AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0393670


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0393670 MtrunA17_Chr3g0079061 84.000 275 32 1 1 263 1 275 8.03e-170 469
Msa0393670 MtrunA17_Chr3g0079131 64.493 276 84 3 1 263 1 275 6.25e-114 328
Msa0393670 MtrunA17_Chr3g0079091 75.706 177 31 1 1 165 1 177 1.08e-81 243
Msa0393670 MtrunA17_Chr4g0018761 29.297 256 155 5 3 255 4 236 5.39e-24 97.1
Msa0393670 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
Msa0393670 AT3G60580.1 26.766 269 147 10 8 254 6 246 1.61e-13 69.3
Msa0393670 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_2:-7767468 None:intergenic
CAGGTACTTGGTTGTTGATT+GGG 0.275325 3_2:-7767377 None:intergenic
TCAGGTACTTGGTTGTTGAT+TGG 0.290946 3_2:-7767378 None:intergenic
CTTCTTGGATTAACAATTGA+TGG 0.303146 3_2:-7767453 None:intergenic
GCCAACTCAGCTGAGTATTC+AGG 0.304238 3_2:-7767396 None:intergenic
TGCTTTGACATCTTTGAATC+TGG 0.309104 3_2:+7767972 Msa0393670:CDS
TTCAAAGATTGAGGATTGTT+TGG 0.332480 3_2:-7767483 None:intergenic
CTTTGAATCTGGTCACGTAT+TGG 0.390852 3_2:+7767983 Msa0393670:CDS
ACAATCAGCGTATAGCGATT+TGG 0.398813 3_2:+7767683 Msa0393670:CDS
CAGCTGAGTATTCAGGTACT+TGG 0.400249 3_2:-7767389 None:intergenic
GAGTGTGTCTCATTTGTAAC+AGG 0.418825 3_2:+7767280 Msa0393670:CDS
AGGTACTTGGTTGTTGATTG+GGG 0.434003 3_2:-7767376 None:intergenic
CAGAATCATAATAATTGTAT+AGG 0.437191 3_2:-7768025 None:intergenic
GTGTTATTCTTAAGAATGAA+TGG 0.439493 3_2:+7767730 Msa0393670:CDS
AATTTCACTTTCAAAGATTG+AGG 0.444853 3_2:-7767492 None:intergenic
AAATGTACCCCGTCAAACTT+TGG 0.446972 3_2:+7767516 Msa0393670:CDS
GATAGAGTGAGTTGGATGTT+TGG 0.448812 3_2:-7767418 None:intergenic
AACAATCTAGCAGGAGAGAT+TGG 0.456742 3_2:+7767894 Msa0393670:CDS
GGATTGGTAGTTTGGCATAG+TGG 0.460724 3_2:-7767344 None:intergenic
TCTTATCCAACAAACCCAAC+TGG 0.466226 3_2:+7767558 Msa0393670:CDS
TATTCCTACCAAAGTTTGAC+GGG 0.471579 3_2:-7767524 None:intergenic
AAGATTGAGGATTGTTTGGT+GGG 0.486813 3_2:-7767479 None:intergenic
TCAGCCATATGAAACTGTCT+TGG 0.489788 3_2:-7767600 None:intergenic
CTATTCCTACCAAAGTTTGA+CGG 0.495952 3_2:-7767525 None:intergenic
GATGTAGAGATAGAGTGAGT+TGG 0.497788 3_2:-7767426 None:intergenic
TGAATCTGGTCACGTATTGG+AGG 0.509112 3_2:+7767986 Msa0393670:CDS
AAAGATTGAGGATTGTTTGG+TGG 0.514150 3_2:-7767480 None:intergenic
GATTGGTAGTTTGGCATAGT+GGG 0.520357 3_2:-7767343 None:intergenic
CAAACCAAGACAGTTTCATA+TGG 0.521057 3_2:+7767596 Msa0393670:CDS
GCAGGAGAGATTGGTAGAAG+TGG 0.524466 3_2:+7767903 Msa0393670:CDS
AGGAAAACTAACAATCTAGC+AGG 0.531732 3_2:+7767885 Msa0393670:CDS
ACCTGAATACTCAGCTGAGT+TGG 0.539000 3_2:+7767395 Msa0393670:CDS
CGTATTGGAGGAACACATGA+AGG 0.564625 3_2:+7767998 Msa0393670:CDS
GGTACTTGGTTGTTGATTGG+GGG 0.573211 3_2:-7767375 None:intergenic
GAATGAATGGAAACAAATTG+AGG 0.585752 3_2:+7767743 Msa0393670:CDS
TCCAATGGAAAAGCTTTGGG+AGG 0.590411 3_2:+7767309 Msa0393670:CDS
TCGGACATGAAGATATCCAT+AGG 0.592226 3_2:+7767865 Msa0393670:CDS
ATAGAAGCTGCTGAAACACT+AGG 0.609115 3_2:+7767708 Msa0393670:CDS
GTACCCCGTCAAACTTTGGT+AGG 0.631191 3_2:+7767520 Msa0393670:CDS
ACAAATATCACACTCAAACA+CGG 0.640237 3_2:-7767811 None:intergenic
TCTCCAACTATGGAGAACAA+TGG 0.649885 3_2:+7767255 None:intergenic
AGAGAATATAGAATTTAACA+TGG 0.705093 3_2:+7767632 Msa0393670:CDS
ATTCCTACCAAAGTTTGACG+GGG 0.741422 3_2:-7767523 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AGAGAATATAGAATTTAACA+TGG + chr3_2:7767632-7767651 Msa0393670:CDS 20.0%
!! CAGAATCATAATAATTGTAT+AGG - chr3_2:7768028-7768047 None:intergenic 20.0%
!! AGAGAATATAGAATTTAACA+TGG + chr3_2:7767632-7767651 Msa0393670:CDS 20.0%
!! CAGAATCATAATAATTGTAT+AGG - chr3_2:7768028-7768047 None:intergenic 20.0%
! AATTTCACTTTCAAAGATTG+AGG - chr3_2:7767495-7767514 None:intergenic 25.0%
!! GTGTTATTCTTAAGAATGAA+TGG + chr3_2:7767730-7767749 Msa0393670:CDS 25.0%
! AAGAAAAAAGCAAGTGAAAA+TGG + chr3_2:7767783-7767802 Msa0393670:CDS 25.0%
! AATTTCACTTTCAAAGATTG+AGG - chr3_2:7767495-7767514 None:intergenic 25.0%
!! GTGTTATTCTTAAGAATGAA+TGG + chr3_2:7767730-7767749 Msa0393670:CDS 25.0%
! AAGAAAAAAGCAAGTGAAAA+TGG + chr3_2:7767783-7767802 Msa0393670:CDS 25.0%
! ATTTTCCAATGGAAAAGCTT+TGG + chr3_2:7767305-7767324 Msa0393670:CDS 30.0%
! TTTTCCAATGGAAAAGCTTT+GGG + chr3_2:7767306-7767325 Msa0393670:CDS 30.0%
CTTCTTGGATTAACAATTGA+TGG - chr3_2:7767456-7767475 None:intergenic 30.0%
TTCAAAGATTGAGGATTGTT+TGG - chr3_2:7767486-7767505 None:intergenic 30.0%
!! GTTTTGATCTTTTTCCAGTT+GGG - chr3_2:7767575-7767594 None:intergenic 30.0%
GAATGAATGGAAACAAATTG+AGG + chr3_2:7767743-7767762 Msa0393670:CDS 30.0%
ACAAATATCACACTCAAACA+CGG - chr3_2:7767814-7767833 None:intergenic 30.0%
! CAATCTAGCAAAGATCTTTT+CGG + chr3_2:7767846-7767865 Msa0393670:CDS 30.0%
!!! CTAGATTGTTAGTTTTCCTA+TGG - chr3_2:7767884-7767903 None:intergenic 30.0%
! ATTTTCCAATGGAAAAGCTT+TGG + chr3_2:7767305-7767324 Msa0393670:CDS 30.0%
! TTTTCCAATGGAAAAGCTTT+GGG + chr3_2:7767306-7767325 Msa0393670:CDS 30.0%
CTTCTTGGATTAACAATTGA+TGG - chr3_2:7767456-7767475 None:intergenic 30.0%
TTCAAAGATTGAGGATTGTT+TGG - chr3_2:7767486-7767505 None:intergenic 30.0%
!! GTTTTGATCTTTTTCCAGTT+GGG - chr3_2:7767575-7767594 None:intergenic 30.0%
GAATGAATGGAAACAAATTG+AGG + chr3_2:7767743-7767762 Msa0393670:CDS 30.0%
ACAAATATCACACTCAAACA+CGG - chr3_2:7767814-7767833 None:intergenic 30.0%
! CAATCTAGCAAAGATCTTTT+CGG + chr3_2:7767846-7767865 Msa0393670:CDS 30.0%
!!! CTAGATTGTTAGTTTTCCTA+TGG - chr3_2:7767884-7767903 None:intergenic 30.0%
!! TGTAACAGGTCATTTTCCAA+TGG + chr3_2:7767294-7767313 Msa0393670:CDS 35.0%
!!! TTTTGGATGGATTGGTAGTT+TGG - chr3_2:7767355-7767374 None:intergenic 35.0%
AAGATTGAGGATTGTTTGGT+GGG - chr3_2:7767482-7767501 None:intergenic 35.0%
AAAGATTGAGGATTGTTTGG+TGG - chr3_2:7767483-7767502 None:intergenic 35.0%
TATTCCTACCAAAGTTTGAC+GGG - chr3_2:7767527-7767546 None:intergenic 35.0%
CTATTCCTACCAAAGTTTGA+CGG - chr3_2:7767528-7767547 None:intergenic 35.0%
!! CGTTTTGATCTTTTTCCAGT+TGG - chr3_2:7767576-7767595 None:intergenic 35.0%
CAAACCAAGACAGTTTCATA+TGG + chr3_2:7767596-7767615 Msa0393670:CDS 35.0%
AGGAAAACTAACAATCTAGC+AGG + chr3_2:7767885-7767904 Msa0393670:CDS 35.0%
TGCTTTGACATCTTTGAATC+TGG + chr3_2:7767972-7767991 Msa0393670:CDS 35.0%
!! TGTAACAGGTCATTTTCCAA+TGG + chr3_2:7767294-7767313 Msa0393670:CDS 35.0%
!!! TTTTGGATGGATTGGTAGTT+TGG - chr3_2:7767355-7767374 None:intergenic 35.0%
AAGATTGAGGATTGTTTGGT+GGG - chr3_2:7767482-7767501 None:intergenic 35.0%
AAAGATTGAGGATTGTTTGG+TGG - chr3_2:7767483-7767502 None:intergenic 35.0%
TATTCCTACCAAAGTTTGAC+GGG - chr3_2:7767527-7767546 None:intergenic 35.0%
CTATTCCTACCAAAGTTTGA+CGG - chr3_2:7767528-7767547 None:intergenic 35.0%
!! CGTTTTGATCTTTTTCCAGT+TGG - chr3_2:7767576-7767595 None:intergenic 35.0%
CAAACCAAGACAGTTTCATA+TGG + chr3_2:7767596-7767615 Msa0393670:CDS 35.0%
AGGAAAACTAACAATCTAGC+AGG + chr3_2:7767885-7767904 Msa0393670:CDS 35.0%
TGCTTTGACATCTTTGAATC+TGG + chr3_2:7767972-7767991 Msa0393670:CDS 35.0%
GAGTGTGTCTCATTTGTAAC+AGG + chr3_2:7767280-7767299 Msa0393670:CDS 40.0%
! GATTGGTAGTTTGGCATAGT+GGG - chr3_2:7767346-7767365 None:intergenic 40.0%
! AGGTACTTGGTTGTTGATTG+GGG - chr3_2:7767379-7767398 None:intergenic 40.0%
! CAGGTACTTGGTTGTTGATT+GGG - chr3_2:7767380-7767399 None:intergenic 40.0%
TCAGGTACTTGGTTGTTGAT+TGG - chr3_2:7767381-7767400 None:intergenic 40.0%
! GATAGAGTGAGTTGGATGTT+TGG - chr3_2:7767421-7767440 None:intergenic 40.0%
GATGTAGAGATAGAGTGAGT+TGG - chr3_2:7767429-7767448 None:intergenic 40.0%
!! TTGTTTGGTGGGTTACTTCT+TGG - chr3_2:7767471-7767490 None:intergenic 40.0%
AAATGTACCCCGTCAAACTT+TGG + chr3_2:7767516-7767535 Msa0393670:CDS 40.0%
ATTCCTACCAAAGTTTGACG+GGG - chr3_2:7767526-7767545 None:intergenic 40.0%
TCTTATCCAACAAACCCAAC+TGG + chr3_2:7767558-7767577 Msa0393670:CDS 40.0%
! CTTTTTCCAGTTGGGTTTGT+TGG - chr3_2:7767567-7767586 None:intergenic 40.0%
TCAGCCATATGAAACTGTCT+TGG - chr3_2:7767603-7767622 None:intergenic 40.0%
ACAATCAGCGTATAGCGATT+TGG + chr3_2:7767683-7767702 Msa0393670:CDS 40.0%
ATAGAAGCTGCTGAAACACT+AGG + chr3_2:7767708-7767727 Msa0393670:CDS 40.0%
TCGGACATGAAGATATCCAT+AGG + chr3_2:7767865-7767884 Msa0393670:CDS 40.0%
AACAATCTAGCAGGAGAGAT+TGG + chr3_2:7767894-7767913 Msa0393670:CDS 40.0%
CTTTGAATCTGGTCACGTAT+TGG + chr3_2:7767983-7768002 Msa0393670:CDS 40.0%
GAGTGTGTCTCATTTGTAAC+AGG + chr3_2:7767280-7767299 Msa0393670:CDS 40.0%
! GATTGGTAGTTTGGCATAGT+GGG - chr3_2:7767346-7767365 None:intergenic 40.0%
! AGGTACTTGGTTGTTGATTG+GGG - chr3_2:7767379-7767398 None:intergenic 40.0%
! CAGGTACTTGGTTGTTGATT+GGG - chr3_2:7767380-7767399 None:intergenic 40.0%
TCAGGTACTTGGTTGTTGAT+TGG - chr3_2:7767381-7767400 None:intergenic 40.0%
! GATAGAGTGAGTTGGATGTT+TGG - chr3_2:7767421-7767440 None:intergenic 40.0%
GATGTAGAGATAGAGTGAGT+TGG - chr3_2:7767429-7767448 None:intergenic 40.0%
!! TTGTTTGGTGGGTTACTTCT+TGG - chr3_2:7767471-7767490 None:intergenic 40.0%
AAATGTACCCCGTCAAACTT+TGG + chr3_2:7767516-7767535 Msa0393670:CDS 40.0%
ATTCCTACCAAAGTTTGACG+GGG - chr3_2:7767526-7767545 None:intergenic 40.0%
TCTTATCCAACAAACCCAAC+TGG + chr3_2:7767558-7767577 Msa0393670:CDS 40.0%
! CTTTTTCCAGTTGGGTTTGT+TGG - chr3_2:7767567-7767586 None:intergenic 40.0%
TCAGCCATATGAAACTGTCT+TGG - chr3_2:7767603-7767622 None:intergenic 40.0%
ACAATCAGCGTATAGCGATT+TGG + chr3_2:7767683-7767702 Msa0393670:CDS 40.0%
ATAGAAGCTGCTGAAACACT+AGG + chr3_2:7767708-7767727 Msa0393670:CDS 40.0%
TCGGACATGAAGATATCCAT+AGG + chr3_2:7767865-7767884 Msa0393670:CDS 40.0%
AACAATCTAGCAGGAGAGAT+TGG + chr3_2:7767894-7767913 Msa0393670:CDS 40.0%
CTTTGAATCTGGTCACGTAT+TGG + chr3_2:7767983-7768002 Msa0393670:CDS 40.0%
!! TCCAATGGAAAAGCTTTGGG+AGG + chr3_2:7767309-7767328 Msa0393670:CDS 45.0%
! TCCTCCCAAAGCTTTTCCAT+TGG - chr3_2:7767313-7767332 None:intergenic 45.0%
! GGATTGGTAGTTTGGCATAG+TGG - chr3_2:7767347-7767366 None:intergenic 45.0%
!!! ATTGGGGGTTTTGGATGGAT+TGG - chr3_2:7767363-7767382 None:intergenic 45.0%
!!! TGTTGATTGGGGGTTTTGGA+TGG - chr3_2:7767368-7767387 None:intergenic 45.0%
!! TGGTTGTTGATTGGGGGTTT+TGG - chr3_2:7767372-7767391 None:intergenic 45.0%
! GGTACTTGGTTGTTGATTGG+GGG - chr3_2:7767378-7767397 None:intergenic 45.0%
CAGCTGAGTATTCAGGTACT+TGG - chr3_2:7767392-7767411 None:intergenic 45.0%
ACCTGAATACTCAGCTGAGT+TGG + chr3_2:7767395-7767414 Msa0393670:CDS 45.0%
TGAATCTGGTCACGTATTGG+AGG + chr3_2:7767986-7768005 Msa0393670:CDS 45.0%
CGTATTGGAGGAACACATGA+AGG + chr3_2:7767998-7768017 Msa0393670:CDS 45.0%
!! TCCAATGGAAAAGCTTTGGG+AGG + chr3_2:7767309-7767328 Msa0393670:CDS 45.0%
! TCCTCCCAAAGCTTTTCCAT+TGG - chr3_2:7767313-7767332 None:intergenic 45.0%
! GGATTGGTAGTTTGGCATAG+TGG - chr3_2:7767347-7767366 None:intergenic 45.0%
!!! ATTGGGGGTTTTGGATGGAT+TGG - chr3_2:7767363-7767382 None:intergenic 45.0%
!!! TGTTGATTGGGGGTTTTGGA+TGG - chr3_2:7767368-7767387 None:intergenic 45.0%
!! TGGTTGTTGATTGGGGGTTT+TGG - chr3_2:7767372-7767391 None:intergenic 45.0%
! GGTACTTGGTTGTTGATTGG+GGG - chr3_2:7767378-7767397 None:intergenic 45.0%
CAGCTGAGTATTCAGGTACT+TGG - chr3_2:7767392-7767411 None:intergenic 45.0%
ACCTGAATACTCAGCTGAGT+TGG + chr3_2:7767395-7767414 Msa0393670:CDS 45.0%
TGAATCTGGTCACGTATTGG+AGG + chr3_2:7767986-7768005 Msa0393670:CDS 45.0%
CGTATTGGAGGAACACATGA+AGG + chr3_2:7767998-7768017 Msa0393670:CDS 45.0%
GCCAACTCAGCTGAGTATTC+AGG - chr3_2:7767399-7767418 None:intergenic 50.0%
GTACCCCGTCAAACTTTGGT+AGG + chr3_2:7767520-7767539 Msa0393670:CDS 50.0%
GCAGGAGAGATTGGTAGAAG+TGG + chr3_2:7767903-7767922 Msa0393670:CDS 50.0%
GCCAACTCAGCTGAGTATTC+AGG - chr3_2:7767399-7767418 None:intergenic 50.0%
GTACCCCGTCAAACTTTGGT+AGG + chr3_2:7767520-7767539 Msa0393670:CDS 50.0%
GCAGGAGAGATTGGTAGAAG+TGG + chr3_2:7767903-7767922 Msa0393670:CDS 50.0%
Chromosome Type Strat End Strand Name
chr3_2 gene 7767264 7768055 7767264 ID=Msa0393670;Name=Msa0393670
chr3_2 mRNA 7767264 7768055 7767264 ID=Msa0393670-mRNA-1;Parent=Msa0393670;Name=Msa0393670-mRNA-1;_AED=0.00;_eAED=0.00;_QI=0|-1|0|1|-1|1|1|0|263
chr3_2 exon 7767264 7768055 7767264 ID=Msa0393670-mRNA-1:exon:2003;Parent=Msa0393670-mRNA-1
chr3_2 CDS 7767264 7768055 7767264 ID=Msa0393670-mRNA-1:cds;Parent=Msa0393670-mRNA-1
Gene Sequence

>Msa0393670

ATGGAGAACAATGGTAGAGTGTGTCTCATTTGTAACAGGTCATTTTCCAATGGAAAAGCTTTGGGAGGACATATGAAATCCCACTATGCCAAACTACCAATCCATCCAAAACCCCCAATCAACAACCAAGTACCTGAATACTCAGCTGAGTTGGCCAAACATCCAACTCACTCTATCTCTACATCTTCACCATCAATTGTTAATCCAAGAAGTAACCCACCAAACAATCCTCAATCTTTGAAAGTGAAATTCAAATGTACCCCGTCAAACTTTGGTAGGAATAGTGTGTTTCAGTCTTATCCAACAAACCCAACTGGAAAAAGATCAAAACGCAAACCAAGACAGTTTCATATGGCTGAAGAAAGAGAAGAGAATATAGAATTTAACATGGCTGAAGAAAAAGAAGATAATACACAATTACAATCAGCGTATAGCGATTTGGATATAGAAGCTGCTGAAACACTAGGTGTTATTCTTAAGAATGAATGGAAACAAATTGAGGACAAATACTACACTGAGAAGAAAAAAGCAAGTGAAAATGGAAACACCGTGTTTGAGTGTGATATTTGTCATGAAGTGTTTCAATCTAGCAAAGATCTTTTCGGACATGAAGATATCCATAGGAAAACTAACAATCTAGCAGGAGAGATTGGTAGAAGTGGAAACATATATGATGTCGTAAATGAAAAAGTGCATAAGTGCGAATATTGCTTTGACATCTTTGAATCTGGTCACGTATTGGAGGAACACATGAAGGTACACCTATACAATTATTATGATTCTGACCCATAG

Protein sequence

>Msa0393670

MENNGRVCLICNRSFSNGKALGGHMKSHYAKLPIHPKPPINNQVPEYSAELAKHPTHSISTSSPSIVNPRSNPPNNPQSLKVKFKCTPSNFGRNSVFQSYPTNPTGKRSKRKPRQFHMAEEREENIEFNMAEEKEDNTQLQSAYSDLDIEAAETLGVILKNEWKQIEDKYYTEKKKASENGNTVFECDICHEVFQSSKDLFGHEDIHRKTNNLAGEIGRSGNIYDVVNEKVHKCEYCFDIFESGHVLEEHMKVHLYNYYDSDP*