AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1211950

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1211950 MtrunA17_Chr4g0060821 81.111 90 16 1 1 89 1 90 7.30e-45 139
Msa1211950 MtrunA17_Chr3g0092121 56.522 92 35 2 1 89 1 90 3.56e-29 100
Msa1211950 MtrunA17_Chr6g0460751 37.778 90 50 3 1 89 1 85 3.12e-11 54.3
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 39 sgRNAs with CRISPR-Local

Find 120 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TTGTTTATGTATGGGATCTT+AGG 0.200401 8_1:-71786247 Msa1211950:three_prime_UTR
TCCATCCTCTCATTAATTCT+TGG 0.236814 8_1:+71786500 None:intergenic
CTCTCATTAATTCTTGGCTT+TGG 0.277804 8_1:+71786506 None:intergenic
TAGAAGAATTTACTTGTAAC+TGG 0.288724 8_1:+71786970 None:intergenic
AATTAATGAGAGGATGGATT+TGG 0.333806 8_1:-71786495 Msa1211950:CDS
AAATCCCCATTGTTTATGTA+TGG 0.334660 8_1:-71786256 Msa1211950:three_prime_UTR
CTCAATGATTATGCACCATC+TGG 0.362640 8_1:-71786470 Msa1211950:CDS
AGAGGAACTAACATTTAATC+AGG 0.368142 8_1:+71786403 None:intergenic
CAACTTGGACATCTTGCATA+AGG 0.415467 8_1:+71786698 None:intergenic
GATGCATGCATATATAATAT+AGG 0.428327 8_1:+71786371 None:intergenic
AATCAGGTTACACACCATTA+CGG 0.442297 8_1:+71786419 None:intergenic
GAGAAGAGCCATTGCAGTGC+AGG 0.444281 8_1:-71787066 Msa1211950:five_prime_UTR
GAGCCATTGCAGTGCAGGAA+TGG 0.454277 8_1:-71787061 Msa1211950:exon
ATAAATTGAGAACTAGCATA+TGG 0.454361 8_1:-71787117 Msa1211950:five_prime_UTR
AGATCCCATACATAAACAAT+GGG 0.456560 8_1:+71786251 None:intergenic
CATTGCAGTGCAGGAATGGC+AGG 0.458130 8_1:-71787057 Msa1211950:exon
ACACACCATTACGGTGCTCT+TGG 0.466740 8_1:+71786428 None:intergenic
TATGCACCATCTGGGGCAAA+TGG 0.473723 8_1:-71786461 Msa1211950:CDS
CTGCCATTCCTGCACTGCAA+TGG 0.493434 8_1:+71787058 None:intergenic
ATCATTGAAATTCTAGTACA+TGG 0.502495 8_1:+71786190 None:intergenic
AATCCCCATTGTTTATGTAT+GGG 0.510722 8_1:-71786255 Msa1211950:three_prime_UTR
TCAATGATTATGCACCATCT+GGG 0.530735 8_1:-71786469 Msa1211950:CDS
ATTTATGTATGATGAAAGAA+AGG 0.544291 8_1:-71786299 Msa1211950:three_prime_UTR
GCCAAGAATTAATGAGAGGA+TGG 0.546052 8_1:-71786501 Msa1211950:CDS
AAATGTTAGTTCCTCTAGCT+AGG 0.547983 8_1:-71786396 Msa1211950:three_prime_UTR
AAGATCCCATACATAAACAA+TGG 0.554557 8_1:+71786250 None:intergenic
TAAATTGAGAACTAGCATAT+GGG 0.561490 8_1:-71787116 Msa1211950:five_prime_UTR
TACTCCGGAAAATACCCCTC+AGG 0.579089 8_1:-71786668 Msa1211950:intron
ACACTCCAAGAGCACCGTAA+TGG 0.580515 8_1:-71786433 Msa1211950:exon
TCTTCTCAGAAACAAGCTCT+AGG 0.580954 8_1:+71787082 None:intergenic
CCAAGTTGACCTAATTACTC+CGG 0.594810 8_1:-71786683 Msa1211950:CDS
TAATATAGGCACCTAGCTAG+AGG 0.625528 8_1:+71786385 None:intergenic
CAAAGCCAAGAATTAATGAG+AGG 0.628754 8_1:-71786505 Msa1211950:CDS
TGACGACCATTTGCCCCAGA+TGG 0.633835 8_1:+71786455 None:intergenic
TCGAGCATAAAAGATGTGAA+AGG 0.635992 8_1:+71787001 None:intergenic
CAATGATTATGCACCATCTG+GGG 0.636327 8_1:-71786468 Msa1211950:CDS
ATTGAGAACTAGCATATGGG+AGG 0.656265 8_1:-71787113 Msa1211950:five_prime_UTR
GATCCCATACATAAACAATG+GGG 0.744720 8_1:+71786252 None:intergenic
AGTATCAAACTGTACCTGAG+GGG 0.746962 8_1:+71786654 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! TTTGTTTTTTATCATTGAAA+AGG - chr8_1:71786387-71786406 Msa1211950:three_prime_UTR 15.0%
!!! TTTGTTTTTTATCATTGAAA+AGG - chr8_1:71786387-71786406 Msa1211950:three_prime_UTR 15.0%
!!! TTTGTGATGTTTTTTTAACA+TGG + chr8_1:71786173-71786192 None:intergenic 20.0%
!! AACAAGATTATATATGTTAC+AGG - chr8_1:71786765-71786784 Msa1211950:intron 20.0%
!!! CTTAATATTGTTTTACATAG+AGG + chr8_1:71786980-71786999 None:intergenic 20.0%
!!! ATATATGAGTTTTATTGTAG+AGG - chr8_1:71787003-71787022 Msa1211950:CDS 20.0%
!! ATTTATGTATGATGAAAGAA+AGG - chr8_1:71787027-71787046 Msa1211950:CDS 20.0%
!!! TTTGTGATGTTTTTTTAACA+TGG + chr8_1:71786173-71786192 None:intergenic 20.0%
!! AACAAGATTATATATGTTAC+AGG - chr8_1:71786765-71786784 Msa1211950:intron 20.0%
!!! CTTAATATTGTTTTACATAG+AGG + chr8_1:71786980-71786999 None:intergenic 20.0%
!!! ATATATGAGTTTTATTGTAG+AGG - chr8_1:71787003-71787022 Msa1211950:CDS 20.0%
!! ATTTATGTATGATGAAAGAA+AGG - chr8_1:71787027-71787046 Msa1211950:CDS 20.0%
! ATAAATTGAGAACTAGCATA+TGG - chr8_1:71786209-71786228 Msa1211950:three_prime_UTR 25.0%
! TAAATTGAGAACTAGCATAT+GGG - chr8_1:71786210-71786229 Msa1211950:three_prime_UTR 25.0%
! TAGAAGAATTTACTTGTAAC+TGG + chr8_1:71786359-71786378 None:intergenic 25.0%
! TACGTCTATATTTGAATTGA+CGG - chr8_1:71786412-71786431 Msa1211950:three_prime_UTR 25.0%
!! AGTCTTAGTCTTCTTATATA+TGG - chr8_1:71786577-71786596 Msa1211950:intron 25.0%
! GATGCATGCATATATAATAT+AGG + chr8_1:71786958-71786977 None:intergenic 25.0%
! ATCATTGAAATTCTAGTACA+TGG + chr8_1:71787139-71787158 None:intergenic 25.0%
! ATAAATTGAGAACTAGCATA+TGG - chr8_1:71786209-71786228 Msa1211950:three_prime_UTR 25.0%
! TAAATTGAGAACTAGCATAT+GGG - chr8_1:71786210-71786229 Msa1211950:three_prime_UTR 25.0%
! TAGAAGAATTTACTTGTAAC+TGG + chr8_1:71786359-71786378 None:intergenic 25.0%
! TACGTCTATATTTGAATTGA+CGG - chr8_1:71786412-71786431 Msa1211950:three_prime_UTR 25.0%
!! AGTCTTAGTCTTCTTATATA+TGG - chr8_1:71786577-71786596 Msa1211950:intron 25.0%
! GATGCATGCATATATAATAT+AGG + chr8_1:71786958-71786977 None:intergenic 25.0%
! ATCATTGAAATTCTAGTACA+TGG + chr8_1:71787139-71787158 None:intergenic 25.0%
! CGTTTATTCGTGATTTTTCT+TGG - chr8_1:71786302-71786321 Msa1211950:three_prime_UTR 30.0%
ATTTGAATTGACGGTGAATT+TGG - chr8_1:71786421-71786440 Msa1211950:exon 30.0%
TGAATTTCATGAAATCATGG+TGG + chr8_1:71786516-71786535 None:intergenic 30.0%
CGATGAATTTCATGAAATCA+TGG + chr8_1:71786519-71786538 None:intergenic 30.0%
GGAAAATTACATGCATGTTT+CGG + chr8_1:71786546-71786565 None:intergenic 30.0%
ATGGTATGTTTGTATTAAGC+AGG - chr8_1:71786596-71786615 Msa1211950:intron 30.0%
TATTGAGAAAAACTTGCACT+TGG - chr8_1:71786792-71786811 Msa1211950:intron 30.0%
! AATTAATGAGAGGATGGATT+TGG - chr8_1:71786831-71786850 Msa1211950:intron 30.0%
AGAGGAACTAACATTTAATC+AGG + chr8_1:71786926-71786945 None:intergenic 30.0%
AAATCCCCATTGTTTATGTA+TGG - chr8_1:71787070-71787089 Msa1211950:five_prime_UTR 30.0%
AATCCCCATTGTTTATGTAT+GGG - chr8_1:71787071-71787090 Msa1211950:five_prime_UTR 30.0%
AGATCCCATACATAAACAAT+GGG + chr8_1:71787078-71787097 None:intergenic 30.0%
AAGATCCCATACATAAACAA+TGG + chr8_1:71787079-71787098 None:intergenic 30.0%
TTGTTTATGTATGGGATCTT+AGG - chr8_1:71787079-71787098 Msa1211950:five_prime_UTR 30.0%
! CGTTTATTCGTGATTTTTCT+TGG - chr8_1:71786302-71786321 Msa1211950:three_prime_UTR 30.0%
ATTTGAATTGACGGTGAATT+TGG - chr8_1:71786421-71786440 Msa1211950:exon 30.0%
TGAATTTCATGAAATCATGG+TGG + chr8_1:71786516-71786535 None:intergenic 30.0%
CGATGAATTTCATGAAATCA+TGG + chr8_1:71786519-71786538 None:intergenic 30.0%
GGAAAATTACATGCATGTTT+CGG + chr8_1:71786546-71786565 None:intergenic 30.0%
ATGGTATGTTTGTATTAAGC+AGG - chr8_1:71786596-71786615 Msa1211950:intron 30.0%
TATTGAGAAAAACTTGCACT+TGG - chr8_1:71786792-71786811 Msa1211950:intron 30.0%
! AATTAATGAGAGGATGGATT+TGG - chr8_1:71786831-71786850 Msa1211950:intron 30.0%
AGAGGAACTAACATTTAATC+AGG + chr8_1:71786926-71786945 None:intergenic 30.0%
AAATCCCCATTGTTTATGTA+TGG - chr8_1:71787070-71787089 Msa1211950:five_prime_UTR 30.0%
AATCCCCATTGTTTATGTAT+GGG - chr8_1:71787071-71787090 Msa1211950:five_prime_UTR 30.0%
AGATCCCATACATAAACAAT+GGG + chr8_1:71787078-71787097 None:intergenic 30.0%
AAGATCCCATACATAAACAA+TGG + chr8_1:71787079-71787098 None:intergenic 30.0%
TTGTTTATGTATGGGATCTT+AGG - chr8_1:71787079-71787098 Msa1211950:five_prime_UTR 30.0%
TCGAGCATAAAAGATGTGAA+AGG + chr8_1:71786328-71786347 None:intergenic 35.0%
GACTAAGACTAAGAAGATGA+AGG + chr8_1:71786567-71786586 None:intergenic 35.0%
CTCTCATTAATTCTTGGCTT+TGG + chr8_1:71786823-71786842 None:intergenic 35.0%
CAAAGCCAAGAATTAATGAG+AGG - chr8_1:71786821-71786840 Msa1211950:intron 35.0%
TCCATCCTCTCATTAATTCT+TGG + chr8_1:71786829-71786848 None:intergenic 35.0%
TCAATGATTATGCACCATCT+GGG - chr8_1:71786857-71786876 Msa1211950:intron 35.0%
AATCAGGTTACACACCATTA+CGG + chr8_1:71786910-71786929 None:intergenic 35.0%
AAATGTTAGTTCCTCTAGCT+AGG - chr8_1:71786930-71786949 Msa1211950:intron 35.0%
GATCCCATACATAAACAATG+GGG + chr8_1:71787077-71787096 None:intergenic 35.0%
TCGAGCATAAAAGATGTGAA+AGG + chr8_1:71786328-71786347 None:intergenic 35.0%
GACTAAGACTAAGAAGATGA+AGG + chr8_1:71786567-71786586 None:intergenic 35.0%
CTCTCATTAATTCTTGGCTT+TGG + chr8_1:71786823-71786842 None:intergenic 35.0%
CAAAGCCAAGAATTAATGAG+AGG - chr8_1:71786821-71786840 Msa1211950:intron 35.0%
TCCATCCTCTCATTAATTCT+TGG + chr8_1:71786829-71786848 None:intergenic 35.0%
TCAATGATTATGCACCATCT+GGG - chr8_1:71786857-71786876 Msa1211950:intron 35.0%
AATCAGGTTACACACCATTA+CGG + chr8_1:71786910-71786929 None:intergenic 35.0%
AAATGTTAGTTCCTCTAGCT+AGG - chr8_1:71786930-71786949 Msa1211950:intron 35.0%
GATCCCATACATAAACAATG+GGG + chr8_1:71787077-71787096 None:intergenic 35.0%
ATTGAGAACTAGCATATGGG+AGG - chr8_1:71786213-71786232 Msa1211950:three_prime_UTR 40.0%
TCTTCTCAGAAACAAGCTCT+AGG + chr8_1:71786247-71786266 None:intergenic 40.0%
TGAATTGACGGTGAATTTGG+TGG - chr8_1:71786424-71786443 Msa1211950:exon 40.0%
CAACTTGGACATCTTGCATA+AGG + chr8_1:71786631-71786650 None:intergenic 40.0%
! CCAAGTTGACCTAATTACTC+CGG - chr8_1:71786643-71786662 Msa1211950:intron 40.0%
! GGGTATTTTCCGGAGTAATT+AGG + chr8_1:71786655-71786674 None:intergenic 40.0%
AGTATCAAACTGTACCTGAG+GGG + chr8_1:71786675-71786694 None:intergenic 40.0%
GAGTATCAAACTGTACCTGA+GGG + chr8_1:71786676-71786695 None:intergenic 40.0%
! AGAGTATCAAACTGTACCTG+AGG + chr8_1:71786677-71786696 None:intergenic 40.0%
GCCAAGAATTAATGAGAGGA+TGG - chr8_1:71786825-71786844 Msa1211950:intron 40.0%
CTCAATGATTATGCACCATC+TGG - chr8_1:71786856-71786875 Msa1211950:intron 40.0%
CAATGATTATGCACCATCTG+GGG - chr8_1:71786858-71786877 Msa1211950:intron 40.0%
TAATATAGGCACCTAGCTAG+AGG + chr8_1:71786944-71786963 None:intergenic 40.0%
ATTGAGAACTAGCATATGGG+AGG - chr8_1:71786213-71786232 Msa1211950:three_prime_UTR 40.0%
TCTTCTCAGAAACAAGCTCT+AGG + chr8_1:71786247-71786266 None:intergenic 40.0%
TGAATTGACGGTGAATTTGG+TGG - chr8_1:71786424-71786443 Msa1211950:exon 40.0%
CAACTTGGACATCTTGCATA+AGG + chr8_1:71786631-71786650 None:intergenic 40.0%
! CCAAGTTGACCTAATTACTC+CGG - chr8_1:71786643-71786662 Msa1211950:intron 40.0%
! GGGTATTTTCCGGAGTAATT+AGG + chr8_1:71786655-71786674 None:intergenic 40.0%
AGTATCAAACTGTACCTGAG+GGG + chr8_1:71786675-71786694 None:intergenic 40.0%
GAGTATCAAACTGTACCTGA+GGG + chr8_1:71786676-71786695 None:intergenic 40.0%
! AGAGTATCAAACTGTACCTG+AGG + chr8_1:71786677-71786696 None:intergenic 40.0%
GCCAAGAATTAATGAGAGGA+TGG - chr8_1:71786825-71786844 Msa1211950:intron 40.0%
CTCAATGATTATGCACCATC+TGG - chr8_1:71786856-71786875 Msa1211950:intron 40.0%
CAATGATTATGCACCATCTG+GGG - chr8_1:71786858-71786877 Msa1211950:intron 40.0%
TAATATAGGCACCTAGCTAG+AGG + chr8_1:71786944-71786963 None:intergenic 40.0%
CCGGAGTAATTAGGTCAACT+TGG + chr8_1:71786646-71786665 None:intergenic 45.0%
!!! TGTACCTGAGGGGTATTTTC+CGG + chr8_1:71786665-71786684 None:intergenic 45.0%
CCGGAGTAATTAGGTCAACT+TGG + chr8_1:71786646-71786665 None:intergenic 45.0%
!!! TGTACCTGAGGGGTATTTTC+CGG + chr8_1:71786665-71786684 None:intergenic 45.0%
TACTCCGGAAAATACCCCTC+AGG - chr8_1:71786658-71786677 Msa1211950:intron 50.0%
! TATGCACCATCTGGGGCAAA+TGG - chr8_1:71786865-71786884 Msa1211950:intron 50.0%
!! ACACTCCAAGAGCACCGTAA+TGG - chr8_1:71786893-71786912 Msa1211950:intron 50.0%
ACACACCATTACGGTGCTCT+TGG + chr8_1:71786901-71786920 None:intergenic 50.0%
TACTCCGGAAAATACCCCTC+AGG - chr8_1:71786658-71786677 Msa1211950:intron 50.0%
! TATGCACCATCTGGGGCAAA+TGG - chr8_1:71786865-71786884 Msa1211950:intron 50.0%
!! ACACTCCAAGAGCACCGTAA+TGG - chr8_1:71786893-71786912 Msa1211950:intron 50.0%
ACACACCATTACGGTGCTCT+TGG + chr8_1:71786901-71786920 None:intergenic 50.0%
GAGAAGAGCCATTGCAGTGC+AGG - chr8_1:71786260-71786279 Msa1211950:three_prime_UTR 55.0%
GAGCCATTGCAGTGCAGGAA+TGG - chr8_1:71786265-71786284 Msa1211950:three_prime_UTR 55.0%
CTGCCATTCCTGCACTGCAA+TGG + chr8_1:71786271-71786290 None:intergenic 55.0%
CATTGCAGTGCAGGAATGGC+AGG - chr8_1:71786269-71786288 Msa1211950:three_prime_UTR 55.0%
TGACGACCATTTGCCCCAGA+TGG + chr8_1:71786874-71786893 None:intergenic 55.0%
GAGAAGAGCCATTGCAGTGC+AGG - chr8_1:71786260-71786279 Msa1211950:three_prime_UTR 55.0%
GAGCCATTGCAGTGCAGGAA+TGG - chr8_1:71786265-71786284 Msa1211950:three_prime_UTR 55.0%
CTGCCATTCCTGCACTGCAA+TGG + chr8_1:71786271-71786290 None:intergenic 55.0%
CATTGCAGTGCAGGAATGGC+AGG - chr8_1:71786269-71786288 Msa1211950:three_prime_UTR 55.0%
TGACGACCATTTGCCCCAGA+TGG + chr8_1:71786874-71786893 None:intergenic 55.0%
Chromosome Type Strat End Strand Name
chr8_1 gene 71786161 71787187 71786161 ID=Msa1211950;Name=Msa1211950
chr8_1 mRNA 71786161 71787187 71786161 ID=Msa1211950-mRNA-1;Parent=Msa1211950;Name=Msa1211950-mRNA-1;_AED=0.03;_eAED=0.03;_QI=123|1|1|1|0.5|0.66|3|275|89
chr8_1 exon 71786161 71786561 71786161 ID=Msa1211950-mRNA-1:exon:24220;Parent=Msa1211950-mRNA-1
chr8_1 exon 71786669 71786730 71786669 ID=Msa1211950-mRNA-1:exon:24219;Parent=Msa1211950-mRNA-1
chr8_1 exon 71786983 71787187 71786983 ID=Msa1211950-mRNA-1:exon:24218;Parent=Msa1211950-mRNA-1
chr8_1 five_prime_UTR 71787065 71787187 71787065 ID=Msa1211950-mRNA-1:five_prime_utr;Parent=Msa1211950-mRNA-1
chr8_1 CDS 71786983 71787064 71786983 ID=Msa1211950-mRNA-1:cds;Parent=Msa1211950-mRNA-1
chr8_1 CDS 71786669 71786730 71786669 ID=Msa1211950-mRNA-1:cds;Parent=Msa1211950-mRNA-1
chr8_1 CDS 71786436 71786561 71786436 ID=Msa1211950-mRNA-1:cds;Parent=Msa1211950-mRNA-1
chr8_1 three_prime_UTR 71786161 71786435 71786161 ID=Msa1211950-mRNA-1:three_prime_utr;Parent=Msa1211950-mRNA-1
Gene Sequence

>Msa1211950

ATGGCAGGAACTTTCTTTCGTTTATTCGTGATTTTTCTTGGCCTTTCACATCTTTTATGCTCGACAGCAGTTCCAGTTACAAGAACTGAAAACCTTATGCAAGATGTCCAAGTTGACCTAATTACTCCGGAAAATACCCCTCAGGTTATTATTGAGAAAAACTTGCACTTGGAAGAGCCAAAGCCAAGAATTAATGAGAGGATGGATTTGGAACTCAATGATTATGCACCATCTGGGGCAAATGGTCGTCACACTCCAAGAGCACCGTAA
Protein sequence

>Msa1211950

MAGTFFRLFVIFLGLSHLLCSTAVPVTRTENLMQDVQVDLITPENTPQVIIEKNLHLEEPKPRINERMDLELNDYAPSGANGRHTPRAP*