AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0317150

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0317150 MtrunA17_Chr2g0290251 99.010 101 1 0 1 101 1 101 6.85e-70 203
Msa0317150 MtrunA17_Chr2g0328651 91.525 59 5 0 1 59 1 59 2.29e-32 107
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0317150 AT4G16450.2 82.178 101 18 0 1 101 1 101 1.27e-58 175
Msa0317150 AT4G16450.1 82.178 101 18 0 1 101 1 101 1.27e-58 175

Find 43 sgRNAs with CRISPR-Local

Find 125 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
AGGGATTATGTGTATCAATT+TGG 0.239012 2_4:-14704776 Msa0317150:three_prime_UTR
TGGTGGATTGATTGGTGTTA+TGG 0.274889 2_4:-14704997 Msa0317150:CDS
GTCACCGTCGGCTATCTTTC+CGG 0.284167 2_4:-14705141 Msa0317150:intron
GGTGGATTGATTGGTGTTAT+GGG 0.287599 2_4:-14704996 Msa0317150:CDS
CGATCAATGACTGGGTATTC+TGG 0.288339 2_4:+14705243 None:intergenic
GGGATTAAGCCTGGAATTAG+AGG 0.339081 2_4:-14705035 Msa0317150:CDS
ATTGAAGGTCCTCTAATTCC+AGG 0.366980 2_4:+14705026 None:intergenic
GATAAATAGCTATCTATTAT+CGG 0.369900 2_4:-14704538 Msa0317150:three_prime_UTR
CGAGCTACCTCAGCATCATT+AGG 0.404008 2_4:+14704921 None:intergenic
ATAAATAGCTATCTATTATC+GGG 0.424113 2_4:-14704537 Msa0317150:three_prime_UTR
TTCATGAAGTTGCATTCAAA+GGG 0.430751 2_4:+14704657 None:intergenic
CCGACGACGGTTGTGAATGG+TGG 0.448497 2_4:+14705216 None:intergenic
TATGCTTATCAGAATTCTGC+TGG 0.449165 2_4:-14704963 Msa0317150:CDS
ATGGTGACTGGTGGATTGAT+TGG 0.453660 2_4:-14705005 Msa0317150:CDS
TTTCCGACGACGGTTGTGAA+TGG 0.455926 2_4:+14705213 None:intergenic
AATCCACCAGTCACCATTGA+AGG 0.467586 2_4:+14705011 None:intergenic
GGTGGGTTGCGATCAATGAC+TGG 0.467714 2_4:+14705234 None:intergenic
CATCACAATAACAACAACAT+AGG 0.473875 2_4:+14704810 None:intergenic
TGTTTGCTACTTATTAGTAA+TGG 0.478345 2_4:-14704626 Msa0317150:three_prime_UTR
GAATTCTGCTGGGAGAATCA+TGG 0.480128 2_4:-14704952 Msa0317150:CDS
ATTCATGAAGTTGCATTCAA+AGG 0.487532 2_4:+14704656 None:intergenic
TGGAATTAGAGGACCTTCAA+TGG 0.490865 2_4:-14705024 Msa0317150:CDS
GGATTGATTGGTGTTATGGG+TGG 0.506463 2_4:-14704993 Msa0317150:CDS
AATTCTGCTGGGAGAATCAT+GGG 0.523726 2_4:-14704951 Msa0317150:CDS
GCCGACGGTGACGGAAATGC+CGG 0.525742 2_4:+14705152 None:intergenic
ATCACAATAACAACAACATA+GGG 0.532707 2_4:+14704811 None:intergenic
TAATGGAACAAATCTTGAGT+TGG 0.544134 2_4:-14704609 Msa0317150:three_prime_UTR
CGACGACGGTTGTGAATGGT+GGG 0.550667 2_4:+14705217 None:intergenic
CTTCGTTTCACCACCATCGC+CGG 0.554404 2_4:-14705171 Msa0317150:CDS
TTTCTTTCCTAATGATGCTG+AGG 0.555841 2_4:-14704928 Msa0317150:CDS
AGTGTTGAAGTTTCCGACGA+CGG 0.565702 2_4:+14705203 None:intergenic
AGAGGACCTTCAATGGTGAC+TGG 0.585809 2_4:-14705017 Msa0317150:CDS
GCCGGCATTTCCGTCACCGT+CGG 0.586235 2_4:-14705153 Msa0317150:CDS
GGTGACGGAAATGCCGGCGA+TGG 0.591153 2_4:+14705158 None:intergenic
GACGGAAATGCCGGCGATGG+TGG 0.600494 2_4:+14705161 None:intergenic
GGACCTTCAATGGTGACTGG+TGG 0.619185 2_4:-14705014 Msa0317150:CDS
GGAAAGATAGCCGACGGTGA+CGG 0.625891 2_4:+14705143 None:intergenic
CCACCATTCACAACCGTCGT+CGG 0.631435 2_4:-14705216 Msa0317150:CDS
TAAATAGCTATCTATTATCG+GGG 0.634351 2_4:-14704536 Msa0317150:three_prime_UTR
ATGCTTATCAGAATTCTGCT+GGG 0.634370 2_4:-14704962 Msa0317150:CDS
CGGCGATGGTGGTGAAACGA+AGG 0.647569 2_4:+14705172 None:intergenic
GTTACCGGAAAGATAGCCGA+CGG 0.709244 2_4:+14705137 None:intergenic
GTGGGTTGCGATCAATGACT+GGG 0.713206 2_4:+14705235 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! AAATTGTAACTTTTTGAAAT+TGG - chr2_4:14704793-14704812 Msa0317150:three_prime_UTR 15.0%
!!! AATTGTAACTTTTTGAAATT+GGG - chr2_4:14704794-14704813 Msa0317150:three_prime_UTR 15.0%
!!! AAATTGTAACTTTTTGAAAT+TGG - chr2_4:14704793-14704812 Msa0317150:three_prime_UTR 15.0%
!!! AATTGTAACTTTTTGAAATT+GGG - chr2_4:14704794-14704813 Msa0317150:three_prime_UTR 15.0%
!! TTAATTCAATTGAAGAAAGA+TGG + chr2_4:14704754-14704773 None:intergenic 20.0%
!! GATAAATAGCTATCTATTAT+CGG - chr2_4:14705328-14705347 Msa0317150:five_prime_UTR 20.0%
!! ATAAATAGCTATCTATTATC+GGG - chr2_4:14705329-14705348 Msa0317150:five_prime_UTR 20.0%
!! TTAATTCAATTGAAGAAAGA+TGG + chr2_4:14704754-14704773 None:intergenic 20.0%
!! GATAAATAGCTATCTATTAT+CGG - chr2_4:14705328-14705347 Msa0317150:five_prime_UTR 20.0%
!! ATAAATAGCTATCTATTATC+GGG - chr2_4:14705329-14705348 Msa0317150:five_prime_UTR 20.0%
! TCAACAACTCATTAAAAAGA+GGG + chr2_4:14705023-14705042 None:intergenic 25.0%
! TTCAACAACTCATTAAAAAG+AGG + chr2_4:14705024-14705043 None:intergenic 25.0%
! ATCACAATAACAACAACATA+GGG + chr2_4:14705058-14705077 None:intergenic 25.0%
!! ATTGTGATGAATGAATTTTG+AGG - chr2_4:14705070-14705089 Msa0317150:intron 25.0%
!! TTGTGATGAATGAATTTTGA+GGG - chr2_4:14705071-14705090 Msa0317150:intron 25.0%
!! TGTTTGCTACTTATTAGTAA+TGG - chr2_4:14705240-14705259 Msa0317150:CDS 25.0%
! TAAATAGCTATCTATTATCG+GGG - chr2_4:14705330-14705349 Msa0317150:five_prime_UTR 25.0%
! TCAACAACTCATTAAAAAGA+GGG + chr2_4:14705023-14705042 None:intergenic 25.0%
! TTCAACAACTCATTAAAAAG+AGG + chr2_4:14705024-14705043 None:intergenic 25.0%
! ATCACAATAACAACAACATA+GGG + chr2_4:14705058-14705077 None:intergenic 25.0%
!! ATTGTGATGAATGAATTTTG+AGG - chr2_4:14705070-14705089 Msa0317150:intron 25.0%
!! TTGTGATGAATGAATTTTGA+GGG - chr2_4:14705071-14705090 Msa0317150:intron 25.0%
!! TGTTTGCTACTTATTAGTAA+TGG - chr2_4:14705240-14705259 Msa0317150:CDS 25.0%
! TAAATAGCTATCTATTATCG+GGG - chr2_4:14705330-14705349 Msa0317150:five_prime_UTR 25.0%
AATTGAAGAAAGATGGTTAC+CGG + chr2_4:14704747-14704766 None:intergenic 30.0%
! AATTGGGAATTCTGTGTTTT+AGG - chr2_4:14704810-14704829 Msa0317150:three_prime_UTR 30.0%
! ATTGGGAATTCTGTGTTTTA+GGG - chr2_4:14704811-14704830 Msa0317150:three_prime_UTR 30.0%
CAACAACTCATTAAAAAGAG+GGG + chr2_4:14705022-14705041 None:intergenic 30.0%
CATCACAATAACAACAACAT+AGG + chr2_4:14705059-14705078 None:intergenic 30.0%
AGGGATTATGTGTATCAATT+TGG - chr2_4:14705090-14705109 Msa0317150:intron 30.0%
! ATTTTGCTGGTAAAGCTTTA+GGG - chr2_4:14705156-14705175 Msa0317150:CDS 30.0%
TTCATGAAGTTGCATTCAAA+GGG + chr2_4:14705212-14705231 None:intergenic 30.0%
ATTCATGAAGTTGCATTCAA+AGG + chr2_4:14705213-14705232 None:intergenic 30.0%
TAATGGAACAAATCTTGAGT+TGG - chr2_4:14705257-14705276 Msa0317150:CDS 30.0%
GCTGAAAACAAGTGAATTTA+CGG - chr2_4:14705362-14705381 Msa0317150:five_prime_UTR 30.0%
AATTGAAGAAAGATGGTTAC+CGG + chr2_4:14704747-14704766 None:intergenic 30.0%
! AATTGGGAATTCTGTGTTTT+AGG - chr2_4:14704810-14704829 Msa0317150:three_prime_UTR 30.0%
! ATTGGGAATTCTGTGTTTTA+GGG - chr2_4:14704811-14704830 Msa0317150:three_prime_UTR 30.0%
CAACAACTCATTAAAAAGAG+GGG + chr2_4:14705022-14705041 None:intergenic 30.0%
CATCACAATAACAACAACAT+AGG + chr2_4:14705059-14705078 None:intergenic 30.0%
AGGGATTATGTGTATCAATT+TGG - chr2_4:14705090-14705109 Msa0317150:intron 30.0%
! ATTTTGCTGGTAAAGCTTTA+GGG - chr2_4:14705156-14705175 Msa0317150:CDS 30.0%
TTCATGAAGTTGCATTCAAA+GGG + chr2_4:14705212-14705231 None:intergenic 30.0%
ATTCATGAAGTTGCATTCAA+AGG + chr2_4:14705213-14705232 None:intergenic 30.0%
TAATGGAACAAATCTTGAGT+TGG - chr2_4:14705257-14705276 Msa0317150:CDS 30.0%
TATGCTTATCAGAATTCTGC+TGG - chr2_4:14704903-14704922 Msa0317150:exon 35.0%
ATGCTTATCAGAATTCTGCT+GGG - chr2_4:14704904-14704923 Msa0317150:exon 35.0%
TTTCTTTCCTAATGATGCTG+AGG - chr2_4:14704938-14704957 Msa0317150:CDS 35.0%
! TGTGTACTTTTGCATTTTGC+TGG - chr2_4:14705143-14705162 Msa0317150:CDS 35.0%
! CATTTTGCTGGTAAAGCTTT+AGG - chr2_4:14705155-14705174 Msa0317150:CDS 35.0%
TATGCTTATCAGAATTCTGC+TGG - chr2_4:14704903-14704922 Msa0317150:exon 35.0%
ATGCTTATCAGAATTCTGCT+GGG - chr2_4:14704904-14704923 Msa0317150:exon 35.0%
TTTCTTTCCTAATGATGCTG+AGG - chr2_4:14704938-14704957 Msa0317150:CDS 35.0%
! TGTGTACTTTTGCATTTTGC+TGG - chr2_4:14705143-14705162 Msa0317150:CDS 35.0%
! CATTTTGCTGGTAAAGCTTT+AGG - chr2_4:14705155-14705174 Msa0317150:CDS 35.0%
!!! TGTGTTTTAGGGATTAAGCC+TGG - chr2_4:14704822-14704841 Msa0317150:three_prime_UTR 40.0%
ATTGAAGGTCCTCTAATTCC+AGG + chr2_4:14704843-14704862 None:intergenic 40.0%
TGGAATTAGAGGACCTTCAA+TGG - chr2_4:14704842-14704861 Msa0317150:three_prime_UTR 40.0%
!! TGGTGGATTGATTGGTGTTA+TGG - chr2_4:14704869-14704888 Msa0317150:three_prime_UTR 40.0%
!! GGTGGATTGATTGGTGTTAT+GGG - chr2_4:14704870-14704889 Msa0317150:three_prime_UTR 40.0%
AATTCTGCTGGGAGAATCAT+GGG - chr2_4:14704915-14704934 Msa0317150:CDS 40.0%
!!! GAGTTGGACCATGTTGTTTT+TGG - chr2_4:14705273-14705292 Msa0317150:CDS 40.0%
!!! GGACCATGTTGTTTTTGGTT+TGG - chr2_4:14705278-14705297 Msa0317150:exon 40.0%
CCACCAAACCAAAAACAACA+TGG + chr2_4:14705284-14705303 None:intergenic 40.0%
!!! CCATGTTGTTTTTGGTTTGG+TGG - chr2_4:14705281-14705300 Msa0317150:exon 40.0%
!!! TGTGTTTTAGGGATTAAGCC+TGG - chr2_4:14704822-14704841 Msa0317150:three_prime_UTR 40.0%
ATTGAAGGTCCTCTAATTCC+AGG + chr2_4:14704843-14704862 None:intergenic 40.0%
TGGAATTAGAGGACCTTCAA+TGG - chr2_4:14704842-14704861 Msa0317150:three_prime_UTR 40.0%
!! TGGTGGATTGATTGGTGTTA+TGG - chr2_4:14704869-14704888 Msa0317150:three_prime_UTR 40.0%
!! GGTGGATTGATTGGTGTTAT+GGG - chr2_4:14704870-14704889 Msa0317150:three_prime_UTR 40.0%
AATTCTGCTGGGAGAATCAT+GGG - chr2_4:14704915-14704934 Msa0317150:CDS 40.0%
!!! GAGTTGGACCATGTTGTTTT+TGG - chr2_4:14705273-14705292 Msa0317150:CDS 40.0%
!!! GGACCATGTTGTTTTTGGTT+TGG - chr2_4:14705278-14705297 Msa0317150:exon 40.0%
CCACCAAACCAAAAACAACA+TGG + chr2_4:14705284-14705303 None:intergenic 40.0%
!!! CCATGTTGTTTTTGGTTTGG+TGG - chr2_4:14705281-14705300 Msa0317150:exon 40.0%
CGATCAATGACTGGGTATTC+TGG + chr2_4:14704626-14704645 None:intergenic 45.0%
! AGTGTTGAAGTTTCCGACGA+CGG + chr2_4:14704666-14704685 None:intergenic 45.0%
GGGATTAAGCCTGGAATTAG+AGG - chr2_4:14704831-14704850 Msa0317150:three_prime_UTR 45.0%
AATCCACCAGTCACCATTGA+AGG + chr2_4:14704858-14704877 None:intergenic 45.0%
!! ATGGTGACTGGTGGATTGAT+TGG - chr2_4:14704861-14704880 Msa0317150:three_prime_UTR 45.0%
!! GGATTGATTGGTGTTATGGG+TGG - chr2_4:14704873-14704892 Msa0317150:three_prime_UTR 45.0%
GAATTCTGCTGGGAGAATCA+TGG - chr2_4:14704914-14704933 Msa0317150:CDS 45.0%
CGATCAATGACTGGGTATTC+TGG + chr2_4:14704626-14704645 None:intergenic 45.0%
! AGTGTTGAAGTTTCCGACGA+CGG + chr2_4:14704666-14704685 None:intergenic 45.0%
GGGATTAAGCCTGGAATTAG+AGG - chr2_4:14704831-14704850 Msa0317150:three_prime_UTR 45.0%
AATCCACCAGTCACCATTGA+AGG + chr2_4:14704858-14704877 None:intergenic 45.0%
!! ATGGTGACTGGTGGATTGAT+TGG - chr2_4:14704861-14704880 Msa0317150:three_prime_UTR 45.0%
!! GGATTGATTGGTGTTATGGG+TGG - chr2_4:14704873-14704892 Msa0317150:three_prime_UTR 45.0%
GAATTCTGCTGGGAGAATCA+TGG - chr2_4:14704914-14704933 Msa0317150:CDS 45.0%
! GTGGGTTGCGATCAATGACT+GGG + chr2_4:14704634-14704653 None:intergenic 50.0%
TTTCCGACGACGGTTGTGAA+TGG + chr2_4:14704656-14704675 None:intergenic 50.0%
GTTACCGGAAAGATAGCCGA+CGG + chr2_4:14704732-14704751 None:intergenic 50.0%
AGAGGACCTTCAATGGTGAC+TGG - chr2_4:14704849-14704868 Msa0317150:three_prime_UTR 50.0%
CGAGCTACCTCAGCATCATT+AGG + chr2_4:14704948-14704967 None:intergenic 50.0%
! GTGGGTTGCGATCAATGACT+GGG + chr2_4:14704634-14704653 None:intergenic 50.0%
TTTCCGACGACGGTTGTGAA+TGG + chr2_4:14704656-14704675 None:intergenic 50.0%
GTTACCGGAAAGATAGCCGA+CGG + chr2_4:14704732-14704751 None:intergenic 50.0%
AGAGGACCTTCAATGGTGAC+TGG - chr2_4:14704849-14704868 Msa0317150:three_prime_UTR 50.0%
CGAGCTACCTCAGCATCATT+AGG + chr2_4:14704948-14704967 None:intergenic 50.0%
!! GGTGGGTTGCGATCAATGAC+TGG + chr2_4:14704635-14704654 None:intergenic 55.0%
CGACGACGGTTGTGAATGGT+GGG + chr2_4:14704652-14704671 None:intergenic 55.0%
CCACCATTCACAACCGTCGT+CGG - chr2_4:14704650-14704669 Msa0317150:three_prime_UTR 55.0%
CTTCGTTTCACCACCATCGC+CGG - chr2_4:14704695-14704714 Msa0317150:three_prime_UTR 55.0%
GGAAAGATAGCCGACGGTGA+CGG + chr2_4:14704726-14704745 None:intergenic 55.0%
! GTCACCGTCGGCTATCTTTC+CGG - chr2_4:14704725-14704744 Msa0317150:three_prime_UTR 55.0%
GGACCTTCAATGGTGACTGG+TGG - chr2_4:14704852-14704871 Msa0317150:three_prime_UTR 55.0%
!! GGTGGGTTGCGATCAATGAC+TGG + chr2_4:14704635-14704654 None:intergenic 55.0%
CGACGACGGTTGTGAATGGT+GGG + chr2_4:14704652-14704671 None:intergenic 55.0%
CCACCATTCACAACCGTCGT+CGG - chr2_4:14704650-14704669 Msa0317150:three_prime_UTR 55.0%
CTTCGTTTCACCACCATCGC+CGG - chr2_4:14704695-14704714 Msa0317150:three_prime_UTR 55.0%
GGAAAGATAGCCGACGGTGA+CGG + chr2_4:14704726-14704745 None:intergenic 55.0%
! GTCACCGTCGGCTATCTTTC+CGG - chr2_4:14704725-14704744 Msa0317150:three_prime_UTR 55.0%
GGACCTTCAATGGTGACTGG+TGG - chr2_4:14704852-14704871 Msa0317150:three_prime_UTR 55.0%
CCGACGACGGTTGTGAATGG+TGG + chr2_4:14704653-14704672 None:intergenic 60.0%
! CGGCGATGGTGGTGAAACGA+AGG + chr2_4:14704697-14704716 None:intergenic 60.0%
CCGACGACGGTTGTGAATGG+TGG + chr2_4:14704653-14704672 None:intergenic 60.0%
! CGGCGATGGTGGTGAAACGA+AGG + chr2_4:14704697-14704716 None:intergenic 60.0%
GACGGAAATGCCGGCGATGG+TGG + chr2_4:14704708-14704727 None:intergenic 65.0%
!! GGTGACGGAAATGCCGGCGA+TGG + chr2_4:14704711-14704730 None:intergenic 65.0%
GCCGGCATTTCCGTCACCGT+CGG - chr2_4:14704713-14704732 Msa0317150:three_prime_UTR 65.0%
!! GCCGACGGTGACGGAAATGC+CGG + chr2_4:14704717-14704736 None:intergenic 65.0%
GACGGAAATGCCGGCGATGG+TGG + chr2_4:14704708-14704727 None:intergenic 65.0%
!! GGTGACGGAAATGCCGGCGA+TGG + chr2_4:14704711-14704730 None:intergenic 65.0%
GCCGGCATTTCCGTCACCGT+CGG - chr2_4:14704713-14704732 Msa0317150:three_prime_UTR 65.0%
!! GCCGACGGTGACGGAAATGC+CGG + chr2_4:14704717-14704736 None:intergenic 65.0%
Chromosome Type Strat End Strand Name
chr2_4 gene 14704505 14705383 14704505 ID=Msa0317150;Name=Msa0317150
chr2_4 mRNA 14704505 14705383 14704505 ID=Msa0317150-mRNA-1;Parent=Msa0317150;Name=Msa0317150-mRNA-1;_AED=0.00;_eAED=0.00;_QI=88|1|1|1|1|1|2|400|101
chr2_4 exon 14704505 14705056 14704505 ID=Msa0317150-mRNA-1:exon:5547;Parent=Msa0317150-mRNA-1
chr2_4 exon 14705142 14705383 14705142 ID=Msa0317150-mRNA-1:exon:5546;Parent=Msa0317150-mRNA-1
chr2_4 five_prime_UTR 14705296 14705383 14705296 ID=Msa0317150-mRNA-1:five_prime_utr;Parent=Msa0317150-mRNA-1
chr2_4 CDS 14705142 14705295 14705142 ID=Msa0317150-mRNA-1:cds;Parent=Msa0317150-mRNA-1
chr2_4 CDS 14704905 14705056 14704905 ID=Msa0317150-mRNA-1:cds;Parent=Msa0317150-mRNA-1
chr2_4 three_prime_UTR 14704505 14704904 14704505 ID=Msa0317150-mRNA-1:three_prime_utr;Parent=Msa0317150-mRNA-1
Gene Sequence

>Msa0317150

ATGAACACAGACATTACAGCGTCAACAAAACCAGAATACCCAGTCATTGATCGCAACCCACCATTCACAACCGTCGTCGGAAACTTCAACACTCTCGATTACCTTCGTTTCACCACCATCGCCGGCATTTCCGTCACCGTCGGCTATCTTTCCGGGATTAAGCCTGGAATTAGAGGACCTTCAATGGTGACTGGTGGATTGATTGGTGTTATGGGTGGATTCATGTATGCTTATCAGAATTCTGCTGGGAGAATCATGGGTTTCTTTCCTAATGATGCTGAGGTAGCTCGTCACAACAAAAAATGA
Protein sequence

>Msa0317150

MNTDITASTKPEYPVIDRNPPFTTVVGNFNTLDYLRFTTIAGISVTVGYLSGIKPGIRGPSMVTGGLIGVMGGFMYAYQNSAGRIMGFFPNDAEVARHNKK*