AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene026879

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene026879.t1 MTR_7g117040 93.678 174 11 0 1 174 1 174 8.32e-124 346
MS.gene026879.t1 MTR_7g117040 91.379 174 11 1 1 174 1 170 2.58e-118 332
MS.gene026879.t1 MTR_7g117040 89.655 174 11 1 1 174 1 167 1.02e-115 325
MS.gene026879.t1 MTR_3g034200 36.424 151 95 1 1 150 1 151 1.46e-28 104
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene026879.t1 AT1G03150 90.230 174 17 0 1 174 1 174 2.02e-120 337
MS.gene026879.t1 AT5G13780 37.179 156 97 1 1 155 1 156 1.41e-28 105

Find 38 sgRNAs with CRISPR-Local

Find 83 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CGAGTGCTACGTTATTATTC+TGG 0.239936 2.2:-17911502 MS.gene026879:CDS
GTAACCCATGATTCGATTTC+CGG 0.242250 2.2:+17912247 None:intergenic
TGATTCGATTTCCGGGGCCT+TGG 0.300853 2.2:+17912255 None:intergenic
GTCAGGCCATCTTGCTAAAT+AGG 0.361124 2.2:+17912292 None:intergenic
TTCCGGGGCCTTGGGCGACT+TGG 0.382516 2.2:+17912264 None:intergenic
GATTCGATTTCCGGGGCCTT+GGG 0.386942 2.2:+17912256 None:intergenic
TAGTCGTATTCTAGTTCATC+AGG 0.393670 2.2:+17911298 None:intergenic
TAACCCATGATTCGATTTCC+GGG 0.408074 2.2:+17912248 None:intergenic
TTCTGGGGAAGAAGATGGAT+TGG 0.420903 2.2:-17911485 MS.gene026879:CDS
AGTCTGTCGTCCCTCTTAAA+CGG 0.427719 2.2:-17911330 MS.gene026879:CDS
TATTATTCTGGGGAAGAAGA+TGG 0.447212 2.2:-17911490 MS.gene026879:CDS
TGCTAAATAGGTCATGTAGA+AGG 0.454880 2.2:+17912304 None:intergenic
GAGTGCTACGTTATTATTCT+GGG 0.470429 2.2:-17911501 MS.gene026879:CDS
TCTGGGGAAGAAGATGGATT+GGG 0.475034 2.2:-17911484 MS.gene026879:intron
TTCCAAGTCGCCCAAGGCCC+CGG 0.485170 2.2:-17912266 MS.gene026879:CDS
TGACATTTGTAAAACGAAGA+AGG 0.486544 2.2:+17912455 None:intergenic
TAGAGGGGCAAGGAGAATCT+TGG 0.499019 2.2:-17912134 MS.gene026879:CDS
TGGGCGACTTGGAAATAGTC+AGG 0.503036 2.2:+17912275 None:intergenic
GGAGTGACACGCCGTTTAAG+AGG 0.508020 2.2:+17911319 None:intergenic
AGCCATCAAGATGTATGAAA+AGG 0.514376 2.2:-17911896 MS.gene026879:intron
AGGCCCCGGAAATCGAATCA+TGG 0.515528 2.2:-17912252 MS.gene026879:CDS
AACGTGAGTACGTACAGTTT+CGG 0.540046 2.2:+17912417 None:intergenic
ACATGACCTATTTAGCAAGA+TGG 0.544945 2.2:-17912298 MS.gene026879:CDS
GCAGTTATGGGTAAAGTAGA+GGG 0.544970 2.2:-17912150 MS.gene026879:intron
GGCCCCGGAAATCGAATCAT+GGG 0.555258 2.2:-17912251 MS.gene026879:CDS
GACTATTTCCAAGTCGCCCA+AGG 0.565815 2.2:-17912272 MS.gene026879:CDS
AACTGCAGTAACCGTTGCTA+CGG 0.572799 2.2:-17912100 MS.gene026879:CDS
ATGGGTAAAGTAGAGGGGCA+AGG 0.572891 2.2:-17912144 MS.gene026879:CDS
TGCAGTTATGGGTAAAGTAG+AGG 0.579669 2.2:-17912151 MS.gene026879:intron
CCGTTGCTACGGAGTATCGC+AGG 0.596977 2.2:-17912089 MS.gene026879:CDS
GAGTGACACGCCGTTTAAGA+GGG 0.600246 2.2:+17911320 None:intergenic
AATAATAACGTAGCACTCGT+CGG 0.603392 2.2:+17911506 None:intergenic
AACCCATGATTCGATTTCCG+GGG 0.619081 2.2:+17912249 None:intergenic
GGGCAAGGAGAATCTTGGCA+TGG 0.661266 2.2:-17912129 MS.gene026879:CDS
AGTGCTACGTTATTATTCTG+GGG 0.665106 2.2:-17911500 MS.gene026879:CDS
CAGTTATGGGTAAAGTAGAG+GGG 0.668038 2.2:-17912149 MS.gene026879:CDS
CCTGCGATACTCCGTAGCAA+CGG 0.679156 2.2:+17912089 None:intergenic
AAGAGATGACGACAATACGT+AGG 0.724152 2.2:-17912492 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! TTAATGTATAACTTAATCAT+TGG - chr2.2:17912129-17912148 MS.gene026879:CDS 15.0%
!! AAAAAACCCTATTAGAATTT+GGG + chr2.2:17912070-17912089 None:intergenic 20.0%
!! ACAGCAAATAAATAATGATA+TGG + chr2.2:17912377-17912396 None:intergenic 20.0%
!! AGATTACTTATCAATAGTTT+AGG - chr2.2:17912103-17912122 MS.gene026879:CDS 20.0%
!! TAAAAAACCCTATTAGAATT+TGG + chr2.2:17912071-17912090 None:intergenic 20.0%
!! TATAACTTAATCATTGGATA+TGG - chr2.2:17912135-17912154 MS.gene026879:CDS 20.0%
!!! GATATGTTTTCTTTTAGATT+AGG - chr2.2:17912178-17912197 MS.gene026879:intron 20.0%
! AATATCATTCATGCAGTTAT+GGG - chr2.2:17911622-17911641 MS.gene026879:intron 25.0%
! TCCTCATATCTGAAAATAAA+GGG + chr2.2:17912407-17912426 None:intergenic 25.0%
! TGTGTAAAAGACTATACTAT+GGG - chr2.2:17911585-17911604 MS.gene026879:intron 25.0%
! TTCCTCATATCTGAAAATAA+AGG + chr2.2:17912408-17912427 None:intergenic 25.0%
! TTGTGTAAAAGACTATACTA+TGG - chr2.2:17911584-17911603 MS.gene026879:intron 25.0%
!!! ACACAAGGTTTGTTTTAAAT+CGG - chr2.2:17911970-17911989 MS.gene026879:intron 25.0%
!!! TTTATTTTCAGATATGAGGA+AGG - chr2.2:17912407-17912426 MS.gene026879:intron 25.0%
ACATATCCTAATCCAACAAA+TGG + chr2.2:17912165-17912184 None:intergenic 30.0%
ATCCAACCCAAATTCTAATA+GGG - chr2.2:17912061-17912080 MS.gene026879:CDS 30.0%
CAAGCTATAAGATGTCAAAA+AGG + chr2.2:17912245-17912264 None:intergenic 30.0%
CAATATCATTCATGCAGTTA+TGG - chr2.2:17911621-17911640 MS.gene026879:intron 30.0%
CATAACTGCATGAATGATAT+TGG + chr2.2:17911623-17911642 None:intergenic 30.0%
TGACATTTGTAAAACGAAGA+AGG + chr2.2:17911332-17911351 None:intergenic 30.0%
! CTTTTTGACATCTTATAGCT+TGG - chr2.2:17912243-17912262 MS.gene026879:intron 30.0%
! TACCTTTTCATACATCTTGA+TGG + chr2.2:17911893-17911912 None:intergenic 30.0%
!! CATAAAGTGAATTGAGTTGA+GGG + chr2.2:17911415-17911434 None:intergenic 30.0%
!!! TCCCTTTATTTTCAGATATG+AGG - chr2.2:17912403-17912422 MS.gene026879:intron 30.0%
AACCCTATTAGAATTTGGGT+TGG + chr2.2:17912066-17912085 None:intergenic 35.0%
AACTGCATGAATGATATTGG+TGG + chr2.2:17911620-17911639 None:intergenic 35.0%
AATAATAACGTAGCACTCGT+CGG + chr2.2:17912281-17912300 None:intergenic 35.0%
ACATGACCTATTTAGCAAGA+TGG - chr2.2:17911486-17911505 MS.gene026879:CDS 35.0%
AGCCATCAAGATGTATGAAA+AGG - chr2.2:17911888-17911907 MS.gene026879:intron 35.0%
AGTGACAATATGTAAGGCAT+CGG - chr2.2:17911760-17911779 MS.gene026879:intron 35.0%
AGTGCTACGTTATTATTCTG+GGG - chr2.2:17912284-17912303 MS.gene026879:CDS 35.0%
AGTGGAAGGTTTAATCTGAA+AGG + chr2.2:17911932-17911951 None:intergenic 35.0%
GACATCAGTGACAATATGTA+AGG - chr2.2:17911754-17911773 MS.gene026879:intron 35.0%
GAGTGCTACGTTATTATTCT+GGG - chr2.2:17912283-17912302 MS.gene026879:CDS 35.0%
GATCCAACCCAAATTCTAAT+AGG - chr2.2:17912060-17912079 MS.gene026879:CDS 35.0%
TGCTAAATAGGTCATGTAGA+AGG + chr2.2:17911483-17911502 None:intergenic 35.0%
! GCATAAAGTGAATTGAGTTG+AGG + chr2.2:17911416-17911435 None:intergenic 35.0%
! TATTATTCTGGGGAAGAAGA+TGG - chr2.2:17912294-17912313 MS.gene026879:CDS 35.0%
!! TAGTCGTATTCTAGTTCATC+AGG + chr2.2:17912489-17912508 None:intergenic 35.0%
!! TGAATTGAGTTGAGGGTTTA+GGG + chr2.2:17911408-17911427 None:intergenic 35.0%
!! TTTTCATACATCTTGATGGC+TGG + chr2.2:17911889-17911908 None:intergenic 35.0%
AACGTGAGTACGTACAGTTT+CGG + chr2.2:17911370-17911389 None:intergenic 40.0%
ACCTTGTGTACAAACCTACA+AGG + chr2.2:17911959-17911978 None:intergenic 40.0%
CAGTTATGGGTAAAGTAGAG+GGG - chr2.2:17911635-17911654 MS.gene026879:intron 40.0%
CGAGTGCTACGTTATTATTC+TGG - chr2.2:17912282-17912301 MS.gene026879:CDS 40.0%
GCAGTTATGGGTAAAGTAGA+GGG - chr2.2:17911634-17911653 MS.gene026879:intron 40.0%
GGATATGGACTTCCATTTGT+TGG - chr2.2:17912150-17912169 MS.gene026879:intron 40.0%
GTAACCCATGATTCGATTTC+CGG + chr2.2:17911540-17911559 None:intergenic 40.0%
TAACCCATGATTCGATTTCC+GGG + chr2.2:17911539-17911558 None:intergenic 40.0%
TATGTGTGTTTGTCTCTGTG+TGG - chr2.2:17911783-17911802 MS.gene026879:intron 40.0%
TCCTTGTAGGTTTGTACACA+AGG - chr2.2:17911955-17911974 MS.gene026879:intron 40.0%
TGCAGTTATGGGTAAAGTAG+AGG - chr2.2:17911633-17911652 MS.gene026879:intron 40.0%
! GGACTTCCATTTGTTGGATT+AGG - chr2.2:17912156-17912175 MS.gene026879:intron 40.0%
!! GTGAATTGAGTTGAGGGTTT+AGG + chr2.2:17911409-17911428 None:intergenic 40.0%
AACCCATGATTCGATTTCCG+GGG + chr2.2:17911538-17911557 None:intergenic 45.0%
AACTGCAGTAACCGTTGCTA+CGG - chr2.2:17911684-17911703 MS.gene026879:intron 45.0%
ACAAACCTACAAGGAAGCAG+TGG + chr2.2:17911950-17911969 None:intergenic 45.0%
AGTCTGTCGTCCCTCTTAAA+CGG - chr2.2:17912454-17912473 MS.gene026879:CDS 45.0%
CCCTACAAAATCAGCTTGTG+CGG + chr2.2:17912032-17912051 None:intergenic 45.0%
GTCAGGCCATCTTGCTAAAT+AGG + chr2.2:17911495-17911514 None:intergenic 45.0%
! TCTGGGGAAGAAGATGGATT+GGG - chr2.2:17912300-17912319 MS.gene026879:CDS 45.0%
! TTCTGGGGAAGAAGATGGAT+TGG - chr2.2:17912299-17912318 MS.gene026879:CDS 45.0%
!! ACCGCACAAGCTGATTTTGT+AGG - chr2.2:17912028-17912047 MS.gene026879:intron 45.0%
!! CCGCACAAGCTGATTTTGTA+GGG - chr2.2:17912029-17912048 MS.gene026879:intron 45.0%
!! GGAAGAAGATGGATTGGGTA+TGG - chr2.2:17912305-17912324 MS.gene026879:CDS 45.0%
ACCTACAAGGAAGCAGTGGA+AGG + chr2.2:17911946-17911965 None:intergenic 50.0%
ACCTTCCACTGCTTCCTTGT+AGG - chr2.2:17911942-17911961 MS.gene026879:CDS 50.0%
ATGGGTAAAGTAGAGGGGCA+AGG - chr2.2:17911640-17911659 MS.gene026879:intron 50.0%
GACTATTTCCAAGTCGCCCA+AGG - chr2.2:17911512-17911531 MS.gene026879:CDS 50.0%
GAGTGACACGCCGTTTAAGA+GGG + chr2.2:17912467-17912486 None:intergenic 50.0%
GTGTGTTTGTCTCTGTGTGG+AGG - chr2.2:17911786-17911805 MS.gene026879:intron 50.0%
TAGAGGGGCAAGGAGAATCT+TGG - chr2.2:17911650-17911669 MS.gene026879:intron 50.0%
! TGGGCGACTTGGAAATAGTC+AGG + chr2.2:17911512-17911531 None:intergenic 50.0%
AGGCCCCGGAAATCGAATCA+TGG - chr2.2:17911532-17911551 MS.gene026879:intron 55.0%
CCTGCGATACTCCGTAGCAA+CGG + chr2.2:17911698-17911717 None:intergenic 55.0%
GATTCGATTTCCGGGGCCTT+GGG + chr2.2:17911531-17911550 None:intergenic 55.0%
GGAGTGACACGCCGTTTAAG+AGG + chr2.2:17912468-17912487 None:intergenic 55.0%
GGCCCCGGAAATCGAATCAT+GGG - chr2.2:17911533-17911552 MS.gene026879:intron 55.0%
GGGCAAGGAGAATCTTGGCA+TGG - chr2.2:17911655-17911674 MS.gene026879:intron 55.0%
TGATTCGATTTCCGGGGCCT+TGG + chr2.2:17911532-17911551 None:intergenic 55.0%
!! CCGTTGCTACGGAGTATCGC+AGG - chr2.2:17911695-17911714 MS.gene026879:intron 60.0%
TTCCAAGTCGCCCAAGGCCC+CGG - chr2.2:17911518-17911537 MS.gene026879:CDS 65.0%
TTCCGGGGCCTTGGGCGACT+TGG + chr2.2:17911523-17911542 None:intergenic 70.0%


Chromosome Type Strat End Strand Name
chr2.2 gene 17911297 17912509 17911297 ID=MS.gene026879
chr2.2 mRNA 17911297 17912509 17911297 ID=MS.gene026879.t1;Parent=MS.gene026879
chr2.2 exon 17912432 17912509 17912432 ID=MS.gene026879.t1.exon1;Parent=MS.gene026879.t1
chr2.2 CDS 17912432 17912509 17912432 ID=cds.MS.gene026879.t1;Parent=MS.gene026879.t1
chr2.2 exon 17912246 17912336 17912246 ID=MS.gene026879.t1.exon2;Parent=MS.gene026879.t1
chr2.2 CDS 17912246 17912336 17912246 ID=cds.MS.gene026879.t1;Parent=MS.gene026879.t1
chr2.2 exon 17912036 17912168 17912036 ID=MS.gene026879.t1.exon3;Parent=MS.gene026879.t1
chr2.2 CDS 17912036 17912168 17912036 ID=cds.MS.gene026879.t1;Parent=MS.gene026879.t1
chr2.2 exon 17911897 17911966 17911897 ID=MS.gene026879.t1.exon4;Parent=MS.gene026879.t1
chr2.2 CDS 17911897 17911966 17911897 ID=cds.MS.gene026879.t1;Parent=MS.gene026879.t1
chr2.2 exon 17911485 17911545 17911485 ID=MS.gene026879.t1.exon5;Parent=MS.gene026879.t1
chr2.2 CDS 17911485 17911545 17911485 ID=cds.MS.gene026879.t1;Parent=MS.gene026879.t1
chr2.2 exon 17911297 17911388 17911297 ID=MS.gene026879.t1.exon6;Parent=MS.gene026879.t1
chr2.2 CDS 17911297 17911388 17911297 ID=cds.MS.gene026879.t1;Parent=MS.gene026879.t1
Gene Sequence

>MS.gene026879

ATGACGACAATACGTAGGTTTTGCTGCAAAGACCTTCTTCGTTTTACAAATGTCAATCTTGATCATCTTACCGAAACTGTACGTACTCACGTTTTTCTTTCTTCTAAACCCTAAACCCTCAACTCAATTCACTTTATGCTTTCGTTCTTAATAAGTTGTTCATTCTGTTTCAGTTTAACATGTCCTTCTACATGACCTATTTAGCAAGATGGCCTGACTATTTCCAAGTCGCCCAAGGCCCCGGAAATCGAATCATGGGTTACAGTAAGTCTTTTTCTTCATCTTTTTTGTGTAAAAGACTATACTATGGGATATTAACACCACCAATATCATTCATGCAGTTATGGGTAAAGTAGAGGGGCAAGGAGAATCTTGGCATGGTCATGTAACTGCAGTAACCGTTGCTACGGAGTATCGCAGGCAACAGTTAGCAAACAAACTAATGAATATTCTCGAAGACATCAGTGACAATATGTAAGGCATCGGTATGTGTGTTTGTCTCTGTGTGGAGGTTTTGATATAATTTAGAATTGAATTTTGCAGTGACAAAGCATACTTTGTTGATCTATTTGTGAGAGCATCAAATGCACCAGCCATCAAGATGTATGAAAAGGTAATGATTTTGTACTTTTCCTTTCAGATTAAACCTTCCACTGCTTCCTTGTAGGTTTGTACACAAGGTTTGTTTTAAATCGGTTTCTTTGTTAGACATCTGTGAAATTAAATAAGACACCGCACAAGCTGATTTTGTAGGGTTGAGTTAGATCCAACCCAAATTCTAATAGGGTTTTTTATCGAGAATTTACAGATTACTTATCAATAGTTTAGGAATTTAATGTATAACTTAATCATTGGATATGGACTTCCATTTGTTGGATTAGGATATGTTTTCTTTTAGATTAGGATTTTCTGATTTTCAAGCTTAAATTGCTAACTAATTATTTTCCTTTTTGACATCTTATAGCTTGGATATGTGATTTACCGACGAGTGCTACGTTATTATTCTGGGGAAGAAGATGGATTGGGTATGGTTTCTTTTTTTTTTTTTTTGTACTTCTCTAACTCTTTGAACAAAGTCCATATCATTATTTATTTGCTGTCGTTTTTCCCTTTATTTTCAGATATGAGGAAGGCGTTATCTCGTGATGTTAATAAGAAGTCTGTCGTCCCTCTTAAACGGCGTGTCACTCCTGATGAACTAGAATACGACTAA
Protein sequence

>MS.gene026879.t1

MTTIRRFCCKDLLRFTNVNLDHLTETFNMSFYMTYLARWPDYFQVAQGPGNRIMGYIMGKVEGQGESWHGHVTAVTVATEYRRQQLANKLMNILEDISDNIDKAYFVDLFVRASNAPAIKMYEKLGYVIYRRVLRYYSGEEDGLDMRKALSRDVNKKSVVPLKRRVTPDELEYD