AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene051290

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 33 sgRNAs with CRISPR-Local

Find 85 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CAATGAGAAATTCACATTTA+AGG 0.174751 7.3:-48919792 MS.gene051290:CDS
TGTTATGAAGTTGATATTCT+TGG 0.275463 7.3:-48919942 MS.gene051290:CDS
GGACAATATGTCTTTCTTCT+TGG 0.280895 7.3:-48919538 MS.gene051290:CDS
AGTATTGCCCTGCTTATTGT+TGG 0.324545 7.3:-48919825 MS.gene051290:CDS
AGAAACATTGACAATTTAAC+AGG 0.337581 7.3:-48919559 MS.gene051290:CDS
GACAATATGTCTTTCTTCTT+GGG 0.345288 7.3:-48919537 MS.gene051290:intron
GAGCACTATACATTCTCAAC+TGG 0.354642 7.3:-48918801 MS.gene051290:CDS
TGAATTTCTCATTGATAAGT+AGG 0.405613 7.3:+48919801 None:intergenic
CAGTACCAGTTGAGGAAGTA+TGG 0.407791 7.3:+48919594 None:intergenic
TGGCAACAGCTTCCAAATAC+AGG 0.408291 7.3:+48919614 None:intergenic
GTTATGAAGTTGATATTCTT+GGG 0.424245 7.3:-48919941 MS.gene051290:CDS
TGTTGCCATACTTCCTCAAC+TGG 0.450840 7.3:-48919599 MS.gene051290:CDS
CCGAGCCCCACTTTGTCCAT+TGG 0.453725 7.3:-48918762 MS.gene051290:CDS
AAGTAGGGCCAACAATAAGC+AGG 0.512666 7.3:+48919817 None:intergenic
TAGATCATATGACAAAGATC+AGG 0.514146 7.3:-48919870 MS.gene051290:CDS
CCAATGGACAAAGTGGGGCT+CGG 0.529481 7.3:+48918762 None:intergenic
TACTTATCCAATGGACAAAG+TGG 0.529817 7.3:+48918755 None:intergenic
CTTTGTAGCAGTACCAGTTG+AGG 0.551696 7.3:+48919586 None:intergenic
TTTCTATTGTATGGTACATG+AGG 0.554169 7.3:-48919910 MS.gene051290:CDS
TCTTCTACTACTATTTCCAA+AGG 0.567268 7.3:-48918561 None:intergenic
TGAGAAATTCACATTTAAGG+AGG 0.576216 7.3:-48919789 MS.gene051290:intron
GAATTTCTCATTGATAAGTA+GGG 0.579233 7.3:+48919802 None:intergenic
GAAATAGTAGTAGAAGAAGT+CGG 0.579721 7.3:+48918567 None:intergenic
ACTTATCCAATGGACAAAGT+GGG 0.585109 7.3:+48918756 None:intergenic
TACTAGAAAATAGTGACGGA+AGG 0.599670 7.3:+48919844 None:intergenic
ACAGAATTATACTTATCCAA+TGG 0.602023 7.3:+48918746 None:intergenic
GGCAACAGCTTCCAAATACA+GGG 0.635959 7.3:+48919615 None:intergenic
CTTATCCAATGGACAAAGTG+GGG 0.636328 7.3:+48918757 None:intergenic
TATACATGGAATAGGTGATG+TGG 0.652075 7.3:-48919645 MS.gene051290:intron
AGCACTATACATTCTCAACT+GGG 0.652774 7.3:-48918800 MS.gene051290:CDS
GCAATACTAGAAAATAGTGA+CGG 0.652982 7.3:+48919840 None:intergenic
ATGATCTACGAACAATCTTG+TGG 0.654874 7.3:+48919885 None:intergenic
AGTAGGGCCAACAATAAGCA+GGG 0.670399 7.3:+48919818 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! ATGCAAATATATAATGTTAA+AGG + chr7.3:48919095-48919114 None:intergenic 15.0%
!! CTATAATAAAAAATAAGCAA+TGG - chr7.3:48919662-48919681 MS.gene051290:intron 15.0%
!! CTAGATAAATTATAGCTAAT+GGG - chr7.3:48919415-48919434 MS.gene051290:intron 20.0%
!! TAAAAACATTCAAACATGTA+TGG + chr7.3:48918877-48918896 None:intergenic 20.0%
!! TAGATAAATTATAGCTAATG+GGG - chr7.3:48919416-48919435 MS.gene051290:intron 20.0%
!!! AGTTGAAAGTTTTTATTTGT+TGG - chr7.3:48919549-48919568 MS.gene051290:CDS 20.0%
!!! TCTTGTTTAATTGTTATCAT+TGG - chr7.3:48919873-48919892 MS.gene051290:CDS 20.0%
! AAAGCTAAAACAAGTTCAAA+TGG + chr7.3:48919710-48919729 None:intergenic 25.0%
! AAGCTAAAACAAGTTCAAAT+GGG + chr7.3:48919709-48919728 None:intergenic 25.0%
! AATTAGCAGCTATTATATTC+TGG - chr7.3:48919147-48919166 MS.gene051290:intron 25.0%
! ACAGAATTATACTTATCCAA+TGG + chr7.3:48919852-48919871 None:intergenic 25.0%
! ACTGTAATGTTTAACAATGA+TGG + chr7.3:48919927-48919946 None:intergenic 25.0%
! AGAAACATTGACAATTTAAC+AGG - chr7.3:48919036-48919055 MS.gene051290:intron 25.0%
! ATATATTTGCATGATTTCTG+TGG - chr7.3:48919103-48919122 MS.gene051290:intron 25.0%
! ATCATTGTTAAACATTACAG+TGG - chr7.3:48919926-48919945 MS.gene051290:CDS 25.0%
! CAATGAGAAATTCACATTTA+AGG - chr7.3:48918803-48918822 MS.gene051290:CDS 25.0%
! CCATTAGCTATAATTTATCT+AGG + chr7.3:48919417-48919436 None:intergenic 25.0%
! CCTAGATAAATTATAGCTAA+TGG - chr7.3:48919414-48919433 MS.gene051290:intron 25.0%
! GAATTTCTCATTGATAAGTA+GGG + chr7.3:48918796-48918815 None:intergenic 25.0%
! TATAATTTATCTAGGTGAGT+TGG + chr7.3:48919409-48919428 None:intergenic 25.0%
! TGAATTTCTCATTGATAAGT+AGG + chr7.3:48918797-48918816 None:intergenic 25.0%
! TTTCATGTAACATGTTGTAT+AGG - chr7.3:48919367-48919386 MS.gene051290:intron 25.0%
!!! GTTATGAAGTTGATATTCTT+GGG - chr7.3:48918654-48918673 MS.gene051290:intron 25.0%
!!! TGTTATGAAGTTGATATTCT+TGG - chr7.3:48918653-48918672 MS.gene051290:intron 25.0%
!!! TTGAACTTGTTTTAGCTTTT+AGG - chr7.3:48919711-48919730 MS.gene051290:intron 25.0%
AAACTGCTTATACATGGAAT+AGG - chr7.3:48918942-48918961 MS.gene051290:intron 30.0%
AACCTTAATAAGCAGAACTT+TGG + chr7.3:48919607-48919626 None:intergenic 30.0%
ATGGTAACTTTGTATATCAG+AGG - chr7.3:48919681-48919700 MS.gene051290:intron 30.0%
CAACTCAAGATCATAATAGA+AGG + chr7.3:48919534-48919553 None:intergenic 30.0%
GAAATAGTAGTAGAAGAAGT+CGG + chr7.3:48920031-48920050 None:intergenic 30.0%
GACAATATGTCTTTCTTCTT+GGG - chr7.3:48919058-48919077 MS.gene051290:intron 30.0%
GCAATACTAGAAAATAGTGA+CGG + chr7.3:48918758-48918777 None:intergenic 30.0%
TAGATCATATGACAAAGATC+AGG - chr7.3:48918725-48918744 MS.gene051290:intron 30.0%
TCTTCTACTACTATTTCCAA+AGG - chr7.3:48920034-48920053 MS.gene051290:CDS 30.0%
TGAGAAATTCACATTTAAGG+AGG - chr7.3:48918806-48918825 MS.gene051290:CDS 30.0%
TTTCTATTGTATGGTACATG+AGG - chr7.3:48918685-48918704 MS.gene051290:intron 30.0%
! ATTCCATGTATAAGCAGTTT+TGG + chr7.3:48918942-48918961 None:intergenic 30.0%
! GAAGCTCATTTTCTATTGTA+TGG - chr7.3:48918676-48918695 MS.gene051290:intron 30.0%
! TTCCATGTATAAGCAGTTTT+GGG + chr7.3:48918941-48918960 None:intergenic 30.0%
! TTTATTTGTTGGAACGAAAC+TGG - chr7.3:48919560-48919579 MS.gene051290:CDS 30.0%
ACTTATCCAATGGACAAAGT+GGG + chr7.3:48919842-48919861 None:intergenic 35.0%
AGCACTATACATTCTCAACT+GGG - chr7.3:48919795-48919814 MS.gene051290:CDS 35.0%
AGCCAAAGTTCTGCTTATTA+AGG - chr7.3:48919602-48919621 MS.gene051290:CDS 35.0%
ATGATCTACGAACAATCTTG+TGG + chr7.3:48918713-48918732 None:intergenic 35.0%
GGACAATATGTCTTTCTTCT+TGG - chr7.3:48919057-48919076 MS.gene051290:intron 35.0%
GGCTTCAAGATCATAATAGA+AGG + chr7.3:48919586-48919605 None:intergenic 35.0%
TACTTATCCAATGGACAAAG+TGG + chr7.3:48919843-48919862 None:intergenic 35.0%
TATACATGGAATAGGTGATG+TGG - chr7.3:48918950-48918969 MS.gene051290:intron 35.0%
TTGAAACTGATCAATGAGAC+TGG - chr7.3:48919508-48919527 MS.gene051290:intron 35.0%
TTTCAATGAAGCCAACAAAC+AGG + chr7.3:48919494-48919513 None:intergenic 35.0%
! CATTACTTCTTTTGCAGCAT+GGG - chr7.3:48919975-48919994 MS.gene051290:CDS 35.0%
! TACTAGAAAATAGTGACGGA+AGG + chr7.3:48918754-48918773 None:intergenic 35.0%
AGACCAACCTTCCAGTTATT+TGG + chr7.3:48919198-48919217 None:intergenic 40.0%
AGTATTGCCCTGCTTATTGT+TGG - chr7.3:48918770-48918789 MS.gene051290:CDS 40.0%
CCATGCTGCAAAAGAAGTAA+TGG + chr7.3:48919977-48919996 None:intergenic 40.0%
CTGATCAACAGCCAAATAAC+TGG - chr7.3:48919184-48919203 MS.gene051290:intron 40.0%
CTTATCCAATGGACAAAGTG+GGG + chr7.3:48919841-48919860 None:intergenic 40.0%
CTTTCTTCTTGGGTAAGCTA+TGG - chr7.3:48919068-48919087 MS.gene051290:intron 40.0%
GAGCACTATACATTCTCAAC+TGG - chr7.3:48919794-48919813 MS.gene051290:CDS 40.0%
GTCCCAAAACTGCTTATACA+TGG - chr7.3:48918936-48918955 MS.gene051290:intron 40.0%
TAGCTAATGGGGACAACAAA+AGG - chr7.3:48919427-48919446 MS.gene051290:intron 40.0%
TCAACAGCCAAATAACTGGA+AGG - chr7.3:48919188-48919207 MS.gene051290:intron 40.0%
TTGGTTTACGCTCTTTAGAC+TGG - chr7.3:48919892-48919911 MS.gene051290:CDS 40.0%
! CCATTACTTCTTTTGCAGCA+TGG - chr7.3:48919974-48919993 MS.gene051290:CDS 40.0%
! GTGAGTTGGATTGACAACTT+TGG + chr7.3:48919395-48919414 None:intergenic 40.0%
! GTGGACATTTTCCCTGTATT+TGG - chr7.3:48918969-48918988 MS.gene051290:intron 40.0%
! TGCTTTGTCTGAAATGCAGT+GGG - chr7.3:48919767-48919786 MS.gene051290:intron 40.0%
! TTGCTTTGTCTGAAATGCAG+TGG - chr7.3:48919766-48919785 MS.gene051290:intron 40.0%
AAGTAGGGCCAACAATAAGC+AGG + chr7.3:48918781-48918800 None:intergenic 45.0%
AATGGCAGGAAGTCAGAACA+AGG + chr7.3:48919959-48919978 None:intergenic 45.0%
AGTAGGGCCAACAATAAGCA+GGG + chr7.3:48918780-48918799 None:intergenic 45.0%
CAGCCAAATAACTGGAAGGT+TGG - chr7.3:48919192-48919211 MS.gene051290:intron 45.0%
CAGTACCAGTTGAGGAAGTA+TGG + chr7.3:48919004-48919023 None:intergenic 45.0%
CTTTGTAGCAGTACCAGTTG+AGG + chr7.3:48919012-48919031 None:intergenic 45.0%
GCATAGAACGAGCTTAGTAG+TGG - chr7.3:48919236-48919255 MS.gene051290:intron 45.0%
GCTGCAAAAGAAGTAATGGC+AGG + chr7.3:48919973-48919992 None:intergenic 45.0%
GGCAACAGCTTCCAAATACA+GGG + chr7.3:48918983-48919002 None:intergenic 45.0%
TGGCAACAGCTTCCAAATAC+AGG + chr7.3:48918984-48919003 None:intergenic 45.0%
TGTTGCCATACTTCCTCAAC+TGG - chr7.3:48918996-48919015 MS.gene051290:intron 45.0%
! CTTTTGCAGCATGGGTTTCT+GGG - chr7.3:48919983-48920002 MS.gene051290:CDS 45.0%
! TCTTTTGCAGCATGGGTTTC+TGG - chr7.3:48919982-48920001 MS.gene051290:CDS 45.0%
!! TTAGTTTGCAGTAGTGCTCG+TGG - chr7.3:48919463-48919482 MS.gene051290:intron 45.0%
TCGTGGACAAGCCTGTTTGT+TGG - chr7.3:48919480-48919499 MS.gene051290:intron 50.0%
CCAATGGACAAAGTGGGGCT+CGG + chr7.3:48919836-48919855 None:intergenic 55.0%
CCGAGCCCCACTTTGTCCAT+TGG - chr7.3:48919833-48919852 MS.gene051290:CDS 60.0%


Chromosome Type Strat End Strand Name
chr7.3 gene 48918562 48920055 48918562 ID=MS.gene051290
chr7.3 mRNA 48918562 48920055 48918562 ID=MS.gene051290.t1;Parent=MS.gene051290
chr7.3 exon 48919790 48920055 48919790 ID=MS.gene051290.t1.exon1;Parent=MS.gene051290.t1
chr7.3 CDS 48919790 48920055 48919790 ID=cds.MS.gene051290.t1;Parent=MS.gene051290.t1
chr7.3 exon 48919538 48919653 48919538 ID=MS.gene051290.t1.exon2;Parent=MS.gene051290.t1
chr7.3 CDS 48919538 48919653 48919538 ID=cds.MS.gene051290.t1;Parent=MS.gene051290.t1
chr7.3 exon 48918758 48918831 48918758 ID=MS.gene051290.t1.exon3;Parent=MS.gene051290.t1
chr7.3 CDS 48918758 48918831 48918758 ID=cds.MS.gene051290.t1;Parent=MS.gene051290.t1
chr7.3 exon 48918562 48918625 48918562 ID=MS.gene051290.t1.exon4;Parent=MS.gene051290.t1
chr7.3 CDS 48918562 48918625 48918562 ID=cds.MS.gene051290.t1;Parent=MS.gene051290.t1
Gene Sequence

>MS.gene051290

GTGTCTCGTTGAAAACTCAAGAACTCTACGCACTTGTTTTTGCTGCTCGCTACTTAGATATCTTTACGAATTACGTATCTCTCTATAATACTGTTATGAAGTTGATATTCTTGGGAAGCTCATTTTCTATTGTATGGTACATGAGGTACCACAAGATTGTTCGTAGATCATATGACAAAGATCAGGATACCTTCCGTCACTATTTTCTAGTATTGCCCTGCTTATTGTTGGCCCTACTTATCAATGAGAAATTCACATTTAAGGAGGTTAGAATGCATTCACTGTTGTCTATCTTCTGTAACTGTTGTGCTGCCATACATGTTTGAATGTTTTTAAGAGATGATGACTTTGCATTAATTTAGCTTTCGTTTGTTGTCCCAAAACTGCTTATACATGGAATAGGTGATGTGGACATTTTCCCTGTATTTGGAAGCTGTTGCCATACTTCCTCAACTGGTACTGCTACAAAGAACTAGAAACATTGACAATTTAACAGGACAATATGTCTTTCTTCTTGGGTAAGCTATGGTCCTTTAACATTATATATTTGCATGATTTCTGTGGCTGTTATTGCATTAGTATTGAAATTAGCAGCTATTATATTCTGGAAGTATTTCAGTTACTGATCAACAGCCAAATAACTGGAAGGTTGGTCTATGTTGATATCTATTTCTGCATAGAACGAGCTTAGTAGTGGTTTCATGCATGATAATGATGATGTAAATCGTAGTTGCAATTTGATACAGTTCTGAGTCATTGAACTAATGCTCTTTAAATAGTGATTCACATGAAGAAAATCATAGCATTTCATGTAACATGTTGTATAGGTTCCAAAGTTGTCAATCCAACTCACCTAGATAAATTATAGCTAATGGGGACAACAAAAGGAATAGAAAAATTATTAGTTTGCAGTAGTGCTCGTGGACAAGCCTGTTTGTTGGCTTCATTGAAACTGATCAATGAGACTGGCCTTCTATTATGATCTTGAGTTGAAAGTTTTTATTTGTTGGAACGAAACTGGCCTTCTATTATGATCTTGAAGCCAAAGTTCTGCTTATTAAGGTTTTCAAGTTTATGCAACTAGCTCTACATATAGTGTGCTATAATAAAAAATAAGCAATGGTAACTTTGTATATCAGAGGAACCCATTTGAACTTGTTTTAGCTTTTAGGCTTTAAGATCTTAGAATTCTGATTCAATAATATTGCTTTGTCTGAAATGCAGTGGGTACAGAGCACTATACATTCTCAACTGGGTCTATCGCTACTTTACCGAGCCCCACTTTGTCCATTGGATAAGTATAATTCTGTCTCTTGTTTAATTGTTATCATTGGTTTACGCTCTTTAGACTGGAAAACTTTTCCATCATTGTTAAACATTACAGTGGCTATAAACCTTGTTCTGACTTCCTGCCATTACTTCTTTTGCAGCATGGGTTTCTGGGCTTGTTCAAACACTGCTATATGCCGACTTCTTCTACTACTATTTCCAAAG
Protein sequence

>MS.gene051290.t1

VSRUKLKNSTHLFLLLATUISLRITYLSIILLUSUYSWEAHFLLYGTUGTTRLFVDHMTKIRIPSVTIFUYCPAYCWPYLSMRNSHLRRUCGHFPCIWKLLPYFLNWYCYKELETLTIUQDNMSFFLVGTEHYTFSTGSIATLPSPTLSIGUHGFLGLFKHCYMPTSSTTISK