AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene031185

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene031185.t1 MTR_8g022970 70.707 99 28 1 1 98 1 99 1.20e-40 132
MS.gene031185.t1 MTR_3g109930 71.622 74 21 0 25 98 10 83 2.81e-31 108
MS.gene031185.t1 MTR_3g437790 61.538 52 19 1 35 85 31 82 9.11e-16 68.9
MS.gene031185.t1 MTR_2g105290 46.575 73 37 2 13 84 8 79 4.37e-13 61.6
MS.gene031185.t1 MTR_1g012570 41.333 75 44 0 13 87 5 79 5.24e-13 62.4
MS.gene031185.t1 MTR_1g047550 38.462 78 48 0 18 95 3 80 9.22e-13 60.8
MS.gene031185.t1 MTR_8g079502 36.709 79 50 0 18 96 3 81 1.07e-12 60.8
MS.gene031185.t1 MTR_1g106070 38.462 78 48 0 13 90 5 82 1.18e-12 60.8
MS.gene031185.t1 MTR_5g053390 42.857 70 40 0 18 87 10 79 2.41e-12 60.8
MS.gene031185.t1 MTR_5g055100 42.857 70 40 0 18 87 10 79 2.78e-12 60.5
MS.gene031185.t1 MTR_3g052920 40.000 75 45 0 13 87 5 79 1.41e-11 58.5
MS.gene031185.t1 MTR_3g052870 37.333 75 47 0 13 87 5 79 2.19e-11 57.8
MS.gene031185.t1 MTR_1g105920 37.333 75 47 0 13 87 5 79 2.34e-11 58.2
MS.gene031185.t1 MTR_1g105910 37.333 75 47 0 13 87 5 79 2.57e-11 57.8
MS.gene031185.t1 MTR_8g043650 37.333 75 47 0 13 87 5 79 2.79e-11 57.8
MS.gene031185.t1 MTR_2g085280 42.647 68 39 0 18 85 10 77 3.71e-11 57.4
MS.gene031185.t1 MTR_2g085250 42.647 68 39 0 18 85 10 77 3.71e-11 57.4
MS.gene031185.t1 MTR_2g030740 37.333 75 47 0 13 87 5 79 4.94e-11 57.0
MS.gene031185.t1 MTR_1g108580 39.474 76 46 0 10 85 2 77 6.42e-11 56.6
MS.gene031185.t1 MTR_5g045560 43.284 67 38 0 18 84 10 76 6.51e-11 57.0
MS.gene031185.t1 MTR_4g131030 37.662 77 48 0 18 94 3 79 7.26e-11 56.6
MS.gene031185.t1 MTR_2g045020 42.667 75 33 3 15 87 20 86 7.95e-11 55.8
MS.gene031185.t1 MTR_2g093190 39.706 68 41 0 18 85 10 77 8.46e-11 56.6
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene031185.t1 AT1G65360 40.789 76 45 0 11 86 1 76 6.83e-14 64.7
MS.gene031185.t1 AT3G66656 40.299 67 40 0 18 84 3 69 2.79e-12 59.7
MS.gene031185.t1 AT1G01530 40.260 77 46 0 11 87 1 77 3.75e-12 60.5

Find 10 sgRNAs with CRISPR-Local

Find 12 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TCAGCTATCGACGCTGAAAA+AGG 0.238437 3.3:+90215227 MS.gene031185:CDS
AAGTGTTTAATGACGATGTT+AGG 0.253299 3.3:-90215188 None:intergenic
CTCTTCTTTCTTGATTTCAA+TGG 0.286601 3.3:-90215018 None:intergenic
TAATGACGATGTTAGGGTTA+GGG 0.414307 3.3:-90215181 None:intergenic
TTAATGACGATGTTAGGGTT+AGG 0.425753 3.3:-90215182 None:intergenic
AGTGTTTAATGACGATGTTA+GGG 0.483491 3.3:-90215187 None:intergenic
TTTCCATCTGAAGAAGCCAT+TGG 0.494665 3.3:-90214957 None:intergenic
GATCCAATGGCTTCTTCAGA+TGG 0.507351 3.3:+90214954 None:intergenic
ACTTTCTCAAAGCTCAAACT+AGG 0.549629 3.3:+90215062 MS.gene031185:CDS
GCATAGAATAGATAATTCTG+TGG 0.670141 3.3:-90215099 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! ATCGTCATTAAACACTTTTT+CGG + chr3.3:90215194-90215213 MS.gene031185:CDS 25.0%
AAGTGTTTAATGACGATGTT+AGG - chr3.3:90215191-90215210 None:intergenic 30.0%
AGTGTTTAATGACGATGTTA+GGG - chr3.3:90215190-90215209 None:intergenic 30.0%
CTCTTCTTTCTTGATTTCAA+TGG - chr3.3:90215021-90215040 None:intergenic 30.0%
GCATAGAATAGATAATTCTG+TGG - chr3.3:90215102-90215121 None:intergenic 30.0%
!!! CATTAAACACTTTTTCGGTA+AGG + chr3.3:90215199-90215218 MS.gene031185:CDS 30.0%
ACTTTCTCAAAGCTCAAACT+AGG + chr3.3:90215062-90215081 MS.gene031185:CDS 35.0%
GACAAAAAACTCTATGCATG+TGG + chr3.3:90215155-90215174 MS.gene031185:CDS 35.0%
TAATGACGATGTTAGGGTTA+GGG - chr3.3:90215184-90215203 None:intergenic 35.0%
TTAATGACGATGTTAGGGTT+AGG - chr3.3:90215185-90215204 None:intergenic 35.0%
CAGCTATCGACGCTGAAAAA+GGG + chr3.3:90215228-90215247 MS.gene031185:CDS 45.0%
TCAGCTATCGACGCTGAAAA+AGG + chr3.3:90215227-90215246 MS.gene031185:CDS 45.0%


Chromosome Type Strat End Strand Name
chr3.3 gene 90214960 90215256 90214960 ID=MS.gene031185
chr3.3 mRNA 90214960 90215256 90214960 ID=MS.gene031185.t1;Parent=MS.gene031185
chr3.3 exon 90214960 90215256 90214960 ID=MS.gene031185.t1.exon1;Parent=MS.gene031185.t1
chr3.3 CDS 90214960 90215256 90214960 ID=cds.MS.gene031185.t1;Parent=MS.gene031185.t1
Gene Sequence

>MS.gene031185

ATGGCTTCTTCAGATGGAAACAACACATCAATAATACGAAGCAACTCACAAAAGAGAACCATTGAAATCAAGAAAGAAGAGACATCGAACAAGCTTCGTAATACTTTCTCAAAGCTCAAACTAGGACTCTTCAACAAAGCCACAGAATTATCTATTCTATGCAATGCAAAAACTGCAATGATCATCACTTCTTCAGACAAAAAACTCTATGCATGTGGATGCCCTAACCCTAACATCGTCATTAAACACTTTTTCGGTAAGGAAAACTCAGCTATCGACGCTGAAAAAGGGAAATAG
Protein sequence

>MS.gene031185.t1

MASSDGNNTSIIRSNSQKRTIEIKKEETSNKLRNTFSKLKLGLFNKATELSILCNAKTAMIITSSDKKLYACGCPNPNIVIKHFFGKENSAIDAEKGK