AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene82459

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene82459.t1 MTR_5g025520 96.721 122 4 0 1 122 12 133 4.62e-84 241
MS.gene82459.t1 MTR_5g025500 37.662 77 48 0 15 91 54 130 1.41e-11 57.8
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 39 sgRNAs with CRISPR-Local

Find 74 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CAAAGCCGTCGCCGAAATTA+TGG 0.132420 5.2:-16141550 MS.gene82459:CDS
TCATCAAACTCTACAGTTTC+CGG 0.200149 5.2:-16141425 MS.gene82459:CDS
CATAATTTCGGCGACGGCTT+TGG 0.257033 5.2:+16141551 None:intergenic
GGAAATGATGGAAGCAATTT+CGG 0.295914 5.2:+16141452 None:intergenic
CAGTGAACTCTGCACTTTCA+TGG 0.368977 5.2:-16141496 MS.gene82459:CDS
CATCAAACTCTACAGTTTCC+GGG 0.376717 5.2:-16141424 MS.gene82459:intron
ATCGCACCCTGGCTGAATTC+CGG 0.377231 5.2:+16140329 None:intergenic
TTTGCCGACACCCATAATTT+CGG 0.382001 5.2:+16141539 None:intergenic
TTTGATGAACTTGGAAATGA+TGG 0.402949 5.2:+16141440 None:intergenic
AAAGCCGTCGCCGAAATTAT+GGG 0.406307 5.2:-16141549 MS.gene82459:CDS
GTATTAAGAAAGACAAGCTT+TGG 0.408648 5.2:-16140424 MS.gene82459:CDS
ACTGGTAGCTTTGCGCGTCT+TGG 0.418961 5.2:+16141515 None:intergenic
ACTGTAGAGTTTGATGAACT+TGG 0.446589 5.2:+16141431 None:intergenic
GGGAAAGGCCAACAGAAGAA+AGG 0.464992 5.2:-16140260 MS.gene82459:CDS
GGATACTAATACGGATTCTT+CGG 0.469159 5.2:-16140297 MS.gene82459:CDS
GACAAAATCTTAGCAATCTC+GGG 0.472491 5.2:+16140353 None:intergenic
TTTGTCTCCGGAATTCAGCC+AGG 0.491203 5.2:-16140336 MS.gene82459:CDS
TAATGTCAAGGATACTAATA+CGG 0.504014 5.2:-16140306 MS.gene82459:CDS
AGACAAAATCTTAGCAATCT+CGG 0.504864 5.2:+16140352 None:intergenic
GGAAAGGCCAACAGAAGAAA+GGG 0.508550 5.2:-16140259 MS.gene82459:CDS
AGTGAACTCTGCACTTTCAT+GGG 0.512210 5.2:-16141495 MS.gene82459:CDS
TATGGTGTTGTGCAGAGTCC+TGG 0.516143 5.2:-16140446 MS.gene82459:intron
TATTAAGAAAGACAAGCTTT+GGG 0.519290 5.2:-16140423 MS.gene82459:CDS
AGCTTGTCTTTCTTAATACC+AGG 0.519823 5.2:+16140428 None:intergenic
CATGAAAGTGCAGAGTTCAC+TGG 0.524418 5.2:+16141497 None:intergenic
GACACCCATAATTTCGGCGA+CGG 0.548577 5.2:+16141545 None:intergenic
TCTTCGGCGGATAACACAAA+GGG 0.549211 5.2:-16140281 MS.gene82459:CDS
GCGGATAACACAAAGGGGAA+AGG 0.574554 5.2:-16140275 MS.gene82459:CDS
GTCGCCGAAATTATGGGTGT+CGG 0.593807 5.2:-16141543 MS.gene82459:CDS
CCAGGGTGCGATTAATGTCA+AGG 0.595433 5.2:-16140318 MS.gene82459:CDS
TTCTTCGGCGGATAACACAA+AGG 0.617908 5.2:-16140282 MS.gene82459:CDS
AATTTGCAAACACTGTTGCG+TGG 0.632781 5.2:-16140395 MS.gene82459:CDS
TTGTCTCCGGAATTCAGCCA+GGG 0.633474 5.2:-16140335 MS.gene82459:CDS
TTGCGTGGCAGAAACAGCGT+TGG 0.639499 5.2:-16140380 MS.gene82459:CDS
ATTTCGGAACGAGATTGATG+AGG 0.642540 5.2:+16141468 None:intergenic
AGGGCGAAGGAGCATGTCGA+CGG 0.655015 5.2:-16141577 None:intergenic
CCTTGACATTAATCGCACCC+TGG 0.658146 5.2:+16140318 None:intergenic
TACTAATACGGATTCTTCGG+CGG 0.662646 5.2:-16140294 MS.gene82459:CDS
CTTCGGCGGATAACACAAAG+GGG 0.722706 5.2:-16140280 MS.gene82459:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AATGAAACAAAAAGAAAAAA+GGG + chr5.2:16140424-16140443 None:intergenic 15.0%
!! TAATGAAACAAAAAGAAAAA+AGG + chr5.2:16140425-16140444 None:intergenic 15.0%
!! ATTAAGCTGTTTATAAAAAC+AGG - chr5.2:16141126-16141145 MS.gene82459:intron 20.0%
!! CTTTCCATAAAATAAGATAT+AGG + chr5.2:16141153-16141172 None:intergenic 20.0%
!! TCAAATAAACCAATTCAAAT+AGG + chr5.2:16140813-16140832 None:intergenic 20.0%
!! TTAAGCTGTTTATAAAAACA+GGG - chr5.2:16141127-16141146 MS.gene82459:intron 20.0%
!!! TCTATTTACTTTTGCTTATT+TGG - chr5.2:16141334-16141353 MS.gene82459:intron 20.0%
! AAGATTAAAGACTAATCAGT+AGG + chr5.2:16140686-16140705 None:intergenic 25.0%
! AGATTAAAGACTAATCAGTA+GGG + chr5.2:16140685-16140704 None:intergenic 25.0%
! TAATGTCAAGGATACTAATA+CGG - chr5.2:16141505-16141524 MS.gene82459:CDS 25.0%
! TATTAAGAAAGACAAGCTTT+GGG - chr5.2:16141388-16141407 MS.gene82459:intron 25.0%
! TGAAAATAAGCTGAAAAACA+TGG + chr5.2:16140501-16140520 None:intergenic 25.0%
! TTGAAAATAATCACTAGTCA+GGG + chr5.2:16140772-16140791 None:intergenic 25.0%
! TTTGAAAATAATCACTAGTC+AGG + chr5.2:16140773-16140792 None:intergenic 25.0%
!! TACTTTTGCTTATTTGGAAA+TGG - chr5.2:16141340-16141359 MS.gene82459:intron 25.0%
!! TTTTCATAAGTTCTCTCAAA+CGG + chr5.2:16140957-16140976 None:intergenic 25.0%
AGACAAAATCTTAGCAATCT+CGG + chr5.2:16141462-16141481 None:intergenic 30.0%
ATTAAAGACTAATCAGTAGG+GGG + chr5.2:16140683-16140702 None:intergenic 30.0%
GATTAAAGACTAATCAGTAG+GGG + chr5.2:16140684-16140703 None:intergenic 30.0%
GCTTATTTGGAAATGGTATA+TGG - chr5.2:16141347-16141366 MS.gene82459:intron 30.0%
GGATAAACAACTTCATTAAG+TGG + chr5.2:16141258-16141277 None:intergenic 30.0%
GTATTAAGAAAGACAAGCTT+TGG - chr5.2:16141387-16141406 MS.gene82459:intron 30.0%
TTTGATGAACTTGGAAATGA+TGG + chr5.2:16140374-16140393 None:intergenic 30.0%
!!! AGGGCCTATATCTTATTTTA+TGG - chr5.2:16141146-16141165 MS.gene82459:intron 30.0%
AAAAGGGTAGAAATGAAACC+CGG + chr5.2:16140408-16140427 None:intergenic 35.0%
AACCAATTCAAATAGGCTCA+TGG + chr5.2:16140806-16140825 None:intergenic 35.0%
AACCATGAGCCTATTTGAAT+TGG - chr5.2:16140801-16140820 MS.gene82459:intron 35.0%
AATGACAACAGCTCTTACTT+AGG + chr5.2:16141288-16141307 None:intergenic 35.0%
ACTGTAGAGTTTGATGAACT+TGG + chr5.2:16140383-16140402 None:intergenic 35.0%
AGCTTGTCTTTCTTAATACC+AGG + chr5.2:16141386-16141405 None:intergenic 35.0%
CAAGTGCTTGTTTCAATACA+TGG + chr5.2:16140842-16140861 None:intergenic 35.0%
GACAAAATCTTAGCAATCTC+GGG + chr5.2:16141461-16141480 None:intergenic 35.0%
GAGAACATTGATCAAACAGT+TGG + chr5.2:16140455-16140474 None:intergenic 35.0%
GCTGAAAAACATGGAAATGA+TGG + chr5.2:16140492-16140511 None:intergenic 35.0%
GGATACTAATACGGATTCTT+CGG - chr5.2:16141514-16141533 MS.gene82459:CDS 35.0%
TCATCAAACTCTACAGTTTC+CGG - chr5.2:16140386-16140405 MS.gene82459:CDS 35.0%
TCATTAAGTGGTTATAGCAC+AGG + chr5.2:16141246-16141265 None:intergenic 35.0%
! AGCGATAAGCTCTTTTCATA+AGG + chr5.2:16141041-16141060 None:intergenic 35.0%
! GATTGCTAAGATTTTGTCTC+CGG - chr5.2:16141463-16141482 MS.gene82459:CDS 35.0%
! GGAAATGATGGAAGCAATTT+CGG + chr5.2:16140362-16140381 None:intergenic 35.0%
! TCTTTTTCCCTTTCTTCTGT+TGG + chr5.2:16141562-16141581 None:intergenic 35.0%
AATTTGCAAACACTGTTGCG+TGG - chr5.2:16141416-16141435 MS.gene82459:intron 40.0%
AGCTCTTACTTAGGCTCATT+TGG + chr5.2:16141279-16141298 None:intergenic 40.0%
AGTCCCTATCAGTGATTAAG+TGG + chr5.2:16140728-16140747 None:intergenic 40.0%
AGTGAACTCTGCACTTTCAT+GGG - chr5.2:16140316-16140335 MS.gene82459:CDS 40.0%
ATTTCGGAACGAGATTGATG+AGG + chr5.2:16140346-16140365 None:intergenic 40.0%
CACCCACTTAATCACTGATA+GGG - chr5.2:16140722-16140741 MS.gene82459:intron 40.0%
CATCAAACTCTACAGTTTCC+GGG - chr5.2:16140387-16140406 MS.gene82459:CDS 40.0%
GTCCCTATCAGTGATTAAGT+GGG + chr5.2:16140727-16140746 None:intergenic 40.0%
TACTAATACGGATTCTTCGG+CGG - chr5.2:16141517-16141536 MS.gene82459:CDS 40.0%
TCACCCACTTAATCACTGAT+AGG - chr5.2:16140721-16140740 MS.gene82459:intron 40.0%
TTAAGTGGTTATAGCACAGG+CGG + chr5.2:16141243-16141262 None:intergenic 40.0%
TTTGCCGACACCCATAATTT+CGG + chr5.2:16140275-16140294 None:intergenic 40.0%
AAAGCCGTCGCCGAAATTAT+GGG - chr5.2:16140262-16140281 MS.gene82459:CDS 45.0%
CAGTGAACTCTGCACTTTCA+TGG - chr5.2:16140315-16140334 MS.gene82459:CDS 45.0%
GGAAAGGCCAACAGAAGAAA+GGG - chr5.2:16141552-16141571 MS.gene82459:CDS 45.0%
TCTTCGGCGGATAACACAAA+GGG - chr5.2:16141530-16141549 MS.gene82459:CDS 45.0%
TTCTTCGGCGGATAACACAA+AGG - chr5.2:16141529-16141548 MS.gene82459:CDS 45.0%
! CATGAAAGTGCAGAGTTCAC+TGG + chr5.2:16140317-16140336 None:intergenic 45.0%
CAAAGCCGTCGCCGAAATTA+TGG - chr5.2:16140261-16140280 MS.gene82459:CDS 50.0%
CATAATTTCGGCGACGGCTT+TGG + chr5.2:16140263-16140282 None:intergenic 50.0%
CCAGGGTGCGATTAATGTCA+AGG - chr5.2:16141493-16141512 MS.gene82459:CDS 50.0%
CCTTGACATTAATCGCACCC+TGG + chr5.2:16141496-16141515 None:intergenic 50.0%
CTTCGGCGGATAACACAAAG+GGG - chr5.2:16141531-16141550 MS.gene82459:CDS 50.0%
GACACCCATAATTTCGGCGA+CGG + chr5.2:16140269-16140288 None:intergenic 50.0%
GCGGATAACACAAAGGGGAA+AGG - chr5.2:16141536-16141555 MS.gene82459:CDS 50.0%
GGGAAAGGCCAACAGAAGAA+AGG - chr5.2:16141551-16141570 MS.gene82459:CDS 50.0%
GTCGCCGAAATTATGGGTGT+CGG - chr5.2:16140268-16140287 MS.gene82459:CDS 50.0%
TTGTCTCCGGAATTCAGCCA+GGG - chr5.2:16141476-16141495 MS.gene82459:CDS 50.0%
TTTGTCTCCGGAATTCAGCC+AGG - chr5.2:16141475-16141494 MS.gene82459:CDS 50.0%
!! TATGGTGTTGTGCAGAGTCC+TGG - chr5.2:16141365-16141384 MS.gene82459:intron 50.0%
ATCGCACCCTGGCTGAATTC+CGG + chr5.2:16141485-16141504 None:intergenic 55.0%
TTGCGTGGCAGAAACAGCGT+TGG - chr5.2:16141431-16141450 MS.gene82459:CDS 55.0%
! ACTGGTAGCTTTGCGCGTCT+TGG + chr5.2:16140299-16140318 None:intergenic 55.0%


Chromosome Type Strat End Strand Name
chr5.2 gene 16140247 16141586 16140247 ID=MS.gene82459
chr5.2 mRNA 16140247 16141586 16140247 ID=MS.gene82459.t1;Parent=MS.gene82459
chr5.2 exon 16141425 16141586 16141425 ID=MS.gene82459.t1.exon1;Parent=MS.gene82459.t1
chr5.2 CDS 16141425 16141586 16141425 ID=cds.MS.gene82459.t1;Parent=MS.gene82459.t1
chr5.2 exon 16140247 16140453 16140247 ID=MS.gene82459.t1.exon2;Parent=MS.gene82459.t1
chr5.2 CDS 16140247 16140453 16140247 ID=cds.MS.gene82459.t1;Parent=MS.gene82459.t1
Gene Sequence

>MS.gene82459

ATGTCGACGGTATCCAAAGCCGTCGCCGAAATTATGGGTGTCGGCAAAACCAAGACGCGCAAAGCTACCAGTGAACTCTGCACTTTCATGGGCATTCCTCATCAATCTCGTTCCGAAATTGCTTCCATCATTTCCAAGTTCATCAAACTCTACAGTTTCCGGGTTTCATTTCTACCCTTTTTTCTTTTTGTTTCATTATTGCATACCAACTGTTTGATCAATGTTCTCACTCACAAAACATGCCATCATTTCCATGTTTTTCAGCTTATTTTCACAATTTCTCTGAGATAGTTTATGAAAATAGCTTAGACTTAACACGAAAACAATTTAACTTTATTTTATTTTTGTTATAGAAATAGCTTAGCAGTTAGCAGCTATAAGCTGCAAATTATTATTATACTATGACACTCAATTTATTTGTTCAAGTTTAACTCCCCCTACTGATTAGTCTTTAATCTTTACATATATGATAACTCACCCACTTAATCACTGATAGGGACTAACGAGATGAATTTTCATATACCCTGACTAGTGATTATTTTCAAATATTTTAGAACCATGAGCCTATTTGAATTGGTTTATTTGAGCTTATCCATGTATTGAAACAAGCACTTGTGAGACTGTTTGAGAGAACATATAGAAACAACGCATGACATAAGAAATTATGACGTATTTGAGCTTATCTCTTGACATATGAACTTGTGAGACCGTTTGAGAGAACTTATGAAAACAAGTTATAGCACATTCATAAGCTGTTTTCAGCTTGTTTGCGTAAGCTCTTAAAAAAAAAACCTTATGAAAAGAGCTTATCGCTTATACTAAAACAATTTAACTTTATTTTATCTTTTGTTATAGAAACAACTTATACATAAGCTGCAAATTAAGCTGTTTATAAAAACAGGGCCTATATCTTATTTTATGGAAAGAAGTTGACTTTATTTTATCTTTTTATTATAGAAATAGCTTATATATACATAAATACTTATGTGAGAACCGCCTGTGCTATAACCACTTAATGAAGTTGTTTATCCAAATGAGCCTAAGTAAGAGCTGTTGTCATTGAGCGACTAAAGTGAAAGTTTACTGTTCTATTTACTTTTGCTTATTTGGAAATGGTATATGGTGTTGTGCAGAGTCCTGGTATTAAGAAAGACAAGCTTTGGGAGCAGAATTTGCAAACACTGTTGCGTGGCAGAAACAGCGTTGGTTTTCCCGAGATTGCTAAGATTTTGTCTCCGGAATTCAGCCAGGGTGCGATTAATGTCAAGGATACTAATACGGATTCTTCGGCGGATAACACAAAGGGGAAAGGCCAACAGAAGAAAGGGAAAAAGAAATAG
Protein sequence

>MS.gene82459.t1

MSTVSKAVAEIMGVGKTKTRKATSELCTFMGIPHQSRSEIASIISKFIKLYSFRSPGIKKDKLWEQNLQTLLRGRNSVGFPEIAKILSPEFSQGAINVKDTNTDSSADNTKGKGQQKKGKKK