AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene49386


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene49386.t1 MTR_1g071630 91.925 161 6 1 1 154 5 165 8.31e-84 243
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene49386.t1 AT4G04614 56.589 129 51 3 27 154 52 176 9.27e-42 137
MS.gene49386.t1 AT4G04614 56.589 129 51 3 27 154 52 176 9.27e-42 137

Find 36 sgRNAs with CRISPR-Local

Find 99 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TTTCTTTGTGTCATCTTCTT+TGG 0.118453 1.1:+53816944 None:intergenic
TTCTTTGTGTCATCTTCTTT+GGG 0.233840 1.1:+53816945 None:intergenic
AGGGACAATGGAGTTTATTC+TGG 0.281268 1.1:-53816690 MS.gene49386:CDS
CTGAAGCGATACGGCTATAA+AGG 0.293708 1.1:-53816996 MS.gene49386:CDS
TAAATCTACAAAGCAGAAAA+AGG 0.315518 1.1:-53817039 MS.gene49386:CDS
AGGCGGACCTTCAGTCTTAA+AGG 0.331123 1.1:-53816976 MS.gene49386:CDS
TCTGAAAATGATAGTGAAAC+TGG 0.358513 1.1:-53818139 MS.gene49386:CDS
CTCAGAAGGAAAAGAAGAAA+AGG 0.400791 1.1:-53816770 MS.gene49386:CDS
GGGATCTTGGTCAAGCAAGC+AGG 0.419342 1.1:-53816749 MS.gene49386:CDS
GAAAAGAAGAAAAGGGATCT+TGG 0.429119 1.1:-53816762 MS.gene49386:CDS
TTCAGAGCTTCAAAGTCAAT+TGG 0.442566 1.1:+53817014 None:intergenic
AAGATGACACAAAGAAAGAT+TGG 0.453949 1.1:-53816938 MS.gene49386:CDS
GTGTCATCTTCTTTGGGTGG+AGG 0.460313 1.1:+53816951 None:intergenic
CAGTTGGCATTTGCTCTCCT+AGG 0.493250 1.1:+53816829 None:intergenic
ATTATGTTGAAGAAGAGAAA+AGG 0.499802 1.1:-53816719 MS.gene49386:CDS
GGATCTTGGTCAAGCAAGCA+GGG 0.515240 1.1:-53816748 MS.gene49386:CDS
TTTGTGTCATCTTCTTTGGG+TGG 0.516808 1.1:+53816948 None:intergenic
TCAGAAGGAAAAGAAGAAAA+GGG 0.533332 1.1:-53816769 MS.gene49386:CDS
AGAAGAGAAAAGGCTGTTGA+GGG 0.535745 1.1:-53816709 MS.gene49386:CDS
TCATTCCTAGTCAGAACAGT+TGG 0.556209 1.1:+53816813 None:intergenic
ACACAAAGAAAGATTGGTCC+TGG 0.556354 1.1:-53816932 MS.gene49386:CDS
ACAAGAGAGGCTCTTTCCCT+AGG 0.557271 1.1:-53816846 MS.gene49386:CDS
AAAAGGCTGTTGAGGGACAA+TGG 0.563867 1.1:-53816702 MS.gene49386:CDS
TTTGAAGCTCTGAAGCGATA+CGG 0.565621 1.1:-53817005 MS.gene49386:CDS
TTGGTCCTGGTCCAGTGGAA+AGG 0.567873 1.1:-53816919 MS.gene49386:CDS
AGTTGGCATTTGCTCTCCTA+GGG 0.578927 1.1:+53816830 None:intergenic
AAGAAGAGAAAAGGCTGTTG+AGG 0.580825 1.1:-53816710 MS.gene49386:CDS
AAAGATTGGTCCTGGTCCAG+TGG 0.594354 1.1:-53816924 MS.gene49386:CDS
GGAGGTACCTTTAAGACTGA+AGG 0.597747 1.1:+53816969 None:intergenic
AAATGCCAACTGTTCTGACT+AGG 0.603014 1.1:-53816818 MS.gene49386:CDS
CTATGAAGAGGACAATGCCA+TGG 0.617111 1.1:-53818192 None:intergenic
TCGTCATCATCATCACTCCA+TGG 0.626378 1.1:+53818175 None:intergenic
ATCTTGGTCAAGCAAGCAGG+GGG 0.627378 1.1:-53816746 MS.gene49386:CDS
GATCTTGGTCAAGCAAGCAG+GGG 0.638659 1.1:-53816747 MS.gene49386:CDS
AGAGAGAAAGAAAACAAGAG+AGG 0.657420 1.1:-53816859 MS.gene49386:CDS
AAGCGATACGGCTATAAAGG+CGG 0.718806 1.1:-53816993 MS.gene49386:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AAATGTAAATTAGAATATCG+GGG - chr1.1:53817575-53817594 MS.gene49386:intron 20.0%
!! AAGAACTATTATAGCATTAT+CGG + chr1.1:53817486-53817505 None:intergenic 20.0%
!! AGACAATAATATATTGCTAA+CGG + chr1.1:53817612-53817631 None:intergenic 20.0%
!! ATAATCACATTAAGATAGAA+CGG + chr1.1:53817068-53817087 None:intergenic 20.0%
!! ATATAATTCAACGTAGTTAT+AGG + chr1.1:53816778-53816797 None:intergenic 20.0%
!! ATATTCTAATTTACATTTCC+TGG + chr1.1:53817573-53817592 None:intergenic 20.0%
!! GAAATCTAATGTGATAAATT+AGG - chr1.1:53817221-53817240 MS.gene49386:intron 20.0%
!! GAAATGTAAATTAGAATATC+GGG - chr1.1:53817574-53817593 MS.gene49386:intron 20.0%
!! GGAAATGTAAATTAGAATAT+CGG - chr1.1:53817573-53817592 MS.gene49386:intron 20.0%
!! TGATAAGTGAAAATAGTATT+TGG - chr1.1:53817005-53817024 MS.gene49386:CDS 20.0%
!!! ATCATTGTTTTAGATTTTGT+TGG - chr1.1:53817368-53817387 MS.gene49386:intron 20.0%
!!! TAAAATACCTTTGGATTTTT+TGG + chr1.1:53816744-53816763 None:intergenic 20.0%
!!! TCATTGTTTTAGATTTTGTT+GGG - chr1.1:53817369-53817388 MS.gene49386:intron 20.0%
! AAAACACAAACACTAATTGT+GGG + chr1.1:53817101-53817120 None:intergenic 25.0%
! AGTGATAGCTGATAATATTA+TGG - chr1.1:53817272-53817291 MS.gene49386:intron 25.0%
! ATTATGTTGAAGAAGAGAAA+AGG - chr1.1:53818136-53818155 MS.gene49386:CDS 25.0%
! CGTTGAATTATATGTTTAAG+TGG - chr1.1:53816785-53816804 MS.gene49386:CDS 25.0%
! GATTTATGAAACACTAACAA+CGG - chr1.1:53816851-53816870 MS.gene49386:CDS 25.0%
! TAAATCTACAAAGCAGAAAA+AGG - chr1.1:53817816-53817835 MS.gene49386:intron 25.0%
!! ACAATTAGTGTTTGTGTTTT+GGG - chr1.1:53817101-53817120 MS.gene49386:intron 25.0%
!! ATTATCTGAAGATCATTTTG+TGG - chr1.1:53817196-53817215 MS.gene49386:intron 25.0%
!!! ACACTTTTAATCTGAAGTAT+CGG - chr1.1:53816968-53816987 MS.gene49386:CDS 25.0%
!!! CATTGTTTTAGATTTTGTTG+GGG - chr1.1:53817370-53817389 MS.gene49386:intron 25.0%
AAATGGTTCATAAACAGTTG+TGG - chr1.1:53817433-53817452 MS.gene49386:intron 30.0%
AAATGTACTTACTTGAACCT+AGG - chr1.1:53817030-53817049 MS.gene49386:CDS 30.0%
AAGATGACACAAAGAAAGAT+TGG - chr1.1:53817917-53817936 MS.gene49386:intron 30.0%
ACCAATAACAAGGAAATACA+AGG + chr1.1:53817340-53817359 None:intergenic 30.0%
ACTAGTAACTAAGCAACATA+TGG + chr1.1:53817773-53817792 None:intergenic 30.0%
ATCACAATACACCAATAACA+AGG + chr1.1:53817350-53817369 None:intergenic 30.0%
ATGTGATAAATTAGGAGTTC+TGG - chr1.1:53817229-53817248 MS.gene49386:intron 30.0%
CAAAACACAAACACTAATTG+TGG + chr1.1:53817102-53817121 None:intergenic 30.0%
CAATAATATATTGCTAACGG+AGG + chr1.1:53817609-53817628 None:intergenic 30.0%
GATACTTCAGATTAAAAGTG+TGG + chr1.1:53816969-53816988 None:intergenic 30.0%
GCTAATTAAGTCACACAATA+TGG + chr1.1:53817643-53817662 None:intergenic 30.0%
TCAGAAGGAAAAGAAGAAAA+GGG - chr1.1:53818086-53818105 MS.gene49386:intron 30.0%
TTCTTTGTGTCATCTTCTTT+GGG + chr1.1:53817913-53817932 None:intergenic 30.0%
TTTCTTTGTGTCATCTTCTT+TGG + chr1.1:53817914-53817933 None:intergenic 30.0%
! AACTAGAGTAGATATTTTCC+AGG - chr1.1:53817552-53817571 MS.gene49386:intron 30.0%
! CACAATTAGTGTTTGTGTTT+TGG - chr1.1:53817100-53817119 MS.gene49386:intron 30.0%
! TCCTTGTATTTCCTTGTTAT+TGG - chr1.1:53817336-53817355 MS.gene49386:intron 30.0%
! TCTGAAAATGATAGTGAAAC+TGG - chr1.1:53816716-53816735 MS.gene49386:CDS 30.0%
!! AAAATCTCATCTCTAGAATG+TGG - chr1.1:53817135-53817154 MS.gene49386:intron 30.0%
AAGGAATCTCTTCTACAATG+GGG + chr1.1:53817321-53817340 None:intergenic 35.0%
AATCTAATCGTGTGTAGTGT+TGG - chr1.1:53816933-53816952 MS.gene49386:CDS 35.0%
ACAAGGAATCTCTTCTACAA+TGG + chr1.1:53817323-53817342 None:intergenic 35.0%
AGAGAGAAAGAAAACAAGAG+AGG - chr1.1:53817996-53818015 MS.gene49386:intron 35.0%
CAAGAGTTTCTTGACTTTCA+AGG - chr1.1:53817528-53817547 MS.gene49386:intron 35.0%
CAAGGAATCTCTTCTACAAT+GGG + chr1.1:53817322-53817341 None:intergenic 35.0%
CTCAGAAGGAAAAGAAGAAA+AGG - chr1.1:53818085-53818104 MS.gene49386:intron 35.0%
GAAAAGAAGAAAAGGGATCT+TGG - chr1.1:53818093-53818112 MS.gene49386:intron 35.0%
GATGCACACTAAAATACCTT+TGG + chr1.1:53816753-53816772 None:intergenic 35.0%
TCAGTTAGTGCAATGCAAAA+TGG - chr1.1:53817416-53817435 MS.gene49386:intron 35.0%
TGACACTAACACTTTGATGT+TGG - chr1.1:53816883-53816902 MS.gene49386:CDS 35.0%
TTAACTTACTTCATGTCTGC+AGG - chr1.1:53817793-53817812 MS.gene49386:intron 35.0%
TTCAGAGCTTCAAAGTCAAT+TGG + chr1.1:53817844-53817863 None:intergenic 35.0%
TTCAGATAATTTCAACGCAG+AGG + chr1.1:53817186-53817205 None:intergenic 35.0%
! ATAGCATTATCGGCTGATTT+AGG + chr1.1:53817476-53817495 None:intergenic 35.0%
! GAATCTTTCCTTTTCTCAGA+AGG - chr1.1:53818071-53818090 MS.gene49386:intron 35.0%
! TTTTGCATTGCACTAACTGA+AGG + chr1.1:53817416-53817435 None:intergenic 35.0%
!! CTTCTTTTCCTTCTGAGAAA+AGG + chr1.1:53818082-53818101 None:intergenic 35.0%
AAATGCCAACTGTTCTGACT+AGG - chr1.1:53818037-53818056 MS.gene49386:intron 40.0%
AACTAAGCAACATATGGCAG+TGG + chr1.1:53817767-53817786 None:intergenic 40.0%
AAGAAGAGAAAAGGCTGTTG+AGG - chr1.1:53818145-53818164 MS.gene49386:CDS 40.0%
ACTAACTGAAGGTCAAGATG+GGG + chr1.1:53817405-53817424 None:intergenic 40.0%
ACTGGAGCCAAAAAATCCAA+AGG - chr1.1:53816734-53816753 MS.gene49386:CDS 40.0%
AGAAGAGAAAAGGCTGTTGA+GGG - chr1.1:53818146-53818165 MS.gene49386:CDS 40.0%
AGGGACAATGGAGTTTATTC+TGG - chr1.1:53818165-53818184 MS.gene49386:CDS 40.0%
AGTATGAAGCCATCATGATG+CGG + chr1.1:53817701-53817720 None:intergenic 40.0%
CACTAACTGAAGGTCAAGAT+GGG + chr1.1:53817406-53817425 None:intergenic 40.0%
CTTGAACCTAGGATGTTGAT+AGG - chr1.1:53817041-53817060 MS.gene49386:CDS 40.0%
TCATTCCTAGTCAGAACAGT+TGG + chr1.1:53818045-53818064 None:intergenic 40.0%
TTTGTGTCATCTTCTTTGGG+TGG + chr1.1:53817910-53817929 None:intergenic 40.0%
! ACACAAAGAAAGATTGGTCC+TGG - chr1.1:53817923-53817942 MS.gene49386:intron 40.0%
!! TTCTGAAATCCGCATCATGA+TGG - chr1.1:53817689-53817708 MS.gene49386:intron 40.0%
!! TTTGAAGCTCTGAAGCGATA+CGG - chr1.1:53817850-53817869 MS.gene49386:intron 40.0%
AAAAGGCTGTTGAGGGACAA+TGG - chr1.1:53818153-53818172 MS.gene49386:CDS 45.0%
AAAGGAAAAACGCGTCGAGA+AGG - chr1.1:53817954-53817973 MS.gene49386:intron 45.0%
AACGCAGAGGTTTCATACCT+TGG + chr1.1:53817173-53817192 None:intergenic 45.0%
AACGGACCTATCAACATCCT+AGG + chr1.1:53817050-53817069 None:intergenic 45.0%
AAGCGATACGGCTATAAAGG+CGG - chr1.1:53817862-53817881 MS.gene49386:intron 45.0%
AGTTGGCATTTGCTCTCCTA+GGG + chr1.1:53818028-53818047 None:intergenic 45.0%
CTGAAGCGATACGGCTATAA+AGG - chr1.1:53817859-53817878 MS.gene49386:intron 45.0%
GCACTAACTGAAGGTCAAGA+TGG + chr1.1:53817407-53817426 None:intergenic 45.0%
TCGTCATCATCATCACTCCA+TGG + chr1.1:53816683-53816702 None:intergenic 45.0%
! TTTTTCCTTTCCACTGGACC+AGG + chr1.1:53817944-53817963 None:intergenic 45.0%
!! GGAGGTACCTTTAAGACTGA+AGG + chr1.1:53817889-53817908 None:intergenic 45.0%
!! TCGTGTGTAGTGTTGGTGTA+CGG - chr1.1:53816940-53816959 MS.gene49386:CDS 45.0%
ACAAGAGAGGCTCTTTCCCT+AGG - chr1.1:53818009-53818028 MS.gene49386:intron 50.0%
AGGCGGACCTTCAGTCTTAA+AGG - chr1.1:53817879-53817898 MS.gene49386:intron 50.0%
ATCTTGGTCAAGCAAGCAGG+GGG - chr1.1:53818109-53818128 MS.gene49386:intron 50.0%
CAGTTGGCATTTGCTCTCCT+AGG + chr1.1:53818029-53818048 None:intergenic 50.0%
GATCTTGGTCAAGCAAGCAG+GGG - chr1.1:53818108-53818127 MS.gene49386:intron 50.0%
GGATCTTGGTCAAGCAAGCA+GGG - chr1.1:53818107-53818126 MS.gene49386:intron 50.0%
GTGTCATCTTCTTTGGGTGG+AGG + chr1.1:53817907-53817926 None:intergenic 50.0%
! AAAGATTGGTCCTGGTCCAG+TGG - chr1.1:53817931-53817950 MS.gene49386:intron 50.0%
! GACGCGTTTTTCCTTTCCAC+TGG + chr1.1:53817950-53817969 None:intergenic 50.0%
! TGTGGATTGACGCTCATCCA+AGG - chr1.1:53817153-53817172 MS.gene49386:intron 50.0%
GGGATCTTGGTCAAGCAAGC+AGG - chr1.1:53818106-53818125 MS.gene49386:intron 55.0%
TTGGTCCTGGTCCAGTGGAA+AGG - chr1.1:53817936-53817955 MS.gene49386:intron 55.0%


Chromosome Type Strat End Strand Name
chr1.1 gene 53816677 53818200 53816677 ID=MS.gene49386
chr1.1 mRNA 53816677 53818200 53816677 ID=MS.gene49386.t1;Parent=MS.gene49386
chr1.1 exon 53818122 53818200 53818122 ID=MS.gene49386.t1.exon1;Parent=MS.gene49386.t1
chr1.1 CDS 53818122 53818200 53818122 ID=cds.MS.gene49386.t1;Parent=MS.gene49386.t1
chr1.1 exon 53816677 53817062 53816677 ID=MS.gene49386.t1.exon2;Parent=MS.gene49386.t1
chr1.1 CDS 53816677 53817062 53816677 ID=cds.MS.gene49386.t1;Parent=MS.gene49386.t1
Gene Sequence

>MS.gene49386

ATGCCATGGAGTGATGATGATGACGACTCATCTTCAGACTCTGAAAATGATAGTGAAACTGGAGCCAAAAAATCCAAAGGTATTTTAGTGTGCATCATCCTATAACTACGTTGAATTATATGTTTAAGTGGAGTATTTTTTGAGTATTTTGTTGACTACAATGTATTCATGTGTGATTTATGAAACACTAACAACGGACATGAACATGACACTAACACTTTGATGTTGGTACTAATTTGAGAAAATAAATTAATTGAATCTAATCGTGTGTAGTGTTGGTGTACGGACACCACACTTTTAATCTGAAGTATCGGTGCTACAAAGTGTTTGATAAGTGAAAATAGTATTTGGACAAATGTACTTACTTGAACCTAGGATGTTGATAGGTCCGTTCTATCTTAATGTGATTATAAGTTTATAACCCACAATTAGTGTTTGTGTTTTGGGTCTATTTAATAAAAATCTCATCTCTAGAATGTGGATTGACGCTCATCCAAGGTATGAAACCTCTGCGTTGAAATTATCTGAAGATCATTTTGTGGCTGAAATCTAATGTGATAAATTAGGAGTTCTGGCGAAAACTAAAAGTTAATTGAGTGATAGCTGATAATATTATGGAGAAATTGCACAATTTCATATTGCCCCATTGTAGAAGAGATTCCTTGTATTTCCTTGTTATTGGTGTATTGTGATCATTGTTTTAGATTTTGTTGGGGATATATATACCCCATCTTGACCTTCAGTTAGTGCAATGCAAAATGGTTCATAAACAGTTGTGGTAGATACATAATGATATCCTAAATCAGCCGATAATGCTATAATAGTTCTTTTTATCTTCACAAAAATTCTTTCAAGAGTTTCTTGACTTTCAAGGCAACTAGAGTAGATATTTTCCAGGAAATGTAAATTAGAATATCGGGGTTGTTATACCTCCGTTAGCAATATATTATTGTCTTTGTTTGACCATATTGTGTGACTTAATTAGCGTTAGTTCATAATTGAAATTGTTAGCTTCTGAAATCCGCATCATGATGGCTTCATACTCATTTGCTTGTAAACTGTGACATCTTGAAAATTCTCACTAATGCCACTGCCATATGTTGCTTAGTTACTAGTTTAACTTACTTCATGTCTGCAGGTAAATCTACAAAGCAGAAAAAGGCTCCAATTGACTTTGAAGCTCTGAAGCGATACGGCTATAAAGGCGGACCTTCAGTCTTAAAGGTACCTCCACCCAAAGAAGATGACACAAAGAAAGATTGGTCCTGGTCCAGTGGAAAGGAAAAACGCGTCGAGAAGGAAGTTGAAGAAACATATGAAGAGAGAAAGAAAACAAGAGAGGCTCTTTCCCTAGGAGAGCAAATGCCAACTGTTCTGACTAGGAATGACAAGAAGAATCTTTCCTTTTCTCAGAAGGAAAAGAAGAAAAGGGATCTTGGTCAAGCAAGCAGGGGGAAAAATTATGTTGAAGAAGAGAAAAGGCTGTTGAGGGACAATGGAGTTTATTCTGGTTTCGATTCTTGA

Protein sequence

>MS.gene49386.t1

MPWSDDDDDSSSDSENDSETGAKKSKGKSTKQKKAPIDFEALKRYGYKGGPSVLKVPPPKEDDTKKDWSWSSGKEKRVEKEVEETYEERKKTREALSLGEQMPTVLTRNDKKNLSFSQKEKKKRDLGQASRGKNYVEEEKRLLRDNGVYSGFDS