AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0090230

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0090230 MtrunA17_Chr1g0210031 94.286 105 4 2 3 106 20 123 8.98e-53 161
Msa0090230 MtrunA17_Chr5g0422991 68.932 103 30 1 2 104 19 119 2.78e-43 137
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0090230 AT1G68585.1 55.000 80 29 2 8 81 24 102 4.89e-19 75.9

Find 34 sgRNAs with CRISPR-Local

Find 130 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TGGGACTAGTCTTGCATCTT+TGG 0.189720 1_2:-72119393 Msa0090230:CDS
AAGATTGTTATTATGATAAA+AGG 0.195948 1_2:-72119466 Msa0090230:five_prime_UTR
CGTTTGATAATGGCAACTTT+AGG 0.228347 1_2:+72118476 None:intergenic
GGGGAAGGAGTCTTGTTTAA+TGG 0.240314 1_2:+72118497 None:intergenic
AGAAGGTGATACTTACATTT+AGG 0.262994 1_2:-72118565 Msa0090230:CDS
GTTTGATAATGGCAACTTTA+GGG 0.304764 1_2:+72118477 None:intergenic
TAATGTCAGCAACTCTCTTC+TGG 0.333777 1_2:+72119208 None:intergenic
GATAGAACAATTTCATCTCT+TGG 0.366031 1_2:+72119563 None:intergenic
ATAGAACAATTTCATCTCTT+GGG 0.377484 1_2:+72119564 None:intergenic
GCGGAATATCCGTTTGATAA+TGG 0.404318 1_2:+72118466 None:intergenic
ATGCTTATGACTTGAGTTGT+TGG 0.430989 1_2:+72119587 None:intergenic
ACTTGAGTTGTTGGTGGGGT+TGG 0.461160 1_2:+72119596 None:intergenic
AATAAACACTCAGTTTCTGT+TGG 0.469610 1_2:-72119528 Msa0090230:five_prime_UTR
GGAGTCTTTATCACTGCCAC+TGG 0.481791 1_2:-72119372 Msa0090230:intron
CTTATGACTTGAGTTGTTGG+TGG 0.494044 1_2:+72119590 None:intergenic
GTCAGCAACTCTCTTCTGGC+AGG 0.495054 1_2:+72119212 None:intergenic
GTCAATTGTGGTGAATGTAT+TGG 0.498672 1_2:-72118591 Msa0090230:CDS
TAAGAAGTTAAATAAAACTA+AGG 0.508098 1_2:-72119495 Msa0090230:five_prime_UTR
TCACAAATAGTAGAGATGTA+AGG 0.514214 1_2:-72118288 Msa0090230:three_prime_UTR
TTATGACTTGAGTTGTTGGT+GGG 0.515275 1_2:+72119591 None:intergenic
TTGTTATTGCTTTCTCAACA+TGG 0.518334 1_2:-72118315 Msa0090230:three_prime_UTR
AGGAATCTTCAGAAATCAGC+TGG 0.529337 1_2:-72119446 Msa0090230:five_prime_UTR
CTAAAGTTGCCATTATCAAA+CGG 0.531333 1_2:-72118475 Msa0090230:CDS
GCAAGACTAGTCCCAGAAAG+AGG 0.539833 1_2:+72119401 None:intergenic
ATAATGGCAACTTTAGGGGA+AGG 0.548777 1_2:+72118482 None:intergenic
TGTAATTACTAATTAACCAC+TGG 0.577763 1_2:+72118439 None:intergenic
GGTGAATGTATTGGAAAAGA+AGG 0.579398 1_2:-72118582 Msa0090230:CDS
CGGATATTCCGCTCATCCAG+TGG 0.579718 1_2:-72118455 Msa0090230:CDS
ACACTCAGTTTCTGTTGGAG+AGG 0.587433 1_2:-72119523 Msa0090230:five_prime_UTR
AACAGAATCTTATGCACATG+TGG 0.606171 1_2:+72118399 None:intergenic
TATGACTTGAGTTGTTGGTG+GGG 0.608328 1_2:+72119592 None:intergenic
CTAATTAACCACTGGATGAG+CGG 0.609688 1_2:+72118447 None:intergenic
TTTGATAATGGCAACTTTAG+GGG 0.615844 1_2:+72118478 None:intergenic
AGCAGAGACAGAGTCAATTG+TGG 0.625282 1_2:-72118603 Msa0090230:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! TAAGAAGTTAAATAAAACTA+AGG - chr1_2:72118415-72118434 Msa0090230:three_prime_UTR 15.0%
!!! AAGATTGTTATTATGATAAA+AGG - chr1_2:72118444-72118463 Msa0090230:exon 15.0%
!! AAAACTCAAAATATAGTAAA+AGG + chr1_2:72118578-72118597 None:intergenic 15.0%
!! TCTATATATATAGTGTTTAA+TGG - chr1_2:72118614-72118633 Msa0090230:intron 15.0%
!! AGTAAATAACAATAATTGTA+AGG + chr1_2:72119066-72119085 None:intergenic 15.0%
!! TAAGAAGTTAAATAAAACTA+AGG - chr1_2:72118415-72118434 Msa0090230:three_prime_UTR 15.0%
!!! AAGATTGTTATTATGATAAA+AGG - chr1_2:72118444-72118463 Msa0090230:exon 15.0%
!! AAAACTCAAAATATAGTAAA+AGG + chr1_2:72118578-72118597 None:intergenic 15.0%
!! TCTATATATATAGTGTTTAA+TGG - chr1_2:72118614-72118633 Msa0090230:intron 15.0%
!! AGTAAATAACAATAATTGTA+AGG + chr1_2:72119066-72119085 None:intergenic 15.0%
!! AAAATGAAAAATAGCCAAAA+AGG + chr1_2:72118291-72118310 None:intergenic 20.0%
!! GACATTATTACAAAAATGAA+TGG - chr1_2:72118718-72118737 Msa0090230:intron 20.0%
!!! CATTTTTGTTCTGTTAAATA+AGG - chr1_2:72118758-72118777 Msa0090230:intron 20.0%
!! AAAATGAAAAATAGCCAAAA+AGG + chr1_2:72118291-72118310 None:intergenic 20.0%
!! GACATTATTACAAAAATGAA+TGG - chr1_2:72118718-72118737 Msa0090230:intron 20.0%
!!! CATTTTTGTTCTGTTAAATA+AGG - chr1_2:72118758-72118777 Msa0090230:intron 20.0%
! ATAGAACAATTTCATCTCTT+GGG + chr1_2:72118349-72118368 None:intergenic 25.0%
! AAATAAGGAGATATCATGTA+TGG - chr1_2:72118773-72118792 Msa0090230:intron 25.0%
!! TCTTTCACTGATTATATACA+TGG - chr1_2:72119121-72119140 Msa0090230:intron 25.0%
! TGCTGAAAAATTATAGATAC+GGG + chr1_2:72119291-72119310 None:intergenic 25.0%
! CTGCTGAAAAATTATAGATA+CGG + chr1_2:72119292-72119311 None:intergenic 25.0%
! TGTAATTACTAATTAACCAC+TGG + chr1_2:72119474-72119493 None:intergenic 25.0%
! ATAGAACAATTTCATCTCTT+GGG + chr1_2:72118349-72118368 None:intergenic 25.0%
! AAATAAGGAGATATCATGTA+TGG - chr1_2:72118773-72118792 Msa0090230:intron 25.0%
!! TCTTTCACTGATTATATACA+TGG - chr1_2:72119121-72119140 Msa0090230:intron 25.0%
! TGCTGAAAAATTATAGATAC+GGG + chr1_2:72119291-72119310 None:intergenic 25.0%
! CTGCTGAAAAATTATAGATA+CGG + chr1_2:72119292-72119311 None:intergenic 25.0%
! TGTAATTACTAATTAACCAC+TGG + chr1_2:72119474-72119493 None:intergenic 25.0%
!! AAAAGCCATTTTCACCTTTT+TGG - chr1_2:72118274-72118293 Msa0090230:three_prime_UTR 30.0%
AATAGCCAAAAAGGTGAAAA+TGG + chr1_2:72118282-72118301 None:intergenic 30.0%
GATAGAACAATTTCATCTCT+TGG + chr1_2:72118350-72118369 None:intergenic 30.0%
AATAAACACTCAGTTTCTGT+TGG - chr1_2:72118382-72118401 Msa0090230:three_prime_UTR 30.0%
GCTGAAAAATTATAGATACG+GGG + chr1_2:72119290-72119309 None:intergenic 30.0%
AGAAGGTGATACTTACATTT+AGG - chr1_2:72119345-72119364 Msa0090230:intron 30.0%
AGGATATCAAAAACAACTGT+TGG - chr1_2:72119365-72119384 Msa0090230:intron 30.0%
!! TTTGATAATGGCAACTTTAG+GGG + chr1_2:72119435-72119454 None:intergenic 30.0%
!! GTTTGATAATGGCAACTTTA+GGG + chr1_2:72119436-72119455 None:intergenic 30.0%
CTAAAGTTGCCATTATCAAA+CGG - chr1_2:72119435-72119454 Msa0090230:exon 30.0%
! TTGTTATTGCTTTCTCAACA+TGG - chr1_2:72119595-72119614 Msa0090230:five_prime_UTR 30.0%
TCACAAATAGTAGAGATGTA+AGG - chr1_2:72119622-72119641 Msa0090230:five_prime_UTR 30.0%
!! AAAAGCCATTTTCACCTTTT+TGG - chr1_2:72118274-72118293 Msa0090230:three_prime_UTR 30.0%
AATAGCCAAAAAGGTGAAAA+TGG + chr1_2:72118282-72118301 None:intergenic 30.0%
GATAGAACAATTTCATCTCT+TGG + chr1_2:72118350-72118369 None:intergenic 30.0%
AATAAACACTCAGTTTCTGT+TGG - chr1_2:72118382-72118401 Msa0090230:three_prime_UTR 30.0%
GCTGAAAAATTATAGATACG+GGG + chr1_2:72119290-72119309 None:intergenic 30.0%
AGAAGGTGATACTTACATTT+AGG - chr1_2:72119345-72119364 Msa0090230:intron 30.0%
AGGATATCAAAAACAACTGT+TGG - chr1_2:72119365-72119384 Msa0090230:intron 30.0%
!! TTTGATAATGGCAACTTTAG+GGG + chr1_2:72119435-72119454 None:intergenic 30.0%
!! GTTTGATAATGGCAACTTTA+GGG + chr1_2:72119436-72119455 None:intergenic 30.0%
CTAAAGTTGCCATTATCAAA+CGG - chr1_2:72119435-72119454 Msa0090230:exon 30.0%
! TTGTTATTGCTTTCTCAACA+TGG - chr1_2:72119595-72119614 Msa0090230:five_prime_UTR 30.0%
TCACAAATAGTAGAGATGTA+AGG - chr1_2:72119622-72119641 Msa0090230:five_prime_UTR 30.0%
! TTATGACTTGAGTTGTTGGT+GGG + chr1_2:72118322-72118341 None:intergenic 35.0%
! ATGCTTATGACTTGAGTTGT+TGG + chr1_2:72118326-72118345 None:intergenic 35.0%
! TCTAAGAGTTTTCCTCTTTC+TGG - chr1_2:72118497-72118516 Msa0090230:CDS 35.0%
! CTAAGAGTTTTCCTCTTTCT+GGG - chr1_2:72118498-72118517 Msa0090230:CDS 35.0%
!! GTGATTGTTTTGTTGAGAAC+AGG - chr1_2:72118636-72118655 Msa0090230:intron 35.0%
TCTTCTTGCAAAGCAAATAG+AGG + chr1_2:72118886-72118905 None:intergenic 35.0%
TCTATTTGCTTTGCAAGAAG+AGG - chr1_2:72118885-72118904 Msa0090230:intron 35.0%
CAGTAGCAACATAAACAGTA+AGG + chr1_2:72118943-72118962 None:intergenic 35.0%
CAAGCTAGAGGAATGTTATA+GGG - chr1_2:72118997-72119016 Msa0090230:intron 35.0%
GTCAATTGTGGTGAATGTAT+TGG - chr1_2:72119319-72119338 Msa0090230:intron 35.0%
GGTGAATGTATTGGAAAAGA+AGG - chr1_2:72119328-72119347 Msa0090230:intron 35.0%
!! CGTTTGATAATGGCAACTTT+AGG + chr1_2:72119437-72119456 None:intergenic 35.0%
AACAGAATCTTATGCACATG+TGG + chr1_2:72119514-72119533 None:intergenic 35.0%
! TTATGACTTGAGTTGTTGGT+GGG + chr1_2:72118322-72118341 None:intergenic 35.0%
! ATGCTTATGACTTGAGTTGT+TGG + chr1_2:72118326-72118345 None:intergenic 35.0%
! TCTAAGAGTTTTCCTCTTTC+TGG - chr1_2:72118497-72118516 Msa0090230:CDS 35.0%
! CTAAGAGTTTTCCTCTTTCT+GGG - chr1_2:72118498-72118517 Msa0090230:CDS 35.0%
!! GTGATTGTTTTGTTGAGAAC+AGG - chr1_2:72118636-72118655 Msa0090230:intron 35.0%
TCTTCTTGCAAAGCAAATAG+AGG + chr1_2:72118886-72118905 None:intergenic 35.0%
TCTATTTGCTTTGCAAGAAG+AGG - chr1_2:72118885-72118904 Msa0090230:intron 35.0%
CAGTAGCAACATAAACAGTA+AGG + chr1_2:72118943-72118962 None:intergenic 35.0%
CAAGCTAGAGGAATGTTATA+GGG - chr1_2:72118997-72119016 Msa0090230:intron 35.0%
GTCAATTGTGGTGAATGTAT+TGG - chr1_2:72119319-72119338 Msa0090230:intron 35.0%
GGTGAATGTATTGGAAAAGA+AGG - chr1_2:72119328-72119347 Msa0090230:intron 35.0%
!! CGTTTGATAATGGCAACTTT+AGG + chr1_2:72119437-72119456 None:intergenic 35.0%
AACAGAATCTTATGCACATG+TGG + chr1_2:72119514-72119533 None:intergenic 35.0%
! TATGACTTGAGTTGTTGGTG+GGG + chr1_2:72118321-72118340 None:intergenic 40.0%
! CTTATGACTTGAGTTGTTGG+TGG + chr1_2:72118323-72118342 None:intergenic 40.0%
AGGAATCTTCAGAAATCAGC+TGG - chr1_2:72118464-72118483 Msa0090230:CDS 40.0%
GGTTCAAAACTACATACCAG+TGG + chr1_2:72118557-72118576 None:intergenic 40.0%
TAATGTCAGCAACTCTCTTC+TGG + chr1_2:72118705-72118724 None:intergenic 40.0%
AAGGAGATATCATGTATGGC+TGG - chr1_2:72118777-72118796 Msa0090230:intron 40.0%
AGAGGTTAAAGAAGACAGAG+AGG - chr1_2:72118903-72118922 Msa0090230:intron 40.0%
! ATAAGCCCTGCATGTGTTTT+TGG - chr1_2:72118971-72118990 Msa0090230:intron 40.0%
GCAAGCTAGAGGAATGTTAT+AGG - chr1_2:72118996-72119015 Msa0090230:intron 40.0%
! ATAATGGCAACTTTAGGGGA+AGG + chr1_2:72119431-72119450 None:intergenic 40.0%
GCGGAATATCCGTTTGATAA+TGG + chr1_2:72119447-72119466 None:intergenic 40.0%
CTAATTAACCACTGGATGAG+CGG + chr1_2:72119466-72119485 None:intergenic 40.0%
! TATGACTTGAGTTGTTGGTG+GGG + chr1_2:72118321-72118340 None:intergenic 40.0%
! CTTATGACTTGAGTTGTTGG+TGG + chr1_2:72118323-72118342 None:intergenic 40.0%
AGGAATCTTCAGAAATCAGC+TGG - chr1_2:72118464-72118483 Msa0090230:CDS 40.0%
GGTTCAAAACTACATACCAG+TGG + chr1_2:72118557-72118576 None:intergenic 40.0%
TAATGTCAGCAACTCTCTTC+TGG + chr1_2:72118705-72118724 None:intergenic 40.0%
AAGGAGATATCATGTATGGC+TGG - chr1_2:72118777-72118796 Msa0090230:intron 40.0%
AGAGGTTAAAGAAGACAGAG+AGG - chr1_2:72118903-72118922 Msa0090230:intron 40.0%
! ATAAGCCCTGCATGTGTTTT+TGG - chr1_2:72118971-72118990 Msa0090230:intron 40.0%
GCAAGCTAGAGGAATGTTAT+AGG - chr1_2:72118996-72119015 Msa0090230:intron 40.0%
! ATAATGGCAACTTTAGGGGA+AGG + chr1_2:72119431-72119450 None:intergenic 40.0%
GCGGAATATCCGTTTGATAA+TGG + chr1_2:72119447-72119466 None:intergenic 40.0%
CTAATTAACCACTGGATGAG+CGG + chr1_2:72119466-72119485 None:intergenic 40.0%
ACACTCAGTTTCTGTTGGAG+AGG - chr1_2:72118387-72118406 Msa0090230:three_prime_UTR 45.0%
!! TGGGACTAGTCTTGCATCTT+TGG - chr1_2:72118517-72118536 Msa0090230:CDS 45.0%
!! GTTTTGTTGAGAACAGGTGC+AGG - chr1_2:72118642-72118661 Msa0090230:intron 45.0%
TGCAGCCAAAAACACATGCA+GGG + chr1_2:72118979-72118998 None:intergenic 45.0%
TTGCAGCCAAAAACACATGC+AGG + chr1_2:72118980-72118999 None:intergenic 45.0%
!!! TGTTTTTGGCTGCAAGCTAG+AGG - chr1_2:72118985-72119004 Msa0090230:intron 45.0%
AGCAGAGACAGAGTCAATTG+TGG - chr1_2:72119307-72119326 Msa0090230:intron 45.0%
!! GGGGAAGGAGTCTTGTTTAA+TGG + chr1_2:72119416-72119435 None:intergenic 45.0%
ACACTCAGTTTCTGTTGGAG+AGG - chr1_2:72118387-72118406 Msa0090230:three_prime_UTR 45.0%
!! TGGGACTAGTCTTGCATCTT+TGG - chr1_2:72118517-72118536 Msa0090230:CDS 45.0%
!! GTTTTGTTGAGAACAGGTGC+AGG - chr1_2:72118642-72118661 Msa0090230:intron 45.0%
TGCAGCCAAAAACACATGCA+GGG + chr1_2:72118979-72118998 None:intergenic 45.0%
TTGCAGCCAAAAACACATGC+AGG + chr1_2:72118980-72118999 None:intergenic 45.0%
!!! TGTTTTTGGCTGCAAGCTAG+AGG - chr1_2:72118985-72119004 Msa0090230:intron 45.0%
AGCAGAGACAGAGTCAATTG+TGG - chr1_2:72119307-72119326 Msa0090230:intron 45.0%
!! GGGGAAGGAGTCTTGTTTAA+TGG + chr1_2:72119416-72119435 None:intergenic 45.0%
! ACTTGAGTTGTTGGTGGGGT+TGG + chr1_2:72118317-72118336 None:intergenic 50.0%
! GCAAGACTAGTCCCAGAAAG+AGG + chr1_2:72118512-72118531 None:intergenic 50.0%
GGAGTCTTTATCACTGCCAC+TGG - chr1_2:72118538-72118557 Msa0090230:CDS 50.0%
GACAGAGAGGAAAAGAGCTG+TGG - chr1_2:72118916-72118935 Msa0090230:intron 50.0%
! ACTTGAGTTGTTGGTGGGGT+TGG + chr1_2:72118317-72118336 None:intergenic 50.0%
! GCAAGACTAGTCCCAGAAAG+AGG + chr1_2:72118512-72118531 None:intergenic 50.0%
GGAGTCTTTATCACTGCCAC+TGG - chr1_2:72118538-72118557 Msa0090230:CDS 50.0%
GACAGAGAGGAAAAGAGCTG+TGG - chr1_2:72118916-72118935 Msa0090230:intron 50.0%
GTCAGCAACTCTCTTCTGGC+AGG + chr1_2:72118701-72118720 None:intergenic 55.0%
CGGATATTCCGCTCATCCAG+TGG - chr1_2:72119455-72119474 Msa0090230:five_prime_UTR 55.0%
GTCAGCAACTCTCTTCTGGC+AGG + chr1_2:72118701-72118720 None:intergenic 55.0%
CGGATATTCCGCTCATCCAG+TGG - chr1_2:72119455-72119474 Msa0090230:five_prime_UTR 55.0%
Chromosome Type Strat End Strand Name
chr1_2 gene 72118272 72119660 72118272 ID=Msa0090230;Name=Msa0090230
chr1_2 mRNA 72118272 72119660 72118272 ID=Msa0090230-mRNA-1;Parent=Msa0090230;Name=Msa0090230-mRNA-1;_AED=0.02;_eAED=0.02;_QI=222|1|1|1|1|1|3|179|106
chr1_2 exon 72118272 72118623 72118272 ID=Msa0090230-mRNA-1:exon:25023;Parent=Msa0090230-mRNA-1
chr1_2 exon 72119193 72119274 72119193 ID=Msa0090230-mRNA-1:exon:25022;Parent=Msa0090230-mRNA-1
chr1_2 exon 72119373 72119660 72119373 ID=Msa0090230-mRNA-1:exon:25021;Parent=Msa0090230-mRNA-1
chr1_2 five_prime_UTR 72119439 72119660 72119439 ID=Msa0090230-mRNA-1:five_prime_utr;Parent=Msa0090230-mRNA-1
chr1_2 CDS 72119373 72119438 72119373 ID=Msa0090230-mRNA-1:cds;Parent=Msa0090230-mRNA-1
chr1_2 CDS 72119193 72119274 72119193 ID=Msa0090230-mRNA-1:cds;Parent=Msa0090230-mRNA-1
chr1_2 CDS 72118451 72118623 72118451 ID=Msa0090230-mRNA-1:cds;Parent=Msa0090230-mRNA-1
chr1_2 three_prime_UTR 72118272 72118450 72118272 ID=Msa0090230-mRNA-1:three_prime_utr;Parent=Msa0090230-mRNA-1
Gene Sequence

>Msa0090230

ATGTCTAAGAGTTTTCCTCTTTCTGGGACTAGTCTTGCATCTTTGGAGTCTTTATCACTGCCACTGGTGCAGGAAGTTGTTCTTTCAGCAGATATGCAATGTGAAACCTGCCAGAAGAGAGTTGCTGACATTATTACAAAAATGAATGCAGAGACAGAGTCAATTGTGGTGAATGTATTGGAAAAGAAGGTGATACTTACATTTAGGATATCAAAAACAACTGTTGGTAAATTAATCTCAAAGAAAGTTACGCCATTAAACAAGACTCCTTCCCCTAAAGTTGCCATTATCAAACGGATATTCCGCTCATCCAGTGGTTAA
Protein sequence

>Msa0090230

MSKSFPLSGTSLASLESLSLPLVQEVVLSADMQCETCQKRVADIITKMNAETESIVVNVLEKKVILTFRISKTTVGKLISKKVTPLNKTPSPKVAIIKRIFRSSSG*