AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1406910

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1406910 MtrunA17_Chr2g0323571 94.505 91 5 0 1 91 1 91 2.18e-60 179
Msa1406910 MtrunA17_Chr2g0323671 93.407 91 6 0 1 91 1 91 6.52e-60 177
Msa1406910 MtrunA17_Chr2g0323631 92.308 91 7 0 1 91 1 91 1.09e-59 177
Msa1406910 MtrunA17_Chr4g0022611 74.118 85 19 2 9 91 6 89 1.78e-37 120
Msa1406910 MtrunA17_Chr2g0323701 67.442 86 23 3 9 91 6 89 8.62e-35 114
Msa1406910 MtrunA17_Chr2g0323721 63.953 86 26 3 9 91 6 89 2.38e-32 108
Msa1406910 MtrunA17_Chr2g0323661 66.667 81 21 3 11 91 10 84 1.10e-31 106
Msa1406910 MtrunA17_Chr2g0323611 66.667 81 21 3 11 91 10 84 1.48e-31 105
Msa1406910 MtrunA17_Chr2g0323601 61.957 92 29 3 5 91 2 92 4.41e-31 104
Msa1406910 MtrunA17_Chr2g0323651 60.440 91 31 2 5 91 2 91 4.09e-30 102
Msa1406910 MtrunA17_Chr2g0323711 60.440 91 31 2 5 91 2 91 4.09e-30 102
Msa1406910 MtrunA17_Chr2g0323681 57.292 96 31 2 5 91 2 96 2.11e-28 98.2
Msa1406910 MtrunA17_Chr2g0318611 54.651 86 36 1 5 90 2 84 2.09e-26 92.8
Msa1406910 MtrunA17_Chr2g0318641 54.444 90 34 3 2 90 32 115 3.26e-26 93.6
Msa1406910 MtrunA17_Chr2g0318601 52.326 86 38 1 5 90 2 84 1.05e-25 91.3
Msa1406910 MtrunA17_Chr2g0323551 56.818 88 34 4 6 91 3 88 1.85e-23 85.5
Msa1406910 MtrunA17_Chr2g0318591 46.512 86 43 2 5 90 2 84 4.85e-17 69.3
Msa1406910 MtrunA17_Chr2g0281091 47.297 74 33 3 21 91 19 89 1.62e-11 55.1
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1406910 AT4G10265.1 67.778 90 21 2 1 90 1 82 4.18e-37 120
Msa1406910 AT4G10270.1 66.292 89 28 1 5 91 2 90 6.95e-36 117

Find 23 sgRNAs with CRISPR-Local

Find 22 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
ATTTCTTTCTACCAAATTTA+AGG 0.083061 tig0023247:+82001 Msa1406910:CDS
CTTCTTCTCATCCTTAAATT+TGG 0.217937 tig0023247:-82012 None:intergenic
CAAGGACTCCTCTGCTTGTT+TGG 0.238006 tig0023247:-82036 None:intergenic
CTATGTACAAATTAATCAAT+TGG 0.386618 tig0023247:-82090 None:intergenic
TGTTATGTATTTAAGCTGCT+GGG 0.439197 tig0023247:+82064 Msa1406910:CDS
CTGTTATGTATTTAAGCTGC+TGG 0.447401 tig0023247:+82063 Msa1406910:CDS
GGCTGCAAGTGTTGGAGTTG+TGG 0.471925 tig0023247:+81860 Msa1406910:CDS
CAACAGCAACAAGCAAAGCC+TGG 0.483623 tig0023247:+81832 Msa1406910:CDS
TATGTACAAATTAATCAATT+GGG 0.486617 tig0023247:-82089 None:intergenic
CAAATTTAAGGATGAGAAGA+AGG 0.489333 tig0023247:+82013 Msa1406910:CDS
TGGATGGTGGCTGCAAGTGT+TGG 0.520041 tig0023247:+81852 Msa1406910:CDS
AACACTTGCAGCCACCATCC+AGG 0.526165 tig0023247:-81850 None:intergenic
CTTGAGAAATTGATCTAACA+CGG 0.546721 tig0023247:-81956 None:intergenic
AGCAACAAGCAAAGCCTGGA+TGG 0.571199 tig0023247:+81836 Msa1406910:CDS
GTTATGTATTTAAGCTGCTG+GGG 0.572155 tig0023247:+82065 Msa1406910:CDS
TGCAAGTGTTGGAGTTGTGG+AGG 0.587512 tig0023247:+81863 Msa1406910:CDS
TAAATACATAACAGTCCTCA+AGG 0.598210 tig0023247:-82054 None:intergenic
AAGATCAAGCAGGTATCTGT+AGG 0.606026 tig0023247:+81892 Msa1406910:CDS
GAAGAAGGCCAAACAAGCAG+AGG 0.609690 tig0023247:+82028 Msa1406910:CDS
ATCAAGCAGGTATCTGTAGG+TGG 0.613271 tig0023247:+81895 Msa1406910:CDS
AACAAGCAGAGGAGTCCTTG+AGG 0.628944 tig0023247:+82039 Msa1406910:CDS
GAGGCTTTGAAAGATCAAGC+AGG 0.651632 tig0023247:+81882 Msa1406910:CDS
AACAAGCAAAGCCTGGATGG+TGG 0.651830 tig0023247:+81839 Msa1406910:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! ATTTCTTTCTACCAAATTTA+AGG + tig0023247:82001-82020 Msa1406910:CDS 20.0%
! TTGATCTAACACGGTTTTTA+AGG - tig0023247:81950-81969 None:intergenic 30.0%
CTTGAGAAATTGATCTAACA+CGG - tig0023247:81959-81978 None:intergenic 30.0%
CTTCTTCTCATCCTTAAATT+TGG - tig0023247:82015-82034 None:intergenic 30.0%
CAAATTTAAGGATGAGAAGA+AGG + tig0023247:82013-82032 Msa1406910:CDS 30.0%
TAAATACATAACAGTCCTCA+AGG - tig0023247:82057-82076 None:intergenic 30.0%
TGTTATGTATTTAAGCTGCT+GGG + tig0023247:82064-82083 Msa1406910:CDS 30.0%
CTGTTATGTATTTAAGCTGC+TGG + tig0023247:82063-82082 Msa1406910:CDS 35.0%
GTTATGTATTTAAGCTGCTG+GGG + tig0023247:82065-82084 Msa1406910:CDS 35.0%
AAGATCAAGCAGGTATCTGT+AGG + tig0023247:81892-81911 Msa1406910:CDS 40.0%
!! GAGGCTTTGAAAGATCAAGC+AGG + tig0023247:81882-81901 Msa1406910:CDS 45.0%
ATCAAGCAGGTATCTGTAGG+TGG + tig0023247:81895-81914 Msa1406910:CDS 45.0%
CAACAGCAACAAGCAAAGCC+TGG + tig0023247:81832-81851 Msa1406910:CDS 50.0%
AGCAACAAGCAAAGCCTGGA+TGG + tig0023247:81836-81855 Msa1406910:CDS 50.0%
AACAAGCAAAGCCTGGATGG+TGG + tig0023247:81839-81858 Msa1406910:CDS 50.0%
!! TGCAAGTGTTGGAGTTGTGG+AGG + tig0023247:81863-81882 Msa1406910:CDS 50.0%
GAAGAAGGCCAAACAAGCAG+AGG + tig0023247:82028-82047 Msa1406910:CDS 50.0%
CAAGGACTCCTCTGCTTGTT+TGG - tig0023247:82039-82058 None:intergenic 50.0%
AACAAGCAGAGGAGTCCTTG+AGG + tig0023247:82039-82058 Msa1406910:CDS 50.0%
AACACTTGCAGCCACCATCC+AGG - tig0023247:81853-81872 None:intergenic 55.0%
! TGGATGGTGGCTGCAAGTGT+TGG + tig0023247:81852-81871 Msa1406910:CDS 55.0%
!! GGCTGCAAGTGTTGGAGTTG+TGG + tig0023247:81860-81879 Msa1406910:CDS 55.0%
Chromosome Type Strat End Strand Name
tig0023247 gene 81822 82097 81822 ID=Msa1406910;Name=Msa1406910
tig0023247 mRNA 81822 82097 81822 ID=Msa1406910-mRNA-1;Parent=Msa1406910;Name=Msa1406910-mRNA-1;_AED=0.25;_eAED=0.25;_QI=0|-1|0|1|-1|1|1|0|91
tig0023247 exon 81822 82097 81822 ID=Msa1406910-mRNA-1:exon:24808;Parent=Msa1406910-mRNA-1
tig0023247 CDS 81822 82097 81822 ID=Msa1406910-mRNA-1:cds;Parent=Msa1406910-mRNA-1
Gene Sequence

>Msa1406910

ATGAGTAGTGCAACAGCAACAAGCAAAGCCTGGATGGTGGCTGCAAGTGTTGGAGTTGTGGAGGCTTTGAAAGATCAAGCAGGTATCTGTAGGTGGAACTATGCTTTAAGACAAGCTCAACAACACCTTAAAAACCGTGTTAGATCAATTTCTCAAGCAAAGAATTTCTCTTCTTCTTCATTTCTTTCTACCAAATTTAAGGATGAGAAGAAGGCCAAACAAGCAGAGGAGTCCTTGAGGACTGTTATGTATTTAAGCTGCTGGGGTCCCAATTGA
Protein sequence

>Msa1406910

MSSATATSKAWMVAASVGVVEALKDQAGICRWNYALRQAQQHLKNRVRSISQAKNFSSSSFLSTKFKDEKKAKQAEESLRTVMYLSCWGPN*