AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0441460


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0441460 MtrunA17_Chr3g0079061 84.000 275 32 1 1 263 1 275 8.03e-170 469
Msa0441460 MtrunA17_Chr3g0079131 64.493 276 84 3 1 263 1 275 6.25e-114 328
Msa0441460 MtrunA17_Chr3g0079091 75.706 177 31 1 1 165 1 177 1.08e-81 243
Msa0441460 MtrunA17_Chr4g0018761 29.297 256 155 5 3 255 4 236 5.39e-24 97.1
Msa0441460 MtrunA17_Chr7g0231181 26.797 306 164 10 8 255 6 309 6.78e-14 70.5
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0441460 AT3G60580.1 26.766 269 147 10 8 254 6 246 1.61e-13 69.3
Msa0441460 AT1G02030.1 26.482 253 152 8 8 254 7 231 1.61e-12 66.2

Find 43 sgRNAs with CRISPR-Local

Find 112 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TTGTTTGGTGGGTTACTTCT+TGG 0.249003 3_3:-9860019 None:intergenic
CAGGTACTTGGTTGTTGATT+GGG 0.275325 3_3:-9859928 None:intergenic
TCAGGTACTTGGTTGTTGAT+TGG 0.290946 3_3:-9859929 None:intergenic
CTTCTTGGATTAACAATTGA+TGG 0.303146 3_3:-9860004 None:intergenic
GCCAACTCAGCTGAGTATTC+AGG 0.304238 3_3:-9859947 None:intergenic
TGCTTTGACATCTTTGAATC+TGG 0.309104 3_3:+9860523 Msa0441460:CDS
TTCAAAGATTGAGGATTGTT+TGG 0.332480 3_3:-9860034 None:intergenic
CTTTGAATCTGGTCACGTAT+TGG 0.390852 3_3:+9860534 Msa0441460:CDS
ACAATCAGCGTATAGCGATT+TGG 0.398813 3_3:+9860234 Msa0441460:CDS
CAGCTGAGTATTCAGGTACT+TGG 0.400249 3_3:-9859940 None:intergenic
GAGTGTGTCTCATTTGTAAC+AGG 0.418825 3_3:+9859831 Msa0441460:CDS
AGGTACTTGGTTGTTGATTG+GGG 0.434003 3_3:-9859927 None:intergenic
CAGAATCATAATAATTGTAT+AGG 0.437191 3_3:-9860576 None:intergenic
GTGTTATTCTTAAGAATGAA+TGG 0.439493 3_3:+9860281 Msa0441460:CDS
AATTTCACTTTCAAAGATTG+AGG 0.444853 3_3:-9860043 None:intergenic
AAATGTACCCCGTCAAACTT+TGG 0.446972 3_3:+9860067 Msa0441460:CDS
GATAGAGTGAGTTGGATGTT+TGG 0.448812 3_3:-9859969 None:intergenic
AACAATCTAGCAGGAGAGAT+TGG 0.456742 3_3:+9860445 Msa0441460:CDS
GGATTGGTAGTTTGGCATAG+TGG 0.460724 3_3:-9859895 None:intergenic
TCTTATCCAACAAACCCAAC+TGG 0.466226 3_3:+9860109 Msa0441460:CDS
TATTCCTACCAAAGTTTGAC+GGG 0.471579 3_3:-9860075 None:intergenic
AAGATTGAGGATTGTTTGGT+GGG 0.486813 3_3:-9860030 None:intergenic
TCAGCCATATGAAACTGTCT+TGG 0.489788 3_3:-9860151 None:intergenic
CTATTCCTACCAAAGTTTGA+CGG 0.495952 3_3:-9860076 None:intergenic
GATGTAGAGATAGAGTGAGT+TGG 0.497788 3_3:-9859977 None:intergenic
TGAATCTGGTCACGTATTGG+AGG 0.509112 3_3:+9860537 Msa0441460:CDS
AAAGATTGAGGATTGTTTGG+TGG 0.514150 3_3:-9860031 None:intergenic
GATTGGTAGTTTGGCATAGT+GGG 0.520357 3_3:-9859894 None:intergenic
CAAACCAAGACAGTTTCATA+TGG 0.521057 3_3:+9860147 Msa0441460:CDS
GCAGGAGAGATTGGTAGAAG+TGG 0.524466 3_3:+9860454 Msa0441460:CDS
AGGAAAACTAACAATCTAGC+AGG 0.531732 3_3:+9860436 Msa0441460:CDS
ACCTGAATACTCAGCTGAGT+TGG 0.539000 3_3:+9859946 Msa0441460:CDS
CGTATTGGAGGAACACATGA+AGG 0.564625 3_3:+9860549 Msa0441460:CDS
GGTACTTGGTTGTTGATTGG+GGG 0.573211 3_3:-9859926 None:intergenic
GAATGAATGGAAACAAATTG+AGG 0.585752 3_3:+9860294 Msa0441460:CDS
TCCAATGGAAAAGCTTTGGG+AGG 0.590411 3_3:+9859860 Msa0441460:CDS
TCGGACATGAAGATATCCAT+AGG 0.592226 3_3:+9860416 Msa0441460:CDS
ATAGAAGCTGCTGAAACACT+AGG 0.609115 3_3:+9860259 Msa0441460:CDS
GTACCCCGTCAAACTTTGGT+AGG 0.631191 3_3:+9860071 Msa0441460:CDS
ACAAATATCACACTCAAACA+CGG 0.640237 3_3:-9860362 None:intergenic
TCTCCAACTATGGAGAACAA+TGG 0.649885 3_3:+9859806 None:intergenic
AGAGAATATAGAATTTAACA+TGG 0.705093 3_3:+9860183 Msa0441460:CDS
ATTCCTACCAAAGTTTGACG+GGG 0.741422 3_3:-9860074 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AGAGAATATAGAATTTAACA+TGG + chr3_3:9860183-9860202 Msa0441460:CDS 20.0%
!! CAGAATCATAATAATTGTAT+AGG - chr3_3:9860579-9860598 None:intergenic 20.0%
!! AGAGAATATAGAATTTAACA+TGG + chr3_3:9860183-9860202 Msa0441460:CDS 20.0%
!! CAGAATCATAATAATTGTAT+AGG - chr3_3:9860579-9860598 None:intergenic 20.0%
! AATTTCACTTTCAAAGATTG+AGG - chr3_3:9860046-9860065 None:intergenic 25.0%
!! GTGTTATTCTTAAGAATGAA+TGG + chr3_3:9860281-9860300 Msa0441460:CDS 25.0%
! AAGAAAAAAGCAAGTGAAAA+TGG + chr3_3:9860334-9860353 Msa0441460:CDS 25.0%
! AATTTCACTTTCAAAGATTG+AGG - chr3_3:9860046-9860065 None:intergenic 25.0%
!! GTGTTATTCTTAAGAATGAA+TGG + chr3_3:9860281-9860300 Msa0441460:CDS 25.0%
! AAGAAAAAAGCAAGTGAAAA+TGG + chr3_3:9860334-9860353 Msa0441460:CDS 25.0%
! ATTTTCCAATGGAAAAGCTT+TGG + chr3_3:9859856-9859875 Msa0441460:CDS 30.0%
! TTTTCCAATGGAAAAGCTTT+GGG + chr3_3:9859857-9859876 Msa0441460:CDS 30.0%
CTTCTTGGATTAACAATTGA+TGG - chr3_3:9860007-9860026 None:intergenic 30.0%
TTCAAAGATTGAGGATTGTT+TGG - chr3_3:9860037-9860056 None:intergenic 30.0%
!! GTTTTGATCTTTTTCCAGTT+GGG - chr3_3:9860126-9860145 None:intergenic 30.0%
GAATGAATGGAAACAAATTG+AGG + chr3_3:9860294-9860313 Msa0441460:CDS 30.0%
ACAAATATCACACTCAAACA+CGG - chr3_3:9860365-9860384 None:intergenic 30.0%
! CAATCTAGCAAAGATCTTTT+CGG + chr3_3:9860397-9860416 Msa0441460:CDS 30.0%
!!! CTAGATTGTTAGTTTTCCTA+TGG - chr3_3:9860435-9860454 None:intergenic 30.0%
! ATTTTCCAATGGAAAAGCTT+TGG + chr3_3:9859856-9859875 Msa0441460:CDS 30.0%
! TTTTCCAATGGAAAAGCTTT+GGG + chr3_3:9859857-9859876 Msa0441460:CDS 30.0%
CTTCTTGGATTAACAATTGA+TGG - chr3_3:9860007-9860026 None:intergenic 30.0%
TTCAAAGATTGAGGATTGTT+TGG - chr3_3:9860037-9860056 None:intergenic 30.0%
!! GTTTTGATCTTTTTCCAGTT+GGG - chr3_3:9860126-9860145 None:intergenic 30.0%
GAATGAATGGAAACAAATTG+AGG + chr3_3:9860294-9860313 Msa0441460:CDS 30.0%
ACAAATATCACACTCAAACA+CGG - chr3_3:9860365-9860384 None:intergenic 30.0%
! CAATCTAGCAAAGATCTTTT+CGG + chr3_3:9860397-9860416 Msa0441460:CDS 30.0%
!!! CTAGATTGTTAGTTTTCCTA+TGG - chr3_3:9860435-9860454 None:intergenic 30.0%
!! TGTAACAGGTCATTTTCCAA+TGG + chr3_3:9859845-9859864 Msa0441460:CDS 35.0%
!!! TTTTGGATGGATTGGTAGTT+TGG - chr3_3:9859906-9859925 None:intergenic 35.0%
AAGATTGAGGATTGTTTGGT+GGG - chr3_3:9860033-9860052 None:intergenic 35.0%
AAAGATTGAGGATTGTTTGG+TGG - chr3_3:9860034-9860053 None:intergenic 35.0%
TATTCCTACCAAAGTTTGAC+GGG - chr3_3:9860078-9860097 None:intergenic 35.0%
CTATTCCTACCAAAGTTTGA+CGG - chr3_3:9860079-9860098 None:intergenic 35.0%
!! CGTTTTGATCTTTTTCCAGT+TGG - chr3_3:9860127-9860146 None:intergenic 35.0%
CAAACCAAGACAGTTTCATA+TGG + chr3_3:9860147-9860166 Msa0441460:CDS 35.0%
AGGAAAACTAACAATCTAGC+AGG + chr3_3:9860436-9860455 Msa0441460:CDS 35.0%
TGCTTTGACATCTTTGAATC+TGG + chr3_3:9860523-9860542 Msa0441460:CDS 35.0%
!! TGTAACAGGTCATTTTCCAA+TGG + chr3_3:9859845-9859864 Msa0441460:CDS 35.0%
!!! TTTTGGATGGATTGGTAGTT+TGG - chr3_3:9859906-9859925 None:intergenic 35.0%
AAGATTGAGGATTGTTTGGT+GGG - chr3_3:9860033-9860052 None:intergenic 35.0%
AAAGATTGAGGATTGTTTGG+TGG - chr3_3:9860034-9860053 None:intergenic 35.0%
TATTCCTACCAAAGTTTGAC+GGG - chr3_3:9860078-9860097 None:intergenic 35.0%
CTATTCCTACCAAAGTTTGA+CGG - chr3_3:9860079-9860098 None:intergenic 35.0%
!! CGTTTTGATCTTTTTCCAGT+TGG - chr3_3:9860127-9860146 None:intergenic 35.0%
CAAACCAAGACAGTTTCATA+TGG + chr3_3:9860147-9860166 Msa0441460:CDS 35.0%
AGGAAAACTAACAATCTAGC+AGG + chr3_3:9860436-9860455 Msa0441460:CDS 35.0%
TGCTTTGACATCTTTGAATC+TGG + chr3_3:9860523-9860542 Msa0441460:CDS 35.0%
GAGTGTGTCTCATTTGTAAC+AGG + chr3_3:9859831-9859850 Msa0441460:CDS 40.0%
! GATTGGTAGTTTGGCATAGT+GGG - chr3_3:9859897-9859916 None:intergenic 40.0%
! AGGTACTTGGTTGTTGATTG+GGG - chr3_3:9859930-9859949 None:intergenic 40.0%
! CAGGTACTTGGTTGTTGATT+GGG - chr3_3:9859931-9859950 None:intergenic 40.0%
TCAGGTACTTGGTTGTTGAT+TGG - chr3_3:9859932-9859951 None:intergenic 40.0%
! GATAGAGTGAGTTGGATGTT+TGG - chr3_3:9859972-9859991 None:intergenic 40.0%
GATGTAGAGATAGAGTGAGT+TGG - chr3_3:9859980-9859999 None:intergenic 40.0%
!! TTGTTTGGTGGGTTACTTCT+TGG - chr3_3:9860022-9860041 None:intergenic 40.0%
AAATGTACCCCGTCAAACTT+TGG + chr3_3:9860067-9860086 Msa0441460:CDS 40.0%
ATTCCTACCAAAGTTTGACG+GGG - chr3_3:9860077-9860096 None:intergenic 40.0%
TCTTATCCAACAAACCCAAC+TGG + chr3_3:9860109-9860128 Msa0441460:CDS 40.0%
! CTTTTTCCAGTTGGGTTTGT+TGG - chr3_3:9860118-9860137 None:intergenic 40.0%
TCAGCCATATGAAACTGTCT+TGG - chr3_3:9860154-9860173 None:intergenic 40.0%
ACAATCAGCGTATAGCGATT+TGG + chr3_3:9860234-9860253 Msa0441460:CDS 40.0%
ATAGAAGCTGCTGAAACACT+AGG + chr3_3:9860259-9860278 Msa0441460:CDS 40.0%
TCGGACATGAAGATATCCAT+AGG + chr3_3:9860416-9860435 Msa0441460:CDS 40.0%
AACAATCTAGCAGGAGAGAT+TGG + chr3_3:9860445-9860464 Msa0441460:CDS 40.0%
CTTTGAATCTGGTCACGTAT+TGG + chr3_3:9860534-9860553 Msa0441460:CDS 40.0%
GAGTGTGTCTCATTTGTAAC+AGG + chr3_3:9859831-9859850 Msa0441460:CDS 40.0%
! GATTGGTAGTTTGGCATAGT+GGG - chr3_3:9859897-9859916 None:intergenic 40.0%
! AGGTACTTGGTTGTTGATTG+GGG - chr3_3:9859930-9859949 None:intergenic 40.0%
! CAGGTACTTGGTTGTTGATT+GGG - chr3_3:9859931-9859950 None:intergenic 40.0%
TCAGGTACTTGGTTGTTGAT+TGG - chr3_3:9859932-9859951 None:intergenic 40.0%
! GATAGAGTGAGTTGGATGTT+TGG - chr3_3:9859972-9859991 None:intergenic 40.0%
GATGTAGAGATAGAGTGAGT+TGG - chr3_3:9859980-9859999 None:intergenic 40.0%
!! TTGTTTGGTGGGTTACTTCT+TGG - chr3_3:9860022-9860041 None:intergenic 40.0%
AAATGTACCCCGTCAAACTT+TGG + chr3_3:9860067-9860086 Msa0441460:CDS 40.0%
ATTCCTACCAAAGTTTGACG+GGG - chr3_3:9860077-9860096 None:intergenic 40.0%
TCTTATCCAACAAACCCAAC+TGG + chr3_3:9860109-9860128 Msa0441460:CDS 40.0%
! CTTTTTCCAGTTGGGTTTGT+TGG - chr3_3:9860118-9860137 None:intergenic 40.0%
TCAGCCATATGAAACTGTCT+TGG - chr3_3:9860154-9860173 None:intergenic 40.0%
ACAATCAGCGTATAGCGATT+TGG + chr3_3:9860234-9860253 Msa0441460:CDS 40.0%
ATAGAAGCTGCTGAAACACT+AGG + chr3_3:9860259-9860278 Msa0441460:CDS 40.0%
TCGGACATGAAGATATCCAT+AGG + chr3_3:9860416-9860435 Msa0441460:CDS 40.0%
AACAATCTAGCAGGAGAGAT+TGG + chr3_3:9860445-9860464 Msa0441460:CDS 40.0%
CTTTGAATCTGGTCACGTAT+TGG + chr3_3:9860534-9860553 Msa0441460:CDS 40.0%
!! TCCAATGGAAAAGCTTTGGG+AGG + chr3_3:9859860-9859879 Msa0441460:CDS 45.0%
! TCCTCCCAAAGCTTTTCCAT+TGG - chr3_3:9859864-9859883 None:intergenic 45.0%
! GGATTGGTAGTTTGGCATAG+TGG - chr3_3:9859898-9859917 None:intergenic 45.0%
!!! ATTGGGGGTTTTGGATGGAT+TGG - chr3_3:9859914-9859933 None:intergenic 45.0%
!!! TGTTGATTGGGGGTTTTGGA+TGG - chr3_3:9859919-9859938 None:intergenic 45.0%
!! TGGTTGTTGATTGGGGGTTT+TGG - chr3_3:9859923-9859942 None:intergenic 45.0%
! GGTACTTGGTTGTTGATTGG+GGG - chr3_3:9859929-9859948 None:intergenic 45.0%
CAGCTGAGTATTCAGGTACT+TGG - chr3_3:9859943-9859962 None:intergenic 45.0%
ACCTGAATACTCAGCTGAGT+TGG + chr3_3:9859946-9859965 Msa0441460:CDS 45.0%
TGAATCTGGTCACGTATTGG+AGG + chr3_3:9860537-9860556 Msa0441460:CDS 45.0%
CGTATTGGAGGAACACATGA+AGG + chr3_3:9860549-9860568 Msa0441460:CDS 45.0%
!! TCCAATGGAAAAGCTTTGGG+AGG + chr3_3:9859860-9859879 Msa0441460:CDS 45.0%
! TCCTCCCAAAGCTTTTCCAT+TGG - chr3_3:9859864-9859883 None:intergenic 45.0%
! GGATTGGTAGTTTGGCATAG+TGG - chr3_3:9859898-9859917 None:intergenic 45.0%
!!! ATTGGGGGTTTTGGATGGAT+TGG - chr3_3:9859914-9859933 None:intergenic 45.0%
!!! TGTTGATTGGGGGTTTTGGA+TGG - chr3_3:9859919-9859938 None:intergenic 45.0%
!! TGGTTGTTGATTGGGGGTTT+TGG - chr3_3:9859923-9859942 None:intergenic 45.0%
! GGTACTTGGTTGTTGATTGG+GGG - chr3_3:9859929-9859948 None:intergenic 45.0%
CAGCTGAGTATTCAGGTACT+TGG - chr3_3:9859943-9859962 None:intergenic 45.0%
ACCTGAATACTCAGCTGAGT+TGG + chr3_3:9859946-9859965 Msa0441460:CDS 45.0%
TGAATCTGGTCACGTATTGG+AGG + chr3_3:9860537-9860556 Msa0441460:CDS 45.0%
CGTATTGGAGGAACACATGA+AGG + chr3_3:9860549-9860568 Msa0441460:CDS 45.0%
GCCAACTCAGCTGAGTATTC+AGG - chr3_3:9859950-9859969 None:intergenic 50.0%
GTACCCCGTCAAACTTTGGT+AGG + chr3_3:9860071-9860090 Msa0441460:CDS 50.0%
GCAGGAGAGATTGGTAGAAG+TGG + chr3_3:9860454-9860473 Msa0441460:CDS 50.0%
GCCAACTCAGCTGAGTATTC+AGG - chr3_3:9859950-9859969 None:intergenic 50.0%
GTACCCCGTCAAACTTTGGT+AGG + chr3_3:9860071-9860090 Msa0441460:CDS 50.0%
GCAGGAGAGATTGGTAGAAG+TGG + chr3_3:9860454-9860473 Msa0441460:CDS 50.0%
Chromosome Type Strat End Strand Name
chr3_3 gene 9859815 9860606 9859815 ID=Msa0441460;Name=Msa0441460
chr3_3 mRNA 9859815 9860606 9859815 ID=Msa0441460-mRNA-1;Parent=Msa0441460;Name=Msa0441460-mRNA-1;_AED=0.00;_eAED=0.00;_QI=0|-1|0|1|-1|1|1|0|263
chr3_3 exon 9859815 9860606 9859815 ID=Msa0441460-mRNA-1:exon:2049;Parent=Msa0441460-mRNA-1
chr3_3 CDS 9859815 9860606 9859815 ID=Msa0441460-mRNA-1:cds;Parent=Msa0441460-mRNA-1
Gene Sequence

>Msa0441460

ATGGAGAACAATGGTAGAGTGTGTCTCATTTGTAACAGGTCATTTTCCAATGGAAAAGCTTTGGGAGGACATATGAAATCCCACTATGCCAAACTACCAATCCATCCAAAACCCCCAATCAACAACCAAGTACCTGAATACTCAGCTGAGTTGGCCAAACATCCAACTCACTCTATCTCTACATCTTCACCATCAATTGTTAATCCAAGAAGTAACCCACCAAACAATCCTCAATCTTTGAAAGTGAAATTCAAATGTACCCCGTCAAACTTTGGTAGGAATAGTGTGTTTCAGTCTTATCCAACAAACCCAACTGGAAAAAGATCAAAACGCAAACCAAGACAGTTTCATATGGCTGAAGAAAGAGAAGAGAATATAGAATTTAACATGGCTGAAGAAAAAGAAGATAATACACAATTACAATCAGCGTATAGCGATTTGGATATAGAAGCTGCTGAAACACTAGGTGTTATTCTTAAGAATGAATGGAAACAAATTGAGGACAAATACTACACTGAGAAGAAAAAAGCAAGTGAAAATGGAAACACCGTGTTTGAGTGTGATATTTGTCATGAAGTGTTTCAATCTAGCAAAGATCTTTTCGGACATGAAGATATCCATAGGAAAACTAACAATCTAGCAGGAGAGATTGGTAGAAGTGGAAACATATATGATGTCGTAAATGAAAAAGTGCATAAGTGCGAATATTGCTTTGACATCTTTGAATCTGGTCACGTATTGGAGGAACACATGAAGGTACACCTATACAATTATTATGATTCTGACCCATAG

Protein sequence

>Msa0441460

MENNGRVCLICNRSFSNGKALGGHMKSHYAKLPIHPKPPINNQVPEYSAELAKHPTHSISTSSPSIVNPRSNPPNNPQSLKVKFKCTPSNFGRNSVFQSYPTNPTGKRSKRKPRQFHMAEEREENIEFNMAEEKEDNTQLQSAYSDLDIEAAETLGVILKNEWKQIEDKYYTEKKKASENGNTVFECDICHEVFQSSKDLFGHEDIHRKTNNLAGEIGRSGNIYDVVNEKVHKCEYCFDIFESGHVLEEHMKVHLYNYYDSDP*