AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0512130


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0512130 MtrunA17_Chr3g0119011 92.969 128 8 1 1 127 1 128 1.02e-82 238
Msa0512130 MtrunA17_Chr3g0118991 73.770 61 13 2 68 127 1 59 8.43e-23 84.3
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0512130 AT5G20935.1 79.012 81 17 0 45 125 37 117 4.46e-41 132
Msa0512130 AT5G20935.2 77.083 48 11 0 45 92 37 84 1.89e-19 77.4

Find 42 sgRNAs with CRISPR-Local

Find 120 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
ACTAATGACACTGAAATATT+TGG 0.193807 3_4:+61763908 None:intergenic
CCTTGCCTCAGAGTTAATTC+TGG 0.251411 3_4:-61763761 Msa0512130:CDS
GATTTGTGGTTTCAATGTTT+TGG 0.261828 3_4:+61764038 None:intergenic
TGGAGCTTCAATGATAATAA+TGG 0.263065 3_4:+61763811 None:intergenic
CGTACTGCCCACACATCTTT+TGG 0.272835 3_4:+61763304 None:intergenic
ACTATACTCAACCAGATCTA+AGG 0.289522 3_4:+61763237 None:intergenic
AAACGTTCAAAGTTGGATAA+AGG 0.314200 3_4:-61763839 Msa0512130:CDS
ATTGGAACTTATCTTATTGA+TGG 0.358224 3_4:-61763274 Msa0512130:CDS
CCCAACCAGCAGGTGGCTCT+TGG 0.375234 3_4:-61763158 Msa0512130:three_prime_UTR
GTTGCAATGTTTCTGATTTG+TGG 0.375721 3_4:+61764024 None:intergenic
GGAGCTTCAATGATAATAAT+GGG 0.378832 3_4:+61763812 None:intergenic
CCAAGAGCCACCTGCTGGTT+GGG 0.395859 3_4:+61763158 None:intergenic
TATGTGTGAGGAAGGATATT+AGG 0.413182 3_4:+61764114 None:intergenic
AACGTTCAAAGTTGGATAAA+GGG 0.431347 3_4:-61763838 Msa0512130:CDS
ATATTTCAAGCCCTTAGATC+TGG 0.435238 3_4:-61763248 Msa0512130:CDS
ACACATACACTGCAAATGAT+TGG 0.445934 3_4:-61764098 Msa0512130:five_prime_UTR
ATATTTCAGTGTCATTAGTA+AGG 0.457947 3_4:-61763904 Msa0512130:CDS
CTGTTGTTGAACTTTAGAAA+TGG 0.461418 3_4:+61763953 None:intergenic
GCCAAGAGCCACCTGCTGGT+TGG 0.499573 3_4:+61763157 None:intergenic
ATGTCTTTGTCCCTTTCTTG+TGG 0.510900 3_4:-61763986 Msa0512130:CDS
CTTTGTGATACCACAAGAAA+GGG 0.530774 3_4:+61763976 None:intergenic
GCTTTGTGATACCACAAGAA+AGG 0.545899 3_4:+61763975 None:intergenic
CAAAAGATGTGTGGGCAGTA+CGG 0.550493 3_4:-61763303 Msa0512130:CDS
AATTCTGGCTTAGTCAAACC+TGG 0.553371 3_4:-61763746 Msa0512130:CDS
AGTCAAGCAAAATATTACAT+TGG 0.554810 3_4:-61763100 Msa0512130:three_prime_UTR
CAGAATTAACTCTGAGGCAA+GGG 0.557005 3_4:+61763762 None:intergenic
CTATACTCAACCAGATCTAA+GGG 0.566149 3_4:+61763238 None:intergenic
TGGGCAGTACGGCTCAACAT+TGG 0.579445 3_4:-61763292 Msa0512130:CDS
TCAAACCTGGTGATGTTGGA+AGG 0.583959 3_4:-61763733 Msa0512130:intron
AAGAAAGCCAAAAGATGTGT+GGG 0.587735 3_4:-61763311 Msa0512130:CDS
CCAGAATTAACTCTGAGGCA+AGG 0.590927 3_4:+61763761 None:intergenic
CAAGAAAGCCAAAAGATGTG+TGG 0.602135 3_4:-61763312 Msa0512130:CDS
TTAGTCAAACCTGGTGATGT+TGG 0.604419 3_4:-61763737 Msa0512130:CDS
AAATACCTTCCAACATCACC+AGG 0.606725 3_4:+61763728 None:intergenic
TTTGTTTCCCAACCAGCAGG+TGG 0.609564 3_4:-61763165 Msa0512130:three_prime_UTR
GTATGCCAAGAGCCACCTGC+TGG 0.623688 3_4:+61763153 None:intergenic
TTGCAGTGTATGTGTGAGGA+AGG 0.631311 3_4:+61764106 None:intergenic
TGAATCAAAAGAGTCATCAG+AGG 0.675313 3_4:-61763879 Msa0512130:CDS
CTAAGCCAGAATTAACTCTG+AGG 0.700737 3_4:+61763756 None:intergenic
ACAGCTTGAAGTATCAACAA+CGG 0.721755 3_4:-61763934 Msa0512130:CDS
TCATTTGCAGTGTATGTGTG+AGG 0.727329 3_4:+61764102 None:intergenic
GCTTGAAGTATCAACAACGG+AGG 0.739120 3_4:-61763931 Msa0512130:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AATGTATAAATGATTTAATT+TGG - chr3_4:61763692-61763711 Msa0512130:intron 10.0%
!! AATTAATATCATGTATAAAA+TGG - chr3_4:61763845-61763864 Msa0512130:CDS 10.0%
!! AATGTATAAATGATTTAATT+TGG - chr3_4:61763692-61763711 Msa0512130:intron 10.0%
!! AATTAATATCATGTATAAAA+TGG - chr3_4:61763845-61763864 Msa0512130:CDS 10.0%
!! GTAAATAATTATATATCACT+TGG - chr3_4:61763875-61763894 Msa0512130:CDS 15.0%
!! GTAAATAATTATATATCACT+TGG - chr3_4:61763875-61763894 Msa0512130:CDS 15.0%
!! GATTAGATACATAGTAAAAA+AGG + chr3_4:61763723-61763742 None:intergenic 20.0%
!! GATTAGATACATAGTAAAAA+AGG + chr3_4:61763723-61763742 None:intergenic 20.0%
!!! TTCAATGTTTTGGAATTTGT+TGG + chr3_4:61763178-61763197 None:intergenic 25.0%
! ACTAATGACACTGAAATATT+TGG + chr3_4:61763318-61763337 None:intergenic 25.0%
!! ATATTTCAGTGTCATTAGTA+AGG - chr3_4:61763319-61763338 Msa0512130:CDS 25.0%
! AGTGAAAAACTTAAAAGATG+AGG + chr3_4:61763523-61763542 None:intergenic 25.0%
!! TTACGTGTAGAAATTTTGTA+AGG - chr3_4:61763814-61763833 Msa0512130:CDS 25.0%
! TATCATGTATAAAATGGCAA+TGG - chr3_4:61763851-61763870 Msa0512130:CDS 25.0%
! ATTGGAACTTATCTTATTGA+TGG - chr3_4:61763949-61763968 Msa0512130:CDS 25.0%
! AGTCAAGCAAAATATTACAT+TGG - chr3_4:61764123-61764142 Msa0512130:five_prime_UTR 25.0%
!!! TTCAATGTTTTGGAATTTGT+TGG + chr3_4:61763178-61763197 None:intergenic 25.0%
! ACTAATGACACTGAAATATT+TGG + chr3_4:61763318-61763337 None:intergenic 25.0%
!! ATATTTCAGTGTCATTAGTA+AGG - chr3_4:61763319-61763338 Msa0512130:CDS 25.0%
! AGTGAAAAACTTAAAAGATG+AGG + chr3_4:61763523-61763542 None:intergenic 25.0%
!! TTACGTGTAGAAATTTTGTA+AGG - chr3_4:61763814-61763833 Msa0512130:CDS 25.0%
! TATCATGTATAAAATGGCAA+TGG - chr3_4:61763851-61763870 Msa0512130:CDS 25.0%
! ATTGGAACTTATCTTATTGA+TGG - chr3_4:61763949-61763968 Msa0512130:CDS 25.0%
! AGTCAAGCAAAATATTACAT+TGG - chr3_4:61764123-61764142 Msa0512130:five_prime_UTR 25.0%
!!! GTTTTGGAATTTGTTGGTTA+TGG + chr3_4:61763172-61763191 None:intergenic 30.0%
! GATTTGTGGTTTCAATGTTT+TGG + chr3_4:61763188-61763207 None:intergenic 30.0%
! CTGTTGTTGAACTTTAGAAA+TGG + chr3_4:61763273-61763292 None:intergenic 30.0%
AAACGTTCAAAGTTGGATAA+AGG - chr3_4:61763384-61763403 Msa0512130:intron 30.0%
AACGTTCAAAGTTGGATAAA+GGG - chr3_4:61763385-61763404 Msa0512130:intron 30.0%
GGAGCTTCAATGATAATAAT+GGG + chr3_4:61763414-61763433 None:intergenic 30.0%
TGGAGCTTCAATGATAATAA+TGG + chr3_4:61763415-61763434 None:intergenic 30.0%
CTTATCCCATTAAATTGGAT+CGG - chr3_4:61763634-61763653 Msa0512130:intron 30.0%
!!! GTTTTGGAATTTGTTGGTTA+TGG + chr3_4:61763172-61763191 None:intergenic 30.0%
! GATTTGTGGTTTCAATGTTT+TGG + chr3_4:61763188-61763207 None:intergenic 30.0%
! CTGTTGTTGAACTTTAGAAA+TGG + chr3_4:61763273-61763292 None:intergenic 30.0%
AAACGTTCAAAGTTGGATAA+AGG - chr3_4:61763384-61763403 Msa0512130:intron 30.0%
AACGTTCAAAGTTGGATAAA+GGG - chr3_4:61763385-61763404 Msa0512130:intron 30.0%
GGAGCTTCAATGATAATAAT+GGG + chr3_4:61763414-61763433 None:intergenic 30.0%
TGGAGCTTCAATGATAATAA+TGG + chr3_4:61763415-61763434 None:intergenic 30.0%
CTTATCCCATTAAATTGGAT+CGG - chr3_4:61763634-61763653 Msa0512130:intron 30.0%
TATGTGTGAGGAAGGATATT+AGG + chr3_4:61763112-61763131 None:intergenic 35.0%
ACACATACACTGCAAATGAT+TGG - chr3_4:61763125-61763144 Msa0512130:three_prime_UTR 35.0%
! GTTGCAATGTTTCTGATTTG+TGG + chr3_4:61763202-61763221 None:intergenic 35.0%
CTTTGTGATACCACAAGAAA+GGG + chr3_4:61763250-61763269 None:intergenic 35.0%
! ACAGCTTGAAGTATCAACAA+CGG - chr3_4:61763289-61763308 Msa0512130:CDS 35.0%
TGAATCAAAAGAGTCATCAG+AGG - chr3_4:61763344-61763363 Msa0512130:intron 35.0%
GCTTGAAAAACGTTCAAAGT+TGG - chr3_4:61763377-61763396 Msa0512130:intron 35.0%
CAATTTAATGGGATAAGGCT+TGG + chr3_4:61763631-61763650 None:intergenic 35.0%
! CAAGCCTTATCCCATTAAAT+TGG - chr3_4:61763629-61763648 Msa0512130:intron 35.0%
CGATCCAATTTAATGGGATA+AGG + chr3_4:61763636-61763655 None:intergenic 35.0%
TGTTGCCGATCCAATTTAAT+GGG + chr3_4:61763642-61763661 None:intergenic 35.0%
ATGTTGCCGATCCAATTTAA+TGG + chr3_4:61763643-61763662 None:intergenic 35.0%
AAGAAAGCCAAAAGATGTGT+GGG - chr3_4:61763912-61763931 Msa0512130:CDS 35.0%
ATATTTCAAGCCCTTAGATC+TGG - chr3_4:61763975-61763994 Msa0512130:CDS 35.0%
CTATACTCAACCAGATCTAA+GGG + chr3_4:61763988-61764007 None:intergenic 35.0%
ACTATACTCAACCAGATCTA+AGG + chr3_4:61763989-61764008 None:intergenic 35.0%
TATGTGTGAGGAAGGATATT+AGG + chr3_4:61763112-61763131 None:intergenic 35.0%
ACACATACACTGCAAATGAT+TGG - chr3_4:61763125-61763144 Msa0512130:three_prime_UTR 35.0%
! GTTGCAATGTTTCTGATTTG+TGG + chr3_4:61763202-61763221 None:intergenic 35.0%
CTTTGTGATACCACAAGAAA+GGG + chr3_4:61763250-61763269 None:intergenic 35.0%
! ACAGCTTGAAGTATCAACAA+CGG - chr3_4:61763289-61763308 Msa0512130:CDS 35.0%
TGAATCAAAAGAGTCATCAG+AGG - chr3_4:61763344-61763363 Msa0512130:intron 35.0%
GCTTGAAAAACGTTCAAAGT+TGG - chr3_4:61763377-61763396 Msa0512130:intron 35.0%
CAATTTAATGGGATAAGGCT+TGG + chr3_4:61763631-61763650 None:intergenic 35.0%
! CAAGCCTTATCCCATTAAAT+TGG - chr3_4:61763629-61763648 Msa0512130:intron 35.0%
CGATCCAATTTAATGGGATA+AGG + chr3_4:61763636-61763655 None:intergenic 35.0%
TGTTGCCGATCCAATTTAAT+GGG + chr3_4:61763642-61763661 None:intergenic 35.0%
ATGTTGCCGATCCAATTTAA+TGG + chr3_4:61763643-61763662 None:intergenic 35.0%
AAGAAAGCCAAAAGATGTGT+GGG - chr3_4:61763912-61763931 Msa0512130:CDS 35.0%
ATATTTCAAGCCCTTAGATC+TGG - chr3_4:61763975-61763994 Msa0512130:CDS 35.0%
CTATACTCAACCAGATCTAA+GGG + chr3_4:61763988-61764007 None:intergenic 35.0%
ACTATACTCAACCAGATCTA+AGG + chr3_4:61763989-61764008 None:intergenic 35.0%
TCATTTGCAGTGTATGTGTG+AGG + chr3_4:61763124-61763143 None:intergenic 40.0%
ATGTCTTTGTCCCTTTCTTG+TGG - chr3_4:61763237-61763256 Msa0512130:CDS 40.0%
GCTTTGTGATACCACAAGAA+AGG + chr3_4:61763251-61763270 None:intergenic 40.0%
!! GCTGCAGTTTTGATCATCTT+TGG + chr3_4:61763435-61763454 None:intergenic 40.0%
!! CAGAATTAACTCTGAGGCAA+GGG + chr3_4:61763464-61763483 None:intergenic 40.0%
CTAAGCCAGAATTAACTCTG+AGG + chr3_4:61763470-61763489 None:intergenic 40.0%
!! AATTCTGGCTTAGTCAAACC+TGG - chr3_4:61763477-61763496 Msa0512130:intron 40.0%
! TTAGTCAAACCTGGTGATGT+TGG - chr3_4:61763486-61763505 Msa0512130:intron 40.0%
AAATACCTTCCAACATCACC+AGG + chr3_4:61763498-61763517 None:intergenic 40.0%
CAAGAAAGCCAAAAGATGTG+TGG - chr3_4:61763911-61763930 Msa0512130:CDS 40.0%
!! ATTTTTGTTTCCCAACCAGC+AGG - chr3_4:61764055-61764074 Msa0512130:five_prime_UTR 40.0%
TCATTTGCAGTGTATGTGTG+AGG + chr3_4:61763124-61763143 None:intergenic 40.0%
ATGTCTTTGTCCCTTTCTTG+TGG - chr3_4:61763237-61763256 Msa0512130:CDS 40.0%
GCTTTGTGATACCACAAGAA+AGG + chr3_4:61763251-61763270 None:intergenic 40.0%
!! GCTGCAGTTTTGATCATCTT+TGG + chr3_4:61763435-61763454 None:intergenic 40.0%
!! CAGAATTAACTCTGAGGCAA+GGG + chr3_4:61763464-61763483 None:intergenic 40.0%
CTAAGCCAGAATTAACTCTG+AGG + chr3_4:61763470-61763489 None:intergenic 40.0%
!! AATTCTGGCTTAGTCAAACC+TGG - chr3_4:61763477-61763496 Msa0512130:intron 40.0%
! TTAGTCAAACCTGGTGATGT+TGG - chr3_4:61763486-61763505 Msa0512130:intron 40.0%
AAATACCTTCCAACATCACC+AGG + chr3_4:61763498-61763517 None:intergenic 40.0%
CAAGAAAGCCAAAAGATGTG+TGG - chr3_4:61763911-61763930 Msa0512130:CDS 40.0%
!! ATTTTTGTTTCCCAACCAGC+AGG - chr3_4:61764055-61764074 Msa0512130:five_prime_UTR 40.0%
TTGCAGTGTATGTGTGAGGA+AGG + chr3_4:61763120-61763139 None:intergenic 45.0%
! GCTTGAAGTATCAACAACGG+AGG - chr3_4:61763292-61763311 Msa0512130:CDS 45.0%
!! CCAGAATTAACTCTGAGGCA+AGG + chr3_4:61763465-61763484 None:intergenic 45.0%
CCTTGCCTCAGAGTTAATTC+TGG - chr3_4:61763462-61763481 Msa0512130:intron 45.0%
! TCAAACCTGGTGATGTTGGA+AGG - chr3_4:61763490-61763509 Msa0512130:intron 45.0%
CAAAAGATGTGTGGGCAGTA+CGG - chr3_4:61763920-61763939 Msa0512130:CDS 45.0%
TTGCAGTGTATGTGTGAGGA+AGG + chr3_4:61763120-61763139 None:intergenic 45.0%
! GCTTGAAGTATCAACAACGG+AGG - chr3_4:61763292-61763311 Msa0512130:CDS 45.0%
!! CCAGAATTAACTCTGAGGCA+AGG + chr3_4:61763465-61763484 None:intergenic 45.0%
CCTTGCCTCAGAGTTAATTC+TGG - chr3_4:61763462-61763481 Msa0512130:intron 45.0%
! TCAAACCTGGTGATGTTGGA+AGG - chr3_4:61763490-61763509 Msa0512130:intron 45.0%
CAAAAGATGTGTGGGCAGTA+CGG - chr3_4:61763920-61763939 Msa0512130:CDS 45.0%
! CGTACTGCCCACACATCTTT+TGG + chr3_4:61763922-61763941 None:intergenic 50.0%
TTTGTTTCCCAACCAGCAGG+TGG - chr3_4:61764058-61764077 Msa0512130:five_prime_UTR 50.0%
! CGTACTGCCCACACATCTTT+TGG + chr3_4:61763922-61763941 None:intergenic 50.0%
TTTGTTTCCCAACCAGCAGG+TGG - chr3_4:61764058-61764077 Msa0512130:five_prime_UTR 50.0%
TGGGCAGTACGGCTCAACAT+TGG - chr3_4:61763931-61763950 Msa0512130:CDS 55.0%
TGGGCAGTACGGCTCAACAT+TGG - chr3_4:61763931-61763950 Msa0512130:CDS 55.0%
! CCAAGAGCCACCTGCTGGTT+GGG + chr3_4:61764068-61764087 None:intergenic 60.0%
GTATGCCAAGAGCCACCTGC+TGG + chr3_4:61764073-61764092 None:intergenic 60.0%
! CCAAGAGCCACCTGCTGGTT+GGG + chr3_4:61764068-61764087 None:intergenic 60.0%
GTATGCCAAGAGCCACCTGC+TGG + chr3_4:61764073-61764092 None:intergenic 60.0%
CCCAACCAGCAGGTGGCTCT+TGG - chr3_4:61764065-61764084 Msa0512130:five_prime_UTR 65.0%
GCCAAGAGCCACCTGCTGGT+TGG + chr3_4:61764069-61764088 None:intergenic 65.0%
CCCAACCAGCAGGTGGCTCT+TGG - chr3_4:61764065-61764084 Msa0512130:five_prime_UTR 65.0%
GCCAAGAGCCACCTGCTGGT+TGG + chr3_4:61764069-61764088 None:intergenic 65.0%
Chromosome Type Strat End Strand Name
chr3_4 gene 61763047 61764198 61763047 ID=Msa0512130;Name=Msa0512130
chr3_4 mRNA 61763047 61764198 61763047 ID=Msa0512130-mRNA-1;Parent=Msa0512130;Name=Msa0512130-mRNA-1;_AED=0.01;_eAED=0.01;_QI=190|1|1|1|1|1|2|187|127
chr3_4 exon 61763047 61763342 61763047 ID=Msa0512130-mRNA-1:exon:15109;Parent=Msa0512130-mRNA-1
chr3_4 exon 61763734 61764198 61763734 ID=Msa0512130-mRNA-1:exon:15108;Parent=Msa0512130-mRNA-1
chr3_4 five_prime_UTR 61764009 61764198 61764009 ID=Msa0512130-mRNA-1:five_prime_utr;Parent=Msa0512130-mRNA-1
chr3_4 CDS 61763734 61764008 61763734 ID=Msa0512130-mRNA-1:cds;Parent=Msa0512130-mRNA-1
chr3_4 CDS 61763234 61763342 61763234 ID=Msa0512130-mRNA-1:cds;Parent=Msa0512130-mRNA-1
chr3_4 three_prime_UTR 61763047 61763233 61763047 ID=Msa0512130-mRNA-1:three_prime_utr;Parent=Msa0512130-mRNA-1
Gene Sequence

>Msa0512130

ATGTCTTTGTCCCTTTCTTGTGGTATCACAAAGCCATTTCTAAAGTTCAACAACAGCTTGAAGTATCAACAACGGAGGCCAAATATTTCAGTGTCATTAGTAAGGTGTGAATCAAAAGAGTCATCAGAGGAGAATGAGTTGCTTGAAAAACGTTCAAAGTTGGATAAAGGGTCTCCCATTATTATCATTGAAGCTCCAAAGATGATCAAAACTGCAGCTTCTGTCCCTTGCCTCAGAGTTAATTCTGGCTTAGTCAAACCTGGTGATGTTGGAAGAATTGTTTCAAGAAAGCCAAAAGATGTGTGGGCAGTACGGCTCAACATTGGAACTTATCTTATTGATGGCAAATATTTCAAGCCCTTAGATCTGGTTGAGTATAGTTAG

Protein sequence

>Msa0512130

MSLSLSCGITKPFLKFNNSLKYQQRRPNISVSLVRCESKESSEENELLEKRSKLDKGSPIIIIEAPKMIKTAASVPCLRVNSGLVKPGDVGRIVSRKPKDVWAVRLNIGTYLIDGKYFKPLDLVEYS*