AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0591290


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0591290 MtrunA17_CPg0492421 91.729 133 9 1 1 131 25 157 1.30e-85 246
Msa0591290 MtrunA17_Chr4g0016101 91.729 133 9 1 1 131 25 157 1.30e-85 246
Msa0591290 MtrunA17_Chr3g0090841 91.729 133 9 1 1 131 25 157 1.30e-85 246
Msa0591290 MtrunA17_Chr4g0002541 83.333 60 10 0 1 60 1 60 3.60e-30 103
Msa0591290 MtrunA17_Chr4g0057401 87.500 40 5 0 92 131 1 40 1.06e-17 71.2
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0591290 ATCG00900.1 95.420 131 6 0 1 131 25 155 7.02e-91 260
Msa0591290 ATCG01240.1 95.420 131 6 0 1 131 25 155 7.02e-91 260
Msa0591290 ATMG01270.1 33.824 136 80 3 2 131 15 146 3.86e-18 75.5
Msa0591290 AT2G07696.1 33.824 136 80 3 2 131 15 146 3.86e-18 75.5

Find 24 sgRNAs with CRISPR-Local

Find 34 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CTTGCCATTCGTTGGTTATT+AGG 0.268444 4_2:+15589114 Msa0591290:CDS
CATCAAGTTCCCGTTGAAAT+AGG 0.307921 4_2:+15589072 Msa0591290:CDS
AAAACGTCCAGGTCGAAATA+TGG 0.317789 4_2:+15589146 Msa0591290:CDS
CAAATTAAGTTCCGAATTAG+TGG 0.342047 4_2:+15589173 Msa0591290:CDS
TGGCGATGCCATACGCAAAA+AGG 0.366109 4_2:+15589212 Msa0591290:CDS
TTTGGCAGCATCCACTAATT+CGG 0.404543 4_2:-15589184 Msa0591280:intron
GCTTGACGTAAAACAGATAG+TGG 0.426676 4_2:-15588991 Msa0591280:intron
GTAAAAGCAAGACGCGTAAA+CGG 0.427761 4_2:+15589042 Msa0591290:CDS
TATGGCATCGCCATTCCCTT+TGG 0.436234 4_2:-15589202 Msa0591280:intron
TGTGTGGATCCTATTTCAAC+GGG 0.470768 4_2:-15589081 Msa0591280:intron
TTATCTATCGAGCTATGAAA+AGG 0.512086 4_2:+15588944 Msa0591290:CDS
GAAAAGCACTTGCCATTCGT+TGG 0.526859 4_2:+15589106 Msa0591290:CDS
GTGGATGCTGCCAAAGGGAA+TGG 0.532446 4_2:+15589192 Msa0591290:CDS
GGCGCATCCCGAAAACGTCC+AGG 0.540732 4_2:+15589135 Msa0591290:CDS
AAAGGAAGAGACTCATAGAA+TGG 0.548096 4_2:+15589230 Msa0591290:CDS
TTGTGTGGATCCTATTTCAA+CGG 0.548545 4_2:-15589082 Msa0591280:intron
AATTAGTGGATGCTGCCAAA+GGG 0.575951 4_2:+15589187 Msa0591290:CDS
GAATTAGTGGATGCTGCCAA+AGG 0.584526 4_2:+15589186 Msa0591290:CDS
AGAGACTCATAGAATGGCAG+AGG 0.593635 4_2:+15589236 Msa0591290:CDS
TTGAAAGCCATATTTCGACC+TGG 0.605724 4_2:-15589153 Msa0591280:intron
TGCGCCTAATAACCAACGAA+TGG 0.620213 4_2:-15589118 Msa0591280:intron
GTTAACCGTATTATGAAACA+CGG 0.650772 4_2:+15588898 Msa0591290:CDS
TTTACGTCAAGCAATACGTG+GGG 0.729232 4_2:+15589002 Msa0591290:CDS
GTTGAAATAGGATCCACACA+AGG 0.731975 4_2:+15589084 Msa0591290:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! TTTTTCCGTGTTTCATAATA+CGG - chr4_2:15588906-15588925 Msa0591280:intron 25.0%
GTTAACCGTATTATGAAACA+CGG + chr4_2:15588898-15588917 Msa0591290:CDS 30.0%
GAAACACGGAAAAAAATCAT+TGG + chr4_2:15588912-15588931 Msa0591290:CDS 30.0%
TTATCTATCGAGCTATGAAA+AGG + chr4_2:15588944-15588963 Msa0591290:CDS 30.0%
!! TCTTGCTTTTACTGCTATAT+CGG - chr4_2:15589034-15589053 Msa0591280:intron 30.0%
CAAATTAAGTTCCGAATTAG+TGG + chr4_2:15589173-15589192 Msa0591290:CDS 30.0%
! TTTTACGTCAAGCAATACGT+GGG + chr4_2:15589001-15589020 Msa0591290:CDS 35.0%
!! CTTGCTTTTACTGCTATATC+GGG - chr4_2:15589033-15589052 Msa0591280:intron 35.0%
TTGTGTGGATCCTATTTCAA+CGG - chr4_2:15589085-15589104 Msa0591280:intron 35.0%
AAAGGAAGAGACTCATAGAA+TGG + chr4_2:15589230-15589249 Msa0591290:CDS 35.0%
GCTTGACGTAAAACAGATAG+TGG - chr4_2:15588994-15589013 Msa0591280:intron 40.0%
! GTTTTACGTCAAGCAATACG+TGG + chr4_2:15589000-15589019 Msa0591290:CDS 40.0%
TTTACGTCAAGCAATACGTG+GGG + chr4_2:15589002-15589021 Msa0591290:CDS 40.0%
GTAAAAGCAAGACGCGTAAA+CGG + chr4_2:15589042-15589061 Msa0591290:CDS 40.0%
CATCAAGTTCCCGTTGAAAT+AGG + chr4_2:15589072-15589091 Msa0591290:CDS 40.0%
TGTGTGGATCCTATTTCAAC+GGG - chr4_2:15589084-15589103 Msa0591280:intron 40.0%
GTTGAAATAGGATCCACACA+AGG + chr4_2:15589084-15589103 Msa0591290:CDS 40.0%
! CTTGCCATTCGTTGGTTATT+AGG + chr4_2:15589114-15589133 Msa0591290:CDS 40.0%
! TATTTCGACCTGGACGTTTT+CGG - chr4_2:15589146-15589165 Msa0591280:intron 40.0%
AAAACGTCCAGGTCGAAATA+TGG + chr4_2:15589146-15589165 Msa0591290:CDS 40.0%
TTGAAAGCCATATTTCGACC+TGG - chr4_2:15589156-15589175 Msa0591280:intron 40.0%
TTTGGCAGCATCCACTAATT+CGG - chr4_2:15589187-15589206 Msa0591280:intron 40.0%
! AATTAGTGGATGCTGCCAAA+GGG + chr4_2:15589187-15589206 Msa0591290:CDS 40.0%
! AGTCTCTTCCTTTTTGCGTA+TGG - chr4_2:15589223-15589242 Msa0591280:intron 40.0%
!! GAAAAGCACTTGCCATTCGT+TGG + chr4_2:15589106-15589125 Msa0591290:CDS 45.0%
TGCGCCTAATAACCAACGAA+TGG - chr4_2:15589121-15589140 Msa0591280:intron 45.0%
! ATTTCGACCTGGACGTTTTC+GGG - chr4_2:15589145-15589164 Msa0591280:intron 45.0%
! GAATTAGTGGATGCTGCCAA+AGG + chr4_2:15589186-15589205 Msa0591290:CDS 45.0%
AGAGACTCATAGAATGGCAG+AGG + chr4_2:15589236-15589255 Msa0591290:CDS 45.0%
! GGCAAGTGCTTTTCCTTGTG+TGG - chr4_2:15589100-15589119 Msa0591280:intron 50.0%
TATGGCATCGCCATTCCCTT+TGG - chr4_2:15589205-15589224 Msa0591280:intron 50.0%
TGGCGATGCCATACGCAAAA+AGG + chr4_2:15589212-15589231 Msa0591290:CDS 50.0%
GTGGATGCTGCCAAAGGGAA+TGG + chr4_2:15589192-15589211 Msa0591290:CDS 55.0%
GGCGCATCCCGAAAACGTCC+AGG + chr4_2:15589135-15589154 Msa0591290:CDS 65.0%
Chromosome Type Strat End Strand Name
chr4_2 gene 15588892 15589287 15588892 ID=Msa0591290;Name=Msa0591290
chr4_2 mRNA 15588892 15589287 15588892 ID=Msa0591290-mRNA-1;Parent=Msa0591290;Name=Msa0591290-mRNA-1;_AED=0.46;_eAED=0.46;_QI=0|-1|0|1|-1|1|1|0|131
chr4_2 exon 15588892 15589287 15588892 ID=Msa0591290-mRNA-1:exon:4490;Parent=Msa0591290-mRNA-1
chr4_2 CDS 15588892 15589287 15588892 ID=Msa0591290-mRNA-1:cds;Parent=Msa0591290-mRNA-1
Gene Sequence

>Msa0591290

ATGTTGGTTAACCGTATTATGAAACACGGAAAAAAATCATTGGCTTATCAAATTATCTATCGAGCTATGAAAAGGATTCAACAAAAGACAGAAACAAATCCACTATCTGTTTTACGTCAAGCAATACGTGGGGTAACTCCCGATATAGCAGTAAAAGCAAGACGCGTAAACGGATCGACTCATCAAGTTCCCGTTGAAATAGGATCCACACAAGGAAAAGCACTTGCCATTCGTTGGTTATTAGGCGCATCCCGAAAACGTCCAGGTCGAAATATGGCTTTCAAATTAAGTTCCGAATTAGTGGATGCTGCCAAAGGGAATGGCGATGCCATACGCAAAAAGGAAGAGACTCATAGAATGGCAGAGGCAAATAGAGCTTTTGCACATTTTCGTTAA

Protein sequence

>Msa0591290

MLVNRIMKHGKKSLAYQIIYRAMKRIQQKTETNPLSVLRQAIRGVTPDIAVKARRVNGSTHQVPVEIGSTQGKALAIRWLLGASRKRPGRNMAFKLSSELVDAAKGNGDAIRKKEETHRMAEANRAFAHFR*