AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0076040


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0076040 MtrunA17_Chr4g0033761 94.030 67 4 0 1 67 1 67 1.99e-41 129
Msa0076040 MtrunA17_Chr2g0285451 91.045 67 6 0 1 67 1 67 1.59e-39 124
Msa0076040 MtrunA17_Chr8g0376751 89.552 67 7 0 1 67 1 67 3.63e-39 123
Msa0076040 MtrunA17_Chr7g0216191 85.075 67 10 0 1 67 1 67 1.30e-34 112
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0076040 AT2G43460.1 89.552 67 7 0 1 67 1 67 1.20e-39 125
Msa0076040 AT3G59540.1 89.552 67 7 0 1 67 1 67 1.20e-39 125

Find 21 sgRNAs with CRISPR-Local

Find 118 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CTCAACCTTGGGGAGAATTT+TGG 0.076151 1_2:+51879004 Msa0076040:five_prime_UTR
TAAGCAAATCAATGAGATTA+AGG 0.290766 1_2:+51879471 Msa0076040:CDS
TTGTTATAGGTGTAAGCTTA+AGG 0.368189 1_2:+51879776 Msa0076040:intron
ACCCTAAAATTCTCAACCTT+GGG 0.395414 1_2:+51878993 Msa0076040:five_prime_UTR
GAACTAAACTCATGATAAAT+CGG 0.406875 1_2:+51878889 Msa0076040:five_prime_UTR
CAAAGATGTTGTCAAGTTCA+AGG 0.413071 1_2:+51879549 Msa0076040:CDS
AACCCTAAAATTCTCAACCT+TGG 0.472712 1_2:+51878992 Msa0076040:five_prime_UTR
ACAAAGTGTGTACAAGTACT+TGG 0.506752 1_2:-51879581 None:intergenic
CATGATAAATCGGCCCAATA+CGG 0.519787 1_2:+51878899 Msa0076040:five_prime_UTR
TTAATCTCATTGATTTGCTT+AGG 0.531275 1_2:-51879469 None:intergenic
TTGAAGCAATCACTTCCTCC+AGG 0.546677 1_2:+51879631 Msa0076040:CDS
AGGACTTCCTCCTCACTGCT+AGG 0.557805 1_2:+51879491 Msa0076040:CDS
CCTCCCCAAAATTCTCCCCA+AGG 0.571486 1_2:-51879009 None:intergenic
CCTCCTCACTGCTAGGAGGA+AGG 0.586231 1_2:+51879498 Msa0076040:CDS
ATAAATCGGCCCAATACGGA+AGG 0.607022 1_2:+51878903 Msa0076040:five_prime_UTR
TACTGTCCTTCTCTCAACGC+GGG 0.615450 1_2:-51878932 None:intergenic
CCCTAAAATTCTCAACCTTG+GGG 0.637055 1_2:+51878994 Msa0076040:five_prime_UTR
CCTTCCTCCTAGCAGTGAGG+AGG 0.655712 1_2:-51879498 None:intergenic
CGTCCTTCCTCCTAGCAGTG+AGG 0.660436 1_2:-51879501 None:intergenic
ACTTCCTCCTCACTGCTAGG+AGG 0.666318 1_2:+51879494 Msa0076040:CDS
GTACTGTCCTTCTCTCAACG+CGG 0.709551 1_2:-51878933 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AAAACATTAAAAATCAAAAT+AGG - chr1_2:51879162-51879181 None:intergenic 10.0%
!!! AATTTTATTTACTCAATTTT+AGG + chr1_2:51879225-51879244 Msa0076040:intron 10.0%
!!! ATTTTATTTACTCAATTTTA+GGG + chr1_2:51879226-51879245 Msa0076040:intron 10.0%
!!! TTTTTTTATTTATTTGGATT+TGG + chr1_2:51879382-51879401 Msa0076040:intron 10.0%
!! AAAACATTAAAAATCAAAAT+AGG - chr1_2:51879162-51879181 None:intergenic 10.0%
!!! AATTTTATTTACTCAATTTT+AGG + chr1_2:51879225-51879244 Msa0076040:intron 10.0%
!!! ATTTTATTTACTCAATTTTA+GGG + chr1_2:51879226-51879245 Msa0076040:intron 10.0%
!!! TTTTTTTATTTATTTGGATT+TGG + chr1_2:51879382-51879401 Msa0076040:intron 10.0%
!! ACATTTCAATAAACATAAAA+AGG - chr1_2:51879447-51879466 None:intergenic 15.0%
!! ATAAGAAATTAAGAATTACA+AGG - chr1_2:51879693-51879712 None:intergenic 15.0%
!! ACATTTCAATAAACATAAAA+AGG - chr1_2:51879447-51879466 None:intergenic 15.0%
!! ATAAGAAATTAAGAATTACA+AGG - chr1_2:51879693-51879712 None:intergenic 15.0%
!!! TACAGTCTTTTCATAATATA+GGG + chr1_2:51878953-51878972 Msa0076040:five_prime_UTR 20.0%
!!! TTATTTTTCGTCATATGTTA+TGG + chr1_2:51879664-51879683 Msa0076040:intron 20.0%
!!! AAATTGTTGTTGTTTGTTAT+AGG + chr1_2:51879763-51879782 Msa0076040:intron 20.0%
!!! TACAGTCTTTTCATAATATA+GGG + chr1_2:51878953-51878972 Msa0076040:five_prime_UTR 20.0%
!!! TTATTTTTCGTCATATGTTA+TGG + chr1_2:51879664-51879683 Msa0076040:intron 20.0%
!!! AAATTGTTGTTGTTTGTTAT+AGG + chr1_2:51879763-51879782 Msa0076040:intron 20.0%
! GAACTAAACTCATGATAAAT+CGG + chr1_2:51878889-51878908 Msa0076040:five_prime_UTR 25.0%
!! GTACAGTCTTTTCATAATAT+AGG + chr1_2:51878952-51878971 Msa0076040:five_prime_UTR 25.0%
!!! TTCCATTCACAGTTTTTTTT+AGG + chr1_2:51879112-51879131 Msa0076040:intron 25.0%
! TTCCTAAAAAAAACTGTGAA+TGG - chr1_2:51879117-51879136 None:intergenic 25.0%
!!! CACAGTTTTTTTTAGGAAAT+TGG + chr1_2:51879119-51879138 Msa0076040:intron 25.0%
! ATTATACACTGATCTGAATT+AGG + chr1_2:51879286-51879305 Msa0076040:intron 25.0%
!!! TTAATCTCATTGATTTGCTT+AGG - chr1_2:51879472-51879491 None:intergenic 25.0%
! TAAGCAAATCAATGAGATTA+AGG + chr1_2:51879471-51879490 Msa0076040:CDS 25.0%
! AAAAATAATTCTCACTAACC+TGG - chr1_2:51879652-51879671 None:intergenic 25.0%
! GAACTAAACTCATGATAAAT+CGG + chr1_2:51878889-51878908 Msa0076040:five_prime_UTR 25.0%
!! GTACAGTCTTTTCATAATAT+AGG + chr1_2:51878952-51878971 Msa0076040:five_prime_UTR 25.0%
!!! TTCCATTCACAGTTTTTTTT+AGG + chr1_2:51879112-51879131 Msa0076040:intron 25.0%
! TTCCTAAAAAAAACTGTGAA+TGG - chr1_2:51879117-51879136 None:intergenic 25.0%
!!! CACAGTTTTTTTTAGGAAAT+TGG + chr1_2:51879119-51879138 Msa0076040:intron 25.0%
! ATTATACACTGATCTGAATT+AGG + chr1_2:51879286-51879305 Msa0076040:intron 25.0%
!!! TTAATCTCATTGATTTGCTT+AGG - chr1_2:51879472-51879491 None:intergenic 25.0%
! TAAGCAAATCAATGAGATTA+AGG + chr1_2:51879471-51879490 Msa0076040:CDS 25.0%
! AAAAATAATTCTCACTAACC+TGG - chr1_2:51879652-51879671 None:intergenic 25.0%
GAACCATGTAATTGAAACAT+TGG + chr1_2:51879255-51879274 Msa0076040:intron 30.0%
ACTCCAATGTTTCAATTACA+TGG - chr1_2:51879261-51879280 None:intergenic 30.0%
TGATCTGAATTAGGTGATTT+AGG + chr1_2:51879295-51879314 Msa0076040:intron 30.0%
GATCTGAATTAGGTGATTTA+GGG + chr1_2:51879296-51879315 Msa0076040:intron 30.0%
! TCAAACTTGGTAGTTGTTAA+AGG + chr1_2:51879329-51879348 Msa0076040:intron 30.0%
! CAAACTTGGTAGTTGTTAAA+GGG + chr1_2:51879330-51879349 Msa0076040:intron 30.0%
! TTTGCTTCTCTTGATTTTCA+CGG - chr1_2:51879533-51879552 None:intergenic 30.0%
TTGTTATAGGTGTAAGCTTA+AGG + chr1_2:51879776-51879795 Msa0076040:intron 30.0%
GAACCATGTAATTGAAACAT+TGG + chr1_2:51879255-51879274 Msa0076040:intron 30.0%
ACTCCAATGTTTCAATTACA+TGG - chr1_2:51879261-51879280 None:intergenic 30.0%
TGATCTGAATTAGGTGATTT+AGG + chr1_2:51879295-51879314 Msa0076040:intron 30.0%
GATCTGAATTAGGTGATTTA+GGG + chr1_2:51879296-51879315 Msa0076040:intron 30.0%
! TCAAACTTGGTAGTTGTTAA+AGG + chr1_2:51879329-51879348 Msa0076040:intron 30.0%
! CAAACTTGGTAGTTGTTAAA+GGG + chr1_2:51879330-51879349 Msa0076040:intron 30.0%
! TTTGCTTCTCTTGATTTTCA+CGG - chr1_2:51879533-51879552 None:intergenic 30.0%
TTGTTATAGGTGTAAGCTTA+AGG + chr1_2:51879776-51879795 Msa0076040:intron 30.0%
AACCCTAAAATTCTCAACCT+TGG + chr1_2:51878992-51879011 Msa0076040:five_prime_UTR 35.0%
ACCCTAAAATTCTCAACCTT+GGG + chr1_2:51878993-51879012 Msa0076040:five_prime_UTR 35.0%
GAAACACTGCAAAGAATCAA+TGG - chr1_2:51879082-51879101 None:intergenic 35.0%
TGGATTTCTGTGTTGTGATT+TGG + chr1_2:51879402-51879421 Msa0076040:intron 35.0%
CAAAGATGTTGTCAAGTTCA+AGG + chr1_2:51879549-51879568 Msa0076040:CDS 35.0%
ACAAAGTGTGTACAAGTACT+TGG - chr1_2:51879584-51879603 None:intergenic 35.0%
AATAATTCTCACTAACCTGG+AGG - chr1_2:51879649-51879668 None:intergenic 35.0%
AACCCTAAAATTCTCAACCT+TGG + chr1_2:51878992-51879011 Msa0076040:five_prime_UTR 35.0%
ACCCTAAAATTCTCAACCTT+GGG + chr1_2:51878993-51879012 Msa0076040:five_prime_UTR 35.0%
GAAACACTGCAAAGAATCAA+TGG - chr1_2:51879082-51879101 None:intergenic 35.0%
TGGATTTCTGTGTTGTGATT+TGG + chr1_2:51879402-51879421 Msa0076040:intron 35.0%
CAAAGATGTTGTCAAGTTCA+AGG + chr1_2:51879549-51879568 Msa0076040:CDS 35.0%
ACAAAGTGTGTACAAGTACT+TGG - chr1_2:51879584-51879603 None:intergenic 35.0%
AATAATTCTCACTAACCTGG+AGG - chr1_2:51879649-51879668 None:intergenic 35.0%
CATGATAAATCGGCCCAATA+CGG + chr1_2:51878899-51878918 Msa0076040:five_prime_UTR 40.0%
! CCCCAAGGTTGAGAATTTTA+GGG - chr1_2:51878997-51879016 None:intergenic 40.0%
CCCTAAAATTCTCAACCTTG+GGG + chr1_2:51878994-51879013 Msa0076040:five_prime_UTR 40.0%
! TCCCCAAGGTTGAGAATTTT+AGG - chr1_2:51878998-51879017 None:intergenic 40.0%
! TCAACCTTGGGGAGAATTTT+GGG + chr1_2:51879005-51879024 Msa0076040:five_prime_UTR 40.0%
TCGCAGCGAAGACAAAAAAA+TGG + chr1_2:51879041-51879060 Msa0076040:exon 40.0%
! GGGCTTTTGATCTTCAAACT+TGG + chr1_2:51879316-51879335 Msa0076040:intron 40.0%
! CTGTGTTGTGATTTGGAAGA+TGG + chr1_2:51879409-51879428 Msa0076040:intron 40.0%
CATGATAAATCGGCCCAATA+CGG + chr1_2:51878899-51878918 Msa0076040:five_prime_UTR 40.0%
! CCCCAAGGTTGAGAATTTTA+GGG - chr1_2:51878997-51879016 None:intergenic 40.0%
CCCTAAAATTCTCAACCTTG+GGG + chr1_2:51878994-51879013 Msa0076040:five_prime_UTR 40.0%
! TCCCCAAGGTTGAGAATTTT+AGG - chr1_2:51878998-51879017 None:intergenic 40.0%
! TCAACCTTGGGGAGAATTTT+GGG + chr1_2:51879005-51879024 Msa0076040:five_prime_UTR 40.0%
TCGCAGCGAAGACAAAAAAA+TGG + chr1_2:51879041-51879060 Msa0076040:exon 40.0%
! GGGCTTTTGATCTTCAAACT+TGG + chr1_2:51879316-51879335 Msa0076040:intron 40.0%
! CTGTGTTGTGATTTGGAAGA+TGG + chr1_2:51879409-51879428 Msa0076040:intron 40.0%
ATAAATCGGCCCAATACGGA+AGG + chr1_2:51878903-51878922 Msa0076040:five_prime_UTR 45.0%
!! GGGCTTTTTCCTTCCGTATT+GGG - chr1_2:51878915-51878934 None:intergenic 45.0%
! CTCAACCTTGGGGAGAATTT+TGG + chr1_2:51879004-51879023 Msa0076040:five_prime_UTR 45.0%
! CAACCTTGGGGAGAATTTTG+GGG + chr1_2:51879006-51879025 Msa0076040:five_prime_UTR 45.0%
TTGAAGCAATCACTTCCTCC+AGG + chr1_2:51879631-51879650 Msa0076040:CDS 45.0%
ATAAATCGGCCCAATACGGA+AGG + chr1_2:51878903-51878922 Msa0076040:five_prime_UTR 45.0%
!! GGGCTTTTTCCTTCCGTATT+GGG - chr1_2:51878915-51878934 None:intergenic 45.0%
! CTCAACCTTGGGGAGAATTT+TGG + chr1_2:51879004-51879023 Msa0076040:five_prime_UTR 45.0%
! CAACCTTGGGGAGAATTTTG+GGG + chr1_2:51879006-51879025 Msa0076040:five_prime_UTR 45.0%
TTGAAGCAATCACTTCCTCC+AGG + chr1_2:51879631-51879650 Msa0076040:CDS 45.0%
!!! ATTCTATTTTTTTATTTATT+TGG + chr1_2:51879376-51879395 Msa0076040:intron 5.0%
!!! ATTCTATTTTTTTATTTATT+TGG + chr1_2:51879376-51879395 Msa0076040:intron 5.0%
!! CGGGCTTTTTCCTTCCGTAT+TGG - chr1_2:51878916-51878935 None:intergenic 50.0%
AAAAAGCCCGCGTTGAGAGA+AGG + chr1_2:51878926-51878945 Msa0076040:five_prime_UTR 50.0%
TACTGTCCTTCTCTCAACGC+GGG - chr1_2:51878935-51878954 None:intergenic 50.0%
GTACTGTCCTTCTCTCAACG+CGG - chr1_2:51878936-51878955 None:intergenic 50.0%
!! GGAGAATTTTGGGGAGGAAG+AGG + chr1_2:51879015-51879034 Msa0076040:five_prime_UTR 50.0%
!! CGGGCTTTTTCCTTCCGTAT+TGG - chr1_2:51878916-51878935 None:intergenic 50.0%
AAAAAGCCCGCGTTGAGAGA+AGG + chr1_2:51878926-51878945 Msa0076040:five_prime_UTR 50.0%
TACTGTCCTTCTCTCAACGC+GGG - chr1_2:51878935-51878954 None:intergenic 50.0%
GTACTGTCCTTCTCTCAACG+CGG - chr1_2:51878936-51878955 None:intergenic 50.0%
!! GGAGAATTTTGGGGAGGAAG+AGG + chr1_2:51879015-51879034 Msa0076040:five_prime_UTR 50.0%
CCTCCCCAAAATTCTCCCCA+AGG - chr1_2:51879012-51879031 None:intergenic 55.0%
!! CCTTGGGGAGAATTTTGGGG+AGG + chr1_2:51879009-51879028 Msa0076040:five_prime_UTR 55.0%
AGGACTTCCTCCTCACTGCT+AGG + chr1_2:51879491-51879510 Msa0076040:CDS 55.0%
ACTTCCTCCTCACTGCTAGG+AGG + chr1_2:51879494-51879513 Msa0076040:CDS 55.0%
CCTCCCCAAAATTCTCCCCA+AGG - chr1_2:51879012-51879031 None:intergenic 55.0%
!! CCTTGGGGAGAATTTTGGGG+AGG + chr1_2:51879009-51879028 Msa0076040:five_prime_UTR 55.0%
AGGACTTCCTCCTCACTGCT+AGG + chr1_2:51879491-51879510 Msa0076040:CDS 55.0%
ACTTCCTCCTCACTGCTAGG+AGG + chr1_2:51879494-51879513 Msa0076040:CDS 55.0%
CCTTCCTCCTAGCAGTGAGG+AGG - chr1_2:51879501-51879520 None:intergenic 60.0%
CCTCCTCACTGCTAGGAGGA+AGG + chr1_2:51879498-51879517 Msa0076040:CDS 60.0%
CGTCCTTCCTCCTAGCAGTG+AGG - chr1_2:51879504-51879523 None:intergenic 60.0%
CCTTCCTCCTAGCAGTGAGG+AGG - chr1_2:51879501-51879520 None:intergenic 60.0%
CCTCCTCACTGCTAGGAGGA+AGG + chr1_2:51879498-51879517 Msa0076040:CDS 60.0%
CGTCCTTCCTCCTAGCAGTG+AGG - chr1_2:51879504-51879523 None:intergenic 60.0%
Chromosome Type Strat End Strand Name
chr1_2 gene 51878886 51879804 51878886 ID=Msa0076040;Name=Msa0076040
chr1_2 mRNA 51878886 51879804 51878886 ID=Msa0076040-mRNA-1;Parent=Msa0076040;Name=Msa0076040-mRNA-1;_AED=0.27;_eAED=0.27;_QI=174|0.5|0.66|0.66|1|1|3|0|68
chr1_2 exon 51878886 51879062 51878886 ID=Msa0076040-mRNA-1:exon:15946;Parent=Msa0076040-mRNA-1
chr1_2 exon 51879469 51879652 51879469 ID=Msa0076040-mRNA-1:exon:15947;Parent=Msa0076040-mRNA-1
chr1_2 exon 51879785 51879804 51879785 ID=Msa0076040-mRNA-1:exon:15948;Parent=Msa0076040-mRNA-1
chr1_2 five_prime_UTR 51878886 51879059 51878886 ID=Msa0076040-mRNA-1:five_prime_utr;Parent=Msa0076040-mRNA-1
chr1_2 CDS 51879060 51879062 51879060 ID=Msa0076040-mRNA-1:cds;Parent=Msa0076040-mRNA-1
chr1_2 CDS 51879469 51879652 51879469 ID=Msa0076040-mRNA-1:cds;Parent=Msa0076040-mRNA-1
chr1_2 CDS 51879785 51879804 51879785 ID=Msa0076040-mRNA-1:cds;Parent=Msa0076040-mRNA-1
Gene Sequence

>Msa0076040

ATGCCTAAGCAAATCAATGAGATTAAGGACTTCCTCCTCACTGCTAGGAGGAAGGACGCACGCTCCGTGAAAATCAAGAGAAGCAAAGATGTTGTCAAGTTCAAGGTTAGATGCTCCAAGTACTTGTACACACTTTGTGTGTTTGATACTGAGAAAGCTGATAAGTTGAAGCAATCACTTCCTCCAGGTGTAAGCTTAAGGATGTAA

Protein sequence

>Msa0076040

MPKQINEIKDFLLTARRKDARSVKIKRSKDVVKFKVRCSKYLYTLCVFDTEKADKLKQSLPPGVSLRM*