AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene28309


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene28309.t1 MTR_4g068300 84.364 275 39 2 1 273 1 273 3.26e-152 426
MS.gene28309.t1 MTR_4g068310 58.537 205 65 8 1 202 1 188 3.39e-66 205
MS.gene28309.t1 MTR_1g021270 32.673 101 66 1 8 108 13 111 5.01e-15 75.1
MS.gene28309.t1 MTR_3g005480 28.972 214 132 9 13 222 24 221 2.60e-13 68.6
MS.gene28309.t1 MTR_1g021440 33.981 103 65 2 23 124 35 135 2.53e-12 66.2
MS.gene28309.t1 MTR_1g021440 33.981 103 65 2 23 124 35 135 2.59e-12 65.9
MS.gene28309.t1 MTR_1g021440 33.981 103 65 2 23 124 35 135 6.07e-12 65.5
MS.gene28309.t1 MTR_1g021440 33.981 103 65 2 23 124 35 135 6.12e-12 65.5
MS.gene28309.t1 MTR_1g021350 34.524 84 53 1 23 106 34 115 4.92e-11 62.8
MS.gene28309.t1 MTR_1g021400 28.249 177 107 4 23 181 43 217 5.36e-11 62.8
MS.gene28309.t1 MTR_7g050710 35.714 98 60 2 11 107 13 108 6.06e-11 62.4
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene28309.t1 AT3G06220 29.565 115 77 2 9 123 8 118 2.49e-13 67.0

Find 45 sgRNAs with CRISPR-Local

Find 97 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TTTCTCTTGGCCGCGATTAT+TGG 0.150855 4.4:+38964352 None:intergenic
AGTGATGCTTGAAGAGTTAT+TGG 0.212786 4.4:-38964503 MS.gene28309:CDS
TGCAGCAACAATCATGTCTA+TGG 0.232377 4.4:-38964173 MS.gene28309:CDS
ATTATTCTGGTAGGCTCTTC+TGG 0.236095 4.4:-38964610 MS.gene28309:CDS
ACAAGAGATTGTTAAGGATT+TGG 0.243204 4.4:-38964659 MS.gene28309:CDS
CATCAATGTTGCTGCAGCTT+TGG 0.244862 4.4:+38964096 None:intergenic
AATGACATTTATCTGCAAAT+TGG 0.269252 4.4:-38964553 MS.gene28309:CDS
CAAGAGATTGTTAAGGATTT+GGG 0.277836 4.4:-38964658 MS.gene28309:CDS
GAAGAATGCATTAATTATTC+TGG 0.319956 4.4:-38964623 MS.gene28309:CDS
TTCTTTGATGATTGCGAAGA+AGG 0.373079 4.4:+38965291 None:intergenic
CAAAGCTGCAGCAACATTGA+TGG 0.380913 4.4:-38964095 MS.gene28309:CDS
TAATGGGGAGAACAAGTTCC+AGG 0.400809 4.4:-38964470 MS.gene28309:CDS
CTGGTGAGAGAGTATGCTTC+AGG 0.408630 4.4:-38964210 MS.gene28309:CDS
TTCTTAAAGCACTCACTCTC+AGG 0.419431 4.4:+38964301 None:intergenic
TAGGCTCTTCTGGTGAGAAA+TGG 0.425803 4.4:-38964600 MS.gene28309:CDS
TGGTCTACCCCTCTTTCTCT+TGG 0.432293 4.4:+38964339 None:intergenic
GAGAAAATCCTGCTGGTGAG+AGG 0.446423 4.4:-38964048 MS.gene28309:CDS
AGGATTTGGGTGAAGAGTTG+TGG 0.456368 4.4:-38964645 MS.gene28309:CDS
CAGTTAACTAAAATAACAAC+TGG 0.461802 4.4:+38963941 None:intergenic
AGGCTCTTCTGGTGAGAAAT+GGG 0.468490 4.4:-38964599 MS.gene28309:CDS
ACATTTATCTGCAAATTGGT+TGG 0.488288 4.4:-38964549 MS.gene28309:CDS
TTCTTCGCAATCATCAAAGA+AGG 0.488553 4.4:-38965289 MS.gene28309:CDS
ATTGTGGTTAAGAGAAATGA+TGG 0.499727 4.4:-38964253 MS.gene28309:CDS
TCTTGTACATTCTTGAAGCA+TGG 0.500756 4.4:+38964415 None:intergenic
AGTACCACAAGAGATTGTTA+AGG 0.512474 4.4:-38964665 MS.gene28309:CDS
CGAAGAAGGATGGTTTGTCT+TGG 0.520720 4.4:+38965305 None:intergenic
TTGATGATTGCGAAGAAGGA+TGG 0.531272 4.4:+38965295 None:intergenic
ATGCATACCCTCTCACCAGC+AGG 0.531521 4.4:+38964040 None:intergenic
TAATCGCGGCCAAGAGAAAG+AGG 0.543608 4.4:-38964348 MS.gene28309:CDS
ACTAAAATAACAACTGGAGC+AGG 0.545360 4.4:+38963947 None:intergenic
AATCGTGGCTGAGAGAAAGA+AGG 0.556974 4.4:-38963987 MS.gene28309:CDS
GCAGCAACAATCATGTCTAT+GGG 0.564847 4.4:-38964172 MS.gene28309:CDS
AGGCTTGAACATCAACCGCC+TGG 0.566829 4.4:-38965269 MS.gene28309:intron
AATGCATTAATTATTCTGGT+AGG 0.572311 4.4:-38964619 MS.gene28309:CDS
AAGCATACTCTCTCACCAGC+AGG 0.573273 4.4:+38964214 None:intergenic
TGCAGCAGCTCCAATAATCG+CGG 0.576668 4.4:-38964362 MS.gene28309:CDS
AGAAAATCCTGCTGGTGAGA+GGG 0.595818 4.4:-38964047 MS.gene28309:CDS
ATTGATGGCTGCGATAAACA+AGG 0.598401 4.4:-38964080 MS.gene28309:CDS
AGAACAAGAGAAAATCCTGC+TGG 0.600152 4.4:-38964055 MS.gene28309:CDS
AATCGCGGCCAAGAGAAAGA+GGG 0.619676 4.4:-38964347 MS.gene28309:CDS
ATCGTGGCTGAGAGAAAGAA+GGG 0.634544 4.4:-38963986 MS.gene28309:CDS
AAATCCTTAACAATCTCTTG+TGG 0.638832 4.4:+38964661 None:intergenic
ATCGCGGCCAAGAGAAAGAG+GGG 0.679157 4.4:-38964346 MS.gene28309:CDS
AAAATCTGCAGAAACAATCG+TGG 0.680787 4.4:-38964002 MS.gene28309:CDS
TTGATGGCTGCGATAAACAA+GGG 0.688503 4.4:-38964079 MS.gene28309:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AGTGTTTCTTATTATTAACA+AGG + chr4.4:38964091-38964110 None:intergenic 20.0%
!!! TATTGGTTTTCACATATAAT+GGG - chr4.4:38964773-38964792 MS.gene28309:intron 20.0%
!!! TGAAAAGTGAGTTTTTTTAA+AGG - chr4.4:38964153-38964172 MS.gene28309:CDS 20.0%
!!! TTATTGGTTTTCACATATAA+TGG - chr4.4:38964772-38964791 MS.gene28309:intron 20.0%
!!! TTTTAGTTATACATAGACAT+AGG - chr4.4:38964310-38964329 MS.gene28309:CDS 20.0%
! AATGACATTTATCTGCAAAT+TGG - chr4.4:38964706-38964725 MS.gene28309:intron 25.0%
! AATGCATTAATTATTCTGGT+AGG - chr4.4:38964640-38964659 MS.gene28309:CDS 25.0%
! AGTACGAATAAATTATTACC+AGG + chr4.4:38964011-38964030 None:intergenic 25.0%
! CAGTTAACTAAAATAACAAC+TGG + chr4.4:38965321-38965340 None:intergenic 25.0%
! GAAGAATGCATTAATTATTC+TGG - chr4.4:38964636-38964655 MS.gene28309:CDS 25.0%
! GACGATGAAAACTAAATTAT+AGG - chr4.4:38964128-38964147 MS.gene28309:CDS 25.0%
! TTATCTACTAGAGACAAATT+GGG - chr4.4:38964271-38964290 MS.gene28309:CDS 25.0%
! TTTATCTACTAGAGACAAAT+TGG - chr4.4:38964270-38964289 MS.gene28309:CDS 25.0%
! TTTGTCTCTAGTAGATAAAT+CGG + chr4.4:38964269-38964288 None:intergenic 25.0%
!! TAAGAAACACTTTGTTTCTT+TGG - chr4.4:38964100-38964119 MS.gene28309:CDS 25.0%
!!! AATTTTTGGTAAGAATGGAT+TGG - chr4.4:38964816-38964835 MS.gene28309:intron 25.0%
!!! ATTGGTTTTCACATATAATG+GGG - chr4.4:38964774-38964793 MS.gene28309:intron 25.0%
AAATCCTTAACAATCTCTTG+TGG + chr4.4:38964601-38964620 None:intergenic 30.0%
AACAGAAAAATTACCAAGCT+TGG + chr4.4:38964421-38964440 None:intergenic 30.0%
ACAAGAGATTGTTAAGGATT+TGG - chr4.4:38964600-38964619 MS.gene28309:CDS 30.0%
ACATTTATCTGCAAATTGGT+TGG - chr4.4:38964710-38964729 MS.gene28309:intron 30.0%
ACGAATAAATTATTACCAGG+CGG + chr4.4:38964008-38964027 None:intergenic 30.0%
ATTGTGGTTAAGAGAAATGA+TGG - chr4.4:38965006-38965025 MS.gene28309:intron 30.0%
CAAGAGATTGTTAAGGATTT+GGG - chr4.4:38964601-38964620 MS.gene28309:CDS 30.0%
TGAAGTTGCAGAAAAAATTG+TGG - chr4.4:38964990-38965009 MS.gene28309:intron 30.0%
TTAGACTATTTGATCTCGAT+TGG - chr4.4:38964440-38964459 MS.gene28309:CDS 30.0%
!! GAAGTGAGTATTTTGAAGAA+AGG - chr4.4:38964682-38964701 MS.gene28309:intron 30.0%
!!! GTCAAGCTACTATGTTTTTT+TGG - chr4.4:38964556-38964575 MS.gene28309:CDS 30.0%
!!! GTGCAAATTTTTGGTAAGAA+TGG - chr4.4:38964811-38964830 MS.gene28309:intron 30.0%
!!! TGACGAACATGATTTTTTCT+TGG + chr4.4:38965117-38965136 None:intergenic 30.0%
AAAATCTGCAGAAACAATCG+TGG - chr4.4:38965257-38965276 MS.gene28309:intron 35.0%
AAAATTACCAAGCTTGGATC+TGG + chr4.4:38964415-38964434 None:intergenic 35.0%
ACATGTTATGCATATGAAGC+TGG + chr4.4:38964507-38964526 None:intergenic 35.0%
ACTAAAATAACAACTGGAGC+AGG + chr4.4:38965315-38965334 None:intergenic 35.0%
ACTATTTGATCTCGATTGGA+AGG - chr4.4:38964444-38964463 MS.gene28309:CDS 35.0%
AGTACCACAAGAGATTGTTA+AGG - chr4.4:38964594-38964613 MS.gene28309:CDS 35.0%
AGTGATGCTTGAAGAGTTAT+TGG - chr4.4:38964756-38964775 MS.gene28309:intron 35.0%
ATGCACACATTCATGAAGTT+TGG - chr4.4:38964358-38964377 MS.gene28309:CDS 35.0%
TCTTACCAAAAATTTGCACC+TGG + chr4.4:38964810-38964829 None:intergenic 35.0%
TCTTGTACATTCTTGAAGCA+TGG + chr4.4:38964847-38964866 None:intergenic 35.0%
TTCTTCGCAATCATCAAAGA+AGG - chr4.4:38963970-38963989 MS.gene28309:CDS 35.0%
! AAGTTCCAGGTGCAAATTTT+TGG - chr4.4:38964802-38964821 MS.gene28309:intron 35.0%
! TCAGGAGAAAGAACTTTTCT+TGG + chr4.4:38964943-38964962 None:intergenic 35.0%
! TTCTTTGATGATTGCGAAGA+AGG + chr4.4:38963971-38963990 None:intergenic 35.0%
AGAACAAGAAAAAGTCCTGC+TGG - chr4.4:38965030-38965049 MS.gene28309:intron 40.0%
AGAACAAGAGAAAATCCTGC+TGG - chr4.4:38965204-38965223 MS.gene28309:intron 40.0%
ATAAATCGGCTGTTGAGCTA+AGG + chr4.4:38964255-38964274 None:intergenic 40.0%
ATAGGAACCTGTATTCCCTT+TGG - chr4.4:38964328-38964347 MS.gene28309:CDS 40.0%
ATTATTCTGGTAGGCTCTTC+TGG - chr4.4:38964649-38964668 MS.gene28309:CDS 40.0%
GCAGCAACAATCATGTCTAT+GGG - chr4.4:38965087-38965106 MS.gene28309:intron 40.0%
GCATGAGATGATGATCATGT+GGG + chr4.4:38964051-38964070 None:intergenic 40.0%
TGATCTCGATTGGAAGGTTA+CGG - chr4.4:38964450-38964469 MS.gene28309:CDS 40.0%
TGCAGCAACAATCATGTCTA+TGG - chr4.4:38965086-38965105 MS.gene28309:intron 40.0%
TGCATGAGATGATGATCATG+TGG + chr4.4:38964052-38964071 None:intergenic 40.0%
! ACTGGAGCAGGATATTTTCT+TGG + chr4.4:38965303-38965322 None:intergenic 40.0%
! ATTGATGGCTGCGATAAACA+AGG - chr4.4:38965179-38965198 MS.gene28309:intron 40.0%
! TTCTTAAAGCACTCACTCTC+AGG + chr4.4:38964961-38964980 None:intergenic 40.0%
! TTGATGATTGCGAAGAAGGA+TGG + chr4.4:38963967-38963986 None:intergenic 40.0%
! TTGATGGCTGCGATAAACAA+GGG - chr4.4:38965180-38965199 MS.gene28309:intron 40.0%
AATCGTGGCTGAGAGAAAGA+AGG - chr4.4:38965272-38965291 MS.gene28309:CDS 45.0%
AGAAAATCCTGCTGGTGAGA+GGG - chr4.4:38965212-38965231 MS.gene28309:intron 45.0%
AGGATTTGGGTGAAGAGTTG+TGG - chr4.4:38964614-38964633 MS.gene28309:CDS 45.0%
AGGCTCTTCTGGTGAGAAAT+GGG - chr4.4:38964660-38964679 MS.gene28309:CDS 45.0%
ATCCATGACCGTCCGAAAAA+TGG - chr4.4:38964383-38964402 MS.gene28309:CDS 45.0%
ATCGTGGCTGAGAGAAAGAA+GGG - chr4.4:38965273-38965292 MS.gene28309:CDS 45.0%
CAAAGCTGCAGCAACATTGA+TGG - chr4.4:38965164-38965183 MS.gene28309:intron 45.0%
CATCAATGTTGCTGCAGCTT+TGG + chr4.4:38965166-38965185 None:intergenic 45.0%
GTGTGCATTCAGTGACCAAA+GGG + chr4.4:38964346-38964365 None:intergenic 45.0%
TAATGGGGAGAACAAGTTCC+AGG - chr4.4:38964789-38964808 MS.gene28309:intron 45.0%
TAGGCTCTTCTGGTGAGAAA+TGG - chr4.4:38964659-38964678 MS.gene28309:CDS 45.0%
TCAGTGACCAAAGGGAATAC+AGG + chr4.4:38964338-38964357 None:intergenic 45.0%
TCCATGACCGTCCGAAAAAT+GGG - chr4.4:38964384-38964403 MS.gene28309:CDS 45.0%
TGCAAGCATTCACAAAGCCA+GGG + chr4.4:38964479-38964498 None:intergenic 45.0%
TGTGTGCATTCAGTGACCAA+AGG + chr4.4:38964347-38964366 None:intergenic 45.0%
TTTCTCTTGGCCGCGATTAT+TGG + chr4.4:38964910-38964929 None:intergenic 45.0%
! CGAAGAAGGATGGTTTGTCT+TGG + chr4.4:38963957-38963976 None:intergenic 45.0%
!! ATCTGGACCACCCCATTTTT+CGG + chr4.4:38964398-38964417 None:intergenic 45.0%
!! TGGCTTTGTGAATGCTTGCA+GGG - chr4.4:38964479-38964498 MS.gene28309:CDS 45.0%
AAGCATACTCTCTCACCAGC+AGG + chr4.4:38965048-38965067 None:intergenic 50.0%
AATCGCGGCCAAGAGAAAGA+GGG - chr4.4:38964912-38964931 MS.gene28309:intron 50.0%
CCATGACCGTCCGAAAAATG+GGG - chr4.4:38964385-38964404 MS.gene28309:CDS 50.0%
CTGCAAGCATTCACAAAGCC+AGG + chr4.4:38964480-38964499 None:intergenic 50.0%
GAGAAAATCCTGCTGGTGAG+AGG - chr4.4:38965211-38965230 MS.gene28309:intron 50.0%
GCAAGCATTCACAAAGCCAG+GGG + chr4.4:38964478-38964497 None:intergenic 50.0%
TAATCGCGGCCAAGAGAAAG+AGG - chr4.4:38964911-38964930 MS.gene28309:intron 50.0%
TGCAGCAGCTCCAATAATCG+CGG - chr4.4:38964897-38964916 MS.gene28309:intron 50.0%
TGGTCTACCCCTCTTTCTCT+TGG + chr4.4:38964923-38964942 None:intergenic 50.0%
! CTGGTGAGAGAGTATGCTTC+AGG - chr4.4:38965049-38965068 MS.gene28309:intron 50.0%
!! CTGGCTTTGTGAATGCTTGC+AGG - chr4.4:38964478-38964497 MS.gene28309:CDS 50.0%
AGGCTTGAACATCAACCGCC+TGG - chr4.4:38963990-38964009 MS.gene28309:CDS 55.0%
ATCGCGGCCAAGAGAAAGAG+GGG - chr4.4:38964913-38964932 MS.gene28309:intron 55.0%
ATGCATACCCTCTCACCAGC+AGG + chr4.4:38965222-38965241 None:intergenic 55.0%
TGACCGTCCGAAAAATGGGG+TGG - chr4.4:38964388-38964407 MS.gene28309:CDS 55.0%
TTGGAAGGTTACGGATCCCC+TGG - chr4.4:38964459-38964478 MS.gene28309:CDS 55.0%
!! CCCCATTTTTCGGACGGTCA+TGG + chr4.4:38964388-38964407 None:intergenic 55.0%
!! GGACCACCCCATTTTTCGGA+CGG + chr4.4:38964394-38964413 None:intergenic 55.0%
GGGTGGTCCAGATCCAAGCT+TGG - chr4.4:38964405-38964424 MS.gene28309:CDS 60.0%


Chromosome Type Strat End Strand Name
chr4.4 gene 38963940 38965341 38963940 ID=MS.gene28309
chr4.4 mRNA 38963940 38965341 38963940 ID=MS.gene28309.t1;Parent=MS.gene28309
chr4.4 exon 38965270 38965341 38965270 ID=MS.gene28309.t1.exon1;Parent=MS.gene28309.t1
chr4.4 CDS 38965270 38965341 38965270 ID=cds.MS.gene28309.t1;Parent=MS.gene28309.t1
chr4.4 exon 38963940 38964689 38963940 ID=MS.gene28309.t1.exon2;Parent=MS.gene28309.t1
chr4.4 CDS 38963940 38964689 38963940 ID=cds.MS.gene28309.t1;Parent=MS.gene28309.t1
Gene Sequence

>MS.gene28309

ATGGATTATGATCACCAAGACAAACCATCCTTCTTCGCAATCATCAAAGAAGGCTTGAACATCAACCGCCTGGTAATAATTTATTCGTACTTTTGTTTATATGTTTCTCCCACATGATCATCATCTCATGCATTCAACAACTTGTTTGCCTTGTTAATAATAAGAAACACTTTGTTTCTTTGGATTCTGACGATGAAAACTAAATTATAGGAATGAAAAGTGAGTTTTTTTAAAGGCGAATGTCATTAAACTAGTTGTATTAATTTACATAGTTTAAATTTGAGACATTCTTCTTAGAACTCATTCGATATTCCTTAGCTCAACAGCCGATTTATCTACTAGAGACAAATTGGGAATTTTAACATTAGCGTTTTAGTTATACATAGACATAGGAACCTGTATTCCCTTTGGTCACTGAATGCACACATTCATGAAGTTTGGAGATCCATGACCGTCCGAAAAATGGGGTGGTCCAGATCCAAGCTTGGTAATTTTTCTGTTTAGACTATTTGATCTCGATTGGAAGGTTACGGATCCCCTGGCTTTGTGAATGCTTGCAGGGATCCAGCTTCATATGCATAACATGTTTAGTTTTAATTTTTAAACATTACATCTTGTCAAGCTACTATGTTTTTTTGGTCATAATCTGCAGAAAGTACCACAAGAGATTGTTAAGGATTTGGGTGAAGAGTTGTGGAAGAATGCATTAATTATTCTGGTAGGCTCTTCTGGTGAGAAATGGGAAGTGAGTATTTTGAAGAAAGGAAATGACATTTATCTGCAAATTGGTTGGCAAAAATTTCTGAAAGACAACACAGTGATGCTTGAAGAGTTATTGGTTTTCACATATAATGGGGAGAACAAGTTCCAGGTGCAAATTTTTGGTAAGAATGGATTGGAGAGACCATGCTTCAAGAATGTACAAGAACAAGAAGAAGTACAAGAAGAAGAAGTTGCTGCAGCAGCTCCAATAATCGCGGCCAAGAGAAAGAGGGGTAGACCAAGAAAAGTTCTTTCTCCTGAGAGTGAGTGCTTTAAGAAGAAAAAAGCTGAAGTTGCAGAAAAAATTGTGGTTAAGAGAAATGATGGTAGAACAAGAAAAAGTCCTGCTGGTGAGAGAGTATGCTTCAGGAAAAAAGAAGAAATTGCAGCAACAATCATGTCTATGGGTAAACCAAGAAAAAATCATGTTCGTCAGAGAGTAAGCGTAAAGAAAGAAGAAGCCAAAGCTGCAGCAACATTGATGGCTGCGATAAACAAGGGTAGAACAAGAGAAAATCCTGCTGGTGAGAGGGTATGCATCATGAAAGAAGAAGCAAAATCTGCAGAAACAATCGTGGCTGAGAGAAAGAAGGGTAGACCAAGAAAATATCCTGCTCCAGTTGTTATTTTAGTTAACTGA

Protein sequence

>MS.gene28309.t1

MDYDHQDKPSFFAIIKEGLNINRLKVPQEIVKDLGEELWKNALIILVGSSGEKWEVSILKKGNDIYLQIGWQKFLKDNTVMLEELLVFTYNGENKFQVQIFGKNGLERPCFKNVQEQEEVQEEEVAAAAPIIAAKRKRGRPRKVLSPESECFKKKKAEVAEKIVVKRNDGRTRKSPAGERVCFRKKEEIAATIMSMGKPRKNHVRQRVSVKKEEAKAAATLMAAINKGRTRENPAGERVCIMKEEAKSAETIVAERKKGRPRKYPAPVVILVN