AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene29155

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene29155.t1 MTR_7g117590 70.988 162 32 2 2 149 12 172 6.57e-78 229
MS.gene29155.t1 MTR_1g054470 52.778 144 42 4 2 145 23 140 1.51e-43 140
MS.gene29155.t1 MTR_2g012700 36.364 110 69 1 40 148 10 119 4.07e-28 100
MS.gene29155.t1 MTR_2g062330 38.793 116 66 3 34 148 27 138 1.50e-26 97.8
MS.gene29155.t1 MTR_5g071400 67.925 53 15 2 3 55 9 59 1.91e-17 72.8
MS.gene29155.t1 MTR_0010s0310 35.556 90 55 1 53 139 151 240 1.34e-15 71.6
MS.gene29155.t1 MTR_6g477950 36.275 102 61 3 48 148 46 144 5.47e-14 67.8
MS.gene29155.t1 MTR_5g078270 33.708 89 56 1 54 139 210 298 2.07e-13 66.2
MS.gene29155.t1 MTR_7g117585 36.905 84 50 2 68 149 64 146 4.03e-12 60.5
MS.gene29155.t1 MTR_3g008190 29.167 96 67 1 54 148 6 101 7.29e-12 58.5
MS.gene29155.t1 MTR_6g087720 34.940 83 53 1 55 136 216 298 9.57e-12 61.6
MS.gene29155.t1 MTR_5g071400 73.684 38 8 2 18 55 1 36 3.65e-11 55.8
MS.gene29155.t1 MTR_0010s0290 31.373 102 63 3 54 149 223 323 4.61e-11 59.7
MS.gene29155.t1 MTR_0010s0320 32.609 92 55 3 54 139 192 282 7.33e-11 58.9
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 29 sgRNAs with CRISPR-Local

Find 41 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
ATCATCAACTATTCGAATTT+TGG 0.090848 5.3:+21844976 None:intergenic
TACAGGTAATGGGTGAAAAT+TGG 0.209416 5.3:+21845264 None:intergenic
CCATCGACTTCTTCTTCATT+TGG 0.245009 5.3:+21845232 None:intergenic
GTGGATGGTTTGAGTTTGTT+AGG 0.256057 5.3:-21844886 MS.gene29155:CDS
GGCTGTTGGACGGAGTGTTC+TGG 0.356206 5.3:-21845134 MS.gene29155:intron
CGAATAGTTGATGATGAAAC+TGG 0.373610 5.3:-21844968 MS.gene29155:CDS
GAATGTGAAGTTCGTGATAA+AGG 0.381874 5.3:-21844935 MS.gene29155:CDS
AAGTTCGTGATAAAGGAAAT+TGG 0.388847 5.3:-21844928 MS.gene29155:CDS
ACAGGTAATGGGTGAAAATT+GGG 0.407202 5.3:+21845265 None:intergenic
ATTAGTTCTGCTACGGCTGT+TGG 0.467637 5.3:-21845148 MS.gene29155:CDS
TGGATGGTTTGAGTTTGTTA+GGG 0.477462 5.3:-21844885 MS.gene29155:CDS
AAATGTCTTCTTCTAGTAGC+AGG 0.479507 5.3:-21845395 MS.gene29155:intron
CTGCAGCCATGTAATTGATC+CGG 0.509939 5.3:-21845305 MS.gene29155:intron
TTTGAAATTGTGCAGATACT+GGG 0.510532 5.3:+21845209 None:intergenic
ATGGAGAAATACGTTGGTAG+TGG 0.538951 5.3:-21844905 MS.gene29155:CDS
CCATGTAATTGATCCGGAGT+TGG 0.545499 5.3:-21845299 MS.gene29155:CDS
GATACAAATAATTTGTGTGG+AGG 0.545934 5.3:+21844815 None:intergenic
GGCATCAATTCGTCCAACTC+CGG 0.549037 5.3:+21845286 None:intergenic
CCAACTCCGGATCAATTACA+TGG 0.550497 5.3:+21845299 None:intergenic
AGAAATACGTTGGTAGTGGA+TGG 0.551017 5.3:-21844901 MS.gene29155:CDS
CTTTGAATTGCAATCTTCCG+AGG 0.557056 5.3:+21845016 None:intergenic
ATTGATACAAATAATTTGTG+TGG 0.558267 5.3:+21844812 None:intergenic
TCGTGATAAAGGAAATTGGA+TGG 0.565929 5.3:-21844924 MS.gene29155:CDS
TGAATGTGTAGCATATTCCT+CGG 0.575111 5.3:-21845033 MS.gene29155:intron
GCATAGTATTAGTTCTGCTA+CGG 0.580120 5.3:-21845155 MS.gene29155:CDS
AGGGCAAAAGAACTCAAAGA+AGG 0.584629 5.3:-21844866 MS.gene29155:CDS
GTTCTGCTACGGCTGTTGGA+CGG 0.598239 5.3:-21845144 MS.gene29155:CDS
AATTGGATGGAGAAATACGT+TGG 0.604235 5.3:-21844911 MS.gene29155:CDS
CCAAATGAAGAAGAAGTCGA+TGG 0.658231 5.3:-21845232 MS.gene29155:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! CAATTTCAAAAATTTCAAAA+CGG - chr5.3:21844999-21845018 MS.gene29155:CDS 15.0%
!!! AGTTTTAATTTTATTTTTGC+TGG - chr5.3:21845086-21845105 MS.gene29155:intron 15.0%
!!! TTTTTGTTTTTTTAATCTTC+TGG - chr5.3:21844844-21844863 MS.gene29155:CDS 15.0%
!!! ATTGATACAAATAATTTGTG+TGG + chr5.3:21845386-21845405 None:intergenic 20.0%
!! ATCATCAACTATTCGAATTT+TGG + chr5.3:21845222-21845241 None:intergenic 25.0%
AAGTTCGTGATAAAGGAAAT+TGG - chr5.3:21845267-21845286 MS.gene29155:CDS 30.0%
! AAAACGGTGATCATACTTTT+TGG - chr5.3:21845015-21845034 MS.gene29155:CDS 30.0%
! GATACAAATAATTTGTGTGG+AGG + chr5.3:21845383-21845402 None:intergenic 30.0%
! TTTGAAATTGTGCAGATACT+GGG + chr5.3:21844989-21845008 None:intergenic 30.0%
!!! TTTTGAAATTGTGCAGATAC+TGG + chr5.3:21844990-21845009 None:intergenic 30.0%
AATTGGATGGAGAAATACGT+TGG - chr5.3:21845284-21845303 MS.gene29155:CDS 35.0%
GAATGTGAAGTTCGTGATAA+AGG - chr5.3:21845260-21845279 MS.gene29155:CDS 35.0%
TCGTGATAAAGGAAATTGGA+TGG - chr5.3:21845271-21845290 MS.gene29155:CDS 35.0%
TGAATGTGTAGCATATTCCT+CGG - chr5.3:21845162-21845181 MS.gene29155:CDS 35.0%
! GATTTTCGTCTACAGGTAAT+GGG + chr5.3:21844944-21844963 None:intergenic 35.0%
! TCATTTGGATTTTCGTCTAC+AGG + chr5.3:21844951-21844970 None:intergenic 35.0%
!! ACAGGTAATGGGTGAAAATT+GGG + chr5.3:21844933-21844952 None:intergenic 35.0%
!! CGAATAGTTGATGATGAAAC+TGG - chr5.3:21845227-21845246 MS.gene29155:CDS 35.0%
!! GCATAGTATTAGTTCTGCTA+CGG - chr5.3:21845040-21845059 MS.gene29155:intron 35.0%
!! TACAGGTAATGGGTGAAAAT+TGG + chr5.3:21844934-21844953 None:intergenic 35.0%
!! TGGATGGTTTGAGTTTGTTA+GGG - chr5.3:21845310-21845329 MS.gene29155:intron 35.0%
AGGGCAAAAGAACTCAAAGA+AGG - chr5.3:21845329-21845348 MS.gene29155:intron 40.0%
CCAAATGAAGAAGAAGTCGA+TGG - chr5.3:21844963-21844982 MS.gene29155:CDS 40.0%
CTTTGAATTGCAATCTTCCG+AGG + chr5.3:21845182-21845201 None:intergenic 40.0%
TTGCTGGATTATTTGCGCAT+GGG - chr5.3:21845102-21845121 MS.gene29155:intron 40.0%
TTTGCTGGATTATTTGCGCA+TGG - chr5.3:21845101-21845120 MS.gene29155:intron 40.0%
! ATGGAGAAATACGTTGGTAG+TGG - chr5.3:21845290-21845309 MS.gene29155:CDS 40.0%
! GGATTTTCGTCTACAGGTAA+TGG + chr5.3:21844945-21844964 None:intergenic 40.0%
! GTGGATGGTTTGAGTTTGTT+AGG - chr5.3:21845309-21845328 MS.gene29155:intron 40.0%
!! AGAAATACGTTGGTAGTGGA+TGG - chr5.3:21845294-21845313 MS.gene29155:CDS 40.0%
!! CCATCGACTTCTTCTTCATT+TGG + chr5.3:21844966-21844985 None:intergenic 40.0%
CCAACTCCGGATCAATTACA+TGG + chr5.3:21844899-21844918 None:intergenic 45.0%
CCATGTAATTGATCCGGAGT+TGG - chr5.3:21844896-21844915 MS.gene29155:CDS 45.0%
CTGCAGCCATGTAATTGATC+CGG - chr5.3:21844890-21844909 MS.gene29155:CDS 45.0%
!! ATTAGTTCTGCTACGGCTGT+TGG - chr5.3:21845047-21845066 MS.gene29155:intron 45.0%
CTGGATTATTTGCGCATGGG+TGG - chr5.3:21845105-21845124 MS.gene29155:intron 50.0%
GATTATTTGCGCATGGGTGG+TGG - chr5.3:21845108-21845127 MS.gene29155:intron 50.0%
GGCATCAATTCGTCCAACTC+CGG + chr5.3:21844912-21844931 None:intergenic 50.0%
GTTCTGCTACGGCTGTTGGA+CGG - chr5.3:21845051-21845070 MS.gene29155:intron 55.0%
! GGCTGTTGGACGGAGTGTTC+TGG - chr5.3:21845061-21845080 MS.gene29155:intron 60.0%
! GCGCATGGGTGGTGGCTTTG+TGG - chr5.3:21845116-21845135 MS.gene29155:intron 65.0%


Chromosome Type Strat End Strand Name
chr5.3 gene 21844802 21845415 21844802 ID=MS.gene29155
chr5.3 mRNA 21844802 21845415 21844802 ID=MS.gene29155.t1;Parent=MS.gene29155
chr5.3 exon 21845396 21845415 21845396 ID=MS.gene29155.t1.exon1;Parent=MS.gene29155.t1
chr5.3 CDS 21845396 21845415 21845396 ID=cds.MS.gene29155.t1;Parent=MS.gene29155.t1
chr5.3 exon 21845135 21845321 21845135 ID=MS.gene29155.t1.exon2;Parent=MS.gene29155.t1
chr5.3 CDS 21845135 21845321 21845135 ID=cds.MS.gene29155.t1;Parent=MS.gene29155.t1
chr5.3 exon 21844802 21845044 21844802 ID=MS.gene29155.t1.exon3;Parent=MS.gene29155.t1
chr5.3 CDS 21844802 21845044 21844802 ID=cds.MS.gene29155.t1;Parent=MS.gene29155.t1
Gene Sequence

>MS.gene29155

ATGTCTTCTTCTAGTAGCAGGTAACTTCAATGTTTGAGTTGTTTTTTGTTTTTTTAATCTTCTGGTTATTTATTAGATTTTGTTGAAACTGCAGCCATGTAATTGATCCGGAGTTGGACGAATTGATGCCCAATTTTCACCCATTACCTGTAGACGAAAATCCAAATGAAGAAGAAGTCGATGGCCCAGTATCTGCACAATTTCAAAAATTTCAAAACGGTGATCATACTTTTTGGATGCATAGTATTAGTTCTGCTACGGCTGTTGGACGGAGTGTTCTGGTTAGTTTTAATTTTATTTTTGCTGGATTATTTGCGCATGGGTGGTGGCTTTGTGGTTGAAAAGTAATATTATTTGTTTTGAATGTGTAGCATATTCCTCGGAAGATTGCAATTCAAAGTATGTATGTGAATCAATCCAAAATTCGAATAGTTGATGATGAAACTGGAGAAGAATATGAATGTGAAGTTCGTGATAAAGGAAATTGGATGGAGAAATACGTTGGTAGTGGATGGTTTGAGTTTGTTAGGGCAAAAGAACTCAAAGAAGGAGATTCGTTGTTCTTCACTATTGATAATCCTCCACACAAATTATTTGTATCAATGATTAGATAG
Protein sequence

>MS.gene29155.t1

MSSSSSSHVIDPELDELMPNFHPLPVDENPNEEEVDGPVSAQFQKFQNGDHTFWMHSISSATAVGRSVLHIPRKIAIQSMYVNQSKIRIVDDETGEEYECEVRDKGNWMEKYVGSGWFEFVRAKELKEGDSLFFTIDNPPHKLFVSMIR