AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1172670


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1172670 MtrunA17_Chr7g0240391 100.000 52 0 0 1 52 1 52 4.25e-31 103
Msa1172670 MtrunA17_Chr8g0351841 98.077 52 1 0 1 52 1 52 3.45e-30 100
Msa1172670 MtrunA17_Chr7g0266561 52.500 40 19 0 10 49 9 48 6.24e-11 52.0
Msa1172670 MtrunA17_Chr6g0477821 52.500 40 19 0 10 49 9 48 9.05e-11 51.6
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1172670 AT2G03870.2 98.077 52 1 0 1 52 1 52 1.72e-30 102
Msa1172670 AT2G03870.1 98.077 52 1 0 1 52 1 52 1.72e-30 102
Msa1172670 AT2G23930.1 57.500 40 17 0 10 49 9 48 1.34e-11 53.9
Msa1172670 AT3G11500.2 55.000 40 18 0 10 49 9 48 9.59e-11 51.6
Msa1172670 AT3G11500.1 55.000 40 18 0 10 49 9 48 9.59e-11 51.6

Find 11 sgRNAs with CRISPR-Local

Find 119 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GTAGTGACAGGTACTCTAAA+AGG 0.295589 8_1:+2785981 Msa1172670:intron
TTAGCAAAATTTGTTGATAA+AGG 0.301879 8_1:+2783595 Msa1172670:CDS
GGTGTTCAAGTCAAGCTTAC+TGG 0.353916 8_1:+2783616 Msa1172670:CDS
CCAGGACAAGGTTAAGTAAC+TGG 0.396790 8_1:-2786010 None:intergenic
TGGGAGGAAAGAAACTGTTC+TGG 0.428213 8_1:+2783570 Msa1172670:CDS
CCAGTTACTTAACCTTGTCC+TGG 0.506664 8_1:+2786010 Msa1172670:CDS
TAGTGACAGGTACTCTAAAA+GGG 0.532671 8_1:+2785982 Msa1172670:intron
AAGCTTACTGGTGGCAGACA+AGG 0.544738 8_1:+2783628 Msa1172670:CDS
AAAACTCAACAGCTTCATCC+AGG 0.561824 8_1:-2786028 None:intergenic
CAACAGCTTCATCCAGGACA+AGG 0.654174 8_1:-2786022 None:intergenic
GTTCAAGTCAAGCTTACTGG+TGG 0.669583 8_1:+2783619 Msa1172670:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! TAAAATAAAGAAAAGAAATT+AGG - chr8_1:2783540-2783559 None:intergenic 10.0%
!! AAATAAAATAAAAAAGAGAA+AGG - chr8_1:2783669-2783688 None:intergenic 10.0%
!!! TTTAAAAAAAATAGATTTTG+AGG + chr8_1:2783985-2784004 Msa1172670:intron 10.0%
!!! ATTTAGAAAAAAATAGATTT+TGG + chr8_1:2784130-2784149 Msa1172670:intron 10.0%
!!! TTGTTAAAAAAATCATTTTT+AGG - chr8_1:2784188-2784207 None:intergenic 10.0%
!!! AAATGATTTTTTTAACAAAA+TGG + chr8_1:2784190-2784209 Msa1172670:intron 10.0%
!!! AAATTTTTTTATTCAAAAGA+TGG - chr8_1:2784985-2785004 None:intergenic 10.0%
!!! TTTATTTTATTTTTCAGTCT+GGG + chr8_1:2783551-2783570 Msa1172670:intron 15.0%
!!! ATCTTCAAAAAATGATTTTT+AGG - chr8_1:2784082-2784101 None:intergenic 15.0%
!!! TCTATTTTTTTCTAAATACA+AGG - chr8_1:2784127-2784146 None:intergenic 15.0%
!!! GTTGATTTAACAAAAATTTA+AGG + chr8_1:2784633-2784652 Msa1172670:intron 15.0%
!! TTTAAGAAAATGAAAATGTT+TGG - chr8_1:2784860-2784879 None:intergenic 15.0%
!!! TTGATTTGCTTTTAATATTA+TGG + chr8_1:2785127-2785146 Msa1172670:intron 15.0%
!!! GTTTTTTTTGTTTTGTTTTA+AGG + chr8_1:2785367-2785386 Msa1172670:intron 15.0%
!!! CTTTATTTTATTTTTCAGTC+TGG + chr8_1:2783550-2783569 Msa1172670:intron 20.0%
!!! TTAGCAAAATTTGTTGATAA+AGG + chr8_1:2783595-2783614 Msa1172670:CDS 20.0%
!!! TCTTATCATTAAATTGATTC+TGG + chr8_1:2783700-2783719 Msa1172670:intron 20.0%
!! TTGGATACATTCATATAAAT+AGG + chr8_1:2783740-2783759 Msa1172670:intron 20.0%
!! TGGATACATTCATATAAATA+GGG + chr8_1:2783741-2783760 Msa1172670:intron 20.0%
!! TCAAAAAAATCCAAAACAAA+CGG + chr8_1:2784288-2784307 Msa1172670:intron 20.0%
!! AATGTAAAATGATACATGTT+TGG + chr8_1:2784594-2784613 Msa1172670:intron 20.0%
!! GAATTGAATTTATGATGTTT+GGG - chr8_1:2784747-2784766 None:intergenic 20.0%
!! AGAATTGAATTTATGATGTT+TGG - chr8_1:2784748-2784767 None:intergenic 20.0%
!!! ATAATTGATTTTGACATGTT+TGG - chr8_1:2784810-2784829 None:intergenic 20.0%
!!! TTATGGATATTCTTATTTGT+AGG + chr8_1:2785144-2785163 Msa1172670:intron 20.0%
!! AAACAAAAAAAACATACACA+AGG - chr8_1:2785360-2785379 None:intergenic 20.0%
!!! AGCTTTTTATCTGAAATAAT+TGG + chr8_1:2785426-2785445 Msa1172670:intron 20.0%
!!! GCTTTTTATCTGAAATAATT+GGG + chr8_1:2785427-2785446 Msa1172670:intron 20.0%
!!! AAATGAGAGATATTCTAAAA+AGG + chr8_1:2785683-2785702 Msa1172670:intron 20.0%
!! CAATAAACATAAAGTAAGTT+TGG - chr8_1:2785825-2785844 None:intergenic 20.0%
!! AAAGTAAACATTGAAGATTA+TGG - chr8_1:2785922-2785941 None:intergenic 20.0%
! AAGTAAGATAAATATGCGAA+AGG - chr8_1:2783471-2783490 None:intergenic 25.0%
! GGCTTAAAGTAATTTATGTT+TGG + chr8_1:2783721-2783740 Msa1172670:intron 25.0%
! TACATTCATATAAATAGGGT+TGG + chr8_1:2783745-2783764 Msa1172670:intron 25.0%
! ATTCACTCAAAATCAATTCT+CGG - chr8_1:2783810-2783829 None:intergenic 25.0%
! TGATTCTGTAAAATTGATTG+TGG + chr8_1:2783830-2783849 Msa1172670:intron 25.0%
! CTACAATTTCTAACTTTGTT+TGG + chr8_1:2783863-2783882 Msa1172670:intron 25.0%
!! CTTTTATCGAGTAGAATTTA+GGG + chr8_1:2783947-2783966 Msa1172670:intron 25.0%
!! CAAGTAAAATCAATTTTGGA+GGG - chr8_1:2784325-2784344 None:intergenic 25.0%
!! TCAAGTAAAATCAATTTTGG+AGG - chr8_1:2784326-2784345 None:intergenic 25.0%
!! GCTTCAAGTAAAATCAATTT+TGG - chr8_1:2784329-2784348 None:intergenic 25.0%
!! ACTAAAAGTGATTTGTGTTT+GGG - chr8_1:2784431-2784450 None:intergenic 25.0%
!! AACTAAAAGTGATTTGTGTT+TGG - chr8_1:2784432-2784451 None:intergenic 25.0%
!! GTATTTTGTAGAATTGCTTT+TGG - chr8_1:2784469-2784488 None:intergenic 25.0%
! CAAAATCAATTATACATGTG+TGG + chr8_1:2784817-2784836 Msa1172670:intron 25.0%
! AAATGAAAATGTTTGGATGA+GGG - chr8_1:2784853-2784872 None:intergenic 25.0%
! AAAATGAAAATGTTTGGATG+AGG - chr8_1:2784854-2784873 None:intergenic 25.0%
! CACAGTTAATAACATACATA+AGG - chr8_1:2785398-2785417 None:intergenic 25.0%
!!! GTGAGTTTTTCAAATTGTAA+GGG + chr8_1:2785449-2785468 Msa1172670:intron 25.0%
!!! TTTCCTATTGAACCATTTTT+GGG + chr8_1:2785478-2785497 Msa1172670:intron 25.0%
!! TTAATACAATTCTTTGCTGT+GGG + chr8_1:2785537-2785556 Msa1172670:intron 25.0%
! GATGAAATAATTGCTCTATT+TGG + chr8_1:2785559-2785578 Msa1172670:intron 25.0%
! AATAATTGCTCTATTTGGAT+TGG + chr8_1:2785564-2785583 Msa1172670:intron 25.0%
! ATAATTGCTCTATTTGGATT+GGG + chr8_1:2785565-2785584 Msa1172670:intron 25.0%
! AATACTTGTTTCAGAACTTA+TGG + chr8_1:2785620-2785639 Msa1172670:intron 25.0%
!! ATGGTTCTTTCAATTTTCAA+TGG + chr8_1:2785866-2785885 Msa1172670:intron 25.0%
!! AATGTTTACTTTAGAGATGA+GGG + chr8_1:2785930-2785949 Msa1172670:intron 25.0%
!!! ATTTTATTTTTCAGTCTGGG+AGG + chr8_1:2783554-2783573 Msa1172670:intron 30.0%
TAAAAAAGAGAAAGGTGAGT+TGG - chr8_1:2783661-2783680 None:intergenic 30.0%
!! TACACCTCTAAAATCAATTC+TGG - chr8_1:2783906-2783925 None:intergenic 30.0%
! GCTTTTATCGAGTAGAATTT+AGG + chr8_1:2783946-2783965 Msa1172670:intron 30.0%
!! TAGATTTTGGAAAAGCTACT+TGG + chr8_1:2784143-2784162 Msa1172670:intron 30.0%
! CTAAAAGTGATTTGTGTTTG+GGG - chr8_1:2784430-2784449 None:intergenic 30.0%
!!! AAGCTACAATTTGTTGCTTT+TGG - chr8_1:2784678-2784697 None:intergenic 30.0%
!!! TAGGTCAATATGTCTTGTTT+TGG + chr8_1:2785163-2785182 Msa1172670:intron 30.0%
!! GGTGAGTTTTTCAAATTGTA+AGG + chr8_1:2785448-2785467 Msa1172670:intron 30.0%
! CTTTCCTATTGAACCATTTT+TGG + chr8_1:2785477-2785496 Msa1172670:intron 30.0%
!! TTCCTATTGAACCATTTTTG+GGG + chr8_1:2785479-2785498 Msa1172670:intron 30.0%
CTTAATACAATTCTTTGCTG+TGG + chr8_1:2785536-2785555 Msa1172670:intron 30.0%
! GAGATATTCTAAAAAGGTTG+AGG + chr8_1:2785689-2785708 Msa1172670:intron 30.0%
! ATATTCTAAAAAGGTTGAGG+TGG + chr8_1:2785692-2785711 Msa1172670:intron 30.0%
!! TTTTCAATGGATTCTTGTCT+TGG + chr8_1:2785879-2785898 Msa1172670:intron 30.0%
! CAATGTTTACTTTAGAGATG+AGG + chr8_1:2785929-2785948 Msa1172670:intron 30.0%
! ATGTTTACTTTAGAGATGAG+GGG + chr8_1:2785931-2785950 Msa1172670:intron 30.0%
! ATTTGTTGAATTGTAGTGAC+AGG + chr8_1:2785969-2785988 Msa1172670:intron 30.0%
! TGCGAAAGGTGATGAAATTT+TGG - chr8_1:2783457-2783476 None:intergenic 35.0%
!! CAATTTTGGAGGGAGAATAA+GGG - chr8_1:2784315-2784334 None:intergenic 35.0%
!! TCAATTTTGGAGGGAGAATA+AGG - chr8_1:2784316-2784335 None:intergenic 35.0%
AATTCTTGTAGAAGCTGAAC+TGG - chr8_1:2784523-2784542 None:intergenic 35.0%
TAGAGAGTCAAAAGTGATTC+TGG - chr8_1:2784778-2784797 None:intergenic 35.0%
!! AGAATCACTTTTGACTCTCT+AGG + chr8_1:2784777-2784796 Msa1172670:intron 35.0%
TACCCCAAAAATGGTTCAAT+AGG - chr8_1:2785484-2785503 None:intergenic 35.0%
!!! AACCATTTTTGGGGTATTCT+TGG + chr8_1:2785488-2785507 Msa1172670:intron 35.0%
! TAGTGACAGGTACTCTAAAA+GGG + chr8_1:2785982-2786001 Msa1172670:intron 35.0%
! TTGTTTGGTTCCACTTCTAG+AGG + chr8_1:2783878-2783897 Msa1172670:intron 40.0%
! TGTTTGGTTCCACTTCTAGA+GGG + chr8_1:2783879-2783898 Msa1172670:intron 40.0%
!! GGGTCCAGAATTGATTTTAG+AGG + chr8_1:2783899-2783918 Msa1172670:intron 40.0%
TACAAGGAGCTCAAGTGTAA+GGG - chr8_1:2784111-2784130 None:intergenic 40.0%
ATACAAGGAGCTCAAGTGTA+AGG - chr8_1:2784112-2784131 None:intergenic 40.0%
! GAATAAGGGTCCGTTTGTTT+TGG - chr8_1:2784301-2784320 None:intergenic 40.0%
AGAGTCAAAAGTGATTCTGG+AGG - chr8_1:2784775-2784794 None:intergenic 40.0%
! ACATGTGTCATTGCAGTGTT+TGG + chr8_1:2784885-2784904 Msa1172670:intron 40.0%
TGTTTGGTATCTGTGTCTGT+CGG + chr8_1:2784901-2784920 Msa1172670:intron 40.0%
CACCAAGAATACCCCAAAAA+TGG - chr8_1:2785493-2785512 None:intergenic 40.0%
! CTCTATTTGGATTGGGTTCT+AGG + chr8_1:2785572-2785591 Msa1172670:intron 40.0%
!!! TTGGATTGGGTTCTAGGTTT+TGG + chr8_1:2785578-2785597 Msa1172670:intron 40.0%
!!! TGGATTGGGTTCTAGGTTTT+GGG + chr8_1:2785579-2785598 Msa1172670:intron 40.0%
TATCCTTAAGCGTTTGTTCG+CGG + chr8_1:2785647-2785666 Msa1172670:intron 40.0%
TCTCCTTTGTGTTCATGCTA+TGG + chr8_1:2785847-2785866 Msa1172670:intron 40.0%
GAACCATAGCATGAACACAA+AGG - chr8_1:2785853-2785872 None:intergenic 40.0%
! TCAATGGATTCTTGTCTTGG+AGG + chr8_1:2785882-2785901 Msa1172670:intron 40.0%
GTAGTGACAGGTACTCTAAA+AGG + chr8_1:2785981-2786000 Msa1172670:intron 40.0%
AAAACTCAACAGCTTCATCC+AGG - chr8_1:2786031-2786050 None:intergenic 40.0%
TGGGAGGAAAGAAACTGTTC+TGG + chr8_1:2783570-2783589 Msa1172670:CDS 45.0%
GGTGTTCAAGTCAAGCTTAC+TGG + chr8_1:2783616-2783635 Msa1172670:CDS 45.0%
GTTCAAGTCAAGCTTACTGG+TGG + chr8_1:2783619-2783638 Msa1172670:CDS 45.0%
! AATTCTGGACCCTCTAGAAG+TGG - chr8_1:2783891-2783910 None:intergenic 45.0%
AAGCTGAACTGGTTGTGCAT+GGG - chr8_1:2784512-2784531 None:intergenic 45.0%
!!! GGATTGGGTTCTAGGTTTTG+GGG + chr8_1:2785580-2785599 Msa1172670:intron 45.0%
!!! GATTGGGTTCTAGGTTTTGG+GGG + chr8_1:2785581-2785600 Msa1172670:intron 45.0%
TAACCGCGAACAAACGCTTA+AGG - chr8_1:2785653-2785672 None:intergenic 45.0%
TAAGCGTTTGTTCGCGGTTA+TGG + chr8_1:2785653-2785672 Msa1172670:intron 45.0%
CCAGGACAAGGTTAAGTAAC+TGG - chr8_1:2786013-2786032 None:intergenic 45.0%
CCAGTTACTTAACCTTGTCC+TGG + chr8_1:2786010-2786029 Msa1172670:CDS 45.0%
AAGCTTACTGGTGGCAGACA+AGG + chr8_1:2783628-2783647 Msa1172670:CDS 50.0%
AGCTGAACTGGTTGTGCATG+GGG - chr8_1:2784511-2784530 None:intergenic 50.0%
GAAGCTGAACTGGTTGTGCA+TGG - chr8_1:2784513-2784532 None:intergenic 50.0%
! GGGGTATTCTTGGTGAGCAT+TGG + chr8_1:2785498-2785517 Msa1172670:intron 50.0%
CAACAGCTTCATCCAGGACA+AGG - chr8_1:2786025-2786044 None:intergenic 50.0%
Chromosome Type Strat End Strand Name
chr8_1 gene 2783438 2786055 2783438 ID=Msa1172670;Name=Msa1172670
chr8_1 mRNA 2783438 2786055 2783438 ID=Msa1172670-mRNA-1;Parent=Msa1172670;Name=Msa1172670-mRNA-1;_AED=0.13;_eAED=0.14;_QI=0|0|0|0.66|1|0.66|3|0|52
chr8_1 exon 2783438 2783440 2783438 ID=Msa1172670-mRNA-1:exon:999;Parent=Msa1172670-mRNA-1
chr8_1 exon 2783568 2783649 2783568 ID=Msa1172670-mRNA-1:exon:1000;Parent=Msa1172670-mRNA-1
chr8_1 exon 2785985 2786055 2785985 ID=Msa1172670-mRNA-1:exon:1001;Parent=Msa1172670-mRNA-1
chr8_1 CDS 2783438 2783440 2783438 ID=Msa1172670-mRNA-1:cds;Parent=Msa1172670-mRNA-1
chr8_1 CDS 2783568 2783649 2783568 ID=Msa1172670-mRNA-1:cds;Parent=Msa1172670-mRNA-1
chr8_1 CDS 2785985 2786055 2785985 ID=Msa1172670-mRNA-1:cds;Parent=Msa1172670-mRNA-1
Gene Sequence

>Msa1172670

ATGTCTGGGAGGAAAGAAACTGTTCTGGATTTAGCAAAATTTGTTGATAAAGGTGTTCAAGTCAAGCTTACTGGTGGCAGACAAGTGACAGGTACTCTAAAAGGGTATGACCAGTTACTTAACCTTGTCCTGGATGAAGCTGTTGAGTTTTTAAGA

Protein sequence

>Msa1172670

MSGRKETVLDLAKFVDKGVQVKLTGGRQVTGTLKGYDQLLNLVLDEAVEFLR