AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene78727


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene78727.t1 MTR_5g053250 97.761 134 3 0 2 135 4 137 2.20e-90 263
MS.gene78727.t1 MTR_5g053250 81.366 161 3 1 2 135 4 164 4.12e-84 248
MS.gene78727.t1 MTR_5g053250 98.701 77 1 0 59 135 1 77 1.39e-49 157
MS.gene78727.t1 MTR_6g017105 39.130 138 79 3 1 137 1 134 7.15e-24 93.2
MS.gene78727.t1 MTR_1g100643 39.456 147 81 5 1 146 1 140 2.82e-22 89.0
MS.gene78727.t1 MTR_1g033360 38.760 129 70 4 20 146 21 142 1.26e-20 84.3
MS.gene78727.t1 MTR_1g100643 42.697 89 48 2 59 146 1 87 1.58e-14 67.4
MS.gene78727.t1 MTR_1g033390 30.894 123 80 4 14 135 9 127 1.82e-11 59.7
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene78727.t1 AT1G26100 62.222 135 40 1 1 135 1 124 6.61e-50 160
MS.gene78727.t1 AT5G38630 44.186 129 63 5 10 135 10 132 1.45e-25 97.4
MS.gene78727.t1 AT4G25570 39.568 139 77 4 9 146 8 140 1.30e-23 92.8
MS.gene78727.t1 AT4G25570 39.568 139 77 4 9 146 49 181 2.31e-23 92.8

Find 45 sgRNAs with CRISPR-Local

Find 60 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GCTTTAGCTTCTGGGATATT+TGG 0.112597 5.3:+42906169 MS.gene78727:CDS
TAGCATTTCTTGTTCTCTTC+TGG 0.118815 5.3:+42905729 MS.gene78727:CDS
CAAGGGGTGGCTTTAGCTTC+TGG 0.175443 5.3:+42906160 MS.gene78727:CDS
GAATGTTTGTGCAGCAATTT+TGG 0.224729 5.3:+42906081 MS.gene78727:intron
CTTTAGCTTCTGGGATATTT+GGG 0.267158 5.3:+42906170 MS.gene78727:CDS
CTTCTGGGATATTTGGGATT+TGG 0.279862 5.3:+42906176 MS.gene78727:CDS
TCCTGTTGAGGAAGAGAATT+AGG 0.298620 5.3:-42905785 None:intergenic
ATTTCTACAGCCTTCATTCA+TGG 0.299138 5.3:+42906233 MS.gene78727:CDS
CTCTTTCTTGCGAGAGTTTG+TGG 0.301862 5.3:+42905698 MS.gene78727:CDS
AAGGGGTGGCTTTAGCTTCT+GGG 0.303519 5.3:+42906161 MS.gene78727:CDS
AGCATTTCTTGTTCTCTTCT+GGG 0.319777 5.3:+42905730 MS.gene78727:CDS
TACTACCTTCTCCACTTAAA+AGG 0.321243 5.3:-42905948 None:intergenic
CCACAATCCCATCATTTACT+TGG 0.326307 5.3:-42906207 None:intergenic
CATCCTGTGCTCATGGTCAT+TGG 0.339718 5.3:+42905919 MS.gene78727:CDS
TCTTGTTCTCTTCTGGGCTC+TGG 0.357755 5.3:+42905736 MS.gene78727:CDS
TGTATCCCTCTTTGAAGCTC+AGG 0.397102 5.3:+42906270 MS.gene78727:CDS
TCCTAATTCTCTTCCTCAAC+AGG 0.404001 5.3:+42905784 MS.gene78727:CDS
TAGATGGTTGCCTGGGTCAA+GGG 0.416984 5.3:+42906108 MS.gene78727:CDS
ACAAAATTCCAAGTAAATGA+TGG 0.437217 5.3:+42906199 MS.gene78727:CDS
TACAGCCTTCATTCATGGAT+GGG 0.445813 5.3:+42906238 MS.gene78727:CDS
ATAGATGGTTGCCTGGGTCA+AGG 0.449560 5.3:+42906107 MS.gene78727:CDS
GAAGAGAATTAGGAGTATTG+AGG 0.459271 5.3:-42905775 None:intergenic
TCGGTGCATTTATGTCTTCA+AGG 0.466772 5.3:+42906142 MS.gene78727:CDS
TTGGTGCATAGATGGTTGCC+TGG 0.471390 5.3:+42906100 MS.gene78727:CDS
GGTTCTCCATCCTGTGCTCA+TGG 0.477323 5.3:+42905912 MS.gene78727:intron
CTACAGCCTTCATTCATGGA+TGG 0.480089 5.3:+42906237 MS.gene78727:CDS
AGATGGTTGCCTGGGTCAAG+GGG 0.483244 5.3:+42906109 MS.gene78727:CDS
AAGAGCAAAGGGAGTAGTGA+GGG 0.491250 5.3:-42905680 None:intergenic
CTCTCGCAAGAAAGAGCAAA+GGG 0.500913 5.3:-42905691 None:intergenic
CGGTGCATTTATGTCTTCAA+GGG 0.507370 5.3:+42906143 MS.gene78727:CDS
CAAAATTCCAAGTAAATGAT+GGG 0.535853 5.3:+42906200 MS.gene78727:CDS
CCAAGTAAATGATGGGATTG+TGG 0.538655 5.3:+42906207 MS.gene78727:CDS
TCAAACCCATCCATGAATGA+AGG 0.539092 5.3:-42906243 None:intergenic
GCATTTATGTCTTCAAGGGG+TGG 0.549961 5.3:+42906147 MS.gene78727:CDS
TGGTGCATAGATGGTTGCCT+GGG 0.586545 5.3:+42906101 MS.gene78727:CDS
AATCCAATGACCATGAGCAC+AGG 0.602677 5.3:-42905922 None:intergenic
TACTCACCTGAGCTTCAAAG+AGG 0.613059 5.3:-42906276 None:intergenic
CAATGACCATGAGCACAGGA+TGG 0.614301 5.3:-42905918 None:intergenic
GATGGTTGCCTGGGTCAAGG+GGG 0.624454 5.3:+42906110 MS.gene78727:CDS
ACTCTCGCAAGAAAGAGCAA+AGG 0.634673 5.3:-42905692 None:intergenic
ACTCACCTGAGCTTCAAAGA+GGG 0.638153 5.3:-42906275 None:intergenic
GGTGCATTTATGTCTTCAAG+GGG 0.646132 5.3:+42906144 MS.gene78727:CDS
AAAGAGCAAAGGGAGTAGTG+AGG 0.647530 5.3:-42905681 None:intergenic
GCATAGATGAGATCCTGTTG+AGG 0.669004 5.3:-42905797 None:intergenic
GAGTAGTGAGGGAAAGACAG+TGG 0.669481 5.3:-42905669 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! TTGATGTAATTAAATAAAAA+GGG - chr5.3:42905853-42905872 None:intergenic 10.0%
!! TTTGATGTAATTAAATAAAA+AGG - chr5.3:42905854-42905873 None:intergenic 10.0%
!!! TTTAATTTTAATTTAATTGC+AGG + chr5.3:42905891-42905910 MS.gene78727:intron 10.0%
!! AAATATTATGTATTGGGATT+AGG + chr5.3:42905991-42906010 MS.gene78727:intron 20.0%
!! AACCCAAAAATATTATGTAT+TGG + chr5.3:42905984-42906003 MS.gene78727:intron 20.0%
!! ACCCAAAAATATTATGTATT+GGG + chr5.3:42905985-42906004 MS.gene78727:intron 20.0%
!! TAATGAAATCAAGTCATTAT+TGG + chr5.3:42906024-42906043 MS.gene78727:intron 20.0%
!!! ATCCCAATACATAATATTTT+TGG - chr5.3:42905990-42906009 None:intergenic 20.0%
!!! TCCCAATACATAATATTTTT+GGG - chr5.3:42905989-42906008 None:intergenic 20.0%
! ACAAAATTCCAAGTAAATGA+TGG + chr5.3:42906199-42906218 MS.gene78727:CDS 25.0%
! CAAAATTCCAAGTAAATGAT+GGG + chr5.3:42906200-42906219 MS.gene78727:CDS 25.0%
!! ATTGGATTTATCCTTTTAAG+TGG + chr5.3:42905937-42905956 MS.gene78727:CDS 25.0%
AAAGGGAATGAAGAAAATAG+AGG - chr5.3:42905836-42905855 None:intergenic 30.0%
!! TTTATCCTTTTAAGTGGAGA+AGG + chr5.3:42905943-42905962 MS.gene78727:CDS 30.0%
AGCATTTCTTGTTCTCTTCT+GGG + chr5.3:42905730-42905749 MS.gene78727:CDS 35.0%
ATTTCTACAGCCTTCATTCA+TGG + chr5.3:42906233-42906252 MS.gene78727:CDS 35.0%
TACTACCTTCTCCACTTAAA+AGG - chr5.3:42905951-42905970 None:intergenic 35.0%
TAGCATTTCTTGTTCTCTTC+TGG + chr5.3:42905729-42905748 MS.gene78727:CDS 35.0%
! GAATGTTTGTGCAGCAATTT+TGG + chr5.3:42906081-42906100 MS.gene78727:intron 35.0%
!! CTTTAGCTTCTGGGATATTT+GGG + chr5.3:42906170-42906189 MS.gene78727:CDS 35.0%
!! GAAGAGAATTAGGAGTATTG+AGG - chr5.3:42905778-42905797 None:intergenic 35.0%
CCACAATCCCATCATTTACT+TGG - chr5.3:42906210-42906229 None:intergenic 40.0%
CGGTGCATTTATGTCTTCAA+GGG + chr5.3:42906143-42906162 MS.gene78727:CDS 40.0%
GGTGCATTTATGTCTTCAAG+GGG + chr5.3:42906144-42906163 MS.gene78727:CDS 40.0%
TACAGCCTTCATTCATGGAT+GGG + chr5.3:42906238-42906257 MS.gene78727:CDS 40.0%
TCAAACCCATCCATGAATGA+AGG - chr5.3:42906246-42906265 None:intergenic 40.0%
TCCTAATTCTCTTCCTCAAC+AGG + chr5.3:42905784-42905803 MS.gene78727:CDS 40.0%
TCCTGTTGAGGAAGAGAATT+AGG - chr5.3:42905788-42905807 None:intergenic 40.0%
TCGGTGCATTTATGTCTTCA+AGG + chr5.3:42906142-42906161 MS.gene78727:CDS 40.0%
! CCAAGTAAATGATGGGATTG+TGG + chr5.3:42906207-42906226 MS.gene78727:CDS 40.0%
!! CAGCAATTTTGGTGCATAGA+TGG + chr5.3:42906092-42906111 MS.gene78727:intron 40.0%
!! CTTCTGGGATATTTGGGATT+TGG + chr5.3:42906176-42906195 MS.gene78727:CDS 40.0%
!! GCTTTAGCTTCTGGGATATT+TGG + chr5.3:42906169-42906188 MS.gene78727:CDS 40.0%
AAAGAGCAAAGGGAGTAGTG+AGG - chr5.3:42905684-42905703 None:intergenic 45.0%
AAGAGCAAAGGGAGTAGTGA+GGG - chr5.3:42905683-42905702 None:intergenic 45.0%
AATCCAATGACCATGAGCAC+AGG - chr5.3:42905925-42905944 None:intergenic 45.0%
ACTCACCTGAGCTTCAAAGA+GGG - chr5.3:42906278-42906297 None:intergenic 45.0%
ACTCTCGCAAGAAAGAGCAA+AGG - chr5.3:42905695-42905714 None:intergenic 45.0%
CTACAGCCTTCATTCATGGA+TGG + chr5.3:42906237-42906256 MS.gene78727:CDS 45.0%
CTCTCGCAAGAAAGAGCAAA+GGG - chr5.3:42905694-42905713 None:intergenic 45.0%
CTCTTTCTTGCGAGAGTTTG+TGG + chr5.3:42905698-42905717 MS.gene78727:CDS 45.0%
GCATAGATGAGATCCTGTTG+AGG - chr5.3:42905800-42905819 None:intergenic 45.0%
GCATTTATGTCTTCAAGGGG+TGG + chr5.3:42906147-42906166 MS.gene78727:CDS 45.0%
GTCAAGGGGGTTGAAGAAAT+CGG + chr5.3:42906123-42906142 MS.gene78727:CDS 45.0%
TACTCACCTGAGCTTCAAAG+AGG - chr5.3:42906279-42906298 None:intergenic 45.0%
!! TGTATCCCTCTTTGAAGCTC+AGG + chr5.3:42906270-42906289 MS.gene78727:CDS 45.0%
ATAGATGGTTGCCTGGGTCA+AGG + chr5.3:42906107-42906126 MS.gene78727:CDS 50.0%
CAATGACCATGAGCACAGGA+TGG - chr5.3:42905921-42905940 None:intergenic 50.0%
CATCCTGTGCTCATGGTCAT+TGG + chr5.3:42905919-42905938 MS.gene78727:CDS 50.0%
GAGTAGTGAGGGAAAGACAG+TGG - chr5.3:42905672-42905691 None:intergenic 50.0%
TAGATGGTTGCCTGGGTCAA+GGG + chr5.3:42906108-42906127 MS.gene78727:CDS 50.0%
TCTTGTTCTCTTCTGGGCTC+TGG + chr5.3:42905736-42905755 MS.gene78727:CDS 50.0%
TGGTGCATAGATGGTTGCCT+GGG + chr5.3:42906101-42906120 MS.gene78727:CDS 50.0%
TTGGTGCATAGATGGTTGCC+TGG + chr5.3:42906100-42906119 MS.gene78727:CDS 50.0%
!! AAGGGGTGGCTTTAGCTTCT+GGG + chr5.3:42906161-42906180 MS.gene78727:CDS 50.0%
AGATGGTTGCCTGGGTCAAG+GGG + chr5.3:42906109-42906128 MS.gene78727:CDS 55.0%
GGTTCTCCATCCTGTGCTCA+TGG + chr5.3:42905912-42905931 MS.gene78727:intron 55.0%
TTCTTCAACCCCCTTGACCC+AGG - chr5.3:42906121-42906140 None:intergenic 55.0%
!! CAAGGGGTGGCTTTAGCTTC+TGG + chr5.3:42906160-42906179 MS.gene78727:CDS 55.0%
GATGGTTGCCTGGGTCAAGG+GGG + chr5.3:42906110-42906129 MS.gene78727:CDS 60.0%


Chromosome Type Strat End Strand Name
chr5.3 gene 42905665 42906342 42905665 ID=MS.gene78727
chr5.3 mRNA 42905665 42906342 42905665 ID=MS.gene78727.t1;Parent=MS.gene78727
chr5.3 exon 42905665 42905820 42905665 ID=MS.gene78727.t1.exon1;Parent=MS.gene78727.t1
chr5.3 CDS 42905665 42905820 42905665 ID=cds.MS.gene78727.t1;Parent=MS.gene78727.t1
chr5.3 exon 42905913 42905964 42905913 ID=MS.gene78727.t1.exon2;Parent=MS.gene78727.t1
chr5.3 CDS 42905913 42905964 42905913 ID=cds.MS.gene78727.t1;Parent=MS.gene78727.t1
chr5.3 exon 42906095 42906342 42906095 ID=MS.gene78727.t1.exon3;Parent=MS.gene78727.t1
chr5.3 CDS 42906095 42906342 42906095 ID=cds.MS.gene78727.t1;Parent=MS.gene78727.t1
Gene Sequence

>MS.gene78727

ATGGCCACTGTCTTTCCCTCACTACTCCCTTTGCTCTTTCTTGCGAGAGTTTGTGGTCTTTCAGTAGCATTTCTTGTTCTCTTCTGGGCTCTGGCTTTCAAATCTAGCTTCCTCAATACTCCTAATTCTCTTCCTCAACAGGATCTCATCTATGCAGTACATACATAACCTCTATTTTCTTCATTCCCTTTTTATTTAATTACATCAAAGAATGCATAAGCTTTATTTTAATTTTAATTTAATTGCAGGTTCTCCATCCTGTGCTCATGGTCATTGGATTTATCCTTTTAAGTGGAGAAGGTAGTACTCTAGTTTTAGCAACCCAAAAATATTATGTATTGGGATTAGGATATTTTACATAATGAAATCAAGTCATTATTGGTCAATTTGTATTTAGTTTAATTGTTTTAATGAATGAATGTTTGTGCAGCAATTTTGGTGCATAGATGGTTGCCTGGGTCAAGGGGGTTGAAGAAATCGGTGCATTTATGTCTTCAAGGGGTGGCTTTAGCTTCTGGGATATTTGGGATTTGGACAAAATTCCAAGTAAATGATGGGATTGTGGCTAATTTCTACAGCCTTCATTCATGGATGGGTTTGATTTGTGTATCCCTCTTTGAAGCTCAGGTGAGTATGCTCTATCATTTCTTTACATTTTTTAAATCAGAGACTTTCTAA

Protein sequence

>MS.gene78727.t1

MATVFPSLLPLLFLARVCGLSVAFLVLFWALAFKSSFLNTPNSLPQQDLIYAVLHPVLMVIGFILLSGEAILVHRWLPGSRGLKKSVHLCLQGVALASGIFGIWTKFQVNDGIVANFYSLHSWMGLICVSLFEAQVSMLYHFFTFFKSETF