AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0517090


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 6 sgRNAs with CRISPR-Local

Find 146 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CAAGAACTACATGATTTAAA+TGG 0.343047 3_4:-68591746 Msa0517090:CDS
GGTTCTTCATTTAAATCAAA+CGG 0.423964 3_4:+68591809 None:intergenic
GAGGAAGAAAACTTTGCTAC+AGG 0.520352 3_4:-68591722 Msa0517090:CDS
ACTACATGATTTAAATGGTG+AGG 0.610476 3_4:-68591741 Msa0517090:CDS
TCTTCATGTAAATCAAACAA+TGG 0.620271 3_4:+68591788 None:intergenic
TCTTGATGTAAATCAAACAG+TGG 0.699392 3_4:+68591764 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AATTAAATTTGTGAGAAATT+TGG - chr3_4:68591772-68591791 Msa0517090:CDS 15.0%
!! ATTAAATTTGTGAGAAATTT+GGG - chr3_4:68591773-68591792 Msa0517090:CDS 15.0%
!!! ACTTTAATTAATTTTGGTAT+TGG + chr3_4:68592587-68592606 None:intergenic 15.0%
!!! TGATTGACTTTAATTAATTT+TGG + chr3_4:68592593-68592612 None:intergenic 15.0%
!! ATTAATTAAAGTCAATCAAA+TGG - chr3_4:68592595-68592614 Msa0517090:intron 15.0%
!! AAGTTGAAAAAAATTTGTAT+TGG + chr3_4:68592709-68592728 None:intergenic 15.0%
!! TAAGATTAGAGTATAAATAA+TGG + chr3_4:68592792-68592811 None:intergenic 15.0%
!! AATTAAATTTGTGAGAAATT+TGG - chr3_4:68591772-68591791 Msa0517090:CDS 15.0%
!! ATTAAATTTGTGAGAAATTT+GGG - chr3_4:68591773-68591792 Msa0517090:CDS 15.0%
!!! ACTTTAATTAATTTTGGTAT+TGG + chr3_4:68592587-68592606 None:intergenic 15.0%
!!! TGATTGACTTTAATTAATTT+TGG + chr3_4:68592593-68592612 None:intergenic 15.0%
!! ATTAATTAAAGTCAATCAAA+TGG - chr3_4:68592595-68592614 Msa0517090:intron 15.0%
!! AAGTTGAAAAAAATTTGTAT+TGG + chr3_4:68592709-68592728 None:intergenic 15.0%
!! TAAGATTAGAGTATAAATAA+TGG + chr3_4:68592792-68592811 None:intergenic 15.0%
!! AAACTAGAAAATAAGAGAAA+GGG + chr3_4:68591910-68591929 None:intergenic 20.0%
!!! TTCTCTTTGTTTTTTCTTAT+AGG - chr3_4:68591981-68592000 Msa0517090:intron 20.0%
!! TGAGGTAAATAAATGTAAAA+TGG + chr3_4:68592544-68592563 None:intergenic 20.0%
!!! TTAATTTTGGTATTGGTATT+GGG + chr3_4:68592580-68592599 None:intergenic 20.0%
!!! ATTAATTTTGGTATTGGTAT+TGG + chr3_4:68592581-68592600 None:intergenic 20.0%
!!! AAATCACATTATTTTTGATG+CGG - chr3_4:68592662-68592681 Msa0517090:intron 20.0%
!!! ATTAGAGTATAAATAATGGA+GGG + chr3_4:68592788-68592807 None:intergenic 20.0%
!! TATAAGTGTTCTTGAAAAAA+CGG + chr3_4:68592857-68592876 None:intergenic 20.0%
!! TTTCACTATATATAAGAGTT+AGG - chr3_4:68592878-68592897 Msa0517090:intron 20.0%
!! AAACTAGAAAATAAGAGAAA+GGG + chr3_4:68591910-68591929 None:intergenic 20.0%
!!! TTCTCTTTGTTTTTTCTTAT+AGG - chr3_4:68591981-68592000 Msa0517090:intron 20.0%
!! TGAGGTAAATAAATGTAAAA+TGG + chr3_4:68592544-68592563 None:intergenic 20.0%
!!! TTAATTTTGGTATTGGTATT+GGG + chr3_4:68592580-68592599 None:intergenic 20.0%
!!! ATTAATTTTGGTATTGGTAT+TGG + chr3_4:68592581-68592600 None:intergenic 20.0%
!!! AAATCACATTATTTTTGATG+CGG - chr3_4:68592662-68592681 Msa0517090:intron 20.0%
!!! ATTAGAGTATAAATAATGGA+GGG + chr3_4:68592788-68592807 None:intergenic 20.0%
!! TATAAGTGTTCTTGAAAAAA+CGG + chr3_4:68592857-68592876 None:intergenic 20.0%
!! TTTCACTATATATAAGAGTT+AGG - chr3_4:68592878-68592897 Msa0517090:intron 20.0%
!! TACAATTTTGGATAAACCAA+CGG + chr3_4:68591742-68591761 None:intergenic 25.0%
! GAAACTAGAAAATAAGAGAA+AGG + chr3_4:68591911-68591930 None:intergenic 25.0%
! AGGAGAAAAAATATTCTGTT+CGG - chr3_4:68592012-68592031 Msa0517090:intron 25.0%
!! ATTTTCATGTTAGGTTTTCT+GGG - chr3_4:68592152-68592171 Msa0517090:intron 25.0%
! TAATAAAATTCAAACTCCAC+TGG - chr3_4:68592284-68592303 Msa0517090:intron 25.0%
!!! AATGGACATGTATTTTGAAA+CGG + chr3_4:68592445-68592464 None:intergenic 25.0%
!! TCAAAATACATGTCCATTTT+AGG - chr3_4:68592447-68592466 Msa0517090:intron 25.0%
!! CAAAATACATGTCCATTTTA+GGG - chr3_4:68592448-68592467 Msa0517090:intron 25.0%
! GGTAAATAAATGTAAAATGG+AGG + chr3_4:68592541-68592560 None:intergenic 25.0%
! GATTAGAGTATAAATAATGG+AGG + chr3_4:68592789-68592808 None:intergenic 25.0%
!! TGAAGAACAAAATTTTGCTA+TGG - chr3_4:68592928-68592947 Msa0517090:intron 25.0%
! GGTTCTTCATTTAAATCAAA+CGG + chr3_4:68592968-68592987 None:intergenic 25.0%
! TCTTCATGTAAATCAAACAA+TGG + chr3_4:68592989-68593008 None:intergenic 25.0%
! CAAGAACTACATGATTTAAA+TGG - chr3_4:68593028-68593047 Msa0517090:intron 25.0%
!! TACAATTTTGGATAAACCAA+CGG + chr3_4:68591742-68591761 None:intergenic 25.0%
! GAAACTAGAAAATAAGAGAA+AGG + chr3_4:68591911-68591930 None:intergenic 25.0%
! AGGAGAAAAAATATTCTGTT+CGG - chr3_4:68592012-68592031 Msa0517090:intron 25.0%
!! ATTTTCATGTTAGGTTTTCT+GGG - chr3_4:68592152-68592171 Msa0517090:intron 25.0%
! TAATAAAATTCAAACTCCAC+TGG - chr3_4:68592284-68592303 Msa0517090:intron 25.0%
!!! AATGGACATGTATTTTGAAA+CGG + chr3_4:68592445-68592464 None:intergenic 25.0%
!! TCAAAATACATGTCCATTTT+AGG - chr3_4:68592447-68592466 Msa0517090:intron 25.0%
!! CAAAATACATGTCCATTTTA+GGG - chr3_4:68592448-68592467 Msa0517090:intron 25.0%
! GGTAAATAAATGTAAAATGG+AGG + chr3_4:68592541-68592560 None:intergenic 25.0%
! GATTAGAGTATAAATAATGG+AGG + chr3_4:68592789-68592808 None:intergenic 25.0%
!! TGAAGAACAAAATTTTGCTA+TGG - chr3_4:68592928-68592947 Msa0517090:intron 25.0%
! GGTTCTTCATTTAAATCAAA+CGG + chr3_4:68592968-68592987 None:intergenic 25.0%
! TCTTCATGTAAATCAAACAA+TGG + chr3_4:68592989-68593008 None:intergenic 25.0%
! CAAGAACTACATGATTTAAA+TGG - chr3_4:68593028-68593047 Msa0517090:intron 25.0%
! GTTGGTTTATCCAAAATTGT+AGG - chr3_4:68591741-68591760 Msa0517090:CDS 30.0%
TTTATCCAAAATTGTAGGTG+AGG - chr3_4:68591746-68591765 Msa0517090:CDS 30.0%
ATGAATGAATGAATGAATGC+TGG + chr3_4:68591855-68591874 None:intergenic 30.0%
AGAAAATAAGAGAAAGGGAA+TGG + chr3_4:68591905-68591924 None:intergenic 30.0%
! TTTTCTTATAGGTTCTGTAG+AGG - chr3_4:68591992-68592011 Msa0517090:intron 30.0%
GGAGAAAAAATATTCTGTTC+GGG - chr3_4:68592013-68592032 Msa0517090:intron 30.0%
ATTCATGTGTAAAGCAATTC+TGG - chr3_4:68592124-68592143 Msa0517090:intron 30.0%
!!! CTGGTTTTGATTTTCATGTT+AGG - chr3_4:68592143-68592162 Msa0517090:intron 30.0%
! GATTTTCATGTTAGGTTTTC+TGG - chr3_4:68592151-68592170 Msa0517090:intron 30.0%
TTACTGCAATTTCCCTAAAA+TGG + chr3_4:68592463-68592482 None:intergenic 30.0%
! ATCAAAGACAAGGGTATAAT+AGG + chr3_4:68592516-68592535 None:intergenic 30.0%
GATTTACTAGTACTCCTAAA+TGG + chr3_4:68592647-68592666 None:intergenic 30.0%
TCTTGATGTAAATCAAACAG+TGG + chr3_4:68593013-68593032 None:intergenic 30.0%
ACTACATGATTTAAATGGTG+AGG - chr3_4:68593033-68593052 Msa0517090:intron 30.0%
! GTTGGTTTATCCAAAATTGT+AGG - chr3_4:68591741-68591760 Msa0517090:CDS 30.0%
TTTATCCAAAATTGTAGGTG+AGG - chr3_4:68591746-68591765 Msa0517090:CDS 30.0%
ATGAATGAATGAATGAATGC+TGG + chr3_4:68591855-68591874 None:intergenic 30.0%
AGAAAATAAGAGAAAGGGAA+TGG + chr3_4:68591905-68591924 None:intergenic 30.0%
! TTTTCTTATAGGTTCTGTAG+AGG - chr3_4:68591992-68592011 Msa0517090:intron 30.0%
GGAGAAAAAATATTCTGTTC+GGG - chr3_4:68592013-68592032 Msa0517090:intron 30.0%
ATTCATGTGTAAAGCAATTC+TGG - chr3_4:68592124-68592143 Msa0517090:intron 30.0%
!!! CTGGTTTTGATTTTCATGTT+AGG - chr3_4:68592143-68592162 Msa0517090:intron 30.0%
! GATTTTCATGTTAGGTTTTC+TGG - chr3_4:68592151-68592170 Msa0517090:intron 30.0%
TTACTGCAATTTCCCTAAAA+TGG + chr3_4:68592463-68592482 None:intergenic 30.0%
! ATCAAAGACAAGGGTATAAT+AGG + chr3_4:68592516-68592535 None:intergenic 30.0%
GATTTACTAGTACTCCTAAA+TGG + chr3_4:68592647-68592666 None:intergenic 30.0%
TCTTGATGTAAATCAAACAG+TGG + chr3_4:68593013-68593032 None:intergenic 30.0%
ACTACATGATTTAAATGGTG+AGG - chr3_4:68593033-68593052 Msa0517090:intron 30.0%
! TTTCACCTCACCTACAATTT+TGG + chr3_4:68591754-68591773 None:intergenic 35.0%
AATAAGAGAAAGGGAATGGA+AGG + chr3_4:68591901-68591920 None:intergenic 35.0%
ACTAGCATCTGCATTACATT+AGG - chr3_4:68591936-68591955 Msa0517090:intron 35.0%
GAAAAAATATTCTGTTCGGG+TGG - chr3_4:68592016-68592035 Msa0517090:intron 35.0%
AGAAAATGAACTTACACGCA+CGG + chr3_4:68592061-68592080 None:intergenic 35.0%
!!! GACATGTATTTTGAAACGGA+TGG + chr3_4:68592441-68592460 None:intergenic 35.0%
ATGGAGGAAATCAAAGACAA+GGG + chr3_4:68592525-68592544 None:intergenic 35.0%
AATGGAGGAAATCAAAGACA+AGG + chr3_4:68592526-68592545 None:intergenic 35.0%
TTGGGAGTAATTATGAGATG+AGG + chr3_4:68592562-68592581 None:intergenic 35.0%
TCAAATGGCAATACCAATAC+TGG - chr3_4:68592610-68592629 Msa0517090:intron 35.0%
TGGCTATACCAATACCATTT+AGG - chr3_4:68592630-68592649 Msa0517090:intron 35.0%
CTAGTACTCCTAAATGGTAT+TGG + chr3_4:68592641-68592660 None:intergenic 35.0%
CAACTTCTCTTATCATGCTT+CGG - chr3_4:68592723-68592742 Msa0517090:intron 35.0%
! TTTCACCTCACCTACAATTT+TGG + chr3_4:68591754-68591773 None:intergenic 35.0%
AATAAGAGAAAGGGAATGGA+AGG + chr3_4:68591901-68591920 None:intergenic 35.0%
ACTAGCATCTGCATTACATT+AGG - chr3_4:68591936-68591955 Msa0517090:intron 35.0%
GAAAAAATATTCTGTTCGGG+TGG - chr3_4:68592016-68592035 Msa0517090:intron 35.0%
AGAAAATGAACTTACACGCA+CGG + chr3_4:68592061-68592080 None:intergenic 35.0%
!!! GACATGTATTTTGAAACGGA+TGG + chr3_4:68592441-68592460 None:intergenic 35.0%
ATGGAGGAAATCAAAGACAA+GGG + chr3_4:68592525-68592544 None:intergenic 35.0%
AATGGAGGAAATCAAAGACA+AGG + chr3_4:68592526-68592545 None:intergenic 35.0%
TTGGGAGTAATTATGAGATG+AGG + chr3_4:68592562-68592581 None:intergenic 35.0%
TCAAATGGCAATACCAATAC+TGG - chr3_4:68592610-68592629 Msa0517090:intron 35.0%
TGGCTATACCAATACCATTT+AGG - chr3_4:68592630-68592649 Msa0517090:intron 35.0%
CTAGTACTCCTAAATGGTAT+TGG + chr3_4:68592641-68592660 None:intergenic 35.0%
CAACTTCTCTTATCATGCTT+CGG - chr3_4:68592723-68592742 Msa0517090:intron 35.0%
ACTCGTGACTTTACACATGT+GGG + chr3_4:68591828-68591847 None:intergenic 40.0%
TACTCGTGACTTTACACATG+TGG + chr3_4:68591829-68591848 None:intergenic 40.0%
TGGGAAGTAGAATATCAACG+AGG - chr3_4:68592171-68592190 Msa0517090:intron 40.0%
GGGAAGTAGAATATCAACGA+GGG - chr3_4:68592172-68592191 Msa0517090:intron 40.0%
AATTCAAACTCCACTGGACT+CGG - chr3_4:68592290-68592309 Msa0517090:intron 40.0%
GTTTGTCACGTGTCAATCAA+TGG - chr3_4:68592337-68592356 Msa0517090:intron 40.0%
!! GTGTCAAACTAGCTTGTTCT+TGG + chr3_4:68592486-68592505 None:intergenic 40.0%
!! GGTATTGGTATAGCCAGTAT+TGG + chr3_4:68592626-68592645 None:intergenic 40.0%
GAGGAAGAAAACTTTGCTAC+AGG - chr3_4:68593052-68593071 Msa0517090:intron 40.0%
ACTCGTGACTTTACACATGT+GGG + chr3_4:68591828-68591847 None:intergenic 40.0%
TACTCGTGACTTTACACATG+TGG + chr3_4:68591829-68591848 None:intergenic 40.0%
TGGGAAGTAGAATATCAACG+AGG - chr3_4:68592171-68592190 Msa0517090:intron 40.0%
GGGAAGTAGAATATCAACGA+GGG - chr3_4:68592172-68592191 Msa0517090:intron 40.0%
AATTCAAACTCCACTGGACT+CGG - chr3_4:68592290-68592309 Msa0517090:intron 40.0%
GTTTGTCACGTGTCAATCAA+TGG - chr3_4:68592337-68592356 Msa0517090:intron 40.0%
!! GTGTCAAACTAGCTTGTTCT+TGG + chr3_4:68592486-68592505 None:intergenic 40.0%
!! GGTATTGGTATAGCCAGTAT+TGG + chr3_4:68592626-68592645 None:intergenic 40.0%
GAGGAAGAAAACTTTGCTAC+AGG - chr3_4:68593052-68593071 Msa0517090:intron 40.0%
AGAAAGATGGTTGGATCCGT+TGG - chr3_4:68591723-68591742 Msa0517090:CDS 45.0%
GGGTTGCATTTAATCCTACG+TGG - chr3_4:68591793-68591812 Msa0517090:CDS 45.0%
CTCGTGACTTTACACATGTG+GGG + chr3_4:68591827-68591846 None:intergenic 45.0%
AGAAAGATGGTTGGATCCGT+TGG - chr3_4:68591723-68591742 Msa0517090:CDS 45.0%
GGGTTGCATTTAATCCTACG+TGG - chr3_4:68591793-68591812 Msa0517090:CDS 45.0%
CTCGTGACTTTACACATGTG+GGG + chr3_4:68591827-68591846 None:intergenic 45.0%
!!! AAATTTTAATTTAATTTTAG+TGG + chr3_4:68592824-68592843 None:intergenic 5.0%
!!! AAATTTTAATTTAATTTTAG+TGG + chr3_4:68592824-68592843 None:intergenic 5.0%
CAGATCTAAACCGAGTCCAG+TGG + chr3_4:68592303-68592322 None:intergenic 50.0%
CGGTTTAGATCTGACGCATG+TGG - chr3_4:68592310-68592329 Msa0517090:intron 50.0%
CAGATCTAAACCGAGTCCAG+TGG + chr3_4:68592303-68592322 None:intergenic 50.0%
CGGTTTAGATCTGACGCATG+TGG - chr3_4:68592310-68592329 Msa0517090:intron 50.0%
GTGGGGTTGACGTTCCACGT+AGG + chr3_4:68591810-68591829 None:intergenic 60.0%
GTGGGGTTGACGTTCCACGT+AGG + chr3_4:68591810-68591829 None:intergenic 60.0%
Chromosome Type Strat End Strand Name
chr3_4 gene 68591715 68593081 68591715 ID=Msa0517090;Name=Msa0517090
chr3_4 mRNA 68591715 68593081 68591715 ID=Msa0517090-mRNA-1;Parent=Msa0517090;Name=Msa0517090-mRNA-1;_AED=0.47;_eAED=0.63;_QI=0|0|0|0.66|1|1|3|0|69
chr3_4 exon 68593078 68593081 68593078 ID=Msa0517090-mRNA-1:exon:18203;Parent=Msa0517090-mRNA-1
chr3_4 exon 68592737 68592793 68592737 ID=Msa0517090-mRNA-1:exon:18202;Parent=Msa0517090-mRNA-1
chr3_4 exon 68591715 68591863 68591715 ID=Msa0517090-mRNA-1:exon:18201;Parent=Msa0517090-mRNA-1
chr3_4 CDS 68593078 68593081 68593078 ID=Msa0517090-mRNA-1:cds;Parent=Msa0517090-mRNA-1
chr3_4 CDS 68592737 68592793 68592737 ID=Msa0517090-mRNA-1:cds;Parent=Msa0517090-mRNA-1
chr3_4 CDS 68591715 68591863 68591715 ID=Msa0517090-mRNA-1:cds;Parent=Msa0517090-mRNA-1
Gene Sequence

>Msa0517090

ATGGGTTCTGTAGAGGAGAAAAAATATTCTGTTCGGGTGGAGCTTCACTTTGCTGAAGACCAACAAAATTTTGCTATGGATCTCAATGCTTTTCCGTTTGATTTAAATGAAGAACCATTGTTTGATTTACATGAAGAGCCACTGTTTGATTTACATCAAGAACTACATGATTTAAATGGTGAGGAAGAAAACTTTGCTACAGGAGAATAA

Protein sequence

>Msa0517090

MGSVEEKKYSVRVELHFAEDQQNFAMDLNAFPFDLNEEPLFDLHEEPLFDLHQELHDLNGEEENFATGE*