AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0716840


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0716840 MtrunA17_Chr5g0404111 88.462 78 8 1 1 78 1 77 8.57e-46 142
Msa0716840 MtrunA17_Chr3g0081641 36.559 93 55 2 14 105 1 90 7.05e-14 62.0
Msa0716840 MtrunA17_Chr1g0173721 35.106 94 48 3 14 106 1 82 2.19e-13 60.5
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0716840 AT2G21640.1 35.052 97 56 2 14 103 1 97 6.30e-12 57.4
Msa0716840 AT4G39235.2 34.783 69 37 1 14 82 1 61 3.19e-11 55.1
Msa0716840 AT4G39235.1 34.783 69 37 1 14 82 1 61 3.19e-11 55.1

Find 22 sgRNAs with CRISPR-Local

Find 29 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TTTAATGCATCAAAGGATTT+TGG 0.124757 5_1:+10418054 Msa0716840:CDS
CTTGAATGTTACACATTAAT+TGG 0.152502 5_1:-10418274 None:intergenic
TCAGCTTTAACTTTCTCCTT+TGG 0.324540 5_1:+10418362 Msa0716840:three_prime_UTR
TTAACTATGTTGATGTCAAC+TGG 0.344256 5_1:+10417727 None:intergenic
ACAGTTTCATATGATTATCA+TGG 0.433286 5_1:+10418306 Msa0716840:three_prime_UTR
AGTCAATCATGTGTTCTCTA+AGG 0.438611 5_1:-10418208 None:intergenic
CAGAATGTGACTCTTTGTGC+TGG 0.447400 5_1:-10417820 None:intergenic
TTCTGTCAAAGAAACAAGTC+CGG 0.465521 5_1:+10417838 Msa0716840:CDS
TCATGTGTTCTCTAAGGTCT+TGG 0.473675 5_1:-10418202 None:intergenic
CTTGAGAAACACAATTCAAA+AGG 0.489220 5_1:+10417939 Msa0716840:CDS
ATTAATGTGTAACATTCAAG+TGG 0.494096 5_1:+10418277 Msa0716840:three_prime_UTR
ACAGATATTTAATGCATCAA+AGG 0.510172 5_1:+10418047 Msa0716840:intron
TCTGTCAAAGAAACAAGTCC+GGG 0.516482 5_1:+10417839 Msa0716840:CDS
CAAAGAAACAAGTCCGGGGA+TGG 0.518949 5_1:+10417844 Msa0716840:CDS
TGTGTTCATCAACGGATGCA+TGG 0.564961 5_1:-10417909 None:intergenic
AGTCACAAAACTCCCATCCC+CGG 0.586279 5_1:-10417857 None:intergenic
AAAGAAACAAGTCCGGGGAT+GGG 0.589500 5_1:+10417845 Msa0716840:CDS
GCATCTCCTGTGTTCATCAA+CGG 0.594973 5_1:-10417917 None:intergenic
TTAATGTGTAACATTCAAGT+GGG 0.633879 5_1:+10418278 Msa0716840:three_prime_UTR
ATGCATCCGTTGATGAACAC+AGG 0.635825 5_1:+10417911 Msa0716840:CDS
TATAAACGAAGATGAAAACT+CGG 0.670859 5_1:+10418092 Msa0716840:CDS
CTGTCAAAGAAACAAGTCCG+GGG 0.697051 5_1:+10417840 Msa0716840:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
! TATTGATGTATATACATCCA+CGG - chr5_1:10417976-10417995 None:intergenic 25.0%
! TTGTTAGCATAATAATCGAA+GGG - chr5_1:10418001-10418020 None:intergenic 25.0%
! ACAGATATTTAATGCATCAA+AGG + chr5_1:10418047-10418066 Msa0716840:intron 25.0%
!! TTTAATGCATCAAAGGATTT+TGG + chr5_1:10418054-10418073 Msa0716840:CDS 25.0%
! TATAAACGAAGATGAAAACT+CGG + chr5_1:10418092-10418111 Msa0716840:CDS 25.0%
!! TTTTCTGAATCATTAGTAGA+TGG + chr5_1:10418149-10418168 Msa0716840:three_prime_UTR 25.0%
! CTTGAATGTTACACATTAAT+TGG - chr5_1:10418277-10418296 None:intergenic 25.0%
! ATTAATGTGTAACATTCAAG+TGG + chr5_1:10418277-10418296 Msa0716840:three_prime_UTR 25.0%
! TTAATGTGTAACATTCAAGT+GGG + chr5_1:10418278-10418297 Msa0716840:three_prime_UTR 25.0%
! ACAGTTTCATATGATTATCA+TGG + chr5_1:10418306-10418325 Msa0716840:three_prime_UTR 25.0%
! AACTGGATTAACTTTTCTTC+AGG + chr5_1:10417744-10417763 Msa0716840:CDS 30.0%
! AACTTTTCTTCAGGTGTTAA+TGG + chr5_1:10417753-10417772 Msa0716840:CDS 30.0%
!!! GTTTTAGTTTTTCATCAGTC+TGG - chr5_1:10417792-10417811 None:intergenic 30.0%
CTTGAGAAACACAATTCAAA+AGG + chr5_1:10417939-10417958 Msa0716840:CDS 30.0%
!! AAAAGGTATATTTTCTACCG+TGG + chr5_1:10417956-10417975 Msa0716840:intron 30.0%
CTTGTTAGCATAATAATCGA+AGG - chr5_1:10418002-10418021 None:intergenic 30.0%
TTCTGTCAAAGAAACAAGTC+CGG + chr5_1:10417838-10417857 Msa0716840:CDS 35.0%
AGTCAATCATGTGTTCTCTA+AGG - chr5_1:10418211-10418230 None:intergenic 35.0%
! TCAGCTTTAACTTTCTCCTT+TGG + chr5_1:10418362-10418381 Msa0716840:three_prime_UTR 35.0%
TCTGTCAAAGAAACAAGTCC+GGG + chr5_1:10417839-10417858 Msa0716840:CDS 40.0%
!! TCATGTGTTCTCTAAGGTCT+TGG - chr5_1:10418205-10418224 None:intergenic 40.0%
CAGAATGTGACTCTTTGTGC+TGG - chr5_1:10417823-10417842 None:intergenic 45.0%
CTGTCAAAGAAACAAGTCCG+GGG + chr5_1:10417840-10417859 Msa0716840:CDS 45.0%
AAAGAAACAAGTCCGGGGAT+GGG + chr5_1:10417845-10417864 Msa0716840:CDS 45.0%
TGTGTTCATCAACGGATGCA+TGG - chr5_1:10417912-10417931 None:intergenic 45.0%
! ATGCATCCGTTGATGAACAC+AGG + chr5_1:10417911-10417930 Msa0716840:CDS 45.0%
GCATCTCCTGTGTTCATCAA+CGG - chr5_1:10417920-10417939 None:intergenic 45.0%
CAAAGAAACAAGTCCGGGGA+TGG + chr5_1:10417844-10417863 Msa0716840:CDS 50.0%
AGTCACAAAACTCCCATCCC+CGG - chr5_1:10417860-10417879 None:intergenic 50.0%
Chromosome Type Strat End Strand Name
chr5_1 gene 10417733 10418396 10417733 ID=Msa0716840;Name=Msa0716840
chr5_1 mRNA 10417733 10418396 10417733 ID=Msa0716840-mRNA-1;Parent=Msa0716840;Name=Msa0716840-mRNA-1;_AED=0.08;_eAED=0.08;_QI=0|1|0.5|1|1|1|2|253|106
chr5_1 exon 10417733 10417960 10417733 ID=Msa0716840-mRNA-1:exon:4183;Parent=Msa0716840-mRNA-1
chr5_1 exon 10418051 10418396 10418051 ID=Msa0716840-mRNA-1:exon:4184;Parent=Msa0716840-mRNA-1
chr5_1 CDS 10417733 10417960 10417733 ID=Msa0716840-mRNA-1:cds;Parent=Msa0716840-mRNA-1
chr5_1 CDS 10418051 10418143 10418051 ID=Msa0716840-mRNA-1:cds;Parent=Msa0716840-mRNA-1
chr5_1 three_prime_UTR 10418144 10418396 10418144 ID=Msa0716840-mRNA-1:three_prime_utr;Parent=Msa0716840-mRNA-1
Gene Sequence

>Msa0716840

ATGTTGATGTCAACTGGATTAACTTTTCTTCAGGTGTTAATGGATTCAAACAGCAACCAGACTGATGAAAAACTAAAACAAGTCAAGCCAGCACAAAGAGTCACATTCTGTCAAAGAAACAAGTCCGGGGATGGGAGTTTTGTGACTAAATTAAGAAATCATTTTCATGAATTTATCCATGCATCCGTTGATGAACACAGGAGATGCTTGAGAAACACAATTCAAAAGATATTTAATGCATCAAAGGATTTTGGAAATAACAGTGAAAGTATAAACGAAGATGAAAACTCGGTACAACTTCATTCATCTACAAAGAACTAG

Protein sequence

>Msa0716840

MLMSTGLTFLQVLMDSNSNQTDEKLKQVKPAQRVTFCQRNKSGDGSFVTKLRNHFHEFIHASVDEHRRCLRNTIQKIFNASKDFGNNSESINEDENSVQLHSSTKN*