AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene002076

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene002076.t1 MTR_2g006900 85.437 103 12 1 63 162 1 103 2.77e-47 149
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene002076.t1 AT3G20750 58.974 39 16 0 101 139 159 197 1.33e-11 60.5

Find 48 sgRNAs with CRISPR-Local

Find 86 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
AATTGCTGCTGTCTCAATTT+TGG 0.174192 2.3:+75491227 MS.gene002076:CDS
CTTCTTCTTCAACTTCCTAA+TGG 0.279260 2.3:+75491869 MS.gene002076:CDS
ACGTCCTCCTCCTCAAAATA+TGG 0.327173 2.3:-75490328 None:intergenic
CGGCCAATGGCATTTCTTGA+TGG 0.368750 2.3:-75491296 None:intergenic
GGTTGGACATTGTTTGCAAT+TGG 0.397971 2.3:-75491189 None:intergenic
CGAGATGTCCCTGCTGCCTC+AGG 0.421876 2.3:+75491811 MS.gene002076:CDS
GCAATTGGAGCAGTAGCAAT+TGG 0.422553 2.3:-75491210 None:intergenic
GGATCTCCTCCCATGATTCC+AGG 0.423283 2.3:-75491847 None:intergenic
TGTCCCACCACCTGGAATCA+TGG 0.424311 2.3:+75491837 MS.gene002076:CDS
AAAATTGAGACAGCAGCAAT+TGG 0.438976 2.3:-75491225 None:intergenic
TCAAGAAATGCCATTGGCCG+TGG 0.443199 2.3:+75491299 MS.gene002076:CDS
AACACTCCTATGTGGCGCTC+TGG 0.449276 2.3:+75491405 MS.gene002076:CDS
TCAGGTTCTGTCCCACCACC+TGG 0.454678 2.3:+75491829 MS.gene002076:CDS
CCTCCCATGATTCCAGGTGG+TGG 0.456756 2.3:-75491841 None:intergenic
CTCGTCCGCGGCGGATGTAA+CGG 0.459014 2.3:-75491329 None:intergenic
TTTCTTGATGGGCACGGACA+TGG 0.477728 2.3:-75491284 None:intergenic
CATTTACTACAAGAAACATA+TGG 0.481434 2.3:+75491783 MS.gene002076:CDS
GGGACAGAACCTGAGGCAGC+AGG 0.482176 2.3:-75491820 None:intergenic
AAATTTACCTTTGGAACCAT+AGG 0.484328 2.3:-75491429 None:intergenic
CGGCGCCGTCCCACGGCCAA+TGG 0.484379 2.3:-75491309 None:intergenic
TATGTGGCGCTCTGGACCTA+TGG 0.489769 2.3:+75491413 MS.gene002076:CDS
GAATTCAGACACTGAAAGTC+AGG 0.494441 2.3:+75490351 MS.gene002076:CDS
GTCCCACCACCTGGAATCAT+GGG 0.504732 2.3:+75491838 MS.gene002076:CDS
CAGAAGGTGGTCGGATCAGA+TGG 0.507419 2.3:-75491357 None:intergenic
TTGGAGCAGTAGCAATTGGT+TGG 0.512553 2.3:-75491206 None:intergenic
CTCCCATGATTCCAGGTGGT+GGG 0.519420 2.3:-75491840 None:intergenic
GATGTAACGGCGCCGTCCCA+CGG 0.521264 2.3:-75491316 None:intergenic
GGCCAATGGCATTTCTTGAT+GGG 0.521674 2.3:-75491295 None:intergenic
CTCTGGACCTATGGTTCCAA+AGG 0.548264 2.3:+75491422 MS.gene002076:CDS
CATTAGGAAGTTGAAGAAGA+AGG 0.548858 2.3:-75491868 None:intergenic
AAATGCCATTGGCCGTGGGA+CGG 0.561985 2.3:+75491304 MS.gene002076:CDS
ATGGCATTTCTTGATGGGCA+CGG 0.572953 2.3:-75491290 None:intergenic
GCAATGAAAATTTGTGCAGA+AGG 0.580559 2.3:-75491373 None:intergenic
TGCCCATCAAGAAATGCCAT+TGG 0.586559 2.3:+75491293 MS.gene002076:CDS
GGACAGAACCTGAGGCAGCA+GGG 0.617193 2.3:-75491819 None:intergenic
AAATTTGTGCAGAAGGTGGT+CGG 0.623430 2.3:-75491366 None:intergenic
CAAGAAATGCCATTGGCCGT+GGG 0.625688 2.3:+75491300 MS.gene002076:CDS
ATGAAAATTTGTGCAGAAGG+TGG 0.644289 2.3:-75491370 None:intergenic
AGACAAGAAACACTCCTATG+TGG 0.647405 2.3:+75491397 MS.gene002076:CDS
ATAGGTCCAGAGCGCCACAT+AGG 0.654562 2.3:-75491411 None:intergenic
CAGACTTTGTGCAATGCGTG+TGG 0.657380 2.3:+75491760 MS.gene002076:intron
AGGTGGTGGGACAGAACCTG+AGG 0.657762 2.3:-75491827 None:intergenic
CAGATGGACGAGCTCGTCCG+CGG 0.664959 2.3:-75491341 None:intergenic
AAAGAATCAGTACAATACAT+CGG 0.676733 2.3:-75491261 None:intergenic
ATGGACGAGCTCGTCCGCGG+CGG 0.680751 2.3:-75491338 None:intergenic
CCACCACCTGGAATCATGGG+AGG 0.682520 2.3:+75491841 MS.gene002076:CDS
TCTCCTCCCATGATTCCAGG+TGG 0.693154 2.3:-75491844 None:intergenic
CGGCGCCGTTACATCCGCCG+CGG 0.715105 2.3:+75491324 MS.gene002076:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AAAAAATTGAAGAAAAATAA+AGG - chr2.3:75490878-75490897 None:intergenic 10.0%
!! TAAGACAAATTAATTTAATT+AGG + chr2.3:75490615-75490634 MS.gene002076:intron 10.0%
!!! GTCTAATATAATTTTTTTTA+AGG - chr2.3:75490568-75490587 None:intergenic 10.0%
!! AAAAATACATCAAATATAAG+TGG - chr2.3:75490721-75490740 None:intergenic 15.0%
!! AGAAAAAAAAACTTACTTTA+GGG - chr2.3:75490411-75490430 None:intergenic 15.0%
!! ATATAAAAAGTAAGGAATTA+AGG + chr2.3:75491526-75491545 MS.gene002076:intron 15.0%
!! GATCTTATATATAAAAAGTA+AGG + chr2.3:75491518-75491537 MS.gene002076:intron 15.0%
!!! TTTTTTAACTAATAATCAGT+TGG - chr2.3:75491461-75491480 None:intergenic 15.0%
!! GAGAAAAAAAAACTTACTTT+AGG - chr2.3:75490412-75490431 None:intergenic 20.0%
! AAAGAATCAGTACAATACAT+CGG - chr2.3:75491264-75491283 None:intergenic 25.0%
! AACATAGAAGACTATTGTTA+TGG - chr2.3:75491731-75491750 None:intergenic 25.0%
! AATGTCTCAAAAATTCAACT+AGG - chr2.3:75491596-75491615 None:intergenic 25.0%
! CATTTACTACAAGAAACATA+TGG + chr2.3:75491783-75491802 MS.gene002076:CDS 25.0%
AAACGTCAGAGACTTAATTA+CGG + chr2.3:75491019-75491038 MS.gene002076:intron 30.0%
AATTAGACGTTTCTTGACTT+TGG + chr2.3:75490933-75490952 MS.gene002076:intron 30.0%
AGTCTAATGCACCAAATAAA+TGG + chr2.3:75490973-75490992 MS.gene002076:intron 30.0%
CAAATTTCCCACCATTTATT+TGG - chr2.3:75490987-75491006 None:intergenic 30.0%
CATGTCGAGAGATAAATTTA+TGG - chr2.3:75490840-75490859 None:intergenic 30.0%
CTAAGAGATGAAAATTGACA+TGG + chr2.3:75490518-75490537 MS.gene002076:intron 30.0%
TAATGCACCAAATAAATGGT+GGG + chr2.3:75490977-75490996 MS.gene002076:intron 30.0%
TTATGTCAAATAGTCTAGTG+TGG + chr2.3:75491482-75491501 MS.gene002076:intron 30.0%
! AATAAATGGTGGGAAATTTG+AGG + chr2.3:75490987-75491006 MS.gene002076:intron 30.0%
! CTTAAACATGCCATATTTTG+AGG + chr2.3:75490318-75490337 MS.gene002076:CDS 30.0%
!! AAATTTACCTTTGGAACCAT+AGG - chr2.3:75491432-75491451 None:intergenic 30.0%
!! TGGTGTTGTAAATTTACCTT+TGG - chr2.3:75491441-75491460 None:intergenic 30.0%
!! TTTATTTGGTGCATTAGACT+TGG - chr2.3:75490973-75490992 None:intergenic 30.0%
!!! ACTCAAAAGTTTTGATTAGC+GGG - chr2.3:75490775-75490794 None:intergenic 30.0%
!!! GACTCAAAAGTTTTGATTAG+CGG - chr2.3:75490776-75490795 None:intergenic 30.0%
!!! GTTAGTTTTGAGTGTATTTG+AGG - chr2.3:75491154-75491173 None:intergenic 30.0%
AAAATTGAGACAGCAGCAAT+TGG - chr2.3:75491228-75491247 None:intergenic 35.0%
ATGAAAATTTGTGCAGAAGG+TGG - chr2.3:75491373-75491392 None:intergenic 35.0%
CAAAACTAACGTTTGTGAAC+AGG + chr2.3:75491164-75491183 MS.gene002076:intron 35.0%
CTAATGCACCAAATAAATGG+TGG + chr2.3:75490976-75490995 MS.gene002076:intron 35.0%
GCAATGAAAATTTGTGCAGA+AGG - chr2.3:75491376-75491395 None:intergenic 35.0%
GTAATTAAGTCTCTGACGTT+TGG - chr2.3:75491020-75491039 None:intergenic 35.0%
TATCTCTCGACATGTGATTT+GGG + chr2.3:75490846-75490865 MS.gene002076:intron 35.0%
TTATCTCTCGACATGTGATT+TGG + chr2.3:75490845-75490864 MS.gene002076:intron 35.0%
! AATTGCTGCTGTCTCAATTT+TGG + chr2.3:75491227-75491246 MS.gene002076:CDS 35.0%
!! AAACATGCCATATTTTGAGG+AGG + chr2.3:75490321-75490340 MS.gene002076:CDS 35.0%
!! GCATGAACATTTTGGTATGT+TGG - chr2.3:75491567-75491586 None:intergenic 35.0%
!!! CTCAAAAGTTTTGATTAGCG+GGG - chr2.3:75490774-75490793 None:intergenic 35.0%
AAATTTGTGCAGAAGGTGGT+CGG - chr2.3:75491369-75491388 None:intergenic 40.0%
AGACAAGAAACACTCCTATG+TGG + chr2.3:75491397-75491416 MS.gene002076:CDS 40.0%
ATCTCTCGACATGTGATTTG+GGG + chr2.3:75490847-75490866 MS.gene002076:intron 40.0%
GAATTCAGACACTGAAAGTC+AGG + chr2.3:75490351-75490370 MS.gene002076:CDS 40.0%
GGTTGGACATTGTTTGCAAT+TGG - chr2.3:75491192-75491211 None:intergenic 40.0%
TTAAGTCTCTGACGTTTGGT+AGG - chr2.3:75491016-75491035 None:intergenic 40.0%
! GGCTAACTGCATGAACATTT+TGG - chr2.3:75491575-75491594 None:intergenic 40.0%
ACGTCCTCCTCCTCAAAATA+TGG - chr2.3:75490331-75490350 None:intergenic 45.0%
GCAATTGGAGCAGTAGCAAT+TGG - chr2.3:75491213-75491232 None:intergenic 45.0%
GGCCAATGGCATTTCTTGAT+GGG - chr2.3:75491298-75491317 None:intergenic 45.0%
TGCCCATCAAGAAATGCCAT+TGG + chr2.3:75491293-75491312 MS.gene002076:CDS 45.0%
TTGGAGCAGTAGCAATTGGT+TGG - chr2.3:75491209-75491228 None:intergenic 45.0%
! ATGGCATTTCTTGATGGGCA+CGG - chr2.3:75491293-75491312 None:intergenic 45.0%
!! CATGCCATATTTTGAGGAGG+AGG + chr2.3:75490324-75490343 MS.gene002076:CDS 45.0%
!! AATTAATTAAAAAAGAAATT+AGG + chr2.3:75491632-75491651 MS.gene002076:intron 5.0%
!!! TTTTTATTGAAATAATAAAA+TGG + chr2.3:75491123-75491142 MS.gene002076:intron 5.0%
CAAGAAATGCCATTGGCCGT+GGG + chr2.3:75491300-75491319 MS.gene002076:CDS 50.0%
CAGACTTTGTGCAATGCGTG+TGG + chr2.3:75491760-75491779 MS.gene002076:intron 50.0%
CGGCCAATGGCATTTCTTGA+TGG - chr2.3:75491299-75491318 None:intergenic 50.0%
CTCTGGACCTATGGTTCCAA+AGG + chr2.3:75491422-75491441 MS.gene002076:CDS 50.0%
TCAAGAAATGCCATTGGCCG+TGG + chr2.3:75491299-75491318 MS.gene002076:CDS 50.0%
! TTTCTTGATGGGCACGGACA+TGG - chr2.3:75491287-75491306 None:intergenic 50.0%
AAATGCCATTGGCCGTGGGA+CGG + chr2.3:75491304-75491323 MS.gene002076:CDS 55.0%
AACACTCCTATGTGGCGCTC+TGG + chr2.3:75491405-75491424 MS.gene002076:CDS 55.0%
CAGAAGGTGGTCGGATCAGA+TGG - chr2.3:75491360-75491379 None:intergenic 55.0%
CTCCCATGATTCCAGGTGGT+GGG - chr2.3:75491843-75491862 None:intergenic 55.0%
GGATCTCCTCCCATGATTCC+AGG - chr2.3:75491850-75491869 None:intergenic 55.0%
GTCCCACCACCTGGAATCAT+GGG + chr2.3:75491838-75491857 MS.gene002076:CDS 55.0%
TCTCCTCCCATGATTCCAGG+TGG - chr2.3:75491847-75491866 None:intergenic 55.0%
TGTCCCACCACCTGGAATCA+TGG + chr2.3:75491837-75491856 MS.gene002076:CDS 55.0%
! ATAGGTCCAGAGCGCCACAT+AGG - chr2.3:75491414-75491433 None:intergenic 55.0%
! TATGTGGCGCTCTGGACCTA+TGG + chr2.3:75491413-75491432 MS.gene002076:CDS 55.0%
CCACCACCTGGAATCATGGG+AGG + chr2.3:75491841-75491860 MS.gene002076:CDS 60.0%
CCTCCCATGATTCCAGGTGG+TGG - chr2.3:75491844-75491863 None:intergenic 60.0%
GGACAGAACCTGAGGCAGCA+GGG - chr2.3:75491822-75491841 None:intergenic 60.0%
TCAGGTTCTGTCCCACCACC+TGG + chr2.3:75491829-75491848 MS.gene002076:CDS 60.0%
!! AGGTGGTGGGACAGAACCTG+AGG - chr2.3:75491830-75491849 None:intergenic 60.0%
CAGATGGACGAGCTCGTCCG+CGG - chr2.3:75491344-75491363 None:intergenic 65.0%
CGAGATGTCCCTGCTGCCTC+AGG + chr2.3:75491811-75491830 MS.gene002076:CDS 65.0%
CTCGTCCGCGGCGGATGTAA+CGG - chr2.3:75491332-75491351 None:intergenic 65.0%
GATGTAACGGCGCCGTCCCA+CGG - chr2.3:75491319-75491338 None:intergenic 65.0%
GGGACAGAACCTGAGGCAGC+AGG - chr2.3:75491823-75491842 None:intergenic 65.0%
ATGGACGAGCTCGTCCGCGG+CGG - chr2.3:75491341-75491360 None:intergenic 70.0%
CGGCGCCGTTACATCCGCCG+CGG + chr2.3:75491324-75491343 MS.gene002076:CDS 75.0%
! CGGCGCCGTCCCACGGCCAA+TGG - chr2.3:75491312-75491331 None:intergenic 80.0%


Chromosome Type Strat End Strand Name
chr2.3 gene 75490307 75491888 75490307 ID=MS.gene002076
chr2.3 mRNA 75490307 75491888 75490307 ID=MS.gene002076.t1;Parent=MS.gene002076
chr2.3 exon 75490307 75490414 75490307 ID=MS.gene002076.t1.exon1;Parent=MS.gene002076.t1
chr2.3 CDS 75490307 75490414 75490307 ID=cds.MS.gene002076.t1;Parent=MS.gene002076.t1
chr2.3 exon 75491186 75491443 75491186 ID=MS.gene002076.t1.exon2;Parent=MS.gene002076.t1
chr2.3 CDS 75491186 75491443 75491186 ID=cds.MS.gene002076.t1;Parent=MS.gene002076.t1
chr2.3 exon 75491763 75491888 75491763 ID=MS.gene002076.t1.exon3;Parent=MS.gene002076.t1
chr2.3 CDS 75491763 75491888 75491763 ID=cds.MS.gene002076.t1;Parent=MS.gene002076.t1
Gene Sequence

>MS.gene002076

ATGGACTTTGACTTAAACATGCCATATTTTGAGGAGGAGGACGTGAATTCAGACACTGAAAGTCAGGTTTCATCACTCATTCAGAGCAATACTGAAAATATCCCTAAAGTAAGTTTTTTTTTCTCTTTCTATAATAATGAATGTCACATACATAATAGTAGTACACATAATGACTGTTAAAAAAAGTTAACATTGTCGATTTTTGTATCATCTAAGAGATGAAAATTGACATGGCTGTTAAAAAAACTAGAACTTTTTCCTTAAAAAAAATTATATTAGACTTAATTCATTTGTACAAAATCGACTTGTAAGACAAATTAATTTAATTAGGATATTTTGTTATTATGCAATTATTTTATACGTGAATCTAATTATGTGTTGTCACTTTTTTTTATATAAAATTATTATTTACCACTTATATTTGATGTATTTTTATAAATATTCATCATAGCATAGAAGTATGTCCCCGCTAATCAAAACTTTTGAGTCTAACTTATAAGATCTTGTGTGTCACTCTTCTATGAATTTTACCATAAATTTATCTCTCGACATGTGATTTGGGGATTTTCCTTTATTTTTCTTCAATTTTTTATGTGATGATGCAATTTAATCATCATGTGAGTAAAAATTAGACGTTTCTTGACTTTGGTATTTAGTCGCATACCAAGTCTAATGCACCAAATAAATGGTGGGAAATTTGAGGATGCCTACCAAACGTCAGAGACTTAATTACGGTAGAATAATTAACATACAAAAAGTGAACAACTAGTGTTATTATGTGATTTTAAATAATTAAATAAAATGATTGTGTATTTATTTTTATTGAAATAATAAAATGGCGACACCTCAAATACACTCAAAACTAACGTTTGTGAACAGGATCCAATTGCAAACAATGTCCAACCAATTGCTACTGCTCCAATTGCTGCTGTCTCAATTTTGGTTGATGCTCAACCGATGTATTGTACTGATTCTTTCCATGTCCGTGCCCATCAAGAAATGCCATTGGCCGTGGGACGGCGCCGTTACATCCGCCGCGGACGAGCTCGTCCATCTGATCCGACCACCTTCTGCACAAATTTTCATTGCAAGACAAGAAACACTCCTATGTGGCGCTCTGGACCTATGGTTCCAAAGGTAAATTTACAACACCAACTGATTATTAGTTAAAAAAATTATGTCAAATAGTCTAGTGTGGAGAATAACACATCGATCTTATATATAAAAAGTAAGGAATTAAGGATTGAAACTCACGCTCCAACATACCAAAATGTTCATGCAGTTAGCCTAGTTGAATTTTTGAGACATTATTTATACAATCTAATAATTAATTAAAAAAGAAATTAGGAAACACACTATTTATTAATAATAGTAATATTAATAACTATTTTACGATCGTCATTATTCTTATCTTTATGTTTCCATAACAATAGTCTTCTATGTTATATATGTGCAGACTTTGTGCAATGCGTGTGGCATTTACTACAAGAAACATATGGTTCGTCGAGATGTCCCTGCTGCCTCAGGTTCTGTCCCACCACCTGGAATCATGGGAGGAGATCCTTCTTCTTCAACTTCCTAA
Protein sequence

>MS.gene002076.t1

MDFDLNMPYFEEEDVNSDTESQVSSLIQSNTENIPKDPIANNVQPIATAPIAAVSILVDAQPMYCTDSFHVRAHQEMPLAVGRRRYIRRGRARPSDPTTFCTNFHCKTRNTPMWRSGPMVPKTLCNACGIYYKKHMVRRDVPAASGSVPPPGIMGGDPSSSTS