AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1349450


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1349450 MtrunA17_Chr5g0395341 99.422 173 1 0 1 173 1 173 1.39e-123 353
Msa1349450 MtrunA17_Chr4g0039841 62.644 174 64 1 1 173 28 201 4.70e-69 216
Msa1349450 MtrunA17_Chr7g0261361 46.061 165 81 2 8 172 5 161 9.46e-44 149
Msa1349450 MtrunA17_Chr3g0139891 43.220 118 63 3 48 163 2 117 1.35e-21 90.9
Msa1349450 MtrunA17_Chr1g0157701 37.984 129 75 4 48 173 2 128 1.79e-21 90.5
Msa1349450 MtrunA17_Chr3g0125541 38.793 116 69 2 46 160 3 117 5.68e-21 89.0
Msa1349450 MtrunA17_Chr7g0244381 35.780 109 68 2 53 160 15 122 1.73e-19 84.7
Msa1349450 MtrunA17_Chr8g0388361 52.308 65 31 0 67 131 1 65 3.07e-17 72.0
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1349450 AT5G16880.3 79.191 173 36 0 1 173 1 173 2.86e-101 293
Msa1349450 AT5G16880.4 79.191 173 36 0 1 173 1 173 6.96e-100 294
Msa1349450 AT5G16880.1 79.191 173 36 0 1 173 1 173 6.96e-100 294
Msa1349450 AT5G16880.2 79.191 173 36 0 1 173 1 173 6.96e-100 294
Msa1349450 AT1G06210.2 46.667 165 80 2 8 172 5 161 1.54e-45 151
Msa1349450 AT1G06210.1 46.667 165 80 2 8 172 5 161 1.19e-44 151
Msa1349450 AT4G32760.1 42.735 117 65 2 48 163 2 117 1.84e-24 99.4
Msa1349450 AT4G32760.2 42.735 117 65 2 48 163 2 117 1.84e-24 99.4
Msa1349450 AT4G32760.3 40.625 128 73 3 48 173 2 128 2.58e-24 98.6
Msa1349450 AT3G08790.1 41.071 112 64 2 48 158 2 112 6.24e-21 89.4
Msa1349450 AT1G76970.2 35.385 130 79 4 46 172 3 130 4.36e-17 78.2
Msa1349450 AT1G76970.3 35.385 130 79 4 46 172 3 130 4.36e-17 78.2
Msa1349450 AT1G76970.6 35.385 130 79 4 46 172 3 130 4.36e-17 78.2
Msa1349450 AT1G76970.1 35.385 130 79 4 46 172 3 130 4.36e-17 78.2
Msa1349450 AT1G21380.1 36.752 117 70 3 46 160 3 117 6.08e-17 77.8
Msa1349450 AT5G01760.1 35.185 108 68 2 52 158 26 132 6.45e-16 74.7
Msa1349450 AT2G38410.1 38.532 109 65 2 53 160 13 120 1.88e-14 70.5

Find 27 sgRNAs with CRISPR-Local

Find 34 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
AACTCCTAGGGTTCAGTATT+TGG 0.146715 tig0010956:+20164 Msa1349450:CDS
CTCAAACTGTTGTTAATAAT+AGG 0.346651 tig0010956:+20289 Msa1349450:CDS
TAGGGTTCAGTATTTGGCTT+TGG 0.352663 tig0010956:+20170 Msa1349450:CDS
GAGTTCTTGATGAGATGGTT+AGG 0.363153 tig0010956:+20253 Msa1349450:CDS
TTTGGTTATGATTGAAGCTT+GGG 0.369449 tig0010956:+20320 Msa1349450:CDS
AATGAGTTCAATGAGTTTCA+AGG 0.404113 tig0010956:+19966 Msa1349450:CDS
ACGAGCTTATCGACTTGGTT+TGG 0.409743 tig0010956:-20009 Msa1349450:intergenic
ATCAGGTTCTTCATGTGCTT+CGG 0.421422 tig0010956:-20046 Msa1349450:intergenic
TAATAATAGGAATAAAGCTT+TGG 0.426379 tig0010956:+20302 Msa1349450:CDS
AGTTCTTGATGAGATGGTTA+GGG 0.461596 tig0010956:+20254 Msa1349450:CDS
CTTCGACGAGCTTATCGACT+TGG 0.463309 tig0010956:-20014 Msa1349450:intergenic
CTTTGGTTATGATTGAAGCT+TGG 0.468467 tig0010956:+20319 Msa1349450:CDS
TCGAGATTCATAGCCCAATC+AGG 0.471193 tig0010956:-20063 Msa1349450:intergenic
CTATTATTAACAACAGTTTG+AGG 0.474784 tig0010956:-20288 Msa1349450:intergenic
AAGCACATGAAGAACCTGAT+TGG 0.475758 tig0010956:+20049 Msa1349450:CDS
AGCACATGAAGAACCTGATT+GGG 0.475868 tig0010956:+20050 Msa1349450:CDS
GGATCATGATTAAAACTCCT+AGG 0.482292 tig0010956:+20151 Msa1349450:CDS
GAAGCTTGGGGAGAGTCTAC+TGG 0.508336 tig0010956:+20333 Msa1349450:CDS
GTAGGTAGAAAAGTAACAGA+AGG 0.533297 tig0010956:+19943 Msa1349450:CDS
TGAAAGAGTTCTTGATGAGA+TGG 0.547601 tig0010956:+20248 Msa1349450:CDS
TGATCCGTGCTATTAAGAAA+CGG 0.554752 tig0010956:+20130 Msa1349450:CDS
AAAGCCAAATACTGAACCCT+AGG 0.558286 tig0010956:-20168 Msa1349450:intergenic
AAGGTTAAAGAATTCTTCAA+CGG 0.559253 tig0010956:+19985 Msa1349450:CDS
GATCATGATTAAAACTCCTA+GGG 0.584994 tig0010956:+20152 Msa1349450:CDS
TGATCCGTTTCTTAATAGCA+CGG 0.604913 tig0010956:-20134 Msa1349450:intergenic
CTCATCAAGAACTCTTTCAG+CGG 0.633474 tig0010956:-20244 Msa1349450:intergenic
TTGGTTATGATTGAAGCTTG+GGG 0.686489 tig0010956:+20321 Msa1349450:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! TAATAATAGGAATAAAGCTT+TGG + tig0010956:20302-20321 Msa1349450:CDS 20.0%
! AAGGTTAAAGAATTCTTCAA+CGG + tig0010956:19985-20004 Msa1349450:CDS 25.0%
! CTATTATTAACAACAGTTTG+AGG - tig0010956:20291-20310 Msa1349450:intergenic 25.0%
! CTCAAACTGTTGTTAATAAT+AGG + tig0010956:20289-20308 Msa1349450:CDS 25.0%
! TTATAGGTTTCTTCAAAAAC+AGG - tig0010956:20375-20394 Msa1349450:intergenic 25.0%
TTCGGTGAAAAGCTAAAAAT+CGG + tig0010956:19910-19929 Msa1349450:CDS 30.0%
AATGAGTTCAATGAGTTTCA+AGG + tig0010956:19966-19985 Msa1349450:CDS 30.0%
GATCATGATTAAAACTCCTA+GGG + tig0010956:20152-20171 Msa1349450:CDS 30.0%
TTTGGTTATGATTGAAGCTT+GGG + tig0010956:20320-20339 Msa1349450:CDS 30.0%
ATGGAAAAAGTGAACGCATT+CGG + tig0010956:19892-19911 Msa1349450:CDS 35.0%
TCGGTGAAAAGCTAAAAATC+GGG + tig0010956:19911-19930 Msa1349450:CDS 35.0%
GTAGGTAGAAAAGTAACAGA+AGG + tig0010956:19943-19962 Msa1349450:CDS 35.0%
! TGATCCGTGCTATTAAGAAA+CGG + tig0010956:20130-20149 Msa1349450:CDS 35.0%
TGATCCGTTTCTTAATAGCA+CGG - tig0010956:20137-20156 Msa1349450:intergenic 35.0%
GGATCATGATTAAAACTCCT+AGG + tig0010956:20151-20170 Msa1349450:CDS 35.0%
TGAAAGAGTTCTTGATGAGA+TGG + tig0010956:20248-20267 Msa1349450:CDS 35.0%
AGTTCTTGATGAGATGGTTA+GGG + tig0010956:20254-20273 Msa1349450:CDS 35.0%
CTTTGGTTATGATTGAAGCT+TGG + tig0010956:20319-20338 Msa1349450:CDS 35.0%
TTGGTTATGATTGAAGCTTG+GGG + tig0010956:20321-20340 Msa1349450:CDS 35.0%
CGGTGAAAAGCTAAAAATCG+GGG + tig0010956:19912-19931 Msa1349450:CDS 40.0%
GGTGAAAAGCTAAAAATCGG+GGG + tig0010956:19913-19932 Msa1349450:CDS 40.0%
ATCAGGTTCTTCATGTGCTT+CGG - tig0010956:20049-20068 Msa1349450:intergenic 40.0%
AAGCACATGAAGAACCTGAT+TGG + tig0010956:20049-20068 Msa1349450:CDS 40.0%
AGCACATGAAGAACCTGATT+GGG + tig0010956:20050-20069 Msa1349450:CDS 40.0%
AACTCCTAGGGTTCAGTATT+TGG + tig0010956:20164-20183 Msa1349450:CDS 40.0%
AAAGCCAAATACTGAACCCT+AGG - tig0010956:20171-20190 Msa1349450:intergenic 40.0%
! TAGGGTTCAGTATTTGGCTT+TGG + tig0010956:20170-20189 Msa1349450:CDS 40.0%
CTCATCAAGAACTCTTTCAG+CGG - tig0010956:20247-20266 Msa1349450:intergenic 40.0%
GAGTTCTTGATGAGATGGTT+AGG + tig0010956:20253-20272 Msa1349450:CDS 40.0%
! AAAATCGGGGGTGTAGAAGT+AGG + tig0010956:19925-19944 Msa1349450:CDS 45.0%
!! ACGAGCTTATCGACTTGGTT+TGG - tig0010956:20012-20031 Msa1349450:intergenic 45.0%
TCGAGATTCATAGCCCAATC+AGG - tig0010956:20066-20085 Msa1349450:intergenic 45.0%
! CTTCGACGAGCTTATCGACT+TGG - tig0010956:20017-20036 Msa1349450:intergenic 50.0%
GAAGCTTGGGGAGAGTCTAC+TGG + tig0010956:20333-20352 Msa1349450:CDS 55.0%
Chromosome Type Strat End Strand Name
tig0010956 gene 19877 20395 19877 ID=Msa1349450;Name=Msa1349450
tig0010956 mRNA 19877 20395 19877 ID=Msa1349450-mRNA-1;Parent=Msa1349450;Name=Msa1349450-mRNA-1;_AED=0.31;_eAED=0.31;_QI=0|-1|0|1|-1|1|1|0|173
tig0010956 exon 19877 20395 19877 ID=Msa1349450-mRNA-1:exon:6926;Parent=Msa1349450-mRNA-1
tig0010956 CDS 19877 20395 19877 ID=Msa1349450-mRNA-1:cds;Parent=Msa1349450-mRNA-1
Gene Sequence

>Msa1349450

ATGAGCGATAATTTGATGGAAAAAGTGAACGCATTCGGTGAAAAGCTAAAAATCGGGGGTGTAGAAGTAGGTAGAAAAGTAACAGAAGGAATGAGTTCAATGAGTTTCAAGGTTAAAGAATTCTTCAACGGTCCAAACCAAGTCGATAAGCTCGTCGAAGATGCTACTTCCGAAGCACATGAAGAACCTGATTGGGCTATGAATCTCGATCTATGTGATTTAATCAATACTGAAAAAGTTAACAGTGTTGAATTGATCCGTGCTATTAAGAAACGGATCATGATTAAAACTCCTAGGGTTCAGTATTTGGCTTTGGTTTTGCTTGAAACTGTTGTTAAGAATTGTGAAAAAGCTTTTTCTGAAGTTGCCGCTGAAAGAGTTCTTGATGAGATGGTTAGGGTTATTGATGATCCTCAAACTGTTGTTAATAATAGGAATAAAGCTTTGGTTATGATTGAAGCTTGGGGAGAGTCTACTGGTGAACTTAGATATCTTCCTGTTTTTGAAGAAACCTATAAG

Protein sequence

>Msa1349450

MSDNLMEKVNAFGEKLKIGGVEVGRKVTEGMSSMSFKVKEFFNGPNQVDKLVEDATSEAHEEPDWAMNLDLCDLINTEKVNSVELIRAIKKRIMIKTPRVQYLALVLLETVVKNCEKAFSEVAAERVLDEMVRVIDDPQTVVNNRNKALVMIEAWGESTGELRYLPVFEETYK