AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1434420


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1434420 MtrunA17_Chr4g0070621 96.035 227 8 1 1 227 42 267 4.21e-161 446
Msa1434420 MtrunA17_Chr4g0070651 96.035 227 8 1 1 227 42 267 4.21e-161 446
Msa1434420 MtrunA17_Chr2g0300451 47.556 225 96 5 6 217 47 262 3.84e-66 205
Msa1434420 MtrunA17_Chr4g0070671 46.119 219 103 6 11 222 5 215 5.86e-57 180
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1434420 AT2G31670.1 55.251 219 94 3 1 217 39 255 1.99e-79 239
Msa1434420 AT1G51360.1 44.811 212 109 6 8 217 2 207 1.68e-53 171

Find 58 sgRNAs with CRISPR-Local

Find 72 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
AGCCACGTCAGCGTTGTTAA+AGG 0.289711 tig0027530:-58652 Msa1434420:CDS
AACGATGTGTTCTATGGTTT+GGG 0.291695 tig0027530:+58879 None:intergenic
GAACGATGTGTTCTATGGTT+TGG 0.301777 tig0027530:+58878 None:intergenic
TATGGTTTGGGATTTGGATT+GGG 0.302144 tig0027530:+58891 None:intergenic
GTGTTCTATGGTTTGGGATT+TGG 0.316340 tig0027530:+58885 None:intergenic
GGATCTTAACGGTGAGGATT+TGG 0.330128 tig0027530:-58578 Msa1434420:CDS
CTATGGTTTGGGATTTGGAT+TGG 0.337633 tig0027530:+58890 None:intergenic
TTTAACAACGCTGACGTGGC+TGG 0.345995 tig0027530:+58654 None:intergenic
GAAGAGAACGATGTGTTCTA+TGG 0.371095 tig0027530:+58873 None:intergenic
ATAAGCTTCGAGATCTTGTT+TGG 0.384276 tig0027530:+58687 None:intergenic
GGAGAATGTTGTTAATGATA+AGG 0.387273 tig0027530:-58506 Msa1434420:CDS
TTAACAACGCTGACGTGGCT+GGG 0.404526 tig0027530:+58655 None:intergenic
AAAATTGACCAACTCATGAT+TGG 0.404994 tig0027530:+58333 None:intergenic
TTTGGATTGGGTTGTTGACA+TGG 0.417990 tig0027530:+58903 None:intergenic
ATGATATCATGGCCGTTGAT+TGG 0.429475 tig0027530:-58609 Msa1434420:CDS
TTCTCTCCGGCGAGAGCTAA+AGG 0.448262 tig0027530:-58415 Msa1434420:CDS
TCCTATCATTGATGATATCA+TGG 0.474974 tig0027530:-58620 Msa1434420:CDS
CAGGTTAAGCAAATTTCCTA+TGG 0.478454 tig0027530:-58445 Msa1434420:CDS
AGTTATGTTCTTGAAATTGA+AGG 0.483665 tig0027530:-58530 Msa1434420:CDS
GATTGAGGAGGTGGTGGCGG+CGG 0.488058 tig0027530:+58253 None:intergenic
CGGTGAGGATTTGGTTCCGA+AGG 0.490577 tig0027530:-58569 Msa1434420:CDS
GATCAAAGACTTGCTGATTG+AGG 0.494091 tig0027530:+58238 None:intergenic
AGAACTGAGATTGTTAATCA+TGG 0.496871 tig0027530:+58813 None:intergenic
TCCTCCATCTCCTTCTCTCC+CGG 0.496909 tig0027530:+58364 None:intergenic
GCTGATTGAGGAGGTGGTGG+CGG 0.503258 tig0027530:+58250 None:intergenic
CTATGGTGAGAATTTCTCTC+CGG 0.505194 tig0027530:-58428 Msa1434420:CDS
GTGAGTGAAGGTTAAGGAAG+TGG 0.505601 tig0027530:+58732 None:intergenic
CTCATCGCAGAACCCTCCTT+CGG 0.509845 tig0027530:+58553 None:intergenic
TGGATCGCTGAGGATCTTAA+CGG 0.519445 tig0027530:-58589 Msa1434420:CDS
TAAGATGGAGGACTTGATCA+AGG 0.519592 tig0027530:+58782 None:intergenic
GCCATGATATCATCAATGAT+AGG 0.521154 tig0027530:+58619 None:intergenic
AGGAAGTGGAGCGATTATGT+AGG 0.524450 tig0027530:+58746 None:intergenic
TTCCTTTAACAACGCTGACG+TGG 0.528577 tig0027530:+58650 None:intergenic
TATGTTCTTGAAATTGAAGG+AGG 0.534187 tig0027530:-58527 Msa1434420:CDS
GCTGACGTGGCTGGGGTGAG+CGG 0.534569 tig0027530:+58663 None:intergenic
ATATTCGATTGCTTCGTTAG+CGG 0.534946 tig0027530:-58392 Msa1434420:CDS
TGAGGATTTGGTTCCGAAGG+AGG 0.542093 tig0027530:-58566 Msa1434420:CDS
GAGCATGTGAGTGAAGGTTA+AGG 0.543953 tig0027530:+58726 None:intergenic
TAACAACGCTGACGTGGCTG+GGG 0.552201 tig0027530:+58656 None:intergenic
AGACTTGCTGATTGAGGAGG+TGG 0.566943 tig0027530:+58244 None:intergenic
CGGAGAGAAATTCTCACCAT+AGG 0.569946 tig0027530:+58429 None:intergenic
GAGGATTTGGTTCCGAAGGA+GGG 0.576392 tig0027530:-58565 Msa1434420:CDS
ACATGATTCCAATCATGAGT+TGG 0.582044 tig0027530:-58341 Msa1434420:CDS
TCCGGGAGAGAAGGAGATGG+AGG 0.592579 tig0027530:-58365 Msa1434420:CDS
ATCCTCAGCGATCCAATCAA+CGG 0.598974 tig0027530:+58597 None:intergenic
CTTGCTGATTGAGGAGGTGG+TGG 0.599722 tig0027530:+58247 None:intergenic
GAATATCCTTTAGCTCTCGC+CGG 0.608110 tig0027530:+58409 None:intergenic
ATTATGTAGGAGAGGGCCTA+CGG 0.610282 tig0027530:+58759 None:intergenic
CAAGTCCTCCATCTTACCGT+AGG 0.617676 tig0027530:-58775 Msa1434420:CDS
CGCTGAGGATCTTAACGGTG+AGG 0.620668 tig0027530:-58584 Msa1434420:CDS
GTGGAGCGATTATGTAGGAG+AGG 0.632936 tig0027530:+58751 None:intergenic
AAGATGGAGGACTTGATCAA+GGG 0.635308 tig0027530:+58783 None:intergenic
TGGAGCGATTATGTAGGAGA+GGG 0.657028 tig0027530:+58752 None:intergenic
GAGGGCCTACGGTAAGATGG+AGG 0.662995 tig0027530:+58770 None:intergenic
GGCCGTTGATTGGATCGCTG+AGG 0.675118 tig0027530:-58599 Msa1434420:CDS
AGTGTGGAGCATGTGAGTGA+AGG 0.676357 tig0027530:+58720 None:intergenic
ACTGAGATTGTTAATCATGG+AGG 0.681157 tig0027530:+58816 None:intergenic
CAAAGACTTGCTGATTGAGG+AGG 0.689083 tig0027530:+58241 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
! AGTTATGTTCTTGAAATTGA+AGG - tig0027530:58611-58630 Msa1434420:CDS 25.0%
!! TGTTAATGATAAGGTTTTAC+AGG - tig0027530:58644-58663 Msa1434420:CDS 25.0%
!! AATTCCAGAAAATTTTCAAC+AGG - tig0027530:58677-58696 Msa1434420:CDS 25.0%
!! TTAACCTGTTGAAAATTTTC+TGG + tig0027530:58684-58703 None:intergenic 25.0%
AGAACTGAGATTGTTAATCA+TGG + tig0027530:58331-58350 None:intergenic 30.0%
! TCCTATCATTGATGATATCA+TGG - tig0027530:58521-58540 Msa1434420:CDS 30.0%
TATGTTCTTGAAATTGAAGG+AGG - tig0027530:58614-58633 Msa1434420:CDS 30.0%
GGAGAATGTTGTTAATGATA+AGG - tig0027530:58635-58654 Msa1434420:CDS 30.0%
AAAATTGACCAACTCATGAT+TGG + tig0027530:58811-58830 None:intergenic 30.0%
! ATTTTCAGAAGGATAAGGTT+AGG - tig0027530:58826-58845 Msa1434420:CDS 30.0%
! TTTTCAGAAGGATAAGGTTA+GGG - tig0027530:58827-58846 Msa1434420:CDS 30.0%
! TATGGTTTGGGATTTGGATT+GGG + tig0027530:58253-58272 None:intergenic 35.0%
AACGATGTGTTCTATGGTTT+GGG + tig0027530:58265-58284 None:intergenic 35.0%
! ATCATGGAGGTGATTTTAGA+GGG + tig0027530:58315-58334 None:intergenic 35.0%
! AATCATGGAGGTGATTTTAG+AGG + tig0027530:58316-58335 None:intergenic 35.0%
ACTGAGATTGTTAATCATGG+AGG + tig0027530:58328-58347 None:intergenic 35.0%
ATAAGCTTCGAGATCTTGTT+TGG + tig0027530:58457-58476 None:intergenic 35.0%
GCCATGATATCATCAATGAT+AGG + tig0027530:58525-58544 None:intergenic 35.0%
CAGGTTAAGCAAATTTCCTA+TGG - tig0027530:58696-58715 Msa1434420:CDS 35.0%
ATATTCGATTGCTTCGTTAG+CGG - tig0027530:58749-58768 Msa1434420:CDS 35.0%
ACATGATTCCAATCATGAGT+TGG - tig0027530:58800-58819 Msa1434420:CDS 35.0%
!!! TGAGTTGGTCAATTTTCAGA+AGG - tig0027530:58815-58834 Msa1434420:CDS 35.0%
! GGTCAATTTTCAGAAGGATA+AGG - tig0027530:58821-58840 Msa1434420:CDS 35.0%
! CTATGGTTTGGGATTTGGAT+TGG + tig0027530:58254-58273 None:intergenic 40.0%
! GTGTTCTATGGTTTGGGATT+TGG + tig0027530:58259-58278 None:intergenic 40.0%
GAACGATGTGTTCTATGGTT+TGG + tig0027530:58266-58285 None:intergenic 40.0%
GAAGAGAACGATGTGTTCTA+TGG + tig0027530:58271-58290 None:intergenic 40.0%
AAGATGGAGGACTTGATCAA+GGG + tig0027530:58361-58380 None:intergenic 40.0%
TAAGATGGAGGACTTGATCA+AGG + tig0027530:58362-58381 None:intergenic 40.0%
!!! GTTTGGTTTTGTAACGAGTG+TGG + tig0027530:58440-58459 None:intergenic 40.0%
ATGATATCATGGCCGTTGAT+TGG - tig0027530:58532-58551 Msa1434420:CDS 40.0%
CTATGGTGAGAATTTCTCTC+CGG - tig0027530:58713-58732 Msa1434420:CDS 40.0%
ATTATGTAGGAGAGGGCCTA+CGG + tig0027530:58385-58404 None:intergenic 45.0%
TGGAGCGATTATGTAGGAGA+GGG + tig0027530:58392-58411 None:intergenic 45.0%
AGGAAGTGGAGCGATTATGT+AGG + tig0027530:58398-58417 None:intergenic 45.0%
GTGAGTGAAGGTTAAGGAAG+TGG + tig0027530:58412-58431 None:intergenic 45.0%
GAGCATGTGAGTGAAGGTTA+AGG + tig0027530:58418-58437 None:intergenic 45.0%
TTCCTTTAACAACGCTGACG+TGG + tig0027530:58494-58513 None:intergenic 45.0%
ATCCTCAGCGATCCAATCAA+CGG + tig0027530:58547-58566 None:intergenic 45.0%
TGGATCGCTGAGGATCTTAA+CGG - tig0027530:58552-58571 Msa1434420:CDS 45.0%
GGATCTTAACGGTGAGGATT+TGG - tig0027530:58563-58582 Msa1434420:CDS 45.0%
CGGAGAGAAATTCTCACCAT+AGG + tig0027530:58715-58734 None:intergenic 45.0%
!! GAATATCCTTTAGCTCTCGC+CGG + tig0027530:58735-58754 None:intergenic 45.0%
! TGCTTCGTTAGCGGTTTTTC+CGG - tig0027530:58758-58777 Msa1434420:CDS 45.0%
!! CAAAGACTTGCTGATTGAGG+AGG + tig0027530:58903-58922 None:intergenic 45.0%
!! GGAGGTGATTTTAGAGGGCT+CGG + tig0027530:58310-58329 None:intergenic 50.0%
CAAGTCCTCCATCTTACCGT+AGG - tig0027530:58366-58385 Msa1434420:CDS 50.0%
GTGGAGCGATTATGTAGGAG+AGG + tig0027530:58393-58412 None:intergenic 50.0%
AGTGTGGAGCATGTGAGTGA+AGG + tig0027530:58424-58443 None:intergenic 50.0%
TTAACAACGCTGACGTGGCT+GGG + tig0027530:58489-58508 None:intergenic 50.0%
TTTAACAACGCTGACGTGGC+TGG + tig0027530:58490-58509 None:intergenic 50.0%
AGCCACGTCAGCGTTGTTAA+AGG - tig0027530:58489-58508 Msa1434420:CDS 50.0%
! TGAGGATTTGGTTCCGAAGG+AGG - tig0027530:58575-58594 Msa1434420:CDS 50.0%
! GAGGATTTGGTTCCGAAGGA+GGG - tig0027530:58576-58595 Msa1434420:CDS 50.0%
! GCTTCGTTAGCGGTTTTTCC+GGG - tig0027530:58759-58778 Msa1434420:CDS 50.0%
! TTTTCCGGGAGAGAAGGAGA+TGG - tig0027530:58773-58792 Msa1434420:CDS 50.0%
!! AGACTTGCTGATTGAGGAGG+TGG + tig0027530:58900-58919 None:intergenic 50.0%
TAACAACGCTGACGTGGCTG+GGG + tig0027530:58488-58507 None:intergenic 55.0%
CGCTGAGGATCTTAACGGTG+AGG - tig0027530:58557-58576 Msa1434420:CDS 55.0%
! CGGTGAGGATTTGGTTCCGA+AGG - tig0027530:58572-58591 Msa1434420:CDS 55.0%
CTCATCGCAGAACCCTCCTT+CGG + tig0027530:58591-58610 None:intergenic 55.0%
TTCTCTCCGGCGAGAGCTAA+AGG - tig0027530:58726-58745 Msa1434420:CDS 55.0%
! AGCGGTTTTTCCGGGAGAGA+AGG - tig0027530:58767-58786 Msa1434420:CDS 55.0%
TCCTCCATCTCCTTCTCTCC+CGG + tig0027530:58780-58799 None:intergenic 55.0%
! CTTGCTGATTGAGGAGGTGG+TGG + tig0027530:58897-58916 None:intergenic 55.0%
GAGGGCCTACGGTAAGATGG+AGG + tig0027530:58374-58393 None:intergenic 60.0%
GGAGAGGGCCTACGGTAAGA+TGG + tig0027530:58377-58396 None:intergenic 60.0%
! GGCCGTTGATTGGATCGCTG+AGG - tig0027530:58542-58561 Msa1434420:CDS 60.0%
TCCGGGAGAGAAGGAGATGG+AGG - tig0027530:58776-58795 Msa1434420:CDS 60.0%
! GCTGATTGAGGAGGTGGTGG+CGG + tig0027530:58894-58913 None:intergenic 60.0%
!! GATTGAGGAGGTGGTGGCGG+CGG + tig0027530:58891-58910 None:intergenic 65.0%
GCTGACGTGGCTGGGGTGAG+CGG + tig0027530:58481-58500 None:intergenic 70.0%
Chromosome Type Strat End Strand Name
tig0027530 gene 58240 58923 58240 ID=Msa1434420;Name=Msa1434420
tig0027530 mRNA 58240 58923 58240 ID=Msa1434420-mRNA-1;Parent=Msa1434420;Name=Msa1434420-mRNA-1;_AED=0.23;_eAED=0.23;_QI=0|-1|0|1|-1|1|1|0|227
tig0027530 exon 58240 58923 58240 ID=Msa1434420-mRNA-1:exon:9201;Parent=Msa1434420-mRNA-1
tig0027530 CDS 58240 58923 58240 ID=Msa1434420-mRNA-1:cds;Parent=Msa1434420-mRNA-1
Gene Sequence

>Msa1434420

ATGTCAACAACCCAATCCAAATCCCAAACCATAGAACACATCGTTCTCTTCAAAGTCAAACAAGACACCGAGCCCTCTAAAATCACCTCCATGATTAACAATCTCAGTTCTCTCATCTCCCTTGATCAAGTCCTCCATCTTACCGTAGGCCCTCTCCTACATAATCGCTCCACTTCCTTAACCTTCACTCACATGCTCCACACTCGTTACAAAACCAAACAAGATCTCGAAGCTTATTCCGCTCACCCCAGCCACGTCAGCGTTGTTAAAGGAAACGTGCTTCCTATCATTGATGATATCATGGCCGTTGATTGGATCGCTGAGGATCTTAACGGTGAGGATTTGGTTCCGAAGGAGGGTTCTGCGATGAGAGTTATGTTCTTGAAATTGAAGGAGGAGAATGTTGTTAATGATAAGGTTTTACAGGTTATTAAAGAAATTCCAGAAAATTTTCAACAGGTTAAGCAAATTTCCTATGGTGAGAATTTCTCTCCGGCGAGAGCTAAAGGATATTCGATTGCTTCGTTAGCGGTTTTTCCGGGAGAGAAGGAGATGGAGGAACATGATTCCAATCATGAGTTGGTCAATTTTCAGAAGGATAAGGTTAGGGATCAGATTGAGAGTGTTGTTGTCGTTGATTATGTTGTGCCGCCGCCACCACCTCCTCAATCAGCAAGTCTTTGA

Protein sequence

>Msa1434420

MSTTQSKSQTIEHIVLFKVKQDTEPSKITSMINNLSSLISLDQVLHLTVGPLLHNRSTSLTFTHMLHTRYKTKQDLEAYSAHPSHVSVVKGNVLPIIDDIMAVDWIAEDLNGEDLVPKEGSAMRVMFLKLKEENVVNDKVLQVIKEIPENFQQVKQISYGENFSPARAKGYSIASLAVFPGEKEMEEHDSNHELVNFQKDKVRDQIESVVVVDYVVPPPPPPQSASL*