AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene027651

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene027651.t1 MTR_5g034030 99.078 217 2 0 1 217 1 217 2.80e-163 449
MS.gene027651.t1 MTR_4g114730 49.686 159 58 4 12 162 14 158 5.66e-45 148
MS.gene027651.t1 MTR_2g087740 51.250 160 62 4 12 162 12 164 2.82e-43 144
MS.gene027651.t1 MTR_4g050300 48.344 151 73 1 12 162 9 154 6.67e-41 137
MS.gene027651.t1 MTR_4g025900 50.000 156 70 2 14 162 25 179 4.13e-40 137
MS.gene027651.t1 MTR_4g101660 51.553 161 64 5 12 162 18 174 1.37e-39 135
MS.gene027651.t1 MTR_5g046230 34.536 194 98 3 12 195 17 191 3.63e-30 111
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene027651.t1 AT1G23420 56.388 227 84 4 2 217 9 231 5.35e-73 221
MS.gene027651.t1 AT1G23420 56.388 227 84 4 2 217 40 262 6.66e-73 222
MS.gene027651.t1 AT2G26580 50.327 153 60 3 12 162 9 147 7.10e-46 150
MS.gene027651.t1 AT2G26580 50.327 153 60 3 12 162 9 147 7.10e-46 150
MS.gene027651.t1 AT2G45190 46.061 165 79 1 8 162 19 183 1.26e-42 144
MS.gene027651.t1 AT1G08465 49.677 155 66 4 12 162 8 154 8.25e-41 137
MS.gene027651.t1 AT4G00180 45.810 179 71 5 8 162 19 195 4.88e-39 135
MS.gene027651.t1 AT4G00180 43.976 166 67 5 21 162 1 164 2.97e-30 111
MS.gene027651.t1 AT1G69180 40.385 156 73 4 12 163 19 158 1.07e-28 106
MS.gene027651.t1 AT2G45190 63.636 66 24 0 97 162 54 119 4.11e-25 97.1

Find 43 sgRNAs with CRISPR-Local

Find 79 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
AATGCAGAGAAGAGATTAAA+AGG 0.220244 5.2:+23978005 MS.gene027651:intron
CATCACCTTTGCACTGAGTT+GGG 0.247070 5.2:-23978268 None:intergenic
GCTTCCTTGTGAGCCATATC+AGG 0.254990 5.2:-23978043 None:intergenic
ACTCATGGTTACCATTAAAA+TGG 0.296363 5.2:-23977269 None:intergenic
CTTTCCAAGATGGAATTTCT+TGG 0.337983 5.2:-23978924 None:intergenic
GATGAGTAAGAGATGCTAAA+AGG 0.346967 5.2:-23977503 None:intergenic
GTCTTGTTTACATCTTCATC+TGG 0.363378 5.2:-23977667 None:intergenic
GGTGTTCTTTGTCTCTTCTC+TGG 0.372695 5.2:-23977875 None:intergenic
TGTACATAGCAAATCTGTTC+TGG 0.376697 5.2:-23977229 None:intergenic
TCATCACCTTTGCACTGAGT+TGG 0.384038 5.2:-23978269 None:intergenic
TATTCATTCATTCACTCAAA+TGG 0.405002 5.2:-23978951 None:intergenic
TTATTGACAACATTGCTGAT+TGG 0.429525 5.2:-23977754 None:intergenic
CAGCTTCATGAGGGTCCACT+TGG 0.437038 5.2:-23978334 None:intergenic
ATCACCTTTGCACTGAGTTG+GGG 0.440172 5.2:-23978267 None:intergenic
GATCCACAAATTGATCTGTC+TGG 0.455209 5.2:-23978304 None:intergenic
ACAAGGATTCCGTGGAAGAA+AGG 0.512794 5.2:+23978899 MS.gene027651:CDS
AGCATCTCTTACTCATCTTG+AGG 0.521370 5.2:+23977509 MS.gene027651:CDS
GGTACCAAGAAATTCCATCT+TGG 0.522438 5.2:+23978920 MS.gene027651:CDS
AGCTTCATGAGGGTCCACTT+GGG 0.522893 5.2:-23978333 None:intergenic
ACAATCAGAATAAGTCATCA+TGG 0.529221 5.2:-23977713 None:intergenic
AAATGGTGTCCTTTCCAAGA+TGG 0.529231 5.2:-23978934 None:intergenic
TAGCCAGACAGATCAATTTG+TGG 0.529249 5.2:+23978301 MS.gene027651:CDS
AGAAGAGATTAAAAGGCTAA+AGG 0.529887 5.2:+23978012 MS.gene027651:CDS
ATATTAATTACTTGATGAAG+CGG 0.533614 5.2:-23977910 None:intergenic
TTCTTGGTACCTTTCTTCCA+CGG 0.541076 5.2:-23978908 None:intergenic
CTTCCTTGTGAGCCATATCA+GGG 0.545406 5.2:-23978042 None:intergenic
GAGATGCTAAAAGGTGGAAA+GGG 0.553103 5.2:-23977494 None:intergenic
AGAGATGCTAAAAGGTGGAA+AGG 0.557063 5.2:-23977495 None:intergenic
GAGTAAGAGATGCTAAAAGG+TGG 0.562368 5.2:-23977500 None:intergenic
ACCATTGTCAAACTGCTGCA+TGG 0.563063 5.2:-23977405 None:intergenic
CAGGTGAATGAAGAAGAACA+AGG 0.564909 5.2:+23978882 MS.gene027651:intron
GAAGAAGAACAAGGATTCCG+TGG 0.572480 5.2:+23978891 MS.gene027651:CDS
AAACCCTGATATGGCTCACA+AGG 0.577441 5.2:+23978039 MS.gene027651:CDS
CAAGAAATTCCATCTTGGAA+AGG 0.597804 5.2:+23978925 MS.gene027651:CDS
TCACCTTTGCACTGAGTTGG+GGG 0.601505 5.2:-23978266 None:intergenic
GATGACTTATTCTGATTGTG+AGG 0.620697 5.2:+23977717 MS.gene027651:CDS
CAGATTTGCTATGTACAATG+TGG 0.632418 5.2:+23977235 MS.gene027651:CDS
AGTGGACCCTCATGAAGCTG+AGG 0.650640 5.2:+23978337 MS.gene027651:CDS
TCCATGCAGCAGTTTGACAA+TGG 0.655787 5.2:+23977404 MS.gene027651:CDS
ATGAAGCGGTTATAAGCTGA+TGG 0.663979 5.2:-23977896 None:intergenic
TGTGGATCTTGACTCCCAAG+TGG 0.667148 5.2:+23978319 MS.gene027651:CDS
ATGCAGCAGTTTGACAATGG+TGG 0.669140 5.2:+23977407 MS.gene027651:CDS
ATGGTGGTGACAGTAAGATG+TGG 0.764759 5.2:+23977423 MS.gene027651:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! TTTTTTTTTATATTTTCAGT+GGG + chr5.2:23978235-23978254 MS.gene027651:intron 10.0%
!!! TTTTTTTTTTATATTTTCAG+TGG + chr5.2:23978234-23978253 MS.gene027651:intron 10.0%
!! AAAGAAAATAAACAAAGTAT+TGG - chr5.2:23977557-23977576 None:intergenic 15.0%
!!! CAAAGCATAATATTTTTAAA+AGG - chr5.2:23978707-23978726 None:intergenic 15.0%
!!! TTGTTTATTTTCTTTTAGTT+AGG + chr5.2:23977562-23977581 MS.gene027651:intron 15.0%
!! ATATTAATTACTTGATGAAG+CGG - chr5.2:23977913-23977932 None:intergenic 20.0%
!!! TATTAAAACTTGCTATAAGT+AGG + chr5.2:23978458-23978477 MS.gene027651:intron 20.0%
! CAATCTTATAAAATTTCCCA+TGG - chr5.2:23978176-23978195 None:intergenic 25.0%
! CTTCTTAACTTCATCATATT+TGG + chr5.2:23977304-23977323 MS.gene027651:intron 25.0%
! TGGTGAATTATTCATAATCT+TGG + chr5.2:23978194-23978213 MS.gene027651:intron 25.0%
! TTAACTCATTTGAAAACCAT+GGG + chr5.2:23978157-23978176 MS.gene027651:intron 25.0%
! TTTAACTCATTTGAAAACCA+TGG + chr5.2:23978156-23978175 MS.gene027651:intron 25.0%
!! ATTCTGCAATACCATTTTAA+TGG + chr5.2:23977258-23977277 MS.gene027651:CDS 25.0%
!! CATGGGAAATTTTATAAGAT+TGG + chr5.2:23978174-23978193 MS.gene027651:intron 25.0%
AAGAGCAATTAGAAAACTCA+TGG - chr5.2:23977287-23977306 None:intergenic 30.0%
AATGCAGAGAAGAGATTAAA+AGG + chr5.2:23978005-23978024 MS.gene027651:intron 30.0%
ACAATCAGAATAAGTCATCA+TGG - chr5.2:23977716-23977735 None:intergenic 30.0%
ACTCATGGTTACCATTAAAA+TGG - chr5.2:23977272-23977291 None:intergenic 30.0%
ACTTTATATCCTCATCTTGT+TGG + chr5.2:23978586-23978605 MS.gene027651:intron 30.0%
AGAAGAGATTAAAAGGCTAA+AGG + chr5.2:23978012-23978031 MS.gene027651:CDS 30.0%
AGTAGGAGATTCTTTAGATT+TGG + chr5.2:23978475-23978494 MS.gene027651:intron 30.0%
GTCTCTTTCTTTATATCACA+TGG + chr5.2:23978524-23978543 MS.gene027651:intron 30.0%
TAAAAGGCTATGTCAAATGA+CGG - chr5.2:23978691-23978710 None:intergenic 30.0%
TATCACATGGTGAATAGTAA+AGG + chr5.2:23978537-23978556 MS.gene027651:intron 30.0%
TTATTGACAACATTGCTGAT+TGG - chr5.2:23977757-23977776 None:intergenic 30.0%
!!! TAGCTAGTTAGTTTTGAACA+TGG - chr5.2:23978132-23978151 None:intergenic 30.0%
AAAGGCTAAAAACCCTGATA+TGG + chr5.2:23978030-23978049 MS.gene027651:CDS 35.0%
CAAGAAATTCCATCTTGGAA+AGG + chr5.2:23978925-23978944 MS.gene027651:CDS 35.0%
CTTTCCAAGATGGAATTTCT+TGG - chr5.2:23978927-23978946 None:intergenic 35.0%
GATGACTTATTCTGATTGTG+AGG + chr5.2:23977717-23977736 MS.gene027651:CDS 35.0%
GATGAGTAAGAGATGCTAAA+AGG - chr5.2:23977506-23977525 None:intergenic 35.0%
GTACAGCTGCAAAAAATGTA+AGG + chr5.2:23978071-23978090 MS.gene027651:intron 35.0%
TCATTTCAATTGTGTGATGC+AGG + chr5.2:23977374-23977393 MS.gene027651:intron 35.0%
TGTACATAGCAAATCTGTTC+TGG - chr5.2:23977232-23977251 None:intergenic 35.0%
! CAATTGTCAAGTACTGCTAT+AGG - chr5.2:23978840-23978859 None:intergenic 35.0%
! TTTTTACCTCAGCTTCATGA+GGG - chr5.2:23978346-23978365 None:intergenic 35.0%
!! CAGATTTGCTATGTACAATG+TGG + chr5.2:23977235-23977254 MS.gene027651:CDS 35.0%
!! GTCTTGTTTACATCTTCATC+TGG - chr5.2:23977670-23977689 None:intergenic 35.0%
!! GTTCTGGAAGATCAAAAAGA+TGG - chr5.2:23977216-23977235 None:intergenic 35.0%
AAATGGTGTCCTTTCCAAGA+TGG - chr5.2:23978937-23978956 None:intergenic 40.0%
AGAGATGCTAAAAGGTGGAA+AGG - chr5.2:23977498-23977517 None:intergenic 40.0%
AGCATCTCTTACTCATCTTG+AGG + chr5.2:23977509-23977528 MS.gene027651:CDS 40.0%
AGTCTTTGCCATTGAATGCA+TGG - chr5.2:23978569-23978588 None:intergenic 40.0%
ATGAAGCGGTTATAAGCTGA+TGG - chr5.2:23977899-23977918 None:intergenic 40.0%
ATGACATTGATCCACCAAAC+TGG + chr5.2:23978621-23978640 MS.gene027651:intron 40.0%
CAGGTGAATGAAGAAGAACA+AGG + chr5.2:23978882-23978901 MS.gene027651:intron 40.0%
GAGATGCTAAAAGGTGGAAA+GGG - chr5.2:23977497-23977516 None:intergenic 40.0%
GAGTAAGAGATGCTAAAAGG+TGG - chr5.2:23977503-23977522 None:intergenic 40.0%
GATCCACAAATTGATCTGTC+TGG - chr5.2:23978307-23978326 None:intergenic 40.0%
GATTGGAAACCAACAAGATG+AGG - chr5.2:23978598-23978617 None:intergenic 40.0%
GGTACCAAGAAATTCCATCT+TGG + chr5.2:23978920-23978939 MS.gene027651:CDS 40.0%
GGTATAGTCCATGCATTCAA+TGG + chr5.2:23978558-23978577 MS.gene027651:intron 40.0%
TAGCCAGACAGATCAATTTG+TGG + chr5.2:23978301-23978320 MS.gene027651:CDS 40.0%
TCTGCAAGAACTTTCCAGTT+TGG - chr5.2:23978638-23978657 None:intergenic 40.0%
TGGATCAATGTCATGCTGAT+TGG - chr5.2:23978615-23978634 None:intergenic 40.0%
TTCTTGGTACCTTTCTTCCA+CGG - chr5.2:23978911-23978930 None:intergenic 40.0%
! GTTTTTACCTCAGCTTCATG+AGG - chr5.2:23978347-23978366 None:intergenic 40.0%
!! GAACTGCATCATCACTTTTC+AGG + chr5.2:23978863-23978882 MS.gene027651:intron 40.0%
AAACCCTGATATGGCTCACA+AGG + chr5.2:23978039-23978058 MS.gene027651:CDS 45.0%
ACAAGGATTCCGTGGAAGAA+AGG + chr5.2:23978899-23978918 MS.gene027651:CDS 45.0%
ACCATTGTCAAACTGCTGCA+TGG - chr5.2:23977408-23977427 None:intergenic 45.0%
ATCACCTTTGCACTGAGTTG+GGG - chr5.2:23978270-23978289 None:intergenic 45.0%
ATGCAGCAGTTTGACAATGG+TGG + chr5.2:23977407-23977426 MS.gene027651:CDS 45.0%
CATCACCTTTGCACTGAGTT+GGG - chr5.2:23978271-23978290 None:intergenic 45.0%
CTTCCTTGTGAGCCATATCA+GGG - chr5.2:23978045-23978064 None:intergenic 45.0%
GAAGAAGAACAAGGATTCCG+TGG + chr5.2:23978891-23978910 MS.gene027651:CDS 45.0%
GCAAGAACTTTCCAGTTTGG+TGG - chr5.2:23978635-23978654 None:intergenic 45.0%
GGCACTGTGTGCATTTATAG+TGG + chr5.2:23978496-23978515 MS.gene027651:intron 45.0%
GGTGTTCTTTGTCTCTTCTC+TGG - chr5.2:23977878-23977897 None:intergenic 45.0%
TCATCACCTTTGCACTGAGT+TGG - chr5.2:23978272-23978291 None:intergenic 45.0%
TCCATGCAGCAGTTTGACAA+TGG + chr5.2:23977404-23977423 MS.gene027651:CDS 45.0%
! ATGGTGGTGACAGTAAGATG+TGG + chr5.2:23977423-23977442 MS.gene027651:CDS 45.0%
AGCTTCATGAGGGTCCACTT+GGG - chr5.2:23978336-23978355 None:intergenic 50.0%
GCTTCCTTGTGAGCCATATC+AGG - chr5.2:23978046-23978065 None:intergenic 50.0%
TGTGGATCTTGACTCCCAAG+TGG + chr5.2:23978319-23978338 MS.gene027651:CDS 50.0%
! TCACCTTTGCACTGAGTTGG+GGG - chr5.2:23978269-23978288 None:intergenic 50.0%
AGTGGACCCTCATGAAGCTG+AGG + chr5.2:23978337-23978356 MS.gene027651:CDS 55.0%
CAGCTTCATGAGGGTCCACT+TGG - chr5.2:23978337-23978356 None:intergenic 55.0%
TGTCCCCCAACTCAGTGCAA+AGG + chr5.2:23978263-23978282 MS.gene027651:CDS 55.0%


Chromosome Type Strat End Strand Name
chr5.2 gene 23977199 23978962 23977199 ID=MS.gene027651
chr5.2 mRNA 23977199 23978962 23977199 ID=MS.gene027651.t1;Parent=MS.gene027651
chr5.2 exon 23977199 23977279 23977199 ID=MS.gene027651.t1.exon1;Parent=MS.gene027651.t1
chr5.2 CDS 23977199 23977279 23977199 ID=cds.MS.gene027651.t1;Parent=MS.gene027651.t1
chr5.2 exon 23977396 23977530 23977396 ID=MS.gene027651.t1.exon2;Parent=MS.gene027651.t1
chr5.2 CDS 23977396 23977530 23977396 ID=cds.MS.gene027651.t1;Parent=MS.gene027651.t1
chr5.2 exon 23977649 23977778 23977649 ID=MS.gene027651.t1.exon3;Parent=MS.gene027651.t1
chr5.2 CDS 23977649 23977778 23977649 ID=cds.MS.gene027651.t1;Parent=MS.gene027651.t1
chr5.2 exon 23977873 23977921 23977873 ID=MS.gene027651.t1.exon4;Parent=MS.gene027651.t1
chr5.2 CDS 23977873 23977921 23977873 ID=cds.MS.gene027651.t1;Parent=MS.gene027651.t1
chr5.2 exon 23978012 23978087 23978012 ID=MS.gene027651.t1.exon5;Parent=MS.gene027651.t1
chr5.2 CDS 23978012 23978087 23978012 ID=cds.MS.gene027651.t1;Parent=MS.gene027651.t1
chr5.2 exon 23978254 23978358 23978254 ID=MS.gene027651.t1.exon6;Parent=MS.gene027651.t1
chr5.2 CDS 23978254 23978358 23978254 ID=cds.MS.gene027651.t1;Parent=MS.gene027651.t1
chr5.2 exon 23978885 23978962 23978885 ID=MS.gene027651.t1.exon7;Parent=MS.gene027651.t1
chr5.2 CDS 23978885 23978962 23978885 ID=cds.MS.gene027651.t1;Parent=MS.gene027651.t1
Gene Sequence

>MS.gene027651

ATGTCAACACTAAACCATCTTTTTGATCTTCCAGAACAGATTTGCTATGTACAATGTGGATTCTGCAATACCATTTTAATGGTAACCATGAGTTTTCTAATTGCTCTTCTTAACTTCATCATATTTGGTTTTAATATCAATTTTTGTTTTCATTTTCAACTTTTTTTCACTGTTTTCATTTCAATTGTGTGATGCAGGTAAGTGTTCCATGCAGCAGTTTGACAATGGTGGTGACAGTAAGATGTGGTCACTGCACAAGTCTCTTATCTGTTAACATGATGAAAGCTTCTTTTGTCCCTTTCCACCTTTTAGCATCTCTTACTCATCTTGAGGTCATAAAGTTAAAGTCACATTTCCAATACTTTGTTTATTTTCTTTTAGTTAGGTATTTGTATTATATATACTTGATACTAACTTATAAAACTATTTGTGAATGTTTTCACTATGCAGCAAAAAGAAAGTAGTAGTCCAGATGAAGATGTAAACAAGACTTTGAACAGTAATACTAGTGCATCCATGATGACTTATTCTGATTGTGAGGAAGATGATGTAATTCCAATCAGCAATGTTGTCAATAAACGTATGTAGTAGATAAATTATTGAGTTTGAAGCAAGTATAGTGTATACAATAATTTTATTTATTTATTTGATGAATGAATCATTGTTCTATGCAGCACCAGAGAAGAGACAAAGAACACCATCAGCTTATAACCGCTTCATCAAGTAATTAATATGTCACATTAACAAAATTTACACTTATTATAAACTTGTAAATTTTTTAATTCTAATATTATGAGTATAATTTTAATGCAGAGAAGAGATTAAAAGGCTAAAGGCTAAAAACCCTGATATGGCTCACAAGGAAGCTTTTAGTACAGCTGCAAAAAATGTAAGGTCTAATTTTCAAAATCACATGATTATATTGCAGAACCATGTTCAAAACTAACTAGCTATTAGTTTAACTCATTTGAAAACCATGGGAAATTTTATAAGATTGGTGAATTATTCATAATCTTGGATTTTTTATTATTATTATTTTTTTTTTATATTTTCAGTGGGCTAATTGTCCCCCAACTCAGTGCAAAGGTGATGAAGAGAGCTGTAGCCAGACAGATCAATTTGTGGATCTTGACTCCCAAGTGGACCCTCATGAAGCTGAGGTAAAAACATAATTATTTGAAGATTAATTAACTAAATTGTTTCTTTGTTTATTTAATAACTGTTTTTCTTATAATTCAAATTTAAAAATTATTTTAGCTTATTAAAACTTGCTATAAGTAGGAGATTCTTTAGATTTGGCACTGTGTGCATTTATAGTGGTACTTGTCTCTTTCTTTATATCACATGGTGAATAGTAAAGGTATAGTCCATGCATTCAATGGCAAAGACTTTATATCCTCATCTTGTTGGTTTCCAATCAGCATGACATTGATCCACCAAACTGGAAAGTTCTTGCAGATTCTCAATACATTATATTATATATTATTGACCGTCATTTGACATAGCCTTTTAAAAATATTATGCTTTGAGTTTAACACATAAATAATATAGTAAATAAATAAATACAACATGATAATACTAATATAAAATGACACAAAATAATCTTGTTATGTTATGTCTAGTTAGTCACTTTCATGACCTATAGCAGTACTTGACAATTGCAAGAACTGCATCATCACTTTTCAGGTGAATGAAGAAGAACAAGGATTCCGTGGAAGAAAGGTACCAAGAAATTCCATCTTGGAAAGGACACCATTTGAGTGA
Protein sequence

>MS.gene027651.t1

MSTLNHLFDLPEQICYVQCGFCNTILMVSVPCSSLTMVVTVRCGHCTSLLSVNMMKASFVPFHLLASLTHLEQKESSSPDEDVNKTLNSNTSASMMTYSDCEEDDVIPISNVVNKPPEKRQRTPSAYNRFIKEEIKRLKAKNPDMAHKEAFSTAAKNWANCPPTQCKGDEESCSQTDQFVDLDSQVDPHEAEVNEEEQGFRGRKVPRNSILERTPFE