AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene75180

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene75180.t1 MTR_1g109630 97.368 114 3 0 1 114 33 146 2.51e-77 227
MS.gene75180.t1 MTR_8g099060 34.234 111 69 1 2 108 84 194 3.15e-18 77.4
MS.gene75180.t1 MTR_8g028450 33.333 111 70 1 2 108 88 198 2.97e-16 72.4
MS.gene75180.t1 MTR_1g099500 34.211 114 71 1 2 111 77 190 3.49e-16 72.0
MS.gene75180.t1 MTR_3g449880 31.193 109 71 1 4 108 49 157 4.98e-14 65.9
MS.gene75180.t1 MTR_3g449880 31.193 109 71 1 4 108 71 179 7.87e-14 65.5
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene75180.t1 AT1G68230 44.737 114 61 1 2 113 41 154 2.96e-26 96.3
MS.gene75180.t1 AT1G68230 44.737 114 61 1 2 113 41 154 7.32e-26 96.7
MS.gene75180.t1 AT3G18260 40.171 117 66 1 2 114 49 165 7.07e-24 91.7
MS.gene75180.t1 AT4G23630 33.333 114 72 1 2 111 99 212 1.97e-22 89.0
MS.gene75180.t1 AT4G23630 33.333 114 72 1 2 111 99 212 1.97e-22 89.0
MS.gene75180.t1 AT4G11220 33.333 114 72 1 2 111 95 208 3.22e-21 85.9
MS.gene75180.t1 AT2G46170 35.088 114 70 1 2 111 78 191 2.01e-19 80.9
MS.gene75180.t1 AT5G41600 33.333 114 72 1 2 111 78 191 3.37e-17 74.7
MS.gene75180.t1 AT1G64090 32.432 111 71 1 2 108 74 184 7.47e-17 73.9
MS.gene75180.t1 AT1G64090 32.432 111 71 1 2 108 90 200 9.54e-17 73.9
MS.gene75180.t1 AT3G61560 32.456 114 73 1 2 111 78 191 7.99e-16 70.5
MS.gene75180.t1 AT3G61560 32.456 114 73 1 2 111 78 191 1.91e-15 70.1
MS.gene75180.t1 AT3G61560 32.456 114 73 1 2 111 78 191 1.91e-15 70.1
MS.gene75180.t1 AT2G46170 31.683 101 65 1 2 98 78 178 2.06e-12 60.8

Find 20 sgRNAs with CRISPR-Local

Find 46 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TTATGCTCATTCTCTTTATT+TGG 0.147832 1.3:-74699309 MS.gene75180:CDS
CTTACTGGTATATAGTAAAT+TGG 0.297591 1.3:+74698641 None:intergenic
CTATGGATCATGTCTACTAT+TGG 0.332384 1.3:-74698682 MS.gene75180:CDS
ATGAATCTAACGGTAGAATC+TGG 0.349110 1.3:+74699121 None:intergenic
TTCAGACAATAGCTGGTCTA+TGG 0.360102 1.3:-74698699 MS.gene75180:intron
ATTTCAAAATCATAGATATC+AGG 0.404128 1.3:+74699145 None:intergenic
TTTATTTGGTATAATGCAGC+TGG 0.406398 1.3:-74699295 MS.gene75180:CDS
AAATAAAGAGAATGAGCATA+AGG 0.427457 1.3:+74699311 None:intergenic
ATTGAATTTCAGACAATAGC+TGG 0.451267 1.3:-74698706 MS.gene75180:intron
AATAAAGAGAATGAGCATAA+GGG 0.486688 1.3:+74699312 None:intergenic
GAAAACAACGGCAGCAATTG+TGG 0.515778 1.3:-74699413 MS.gene75180:CDS
ATGCAGCTGGATTAATCACT+TGG 0.517496 1.3:-74699282 MS.gene75180:intron
AAAAGTTCAACTTGTTCTTG+AGG 0.520276 1.3:-74699093 MS.gene75180:CDS
TGAATCTAACGGTAGAATCT+GGG 0.523175 1.3:+74699122 None:intergenic
AGATCTTAGATTCTTCTTTG+TGG 0.523221 1.3:-74699044 MS.gene75180:intron
ACAACGGCAGCAATTGTGGC+TGG 0.528525 1.3:-74699409 MS.gene75180:CDS
GAATGAGCATAAGGGCTATG+AGG 0.566119 1.3:+74699320 None:intergenic
GCATAAGGGCTATGAGGATG+TGG 0.569062 1.3:+74699326 None:intergenic
GGTTTGGTTTCTCTTTGAAG+TGG 0.581573 1.3:-74699377 MS.gene75180:CDS
ATGGAAAGACATGAAAACAA+CGG 0.698215 1.3:-74699425 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AAAAATTGATAAAAACTTAT+AGG - chr1.3:74699245-74699264 MS.gene75180:intron 10.0%
!! AATATAGTCAAAAAATTTAT+AGG + chr1.3:74699162-74699181 None:intergenic 10.0%
!!! ACATATTCATAATTTTTATA+AGG + chr1.3:74698820-74698839 None:intergenic 10.0%
!! AAATAAGATAGCATAAATTA+TGG - chr1.3:74699273-74699292 MS.gene75180:intron 15.0%
!! AATAAGATAGCATAAATTAT+GGG - chr1.3:74699274-74699293 MS.gene75180:intron 15.0%
!! ACAAATCAATTCAAATCAAA+AGG + chr1.3:74699318-74699337 None:intergenic 20.0%
!! ATAAGATAGCATAAATTATG+GGG - chr1.3:74699275-74699294 MS.gene75180:intron 20.0%
!! ATAGTCAAAAAATTTATAGG+AGG + chr1.3:74699159-74699178 None:intergenic 20.0%
!! ATTTCAAAATCATAGATATC+AGG + chr1.3:74698919-74698938 None:intergenic 20.0%
!! TAATTCAGAAAGAAAAGAAA+TGG + chr1.3:74699090-74699109 None:intergenic 20.0%
!!! AAATTTTATGACATTTCAAC+TGG - chr1.3:74698991-74699010 MS.gene75180:intron 20.0%
!!! AATTTTATGACATTTCAACT+GGG - chr1.3:74698992-74699011 MS.gene75180:intron 20.0%
!!! CTTTTTATGAATGAATCTAA+CGG + chr1.3:74698953-74698972 None:intergenic 20.0%
!!! GCATCTTTTATAAAAATAGA+GGG - chr1.3:74699188-74699207 MS.gene75180:intron 20.0%
! AAAAATAAGGCTTCTGAATA+GGG + chr1.3:74698848-74698867 None:intergenic 25.0%
! AAATAAAGAGAATGAGCATA+AGG + chr1.3:74698753-74698772 None:intergenic 25.0%
! AAATGTACCTGTGTTTAAAA+AGG - chr1.3:74699214-74699233 MS.gene75180:intron 25.0%
! AATAAAGAGAATGAGCATAA+GGG + chr1.3:74698752-74698771 None:intergenic 25.0%
! CACCAAATGTTACAAAAATA+AGG + chr1.3:74698861-74698880 None:intergenic 25.0%
! GAGGTGATAATAATTGAAAA+TGG + chr1.3:74699057-74699076 None:intergenic 25.0%
! TTATGCTCATTCTCTTTATT+TGG - chr1.3:74698752-74698771 MS.gene75180:intron 25.0%
!! CGCATCTTTTATAAAAATAG+AGG - chr1.3:74699187-74699206 MS.gene75180:intron 25.0%
!!! AGCCTTATTTTTGTAACATT+TGG - chr1.3:74698856-74698875 MS.gene75180:intron 25.0%
AGATCTTAGATTCTTCTTTG+TGG - chr1.3:74699017-74699036 MS.gene75180:intron 30.0%
ATTGAATTTCAGACAATAGC+TGG - chr1.3:74699355-74699374 MS.gene75180:CDS 30.0%
CAAAAATAAGGCTTCTGAAT+AGG + chr1.3:74698849-74698868 None:intergenic 30.0%
TTATTTATGTGTTGCATTGC+AGG - chr1.3:74698887-74698906 MS.gene75180:intron 30.0%
TTTATTTGGTATAATGCAGC+TGG - chr1.3:74698766-74698785 MS.gene75180:intron 30.0%
! AAAAGTTCAACTTGTTCTTG+AGG - chr1.3:74698968-74698987 MS.gene75180:intron 30.0%
AAGAAAAGAAATGGTCTCAG+TGG + chr1.3:74699081-74699100 None:intergenic 35.0%
ATGAATCTAACGGTAGAATC+TGG + chr1.3:74698943-74698962 None:intergenic 35.0%
CTATGGATCATGTCTACTAT+TGG - chr1.3:74699379-74699398 MS.gene75180:CDS 35.0%
GTACCTGTGTTTAAAAAGGT+AGG - chr1.3:74699218-74699237 MS.gene75180:intron 35.0%
TGAATCTAACGGTAGAATCT+GGG + chr1.3:74698942-74698961 None:intergenic 35.0%
! AATTGTGGCTGGATTTTCAA+TGG - chr1.3:74698663-74698682 MS.gene75180:CDS 35.0%
! GTTCCTACCTTTTTAAACAC+AGG + chr1.3:74699224-74699243 None:intergenic 35.0%
ATGCAGCTGGATTAATCACT+TGG - chr1.3:74698779-74698798 MS.gene75180:intron 40.0%
! GGTTTGGTTTCTCTTTGAAG+TGG - chr1.3:74698684-74698703 MS.gene75180:CDS 40.0%
! TGGCTGGATTTTCAATGGTT+TGG - chr1.3:74698668-74698687 MS.gene75180:CDS 40.0%
! TTCAGACAATAGCTGGTCTA+TGG - chr1.3:74699362-74699381 MS.gene75180:CDS 40.0%
!! ATTGCTGCCGTTGTTTTCAT+TGG + chr1.3:74698646-74698665 None:intergenic 40.0%
AAGAAATGGTCTCAGTGGAG+AGG + chr1.3:74699076-74699095 None:intergenic 45.0%
GAAAACAACGGCAGCAATTG+TGG - chr1.3:74698648-74698667 MS.gene75180:CDS 45.0%
GAATGAGCATAAGGGCTATG+AGG + chr1.3:74698744-74698763 None:intergenic 45.0%
GCATAAGGGCTATGAGGATG+TGG + chr1.3:74698738-74698757 None:intergenic 50.0%
ACAACGGCAGCAATTGTGGC+TGG - chr1.3:74698652-74698671 MS.gene75180:CDS 55.0%


Chromosome Type Strat End Strand Name
chr1.3 gene 74698646 74699437 74698646 ID=MS.gene75180
chr1.3 mRNA 74698646 74699437 74698646 ID=MS.gene75180.t1;Parent=MS.gene75180
chr1.3 exon 74699283 74699437 74699283 ID=MS.gene75180.t1.exon1;Parent=MS.gene75180.t1
chr1.3 CDS 74699283 74699437 74699283 ID=cds.MS.gene75180.t1;Parent=MS.gene75180.t1
chr1.3 exon 74699045 74699174 74699045 ID=MS.gene75180.t1.exon2;Parent=MS.gene75180.t1
chr1.3 CDS 74699045 74699174 74699045 ID=cds.MS.gene75180.t1;Parent=MS.gene75180.t1
chr1.3 exon 74698646 74698716 74698646 ID=MS.gene75180.t1.exon3;Parent=MS.gene75180.t1
chr1.3 CDS 74698646 74698716 74698646 ID=cds.MS.gene75180.t1;Parent=MS.gene75180.t1
Gene Sequence

>MS.gene75180

ATGAAAACAACGGCAGCAATTGTGGCTGGATTTTCAATGGTTTGGTTTCTCTTTGAAGTGGTTGAATATAATCTTGTTACTCTGCTATGCCACATCCTCATAGCCCTTATGCTCATTCTCTTTATTTGGTATAATGCAGCTGGATTAATCACTTGGTAATTGTATTTTTAACCTTATAAAAATTATGAATATGTGCAGTCCCTATTCAGAAGCCTTATTTTTGTAACATTTGGTGTAAACATTATTTATGTGTTGCATTGCAGGAAACTTCCTGATATCTATGATTTTGAAATCCCAGATTCTACCGTTAGATTCATTCATAAAAAGTTCAACTTGTTCTTGAGGAAATTTTATGACATTTCAACTGGGAAAGATCTTAGATTCTTCTTTGTGGTATTATGAAATAGACCATTTTCAATTATTATCACCTCTCCACTGAGACCATTTCTTTTCTTTCTGAATTAAATATATTTTTAATCTCTATAAAACTATAAATCTTTCAAGTTGAATCCTCCTATAAATTTTTTGACTATATTTAGTTCGCATCTTTTATAAAAATAGAGGGATTAAATGTACCTGTGTTTAAAAAGGTAGGAACTAAAAATTGATAAAAACTTATAGGTACTAAAATAAGATAGCATAAATTATGGGGACTAAAAAATATTTAAGCCTTTTGATTTGAATTGATTTGTTTATTGACATCAAAGTGATTGAATTTCAGACAATAGCTGGTCTATGGATCATGTCTACTATTGGAAATTTCTTCAGCACTGTCCAATTTACTATATACCA
Protein sequence

>MS.gene75180.t1

MKTTAAIVAGFSMVWFLFEVVEYNLVTLLCHILIALMLILFIWYNAAGLITWKLPDIYDFEIPDSTVRFIHKKFNLFLRKFYDISTGKDLRFFFVTIAGLWIMSTIGNFFSTVQFTIY