AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0836340


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0836340 MtrunA17_Chr5g0402081 97.842 139 3 0 1 139 1 139 1.06e-99 291
Msa0836340 MtrunA17_Chr4g0044651 63.448 145 46 3 1 138 1 145 4.99e-61 192
Msa0836340 MtrunA17_Chr4g0053041 47.887 142 66 2 5 138 19 160 1.52e-39 137
Msa0836340 MtrunA17_Chr5g0401931 50.820 122 56 2 21 138 27 148 2.59e-36 128
Msa0836340 MtrunA17_Chr4g0044681 50.407 123 50 3 20 138 23 138 2.28e-35 124
Msa0836340 MtrunA17_Chr7g0219811 40.940 149 76 4 1 138 1 148 8.92e-30 110
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0836340 AT4G36945.1 63.971 136 46 1 6 138 9 144 2.22e-62 196
Msa0836340 AT1G49740.1 66.667 129 40 1 13 138 20 148 2.76e-56 179
Msa0836340 AT3G19310.1 65.600 125 40 1 17 138 24 148 3.39e-55 178
Msa0836340 AT5G67130.1 53.636 110 51 0 29 138 46 155 1.98e-38 134
Msa0836340 AT1G13680.1 39.855 138 69 4 5 138 15 142 5.14e-25 97.8

Find 33 sgRNAs with CRISPR-Local

Find 109 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
AAAGATACAAACTTTGTTAA+TGG 0.244124 5_4:+9837452 None:intergenic
AAGATACAAACTTTGTTAAT+GGG 0.302320 5_4:+9837453 None:intergenic
GACACATAATTCATTTGCTT+TGG 0.348095 5_4:-9837306 Msa0836340:CDS
TGACGATTAATACAAAGATT+TGG 0.359042 5_4:+9837704 None:intergenic
GGACGTGTATTTCCATTTGC+AGG 0.360507 5_4:+9837504 None:intergenic
AGATAGCAACAGAAAGGATA+TGG 0.370036 5_4:+9838002 None:intergenic
AGATAGTATCCTGCTACATC+TGG 0.382095 5_4:+9837482 None:intergenic
TGAAAGGTTTGCCGTTTAAT+CGG 0.388517 5_4:-9837343 Msa0836340:CDS
CACATATTCATCCAGCTTGA+AGG 0.392390 5_4:-9837671 Msa0836340:intron
CATAATTCATTTGCTTTGGC+TGG 0.394141 5_4:-9837302 Msa0836340:CDS
AACCATGAATACCGATTAAA+CGG 0.395061 5_4:+9837332 None:intergenic
TGCCGTTTAATCGGTATTCA+TGG 0.399726 5_4:-9837334 Msa0836340:CDS
TGTCAAACATGTCCTGCAAA+TGG 0.461549 5_4:-9837516 Msa0836340:CDS
AATTATTATTACCTTCAAGC+TGG 0.464784 5_4:+9837660 None:intergenic
AATGATAATGTGAAGGTGAA+AGG 0.477711 5_4:-9837359 Msa0836340:intron
GTATGGTTGTGTCATTCTAC+TGG 0.479005 5_4:-9835508 Msa0836340:CDS
ATAGTGTCATCCTGGTTCAT+AGG 0.494246 5_4:+9837245 None:intergenic
TAAACACAAAAGTAGAATGA+AGG 0.537079 5_4:-9837910 Msa0836340:intron
AGATACAAACTTTGTTAATG+GGG 0.540888 5_4:+9837454 None:intergenic
ATATGGATTTGTGAAGGAAG+AGG 0.558800 5_4:+9838019 None:intergenic
GATCAGCAATAGTGTCATCC+TGG 0.565278 5_4:+9837237 None:intergenic
GATAGTATCCTGCTACATCT+GGG 0.566644 5_4:+9837483 None:intergenic
ATACACGTCCCAGATGTAGC+AGG 0.568124 5_4:-9837491 Msa0836340:CDS
AGTTGAAGATAGCAACAGAA+AGG 0.574228 5_4:+9837996 None:intergenic
TCTTAACAGAATGGTGTTCG+AGG 0.581911 5_4:-9835565 Msa0836340:intron
GAAAGGATATGGATTTGTGA+AGG 0.585887 5_4:+9838013 None:intergenic
TATCCTTGCACCTATGAACC+AGG 0.595518 5_4:-9837255 Msa0836340:CDS
GCTGGTGCAAGATCAGCCAC+AGG 0.596230 5_4:-9837284 Msa0836340:CDS
ACATGCGGTTCATGTGATGC+TGG 0.602805 5_4:-9837546 Msa0836340:CDS
CATCCTGGTTCATAGGTGCA+AGG 0.632672 5_4:+9837252 None:intergenic
TGGTTGTGTCATTCTACTGG+AGG 0.640950 5_4:-9835505 Msa0836340:CDS
TGCAAGGATAATTGAACCTG+TGG 0.658279 5_4:+9837268 None:intergenic
TAGCAGATCGGAGAAACATG+CGG 0.699281 5_4:-9837561 Msa0836340:intron

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! AAATTTTTCAATTAGAATAT+AGG + chr5_4:9836092-9836111 None:intergenic 10.0%
!! ATTTATTAGTTAAAATTACT+TGG - chr5_4:9836527-9836546 Msa0836340:intron 10.0%
!!! AAAAATGATAAATTTTTCAT+TGG - chr5_4:9837077-9837096 Msa0836340:intron 10.0%
!! GTAGTAAATAAATAAATAAT+TGG - chr5_4:9837272-9837291 Msa0836340:CDS 10.0%
!! AATAAAATGATAATTGAAAA+AGG + chr5_4:9837584-9837603 None:intergenic 10.0%
!! TTTATTCTATCATAAAAAAT+GGG + chr5_4:9837665-9837684 None:intergenic 10.0%
!! ATTTATTCTATCATAAAAAA+TGG + chr5_4:9837666-9837685 None:intergenic 10.0%
!!! TTTTTATAATGATAATGTGA+AGG - chr5_4:9836151-9836170 Msa0836340:intron 15.0%
!! TGACTTATTAAAATTAATTC+TGG + chr5_4:9836808-9836827 None:intergenic 15.0%
!!! TATAATGTCTTTTTCTTTTA+GGG - chr5_4:9837120-9837139 Msa0836340:intron 15.0%
!! AAGATACAAACTTTGTTAAT+GGG + chr5_4:9836067-9836086 None:intergenic 20.0%
!! AAAGATACAAACTTTGTTAA+TGG + chr5_4:9836068-9836087 None:intergenic 20.0%
!! AAGATTGAATATTGAAATTG+AGG - chr5_4:9836484-9836503 Msa0836340:intron 20.0%
!! ACAATAGGTTTGATAAAATA+TGG - chr5_4:9836895-9836914 Msa0836340:intron 20.0%
!!! GTATAATGTCTTTTTCTTTT+AGG - chr5_4:9837119-9837138 Msa0836340:intron 20.0%
!!! ATAATGTCTTTTTCTTTTAG+GGG - chr5_4:9837121-9837140 Msa0836340:intron 20.0%
!!! CAAGCAATATATTTTTATAG+TGG + chr5_4:9837531-9837550 None:intergenic 20.0%
! TAAACACAAAAGTAGAATGA+AGG - chr5_4:9835607-9835626 Msa0836340:intron 25.0%
!! TTGTATGGATTAAAAACAAC+AGG + chr5_4:9835774-9835793 None:intergenic 25.0%
! TGACGATTAATACAAAGATT+TGG + chr5_4:9835816-9835835 None:intergenic 25.0%
! AATTATTATTACCTTCAAGC+TGG + chr5_4:9835860-9835879 None:intergenic 25.0%
! AGATACAAACTTTGTTAATG+GGG + chr5_4:9836066-9836085 None:intergenic 25.0%
! TATGAATGTGAATAGTCTAT+TGG - chr5_4:9836385-9836404 Msa0836340:intron 25.0%
! TAAATAAAAACTAGTTGAGC+TGG + chr5_4:9836512-9836531 None:intergenic 25.0%
!!! ATTTCTTTTTCGTGTATGTT+TGG - chr5_4:9836622-9836641 Msa0836340:intron 25.0%
! CGGGAATTATCAATAAAAAA+GGG + chr5_4:9836963-9836982 None:intergenic 25.0%
! ACGGGAATTATCAATAAAAA+AGG + chr5_4:9836964-9836983 None:intergenic 25.0%
!!! TTTTTTATTGATAATTCCCG+TGG - chr5_4:9836963-9836982 Msa0836340:intron 25.0%
!! ATTGGATGTCTTTTTCTTTT+AGG - chr5_4:9837095-9837114 Msa0836340:intron 25.0%
!! TTGGATGTCTTTTTCTTTTA+GGG - chr5_4:9837096-9837115 Msa0836340:intron 25.0%
! TATACATGTTCATTGTTCAA+TGG - chr5_4:9837444-9837463 Msa0836340:intron 25.0%
! ATACATGTTCATTGTTCAAT+GGG - chr5_4:9837445-9837464 Msa0836340:intron 25.0%
! CAGCATCTAATCTTAAAATA+TGG + chr5_4:9837617-9837636 None:intergenic 25.0%
!! GCAATTTTATAAACCAAAGA+AGG - chr5_4:9837742-9837761 Msa0836340:intron 25.0%
AAGAGGAAAAAAGCTGATTA+AGG + chr5_4:9835484-9835503 None:intergenic 30.0%
!! TCTACTTTTGTGTTTAGAGA+GGG + chr5_4:9835603-9835622 None:intergenic 30.0%
!! TTCTACTTTTGTGTTTAGAG+AGG + chr5_4:9835604-9835623 None:intergenic 30.0%
! ATGATTAGTTGAAGATGCAT+AGG + chr5_4:9835648-9835667 None:intergenic 30.0%
! AATGATAATGTGAAGGTGAA+AGG - chr5_4:9836158-9836177 Msa0836340:intron 30.0%
! AACCATGAATACCGATTAAA+CGG + chr5_4:9836188-9836207 None:intergenic 30.0%
GACACATAATTCATTTGCTT+TGG - chr5_4:9836211-9836230 Msa0836340:intron 30.0%
CTTATGTGACAACTAAGAAA+TGG - chr5_4:9836555-9836574 Msa0836340:intron 30.0%
! GCTACAAGTAGAATCAATTT+TGG + chr5_4:9836664-9836683 None:intergenic 30.0%
TTCTACTTGTAGCTATAGAT+TGG - chr5_4:9836671-9836690 Msa0836340:intron 30.0%
ACAATGCATCATGTTAAAGA+AGG + chr5_4:9836990-9837009 None:intergenic 30.0%
TCTTTAACATGATGCATTGT+AGG - chr5_4:9836990-9837009 Msa0836340:intron 30.0%
! TGGATGTCTTTTTCTTTTAG+GGG - chr5_4:9837097-9837116 Msa0836340:intron 30.0%
CTAGTAGTTGTTGAATTAGT+TGG - chr5_4:9837309-9837328 Msa0836340:CDS 30.0%
GTCACAATTACAACATGATA+CGG - chr5_4:9837687-9837706 Msa0836340:CDS 30.0%
TGTTGTGTATCTTAACAGAA+TGG - chr5_4:9837943-9837962 Msa0836340:five_prime_UTR 30.0%
! ATGATTTTCAAAACGACGTA+TGG - chr5_4:9837992-9838011 Msa0836340:five_prime_UTR 30.0%
ATATGGATTTGTGAAGGAAG+AGG + chr5_4:9835501-9835520 None:intergenic 35.0%
GAAAGGATATGGATTTGTGA+AGG + chr5_4:9835507-9835526 None:intergenic 35.0%
AGATAGCAACAGAAAGGATA+TGG + chr5_4:9835518-9835537 None:intergenic 35.0%
AGTTGAAGATAGCAACAGAA+AGG + chr5_4:9835524-9835543 None:intergenic 35.0%
GCAGAAAACGAAACATTGTA+TGG + chr5_4:9835789-9835808 None:intergenic 35.0%
!!! GTTGTTTTTAACCATGTACG+AGG - chr5_4:9835933-9835952 Msa0836340:intron 35.0%
! TGAAAGGTTTGCCGTTTAAT+CGG - chr5_4:9836174-9836193 Msa0836340:intron 35.0%
CATAATTCATTTGCTTTGGC+TGG - chr5_4:9836215-9836234 Msa0836340:intron 35.0%
GACAACTAAGAAATGGTCTA+TGG - chr5_4:9836562-9836581 Msa0836340:intron 35.0%
TTTGACCGTAGAAACTAGAA+AGG + chr5_4:9836870-9836889 None:intergenic 35.0%
TACGGTCAAACAAACACAAT+AGG - chr5_4:9836880-9836899 Msa0836340:intron 35.0%
ATTAATCCTTCTCTTCCTTG+TGG - chr5_4:9836937-9836956 Msa0836340:intron 35.0%
ATCAATAAAAAAGGGCCACA+AGG + chr5_4:9836955-9836974 None:intergenic 35.0%
ATCATGTTAAAGAAGGTCCA+CGG + chr5_4:9836983-9837002 None:intergenic 35.0%
TGTTGACCACATAAATGAAG+TGG - chr5_4:9837202-9837221 Msa0836340:intron 35.0%
GTTGACCACATAAATGAAGT+GGG - chr5_4:9837203-9837222 Msa0836340:intron 35.0%
TGGCACGGTTGAAATAAAAT+TGG - chr5_4:9837237-9837256 Msa0836340:CDS 35.0%
AAGTAAGATGTGTGCTTTCA+AGG + chr5_4:9837413-9837432 None:intergenic 35.0%
! AGCACACATCTTACTTGTTA+AGG - chr5_4:9837417-9837436 Msa0836340:intron 35.0%
GGCAATCGTGTATTCTAATT+TGG - chr5_4:9837763-9837782 Msa0836340:intron 35.0%
CACATATTCATCCAGCTTGA+AGG - chr5_4:9835846-9835865 Msa0836340:intron 40.0%
TGTCAAACATGTCCTGCAAA+TGG - chr5_4:9836001-9836020 Msa0836340:intron 40.0%
GATAGTATCCTGCTACATCT+GGG + chr5_4:9836037-9836056 None:intergenic 40.0%
AGATAGTATCCTGCTACATC+TGG + chr5_4:9836038-9836057 None:intergenic 40.0%
! TGCCGTTTAATCGGTATTCA+TGG - chr5_4:9836183-9836202 Msa0836340:intron 40.0%
TGCAAGGATAATTGAACCTG+TGG + chr5_4:9836252-9836271 None:intergenic 40.0%
ATAGTGTCATCCTGGTTCAT+AGG + chr5_4:9836275-9836294 None:intergenic 40.0%
CTAGAAAGGTCGTGTATGTT+TGG + chr5_4:9836856-9836875 None:intergenic 40.0%
!! CACGACCTTTCTAGTTTCTA+CGG - chr5_4:9836862-9836881 Msa0836340:intron 40.0%
TATGGAAGTCCATGCATACA+CGG - chr5_4:9836913-9836932 Msa0836340:intron 40.0%
TCATGTTAAAGAAGGTCCAC+GGG + chr5_4:9836982-9837001 None:intergenic 40.0%
CTACACCCACTTCATTTATG+TGG + chr5_4:9837211-9837230 None:intergenic 40.0%
TGTATGCAGTAGTTGTCTCA+TGG - chr5_4:9837496-9837515 Msa0836340:CDS 40.0%
GTATGCAGTAGTTGTCTCAT+GGG - chr5_4:9837497-9837516 Msa0836340:CDS 40.0%
TATGCAGTAGTTGTCTCATG+GGG - chr5_4:9837498-9837517 Msa0836340:CDS 40.0%
GAATACACGATTGCCTTCTT+TGG + chr5_4:9837758-9837777 None:intergenic 40.0%
TCTTAACAGAATGGTGTTCG+AGG - chr5_4:9837952-9837971 Msa0836340:five_prime_UTR 40.0%
! GTATGGTTGTGTCATTCTAC+TGG - chr5_4:9838009-9838028 Msa0836340:five_prime_UTR 40.0%
TAGCAGATCGGAGAAACATG+CGG - chr5_4:9835956-9835975 Msa0836340:intron 45.0%
GGACGTGTATTTCCATTTGC+AGG + chr5_4:9836016-9836035 None:intergenic 45.0%
TATCCTTGCACCTATGAACC+AGG - chr5_4:9836262-9836281 Msa0836340:intron 45.0%
GATCAGCAATAGTGTCATCC+TGG + chr5_4:9836283-9836302 None:intergenic 45.0%
ATGGAAGTCCATGCATACAC+GGG - chr5_4:9836914-9836933 Msa0836340:intron 45.0%
GGATTAATCCCGTGTATGCA+TGG + chr5_4:9836925-9836944 None:intergenic 45.0%
TGAAGTGGGTGTAGTGTAGA+TGG - chr5_4:9837217-9837236 Msa0836340:intron 45.0%
ATGCAGTAGTTGTCTCATGG+GGG - chr5_4:9837499-9837518 Msa0836340:CDS 45.0%
! TGGTTGTGTCATTCTACTGG+AGG - chr5_4:9838012-9838031 Msa0836340:five_prime_UTR 45.0%
!! AATAATAAAAAATATGAAAA+GGG + chr5_4:9836328-9836347 None:intergenic 5.0%
!! TAATAATAAAAAATATGAAA+AGG + chr5_4:9836329-9836348 None:intergenic 5.0%
!!! CATATTTTTTATTATTATTA+TGG - chr5_4:9836332-9836351 Msa0836340:intron 5.0%
CCATGTACGAGGTAGCAGAT+CGG - chr5_4:9835944-9835963 Msa0836340:intron 50.0%
ACATGCGGTTCATGTGATGC+TGG - chr5_4:9835971-9835990 Msa0836340:intron 50.0%
ATACACGTCCCAGATGTAGC+AGG - chr5_4:9836026-9836045 Msa0836340:intron 50.0%
CATCCTGGTTCATAGGTGCA+AGG + chr5_4:9836268-9836287 None:intergenic 50.0%
AAAGGGCCACAAGGAAGAGA+AGG + chr5_4:9836946-9836965 None:intergenic 50.0%
TGGGTGTAGTGTAGATGGCA+CGG - chr5_4:9837222-9837241 Msa0836340:intron 50.0%
CCGATCTGCTACCTCGTACA+TGG + chr5_4:9835947-9835966 None:intergenic 55.0%
GCTGGTGCAAGATCAGCCAC+AGG - chr5_4:9836233-9836252 Msa0836340:intron 60.0%
Chromosome Type Strat End Strand Name
chr5_4 gene 9835474 9838065 9835474 ID=Msa0836340;Name=Msa0836340
chr5_4 mRNA 9835474 9838065 9835474 ID=Msa0836340-mRNA-1;Parent=Msa0836340;Name=Msa0836340-mRNA-1;_AED=0.00;_eAED=0.00;_QI=149|1|0.8|1|0|0|5|0|140
chr5_4 exon 9835474 9835578 9835474 ID=Msa0836340-mRNA-1:exon:4385;Parent=Msa0836340-mRNA-1
chr5_4 exon 9837229 9837366 9837229 ID=Msa0836340-mRNA-1:exon:4384;Parent=Msa0836340-mRNA-1
chr5_4 exon 9837464 9837577 9837464 ID=Msa0836340-mRNA-1:exon:4383;Parent=Msa0836340-mRNA-1
chr5_4 exon 9837672 9837728 9837672 ID=Msa0836340-mRNA-1:exon:4382;Parent=Msa0836340-mRNA-1
chr5_4 exon 9837911 9838065 9837911 ID=Msa0836340-mRNA-1:exon:4381;Parent=Msa0836340-mRNA-1
chr5_4 five_prime_UTR 9837917 9838065 9837917 ID=Msa0836340-mRNA-1:five_prime_utr;Parent=Msa0836340-mRNA-1
chr5_4 CDS 9837911 9837916 9837911 ID=Msa0836340-mRNA-1:cds;Parent=Msa0836340-mRNA-1
chr5_4 CDS 9837672 9837728 9837672 ID=Msa0836340-mRNA-1:cds;Parent=Msa0836340-mRNA-1
chr5_4 CDS 9837464 9837577 9837464 ID=Msa0836340-mRNA-1:cds;Parent=Msa0836340-mRNA-1
chr5_4 CDS 9837229 9837366 9837229 ID=Msa0836340-mRNA-1:cds;Parent=Msa0836340-mRNA-1
chr5_4 CDS 9835474 9835578 9835474 ID=Msa0836340-mRNA-1:cds;Parent=Msa0836340-mRNA-1
Gene Sequence

>Msa0836340

ATGAAGAGCCAAATCTTTGTATTAATCGTCATTTGTTTCTTCACATATTCATCCAGCTTGAAGATCGGAGAAACATGCGGTTCATGTGATGCTGGTCTTACATGTCAAACATGTCCTGCAAATGGAAATACACGTCCCAGATGTAGCAGGATACTATCTTCAAACCCCATTAACAAAGTGAAAGGTTTGCCGTTTAATCGGTATTCATGGTTAACGACACATAATTCATTTGCTTTGGCTGGTGCAAGATCAGCCACAGGTTCAATTATCCTTGCACCTATGAACCAGGATGACACTATTGCTGATCAACTCAAAAATGGTGTTCGAGGATTTATGTTAGATATGTATGATTTTCAAAACGACGTATGGTTGTGTCATTCTACTGGAGGCAAATGTTTCAACTTCAGTTCATTCGTAAGT

Protein sequence

>Msa0836340

MKSQIFVLIVICFFTYSSSLKIGETCGSCDAGLTCQTCPANGNTRPRCSRILSSNPINKVKGLPFNRYSWLTTHNSFALAGARSATGSIILAPMNQDDTIADQLKNGVRGFMLDMYDFQNDVWLCHSTGGKCFNFSSFVS