AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene58691

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene58691.t1 MTR_2g035850 96.624 237 7 1 1 236 1 237 1.31e-169 467
MS.gene58691.t1 MTR_4g094698 49.254 134 45 5 1 131 1 114 5.01e-32 115
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 43 sgRNAs with CRISPR-Local

Find 45 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
ACTACCTTGTTGAAAGTTTA+AGG 0.076288 2.3:+53287262 None:intergenic
TCATCACATAAAAGTATTAT+TGG 0.207412 2.3:+53286947 None:intergenic
GCTCTAGATCTTCTTCTAAT+TGG 0.209397 2.3:+53287419 None:intergenic
TTGCACAAGTTGTCTAAAAT+TGG 0.266497 2.3:+53287355 None:intergenic
GATAGTATTGCATCCAATAT+TGG 0.285397 2.3:+53287609 None:intergenic
TTGGTTGTGGATAATGATTT+TGG 0.308541 2.3:-53286999 MS.gene58691:CDS
TGTTGAAAGTTTAAGGTAAT+AGG 0.323637 2.3:+53287269 None:intergenic
CTGCTTCTACTGACCAATAT+TGG 0.333962 2.3:-53287622 MS.gene58691:CDS
AGATCTTCTTCTAATTGGTT+TGG 0.337371 2.3:+53287424 None:intergenic
CTCAAAATCATAGTCTCTAA+TGG 0.337812 2.3:+53287506 None:intergenic
TGCTCCTTGTTCCATGGAAA+TGG 0.342079 2.3:+53287146 None:intergenic
CTTGGATGTTTCTGATGGTT+TGG 0.350629 2.3:-53287018 MS.gene58691:CDS
GACGACGAGTTACCCGAATT+CGG 0.392141 2.3:+53287053 None:intergenic
TTGGATATATTACCACCCTT+TGG 0.400197 2.3:+53287443 None:intergenic
ATCATAGTCTCTAATGGAAC+AGG 0.408085 2.3:+53287512 None:intergenic
GTGTTTGTGTATGAATTTGT+AGG 0.408854 2.3:+53287482 None:intergenic
TACCACCCTTTGGTGTCAAT+TGG 0.410144 2.3:+53287453 None:intergenic
TTTGCATTAAGTAGTGTTGT+TGG 0.420896 2.3:+53287383 None:intergenic
GTCGTCAAGGCCTAGTAACT+TGG 0.429524 2.3:-53287036 MS.gene58691:CDS
TGTTTCTGATGGTTTGGTTG+TGG 0.449182 2.3:-53287012 MS.gene58691:CDS
TGAATTTGCTCCTTGTTCCA+TGG 0.471507 2.3:+53287140 None:intergenic
TTGTCCTCGTCGTCGTCGCT+AGG 0.494806 2.3:-53287305 MS.gene58691:CDS
ATACTATCAACAACCTCTCA+TGG 0.500539 2.3:-53287594 MS.gene58691:CDS
AGTAACTTGGATGTTTCTGA+TGG 0.501901 2.3:-53287023 MS.gene58691:CDS
TCGTCGCTAGGTGTTCATAA+AGG 0.509070 2.3:-53287293 MS.gene58691:CDS
TGTTTGTGTATGAATTTGTA+GGG 0.517144 2.3:+53287483 None:intergenic
GACGAGGACAAAGCTGTACT+AGG 0.537020 2.3:+53287317 None:intergenic
TCAGAAACATCCAAGTTACT+AGG 0.537297 2.3:+53287026 None:intergenic
AGTGACCAATTGACACCAAA+GGG 0.545409 2.3:-53287458 MS.gene58691:CDS
CAACTTGTGCAACAATTCAC+AGG 0.545584 2.3:-53287344 MS.gene58691:CDS
AGGAGCAAATTCAAGCGCCT+CGG 0.584501 2.3:-53287130 MS.gene58691:CDS
TAACCACTCTGCTGTTGCCG+AGG 0.590379 2.3:+53287113 None:intergenic
TTGGTCAGTAGAAGCAGTCA+TGG 0.595873 2.3:+53287628 None:intergenic
AAGTGACTAAGCCATTTCCA+TGG 0.609099 2.3:-53287157 MS.gene58691:CDS
TAGTGACCAATTGACACCAA+AGG 0.616846 2.3:-53287459 MS.gene58691:CDS
AACACCTAGCGACGACGACG+AGG 0.626702 2.3:+53287301 None:intergenic
ATTCGGGTAACTCGTCGTCA+AGG 0.628642 2.3:-53287049 MS.gene58691:CDS
TAAGCCATTTCCATGGAACA+AGG 0.637693 2.3:-53287150 MS.gene58691:CDS
TTCAATCCATAACACATGAG+TGG 0.650240 2.3:-53287653 None:intergenic
TTTAGAGTATGATCCATGAG+AGG 0.654825 2.3:+53287581 None:intergenic
ATTACCTTAAACTTTCAACA+AGG 0.690320 2.3:-53287266 MS.gene58691:CDS
GACCAATTGACACCAAAGGG+TGG 0.701501 2.3:-53287455 MS.gene58691:CDS
GCGCCTCGGCAACAGCAGAG+TGG 0.703474 2.3:-53287116 MS.gene58691:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
! ATTACCTTAAACTTTCAACA+AGG - chr2.3:53287322-53287341 MS.gene58691:CDS 25.0%
! TGTTTGTGTATGAATTTGTA+GGG + chr2.3:53287108-53287127 None:intergenic 25.0%
!! GAATCAGAGAAATTTTCTAT+AGG + chr2.3:53287037-53287056 None:intergenic 25.0%
!! TGTTGAAAGTTTAAGGTAAT+AGG + chr2.3:53287322-53287341 None:intergenic 25.0%
ACTACCTTGTTGAAAGTTTA+AGG + chr2.3:53287329-53287348 None:intergenic 30.0%
AGATCTTCTTCTAATTGGTT+TGG + chr2.3:53287167-53287186 None:intergenic 30.0%
CTCAAAATCATAGTCTCTAA+TGG + chr2.3:53287085-53287104 None:intergenic 30.0%
GATAGTATTGCATCCAATAT+TGG + chr2.3:53286982-53287001 None:intergenic 30.0%
GTGTTTGTGTATGAATTTGT+AGG + chr2.3:53287109-53287128 None:intergenic 30.0%
TTTGCATTAAGTAGTGTTGT+TGG + chr2.3:53287208-53287227 None:intergenic 30.0%
! AACAATTTTGTTCCGAATTC+GGG - chr2.3:53287523-53287542 MS.gene58691:CDS 30.0%
! CAACAATTTTGTTCCGAATT+CGG - chr2.3:53287522-53287541 MS.gene58691:CDS 30.0%
! TCAGAGAAATTTTCTATAGG+TGG + chr2.3:53287034-53287053 None:intergenic 30.0%
! TTGCACAAGTTGTCTAAAAT+TGG + chr2.3:53287236-53287255 None:intergenic 30.0%
! TTGGTTGTGGATAATGATTT+TGG - chr2.3:53287589-53287608 MS.gene58691:CDS 30.0%
ATACTATCAACAACCTCTCA+TGG - chr2.3:53286994-53287013 MS.gene58691:CDS 35.0%
ATCATAGTCTCTAATGGAAC+AGG + chr2.3:53287079-53287098 None:intergenic 35.0%
TCAGAAACATCCAAGTTACT+AGG + chr2.3:53287565-53287584 None:intergenic 35.0%
TTGGATATATTACCACCCTT+TGG + chr2.3:53287148-53287167 None:intergenic 35.0%
! AGTAACTTGGATGTTTCTGA+TGG - chr2.3:53287565-53287584 MS.gene58691:CDS 35.0%
! GCTCTAGATCTTCTTCTAAT+TGG + chr2.3:53287172-53287191 None:intergenic 35.0%
! TTTAGAGTATGATCCATGAG+AGG + chr2.3:53287010-53287029 None:intergenic 35.0%
AAGTGACTAAGCCATTTCCA+TGG - chr2.3:53287431-53287450 MS.gene58691:CDS 40.0%
AGTGACCAATTGACACCAAA+GGG - chr2.3:53287130-53287149 MS.gene58691:CDS 40.0%
CAACTTGTGCAACAATTCAC+AGG - chr2.3:53287244-53287263 MS.gene58691:CDS 40.0%
CTGCTTCTACTGACCAATAT+TGG - chr2.3:53286966-53286985 MS.gene58691:CDS 40.0%
TAAGCCATTTCCATGGAACA+AGG - chr2.3:53287438-53287457 MS.gene58691:CDS 40.0%
TAGTGACCAATTGACACCAA+AGG - chr2.3:53287129-53287148 MS.gene58691:CDS 40.0%
! CTTGGATGTTTCTGATGGTT+TGG - chr2.3:53287570-53287589 MS.gene58691:CDS 40.0%
! TGAATTTGCTCCTTGTTCCA+TGG + chr2.3:53287451-53287470 None:intergenic 40.0%
!! TGTTTCTGATGGTTTGGTTG+TGG - chr2.3:53287576-53287595 MS.gene58691:CDS 40.0%
TCGTCGCTAGGTGTTCATAA+AGG - chr2.3:53287295-53287314 MS.gene58691:CDS 45.0%
TGCTCCTTGTTCCATGGAAA+TGG + chr2.3:53287445-53287464 None:intergenic 45.0%
TTGGTCAGTAGAAGCAGTCA+TGG + chr2.3:53286963-53286982 None:intergenic 45.0%
!! TACCACCCTTTGGTGTCAAT+TGG + chr2.3:53287138-53287157 None:intergenic 45.0%
AGGAGCAAATTCAAGCGCCT+CGG - chr2.3:53287458-53287477 MS.gene58691:CDS 50.0%
ATTCGGGTAACTCGTCGTCA+AGG - chr2.3:53287539-53287558 MS.gene58691:CDS 50.0%
GACCAATTGACACCAAAGGG+TGG - chr2.3:53287133-53287152 MS.gene58691:CDS 50.0%
GACGACGAGTTACCCGAATT+CGG + chr2.3:53287538-53287557 None:intergenic 50.0%
GACGAGGACAAAGCTGTACT+AGG + chr2.3:53287274-53287293 None:intergenic 50.0%
GTCGTCAAGGCCTAGTAACT+TGG - chr2.3:53287552-53287571 MS.gene58691:CDS 50.0%
TAACCACTCTGCTGTTGCCG+AGG + chr2.3:53287478-53287497 None:intergenic 55.0%
AACACCTAGCGACGACGACG+AGG + chr2.3:53287290-53287309 None:intergenic 60.0%
TTGTCCTCGTCGTCGTCGCT+AGG - chr2.3:53287283-53287302 MS.gene58691:CDS 60.0%
GCGCCTCGGCAACAGCAGAG+TGG - chr2.3:53287472-53287491 MS.gene58691:CDS 70.0%


Chromosome Type Strat End Strand Name
chr2.3 gene 53286950 53287660 53286950 ID=MS.gene58691
chr2.3 mRNA 53286950 53287660 53286950 ID=MS.gene58691.t1;Parent=MS.gene58691
chr2.3 exon 53286950 53287660 53286950 ID=MS.gene58691.t1.exon1;Parent=MS.gene58691.t1
chr2.3 CDS 53286950 53287660 53286950 ID=cds.MS.gene58691.t1;Parent=MS.gene58691.t1
Gene Sequence

>MS.gene58691

ATGAGTGGTACCATGACTGCTTCTACTGACCAATATTGGATGCAATACTATCAACAACCTCTCATGGATCATACTCTAAATCCACCTATAGAAAATTTCTCTGATTCAACTGTGATGACAACAAATCCTGTTCCATTAGAGACTATGATTTTGAGCCCTACAAATTCATACACAAACACTAGTGACCAATTGACACCAAAGGGTGGTAATATATCCAAACCAATTAGAAGAAGATCTAGAGCTTCTAAGAGAACACCAACAACACTACTTAATGCAAACACAACCAATTTTAGACAACTTGTGCAACAATTCACAGGTTGTCCTAGTACAGCTTTGTCCTCGTCGTCGTCGCTAGGTGTTCATAAAGGACCTATTACCTTAAACTTTCAACAAGGTAGTAGCAAACAGAATGTTCAACATGACACAACAGCTAGATTAATGACACAACTTAGTAGCACAAGTTACAATCAAGTTCATCATCAAGTGACTAAGCCATTTCCATGGAACAAGGAGCAAATTCAAGCGCCTCGGCAACAGCAGAGTGGTTATAACTCATTTGAATATGTCAAGAACAACAATTTTGTTCCGAATTCGGGTAACTCGTCGTCAAGGCCTAGTAACTTGGATGTTTCTGATGGTTTGGTTGTGGATAATGATTTTGGTTTGCATGATCTAACTGTTAATGAATTCTCCAATAATACTTTTATGTGA
Protein sequence

>MS.gene58691.t1

MSGTMTASTDQYWMQYYQQPLMDHTLNPPIENFSDSTVMTTNPVPLETMILSPTNSYTNTSDQLTPKGGNISKPIRRRSRASKRTPTTLLNANTTNFRQLVQQFTGCPSTALSSSSSLGVHKGPITLNFQQGSSKQNVQHDTTARLMTQLSSTSYNQVHHQVTKPFPWNKEQIQAPRQQQSGYNSFEYVKNNNFVPNSGNSSSRPSNLDVSDGLVVDNDFGLHDLTVNEFSNNTFM