AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0903390


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0903390 MtrunA17_Chr6g0451531 81.720 93 12 3 1 88 1 93 2.57e-39 137
Msa0903390 MtrunA17_Chr6g0451541 81.720 93 12 3 1 88 1 93 3.24e-39 137
Msa0903390 MtrunA17_Chr6g0451561 78.947 95 13 3 1 88 1 95 1.07e-37 132
Msa0903390 MtrunA17_Chr3g0107671 61.798 89 31 2 1 88 1 87 2.79e-24 95.5
Msa0903390 MtrunA17_Chr6g0451511 56.667 90 37 2 1 88 1 90 7.72e-24 94.4
Msa0903390 MtrunA17_Chr3g0107661 60.000 90 32 2 1 88 1 88 2.41e-23 90.1
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 24 sgRNAs with CRISPR-Local

Find 114 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GAAGTGAGTTATTGGAATTT+TGG 0.204889 6_2:-476436 None:intergenic
TTCCAATCTTCAAAGTGATT+TGG 0.278610 6_2:+476822 Msa0903390:CDS
CGGAGCCACTCACATGGTTG+TGG 0.324121 6_2:-477337 None:intergenic
TCAATTATTACATACAGTTT+AGG 0.324280 6_2:-476522 None:intergenic
TTGAAGATTGGAAGAATCTA+TGG 0.335987 6_2:-476812 None:intergenic
AGCCAAATCACTTTGAAGAT+TGG 0.364954 6_2:-476824 None:intergenic
ATGTGATGGAAGTGAGTTAT+TGG 0.376355 6_2:-476444 None:intergenic
GGTAGCTTCAAAGGCTATAA+TGG 0.391709 6_2:-476791 None:intergenic
GGAGCCACTCACATGGTTGT+GGG 0.413731 6_2:-477336 None:intergenic
TTTGAATCATTATCATACTC+AGG 0.449724 6_2:-477362 None:intergenic
GAACACATAGTTACAATTTG+TGG 0.454235 6_2:+476721 Msa0903390:CDS
ATAGTTACAATTTGTGGTGT+TGG 0.455361 6_2:+476727 Msa0903390:CDS
AGAATCTATGGTAGCTTCAA+AGG 0.487090 6_2:-476800 None:intergenic
TTAGGTTGTGCCATGGTGCT+AGG 0.502151 6_2:-476504 None:intergenic
TTGAATCATTATCATACTCA+GGG 0.505249 6_2:-477361 None:intergenic
GAGCCACTCACATGGTTGTG+GGG 0.506735 6_2:-477335 None:intergenic
TAGAAGCTTATGTTATGTGA+TGG 0.544167 6_2:-476458 None:intergenic
TTTGTGGTGTTGGATTGTGT+TGG 0.587547 6_2:+476737 Msa0903390:CDS
AGCCACTCACATGGTTGTGG+GGG 0.591757 6_2:-477334 None:intergenic
ATACAGTTTAGGTTGTGCCA+TGG 0.608316 6_2:-476511 None:intergenic
ATCATTATCATACTCAGGGG+CGG 0.655258 6_2:-477357 None:intergenic
CAGGGGCGGAGCCACTCACA+TGG 0.657826 6_2:-477343 None:intergenic
ATTTAATCTTCCTAGCACCA+TGG 0.668100 6_2:+476494 Msa0903390:exon
TGAATCATTATCATACTCAG+GGG 0.669781 6_2:-477360 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! TTATTTAGTTAATTTGTATT+TGG + chr6_2:476606-476625 Msa0903390:intron 10.0%
!!! TTATTTAGTTAATTTGTATT+TGG + chr6_2:476606-476625 Msa0903390:intron 10.0%
!! AAATCGGTAATAAATAATAA+TGG - chr6_2:476556-476575 None:intergenic 15.0%
!! AAATCGGTAATAAATAATAA+TGG - chr6_2:476556-476575 None:intergenic 15.0%
!! TCAATTATTACATACAGTTT+AGG - chr6_2:476525-476544 None:intergenic 20.0%
!! AAGTATCATGCAATATAAAT+CGG - chr6_2:476572-476591 None:intergenic 20.0%
!! ATCAAATCCTTAAAAAAACA+TGG + chr6_2:476683-476702 Msa0903390:CDS 20.0%
!!! TAACATTCCATGTTTTTTTA+AGG - chr6_2:476693-476712 None:intergenic 20.0%
!! TGAAATTACTAAAACAATTG+TGG + chr6_2:477242-477261 Msa0903390:intron 20.0%
!! GAAATTACTAAAACAATTGT+GGG + chr6_2:477243-477262 Msa0903390:intron 20.0%
!! TCAATTATTACATACAGTTT+AGG - chr6_2:476525-476544 None:intergenic 20.0%
!! AAGTATCATGCAATATAAAT+CGG - chr6_2:476572-476591 None:intergenic 20.0%
!! ATCAAATCCTTAAAAAAACA+TGG + chr6_2:476683-476702 Msa0903390:CDS 20.0%
!!! TAACATTCCATGTTTTTTTA+AGG - chr6_2:476693-476712 None:intergenic 20.0%
!! TGAAATTACTAAAACAATTG+TGG + chr6_2:477242-477261 Msa0903390:intron 20.0%
!! GAAATTACTAAAACAATTGT+GGG + chr6_2:477243-477262 Msa0903390:intron 20.0%
! TACTATTAAGAGAGAAAGAA+GGG - chr6_2:476912-476931 None:intergenic 25.0%
! NNNNNNTTGTTGAAACAGAG+AGG + chr6_2:477060-477079 Msa0903390:intron 25.0%
! NNNNNTTGTTGAAACAGAGA+GGG + chr6_2:477061-477080 Msa0903390:intron 25.0%
! AAAAATAGCAAAATTTGTGC+AGG + chr6_2:477305-477324 Msa0903390:intron 25.0%
! TTGAATCATTATCATACTCA+GGG - chr6_2:477364-477383 None:intergenic 25.0%
! TTTGAATCATTATCATACTC+AGG - chr6_2:477365-477384 None:intergenic 25.0%
! TACTATTAAGAGAGAAAGAA+GGG - chr6_2:476912-476931 None:intergenic 25.0%
! NNNNNNTTGTTGAAACAGAG+AGG + chr6_2:477060-477079 Msa0903390:intron 25.0%
! NNNNNTTGTTGAAACAGAGA+GGG + chr6_2:477061-477080 Msa0903390:intron 25.0%
! AAAAATAGCAAAATTTGTGC+AGG + chr6_2:477305-477324 Msa0903390:intron 25.0%
! TTGAATCATTATCATACTCA+GGG - chr6_2:477364-477383 None:intergenic 25.0%
! TTTGAATCATTATCATACTC+AGG - chr6_2:477365-477384 None:intergenic 25.0%
TAGAAGCTTATGTTATGTGA+TGG - chr6_2:476461-476480 None:intergenic 30.0%
!! TATTTTTGCAGATTTAGCAG+TGG + chr6_2:476631-476650 Msa0903390:intron 30.0%
GAACACATAGTTACAATTTG+TGG + chr6_2:476721-476740 Msa0903390:CDS 30.0%
ATAGTTACAATTTGTGGTGT+TGG + chr6_2:476727-476746 Msa0903390:CDS 30.0%
TTGAAGATTGGAAGAATCTA+TGG - chr6_2:476815-476834 None:intergenic 30.0%
TTCCAATCTTCAAAGTGATT+TGG + chr6_2:476822-476841 Msa0903390:CDS 30.0%
GTACTATTAAGAGAGAAAGA+AGG - chr6_2:476913-476932 None:intergenic 30.0%
TTCTTTCATTCTATGTCACA+AGG - chr6_2:477099-477118 None:intergenic 30.0%
! CAGATTTTTGTTAGCCAATT+GGG + chr6_2:477178-477197 Msa0903390:intron 30.0%
ATTACTAAAACAATTGTGGG+TGG + chr6_2:477246-477265 Msa0903390:intron 30.0%
TTACTAAAACAATTGTGGGT+GGG + chr6_2:477247-477266 Msa0903390:intron 30.0%
TGAATCATTATCATACTCAG+GGG - chr6_2:477363-477382 None:intergenic 30.0%
TAGAAGCTTATGTTATGTGA+TGG - chr6_2:476461-476480 None:intergenic 30.0%
!! TATTTTTGCAGATTTAGCAG+TGG + chr6_2:476631-476650 Msa0903390:intron 30.0%
GAACACATAGTTACAATTTG+TGG + chr6_2:476721-476740 Msa0903390:CDS 30.0%
ATAGTTACAATTTGTGGTGT+TGG + chr6_2:476727-476746 Msa0903390:CDS 30.0%
TTGAAGATTGGAAGAATCTA+TGG - chr6_2:476815-476834 None:intergenic 30.0%
TTCCAATCTTCAAAGTGATT+TGG + chr6_2:476822-476841 Msa0903390:CDS 30.0%
GTACTATTAAGAGAGAAAGA+AGG - chr6_2:476913-476932 None:intergenic 30.0%
TTCTTTCATTCTATGTCACA+AGG - chr6_2:477099-477118 None:intergenic 30.0%
! CAGATTTTTGTTAGCCAATT+GGG + chr6_2:477178-477197 Msa0903390:intron 30.0%
ATTACTAAAACAATTGTGGG+TGG + chr6_2:477246-477265 Msa0903390:intron 30.0%
TTACTAAAACAATTGTGGGT+GGG + chr6_2:477247-477266 Msa0903390:intron 30.0%
TGAATCATTATCATACTCAG+GGG - chr6_2:477363-477382 None:intergenic 30.0%
! ATGTGATGGAAGTGAGTTAT+TGG - chr6_2:476447-476466 None:intergenic 35.0%
ATTTAATCTTCCTAGCACCA+TGG + chr6_2:476494-476513 Msa0903390:exon 35.0%
AGAATCTATGGTAGCTTCAA+AGG - chr6_2:476803-476822 None:intergenic 35.0%
! AGCCAAATCACTTTGAAGAT+TGG - chr6_2:476827-476846 None:intergenic 35.0%
! CTGTGATTTTGTGAACTGAT+GGG + chr6_2:477128-477147 Msa0903390:intron 35.0%
! TGTGATTTTGTGAACTGATG+GGG + chr6_2:477129-477148 Msa0903390:intron 35.0%
! GCAGATTTTTGTTAGCCAAT+TGG + chr6_2:477177-477196 Msa0903390:intron 35.0%
TACTAAAACAATTGTGGGTG+GGG + chr6_2:477248-477267 Msa0903390:intron 35.0%
! ATGTGATGGAAGTGAGTTAT+TGG - chr6_2:476447-476466 None:intergenic 35.0%
ATTTAATCTTCCTAGCACCA+TGG + chr6_2:476494-476513 Msa0903390:exon 35.0%
AGAATCTATGGTAGCTTCAA+AGG - chr6_2:476803-476822 None:intergenic 35.0%
! AGCCAAATCACTTTGAAGAT+TGG - chr6_2:476827-476846 None:intergenic 35.0%
! CTGTGATTTTGTGAACTGAT+GGG + chr6_2:477128-477147 Msa0903390:intron 35.0%
! TGTGATTTTGTGAACTGATG+GGG + chr6_2:477129-477148 Msa0903390:intron 35.0%
! GCAGATTTTTGTTAGCCAAT+TGG + chr6_2:477177-477196 Msa0903390:intron 35.0%
TACTAAAACAATTGTGGGTG+GGG + chr6_2:477248-477267 Msa0903390:intron 35.0%
!! ATACAGTTTAGGTTGTGCCA+TGG - chr6_2:476514-476533 None:intergenic 40.0%
! TTTGTGGTGTTGGATTGTGT+TGG + chr6_2:476737-476756 Msa0903390:CDS 40.0%
GGTAGCTTCAAAGGCTATAA+TGG - chr6_2:476794-476813 None:intergenic 40.0%
! GCTGTGATTTTGTGAACTGA+TGG + chr6_2:477127-477146 Msa0903390:intron 40.0%
ATAGCAAAATTTGTGCAGGC+AGG + chr6_2:477309-477328 Msa0903390:intron 40.0%
ATCATTATCATACTCAGGGG+CGG - chr6_2:477360-477379 None:intergenic 40.0%
!! ATACAGTTTAGGTTGTGCCA+TGG - chr6_2:476514-476533 None:intergenic 40.0%
! TTTGTGGTGTTGGATTGTGT+TGG + chr6_2:476737-476756 Msa0903390:CDS 40.0%
GGTAGCTTCAAAGGCTATAA+TGG - chr6_2:476794-476813 None:intergenic 40.0%
! GCTGTGATTTTGTGAACTGA+TGG + chr6_2:477127-477146 Msa0903390:intron 40.0%
ATAGCAAAATTTGTGCAGGC+AGG + chr6_2:477309-477328 Msa0903390:intron 40.0%
ATCATTATCATACTCAGGGG+CGG - chr6_2:477360-477379 None:intergenic 40.0%
! GATTTTGTGAACTGATGGGG+CGG + chr6_2:477132-477151 Msa0903390:intron 45.0%
TTTGTTAGCCAATTGGGCCT+TGG + chr6_2:477184-477203 Msa0903390:intron 45.0%
TTGTTAGCCAATTGGGCCTT+GGG + chr6_2:477185-477204 Msa0903390:intron 45.0%
! GATTTTGTGAACTGATGGGG+CGG + chr6_2:477132-477151 Msa0903390:intron 45.0%
TTTGTTAGCCAATTGGGCCT+TGG + chr6_2:477184-477203 Msa0903390:intron 45.0%
TTGTTAGCCAATTGGGCCTT+GGG + chr6_2:477185-477204 Msa0903390:intron 45.0%
! TTAGGTTGTGCCATGGTGCT+AGG - chr6_2:476507-476526 None:intergenic 50.0%
!! GGCGGCTGTTTTGTGTTGTT+TGG + chr6_2:477150-477169 Msa0903390:intron 50.0%
! TTAGGTTGTGCCATGGTGCT+AGG - chr6_2:476507-476526 None:intergenic 50.0%
!! GGCGGCTGTTTTGTGTTGTT+TGG + chr6_2:477150-477169 Msa0903390:intron 50.0%
AACCCAACTTCCCAAGCCCA+AGG - chr6_2:477204-477223 None:intergenic 55.0%
AGCCACTCACATGGTTGTGG+GGG - chr6_2:477337-477356 None:intergenic 55.0%
GAGCCACTCACATGGTTGTG+GGG - chr6_2:477338-477357 None:intergenic 55.0%
GGAGCCACTCACATGGTTGT+GGG - chr6_2:477339-477358 None:intergenic 55.0%
AACCCAACTTCCCAAGCCCA+AGG - chr6_2:477204-477223 None:intergenic 55.0%
AGCCACTCACATGGTTGTGG+GGG - chr6_2:477337-477356 None:intergenic 55.0%
GAGCCACTCACATGGTTGTG+GGG - chr6_2:477338-477357 None:intergenic 55.0%
GGAGCCACTCACATGGTTGT+GGG - chr6_2:477339-477358 None:intergenic 55.0%
AGCCAATTGGGCCTTGGGCT+TGG + chr6_2:477190-477209 Msa0903390:intron 60.0%
GCCAATTGGGCCTTGGGCTT+GGG + chr6_2:477191-477210 Msa0903390:intron 60.0%
TCCCAAGCCCAAGGCCCAAT+TGG - chr6_2:477195-477214 None:intergenic 60.0%
GGCCTTGGGCTTGGGAAGTT+GGG + chr6_2:477199-477218 Msa0903390:intron 60.0%
AGCCCCCACAACCATGTGAG+TGG + chr6_2:477332-477351 Msa0903390:CDS 60.0%
CGGAGCCACTCACATGGTTG+TGG - chr6_2:477340-477359 None:intergenic 60.0%
AGCCAATTGGGCCTTGGGCT+TGG + chr6_2:477190-477209 Msa0903390:intron 60.0%
GCCAATTGGGCCTTGGGCTT+GGG + chr6_2:477191-477210 Msa0903390:intron 60.0%
TCCCAAGCCCAAGGCCCAAT+TGG - chr6_2:477195-477214 None:intergenic 60.0%
GGCCTTGGGCTTGGGAAGTT+GGG + chr6_2:477199-477218 Msa0903390:intron 60.0%
AGCCCCCACAACCATGTGAG+TGG + chr6_2:477332-477351 Msa0903390:CDS 60.0%
CGGAGCCACTCACATGGTTG+TGG - chr6_2:477340-477359 None:intergenic 60.0%
GGGCCTTGGGCTTGGGAAGT+TGG + chr6_2:477198-477217 Msa0903390:intron 65.0%
GGGCCTTGGGCTTGGGAAGT+TGG + chr6_2:477198-477217 Msa0903390:intron 65.0%
CAGGGGCGGAGCCACTCACA+TGG - chr6_2:477346-477365 None:intergenic 70.0%
CAGGGGCGGAGCCACTCACA+TGG - chr6_2:477346-477365 None:intergenic 70.0%
Chromosome Type Strat End Strand Name
chr6_2 gene 476437 477388 476437 ID=Msa0903390;Name=Msa0903390
chr6_2 mRNA 476437 477388 476437 ID=Msa0903390-mRNA-1;Parent=Msa0903390;Name=Msa0903390-mRNA-1;_AED=0.17;_eAED=0.17;_QI=76|0.5|0.33|0.66|0.5|0.66|3|0|106
chr6_2 exon 476437 476529 476437 ID=Msa0903390-mRNA-1:exon:219;Parent=Msa0903390-mRNA-1
chr6_2 exon 476642 476887 476642 ID=Msa0903390-mRNA-1:exon:220;Parent=Msa0903390-mRNA-1
chr6_2 exon 477331 477388 477331 ID=Msa0903390-mRNA-1:exon:221;Parent=Msa0903390-mRNA-1
chr6_2 five_prime_UTR 476437 476512 476437 ID=Msa0903390-mRNA-1:five_prime_utr;Parent=Msa0903390-mRNA-1
chr6_2 CDS 476513 476529 476513 ID=Msa0903390-mRNA-1:cds;Parent=Msa0903390-mRNA-1
chr6_2 CDS 476642 476887 476642 ID=Msa0903390-mRNA-1:cds;Parent=Msa0903390-mRNA-1
chr6_2 CDS 477331 477388 477331 ID=Msa0903390-mRNA-1:cds;Parent=Msa0903390-mRNA-1
Gene Sequence

>Msa0903390

ATGGCACAACCTAAACTATTTAGCAGTGGAATTGAGCATGCATCATTTGTGACAAGCTATCAAATCCTTAAAAAAACATGGAATGTTATCTCATCTGAACACATAGTTACAATTTGTGGTGTTGGATTGTGTTGGAAAGTTTACAAAGAACAAAGTTCTGATTTGACCATTATAGCCTTTGAAGCTACCATAGATTCTTCCAATCTTCAAAGTGATTTGGCTTCATCTTCTGATCTTAAAGAGAAGAATTTTCTTCAGTTTGAGAGCCCCCACAACCATGTGAGTGGCTCCGCCCCTGAGTATGATAATGATTCAAAATGA

Protein sequence

>Msa0903390

MAQPKLFSSGIEHASFVTSYQILKKTWNVISSEHIVTICGVGLCWKVYKEQSSDLTIIAFEATIDSSNLQSDLASSSDLKEKNFLQFESPHNHVSGSAPEYDNDSK*