AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene060326

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene060326.t1 MTR_2g035850 97.046 237 6 1 1 236 1 237 5.12e-169 465
MS.gene060326.t1 MTR_4g094698 50.746 134 43 6 1 131 1 114 4.80e-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 42 sgRNAs with CRISPR-Local

Find 44 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
ACTACCTTGTTGAAAGTTTA+AGG 0.076288 2.4:+53450403 None:intergenic
TCATCACATAAAAGTATTAT+TGG 0.207412 2.4:+53450088 None:intergenic
GCTCTAGATCTTCTTCTAAT+TGG 0.209397 2.4:+53450560 None:intergenic
TTGCACAAGTTGTCTAAAAT+TGG 0.266497 2.4:+53450496 None:intergenic
GATAGTATTGCATCCAATAT+TGG 0.285397 2.4:+53450750 None:intergenic
TTGGTTGTGGATAATGATTT+TGG 0.308541 2.4:-53450140 MS.gene060326:CDS
CTCAAAATCATAGTCTCTAA+TGG 0.318292 2.4:+53450647 None:intergenic
TGTTGAAAGTTTAAGGTAAT+AGG 0.323637 2.4:+53450410 None:intergenic
CTGCTTCTACTGACCAATAT+TGG 0.333962 2.4:-53450763 MS.gene060326:CDS
AGATCTTCTTCTAATTGGTT+TGG 0.337371 2.4:+53450565 None:intergenic
CTTGGATGTTTCTGATGGTT+TGG 0.350629 2.4:-53450159 MS.gene060326:CDS
TGCTCCTTGTTCCATTGAAA+TGG 0.351870 2.4:+53450287 None:intergenic
GACGACGAGTTACCCGAATT+CGG 0.392141 2.4:+53450194 None:intergenic
TTGGATATATTACCACCCTT+TGG 0.400197 2.4:+53450584 None:intergenic
TACCACCCTTTGGTGTCAAT+TGG 0.410144 2.4:+53450594 None:intergenic
ATCATAGTCTCTAATGGAAT+AGG 0.414200 2.4:+53450653 None:intergenic
GTGTTTGTGTATGAATTTGT+TGG 0.422157 2.4:+53450623 None:intergenic
GTCGTCAAGGCCTAGTAACT+TGG 0.429524 2.4:-53450177 MS.gene060326:CDS
TTTGCATTGAGTAGTGTTGT+TGG 0.438305 2.4:+53450524 None:intergenic
TGTTTGTGTATGAATTTGTT+GGG 0.446949 2.4:+53450624 None:intergenic
TGTTTCTGATGGTTTGGTTG+TGG 0.449182 2.4:-53450153 MS.gene060326:CDS
TTGTCCTCGTCGTCGTCGCT+AGG 0.494806 2.4:-53450446 MS.gene060326:CDS
ATACTATCAACAACCTCTCA+TGG 0.500539 2.4:-53450735 MS.gene060326:CDS
AGTAACTTGGATGTTTCTGA+TGG 0.501901 2.4:-53450164 MS.gene060326:CDS
TCGTCGCTAGGTGTTCATAA+AGG 0.509070 2.4:-53450434 MS.gene060326:CDS
CAACTTGTGCAACAATTCAC+TGG 0.519474 2.4:-53450485 MS.gene060326:CDS
GACGAGGACAAAGCTGTACT+AGG 0.537020 2.4:+53450458 None:intergenic
TCAGAAACATCCAAGTTACT+AGG 0.537297 2.4:+53450167 None:intergenic
AGTGACCAATTGACACCAAA+GGG 0.545409 2.4:-53450599 MS.gene060326:CDS
AAGTGACTAAGCCATTTCAA+TGG 0.546067 2.4:-53450298 MS.gene060326:CDS
AGGAGCAAATTCAAGCGCCT+CGG 0.584501 2.4:-53450271 MS.gene060326:CDS
TAACCACTCTGCTGTTGCCG+AGG 0.590379 2.4:+53450254 None:intergenic
TTGGTCAGTAGAAGCAGTCA+TGG 0.595873 2.4:+53450769 None:intergenic
TAGTGACCAATTGACACCAA+AGG 0.616846 2.4:-53450600 MS.gene060326:CDS
AACACCTAGCGACGACGACG+AGG 0.626702 2.4:+53450442 None:intergenic
ATTCGGGTAACTCGTCGTCA+AGG 0.628642 2.4:-53450190 MS.gene060326:CDS
TTCAATCCATAACACATGAG+TGG 0.650240 2.4:-53450794 None:intergenic
TTTAGAGTATGATCCATGAG+AGG 0.654825 2.4:+53450722 None:intergenic
ATTACCTTAAACTTTCAACA+AGG 0.690320 2.4:-53450407 MS.gene060326:CDS
TAAGCCATTTCAATGGAACA+AGG 0.693366 2.4:-53450291 MS.gene060326:CDS
GACCAATTGACACCAAAGGG+TGG 0.701501 2.4:-53450596 MS.gene060326:CDS
GCGCCTCGGCAACAGCAGAG+TGG 0.703474 2.4:-53450257 MS.gene060326:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
! ATTACCTTAAACTTTCAACA+AGG - chr2.4:53450463-53450482 MS.gene060326:CDS 25.0%
!! GAATCAGAGAAATTTTCTAT+AGG + chr2.4:53450178-53450197 None:intergenic 25.0%
!! TGTTGAAAGTTTAAGGTAAT+AGG + chr2.4:53450463-53450482 None:intergenic 25.0%
!! TGTTTGTGTATGAATTTGTT+GGG + chr2.4:53450249-53450268 None:intergenic 25.0%
ACTACCTTGTTGAAAGTTTA+AGG + chr2.4:53450470-53450489 None:intergenic 30.0%
AGATCTTCTTCTAATTGGTT+TGG + chr2.4:53450308-53450327 None:intergenic 30.0%
ATCATAGTCTCTAATGGAAT+AGG + chr2.4:53450220-53450239 None:intergenic 30.0%
CTCAAAATCATAGTCTCTAA+TGG + chr2.4:53450226-53450245 None:intergenic 30.0%
GATAGTATTGCATCCAATAT+TGG + chr2.4:53450123-53450142 None:intergenic 30.0%
GTGTTTGTGTATGAATTTGT+TGG + chr2.4:53450250-53450269 None:intergenic 30.0%
! AACAATTTTGTTCCGAATTC+GGG - chr2.4:53450664-53450683 MS.gene060326:CDS 30.0%
! CAACAATTTTGTTCCGAATT+CGG - chr2.4:53450663-53450682 MS.gene060326:CDS 30.0%
! TCAGAGAAATTTTCTATAGG+TGG + chr2.4:53450175-53450194 None:intergenic 30.0%
! TTGCACAAGTTGTCTAAAAT+TGG + chr2.4:53450377-53450396 None:intergenic 30.0%
! TTGGTTGTGGATAATGATTT+TGG - chr2.4:53450730-53450749 MS.gene060326:CDS 30.0%
AAGTGACTAAGCCATTTCAA+TGG - chr2.4:53450572-53450591 MS.gene060326:CDS 35.0%
ATACTATCAACAACCTCTCA+TGG - chr2.4:53450135-53450154 MS.gene060326:CDS 35.0%
TAAGCCATTTCAATGGAACA+AGG - chr2.4:53450579-53450598 MS.gene060326:CDS 35.0%
TCAGAAACATCCAAGTTACT+AGG + chr2.4:53450706-53450725 None:intergenic 35.0%
TTGGATATATTACCACCCTT+TGG + chr2.4:53450289-53450308 None:intergenic 35.0%
TTTGCATTGAGTAGTGTTGT+TGG + chr2.4:53450349-53450368 None:intergenic 35.0%
! AGTAACTTGGATGTTTCTGA+TGG - chr2.4:53450706-53450725 MS.gene060326:CDS 35.0%
! GCTCTAGATCTTCTTCTAAT+TGG + chr2.4:53450313-53450332 None:intergenic 35.0%
! TTTAGAGTATGATCCATGAG+AGG + chr2.4:53450151-53450170 None:intergenic 35.0%
AGTGACCAATTGACACCAAA+GGG - chr2.4:53450271-53450290 MS.gene060326:CDS 40.0%
CAACTTGTGCAACAATTCAC+TGG - chr2.4:53450385-53450404 MS.gene060326:CDS 40.0%
CTGCTTCTACTGACCAATAT+TGG - chr2.4:53450107-53450126 MS.gene060326:CDS 40.0%
TAGTGACCAATTGACACCAA+AGG - chr2.4:53450270-53450289 MS.gene060326:CDS 40.0%
TGCTCCTTGTTCCATTGAAA+TGG + chr2.4:53450586-53450605 None:intergenic 40.0%
! CTTGGATGTTTCTGATGGTT+TGG - chr2.4:53450711-53450730 MS.gene060326:CDS 40.0%
!! TGTTTCTGATGGTTTGGTTG+TGG - chr2.4:53450717-53450736 MS.gene060326:CDS 40.0%
TCGTCGCTAGGTGTTCATAA+AGG - chr2.4:53450436-53450455 MS.gene060326:CDS 45.0%
TTGGTCAGTAGAAGCAGTCA+TGG + chr2.4:53450104-53450123 None:intergenic 45.0%
!! TACCACCCTTTGGTGTCAAT+TGG + chr2.4:53450279-53450298 None:intergenic 45.0%
AGGAGCAAATTCAAGCGCCT+CGG - chr2.4:53450599-53450618 MS.gene060326:CDS 50.0%
ATTCGGGTAACTCGTCGTCA+AGG - chr2.4:53450680-53450699 MS.gene060326:CDS 50.0%
GACCAATTGACACCAAAGGG+TGG - chr2.4:53450274-53450293 MS.gene060326:CDS 50.0%
GACGACGAGTTACCCGAATT+CGG + chr2.4:53450679-53450698 None:intergenic 50.0%
GACGAGGACAAAGCTGTACT+AGG + chr2.4:53450415-53450434 None:intergenic 50.0%
GTCGTCAAGGCCTAGTAACT+TGG - chr2.4:53450693-53450712 MS.gene060326:CDS 50.0%
TAACCACTCTGCTGTTGCCG+AGG + chr2.4:53450619-53450638 None:intergenic 55.0%
AACACCTAGCGACGACGACG+AGG + chr2.4:53450431-53450450 None:intergenic 60.0%
TTGTCCTCGTCGTCGTCGCT+AGG - chr2.4:53450424-53450443 MS.gene060326:CDS 60.0%
GCGCCTCGGCAACAGCAGAG+TGG - chr2.4:53450613-53450632 MS.gene060326:CDS 70.0%


Chromosome Type Strat End Strand Name
chr2.4 gene 53450091 53450801 53450091 ID=MS.gene060326
chr2.4 mRNA 53450091 53450801 53450091 ID=MS.gene060326.t1;Parent=MS.gene060326
chr2.4 exon 53450091 53450801 53450091 ID=MS.gene060326.t1.exon1;Parent=MS.gene060326.t1
chr2.4 CDS 53450091 53450801 53450091 ID=cds.MS.gene060326.t1;Parent=MS.gene060326.t1
Gene Sequence

>MS.gene060326

ATGAGTGGTACCATGACTGCTTCTACTGACCAATATTGGATGCAATACTATCAACAACCTCTCATGGATCATACTCTAAATCCACCTATAGAAAATTTCTCTGATTCAACTGTGATGACAACAAATCCTATTCCATTAGAGACTATGATTTTGAGCCCAACAAATTCATACACAAACACTAGTGACCAATTGACACCAAAGGGTGGTAATATATCCAAACCAATTAGAAGAAGATCTAGAGCTTCTAAGAGAACACCAACAACACTACTCAATGCAAATACAACCAATTTTAGACAACTTGTGCAACAATTCACTGGTTGTCCTAGTACAGCTTTGTCCTCGTCGTCGTCGCTAGGTGTTCATAAAGGACCTATTACCTTAAACTTTCAACAAGGTAGTAGCAAACAGAATGTTCAACATGACACAACAGCTAGATTAATGTCACAACTTAGTAGCACAAGTTACAATCAAGTTCATCATCAAGTGACTAAGCCATTTCAATGGAACAAGGAGCAAATTCAAGCGCCTCGGCAACAGCAGAGTGGTTATAACTCATTTGAATATGTCAAGAACAACAATTTTGTTCCGAATTCGGGTAACTCGTCGTCAAGGCCTAGTAACTTGGATGTTTCTGATGGTTTGGTTGTGGATAATGATTTTGGTTTGCATGATCTAACTGTTAATGAATTCTCCAATAATACTTTTATGTGA
Protein sequence

>MS.gene060326.t1

MSGTMTASTDQYWMQYYQQPLMDHTLNPPIENFSDSTVMTTNPIPLETMILSPTNSYTNTSDQLTPKGGNISKPIRRRSRASKRTPTTLLNANTTNFRQLVQQFTGCPSTALSSSSSLGVHKGPITLNFQQGSSKQNVQHDTTARLMSQLSSTSYNQVHHQVTKPFQWNKEQIQAPRQQQSGYNSFEYVKNNNFVPNSGNSSSRPSNLDVSDGLVVDNDFGLHDLTVNEFSNNTFM