AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene25039


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene25039.t1 MTR_7g109250 85.366 328 38 3 1 319 1 327 0.0 562
MS.gene25039.t1 MTR_7g109250 85.366 328 38 3 1 319 61 387 0.0 560
MS.gene25039.t1 MTR_8g058607 50.000 172 32 5 60 231 24 141 1.58e-43 146
MS.gene25039.t1 MTR_7g108868 47.368 171 35 3 60 229 11 127 1.35e-41 143
MS.gene25039.t1 MTR_8g058593 47.368 171 35 3 60 229 11 127 1.35e-41 143
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene25039.t1 AT1G01350 66.879 314 95 5 13 319 25 336 2.11e-148 421
MS.gene25039.t1 AT5G06420 65.815 313 101 4 11 319 61 371 2.46e-148 422
MS.gene25039.t1 AT5G06420 65.815 313 101 4 11 319 61 371 2.46e-148 422
MS.gene25039.t1 AT4G01023 65.625 64 20 1 245 308 73 134 3.69e-27 107
MS.gene25039.t1 AT4G01023 65.625 64 20 1 245 308 92 153 7.93e-27 106
MS.gene25039.t1 AT4G01023 65.625 64 20 1 245 308 92 153 1.13e-26 105

Find 70 sgRNAs with CRISPR-Local

Find 77 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
AAAATGAAAGCTAGGTTTCT+TGG 0.236965 8.1:-77420062 None:intergenic
TTGGTGATTTGCAGGAGATT+TGG 0.316183 8.1:-77419742 None:intergenic
GTGGGTCACACAGTCCTCTC+AGG 0.317320 8.1:+77420326 MS.gene25039:CDS
TGTTCAGTTTGGTGATTTGC+AGG 0.323435 8.1:-77419750 None:intergenic
GATCGAGGCGATTACAAATC+TGG 0.345615 8.1:+77420460 MS.gene25039:CDS
GTCATATTCTTCTTATTAAG+AGG 0.347081 8.1:-77419911 None:intergenic
TATACATACCTTGTTCAGTT+TGG 0.352276 8.1:-77419761 None:intergenic
CTTGTATAATTGTACATCTT+CGG 0.375485 8.1:-77420233 None:intergenic
GGATATATGCAAGGATTATA+AGG 0.382708 8.1:+77420393 MS.gene25039:CDS
TGCAAGGATTATAAGGAAAC+TGG 0.390916 8.1:+77420400 MS.gene25039:CDS
GCTAGGTTTCTTGGATTCTT+CGG 0.398397 8.1:-77420053 None:intergenic
TTATAATCCTTGCATATATC+CGG 0.408034 8.1:-77420391 None:intergenic
TAGCAAAGCAACCGCAACTT+TGG 0.426930 8.1:+77420117 MS.gene25039:CDS
CTTGCTTAAGAGCTCTTTCA+CGG 0.431115 8.1:-77420177 None:intergenic
CTGTGAGCATTGTGCATTGA+AGG 0.436410 8.1:+77420678 MS.gene25039:CDS
GTCTGCAACCAGCCTACGCT+TGG 0.437064 8.1:+77420843 MS.gene25039:CDS
TGCTTGCACTTGGTTGAGAC+AGG 0.443250 8.1:-77420649 None:intergenic
CATTTGTAGAAATCCATTTG+TGG 0.461066 8.1:+77420624 MS.gene25039:CDS
AAAGACTCAAAATGAAAGCT+AGG 0.461332 8.1:-77420070 None:intergenic
TTCGGTCTTTGAAGAGGAGG+TGG 0.474323 8.1:-77420035 None:intergenic
GAAAGCAAGGAGGATGAGAT+TGG 0.475774 8.1:+77420516 MS.gene25039:CDS
CAATAATTACACAGATCATA+AGG 0.476447 8.1:+77420261 MS.gene25039:CDS
CGAAGATGTACAATTATACA+AGG 0.488171 8.1:+77420234 MS.gene25039:CDS
GTGGCTGATGGAGAAGGAAT+GGG 0.493010 8.1:+77420483 MS.gene25039:CDS
GCAAACAATTGCTAGTGAAA+AGG 0.493544 8.1:+77420300 MS.gene25039:CDS
TTACAAATCTGGGTGGCTGA+TGG 0.500708 8.1:+77420471 MS.gene25039:CDS
GTTGAGACAGGATCCACAAA+TGG 0.505798 8.1:-77420637 None:intergenic
TTCTTCGGTCTTTGAAGAGG+AGG 0.521939 8.1:-77420038 None:intergenic
ATCGAGGCGATTACAAATCT+GGG 0.523125 8.1:+77420461 MS.gene25039:CDS
GAGCTCTTTCACGGATGGCA+CGG 0.524231 8.1:-77420168 None:intergenic
AGCAAGATTTGATTATCAGC+CGG 0.527438 8.1:+77420372 MS.gene25039:CDS
TGGATGAGTTTATTTATCCT+CGG 0.527485 8.1:-77420904 None:intergenic
GAGGAGGGTGCTAATTTGAA+TGG 0.530598 8.1:+77420559 MS.gene25039:CDS
TGCAGGTGAGGATGCAGAAG+AGG 0.532110 8.1:+77420540 MS.gene25039:CDS
GGATTCTTCGGTCTTTGAAG+AGG 0.535410 8.1:-77420041 None:intergenic
CTTAAGAGCTCTTTCACGGA+TGG 0.538525 8.1:-77420173 None:intergenic
AATTACACAGATCATAAGGC+TGG 0.540860 8.1:+77420265 MS.gene25039:CDS
GGTGGCTGATGGAGAAGGAA+TGG 0.541112 8.1:+77420482 MS.gene25039:CDS
GCGAAGCACTATTGAGAATG+AGG 0.543921 8.1:+77419937 MS.gene25039:CDS
TGGGTCACACAGTCCTCTCA+GGG 0.547131 8.1:+77420327 MS.gene25039:CDS
TATTAGTATGGAAGATTCTG+AGG 0.556688 8.1:+77419719 None:intergenic
ACAGAAGTAGTGCTTGCACT+TGG 0.557721 8.1:-77420659 None:intergenic
ATCTGGGTGGCTGATGGAGA+AGG 0.558711 8.1:+77420477 MS.gene25039:CDS
AGCTCTTTCACGGATGGCAC+GGG 0.560125 8.1:-77420167 None:intergenic
GAAACTGGTTACTGTGGGTA+TGG 0.560524 8.1:+77420415 MS.gene25039:CDS
TCATGAGATACGAAAGAAGA+TGG 0.562670 8.1:+77420881 MS.gene25039:CDS
AGGTGAGGATGCAGAAGAGG+AGG 0.575195 8.1:+77420543 MS.gene25039:CDS
GGGATGAAGCTGAGAAAGCA+AGG 0.584805 8.1:+77420503 MS.gene25039:CDS
TATAAGGAAACTGGTTACTG+TGG 0.586008 8.1:+77420409 MS.gene25039:CDS
ACAATTGCTAGTGAAAAGGC+TGG 0.588134 8.1:+77420304 MS.gene25039:CDS
TTGCTAGTGAAAAGGCTGGT+GGG 0.588909 8.1:+77420308 MS.gene25039:CDS
GATGAGATTGGCTGCAGGTG+AGG 0.590274 8.1:+77420528 MS.gene25039:CDS
GCAAATCACCAAACTGAACA+AGG 0.596043 8.1:+77419753 MS.gene25039:CDS
AGGAGGATGAGATTGGCTGC+AGG 0.603143 8.1:+77420523 MS.gene25039:CDS
GCAAGCGACAAAGAGTCTCA+AGG 0.605902 8.1:+77420195 MS.gene25039:CDS
CAAGCGACAAAGAGTCTCAA+GGG 0.609568 8.1:+77420196 MS.gene25039:CDS
ATTGCTAGTGAAAAGGCTGG+TGG 0.609608 8.1:+77420307 MS.gene25039:CDS
AGCACTATTGAGAATGAGGA+TGG 0.610986 8.1:+77419941 MS.gene25039:CDS
GGTGAGGATGCAGAAGAGGA+GGG 0.615274 8.1:+77420544 MS.gene25039:CDS
ATAAGGAAACTGGTTACTGT+GGG 0.628079 8.1:+77420410 MS.gene25039:CDS
GATACGAAAGAAGATGGCCG+AGG 0.629597 8.1:+77420887 MS.gene25039:CDS
TTATCAGCCGGATATATGCA+AGG 0.629970 8.1:+77420384 MS.gene25039:CDS
CTACAAATGAAACACGCAGA+TGG 0.636028 8.1:-77420610 None:intergenic
TGTAAGTTTATGCATGATCG+AGG 0.641112 8.1:+77420445 MS.gene25039:CDS
AGTCTCAGTCTCCAAAGTTG+CGG 0.641815 8.1:-77420128 None:intergenic
TGAGGATGGCTTGAACAATG+AGG 0.672716 8.1:+77419955 MS.gene25039:CDS
ATGTGAGCTGAAGCCCTGAG+AGG 0.679042 8.1:-77420340 None:intergenic
GAAGATGTACAATTATACAA+GGG 0.702149 8.1:+77420235 MS.gene25039:CDS
ATGAAGCTGAGAAAGCAAGG+AGG 0.730792 8.1:+77420506 MS.gene25039:CDS
GAGGCGATTACAAATCTGGG+TGG 0.743333 8.1:+77420464 MS.gene25039:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
! AAGTAAAATGAACAGAAGTT+AGG - chr8.1:77420792-77420811 None:intergenic 25.0%
! AGAAGTTAGGCATAATTAAA+AGG - chr8.1:77420779-77420798 None:intergenic 25.0%
! CAATAATTACACAGATCATA+AGG + chr8.1:77420261-77420280 MS.gene25039:CDS 25.0%
! CTTGTATAATTGTACATCTT+CGG - chr8.1:77420236-77420255 None:intergenic 25.0%
! GAAGATGTACAATTATACAA+GGG + chr8.1:77420235-77420254 MS.gene25039:CDS 25.0%
! GAAGTTAGGCATAATTAAAA+GGG - chr8.1:77420778-77420797 None:intergenic 25.0%
! GTCATATTCTTCTTATTAAG+AGG - chr8.1:77419914-77419933 None:intergenic 25.0%
! TTATAATCCTTGCATATATC+CGG - chr8.1:77420394-77420413 None:intergenic 25.0%
!!! ACTTATTTGCTTTGAAGTTA+AGG - chr8.1:77420709-77420728 None:intergenic 25.0%
!!! CTTATTTGCTTTGAAGTTAA+GGG - chr8.1:77420708-77420727 None:intergenic 25.0%
AAAATGAAAGCTAGGTTTCT+TGG - chr8.1:77420065-77420084 None:intergenic 30.0%
AAAGACTCAAAATGAAAGCT+AGG - chr8.1:77420073-77420092 None:intergenic 30.0%
CATTTGTAGAAATCCATTTG+TGG + chr8.1:77420624-77420643 MS.gene25039:CDS 30.0%
CGAAGATGTACAATTATACA+AGG + chr8.1:77420234-77420253 MS.gene25039:CDS 30.0%
GGATATATGCAAGGATTATA+AGG + chr8.1:77420393-77420412 MS.gene25039:CDS 30.0%
GTACAAAGAAATAAATGCAG+AGG - chr8.1:77419831-77419850 None:intergenic 30.0%
TATACATACCTTGTTCAGTT+TGG - chr8.1:77419764-77419783 None:intergenic 30.0%
AATTACACAGATCATAAGGC+TGG + chr8.1:77420265-77420284 MS.gene25039:CDS 35.0%
ACATTAAAAATGCCAAGCGT+AGG - chr8.1:77420858-77420877 None:intergenic 35.0%
AGCAAGATTTGATTATCAGC+CGG + chr8.1:77420372-77420391 MS.gene25039:CDS 35.0%
ATAAGGAAACTGGTTACTGT+GGG + chr8.1:77420410-77420429 MS.gene25039:CDS 35.0%
GCAAACAATTGCTAGTGAAA+AGG + chr8.1:77420300-77420319 MS.gene25039:CDS 35.0%
TATAAGGAAACTGGTTACTG+TGG + chr8.1:77420409-77420428 MS.gene25039:CDS 35.0%
TCATGAGATACGAAAGAAGA+TGG + chr8.1:77420881-77420900 MS.gene25039:CDS 35.0%
TGCAAGGATTATAAGGAAAC+TGG + chr8.1:77420400-77420419 MS.gene25039:CDS 35.0%
TGTAAGTTTATGCATGATCG+AGG + chr8.1:77420445-77420464 MS.gene25039:CDS 35.0%
! TACGCTTGGCATTTTTAATG+TGG + chr8.1:77420857-77420876 MS.gene25039:CDS 35.0%
ACAATTGCTAGTGAAAAGGC+TGG + chr8.1:77420304-77420323 MS.gene25039:CDS 40.0%
AGCACTATTGAGAATGAGGA+TGG + chr8.1:77419941-77419960 MS.gene25039:CDS 40.0%
ATCGAGGCGATTACAAATCT+GGG + chr8.1:77420461-77420480 MS.gene25039:CDS 40.0%
CTACAAATGAAACACGCAGA+TGG - chr8.1:77420613-77420632 None:intergenic 40.0%
CTTGCTTAAGAGCTCTTTCA+CGG - chr8.1:77420180-77420199 None:intergenic 40.0%
GCAAATCACCAAACTGAACA+AGG + chr8.1:77419753-77419772 MS.gene25039:CDS 40.0%
GCTAGGTTTCTTGGATTCTT+CGG - chr8.1:77420056-77420075 None:intergenic 40.0%
TTATCAGCCGGATATATGCA+AGG + chr8.1:77420384-77420403 MS.gene25039:CDS 40.0%
! TGTTCAGTTTGGTGATTTGC+AGG - chr8.1:77419753-77419772 None:intergenic 40.0%
! TTGGTGATTTGCAGGAGATT+TGG - chr8.1:77419745-77419764 None:intergenic 40.0%
ACAGAAGTAGTGCTTGCACT+TGG - chr8.1:77420662-77420681 None:intergenic 45.0%
AGTCTCAGTCTCCAAAGTTG+CGG - chr8.1:77420131-77420150 None:intergenic 45.0%
ATGAAGCTGAGAAAGCAAGG+AGG + chr8.1:77420506-77420525 MS.gene25039:CDS 45.0%
ATTGCTAGTGAAAAGGCTGG+TGG + chr8.1:77420307-77420326 MS.gene25039:CDS 45.0%
CAAGCGACAAAGAGTCTCAA+GGG + chr8.1:77420196-77420215 MS.gene25039:CDS 45.0%
CTTAAGAGCTCTTTCACGGA+TGG - chr8.1:77420176-77420195 None:intergenic 45.0%
GAAACTGGTTACTGTGGGTA+TGG + chr8.1:77420415-77420434 MS.gene25039:CDS 45.0%
GAAAGCAAGGAGGATGAGAT+TGG + chr8.1:77420516-77420535 MS.gene25039:CDS 45.0%
GATCGAGGCGATTACAAATC+TGG + chr8.1:77420460-77420479 MS.gene25039:CDS 45.0%
GTTGAGACAGGATCCACAAA+TGG - chr8.1:77420640-77420659 None:intergenic 45.0%
TAAAAATGCCAAGCGTAGGC+TGG - chr8.1:77420854-77420873 None:intergenic 45.0%
TAGCAAAGCAACCGCAACTT+TGG + chr8.1:77420117-77420136 MS.gene25039:CDS 45.0%
TGAGGATGGCTTGAACAATG+AGG + chr8.1:77419955-77419974 MS.gene25039:CDS 45.0%
TTACAAATCTGGGTGGCTGA+TGG + chr8.1:77420471-77420490 MS.gene25039:CDS 45.0%
TTGCTAGTGAAAAGGCTGGT+GGG + chr8.1:77420308-77420327 MS.gene25039:CDS 45.0%
! CTGTGAGCATTGTGCATTGA+AGG + chr8.1:77420678-77420697 MS.gene25039:CDS 45.0%
! GCGAAGCACTATTGAGAATG+AGG + chr8.1:77419937-77419956 MS.gene25039:CDS 45.0%
! GGATTCTTCGGTCTTTGAAG+AGG - chr8.1:77420044-77420063 None:intergenic 45.0%
! TTCTTCGGTCTTTGAAGAGG+AGG - chr8.1:77420041-77420060 None:intergenic 45.0%
!! GAGGAGGGTGCTAATTTGAA+TGG + chr8.1:77420559-77420578 MS.gene25039:CDS 45.0%
GAGGCGATTACAAATCTGGG+TGG + chr8.1:77420464-77420483 MS.gene25039:CDS 50.0%
GATACGAAAGAAGATGGCCG+AGG + chr8.1:77420887-77420906 MS.gene25039:CDS 50.0%
GCAAGCGACAAAGAGTCTCA+AGG + chr8.1:77420195-77420214 MS.gene25039:CDS 50.0%
GGGATGAAGCTGAGAAAGCA+AGG + chr8.1:77420503-77420522 MS.gene25039:CDS 50.0%
GTGGCTGATGGAGAAGGAAT+GGG + chr8.1:77420483-77420502 MS.gene25039:CDS 50.0%
TGCTTGCACTTGGTTGAGAC+AGG - chr8.1:77420652-77420671 None:intergenic 50.0%
! TTCGGTCTTTGAAGAGGAGG+TGG - chr8.1:77420038-77420057 None:intergenic 50.0%
AGCTCTTTCACGGATGGCAC+GGG - chr8.1:77420170-77420189 None:intergenic 55.0%
AGGTGAGGATGCAGAAGAGG+AGG + chr8.1:77420543-77420562 MS.gene25039:CDS 55.0%
ATCTGGGTGGCTGATGGAGA+AGG + chr8.1:77420477-77420496 MS.gene25039:CDS 55.0%
ATGTGAGCTGAAGCCCTGAG+AGG - chr8.1:77420343-77420362 None:intergenic 55.0%
GAGCTCTTTCACGGATGGCA+CGG - chr8.1:77420171-77420190 None:intergenic 55.0%
GGTGAGGATGCAGAAGAGGA+GGG + chr8.1:77420544-77420563 MS.gene25039:CDS 55.0%
GGTGGCTGATGGAGAAGGAA+TGG + chr8.1:77420482-77420501 MS.gene25039:CDS 55.0%
TGCAGGTGAGGATGCAGAAG+AGG + chr8.1:77420540-77420559 MS.gene25039:CDS 55.0%
TGGGTCACACAGTCCTCTCA+GGG + chr8.1:77420327-77420346 MS.gene25039:CDS 55.0%
! AGGAGGATGAGATTGGCTGC+AGG + chr8.1:77420523-77420542 MS.gene25039:CDS 55.0%
! GATGAGATTGGCTGCAGGTG+AGG + chr8.1:77420528-77420547 MS.gene25039:CDS 55.0%
GTCTGCAACCAGCCTACGCT+TGG + chr8.1:77420843-77420862 MS.gene25039:CDS 60.0%
GTGGGTCACACAGTCCTCTC+AGG + chr8.1:77420326-77420345 MS.gene25039:CDS 60.0%


Chromosome Type Strat End Strand Name
chr8.1 gene 77419726 77420917 77419726 ID=MS.gene25039
chr8.1 mRNA 77419726 77420917 77419726 ID=MS.gene25039.t1;Parent=MS.gene25039
chr8.1 exon 77419726 77419774 77419726 ID=MS.gene25039.t1.exon1;Parent=MS.gene25039.t1
chr8.1 CDS 77419726 77419774 77419726 ID=cds.MS.gene25039.t1;Parent=MS.gene25039.t1
chr8.1 exon 77419891 77420699 77419891 ID=MS.gene25039.t1.exon2;Parent=MS.gene25039.t1
chr8.1 CDS 77419891 77420699 77419891 ID=cds.MS.gene25039.t1;Parent=MS.gene25039.t1
chr8.1 exon 77420816 77420917 77420816 ID=MS.gene25039.t1.exon3;Parent=MS.gene25039.t1
chr8.1 CDS 77420816 77420917 77420816 ID=cds.MS.gene25039.t1;Parent=MS.gene25039.t1
Gene Sequence

>MS.gene25039

ATGGAAGATTCTGAGGCCAAATCTCCTGCAAATCACCAAACTGAACAAGGTATGTATAATTAATTTCTTGCATTACTAGACTCACAATTGTTATCTTATGCACCTCTGCATTTATTTCTTTGTACTGTCATTAACTTTTCTTTTTACGTGTTTGTTGATCTTCAGTGTGCAGTTTCTTTAGAAAACCTCTTAATAAGAAGAATATGACGAAGCGAAGCACTATTGAGAATGAGGATGGCTTGAACAATGAGGAGTCTTTGATGCATGTTCAGAAAAAGAACATGAAAGCTGACAATAACTTATTCTTTTCCACCTCCTCTTCAAAGACCGAAGAATCCAAGAAACCTAGCTTTCATTTTGAGTCTTTTAAAGAGATTCAAGTTCAACATGATAGCAAAGCAACCGCAACTTTGGAGACTGAGACTGATTTTTCAAGAGATGCCCGTGCCATCCGTGAAAGAGCTCTTAAGCAAGCGACAAAGAGTCTCAAGGGAAAGAGTAATCGTTCCGAAGATGTACAATTATACAAGGGAATCAATAATTACACAGATCATAAGGCTGGATTTCGTAGAGAGCAAACAATTGCTAGTGAAAAGGCTGGTGGGTCACACAGTCCTCTCAGGGCTTCAGCTCACATAAGAGTTTCAGCAAGATTTGATTATCAGCCGGATATATGCAAGGATTATAAGGAAACTGGTTACTGTGGGTATGGTGATTCGTGTAAGTTTATGCATGATCGAGGCGATTACAAATCTGGGTGGCTGATGGAGAAGGAATGGGATGAAGCTGAGAAAGCAAGGAGGATGAGATTGGCTGCAGGTGAGGATGCAGAAGAGGAGGGTGCTAATTTGAATGGTGAAGATGATGACGACGAAGACTCGTTACCATCTGCGTGTTTCATTTGTAGAAATCCATTTGTGGATCCTGTCTCAACCAAGTGCAAGCACTACTTCTGTGAGCATTGTGCATTGAAGGTACACCCTTAACTTCAAAGCAAATAAGTTTCAATTTATAACAGTTTCAAGTTATTTAGTAATGCTTAACTTTTTCCCTTTTAATTATGCCTAACTTCTGTTCATTTTACTTGCAGCATCATGCAAAGAATAAAAAGTGTTTTGTCTGCAACCAGCCTACGCTTGGCATTTTTAATGTGGCTCATGAGATACGAAAGAAGATGGCCGAGGATAAATAA

Protein sequence

>MS.gene25039.t1

MEDSEAKSPANHQTEQVCSFFRKPLNKKNMTKRSTIENEDGLNNEESLMHVQKKNMKADNNLFFSTSSSKTEESKKPSFHFESFKEIQVQHDSKATATLETETDFSRDARAIRERALKQATKSLKGKSNRSEDVQLYKGINNYTDHKAGFRREQTIASEKAGGSHSPLRASAHIRVSARFDYQPDICKDYKETGYCGYGDSCKFMHDRGDYKSGWLMEKEWDEAEKARRMRLAAGEDAEEEGANLNGEDDDDEDSLPSACFICRNPFVDPVSTKCKHYFCEHCALKHHAKNKKCFVCNQPTLGIFNVAHEIRKKMAEDK