AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1065380

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1065380 MtrunA17_Chr7g0245951 97.895 95 2 0 1 95 1 95 1.29e-63 187
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1065380 AT3G60890.2 47.692 65 33 1 23 86 34 98 6.34e-13 59.7

Find 43 sgRNAs with CRISPR-Local

Find 119 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
ATTTGATATAAGAAACTAAA+AGG 0.249578 7_2:-59023035 None:intergenic
CAAGCTATTAATTAAATTCA+TGG 0.344700 7_2:+59023946 Msa1065380:three_prime_UTR
GTGAAATATTGTTGGTGTAT+TGG 0.350232 7_2:+59023817 Msa1065380:three_prime_UTR
TGACATCCTAAGGGTATGTT+TGG 0.359081 7_2:+59023850 Msa1065380:three_prime_UTR
TGAGGTGAGGTGTAACAATT+AGG 0.362948 7_2:-59023088 None:intergenic
CAATATTATGTTCTATGTAA+TGG 0.366989 7_2:-59023795 None:intergenic
GTGATATAATAAAGATGAAT+AGG 0.370948 7_2:+59023755 Msa1065380:three_prime_UTR
GGTGTAACAATTAGGAAATA+AGG 0.376836 7_2:-59023080 None:intergenic
TTCAAATGTTTGACATCCTA+AGG 0.376934 7_2:+59023840 Msa1065380:three_prime_UTR
GAGAAACCTTATCTCTCAAA+AGG 0.386939 7_2:+59023164 Msa1065380:five_prime_UTR
TTTGTTGTGAAAGTTTCATT+TGG 0.391141 7_2:-59023552 None:intergenic
CATGAATTTAATTAATAGCT+TGG 0.405233 7_2:-59023945 None:intergenic
TTCTATGTAATGGTTACAAT+TGG 0.414110 7_2:-59023785 None:intergenic
CTTCTCATTCTGCTCTATGA+TGG 0.425083 7_2:-59023473 None:intergenic
ATAATATTGTGAAATATTGT+TGG 0.425924 7_2:+59023809 Msa1065380:three_prime_UTR
GTGTAACAATTAGGAAATAA+GGG 0.425973 7_2:-59023079 None:intergenic
CCTTCTCCAAACATACCCTT+AGG 0.436649 7_2:-59023856 None:intergenic
AAATAATAGCTAGTTATTGT+TGG 0.453707 7_2:-59023584 None:intergenic
GTGCCTACAGTTGTGTCTCT+TGG 0.458566 7_2:-59023241 None:intergenic
TCATTTGGAGCTGAGACATA+AGG 0.458680 7_2:-59023537 None:intergenic
TTAGGTTGAGCCACCTCAAA+AGG 0.471420 7_2:+59023265 Msa1065380:CDS
GACACAACTGTAGGCACCTT+AGG 0.478643 7_2:+59023247 Msa1065380:CDS
ATTCTCTTTGTGAAGAAGCA+TGG 0.505800 7_2:-59023509 None:intergenic
TTTGATATAAGAAACTAAAA+GGG 0.512408 7_2:-59023034 None:intergenic
GACTCATGATTACAAAGGGC+AGG 0.516917 7_2:-59022917 None:intergenic
AAGCTATTAATTAAATTCAT+GGG 0.521024 7_2:+59023947 Msa1065380:three_prime_UTR
CCTAAGGGTATGTTTGGAGA+AGG 0.529938 7_2:+59023856 Msa1065380:three_prime_UTR
ATTGGTGATGCAGAAGGAAA+AGG 0.539434 7_2:+59023389 Msa1065380:intron
GTTTGATAGTTAGTGAGGTG+AGG 0.540735 7_2:-59023101 None:intergenic
TGATAGTTTGATAGTTAGTG+AGG 0.542097 7_2:-59023106 None:intergenic
TGTAACAATTAGGAAATAAG+GGG 0.546354 7_2:-59023078 None:intergenic
AGAAACCTTATCTCTCAAAA+GGG 0.550420 7_2:+59023165 Msa1065380:five_prime_UTR
TAAGGACTCATGATTACAAA+GGG 0.567020 7_2:-59022921 None:intergenic
CAGTTGTGTCTCTTGGAAAG+AGG 0.570084 7_2:-59023234 None:intergenic
TTTATGGTAATGATGGCGTA+AGG 0.575171 7_2:-59022939 None:intergenic
CTAAGGGTATGTTTGGAGAA+GGG 0.575665 7_2:+59023857 Msa1065380:three_prime_UTR
CAGAAGGAAAAGGATGATTG+AGG 0.594182 7_2:+59023399 Msa1065380:intron
TCAAATGTTTGACATCCTAA+GGG 0.607895 7_2:+59023841 Msa1065380:three_prime_UTR
ACAAAGGGCAGGAATAGAAG+AGG 0.621775 7_2:-59022906 None:intergenic
GTAAGGACTCATGATTACAA+AGG 0.633201 7_2:-59022922 None:intergenic
GTAACAATTAGGAAATAAGG+GGG 0.644045 7_2:-59023077 None:intergenic
TTTCCAAGAGACACAACTGT+AGG 0.666230 7_2:+59023238 Msa1065380:CDS
TAACAATTAGGAAATAAGGG+GGG 0.750535 7_2:-59023076 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! TTTGATATAAGAAACTAAAA+GGG - chr7_2:59023037-59023056 None:intergenic 15.0%
!! ATTTGATATAAGAAACTAAA+AGG - chr7_2:59023038-59023057 None:intergenic 15.0%
!!! GAAAAATTTGAAATTGTATA+TGG + chr7_2:59023441-59023460 Msa1065380:CDS 15.0%
!! TTAAAAAACTAAAACAAACA+AGG - chr7_2:59023705-59023724 None:intergenic 15.0%
!! ATAATATTGTGAAATATTGT+TGG + chr7_2:59023809-59023828 Msa1065380:three_prime_UTR 15.0%
!! AAGCTATTAATTAAATTCAT+GGG + chr7_2:59023947-59023966 Msa1065380:three_prime_UTR 15.0%
!! TTTGATATAAGAAACTAAAA+GGG - chr7_2:59023037-59023056 None:intergenic 15.0%
!! ATTTGATATAAGAAACTAAA+AGG - chr7_2:59023038-59023057 None:intergenic 15.0%
!!! GAAAAATTTGAAATTGTATA+TGG + chr7_2:59023441-59023460 Msa1065380:CDS 15.0%
!! TTAAAAAACTAAAACAAACA+AGG - chr7_2:59023705-59023724 None:intergenic 15.0%
!! ATAATATTGTGAAATATTGT+TGG + chr7_2:59023809-59023828 Msa1065380:three_prime_UTR 15.0%
!! AAGCTATTAATTAAATTCAT+GGG + chr7_2:59023947-59023966 Msa1065380:three_prime_UTR 15.0%
!!! GATTAATTAACTTGTATGAT+TGG + chr7_2:59023371-59023390 Msa1065380:intron 20.0%
!! AAATAATAGCTAGTTATTGT+TGG - chr7_2:59023587-59023606 None:intergenic 20.0%
!! GTGATATAATAAAGATGAAT+AGG + chr7_2:59023755-59023774 Msa1065380:three_prime_UTR 20.0%
!! CAATATTATGTTCTATGTAA+TGG - chr7_2:59023798-59023817 None:intergenic 20.0%
!! CATGAATTTAATTAATAGCT+TGG - chr7_2:59023948-59023967 None:intergenic 20.0%
!! CAAGCTATTAATTAAATTCA+TGG + chr7_2:59023946-59023965 Msa1065380:three_prime_UTR 20.0%
!!! GATTAATTAACTTGTATGAT+TGG + chr7_2:59023371-59023390 Msa1065380:intron 20.0%
!! AAATAATAGCTAGTTATTGT+TGG - chr7_2:59023587-59023606 None:intergenic 20.0%
!! GTGATATAATAAAGATGAAT+AGG + chr7_2:59023755-59023774 Msa1065380:three_prime_UTR 20.0%
!! CAATATTATGTTCTATGTAA+TGG - chr7_2:59023798-59023817 None:intergenic 20.0%
!! CATGAATTTAATTAATAGCT+TGG - chr7_2:59023948-59023967 None:intergenic 20.0%
!! CAAGCTATTAATTAAATTCA+TGG + chr7_2:59023946-59023965 Msa1065380:three_prime_UTR 20.0%
! TGTAACAATTAGGAAATAAG+GGG - chr7_2:59023081-59023100 None:intergenic 25.0%
! GTGTAACAATTAGGAAATAA+GGG - chr7_2:59023082-59023101 None:intergenic 25.0%
!! TATTAGAAGAATACCTTTTG+AGG - chr7_2:59023281-59023300 None:intergenic 25.0%
!! TTTGTTGTGAAAGTTTCATT+TGG - chr7_2:59023555-59023574 None:intergenic 25.0%
! TTCTATGTAATGGTTACAAT+TGG - chr7_2:59023788-59023807 None:intergenic 25.0%
! GAATAGAGAAAAAAATGTCT+TGG + chr7_2:59023886-59023905 Msa1065380:three_prime_UTR 25.0%
! TGTAACAATTAGGAAATAAG+GGG - chr7_2:59023081-59023100 None:intergenic 25.0%
! GTGTAACAATTAGGAAATAA+GGG - chr7_2:59023082-59023101 None:intergenic 25.0%
!! TATTAGAAGAATACCTTTTG+AGG - chr7_2:59023281-59023300 None:intergenic 25.0%
!! TTTGTTGTGAAAGTTTCATT+TGG - chr7_2:59023555-59023574 None:intergenic 25.0%
! TTCTATGTAATGGTTACAAT+TGG - chr7_2:59023788-59023807 None:intergenic 25.0%
! GAATAGAGAAAAAAATGTCT+TGG + chr7_2:59023886-59023905 Msa1065380:three_prime_UTR 25.0%
TAAGGACTCATGATTACAAA+GGG - chr7_2:59022924-59022943 None:intergenic 30.0%
!! AGAGACTTTTATGGTAATGA+TGG - chr7_2:59022949-59022968 None:intergenic 30.0%
! AGATAAGAGAGAGACTTTTA+TGG - chr7_2:59022958-59022977 None:intergenic 30.0%
TAACAATTAGGAAATAAGGG+GGG - chr7_2:59023079-59023098 None:intergenic 30.0%
GTAACAATTAGGAAATAAGG+GGG - chr7_2:59023080-59023099 None:intergenic 30.0%
GGTGTAACAATTAGGAAATA+AGG - chr7_2:59023083-59023102 None:intergenic 30.0%
! TGATAGTTTGATAGTTAGTG+AGG - chr7_2:59023109-59023128 None:intergenic 30.0%
TCTTGCAACGAAAAAAATAG+GGG - chr7_2:59023146-59023165 None:intergenic 30.0%
CTCTTGCAACGAAAAAAATA+GGG - chr7_2:59023147-59023166 None:intergenic 30.0%
TCTCTTGCAACGAAAAAAAT+AGG - chr7_2:59023148-59023167 None:intergenic 30.0%
AGAAACCTTATCTCTCAAAA+GGG + chr7_2:59023165-59023184 Msa1065380:five_prime_UTR 30.0%
GTGAAATATTGTTGGTGTAT+TGG + chr7_2:59023817-59023836 Msa1065380:three_prime_UTR 30.0%
TTCAAATGTTTGACATCCTA+AGG + chr7_2:59023840-59023859 Msa1065380:three_prime_UTR 30.0%
TCAAATGTTTGACATCCTAA+GGG + chr7_2:59023841-59023860 Msa1065380:three_prime_UTR 30.0%
TAAGGACTCATGATTACAAA+GGG - chr7_2:59022924-59022943 None:intergenic 30.0%
!! AGAGACTTTTATGGTAATGA+TGG - chr7_2:59022949-59022968 None:intergenic 30.0%
! AGATAAGAGAGAGACTTTTA+TGG - chr7_2:59022958-59022977 None:intergenic 30.0%
TAACAATTAGGAAATAAGGG+GGG - chr7_2:59023079-59023098 None:intergenic 30.0%
GTAACAATTAGGAAATAAGG+GGG - chr7_2:59023080-59023099 None:intergenic 30.0%
GGTGTAACAATTAGGAAATA+AGG - chr7_2:59023083-59023102 None:intergenic 30.0%
! TGATAGTTTGATAGTTAGTG+AGG - chr7_2:59023109-59023128 None:intergenic 30.0%
TCTTGCAACGAAAAAAATAG+GGG - chr7_2:59023146-59023165 None:intergenic 30.0%
CTCTTGCAACGAAAAAAATA+GGG - chr7_2:59023147-59023166 None:intergenic 30.0%
TCTCTTGCAACGAAAAAAAT+AGG - chr7_2:59023148-59023167 None:intergenic 30.0%
AGAAACCTTATCTCTCAAAA+GGG + chr7_2:59023165-59023184 Msa1065380:five_prime_UTR 30.0%
GTGAAATATTGTTGGTGTAT+TGG + chr7_2:59023817-59023836 Msa1065380:three_prime_UTR 30.0%
TTCAAATGTTTGACATCCTA+AGG + chr7_2:59023840-59023859 Msa1065380:three_prime_UTR 30.0%
TCAAATGTTTGACATCCTAA+GGG + chr7_2:59023841-59023860 Msa1065380:three_prime_UTR 30.0%
GTAAGGACTCATGATTACAA+AGG - chr7_2:59022925-59022944 None:intergenic 35.0%
! TTTATGGTAATGATGGCGTA+AGG - chr7_2:59022942-59022961 None:intergenic 35.0%
! GAAATAAGGGGGGTATATAT+AGG - chr7_2:59023069-59023088 None:intergenic 35.0%
GAGAAACCTTATCTCTCAAA+AGG + chr7_2:59023164-59023183 Msa1065380:five_prime_UTR 35.0%
!! TGTTTCCCTTTTGAGAGATA+AGG - chr7_2:59023173-59023192 None:intergenic 35.0%
!! TAGAAGAATACCTTTTGAGG+TGG - chr7_2:59023278-59023297 None:intergenic 35.0%
ATTCTCTTTGTGAAGAAGCA+TGG - chr7_2:59023512-59023531 None:intergenic 35.0%
!! TGTCTTGGTTTTCTTCTCTT+AGG + chr7_2:59023901-59023920 Msa1065380:three_prime_UTR 35.0%
GTAAGGACTCATGATTACAA+AGG - chr7_2:59022925-59022944 None:intergenic 35.0%
! TTTATGGTAATGATGGCGTA+AGG - chr7_2:59022942-59022961 None:intergenic 35.0%
! GAAATAAGGGGGGTATATAT+AGG - chr7_2:59023069-59023088 None:intergenic 35.0%
GAGAAACCTTATCTCTCAAA+AGG + chr7_2:59023164-59023183 Msa1065380:five_prime_UTR 35.0%
!! TGTTTCCCTTTTGAGAGATA+AGG - chr7_2:59023173-59023192 None:intergenic 35.0%
!! TAGAAGAATACCTTTTGAGG+TGG - chr7_2:59023278-59023297 None:intergenic 35.0%
ATTCTCTTTGTGAAGAAGCA+TGG - chr7_2:59023512-59023531 None:intergenic 35.0%
!! TGTCTTGGTTTTCTTCTCTT+AGG + chr7_2:59023901-59023920 Msa1065380:three_prime_UTR 35.0%
TGAGGTGAGGTGTAACAATT+AGG - chr7_2:59023091-59023110 None:intergenic 40.0%
! GTTTGATAGTTAGTGAGGTG+AGG - chr7_2:59023104-59023123 None:intergenic 40.0%
TTTCCAAGAGACACAACTGT+AGG + chr7_2:59023238-59023257 Msa1065380:CDS 40.0%
!! TGTATGATTGGTGATGCAGA+AGG + chr7_2:59023383-59023402 Msa1065380:intron 40.0%
!! ATTGGTGATGCAGAAGGAAA+AGG + chr7_2:59023389-59023408 Msa1065380:intron 40.0%
CAGAAGGAAAAGGATGATTG+AGG + chr7_2:59023399-59023418 Msa1065380:intron 40.0%
CTTCTCATTCTGCTCTATGA+TGG - chr7_2:59023476-59023495 None:intergenic 40.0%
! TCATTTGGAGCTGAGACATA+AGG - chr7_2:59023540-59023559 None:intergenic 40.0%
! TGACATCCTAAGGGTATGTT+TGG + chr7_2:59023850-59023869 Msa1065380:three_prime_UTR 40.0%
! CTAAGGGTATGTTTGGAGAA+GGG + chr7_2:59023857-59023876 Msa1065380:three_prime_UTR 40.0%
TGAGGTGAGGTGTAACAATT+AGG - chr7_2:59023091-59023110 None:intergenic 40.0%
! GTTTGATAGTTAGTGAGGTG+AGG - chr7_2:59023104-59023123 None:intergenic 40.0%
TTTCCAAGAGACACAACTGT+AGG + chr7_2:59023238-59023257 Msa1065380:CDS 40.0%
!! TGTATGATTGGTGATGCAGA+AGG + chr7_2:59023383-59023402 Msa1065380:intron 40.0%
!! ATTGGTGATGCAGAAGGAAA+AGG + chr7_2:59023389-59023408 Msa1065380:intron 40.0%
CAGAAGGAAAAGGATGATTG+AGG + chr7_2:59023399-59023418 Msa1065380:intron 40.0%
CTTCTCATTCTGCTCTATGA+TGG - chr7_2:59023476-59023495 None:intergenic 40.0%
! TCATTTGGAGCTGAGACATA+AGG - chr7_2:59023540-59023559 None:intergenic 40.0%
! TGACATCCTAAGGGTATGTT+TGG + chr7_2:59023850-59023869 Msa1065380:three_prime_UTR 40.0%
! CTAAGGGTATGTTTGGAGAA+GGG + chr7_2:59023857-59023876 Msa1065380:three_prime_UTR 40.0%
GACTCATGATTACAAAGGGC+AGG - chr7_2:59022920-59022939 None:intergenic 45.0%
! AAGGGGGGTATATATAGGTG+AGG - chr7_2:59023064-59023083 None:intergenic 45.0%
CAGTTGTGTCTCTTGGAAAG+AGG - chr7_2:59023237-59023256 None:intergenic 45.0%
!!! TTTTGAGGTGGCTCAACCTA+AGG - chr7_2:59023266-59023285 None:intergenic 45.0%
!! TTAGGTTGAGCCACCTCAAA+AGG + chr7_2:59023265-59023284 Msa1065380:CDS 45.0%
CCTTCTCCAAACATACCCTT+AGG - chr7_2:59023859-59023878 None:intergenic 45.0%
! CCTAAGGGTATGTTTGGAGA+AGG + chr7_2:59023856-59023875 Msa1065380:three_prime_UTR 45.0%
ACAAAGGGCAGGAATAGAAG+TGG - chr7_2:59022909-59022928 None:intergenic 45.0%
GACTCATGATTACAAAGGGC+AGG - chr7_2:59022920-59022939 None:intergenic 45.0%
! AAGGGGGGTATATATAGGTG+AGG - chr7_2:59023064-59023083 None:intergenic 45.0%
CAGTTGTGTCTCTTGGAAAG+AGG - chr7_2:59023237-59023256 None:intergenic 45.0%
!!! TTTTGAGGTGGCTCAACCTA+AGG - chr7_2:59023266-59023285 None:intergenic 45.0%
!! TTAGGTTGAGCCACCTCAAA+AGG + chr7_2:59023265-59023284 Msa1065380:CDS 45.0%
CCTTCTCCAAACATACCCTT+AGG - chr7_2:59023859-59023878 None:intergenic 45.0%
! CCTAAGGGTATGTTTGGAGA+AGG + chr7_2:59023856-59023875 Msa1065380:three_prime_UTR 45.0%
GTGCCTACAGTTGTGTCTCT+TGG - chr7_2:59023244-59023263 None:intergenic 50.0%
GACACAACTGTAGGCACCTT+AGG + chr7_2:59023247-59023266 Msa1065380:CDS 50.0%
GTGCCTACAGTTGTGTCTCT+TGG - chr7_2:59023244-59023263 None:intergenic 50.0%
GACACAACTGTAGGCACCTT+AGG + chr7_2:59023247-59023266 Msa1065380:CDS 50.0%
Chromosome Type Strat End Strand Name
chr7_2 gene 59022909 59023996 59022909 ID=Msa1065380;Name=Msa1065380
chr7_2 mRNA 59022909 59023996 59022909 ID=Msa1065380-mRNA-1;Parent=Msa1065380;Name=Msa1065380-mRNA-1;_AED=0.00;_eAED=0.00;_QI=286|1|1|1|1|1|2|399|95
chr7_2 exon 59022909 59023286 59022909 ID=Msa1065380-mRNA-1:exon:11223;Parent=Msa1065380-mRNA-1
chr7_2 exon 59023402 59023996 59023402 ID=Msa1065380-mRNA-1:exon:11224;Parent=Msa1065380-mRNA-1
chr7_2 five_prime_UTR 59022909 59023194 59022909 ID=Msa1065380-mRNA-1:five_prime_utr;Parent=Msa1065380-mRNA-1
chr7_2 CDS 59023195 59023286 59023195 ID=Msa1065380-mRNA-1:cds;Parent=Msa1065380-mRNA-1
chr7_2 CDS 59023402 59023597 59023402 ID=Msa1065380-mRNA-1:cds;Parent=Msa1065380-mRNA-1
chr7_2 three_prime_UTR 59023598 59023996 59023598 ID=Msa1065380-mRNA-1:three_prime_utr;Parent=Msa1065380-mRNA-1
Gene Sequence

>Msa1065380

ATGTGTTGTTTCTCTTCACAACATGACACTCTTTATGCTCCTCTTTCCAAGAGACACAACTGTAGGCACCTTAGGTTGAGCCACCTCAAAAGAAGGAAAAGGATGATTGAGGTGAAAGCACAGATTAAGATGAAAAATTTGAAATTGTATATGGAGAATCAAACCATCATAGAGCAGAATGAGAAGTTGAGAAAACAAGCCATGCTTCTTCACAAAGAGAATCAAGACCTTATGTCTCAGCTCCAAATGAAACTTTCACAACAAAATATCAATACCAACAATAACTAG
Protein sequence

>Msa1065380

MCCFSSQHDTLYAPLSKRHNCRHLRLSHLKRRKRMIEVKAQIKMKNLKLYMENQTIIEQNEKLRKQAMLLHKENQDLMSQLQMKLSQQNINTNNN*