AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1182690


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1182690 MtrunA17_Chr8g0337781 98.630 73 1 0 1 73 1 73 1.16e-46 142
Msa1182690 MtrunA17_Chr8g0337711 65.753 73 25 0 1 73 1 73 4.95e-30 100
Msa1182690 MtrunA17_Chr6g0458744 62.162 74 26 2 1 73 37 109 1.80e-22 82.8
Msa1182690 MtrunA17_Chr6g0458644 62.162 74 26 2 1 73 37 109 1.80e-22 82.8
Msa1182690 MtrunA17_Chr8g0337731 56.757 74 31 1 1 73 1 74 2.80e-22 81.3
Msa1182690 MtrunA17_Chr6g0458787 60.811 74 27 2 1 73 1 73 4.18e-22 80.9
Msa1182690 MtrunA17_Chr6g0458701 60.811 74 27 2 1 73 37 109 6.75e-22 81.3
Msa1182690 MtrunA17_Chr8g0337741 57.353 68 29 0 6 73 5 72 5.06e-21 78.2
Msa1182690 MtrunA17_Chr6g0458807 59.459 74 28 2 1 73 1 73 5.93e-21 77.8
Msa1182690 MtrunA17_Chr8g0337061 49.315 73 36 1 1 72 9 81 1.43e-20 77.4
Msa1182690 MtrunA17_Chr8g0337721 55.405 74 32 1 1 73 1 74 2.47e-20 76.3
Msa1182690 MtrunA17_Chr8g0337771 50.000 72 35 1 1 71 1 72 3.61e-20 75.9
Msa1182690 MtrunA17_Chr8g0337761 56.250 48 21 0 1 48 1 48 1.19e-12 57.0
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 24 sgRNAs with CRISPR-Local

Find 98 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TCATAGCTAGATTATGTTCA+TGG 0.337702 8_1:-17852022 Msa1182690:three_prime_UTR
ATTAATTCTCTTCTCACTAA+AGG 0.348898 8_1:+17851974 None:intergenic
AACAATGTGGCTATCTTTGC+AGG 0.350015 8_1:-17852159 Msa1182690:CDS
TTCTTCAGTGGTGCATGTAT+TGG 0.373930 8_1:-17852196 Msa1182690:CDS
ACATCTATCAGCAATGTGAT+AGG 0.375987 8_1:-17852978 None:intergenic
TTAATTCTCTTCTCACTAAA+GGG 0.376554 8_1:+17851975 None:intergenic
GTCTTCTAAAATAATGTAAG+TGG 0.421980 8_1:+17852945 None:intergenic
TGCAAAGATAGCCACATTGT+TGG 0.437931 8_1:+17852161 None:intergenic
AGTAATATGTGTGACAAGAT+AGG 0.451632 8_1:-17851941 Msa1182690:three_prime_UTR
GGTGCATGTATTGGTTCATC+TGG 0.472404 8_1:-17852187 Msa1182690:CDS
GCACCACTGAAGAATTTACT+TGG 0.486888 8_1:+17852205 None:intergenic
TTCTCTTCTCACTAAAGGGA+AGG 0.498958 8_1:+17851979 None:intergenic
TCTCTTCTCACTAAAGGGAA+GGG 0.523534 8_1:+17851980 None:intergenic
TATCTTTGCAGGAGAGGAGA+AGG 0.527260 8_1:-17852148 Msa1182690:CDS
AGAAGCAGTGGTGCAAATTG+AGG 0.543400 8_1:-17852239 Msa1182690:CDS
TTATGTATTATATCTCATAG+TGG 0.561009 8_1:+17852070 None:intergenic
CATCTATCAGCAATGTGATA+GGG 0.583085 8_1:-17852977 None:intergenic
GAAGAGAATTAATTAATGCA+TGG 0.594544 8_1:-17851964 Msa1182690:three_prime_UTR
TGTGGCTATCTTTGCAGGAG+AGG 0.598922 8_1:-17852154 Msa1182690:CDS
GGAAATTGCAGAAGAAGCAG+TGG 0.602727 8_1:-17852251 Msa1182690:intron
AAACCAAGTAAATTCTTCAG+TGG 0.617297 8_1:-17852208 Msa1182690:CDS
GTAGTTCTGTTACACTACGT+TGG 0.632099 8_1:+17851705 None:intergenic
AGAGGAGAAGGCTTACTCAG+TGG 0.689859 8_1:-17852136 Msa1182690:CDS
TCATCTGGCAACCAACAATG+TGG 0.698688 8_1:-17852172 Msa1182690:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AGTTTATATTAAAGTAAATT+TGG - chr8_1:17851826-17851845 Msa1182690:intron 10.0%
!! GTTTATATTAAAGTAAATTT+GGG - chr8_1:17851827-17851846 Msa1182690:intron 10.0%
!!! TTTTTAATGAATTTTTTATC+CGG - chr8_1:17851963-17851982 Msa1182690:three_prime_UTR 10.0%
!! ATTACTTAAGAAAAATAATA+TGG - chr8_1:17852393-17852412 Msa1182690:intron 10.0%
!! AGTTTATATTAAAGTAAATT+TGG - chr8_1:17851826-17851845 Msa1182690:intron 10.0%
!! GTTTATATTAAAGTAAATTT+GGG - chr8_1:17851827-17851846 Msa1182690:intron 10.0%
!!! TTTTTAATGAATTTTTTATC+CGG - chr8_1:17851963-17851982 Msa1182690:three_prime_UTR 10.0%
!! ATTACTTAAGAAAAATAATA+TGG - chr8_1:17852393-17852412 Msa1182690:intron 10.0%
!! ATATTCATATCAAAATTAAC+TGG - chr8_1:17852056-17852075 Msa1182690:three_prime_UTR 15.0%
!! GATCAAATTATATATCAATA+TGG - chr8_1:17852175-17852194 Msa1182690:CDS 15.0%
!! ATATTCATATCAAAATTAAC+TGG - chr8_1:17852056-17852075 Msa1182690:three_prime_UTR 15.0%
!! GATCAAATTATATATCAATA+TGG - chr8_1:17852175-17852194 Msa1182690:CDS 15.0%
!! TGATATATAATTTGATCAAG+AGG + chr8_1:17852172-17852191 None:intergenic 20.0%
!!! TTTTCTTCCTTCAATTATTA+TGG + chr8_1:17852209-17852228 None:intergenic 20.0%
!!! GTTTCATCAAATTTAAGATT+TGG + chr8_1:17852239-17852258 None:intergenic 20.0%
!!! GAAAAATAATATGGTTCTTT+TGG - chr8_1:17852402-17852421 Msa1182690:intron 20.0%
!! TTATGTATTATATCTCATAG+TGG + chr8_1:17852607-17852626 None:intergenic 20.0%
!! TGATATATAATTTGATCAAG+AGG + chr8_1:17852172-17852191 None:intergenic 20.0%
!!! TTTTCTTCCTTCAATTATTA+TGG + chr8_1:17852209-17852228 None:intergenic 20.0%
!!! GTTTCATCAAATTTAAGATT+TGG + chr8_1:17852239-17852258 None:intergenic 20.0%
!!! GAAAAATAATATGGTTCTTT+TGG - chr8_1:17852402-17852421 Msa1182690:intron 20.0%
!! TTATGTATTATATCTCATAG+TGG + chr8_1:17852607-17852626 None:intergenic 20.0%
!!! GTCTTCTAAAATAATGTAAG+TGG + chr8_1:17851732-17851751 None:intergenic 25.0%
! GAAGACAAAAAAAAAAGTGA+TGG - chr8_1:17851746-17851765 Msa1182690:three_prime_UTR 25.0%
! ATTAACTGGTTAATGAGATT+CGG - chr8_1:17852070-17852089 Msa1182690:three_prime_UTR 25.0%
! CATCTTTCCATAATAATTGA+AGG - chr8_1:17852199-17852218 Msa1182690:CDS 25.0%
! TTAATTCTCTTCTCACTAAA+GGG + chr8_1:17852702-17852721 None:intergenic 25.0%
! ATTAATTCTCTTCTCACTAA+AGG + chr8_1:17852703-17852722 None:intergenic 25.0%
! GAAGAGAATTAATTAATGCA+TGG - chr8_1:17852710-17852729 Msa1182690:intron 25.0%
!!! GTCTTCTAAAATAATGTAAG+TGG + chr8_1:17851732-17851751 None:intergenic 25.0%
! GAAGACAAAAAAAAAAGTGA+TGG - chr8_1:17851746-17851765 Msa1182690:three_prime_UTR 25.0%
! ATTAACTGGTTAATGAGATT+CGG - chr8_1:17852070-17852089 Msa1182690:three_prime_UTR 25.0%
! CATCTTTCCATAATAATTGA+AGG - chr8_1:17852199-17852218 Msa1182690:CDS 25.0%
! TTAATTCTCTTCTCACTAAA+GGG + chr8_1:17852702-17852721 None:intergenic 25.0%
! ATTAATTCTCTTCTCACTAA+AGG + chr8_1:17852703-17852722 None:intergenic 25.0%
! GAAGAGAATTAATTAATGCA+TGG - chr8_1:17852710-17852729 Msa1182690:intron 25.0%
! CAAAAAAAAAAGTGATGGAG+AGG - chr8_1:17851751-17851770 Msa1182690:three_prime_UTR 30.0%
TACACACATAATTGATTGAC+CGG + chr8_1:17851985-17852004 None:intergenic 30.0%
AAACCAAGTAAATTCTTCAG+TGG - chr8_1:17852466-17852485 Msa1182690:intron 30.0%
TCATAGCTAGATTATGTTCA+TGG - chr8_1:17852652-17852671 Msa1182690:intron 30.0%
AGTAATATGTGTGACAAGAT+AGG - chr8_1:17852733-17852752 Msa1182690:intron 30.0%
!!! AGTTTTGTTCACTTTGATGT+TGG - chr8_1:17852811-17852830 Msa1182690:intron 30.0%
!! GTTTTGTTCACTTTGATGTT+GGG - chr8_1:17852812-17852831 Msa1182690:intron 30.0%
! CAAAAAAAAAAGTGATGGAG+AGG - chr8_1:17851751-17851770 Msa1182690:three_prime_UTR 30.0%
TACACACATAATTGATTGAC+CGG + chr8_1:17851985-17852004 None:intergenic 30.0%
AAACCAAGTAAATTCTTCAG+TGG - chr8_1:17852466-17852485 Msa1182690:intron 30.0%
TCATAGCTAGATTATGTTCA+TGG - chr8_1:17852652-17852671 Msa1182690:intron 30.0%
AGTAATATGTGTGACAAGAT+AGG - chr8_1:17852733-17852752 Msa1182690:intron 30.0%
!!! AGTTTTGTTCACTTTGATGT+TGG - chr8_1:17852811-17852830 Msa1182690:intron 30.0%
!! GTTTTGTTCACTTTGATGTT+GGG - chr8_1:17852812-17852831 Msa1182690:intron 30.0%
GCACCACTGAAGAATTTACT+TGG + chr8_1:17852472-17852491 None:intergenic 40.0%
TTCTTCAGTGGTGCATGTAT+TGG - chr8_1:17852478-17852497 Msa1182690:intron 40.0%
TGCAAAGATAGCCACATTGT+TGG + chr8_1:17852516-17852535 None:intergenic 40.0%
AACAATGTGGCTATCTTTGC+AGG - chr8_1:17852515-17852534 Msa1182690:intron 40.0%
TCTCTTCTCACTAAAGGGAA+GGG + chr8_1:17852697-17852716 None:intergenic 40.0%
TTCTCTTCTCACTAAAGGGA+AGG + chr8_1:17852698-17852717 None:intergenic 40.0%
GTTCACTTTGATGTTGGGTT+CGG - chr8_1:17852817-17852836 Msa1182690:intron 40.0%
! GTAGTTCTGTTACACTACGT+TGG + chr8_1:17852972-17852991 None:intergenic 40.0%
GCACCACTGAAGAATTTACT+TGG + chr8_1:17852472-17852491 None:intergenic 40.0%
TTCTTCAGTGGTGCATGTAT+TGG - chr8_1:17852478-17852497 Msa1182690:intron 40.0%
TGCAAAGATAGCCACATTGT+TGG + chr8_1:17852516-17852535 None:intergenic 40.0%
AACAATGTGGCTATCTTTGC+AGG - chr8_1:17852515-17852534 Msa1182690:intron 40.0%
TCTCTTCTCACTAAAGGGAA+GGG + chr8_1:17852697-17852716 None:intergenic 40.0%
TTCTCTTCTCACTAAAGGGA+AGG + chr8_1:17852698-17852717 None:intergenic 40.0%
GTTCACTTTGATGTTGGGTT+CGG - chr8_1:17852817-17852836 Msa1182690:intron 40.0%
! GTAGTTCTGTTACACTACGT+TGG + chr8_1:17852972-17852991 None:intergenic 40.0%
GGAAATTGCAGAAGAAGCAG+TGG - chr8_1:17852423-17852442 Msa1182690:intron 45.0%
AGAAGCAGTGGTGCAAATTG+AGG - chr8_1:17852435-17852454 Msa1182690:intron 45.0%
!! GGTGCATGTATTGGTTCATC+TGG - chr8_1:17852487-17852506 Msa1182690:intron 45.0%
TCATCTGGCAACCAACAATG+TGG - chr8_1:17852502-17852521 Msa1182690:intron 45.0%
TATCTTTGCAGGAGAGGAGA+AGG - chr8_1:17852526-17852545 Msa1182690:intron 45.0%
CCACACAACATGCTAGTGAA+CGG + chr8_1:17852759-17852778 None:intergenic 45.0%
CGTTCACTAGCATGTTGTGT+GGG - chr8_1:17852757-17852776 Msa1182690:intron 45.0%
TCTCTGCAACCCTTCATAGA+AGG - chr8_1:17852781-17852800 Msa1182690:intron 45.0%
TGCAACCCTTCATAGAAGGT+GGG - chr8_1:17852785-17852804 Msa1182690:intron 45.0%
CTCTACCCACCTTCTATGAA+GGG + chr8_1:17852793-17852812 None:intergenic 45.0%
ACTCTACCCACCTTCTATGA+AGG + chr8_1:17852794-17852813 None:intergenic 45.0%
GGAAATTGCAGAAGAAGCAG+TGG - chr8_1:17852423-17852442 Msa1182690:intron 45.0%
AGAAGCAGTGGTGCAAATTG+AGG - chr8_1:17852435-17852454 Msa1182690:intron 45.0%
!! GGTGCATGTATTGGTTCATC+TGG - chr8_1:17852487-17852506 Msa1182690:intron 45.0%
TCATCTGGCAACCAACAATG+TGG - chr8_1:17852502-17852521 Msa1182690:intron 45.0%
TATCTTTGCAGGAGAGGAGA+AGG - chr8_1:17852526-17852545 Msa1182690:intron 45.0%
CCACACAACATGCTAGTGAA+CGG + chr8_1:17852759-17852778 None:intergenic 45.0%
CGTTCACTAGCATGTTGTGT+GGG - chr8_1:17852757-17852776 Msa1182690:intron 45.0%
TCTCTGCAACCCTTCATAGA+AGG - chr8_1:17852781-17852800 Msa1182690:intron 45.0%
TGCAACCCTTCATAGAAGGT+GGG - chr8_1:17852785-17852804 Msa1182690:intron 45.0%
CTCTACCCACCTTCTATGAA+GGG + chr8_1:17852793-17852812 None:intergenic 45.0%
ACTCTACCCACCTTCTATGA+AGG + chr8_1:17852794-17852813 None:intergenic 45.0%
!!! TTTTATTTTGTAATAAAAAA+TGG + chr8_1:17851895-17851914 None:intergenic 5.0%
!!! TTTTATTTTGTAATAAAAAA+TGG + chr8_1:17851895-17851914 None:intergenic 5.0%
TGTGGCTATCTTTGCAGGAG+AGG - chr8_1:17852520-17852539 Msa1182690:intron 50.0%
AGAGGAGAAGGCTTACTCAG+TGG - chr8_1:17852538-17852557 Msa1182690:intron 50.0%
CCGTTCACTAGCATGTTGTG+TGG - chr8_1:17852756-17852775 Msa1182690:intron 50.0%
CTGCAACCCTTCATAGAAGG+TGG - chr8_1:17852784-17852803 Msa1182690:intron 50.0%
TGTGGCTATCTTTGCAGGAG+AGG - chr8_1:17852520-17852539 Msa1182690:intron 50.0%
AGAGGAGAAGGCTTACTCAG+TGG - chr8_1:17852538-17852557 Msa1182690:intron 50.0%
CCGTTCACTAGCATGTTGTG+TGG - chr8_1:17852756-17852775 Msa1182690:intron 50.0%
CTGCAACCCTTCATAGAAGG+TGG - chr8_1:17852784-17852803 Msa1182690:intron 50.0%
Chromosome Type Strat End Strand Name
chr8_1 gene 17851704 17852992 17851704 ID=Msa1182690;Name=Msa1182690
chr8_1 mRNA 17851704 17852992 17851704 ID=Msa1182690-mRNA-1;Parent=Msa1182690;Name=Msa1182690-mRNA-1;_AED=0.10;_eAED=0.10;_QI=61|1|1|1|0|0|3|256|73
chr8_1 exon 17851704 17851799 17851704 ID=Msa1182690-mRNA-1:exon:6745;Parent=Msa1182690-mRNA-1
chr8_1 exon 17851939 17852262 17851939 ID=Msa1182690-mRNA-1:exon:6744;Parent=Msa1182690-mRNA-1
chr8_1 exon 17852874 17852992 17852874 ID=Msa1182690-mRNA-1:exon:6743;Parent=Msa1182690-mRNA-1
chr8_1 five_prime_UTR 17852932 17852992 17852932 ID=Msa1182690-mRNA-1:five_prime_utr;Parent=Msa1182690-mRNA-1
chr8_1 CDS 17852874 17852931 17852874 ID=Msa1182690-mRNA-1:cds;Parent=Msa1182690-mRNA-1
chr8_1 CDS 17852099 17852262 17852099 ID=Msa1182690-mRNA-1:cds;Parent=Msa1182690-mRNA-1
chr8_1 three_prime_UTR 17851939 17852098 17851939 ID=Msa1182690-mRNA-1:three_prime_utr;Parent=Msa1182690-mRNA-1
chr8_1 three_prime_UTR 17851704 17851799 17851704 ID=Msa1182690-mRNA-1:three_prime_utr;Parent=Msa1182690-mRNA-1
Gene Sequence

>Msa1182690

ATGGAGAGGAAAACACTTGCTAGCTTGTGCTTCTTTCTCATTGTTCTCTTAGCTGCTCAAGAAGCAGTGGTGCAAATTGAGGCTTGTGAGAAACCAAGTAAATTCTTCAGTGGTGCATGTATTGGTTCATCTGGCAACCAACAATGTGGCTATCTTTGCAGGAGAGGAGAAGGCTTACTCAGTGGTTCTTGCAAAAATCTAAAATGTGTTTGTGCTTGTTGA

Protein sequence

>Msa1182690

MERKTLASLCFFLIVLLAAQEAVVQIEACEKPSKFFSGACIGSSGNQQCGYLCRRGEGLLSGSCKNLKCVCAC*