr6_2:28676104-28676123 None:intergenic 30.0%
! CTAAAGGGACCAAAAATTTT+AGG + chr6_2:28676102-28676121 Msa0914460:intron 30.0%
! AAAGGGACCAAAAATTTTAG+GGG + chr6_2:28676104-28676123 Msa0914460:intron 30.0%
!!! TCACTGTTGAATTTTTTAGG+GGG + chr6_2:28676171-28676190 Msa0914460:intron 30.0%
CCAATCAAAATCCATAATCT+AGG - chr6_2:28676371-28676390 None:intergenic 30.0%
!! CCTAGATTATGGATTTTGAT+TGG + chr6_2:28676368-28676387 Msa0914460:intron 30.0%
TGTGTCTTCACAAATTCATT+TGG - chr6_2:28676492-28676511 None:intergenic 30.0%
TTGTTGATCAAGATAGAACA+TGG + chr6_2:28676547-28676566 Msa0914460:CDS 30.0%
AAACAATTTGCACTAACAAG+TGG + chr6_2:28676597-28676616 Msa0914460:CDS 30.0%
! AACTTTTGTACTCAATTAGG+TGG + chr6_2:28676921-28676940 Msa0914460:intron 30.0%
TCGATAAAAAGATGCTTGAT+AGG - chr6_2:28677061-28677080 None:intergenic 30.0%
GTCTACCAATAAACTACATT+AGG + chr6_2:28677201-28677220 Msa0914460:intron 30.0%
! AAGGATTGTTACTTCAAAGA+GGG + chr6_2:28677348-28677367 Msa0914460:CDS 30.0%
!!! TTCGTGCTTAGCTTTTTTTG+TGG + chr6_2:28675899-28675918 Msa0914460:CDS 35.0%
ATGCAAAAAAGTCCTTGTCA+TGG - chr6_2:28676000-28676019 None:intergenic 35.0%
! ACACATTGAGAGAGATCTTT+TGG + chr6_2:28676036-28676055 Msa0914460:CDS 35.0%
! AAGGGACCAAAAATTTTAGG+GGG + chr6_2:28676105-28676124 Msa0914460:intron 35.0%
! TTTGGTCCCCCTAAAATTTT+TGG - chr6_2:28676114-28676133 None:intergenic 35.0%
CATATGCACATGATGAAAGA+AGG + chr6_2:28676510-28676529 Msa0914460:CDS 35.0%
! TAGAACATGGAATGCTGATT+TGG + chr6_2:28676560-28676579 Msa0914460:CDS 35.0%
AATTTGCACTAACAAGTGGT+TGG + chr6_2:28676601-28676620 Msa0914460:CDS 35.0%
!!! TGCTATTTTCTCTCTTGAAG+AGG + chr6_2:28676713-28676732 Msa0914460:intron 35.0%
! AAATTGTGACCTTGCGATTT+TGG + chr6_2:28677246-28677265 Msa0914460:intron 35.0%
ATTTATGTGTGAACTCTCTC+AGG + chr6_2:28677308-28677327 Msa0914460:intron 35.0%
TTTATGTGTGAACTCTCTCA+GGG + chr6_2:28677309-28677328 Msa0914460:intron 35.0%
! GAAGGATTGTTACTTCAAAG+AGG + chr6_2:28677347-28677366 Msa0914460:CDS 35.0%
TGATACTTGCCTATTGAAGA+TGG + chr6_2:28677371-28677390 Msa0914460:CDS 35.0%
CTATTGAAGATGGTCGATTA+GGG + chr6_2:28677381-28677400 Msa0914460:CDS 35.0%
TATTGAAGATGGTCGATTAG+GGG + chr6_2:28677382-28677401 Msa0914460:CDS 35.0%
!!! TTCGTGCTTAGCTTTTTTTG+TGG + chr6_2:28675899-28675918 Msa0914460:CDS 35.0%
ATGCAAAAAAGTCCTTGTCA+TGG - chr6_2:28676000-28676019 None:intergenic 35.0%
! ACACATTGAGAGAGATCTTT+TGG + chr6_2:28676036-28676055 Msa0914460:CDS 35.0%
! AAGGGACCAAAAATTTTAGG+GGG + chr6_2:28676105-28676124 Msa0914460:intron 35.0%
! TTTGGTCCCCCTAAAATTTT+TGG - chr6_2:28676114-28676133 None:intergenic 35.0%
CATATGCACATGATGAAAGA+AGG + chr6_2:28676510-28676529 Msa0914460:CDS 35.0%
! TAGAACATGGAATGCTGATT+TGG + chr6_2:28676560-28676579 Msa0914460:CDS 35.0%
AATTTGCACTAACAAGTGGT+TGG + chr6_2:28676601-28676620 Msa0914460:CDS 35.0%
!!! TGCTATTTTCTCTCTTGAAG+AGG + chr6_2:28676713-28676732 Msa0914460:intron 35.0%
! AAATTGTGACCTTGCGATTT+TGG + chr6_2:28677246-28677265 Msa0914460:intron 35.0%
ATTTATGTGTGAACTCTCTC+AGG + chr6_2:28677308-28677327 Msa0914460:intron 35.0%
TTTATGTGTGAACTCTCTCA+GGG + chr6_2:28677309-28677328 Msa0914460:intron 35.0%
! GAAGGATTGTTACTTCAAAG+AGG + chr6_2:28677347-28677366 Msa0914460:CDS 35.0%
TGATACTTGCCTATTGAAGA+TGG + chr6_2:28677371-28677390 Msa0914460:CDS 35.0%
!!! AGCTTTTTTTGTGGTGTAGC+AGG + chr6_2:28675908-28675927 Msa0914460:CDS 40.0%
CGAAAAATTCAGCCATGACA+AGG + chr6_2:28675985-28676004 Msa0914460:CDS 40.0%
! GCTGAAGTACTCGATTAAAG+CGG - chr6_2:28677039-28677058 None:intergenic 40.0%
CCTATTGAAGATGGTCGATT+AGG + chr6_2:28677380-28677399 Msa0914460:CDS 40.0%
!!! AGCTTTTTTTGTGGTGTAGC+AGG + chr6_2:28675908-28675927 Msa0914460:CDS 40.0%
CGAAAAATTCAGCCATGACA+AGG + chr6_2:28675985-28676004 Msa0914460:CDS 40.0%
! GCTGAAGTACTCGATTAAAG+CGG - chr6_2:28677039-28677058 None:intergenic 40.0%
CTCTCTCAATGTGTGTCTTC+TGG - chr6_2:28676030-28676049 None:intergenic 45.0%
GTCGTACAAAGAGTCTAGAG+AGG - chr6_2:28676858-28676877 None:intergenic 45.0%
!! GGGTTGGCTAGAATTTGTGA+AGG + chr6_2:28677329-28677348 Msa0914460:intron 45.0%
CTCTCTCAATGTGTGTCTTC+TGG - chr6_2:28676030-28676049 None:intergenic 45.0%
GTCGTACAAAGAGTCTAGAG+AGG - chr6_2:28676858-28676877 None:intergenic 45.0%
!! GGGTTGGCTAGAATTTGTGA+AGG + chr6_2:28677329-28677348 Msa0914460:intron 45.0%
TGTGTGAACTCTCTCAGGGT+TGG + chr6_2:28677313-28677332 Msa0914460:intron 50.0%
TGTGTGAACTCTCTCAGGGT+TGG + chr6_2:28677313-28677332 Msa0914460:intron 50.0%
Chromosome Type Strat End Strand Name
chr6_2 gene 28675896 28677401 28675896 ID=Msa0914460;Name=Msa0914460
chr6_2 mRNA 28675896 28677401 28675896 ID=Msa0914460-mRNA-1;Parent=Msa0914460;Name=Msa0914460-mRNA-1;_AED=0.40;_eAED=0.40;_QI=0|0|0|1|0.5|0.66|3|0|153
chr6_2 exon 28675896 28676057 28675896 ID=Msa0914460-mRNA-1:exon:5220;Parent=Msa0914460-mRNA-1
chr6_2 exon 28676483 28676710 28676483 ID=Msa0914460-mRNA-1:exon:5221;Parent=Msa0914460-mRNA-1
chr6_2 exon 28677330 28677401 28677330 ID=Msa0914460-mRNA-1:exon:5222;Parent=Msa0914460-mRNA-1
chr6_2 CDS 28675896 28676057 28675896 ID=Msa0914460-mRNA-1:cds;Parent=Msa0914460-mRNA-1
chr6_2 CDS 28676483 28676710 28676483 ID=Msa0914460-mRNA-1:cds;Parent=Msa0914460-mRNA-1
chr6_2 CDS 28677330 28677401 28677330 ID=Msa0914460-mRNA-1:cds;Parent=Msa0914460-mRNA-1
Gene Sequence

>Msa0914460

GGGTTCGTGCTTAGCTTTTTTTGTGGTGTAGCAGGTAATAGTCATGATGATATCAAGGAGAGAAGCAAAGTTCTGTACGAGAAAGTGAACGAAAAATTCAGCCATGACAAGGACTTTTTTGCATGTTCGATCCAGAAGACACACATTGAGAGAGATCTTTTGGTGATACCAAATGAATTTGTGAAGACACATATGCACATGATGAAAGAAGGAAATGCTATCCTTTTTGTTGATCAAGATAGAACATGGAATGCTGATTTGGATCTCACTCTAAATAAACAATTTGCACTAACAAGTGGTTGGAGTGAATTCTGTGCTCACAATAATTTGAAATTTGGTGATGTTTGTGCTTTTTTGCTACACAAATGCAAAACAACAATTTTAGTTCAAGGTTGGCTAGAATTTGTGAAGGATTGTTACTTCAAAGAGGGTGATACTTGCCTATTGAAGATGGTCGATTAG

Protein sequence

>Msa0914460

GFVLSFFCGVAGNSHDDIKERSKVLYEKVNEKFSHDKDFFACSIQKTHIERDLLVIPNEFVKTHMHMMKEGNAILFVDQDRTWNADLDLTLNKQFALTSGWSEFCAHNNLKFGDVCAFLLHKCKTTILVQGWLEFVKDCYFKEGDTCLLKMVD*