AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0335120

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0335120 MtrunA17_Chr2g0320521 74.627 134 22 1 1 122 2 135 9.74e-70 209
Msa0335120 MtrunA17_Chr4g0020811 58.209 134 44 1 1 122 2 135 2.35e-47 149
Msa0335120 MtrunA17_Chr2g0308401 57.143 133 45 1 2 122 1 133 7.73e-46 145
Msa0335120 MtrunA17_Chr2g0320561 49.624 133 55 1 2 122 1 133 7.90e-42 138
Msa0335120 MtrunA17_Chr2g0320551 51.128 133 53 1 2 122 1 133 1.09e-41 135
Msa0335120 MtrunA17_Chr1g0179781 41.481 135 57 4 1 122 2 127 2.66e-27 100
Msa0335120 MtrunA17_Chr7g0265291 37.778 135 61 3 2 122 4 129 5.66e-24 91.7
Msa0335120 MtrunA17_Chr5g0411151 35.338 133 66 4 1 122 31 154 1.53e-22 88.6
Msa0335120 MtrunA17_Chr5g0395181 35.156 128 63 4 6 122 22 140 6.36e-22 86.3
Msa0335120 MtrunA17_Chr8g0366581 35.156 128 63 3 6 122 34 152 2.39e-21 85.5
Msa0335120 MtrunA17_Chr4g0040071 35.938 128 62 4 6 122 16 134 1.70e-20 82.8
Msa0335120 MtrunA17_Chr2g0297251 33.333 126 65 3 7 122 39 155 1.43e-15 70.5
Msa0335120 MtrunA17_Chr7g0230511 31.538 130 68 4 4 122 7 126 6.96e-15 68.6
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0335120 AT4G17900.2 40.650 123 53 4 6 117 21 134 3.19e-22 87.4
Msa0335120 AT4G17900.1 40.650 123 53 4 6 117 35 148 3.30e-22 87.8
Msa0335120 AT1G43000.2 36.090 133 65 3 1 122 12 135 1.74e-21 85.9
Msa0335120 AT1G43000.1 36.090 133 65 3 1 122 5 128 1.92e-21 85.5
Msa0335120 AT1G32700.1 37.795 127 59 4 7 122 14 131 3.51e-21 84.7
Msa0335120 AT2G27930.3 34.884 129 70 3 7 122 6 133 8.88e-19 77.4
Msa0335120 AT2G27930.2 34.884 129 70 3 7 122 6 133 8.88e-19 77.4
Msa0335120 AT2G27930.1 34.884 129 70 3 7 122 6 133 1.20e-18 77.8
Msa0335120 AT2G27930.4 34.884 129 70 3 7 122 6 133 1.20e-18 77.8
Msa0335120 AT1G21000.1 33.083 133 69 3 1 122 12 135 9.49e-18 76.6
Msa0335120 AT1G21000.2 33.083 133 69 3 1 122 9 132 9.98e-18 76.3
Msa0335120 AT1G32700.2 44.048 84 39 2 39 122 17 92 2.93e-17 73.6
Msa0335120 AT1G76590.1 32.812 128 66 3 6 122 19 137 1.88e-16 73.2
Msa0335120 AT5G46710.2 34.426 122 60 3 7 117 30 142 2.16e-14 66.2
Msa0335120 AT3G60670.1 33.333 129 67 3 7 125 9 128 2.66e-14 67.4
Msa0335120 AT5G46710.3 34.426 122 60 3 7 117 14 126 4.16e-14 66.2
Msa0335120 AT5G46710.1 34.426 122 60 3 7 117 30 142 4.58e-14 66.2
Msa0335120 AT1G31040.1 31.746 126 66 4 7 122 21 136 1.10e-13 65.5
Msa0335120 AT2G27930.5 38.158 76 46 1 48 122 61 136 5.95e-12 60.1
Msa0335120 AT2G27930.6 38.158 76 46 1 48 122 61 136 5.95e-12 60.1
Msa0335120 AT2G12646.3 32.812 128 67 4 3 120 1 119 1.35e-11 60.1
Msa0335120 AT2G12646.1 33.065 124 64 4 7 120 8 122 2.13e-11 59.3
Msa0335120 AT2G12646.2 33.065 124 64 4 7 120 8 122 2.13e-11 59.3

Find 12 sgRNAs with CRISPR-Local

Find 23 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TATCTCATTGATTGGGAATA+AGG 0.167816 2_4:+54190835 None:intergenic
GATTGATATTTACAAGTATT+TGG 0.197324 2_4:-54190920 Msa0335120:CDS
AGATACAAGATTGGTATAAT+TGG 0.287922 2_4:-54190817 Msa0335120:CDS
AACATTATGTAAAAGTAATA+AGG 0.320284 2_4:+54190745 None:intergenic
CAATCTTGTATCTCATTGAT+TGG 0.323377 2_4:+54190827 None:intergenic
TACAAGTATTTGGACTTTCT+AGG 0.323760 2_4:-54190910 Msa0335120:CDS
AATCTTGTATCTCATTGATT+GGG 0.448397 2_4:+54190828 None:intergenic
CAATCAATGAGATACAAGAT+TGG 0.552028 2_4:-54190826 Msa0335120:CDS
GATATGTCAAAGAAATCTTG+TGG 0.556486 2_4:-54190770 Msa0335120:CDS
CGACTGTATTCATAAACAAG+AGG 0.573759 2_4:-54190858 Msa0335120:CDS
ATATGTCAAAGAAATCTTGT+GGG 0.576587 2_4:-54190769 Msa0335120:CDS
AGGATATGATGGTTATGCCC+TGG 0.608474 2_4:-54191310 Msa0335120:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! TTATTTGATTTTTTTTACTT+TGG - chr2_4:54191031-54191050 Msa0335120:intron 10.0%
!!! TATTTGATTTTTTTTACTTT+GGG - chr2_4:54191032-54191051 Msa0335120:intron 10.0%
!! AACATTATGTAAAAGTAATA+AGG + chr2_4:54191307-54191326 None:intergenic 15.0%
!! TTTATGCAAAATCTTCAAAA+TGG + chr2_4:54190870-54190889 None:intergenic 20.0%
!! TAAATTTGAACCTTGATATT+TGG - chr2_4:54191058-54191077 Msa0335120:intron 20.0%
!! GATTGATATTTACAAGTATT+TGG - chr2_4:54191129-54191148 Msa0335120:intron 20.0%
! ATTTGTAGTTCCAAATATCA+AGG + chr2_4:54191071-54191090 None:intergenic 25.0%
!! AATCTTGTATCTCATTGATT+GGG + chr2_4:54191224-54191243 None:intergenic 25.0%
! AGATACAAGATTGGTATAAT+TGG - chr2_4:54191232-54191251 Msa0335120:CDS 25.0%
! ATATGTCAAAGAAATCTTGT+GGG - chr2_4:54191280-54191299 Msa0335120:CDS 25.0%
!! GAAAGCAAATTTTTCAACCA+GGG + chr2_4:54190759-54190778 None:intergenic 30.0%
!! TGAAAGCAAATTTTTCAACC+AGG + chr2_4:54190760-54190779 None:intergenic 30.0%
! TGACTGTTGTTTAAAGTGAT+AGG - chr2_4:54190922-54190941 Msa0335120:CDS 30.0%
! GATATTTGGAACTACAAATC+AGG - chr2_4:54191072-54191091 Msa0335120:intron 30.0%
TACAAGTATTTGGACTTTCT+AGG - chr2_4:54191139-54191158 Msa0335120:intron 30.0%
! TATCTCATTGATTGGGAATA+AGG + chr2_4:54191217-54191236 None:intergenic 30.0%
CAATCTTGTATCTCATTGAT+TGG + chr2_4:54191225-54191244 None:intergenic 30.0%
CAATCAATGAGATACAAGAT+TGG - chr2_4:54191223-54191242 Msa0335120:intron 30.0%
GATATGTCAAAGAAATCTTG+TGG - chr2_4:54191279-54191298 Msa0335120:CDS 30.0%
CACTTTAAACAACAGTCACT+TGG + chr2_4:54190920-54190939 None:intergenic 35.0%
CGACTGTATTCATAAACAAG+AGG - chr2_4:54191191-54191210 Msa0335120:intron 35.0%
!!! CGCTCATATTTTGACTCGTT+CGG + chr2_4:54190816-54190835 None:intergenic 40.0%
TTGGAACTACAAATCAGGTG+AGG - chr2_4:54191077-54191096 Msa0335120:intron 40.0%
Chromosome Type Strat End Strand Name
chr2_4 gene 54190741 54191330 54190741 ID=Msa0335120;Name=Msa0335120
chr2_4 mRNA 54190741 54191330 54190741 ID=Msa0335120-mRNA-1;Parent=Msa0335120;Name=Msa0335120-mRNA-1;_AED=0.15;_eAED=0.15;_QI=0|0|0|1|0|0|3|0|126
chr2_4 exon 54191230 54191330 54191230 ID=Msa0335120-mRNA-1:exon:16389;Parent=Msa0335120-mRNA-1
chr2_4 exon 54191151 54191193 54191151 ID=Msa0335120-mRNA-1:exon:16388;Parent=Msa0335120-mRNA-1
chr2_4 exon 54190741 54190977 54190741 ID=Msa0335120-mRNA-1:exon:16387;Parent=Msa0335120-mRNA-1
chr2_4 CDS 54191230 54191330 54191230 ID=Msa0335120-mRNA-1:cds;Parent=Msa0335120-mRNA-1
chr2_4 CDS 54191151 54191193 54191151 ID=Msa0335120-mRNA-1:cds;Parent=Msa0335120-mRNA-1
chr2_4 CDS 54190741 54190977 54190741 ID=Msa0335120-mRNA-1:cds;Parent=Msa0335120-mRNA-1
Gene Sequence

>Msa0335120

GATATGATGGTTATGCCCTGGTTGAAAAATTTGCTTTCAATCACTGCATTTTTCACTAAATGTGAAGTTCAACCGAACGAGTCAAAATATGAGCGCATCATATTTTGCATAAAATCTCATCACAAAGATCATCAAGTAATCCAAGTGAGGAGATCATCTTATACTGACGTTGTTAAGACGATTGATATTTACAAGTATTTGGACTTTCTAGGAATTCAAACGTATGTGATTAGCAACTTTACGACTGTATTCATAAACAAGAGGCCTTATTCCCAATCAATGAGATACAAGATTGGTATAATTGGTTGTAGTAGTGACTATCTTTGTAAGATATGTCAAAGAAATCTTGTGGGTCCTTATTACTTTTACATAATGTTTTAA
Protein sequence

>Msa0335120

DMMVMPWLKNLLSITAFFTKCEVQPNESKYERIIFCIKSHHKDHQVIQVRRSSYTDVVKTIDIYKYLDFLGIQTYVISNFTTVFINKRPYSQSMRYKIGIIGCSSDYLCKICQRNLVGPYYFYIMF*