AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1280020


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1280020 MtrunA17_Chr8g0349971 94.262 244 14 0 1 244 1 244 1.07e-170 470
Msa1280020 MtrunA17_Chr7g0246981 50.704 142 63 2 1 142 1 135 1.17e-40 137
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1280020 AT4G23890.1 54.656 247 95 6 2 240 3 240 5.53e-87 258

Find 63 sgRNAs with CRISPR-Local

Find 69 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TCTCCGACGAAGAAAGTTTA+AGG 0.169983 8_3:+18004676 None:intergenic
ATACCACAGTACATGTAAAA+AGG 0.226887 8_3:+18004585 None:intergenic
GTTGCCCTTCATAGCCTTCA+TGG 0.229693 8_3:-18005119 Msa1280020:CDS
CTTCTTAGATCCAAGTTCTT+AGG 0.247457 8_3:-18005092 Msa1280020:CDS
GAACTTGAGAGAAGAGAAAA+AGG 0.270077 8_3:-18004480 Msa1280020:CDS
GGGTTTCCTGGTGGTGAAAA+AGG 0.277133 8_3:-18004756 Msa1280020:CDS
TTGTCACCTCTACCAGGTTT+TGG 0.284174 8_3:+18004702 None:intergenic
GATCTGCAGCAAATCGAATT+TGG 0.295479 8_3:+18004980 None:intergenic
GGGTTAACTGGAGGGTTTCC+TGG 0.308952 8_3:-18004768 Msa1280020:CDS
TATGATTTCTTTACAAGAAA+TGG 0.313320 8_3:+18004420 None:intergenic
AAAGAGTTGATGGGGTTAAC+TGG 0.314813 8_3:-18004780 Msa1280020:CDS
TACTGTTTGAAGGAGGGAAT+TGG 0.328753 8_3:-18004530 Msa1280020:CDS
ACTGTTTGAAGGAGGGAATT+GGG 0.336476 8_3:-18004529 Msa1280020:CDS
GGGATAAGTTGATCACCTTT+AGG 0.350751 8_3:-18004509 Msa1280020:CDS
TTGTTCTTCGTTACTTGCTT+CGG 0.370219 8_3:+18004863 None:intergenic
CTTCACAATAGCAATCATTC+CGG 0.373797 8_3:+18004620 None:intergenic
ACAAGACTTGGGATTCTTCA+TGG 0.388142 8_3:+18004452 None:intergenic
GAATTTGGCACATGTTTGTA+TGG 0.394434 8_3:+18004995 None:intergenic
ATTCGATTTGCTGCAGATCA+TGG 0.403942 8_3:-18004976 Msa1280020:CDS
ATTCTCTTGGCCTAAGAACT+TGG 0.403982 8_3:+18005082 None:intergenic
AGGGTTTGATAAAGAGTTGA+TGG 0.404058 8_3:-18004790 Msa1280020:CDS
GGAAGTAACATAGGAAGTTC+TGG 0.409953 8_3:+18004642 None:intergenic
GAGAGCCATGAAGGCTATGA+AGG 0.426665 8_3:+18005114 None:intergenic
TTCACAATAGCAATCATTCC+GGG 0.441701 8_3:+18004621 None:intergenic
GAACTTCCTATGTTACTTCC+CGG 0.446985 8_3:-18004639 Msa1280020:CDS
TTTGTAAGTGTTGCAGAAGA+AGG 0.447129 8_3:-18004810 Msa1280020:CDS
AAAGAGCTTAAAAGAGAAGT+TGG 0.459053 8_3:-18004915 Msa1280020:CDS
GGGTTTGATAAAGAGTTGAT+GGG 0.470608 8_3:-18004789 Msa1280020:CDS
GGACTCTGCAAAGGAGAAGA+AGG 0.493957 8_3:-18004945 Msa1280020:CDS
TAAACTTTCTTCGTCGGAGA+AGG 0.497501 8_3:-18004673 Msa1280020:CDS
CTCAAGTTCCTCAAGCCTAA+AGG 0.506721 8_3:+18004494 None:intergenic
CGTCGATTTGCTGTGAAAGA+TGG 0.508364 8_3:+18005025 None:intergenic
TTACTTGCTTCGGATGATGT+TGG 0.510598 8_3:+18004873 None:intergenic
TTCGATTTGCTGCAGATCAT+GGG 0.510808 8_3:-18004975 Msa1280020:CDS
CTGCAGATCATGGGAGGCAG+AGG 0.514988 8_3:-18004966 Msa1280020:CDS
AGAATCACTGATGGTAAAGC+AGG 0.515714 8_3:-18004555 Msa1280020:CDS
AGTTGATGGGGTTAACTGGA+GGG 0.519714 8_3:-18004776 Msa1280020:CDS
GTTGATCACCTTTAGGCTTG+AGG 0.527881 8_3:-18004502 Msa1280020:CDS
AAAGATGAGTGAGATTCTCT+TGG 0.529880 8_3:+18005069 None:intergenic
GAAAACCCTGTTCCAAAACC+TGG 0.534181 8_3:-18004714 Msa1280020:CDS
AAGCCTTAAACTTTCTTCGT+CGG 0.537850 8_3:-18004679 Msa1280020:CDS
TTGTAAGTGTTGCAGAAGAA+GGG 0.538779 8_3:-18004809 Msa1280020:CDS
TTCTTCTGCAACACTTACAA+AGG 0.552410 8_3:+18004812 None:intergenic
TGGTTCAAGAACACAAGACT+TGG 0.554025 8_3:+18004440 None:intergenic
CAAGACTTGGGATTCTTCAT+GGG 0.554949 8_3:+18004453 None:intergenic
AAAGCAGGAGTACTGTTTGA+AGG 0.555664 8_3:-18004540 Msa1280020:CDS
ATCTAAGAAGAGAGCCATGA+AGG 0.565588 8_3:+18005105 None:intergenic
GAGTTGATGGGGTTAACTGG+AGG 0.584401 8_3:-18004777 Msa1280020:CDS
GGTTTGATAAAGAGTTGATG+GGG 0.584525 8_3:-18004788 Msa1280020:CDS
GGTTCAAGAACACAAGACTT+GGG 0.586922 8_3:+18004441 None:intergenic
AAGGCTATGAAGGGCAACAA+AGG 0.600980 8_3:+18005124 None:intergenic
GCAGGAGTACTGTTTGAAGG+AGG 0.603818 8_3:-18004537 Msa1280020:CDS
TTAACTGGAGGGTTTCCTGG+TGG 0.603897 8_3:-18004765 Msa1280020:CDS
CCTGTTCCAAAACCTGGTAG+AGG 0.604649 8_3:-18004708 Msa1280020:CDS
GACTTGGGATTCTTCATGGG+AGG 0.605015 8_3:+18004456 None:intergenic
ATCATTCCGGGAAGTAACAT+AGG 0.609248 8_3:+18004633 None:intergenic
CAGGAGTACTGTTTGAAGGA+GGG 0.618790 8_3:-18004536 Msa1280020:CDS
ATTGTTCAAAGAATCACTGA+TGG 0.621968 8_3:-18004564 Msa1280020:CDS
GGAGGCAGAGGACTCTGCAA+AGG 0.631448 8_3:-18004954 Msa1280020:CDS
GATTTGCTGCAGATCATGGG+AGG 0.641733 8_3:-18004972 Msa1280020:CDS
AGAGCCATGAAGGCTATGAA+GGG 0.649789 8_3:+18005115 None:intergenic
ATGGAAGCTTTATTGCTGTG+AGG 0.676809 8_3:+18005044 None:intergenic
AGTAACATAGGAAGTTCTGG+TGG 0.681209 8_3:+18004645 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! TATGATTTCTTTACAAGAAA+TGG + chr8_3:18005133-18005152 None:intergenic 20.0%
AAAGAGCTTAAAAGAGAAGT+TGG - chr8_3:18004635-18004654 Msa1280020:CDS 30.0%
TACCACAGTACATGTAAAAA+GGG + chr8_3:18004967-18004986 None:intergenic 30.0%
ATACCACAGTACATGTAAAA+AGG + chr8_3:18004968-18004987 None:intergenic 30.0%
ATTGTTCAAAGAATCACTGA+TGG - chr8_3:18004986-18005005 Msa1280020:CDS 30.0%
CTTCTTAGATCCAAGTTCTT+AGG - chr8_3:18004458-18004477 Msa1280020:CDS 35.0%
AAAGATGAGTGAGATTCTCT+TGG + chr8_3:18004484-18004503 None:intergenic 35.0%
GAATTTGGCACATGTTTGTA+TGG + chr8_3:18004558-18004577 None:intergenic 35.0%
TTGTTCTTCGTTACTTGCTT+CGG + chr8_3:18004690-18004709 None:intergenic 35.0%
TTCTTCTGCAACACTTACAA+AGG + chr8_3:18004741-18004760 None:intergenic 35.0%
! TTTGTAAGTGTTGCAGAAGA+AGG - chr8_3:18004740-18004759 Msa1280020:CDS 35.0%
! TTGTAAGTGTTGCAGAAGAA+GGG - chr8_3:18004741-18004760 Msa1280020:CDS 35.0%
AGGGTTTGATAAAGAGTTGA+TGG - chr8_3:18004760-18004779 Msa1280020:CDS 35.0%
! GGGTTTGATAAAGAGTTGAT+GGG - chr8_3:18004761-18004780 Msa1280020:CDS 35.0%
!! GGTTTGATAAAGAGTTGATG+GGG - chr8_3:18004762-18004781 Msa1280020:CDS 35.0%
AAGCCTTAAACTTTCTTCGT+CGG - chr8_3:18004871-18004890 Msa1280020:CDS 35.0%
TTCACAATAGCAATCATTCC+GGG + chr8_3:18004932-18004951 None:intergenic 35.0%
CTTCACAATAGCAATCATTC+CGG + chr8_3:18004933-18004952 None:intergenic 35.0%
! AACCCTTTTTACATGTACTG+TGG - chr8_3:18004962-18004981 Msa1280020:CDS 35.0%
GAACTTGAGAGAAGAGAAAA+AGG - chr8_3:18005070-18005089 Msa1280020:CDS 35.0%
ATCTAAGAAGAGAGCCATGA+AGG + chr8_3:18004448-18004467 None:intergenic 40.0%
ATTCTCTTGGCCTAAGAACT+TGG + chr8_3:18004471-18004490 None:intergenic 40.0%
!! ATGGAAGCTTTATTGCTGTG+AGG + chr8_3:18004509-18004528 None:intergenic 40.0%
GATCTGCAGCAAATCGAATT+TGG + chr8_3:18004573-18004592 None:intergenic 40.0%
!! ATTCGATTTGCTGCAGATCA+TGG - chr8_3:18004574-18004593 Msa1280020:CDS 40.0%
!! TTCGATTTGCTGCAGATCAT+GGG - chr8_3:18004575-18004594 Msa1280020:CDS 40.0%
TTACTTGCTTCGGATGATGT+TGG + chr8_3:18004680-18004699 None:intergenic 40.0%
!! AAAGAGTTGATGGGGTTAAC+TGG - chr8_3:18004770-18004789 Msa1280020:CDS 40.0%
!! TTCAAACCTTTTTCACCACC+AGG + chr8_3:18004803-18004822 None:intergenic 40.0%
TCTCCGACGAAGAAAGTTTA+AGG + chr8_3:18004877-18004896 None:intergenic 40.0%
TAAACTTTCTTCGTCGGAGA+AGG - chr8_3:18004877-18004896 Msa1280020:CDS 40.0%
! AGTAACATAGGAAGTTCTGG+TGG + chr8_3:18004908-18004927 None:intergenic 40.0%
GGAAGTAACATAGGAAGTTC+TGG + chr8_3:18004911-18004930 None:intergenic 40.0%
! GAACTTCCTATGTTACTTCC+CGG - chr8_3:18004911-18004930 Msa1280020:CDS 40.0%
ATCATTCCGGGAAGTAACAT+AGG + chr8_3:18004920-18004939 None:intergenic 40.0%
AGAATCACTGATGGTAAAGC+AGG - chr8_3:18004995-18005014 Msa1280020:CDS 40.0%
!! AAAGCAGGAGTACTGTTTGA+AGG - chr8_3:18005010-18005029 Msa1280020:CDS 40.0%
TACTGTTTGAAGGAGGGAAT+TGG - chr8_3:18005020-18005039 Msa1280020:CDS 40.0%
ACTGTTTGAAGGAGGGAATT+GGG - chr8_3:18005021-18005040 Msa1280020:CDS 40.0%
!! GGGATAAGTTGATCACCTTT+AGG - chr8_3:18005041-18005060 Msa1280020:CDS 40.0%
CAAGACTTGGGATTCTTCAT+GGG + chr8_3:18005100-18005119 None:intergenic 40.0%
ACAAGACTTGGGATTCTTCA+TGG + chr8_3:18005101-18005120 None:intergenic 40.0%
GGTTCAAGAACACAAGACTT+GGG + chr8_3:18005112-18005131 None:intergenic 40.0%
TGGTTCAAGAACACAAGACT+TGG + chr8_3:18005113-18005132 None:intergenic 40.0%
AAGGCTATGAAGGGCAACAA+AGG + chr8_3:18004429-18004448 None:intergenic 45.0%
AGAGCCATGAAGGCTATGAA+GGG + chr8_3:18004438-18004457 None:intergenic 45.0%
!! CGTCGATTTGCTGTGAAAGA+TGG + chr8_3:18004528-18004547 None:intergenic 45.0%
!! AGTTGATGGGGTTAACTGGA+GGG - chr8_3:18004774-18004793 Msa1280020:CDS 45.0%
GAAAACCCTGTTCCAAAACC+TGG - chr8_3:18004836-18004855 Msa1280020:CDS 45.0%
!!! CTCTACCAGGTTTTGGAACA+GGG + chr8_3:18004844-18004863 None:intergenic 45.0%
! TTGTCACCTCTACCAGGTTT+TGG + chr8_3:18004851-18004870 None:intergenic 45.0%
!! CAGGAGTACTGTTTGAAGGA+GGG - chr8_3:18005014-18005033 Msa1280020:CDS 45.0%
GTTGATCACCTTTAGGCTTG+AGG - chr8_3:18005048-18005067 Msa1280020:CDS 45.0%
CTCAAGTTCCTCAAGCCTAA+AGG + chr8_3:18005059-18005078 None:intergenic 45.0%
GTTGCCCTTCATAGCCTTCA+TGG - chr8_3:18004431-18004450 Msa1280020:CDS 50.0%
GAGAGCCATGAAGGCTATGA+AGG + chr8_3:18004439-18004458 None:intergenic 50.0%
!! GATTTGCTGCAGATCATGGG+AGG - chr8_3:18004578-18004597 Msa1280020:CDS 50.0%
GGACTCTGCAAAGGAGAAGA+AGG - chr8_3:18004605-18004624 Msa1280020:CDS 50.0%
!! GAGTTGATGGGGTTAACTGG+AGG - chr8_3:18004773-18004792 Msa1280020:CDS 50.0%
TTAACTGGAGGGTTTCCTGG+TGG - chr8_3:18004785-18004804 Msa1280020:CDS 50.0%
! GGGTTTCCTGGTGGTGAAAA+AGG - chr8_3:18004794-18004813 Msa1280020:CDS 50.0%
!!! CCTCTACCAGGTTTTGGAAC+AGG + chr8_3:18004845-18004864 None:intergenic 50.0%
CCTGTTCCAAAACCTGGTAG+AGG - chr8_3:18004842-18004861 Msa1280020:CDS 50.0%
! AGGCTTTTGTCACCTCTACC+AGG + chr8_3:18004857-18004876 None:intergenic 50.0%
!! GCAGGAGTACTGTTTGAAGG+AGG - chr8_3:18005013-18005032 Msa1280020:CDS 50.0%
GACTTGGGATTCTTCATGGG+AGG + chr8_3:18005097-18005116 None:intergenic 50.0%
GGGTTAACTGGAGGGTTTCC+TGG - chr8_3:18004782-18004801 Msa1280020:CDS 55.0%
CTGCAGATCATGGGAGGCAG+AGG - chr8_3:18004584-18004603 Msa1280020:CDS 60.0%
GGAGGCAGAGGACTCTGCAA+AGG - chr8_3:18004596-18004615 Msa1280020:CDS 60.0%
Chromosome Type Strat End Strand Name
chr8_3 gene 18004419 18005153 18004419 ID=Msa1280020;Name=Msa1280020
chr8_3 mRNA 18004419 18005153 18004419 ID=Msa1280020-mRNA-1;Parent=Msa1280020;Name=Msa1280020-mRNA-1;_AED=0.35;_eAED=0.35;_QI=0|-1|0|1|-1|1|1|0|244
chr8_3 exon 18004419 18005153 18004419 ID=Msa1280020-mRNA-1:exon:6899;Parent=Msa1280020-mRNA-1
chr8_3 CDS 18004419 18005153 18004419 ID=Msa1280020-mRNA-1:cds;Parent=Msa1280020-mRNA-1
Gene Sequence

>Msa1280020

ATGTCTTCCTTTGTTGCCCTTCATAGCCTTCATGGCTCTCTTCTTAGATCCAAGTTCTTAGGCCAAGAGAATCTCACTCATCTTTATCCTCACAGCAATAAAGCTTCCATCTTTCACAGCAAATCGACGTACAAAACCATACAAACATGTGCCAAATTCGATTTGCTGCAGATCATGGGAGGCAGAGGACTCTGCAAAGGAGAAGAAGGTCTTCAAAAAGAGCTTAAAAGAGAAGTTGGTCTTGATGATCAGAATCAGCCAACATCATCCGAAGCAAGTAACGAAGAACAAGAAGACTCAACAAGTAGCTCAACGAAATCCTTTGTAAGTGTTGCAGAAGAAGGGTTTGATAAAGAGTTGATGGGGTTAACTGGAGGGTTTCCTGGTGGTGAAAAAGGTTTGAAAAAATTCATTGAAGAAAACCCTGTTCCAAAACCTGGTAGAGGTGACAAAAGCCTTAAACTTTCTTCGTCGGAGAAGGCAAAACCACCAGAACTTCCTATGTTACTTCCCGGAATGATTGCTATTGTGAAGAATCAAAATAACCCTTTTTACATGTACTGTGGTATTGTTCAAAGAATCACTGATGGTAAAGCAGGAGTACTGTTTGAAGGAGGGAATTGGGATAAGTTGATCACCTTTAGGCTTGAGGAACTTGAGAGAAGAGAAAAAGGTCCTCCCATGAAGAATCCCAAGTCTTGTGTTCTTGAACCATTTCTTGTAAAGAAATCATAG

Protein sequence

>Msa1280020

MSSFVALHSLHGSLLRSKFLGQENLTHLYPHSNKASIFHSKSTYKTIQTCAKFDLLQIMGGRGLCKGEEGLQKELKREVGLDDQNQPTSSEASNEEQEDSTSSSTKSFVSVAEEGFDKELMGLTGGFPGGEKGLKKFIEENPVPKPGRGDKSLKLSSSEKAKPPELPMLLPGMIAIVKNQNNPFYMYCGIVQRITDGKAGVLFEGGNWDKLITFRLEELERREKGPPMKNPKSCVLEPFLVKKS*