AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1386840

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1386840 MtrunA17_Chr4g0060821 82.222 90 15 1 1 89 1 90 5.67e-45 139
Msa1386840 MtrunA17_Chr3g0092121 55.435 92 36 2 1 89 1 90 9.53e-29 99.0
Msa1386840 MtrunA17_Chr6g0460751 38.889 90 49 3 1 89 1 85 2.11e-12 57.4
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 43 sgRNAs with CRISPR-Local

Find 131 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CGTTTATTCGTGATTCTTCT+TGG 0.169086 tig0020872:-46023 Msa1386840:CDS
ATTAAGCACAAAACTGAAAA+AGG 0.192325 tig0020872:-45114 Msa1386840:three_prime_UTR
TTGTTTATGTATGGGATCTT+AGG 0.200401 tig0020872:-45284 Msa1386840:three_prime_UTR
TCCATCCTCTCATTAATTCT+TGG 0.236814 tig0020872:+45501 None:intergenic
CTCTCATTAATTCTTGGCTT+TGG 0.277804 tig0020872:+45507 None:intergenic
TAGAAGAATTTACTTGTAAC+TGG 0.288724 tig0020872:+45969 None:intergenic
AATTAATGAGAGGATGGATT+TGG 0.333806 tig0020872:-45496 Msa1386840:CDS
AAATCCCCATTGTTTATGTA+TGG 0.334660 tig0020872:-45293 Msa1386840:three_prime_UTR
CTCAATGATTATGCACCATC+TGG 0.362640 tig0020872:-45471 Msa1386840:CDS
AGAGGAACTAACATTTAATC+AGG 0.392881 tig0020872:+45404 None:intergenic
AAAAGGGTCCATATTCATAT+TGG 0.393272 tig0020872:-45097 Msa1386840:three_prime_UTR
CAACTTGGACATCTTGCATA+AGG 0.415467 tig0020872:+45698 None:intergenic
AATCAGGTTACACACCATTA+CGG 0.442297 tig0020872:+45420 None:intergenic
ATAAATTGAGAACTAGCATA+TGG 0.454361 tig0020872:-46116 Msa1386840:five_prime_UTR
AGATCCCATACATAAACAAT+GGG 0.456560 tig0020872:+45288 None:intergenic
AATATATAGGTGGACGGTAG+AGG 0.459504 tig0020872:+45064 None:intergenic
ACACACCATTACGGTGCTCT+TGG 0.466740 tig0020872:+45429 None:intergenic
TATGCACCATCTGGGGCAAA+TGG 0.473723 tig0020872:-45462 Msa1386840:CDS
GAGAAGGGTCATTGCAGTGC+AGG 0.473866 tig0020872:-46065 Msa1386840:five_prime_UTR
CATTGCAGTGCAGGAATGGC+AGG 0.490014 tig0020872:-46056 Msa1386840:exon
GGGTCATTGCAGTGCAGGAA+TGG 0.499077 tig0020872:-46060 Msa1386840:exon
ATCATTGAAATTCTAGTACA+TGG 0.502495 tig0020872:+45226 None:intergenic
ATAAAATAAGACAAAATCAA+TGG 0.507774 tig0020872:+45172 None:intergenic
AATCCCCATTGTTTATGTAT+GGG 0.510722 tig0020872:-45292 Msa1386840:three_prime_UTR
AAGACAAAATCAATGGCTGT+TGG 0.520940 tig0020872:+45179 None:intergenic
TCAATGATTATGCACCATCT+GGG 0.530735 tig0020872:-45470 Msa1386840:CDS
ATTTATGTATGATGAAAGAA+AGG 0.544291 tig0020872:-45336 Msa1386840:three_prime_UTR
GCCAAGAATTAATGAGAGGA+TGG 0.546052 tig0020872:-45502 Msa1386840:CDS
AAGATCCCATACATAAACAA+TGG 0.554557 tig0020872:+45287 None:intergenic
ATATATAGGTGGACGGTAGA+GGG 0.556953 tig0020872:+45065 None:intergenic
GTGTTACATGCAGGTTAAAG+TGG 0.557750 tig0020872:+45141 None:intergenic
TAAATTGAGAACTAGCATAT+GGG 0.561490 tig0020872:-46115 Msa1386840:five_prime_UTR
TACTCCGGAAAATACCCCTC+AGG 0.579089 tig0020872:-45668 Msa1386840:intron
ACACTCCAAGAGCACCGTAA+TGG 0.580515 tig0020872:-45434 Msa1386840:exon
TTAATGCTTGTGTTACATGC+AGG 0.582300 tig0020872:+45132 None:intergenic
CCAAGTTGACCTAATTACTC+CGG 0.594810 tig0020872:-45683 Msa1386840:CDS
CAAAGCCAAGAATTAATGAG+AGG 0.628754 tig0020872:-45506 Msa1386840:CDS
TGACGACCATTTGCCCCAGA+TGG 0.633835 tig0020872:+45456 None:intergenic
CAATGATTATGCACCATCTG+GGG 0.636327 tig0020872:-45469 Msa1386840:CDS
TTAAGCATAGAAGATGTGAA+AGG 0.652061 tig0020872:+46000 None:intergenic
ATTGAGAACTAGCATATGGG+AGG 0.656265 tig0020872:-46112 Msa1386840:five_prime_UTR
GATCCCATACATAAACAATG+GGG 0.744720 tig0020872:+45289 None:intergenic
AGTATCAAACTGTACCTGAG+GGG 0.746962 tig0020872:+45654 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! ATAAAATAAGACAAAATCAA+TGG + tig0020872:46069-46088 None:intergenic 15.0%
!! ATAAAATAAGACAAAATCAA+TGG + tig0020872:46069-46088 None:intergenic 15.0%
!!! TTTGTGATGTTTTTTTAACA+TGG + tig0020872:45086-45105 None:intergenic 20.0%
!! AACAAGATTATATATGTTAC+AGG - tig0020872:45676-45695 Msa1386840:CDS 20.0%
!!! CTTAATATTGTTTTACATAG+AGG + tig0020872:45855-45874 None:intergenic 20.0%
!!! ATATATGAGTTTTATTGTAG+AGG - tig0020872:45878-45897 Msa1386840:intron 20.0%
!! ATTTATGTATGATGAAAGAA+AGG - tig0020872:45902-45921 Msa1386840:intron 20.0%
!!! TTTGTGATGTTTTTTTAACA+TGG + tig0020872:45086-45105 None:intergenic 20.0%
!! AACAAGATTATATATGTTAC+AGG - tig0020872:45676-45695 Msa1386840:CDS 20.0%
!!! CTTAATATTGTTTTACATAG+AGG + tig0020872:45855-45874 None:intergenic 20.0%
!!! ATATATGAGTTTTATTGTAG+AGG - tig0020872:45878-45897 Msa1386840:intron 20.0%
!! ATTTATGTATGATGAAAGAA+AGG - tig0020872:45902-45921 Msa1386840:intron 20.0%
! ATAAATTGAGAACTAGCATA+TGG - tig0020872:45122-45141 Msa1386840:three_prime_UTR 25.0%
! TAAATTGAGAACTAGCATAT+GGG - tig0020872:45123-45142 Msa1386840:three_prime_UTR 25.0%
! TAGAAGAATTTACTTGTAAC+TGG + tig0020872:45272-45291 None:intergenic 25.0%
! TACGTCTATATTTGAATTGA+CGG - tig0020872:45324-45343 Msa1386840:three_prime_UTR 25.0%
!! AGTCTTAGTCTTCTTATATA+TGG - tig0020872:45489-45508 Msa1386840:CDS 25.0%
! ATCATTGAAATTCTAGTACA+TGG + tig0020872:46015-46034 None:intergenic 25.0%
! ATTAAGCACAAAACTGAAAA+AGG - tig0020872:46124-46143 Msa1386840:five_prime_UTR 25.0%
! TTAAGCACAAAACTGAAAAA+GGG - tig0020872:46125-46144 Msa1386840:five_prime_UTR 25.0%
!! TTTTTGCACCAATATGAATA+TGG + tig0020872:46152-46171 None:intergenic 25.0%
! ATAAATTGAGAACTAGCATA+TGG - tig0020872:45122-45141 Msa1386840:three_prime_UTR 25.0%
! TAAATTGAGAACTAGCATAT+GGG - tig0020872:45123-45142 Msa1386840:three_prime_UTR 25.0%
! TAGAAGAATTTACTTGTAAC+TGG + tig0020872:45272-45291 None:intergenic 25.0%
! TACGTCTATATTTGAATTGA+CGG - tig0020872:45324-45343 Msa1386840:three_prime_UTR 25.0%
!! AGTCTTAGTCTTCTTATATA+TGG - tig0020872:45489-45508 Msa1386840:CDS 25.0%
! ATCATTGAAATTCTAGTACA+TGG + tig0020872:46015-46034 None:intergenic 25.0%
! ATTAAGCACAAAACTGAAAA+AGG - tig0020872:46124-46143 Msa1386840:five_prime_UTR 25.0%
! TTAAGCACAAAACTGAAAAA+GGG - tig0020872:46125-46144 Msa1386840:five_prime_UTR 25.0%
!! TTTTTGCACCAATATGAATA+TGG + tig0020872:46152-46171 None:intergenic 25.0%
TTAAGCATAGAAGATGTGAA+AGG + tig0020872:45241-45260 None:intergenic 30.0%
ATTTGAATTGACGGTGAATT+TGG - tig0020872:45333-45352 Msa1386840:three_prime_UTR 30.0%
TGTATTTCATGAAATCATGG+TGG + tig0020872:45428-45447 None:intergenic 30.0%
CGATGTATTTCATGAAATCA+TGG + tig0020872:45431-45450 None:intergenic 30.0%
GGAAAATTACATGCATGTTT+CGG + tig0020872:45458-45477 None:intergenic 30.0%
ATGGTATGTTTGTATTAAGC+AGG - tig0020872:45508-45527 Msa1386840:CDS 30.0%
TATTGAGAAAAACTTGCACT+TGG - tig0020872:45703-45722 Msa1386840:CDS 30.0%
! AATTAATGAGAGGATGGATT+TGG - tig0020872:45742-45761 Msa1386840:intron 30.0%
AGAGGAACTAACATTTAATC+AGG + tig0020872:45837-45856 None:intergenic 30.0%
AAATCCCCATTGTTTATGTA+TGG - tig0020872:45945-45964 Msa1386840:intron 30.0%
AATCCCCATTGTTTATGTAT+GGG - tig0020872:45946-45965 Msa1386840:intron 30.0%
AGATCCCATACATAAACAAT+GGG + tig0020872:45953-45972 None:intergenic 30.0%
AAGATCCCATACATAAACAA+TGG + tig0020872:45954-45973 None:intergenic 30.0%
TTGTTTATGTATGGGATCTT+AGG - tig0020872:45954-45973 Msa1386840:intron 30.0%
AAAAGGGTCCATATTCATAT+TGG - tig0020872:46141-46160 Msa1386840:five_prime_UTR 30.0%
! TTTTAACATGGAATGTCGAT+TGG + tig0020872:45074-45093 None:intergenic 30.0%
TTAAGCATAGAAGATGTGAA+AGG + tig0020872:45241-45260 None:intergenic 30.0%
ATTTGAATTGACGGTGAATT+TGG - tig0020872:45333-45352 Msa1386840:three_prime_UTR 30.0%
TGTATTTCATGAAATCATGG+TGG + tig0020872:45428-45447 None:intergenic 30.0%
CGATGTATTTCATGAAATCA+TGG + tig0020872:45431-45450 None:intergenic 30.0%
GGAAAATTACATGCATGTTT+CGG + tig0020872:45458-45477 None:intergenic 30.0%
ATGGTATGTTTGTATTAAGC+AGG - tig0020872:45508-45527 Msa1386840:CDS 30.0%
TATTGAGAAAAACTTGCACT+TGG - tig0020872:45703-45722 Msa1386840:CDS 30.0%
! AATTAATGAGAGGATGGATT+TGG - tig0020872:45742-45761 Msa1386840:intron 30.0%
AGAGGAACTAACATTTAATC+AGG + tig0020872:45837-45856 None:intergenic 30.0%
AAATCCCCATTGTTTATGTA+TGG - tig0020872:45945-45964 Msa1386840:intron 30.0%
AATCCCCATTGTTTATGTAT+GGG - tig0020872:45946-45965 Msa1386840:intron 30.0%
AGATCCCATACATAAACAAT+GGG + tig0020872:45953-45972 None:intergenic 30.0%
AAGATCCCATACATAAACAA+TGG + tig0020872:45954-45973 None:intergenic 30.0%
TTGTTTATGTATGGGATCTT+AGG - tig0020872:45954-45973 Msa1386840:intron 30.0%
AAAAGGGTCCATATTCATAT+TGG - tig0020872:46141-46160 Msa1386840:five_prime_UTR 30.0%
!!! CTAGAGCTTGTTTTTGAGAA+GGG - tig0020872:45158-45177 Msa1386840:three_prime_UTR 35.0%
CGTTTATTCGTGATTCTTCT+TGG - tig0020872:45215-45234 Msa1386840:three_prime_UTR 35.0%
GACTAAGACTAAGAAGATGA+AGG + tig0020872:45479-45498 None:intergenic 35.0%
CTCTCATTAATTCTTGGCTT+TGG + tig0020872:45734-45753 None:intergenic 35.0%
CAAAGCCAAGAATTAATGAG+AGG - tig0020872:45732-45751 Msa1386840:intron 35.0%
TCCATCCTCTCATTAATTCT+TGG + tig0020872:45740-45759 None:intergenic 35.0%
TCAATGATTATGCACCATCT+GGG - tig0020872:45768-45787 Msa1386840:intron 35.0%
AATCAGGTTACACACCATTA+CGG + tig0020872:45821-45840 None:intergenic 35.0%
GATCCCATACATAAACAATG+GGG + tig0020872:45952-45971 None:intergenic 35.0%
AAGACAAAATCAATGGCTGT+TGG + tig0020872:46062-46081 None:intergenic 35.0%
TTAATGCTTGTGTTACATGC+AGG + tig0020872:46109-46128 None:intergenic 35.0%
!!! CTAGAGCTTGTTTTTGAGAA+GGG - tig0020872:45158-45177 Msa1386840:three_prime_UTR 35.0%
CGTTTATTCGTGATTCTTCT+TGG - tig0020872:45215-45234 Msa1386840:three_prime_UTR 35.0%
GACTAAGACTAAGAAGATGA+AGG + tig0020872:45479-45498 None:intergenic 35.0%
CTCTCATTAATTCTTGGCTT+TGG + tig0020872:45734-45753 None:intergenic 35.0%
CAAAGCCAAGAATTAATGAG+AGG - tig0020872:45732-45751 Msa1386840:intron 35.0%
TCCATCCTCTCATTAATTCT+TGG + tig0020872:45740-45759 None:intergenic 35.0%
TCAATGATTATGCACCATCT+GGG - tig0020872:45768-45787 Msa1386840:intron 35.0%
AATCAGGTTACACACCATTA+CGG + tig0020872:45821-45840 None:intergenic 35.0%
GATCCCATACATAAACAATG+GGG + tig0020872:45952-45971 None:intergenic 35.0%
AAGACAAAATCAATGGCTGT+TGG + tig0020872:46062-46081 None:intergenic 35.0%
TTAATGCTTGTGTTACATGC+AGG + tig0020872:46109-46128 None:intergenic 35.0%
ATTGAGAACTAGCATATGGG+AGG - tig0020872:45126-45145 Msa1386840:three_prime_UTR 40.0%
CCTTCTCAAAAACAAGCTCT+AGG + tig0020872:45160-45179 None:intergenic 40.0%
!!! CCTAGAGCTTGTTTTTGAGA+AGG - tig0020872:45157-45176 Msa1386840:three_prime_UTR 40.0%
TGAATTGACGGTGAATTTGG+TGG - tig0020872:45336-45355 Msa1386840:three_prime_UTR 40.0%
CAACTTGGACATCTTGCATA+AGG + tig0020872:45543-45562 None:intergenic 40.0%
! CCAAGTTGACCTAATTACTC+CGG - tig0020872:45555-45574 Msa1386840:intron 40.0%
! GGGTATTTTCCGGAGTAATT+AGG + tig0020872:45567-45586 None:intergenic 40.0%
AGTATCAAACTGTACCTGAG+GGG + tig0020872:45587-45606 None:intergenic 40.0%
GAGTATCAAACTGTACCTGA+GGG + tig0020872:45588-45607 None:intergenic 40.0%
! AGAGTATCAAACTGTACCTG+AGG + tig0020872:45589-45608 None:intergenic 40.0%
GCCAAGAATTAATGAGAGGA+TGG - tig0020872:45736-45755 Msa1386840:intron 40.0%
CTCAATGATTATGCACCATC+TGG - tig0020872:45767-45786 Msa1386840:intron 40.0%
CAATGATTATGCACCATCTG+GGG - tig0020872:45769-45788 Msa1386840:intron 40.0%
GTGTTACATGCAGGTTAAAG+TGG + tig0020872:46100-46119 None:intergenic 40.0%
ATTGAGAACTAGCATATGGG+AGG - tig0020872:45126-45145 Msa1386840:three_prime_UTR 40.0%
CCTTCTCAAAAACAAGCTCT+AGG + tig0020872:45160-45179 None:intergenic 40.0%
!!! CCTAGAGCTTGTTTTTGAGA+AGG - tig0020872:45157-45176 Msa1386840:three_prime_UTR 40.0%
TGAATTGACGGTGAATTTGG+TGG - tig0020872:45336-45355 Msa1386840:three_prime_UTR 40.0%
CAACTTGGACATCTTGCATA+AGG + tig0020872:45543-45562 None:intergenic 40.0%
! CCAAGTTGACCTAATTACTC+CGG - tig0020872:45555-45574 Msa1386840:intron 40.0%
! GGGTATTTTCCGGAGTAATT+AGG + tig0020872:45567-45586 None:intergenic 40.0%
AGTATCAAACTGTACCTGAG+GGG + tig0020872:45587-45606 None:intergenic 40.0%
GAGTATCAAACTGTACCTGA+GGG + tig0020872:45588-45607 None:intergenic 40.0%
! AGAGTATCAAACTGTACCTG+AGG + tig0020872:45589-45608 None:intergenic 40.0%
GCCAAGAATTAATGAGAGGA+TGG - tig0020872:45736-45755 Msa1386840:intron 40.0%
CTCAATGATTATGCACCATC+TGG - tig0020872:45767-45786 Msa1386840:intron 40.0%
CAATGATTATGCACCATCTG+GGG - tig0020872:45769-45788 Msa1386840:intron 40.0%
GTGTTACATGCAGGTTAAAG+TGG + tig0020872:46100-46119 None:intergenic 40.0%
CCGGAGTAATTAGGTCAACT+TGG + tig0020872:45558-45577 None:intergenic 45.0%
!!! TGTACCTGAGGGGTATTTTC+CGG + tig0020872:45577-45596 None:intergenic 45.0%
CCGGAGTAATTAGGTCAACT+TGG + tig0020872:45558-45577 None:intergenic 45.0%
!!! TGTACCTGAGGGGTATTTTC+CGG + tig0020872:45577-45596 None:intergenic 45.0%
TACTCCGGAAAATACCCCTC+AGG - tig0020872:45570-45589 Msa1386840:intron 50.0%
! TATGCACCATCTGGGGCAAA+TGG - tig0020872:45776-45795 Msa1386840:intron 50.0%
!! ACACTCCAAGAGCACCGTAA+TGG - tig0020872:45804-45823 Msa1386840:intron 50.0%
ACACACCATTACGGTGCTCT+TGG + tig0020872:45812-45831 None:intergenic 50.0%
TACTCCGGAAAATACCCCTC+AGG - tig0020872:45570-45589 Msa1386840:intron 50.0%
! TATGCACCATCTGGGGCAAA+TGG - tig0020872:45776-45795 Msa1386840:intron 50.0%
!! ACACTCCAAGAGCACCGTAA+TGG - tig0020872:45804-45823 Msa1386840:intron 50.0%
ACACACCATTACGGTGCTCT+TGG + tig0020872:45812-45831 None:intergenic 50.0%
GAGAAGGGTCATTGCAGTGC+AGG - tig0020872:45173-45192 Msa1386840:three_prime_UTR 55.0%
GGGTCATTGCAGTGCAGGAA+TGG - tig0020872:45178-45197 Msa1386840:three_prime_UTR 55.0%
CATTGCAGTGCAGGAATGGC+AGG - tig0020872:45182-45201 Msa1386840:three_prime_UTR 55.0%
TGACGACCATTTGCCCCAGA+TGG + tig0020872:45785-45804 None:intergenic 55.0%
GAGAAGGGTCATTGCAGTGC+AGG - tig0020872:45173-45192 Msa1386840:three_prime_UTR 55.0%
GGGTCATTGCAGTGCAGGAA+TGG - tig0020872:45178-45197 Msa1386840:three_prime_UTR 55.0%
CATTGCAGTGCAGGAATGGC+AGG - tig0020872:45182-45201 Msa1386840:three_prime_UTR 55.0%
TGACGACCATTTGCCCCAGA+TGG + tig0020872:45785-45804 None:intergenic 55.0%
Chromosome Type Strat End Strand Name
tig0020872 gene 45074 46186 45074 ID=Msa1386840;Name=Msa1386840
tig0020872 mRNA 45074 46186 45074 ID=Msa1386840-mRNA-1;Parent=Msa1386840;Name=Msa1386840-mRNA-1;_AED=0.03;_eAED=0.03;_QI=123|1|1|1|1|1|3|363|89
tig0020872 exon 45074 45562 45074 ID=Msa1386840-mRNA-1:exon:10391;Parent=Msa1386840-mRNA-1
tig0020872 exon 45669 45730 45669 ID=Msa1386840-mRNA-1:exon:10390;Parent=Msa1386840-mRNA-1
tig0020872 exon 45982 46186 45982 ID=Msa1386840-mRNA-1:exon:10389;Parent=Msa1386840-mRNA-1
tig0020872 five_prime_UTR 46064 46186 46064 ID=Msa1386840-mRNA-1:five_prime_utr;Parent=Msa1386840-mRNA-1
tig0020872 CDS 45982 46063 45982 ID=Msa1386840-mRNA-1:cds;Parent=Msa1386840-mRNA-1
tig0020872 CDS 45669 45730 45669 ID=Msa1386840-mRNA-1:cds;Parent=Msa1386840-mRNA-1
tig0020872 CDS 45437 45562 45437 ID=Msa1386840-mRNA-1:cds;Parent=Msa1386840-mRNA-1
tig0020872 three_prime_UTR 45074 45436 45074 ID=Msa1386840-mRNA-1:three_prime_utr;Parent=Msa1386840-mRNA-1
Gene Sequence

>Msa1386840

ATGGCAGGAACTTTCTTTCGTTTATTCGTGATTCTTCTTGGCCTTTCACATCTTCTATGCTTAACAGCAGTTCCAGTTACAAGAACTGAAAACCTTATGCAAGATGTCCAAGTTGACCTAATTACTCCGGAAAATACCCCTCAGGTTATTATTGAGAAAAACTTGCACTTGGAAGAGCCAAAGCCAAGAATTAATGAGAGGATGGATTTGGAACTCAATGATTATGCACCATCTGGGGCAAATGGTCGTCACACTCCAAGAGCACCGTAA
Protein sequence

>Msa1386840

MAGTFFRLFVILLGLSHLLCLTAVPVTRTENLMQDVQVDLITPENTPQVIIEKNLHLEEPKPRINERMDLELNDYAPSGANGRHTPRAP*