AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene010343

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene010343.t1 MTR_5g094680 75.000 108 26 1 1 107 113 220 2.29e-55 171
MS.gene010343.t1 MTR_7g092960 65.714 105 27 2 1 105 1 96 4.96e-43 136
MS.gene010343.t1 MTR_7g093310 73.171 82 22 0 26 107 56 137 4.35e-38 125
MS.gene010343.t1 MTR_5g037840 35.484 124 60 3 1 106 8 129 1.04e-16 70.9
MS.gene010343.t1 MTR_8g085520 37.500 112 64 2 1 106 37 148 1.56e-16 71.2
MS.gene010343.t1 MTR_8g085550 47.059 68 36 0 39 106 81 148 1.96e-16 70.5
MS.gene010343.t1 MTR_5g037810 33.065 124 63 2 1 106 8 129 3.67e-16 69.3
MS.gene010343.t1 MTR_5g006240 32.759 116 65 2 1 105 110 223 4.05e-14 65.9
MS.gene010343.t1 MTR_8g085530 51.923 52 25 0 55 106 245 296 4.97e-13 63.5
MS.gene010343.t1 MTR_1g029910 41.935 62 35 1 46 106 131 192 4.64e-11 57.4
MS.gene010343.t1 MTR_1g029860 29.091 110 61 4 1 106 80 176 5.44e-11 57.0
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 21 sgRNAs with CRISPR-Local

Find 24 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
ACGACGAAGATCAGAAAATC+TGG 0.344881 5.4:+10310986 MS.gene010343:CDS
GGACCGGTGTGCAATTTGTT+TGG 0.399227 5.4:+10311131 MS.gene010343:CDS
TTGTCGTGGATGGGTTGAAA+AGG 0.454657 5.4:+10311076 MS.gene010343:CDS
AAGGCCCTACTTGTCGTGGA+TGG 0.483342 5.4:+10311066 MS.gene010343:CDS
GTGGATGGGTTGAAAAGGGT+TGG 0.497843 5.4:+10311081 MS.gene010343:CDS
TGGGTTGAAAAGGGTTGGAA+TGG 0.527182 5.4:+10311086 MS.gene010343:CDS
TCAACCCATCCACGACAAGT+AGG 0.539164 5.4:-10311071 None:intergenic
CAACCCATCCACGACAAGTA+GGG 0.539800 5.4:-10311070 None:intergenic
TGTTTGGAAGAGCTCTTCGA+TGG 0.552068 5.4:+10311147 MS.gene010343:CDS
TCATTCATCTCGTTACTCTA+CGG 0.565153 5.4:+10311110 MS.gene010343:CDS
TGTCGTGGATGGGTTGAAAA+GGG 0.570487 5.4:+10311077 MS.gene010343:CDS
CGACGAAGATCAGAAAATCT+GGG 0.572391 5.4:+10310987 MS.gene010343:CDS
AGGCCCTACTTGTCGTGGAT+GGG 0.574481 5.4:+10311067 MS.gene010343:CDS
GCGACACAATGGACACGAGA+GGG 0.606474 5.4:-10311265 None:intergenic
TGAAGATAATGATGCTGTGA+AGG 0.607686 5.4:+10311047 MS.gene010343:CDS
TGAAGCTTGATGTCAATACA+TGG 0.634786 5.4:+10311019 MS.gene010343:CDS
CATCTCGTTACTCTACGGAC+CGG 0.636560 5.4:+10311115 MS.gene010343:CDS
TGCGACACAATGGACACGAG+AGG 0.660737 5.4:-10311266 None:intergenic
ACGAGAGGGATGATTGACGA+TGG 0.663362 5.4:-10311251 None:intergenic
TGTGAAGGCCCTACTTGTCG+TGG 0.664403 5.4:+10311062 MS.gene010343:CDS
CTTCCAAACAAATTGCACAC+CGG 0.732526 5.4:-10311134 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! ATAAAGAGTGTATTTTTCAA+TGG + chr5.4:10311214-10311233 MS.gene010343:CDS 20.0%
! ATGAAAAACATGCAAACAAT+TGG - chr5.4:10311196-10311215 None:intergenic 25.0%
TCATTCATCTCGTTACTCTA+CGG + chr5.4:10311110-10311129 MS.gene010343:CDS 35.0%
TGAAGATAATGATGCTGTGA+AGG + chr5.4:10311047-10311066 MS.gene010343:CDS 35.0%
TGAAGCTTGATGTCAATACA+TGG + chr5.4:10311019-10311038 MS.gene010343:CDS 35.0%
ACGACGAAGATCAGAAAATC+TGG + chr5.4:10310986-10311005 MS.gene010343:CDS 40.0%
CGACGAAGATCAGAAAATCT+GGG + chr5.4:10310987-10311006 MS.gene010343:CDS 40.0%
CTTCCAAACAAATTGCACAC+CGG - chr5.4:10311137-10311156 None:intergenic 40.0%
! TCATCAGTTTTGCGACACAA+TGG - chr5.4:10311279-10311298 None:intergenic 40.0%
TGTTTGGAAGAGCTCTTCGA+TGG + chr5.4:10311147-10311166 MS.gene010343:CDS 45.0%
! TGGGTTGAAAAGGGTTGGAA+TGG + chr5.4:10311086-10311105 MS.gene010343:CDS 45.0%
!! TGTCGTGGATGGGTTGAAAA+GGG + chr5.4:10311077-10311096 MS.gene010343:CDS 45.0%
!! TTGTCGTGGATGGGTTGAAA+AGG + chr5.4:10311076-10311095 MS.gene010343:CDS 45.0%
ACGAGAGGGATGATTGACGA+TGG - chr5.4:10311254-10311273 None:intergenic 50.0%
CAACCCATCCACGACAAGTA+GGG - chr5.4:10311073-10311092 None:intergenic 50.0%
CATCTCGTTACTCTACGGAC+CGG + chr5.4:10311115-10311134 MS.gene010343:CDS 50.0%
TCAACCCATCCACGACAAGT+AGG - chr5.4:10311074-10311093 None:intergenic 50.0%
! GGACCGGTGTGCAATTTGTT+TGG + chr5.4:10311131-10311150 MS.gene010343:CDS 50.0%
!! GTGGATGGGTTGAAAAGGGT+TGG + chr5.4:10311081-10311100 MS.gene010343:CDS 50.0%
AAGGCCCTACTTGTCGTGGA+TGG + chr5.4:10311066-10311085 MS.gene010343:CDS 55.0%
AGGCCCTACTTGTCGTGGAT+GGG + chr5.4:10311067-10311086 MS.gene010343:CDS 55.0%
GCGACACAATGGACACGAGA+GGG - chr5.4:10311268-10311287 None:intergenic 55.0%
TGCGACACAATGGACACGAG+AGG - chr5.4:10311269-10311288 None:intergenic 55.0%
TGTGAAGGCCCTACTTGTCG+TGG + chr5.4:10311062-10311081 MS.gene010343:CDS 55.0%


Chromosome Type Strat End Strand Name
chr5.4 gene 10310973 10311311 10310973 ID=MS.gene010343
chr5.4 mRNA 10310973 10311311 10310973 ID=MS.gene010343.t1;Parent=MS.gene010343
chr5.4 exon 10310973 10311311 10310973 ID=MS.gene010343.t1.exon1;Parent=MS.gene010343.t1
chr5.4 CDS 10310973 10311311 10310973 ID=cds.MS.gene010343.t1;Parent=MS.gene010343.t1
Gene Sequence

>MS.gene010343

ATGGTCGCTAATGACGACGAAGATCAGAAAATCTGGGAGATAGACGTGAAGCTTGATGTCAATACATGGTATATTGAAGATAATGATGCTGTGAAGGCCCTACTTGTCGTGGATGGGTTGAAAAGGGTTGGAATGGATCATTCATCTCGTTACTCTACGGACCGGTGTGCAATTTGTTTGGAAGAGCTCTTCGATGGATCAAAGTCAGAACATGTTATGACCAATTGTTTGCATGTTTTTCATAAAGAGTGTATTTTTCAATGGCTCAAAAGATGCTTCCATCGTCAATCATCCCTCTCGTGTCCATTGTGTCGCAAAACTGATGAAGCTTTTGAATGA
Protein sequence

>MS.gene010343.t1

MVANDDEDQKIWEIDVKLDVNTWYIEDNDAVKALLVVDGLKRVGMDHSSRYSTDRCAICLEELFDGSKSEHVMTNCLHVFHKECIFQWLKRCFHRQSSLSCPLCRKTDEAFE