AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0708610


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0708610 MtrunA17_Chr1g0201701 94.565 184 10 0 1 184 1 184 2.67e-128 358
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0708610 AT5G09270.1 55.789 95 37 2 90 184 19 108 4.23e-31 109
Msa0708610 AT5G09270.2 55.789 95 37 2 90 184 19 108 4.23e-31 109

Find 52 sgRNAs with CRISPR-Local

Find 56 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CTCTTCTGCTAAGGGCTTTA+TGG 0.055488 4_4:+82174952 Msa0708610:CDS
CCCTCCTGCTGCAGGCTTTA+TGG 0.092653 4_4:+82175123 Msa0708610:CDS
TATATGGCGGCTTTGGTCTT+TGG 0.247259 4_4:+82175224 Msa0708610:CDS
ATAGATATAGAAAGCTTCTT+AGG 0.309898 4_4:+82175254 Msa0708610:CDS
GGTTCCTATATTCTTGTATA+TGG 0.337081 4_4:+82175208 Msa0708610:CDS
ATTCTTGTATATGGCGGCTT+TGG 0.347000 4_4:+82175217 Msa0708610:CDS
TTCTGCCAAAGTGGTTGAAA+AGG 0.353945 4_4:+82175363 Msa0708610:CDS
CTTGGTCCTCACCAGTTTCC+AGG 0.356142 4_4:-82175090 None:intergenic
TGCAGGCTTTATGGATTCAT+TGG 0.369416 4_4:+82175132 Msa0708610:CDS
CAGAAACTTATCCTTATGTA+TGG 0.372733 4_4:+82175185 Msa0708610:CDS
TGGATAAGTGCTTCAGAACT+TGG 0.383586 4_4:-82174899 None:intergenic
TTATGGATTCATTGGAAAAT+CGG 0.384322 4_4:+82175140 Msa0708610:CDS
TGATTTGCCATGTCCTTGGC+TGG 0.408407 4_4:-82175022 None:intergenic
AAGAAGCTTTCTATATCTAT+AGG 0.413891 4_4:-82175251 None:intergenic
GTCGGTGCCCCTCCTGCTGC+AGG 0.419080 4_4:+82175115 Msa0708610:CDS
CAGGAGGGGCACCGACTACT+TGG 0.421600 4_4:-82175108 None:intergenic
AAGTTCTGCAGCACCTATCC+TGG 0.422828 4_4:+82175072 Msa0708610:CDS
AGGATAGGTGCTGCAGAACT+TGG 0.446859 4_4:-82175070 None:intergenic
AGTCGGTGGCTCTTCTGCTA+AGG 0.456570 4_4:+82174943 Msa0708610:CDS
GCAGCACCTATCCTGGAAAC+TGG 0.465240 4_4:+82175079 Msa0708610:CDS
GAAGCACTTATCCAGAAAAC+TGG 0.468163 4_4:+82174908 Msa0708610:CDS
GCCGCCATATACAAGAATAT+AGG 0.480158 4_4:-82175212 None:intergenic
TGGTTGATTTGCCATGTCCT+TGG 0.486730 4_4:-82175026 None:intergenic
ACTACGTGAGATGGTTGAAA+AGG 0.493284 4_4:+82175309 Msa0708610:CDS
AGCTTCTTAGGACAGAGGAC+AGG 0.494425 4_4:+82175266 Msa0708610:CDS
AGAAACTTATCCTTATGTAT+GGG 0.501079 4_4:+82175186 Msa0708610:CDS
TTCTAATAATTCTGCCAAAG+TGG 0.501415 4_4:+82175354 Msa0708610:CDS
TCTGCCAAAGTGGTTGAAAA+GGG 0.502981 4_4:+82175364 Msa0708610:CDS
ATATAGGAACCCCATACATA+AGG 0.508413 4_4:-82175196 None:intergenic
TCCTATATTCTTGTATATGG+CGG 0.516713 4_4:+82175211 Msa0708610:CDS
ATGTTGCAATGTAGGCTACT+TGG 0.523428 4_4:-82175410 None:intergenic
CATAAAGCCTGCAGCAGGAG+GGG 0.525453 4_4:-82175122 None:intergenic
TCCTCACCAGTTTCCAGGAT+AGG 0.526596 4_4:-82175085 None:intergenic
TCCATAAAGCCTGCAGCAGG+AGG 0.530529 4_4:-82175124 None:intergenic
TTAGGACAGAGGACAGGGTA+CGG 0.537011 4_4:+82175272 Msa0708610:CDS
GTCGGTGGCTCTTCTGCTAA+GGG 0.540392 4_4:+82174944 Msa0708610:CDS
GAATCCATAAAGCCTGCAGC+AGG 0.543830 4_4:-82175127 None:intergenic
TAGGACAGAGGACAGGGTAC+GGG 0.558112 4_4:+82175273 Msa0708610:CDS
GGAAGGAATCTCAGAAGATG+TGG 0.565631 4_4:-82175389 None:intergenic
GAAACTTATCCTTATGTATG+GGG 0.570070 4_4:+82175187 Msa0708610:CDS
TCAAGCAAGACTACGTGAGA+TGG 0.592566 4_4:+82175300 Msa0708610:CDS
CCATAAAGCCTGCAGCAGGA+GGG 0.618716 4_4:-82175123 None:intergenic
TAGCTGGAACACTCCAGCCA+AGG 0.621030 4_4:+82175009 Msa0708610:CDS
GAACACTCCAGCCAAGGACA+TGG 0.636957 4_4:+82175015 Msa0708610:CDS
GCTTCTTAGGACAGAGGACA+GGG 0.639564 4_4:+82175267 Msa0708610:CDS
ACCTATCCTGGAAACTGGTG+AGG 0.641675 4_4:+82175084 Msa0708610:CDS
TGCAATGTAGGCTACTTGGA+AGG 0.646398 4_4:-82175406 None:intergenic
ACTGGCGAGGATCAAGTAGT+CGG 0.654403 4_4:+82174926 Msa0708610:CDS
TAGAAAGCTTCTTAGGACAG+AGG 0.663471 4_4:+82175261 Msa0708610:CDS
ACTGGTGAGGACCAAGTAGT+CGG 0.664340 4_4:+82175097 Msa0708610:CDS
GGCGAGGATCAAGTAGTCGG+TGG 0.665719 4_4:+82174929 Msa0708610:CDS
ACTTATCCAGAAAACTGGCG+AGG 0.696112 4_4:+82174913 Msa0708610:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! TTATGGATTCATTGAAAAAT+CGG + chr4_4:82174969-82174988 Msa0708610:CDS 20.0%
! ATCAAAAAATCATAGATAGC+TGG + chr4_4:82174993-82175012 Msa0708610:CDS 25.0%
! TTATGGATTCATTGGAAAAT+CGG + chr4_4:82175140-82175159 Msa0708610:CDS 25.0%
! AGAAACTTATCCTTATGTAT+GGG + chr4_4:82175186-82175205 Msa0708610:CDS 25.0%
! AAGAAGCTTTCTATATCTAT+AGG - chr4_4:82175254-82175273 None:intergenic 25.0%
! ATAGATATAGAAAGCTTCTT+AGG + chr4_4:82175254-82175273 Msa0708610:CDS 25.0%
!!! GCTTGTTGCTTTTCATTATT+TGG - chr4_4:82175049-82175068 None:intergenic 30.0%
CAGAAACTTATCCTTATGTA+TGG + chr4_4:82175185-82175204 Msa0708610:CDS 30.0%
GAAACTTATCCTTATGTATG+GGG + chr4_4:82175187-82175206 Msa0708610:CDS 30.0%
GGTTCCTATATTCTTGTATA+TGG + chr4_4:82175208-82175227 Msa0708610:CDS 30.0%
TCCTATATTCTTGTATATGG+CGG + chr4_4:82175211-82175230 Msa0708610:CDS 30.0%
TTCTAATAATTCTGCCAAAG+TGG + chr4_4:82175354-82175373 Msa0708610:CDS 30.0%
!!! GCTTGCTGCTTTTCATTATT+TGG - chr4_4:82174878-82174897 None:intergenic 35.0%
ATATAGGAACCCCATACATA+AGG - chr4_4:82175199-82175218 None:intergenic 35.0%
TGGATAAGTGCTTCAGAACT+TGG - chr4_4:82174902-82174921 None:intergenic 40.0%
! GAAGCACTTATCCAGAAAAC+TGG + chr4_4:82174908-82174927 Msa0708610:CDS 40.0%
! TGCAGGCTTTATGGATTCAT+TGG + chr4_4:82175132-82175151 Msa0708610:CDS 40.0%
GCCGCCATATACAAGAATAT+AGG - chr4_4:82175215-82175234 None:intergenic 40.0%
ATTCTTGTATATGGCGGCTT+TGG + chr4_4:82175217-82175236 Msa0708610:CDS 40.0%
TAGAAAGCTTCTTAGGACAG+AGG + chr4_4:82175261-82175280 Msa0708610:CDS 40.0%
ACTACGTGAGATGGTTGAAA+AGG + chr4_4:82175309-82175328 Msa0708610:CDS 40.0%
TTCTGCCAAAGTGGTTGAAA+AGG + chr4_4:82175363-82175382 Msa0708610:CDS 40.0%
TCTGCCAAAGTGGTTGAAAA+GGG + chr4_4:82175364-82175383 Msa0708610:CDS 40.0%
ACTTATCCAGAAAACTGGCG+AGG + chr4_4:82174913-82174932 Msa0708610:CDS 45.0%
CTCTTCTGCTAAGGGCTTTA+TGG + chr4_4:82174952-82174971 Msa0708610:CDS 45.0%
!! TGGTTGATTTGCCATGTCCT+TGG - chr4_4:82175029-82175048 None:intergenic 45.0%
! TATATGGCGGCTTTGGTCTT+TGG + chr4_4:82175224-82175243 Msa0708610:CDS 45.0%
TCAAGCAAGACTACGTGAGA+TGG + chr4_4:82175300-82175319 Msa0708610:CDS 45.0%
! GGAACCCTTTTCAACCACTT+TGG - chr4_4:82175371-82175390 None:intergenic 45.0%
GGAAGGAATCTCAGAAGATG+TGG - chr4_4:82175392-82175411 None:intergenic 45.0%
! CTTGATCCTCGCCAGTTTTC+TGG - chr4_4:82174922-82174941 None:intergenic 50.0%
ACTGGCGAGGATCAAGTAGT+CGG + chr4_4:82174926-82174945 Msa0708610:CDS 50.0%
! TGATTTGCCATGTCCTTGGC+TGG - chr4_4:82175025-82175044 None:intergenic 50.0%
! AGGATAGGTGCTGCAGAACT+TGG - chr4_4:82175073-82175092 None:intergenic 50.0%
AAGTTCTGCAGCACCTATCC+TGG + chr4_4:82175072-82175091 Msa0708610:CDS 50.0%
ACCTATCCTGGAAACTGGTG+AGG + chr4_4:82175084-82175103 Msa0708610:CDS 50.0%
TCCTCACCAGTTTCCAGGAT+AGG - chr4_4:82175088-82175107 None:intergenic 50.0%
ACTGGTGAGGACCAAGTAGT+CGG + chr4_4:82175097-82175116 Msa0708610:CDS 50.0%
GAATCCATAAAGCCTGCAGC+AGG - chr4_4:82175130-82175149 None:intergenic 50.0%
AGCTTCTTAGGACAGAGGAC+AGG + chr4_4:82175266-82175285 Msa0708610:CDS 50.0%
GCTTCTTAGGACAGAGGACA+GGG + chr4_4:82175267-82175286 Msa0708610:CDS 50.0%
TTAGGACAGAGGACAGGGTA+CGG + chr4_4:82175272-82175291 Msa0708610:CDS 50.0%
AGTCGGTGGCTCTTCTGCTA+AGG + chr4_4:82174943-82174962 Msa0708610:CDS 55.0%
GTCGGTGGCTCTTCTGCTAA+GGG + chr4_4:82174944-82174963 Msa0708610:CDS 55.0%
TAGCTGGAACACTCCAGCCA+AGG + chr4_4:82175009-82175028 Msa0708610:CDS 55.0%
GAACACTCCAGCCAAGGACA+TGG + chr4_4:82175015-82175034 Msa0708610:CDS 55.0%
GCAGCACCTATCCTGGAAAC+TGG + chr4_4:82175079-82175098 Msa0708610:CDS 55.0%
CTTGGTCCTCACCAGTTTCC+AGG - chr4_4:82175093-82175112 None:intergenic 55.0%
CATAAAGCCTGCAGCAGGAG+GGG - chr4_4:82175125-82175144 None:intergenic 55.0%
CCATAAAGCCTGCAGCAGGA+GGG - chr4_4:82175126-82175145 None:intergenic 55.0%
TCCATAAAGCCTGCAGCAGG+AGG - chr4_4:82175127-82175146 None:intergenic 55.0%
TAGGACAGAGGACAGGGTAC+GGG + chr4_4:82175273-82175292 Msa0708610:CDS 55.0%
GGCGAGGATCAAGTAGTCGG+TGG + chr4_4:82174929-82174948 Msa0708610:CDS 60.0%
CCCTCCTGCTGCAGGCTTTA+TGG + chr4_4:82175123-82175142 Msa0708610:CDS 60.0%
!! CAGGAGGGGCACCGACTACT+TGG - chr4_4:82175111-82175130 None:intergenic 65.0%
! GTCGGTGCCCCTCCTGCTGC+AGG + chr4_4:82175115-82175134 Msa0708610:CDS 75.0%
Chromosome Type Strat End Strand Name
chr4_4 gene 82174863 82175417 82174863 ID=Msa0708610;Name=Msa0708610
chr4_4 mRNA 82174863 82175417 82174863 ID=Msa0708610-mRNA-1;Parent=Msa0708610;Name=Msa0708610-mRNA-1;_AED=0.21;_eAED=0.21;_QI=0|-1|0|1|-1|1|1|0|184
chr4_4 exon 82174863 82175417 82174863 ID=Msa0708610-mRNA-1:exon:27032;Parent=Msa0708610-mRNA-1
chr4_4 CDS 82174863 82175417 82174863 ID=Msa0708610-mRNA-1:cds;Parent=Msa0708610-mRNA-1
Gene Sequence

>Msa0708610

ATGGCAAATCAACCAAATAATGAAAAGCAGCAAGCACCAAGTTCTGAAGCACTTATCCAGAAAACTGGCGAGGATCAAGTAGTCGGTGGCTCTTCTGCTAAGGGCTTTATGGATTCATTGAAAAATCGGTATCAAAAAATCATAGATAGCTGGAACACTCCAGCCAAGGACATGGCAAATCAACCAAATAATGAAAAGCAACAAGCACCAAGTTCTGCAGCACCTATCCTGGAAACTGGTGAGGACCAAGTAGTCGGTGCCCCTCCTGCTGCAGGCTTTATGGATTCATTGGAAAATCGGTATAAAAAAATCAAAGAGCATGCAGAAACTTATCCTTATGTATGGGGTTCCTATATTCTTGTATATGGCGGCTTTGGTCTTTGGTTTGCCTATAGATATAGAAAGCTTCTTAGGACAGAGGACAGGGTACGGGCACTTCAAGCAAGACTACGTGAGATGGTTGAAAAGGATAAGATTGTTGAAGCTGAAAATTCTAATAATTCTGCCAAAGTGGTTGAAAAGGGTTCCACATCTTCTGAGATTCCTTCCAAGTAG

Protein sequence

>Msa0708610

MANQPNNEKQQAPSSEALIQKTGEDQVVGGSSAKGFMDSLKNRYQKIIDSWNTPAKDMANQPNNEKQQAPSSAAPILETGEDQVVGAPPAAGFMDSLENRYKKIKEHAETYPYVWGSYILVYGGFGLWFAYRYRKLLRTEDRVRALQARLREMVEKDKIVEAENSNNSAKVVEKGSTSSEIPSK*