AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0488980


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0488980 MtrunA17_Chr3g0079061 85.455 275 28 1 1 263 1 275 3.09e-173 478
Msa0488980 MtrunA17_Chr3g0079131 64.493 276 84 3 1 263 1 275 1.72e-114 330
Msa0488980 MtrunA17_Chr3g0079091 76.836 177 29 1 1 165 1 177 2.02e-83 247
Msa0488980 MtrunA17_Chr4g0018761 29.688 256 154 6 3 255 4 236 3.91e-24 97.4
Msa0488980 MtrunA17_Chr7g0231181 26.471 306 165 10 8 255 6 309 2.16e-14 72.0
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0488980 AT3G60580.1 27.138 269 146 10 8 254 6 246 3.33e-14 71.2
Msa0488980 AT1G02030.1 25.692 253 154 8 8 254 7 231 5.50e-12 64.7

Find 43 sgRNAs with CRISPR-Local

Find 112 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TTGTTTGTTGGGTTATTTCT+TGG 0.241989 3_4:-9138407 None:intergenic
CAGGTACTTGGTTGTTGATT+GGG 0.275325 3_4:-9138316 None:intergenic
TCAGGTACTTGGTTGTTGAT+TGG 0.290946 3_4:-9138317 None:intergenic
GCCAACTCAGCTGAGTATTC+AGG 0.304238 3_4:-9138335 None:intergenic
TGCTTTGACATCTTTGAATC+TGG 0.309104 3_4:+9138911 Msa0488980:CDS
TTTCTTGGATTAACAATTGA+TGG 0.326711 3_4:-9138392 None:intergenic
ACAATCAGCGTATAGTGATT+TGG 0.373049 3_4:+9138622 Msa0488980:CDS
CTTTGAATCTGGTCATGTAT+TGG 0.374462 3_4:+9138922 Msa0488980:CDS
AAGATTGAGGATTGTTTGTT+GGG 0.385971 3_4:-9138418 None:intergenic
CAGCTGAGTATTCAGGTACT+TGG 0.400249 3_4:-9138328 None:intergenic
AAAGATTGAGGATTGTTTGT+TGG 0.403304 3_4:-9138419 None:intergenic
TGTCATGAAGTGTTTCAATC+TGG 0.407883 3_4:+9138770 Msa0488980:CDS
GAGTGTGTCTCATTTGTAAC+AGG 0.418825 3_4:+9138219 Msa0488980:CDS
AGGTACTTGGTTGTTGATTG+GGG 0.434003 3_4:-9138315 None:intergenic
CAGAATCATAATAATTGTAT+AGG 0.437191 3_4:-9138964 None:intergenic
GTGTTATTCTTAAGAATGAA+TGG 0.439493 3_4:+9138669 Msa0488980:CDS
AATTTCACTTTCAAAGATTG+AGG 0.444853 3_4:-9138431 None:intergenic
AAATGTACCCCGTCAAACTT+TGG 0.446972 3_4:+9138455 Msa0488980:CDS
TATTCCTACCAAAGTTTGAC+GGG 0.447395 3_4:-9138463 None:intergenic
GATAGAGTGAGTTGGATGTT+TGG 0.448812 3_4:-9138357 None:intergenic
AACAATCTAGCAGGAGAGAT+TGG 0.456742 3_4:+9138833 Msa0488980:CDS
GGATTGGTAGTTTGGCATAG+TGG 0.460724 3_4:-9138283 None:intergenic
TCTTATCCAACAAACCCAAC+TGG 0.466226 3_4:+9138497 Msa0488980:CDS
TCAGCCATATGAAACTGTCT+TGG 0.489788 3_4:-9138539 None:intergenic
GATGTAGAGATAGAGTGAGT+TGG 0.497788 3_4:-9138365 None:intergenic
TGAATCTGGTCATGTATTGG+AGG 0.500943 3_4:+9138925 Msa0488980:CDS
TTATTCCTACCAAAGTTTGA+CGG 0.514338 3_4:-9138464 None:intergenic
GATTGGTAGTTTGGCATAGT+GGG 0.520357 3_4:-9138282 None:intergenic
CAAACCAAGACAGTTTCATA+TGG 0.521057 3_4:+9138535 Msa0488980:CDS
GCAGGAGAGATTGGTAGAAG+TGG 0.524466 3_4:+9138842 Msa0488980:CDS
AGGAAAACTAACAATCTAGC+AGG 0.531732 3_4:+9138824 Msa0488980:CDS
ACCTGAATACTCAGCTGAGT+TGG 0.539000 3_4:+9138334 Msa0488980:CDS
TTGGACATGAAGAGATCCAT+AGG 0.540507 3_4:+9138804 Msa0488980:CDS
GGTACTTGGTTGTTGATTGG+GGG 0.573211 3_4:-9138314 None:intergenic
GAATGAATGGAAACAAATTG+AGG 0.585752 3_4:+9138682 Msa0488980:CDS
TGTATTGGAGGAACACATGA+AGG 0.585882 3_4:+9138937 Msa0488980:CDS
TCCAATGGAAAAGCTTTGGG+AGG 0.590411 3_4:+9138248 Msa0488980:CDS
ATAGAAGCTGCTGAAACACT+AGG 0.609115 3_4:+9138647 Msa0488980:CDS
GTACCCCGTCAAACTTTGGT+AGG 0.631191 3_4:+9138459 Msa0488980:CDS
ACAAATATCACACTCAAACA+CGG 0.640237 3_4:-9138750 None:intergenic
TCTCCAACTATGGAGAACAA+TGG 0.649885 3_4:+9138194 None:intergenic
AGAGAATACACAATTTAACA+TGG 0.696888 3_4:+9138571 Msa0488980:CDS
ATTCCTACCAAAGTTTGACG+GGG 0.736639 3_4:-9138462 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! CAGAATCATAATAATTGTAT+AGG - chr3_4:9138967-9138986 None:intergenic 20.0%
!! CAGAATCATAATAATTGTAT+AGG - chr3_4:9138967-9138986 None:intergenic 20.0%
! TTTCTTGGATTAACAATTGA+TGG - chr3_4:9138395-9138414 None:intergenic 25.0%
! AATTTCACTTTCAAAGATTG+AGG - chr3_4:9138434-9138453 None:intergenic 25.0%
! AGAGAATACACAATTTAACA+TGG + chr3_4:9138571-9138590 Msa0488980:CDS 25.0%
!! GTGTTATTCTTAAGAATGAA+TGG + chr3_4:9138669-9138688 Msa0488980:CDS 25.0%
! AAGAAAAAAGCAAGTGAAAA+TGG + chr3_4:9138722-9138741 Msa0488980:CDS 25.0%
! TTTCTTGGATTAACAATTGA+TGG - chr3_4:9138395-9138414 None:intergenic 25.0%
! AATTTCACTTTCAAAGATTG+AGG - chr3_4:9138434-9138453 None:intergenic 25.0%
! AGAGAATACACAATTTAACA+TGG + chr3_4:9138571-9138590 Msa0488980:CDS 25.0%
!! GTGTTATTCTTAAGAATGAA+TGG + chr3_4:9138669-9138688 Msa0488980:CDS 25.0%
! AAGAAAAAAGCAAGTGAAAA+TGG + chr3_4:9138722-9138741 Msa0488980:CDS 25.0%
! ATTTTCCAATGGAAAAGCTT+TGG + chr3_4:9138244-9138263 Msa0488980:CDS 30.0%
! TTTTCCAATGGAAAAGCTTT+GGG + chr3_4:9138245-9138264 Msa0488980:CDS 30.0%
!! TTGTTTGTTGGGTTATTTCT+TGG - chr3_4:9138410-9138429 None:intergenic 30.0%
AAGATTGAGGATTGTTTGTT+GGG - chr3_4:9138421-9138440 None:intergenic 30.0%
AAAGATTGAGGATTGTTTGT+TGG - chr3_4:9138422-9138441 None:intergenic 30.0%
TTATTCCTACCAAAGTTTGA+CGG - chr3_4:9138467-9138486 None:intergenic 30.0%
!! GTTTTGATCTTTTTCCAGTT+GGG - chr3_4:9138514-9138533 None:intergenic 30.0%
GAATGAATGGAAACAAATTG+AGG + chr3_4:9138682-9138701 Msa0488980:CDS 30.0%
ACAAATATCACACTCAAACA+CGG - chr3_4:9138753-9138772 None:intergenic 30.0%
!!! CTAGATTGTTAGTTTTCCTA+TGG - chr3_4:9138823-9138842 None:intergenic 30.0%
! ATTTTCCAATGGAAAAGCTT+TGG + chr3_4:9138244-9138263 Msa0488980:CDS 30.0%
! TTTTCCAATGGAAAAGCTTT+GGG + chr3_4:9138245-9138264 Msa0488980:CDS 30.0%
!! TTGTTTGTTGGGTTATTTCT+TGG - chr3_4:9138410-9138429 None:intergenic 30.0%
AAGATTGAGGATTGTTTGTT+GGG - chr3_4:9138421-9138440 None:intergenic 30.0%
AAAGATTGAGGATTGTTTGT+TGG - chr3_4:9138422-9138441 None:intergenic 30.0%
TTATTCCTACCAAAGTTTGA+CGG - chr3_4:9138467-9138486 None:intergenic 30.0%
!! GTTTTGATCTTTTTCCAGTT+GGG - chr3_4:9138514-9138533 None:intergenic 30.0%
GAATGAATGGAAACAAATTG+AGG + chr3_4:9138682-9138701 Msa0488980:CDS 30.0%
ACAAATATCACACTCAAACA+CGG - chr3_4:9138753-9138772 None:intergenic 30.0%
!!! CTAGATTGTTAGTTTTCCTA+TGG - chr3_4:9138823-9138842 None:intergenic 30.0%
!! TGTAACAGGTCATTTTCCAA+TGG + chr3_4:9138233-9138252 Msa0488980:CDS 35.0%
!!! TTTTGGATGGATTGGTAGTT+TGG - chr3_4:9138294-9138313 None:intergenic 35.0%
TATTCCTACCAAAGTTTGAC+GGG - chr3_4:9138466-9138485 None:intergenic 35.0%
!! CGTTTTGATCTTTTTCCAGT+TGG - chr3_4:9138515-9138534 None:intergenic 35.0%
CAAACCAAGACAGTTTCATA+TGG + chr3_4:9138535-9138554 Msa0488980:CDS 35.0%
ACAATCAGCGTATAGTGATT+TGG + chr3_4:9138622-9138641 Msa0488980:CDS 35.0%
! TGTCATGAAGTGTTTCAATC+TGG + chr3_4:9138770-9138789 Msa0488980:CDS 35.0%
! CAATCTGGCAAAGATCTTTT+TGG + chr3_4:9138785-9138804 Msa0488980:CDS 35.0%
AGGAAAACTAACAATCTAGC+AGG + chr3_4:9138824-9138843 Msa0488980:CDS 35.0%
TGCTTTGACATCTTTGAATC+TGG + chr3_4:9138911-9138930 Msa0488980:CDS 35.0%
CTTTGAATCTGGTCATGTAT+TGG + chr3_4:9138922-9138941 Msa0488980:CDS 35.0%
!! TGTAACAGGTCATTTTCCAA+TGG + chr3_4:9138233-9138252 Msa0488980:CDS 35.0%
!!! TTTTGGATGGATTGGTAGTT+TGG - chr3_4:9138294-9138313 None:intergenic 35.0%
TATTCCTACCAAAGTTTGAC+GGG - chr3_4:9138466-9138485 None:intergenic 35.0%
!! CGTTTTGATCTTTTTCCAGT+TGG - chr3_4:9138515-9138534 None:intergenic 35.0%
CAAACCAAGACAGTTTCATA+TGG + chr3_4:9138535-9138554 Msa0488980:CDS 35.0%
ACAATCAGCGTATAGTGATT+TGG + chr3_4:9138622-9138641 Msa0488980:CDS 35.0%
! TGTCATGAAGTGTTTCAATC+TGG + chr3_4:9138770-9138789 Msa0488980:CDS 35.0%
! CAATCTGGCAAAGATCTTTT+TGG + chr3_4:9138785-9138804 Msa0488980:CDS 35.0%
AGGAAAACTAACAATCTAGC+AGG + chr3_4:9138824-9138843 Msa0488980:CDS 35.0%
TGCTTTGACATCTTTGAATC+TGG + chr3_4:9138911-9138930 Msa0488980:CDS 35.0%
CTTTGAATCTGGTCATGTAT+TGG + chr3_4:9138922-9138941 Msa0488980:CDS 35.0%
GAGTGTGTCTCATTTGTAAC+AGG + chr3_4:9138219-9138238 Msa0488980:CDS 40.0%
! GATTGGTAGTTTGGCATAGT+GGG - chr3_4:9138285-9138304 None:intergenic 40.0%
! AGGTACTTGGTTGTTGATTG+GGG - chr3_4:9138318-9138337 None:intergenic 40.0%
! CAGGTACTTGGTTGTTGATT+GGG - chr3_4:9138319-9138338 None:intergenic 40.0%
TCAGGTACTTGGTTGTTGAT+TGG - chr3_4:9138320-9138339 None:intergenic 40.0%
! GATAGAGTGAGTTGGATGTT+TGG - chr3_4:9138360-9138379 None:intergenic 40.0%
GATGTAGAGATAGAGTGAGT+TGG - chr3_4:9138368-9138387 None:intergenic 40.0%
AAATGTACCCCGTCAAACTT+TGG + chr3_4:9138455-9138474 Msa0488980:CDS 40.0%
ATTCCTACCAAAGTTTGACG+GGG - chr3_4:9138465-9138484 None:intergenic 40.0%
TCTTATCCAACAAACCCAAC+TGG + chr3_4:9138497-9138516 Msa0488980:CDS 40.0%
! CTTTTTCCAGTTGGGTTTGT+TGG - chr3_4:9138506-9138525 None:intergenic 40.0%
TCAGCCATATGAAACTGTCT+TGG - chr3_4:9138542-9138561 None:intergenic 40.0%
ATAGAAGCTGCTGAAACACT+AGG + chr3_4:9138647-9138666 Msa0488980:CDS 40.0%
TTGGACATGAAGAGATCCAT+AGG + chr3_4:9138804-9138823 Msa0488980:CDS 40.0%
AACAATCTAGCAGGAGAGAT+TGG + chr3_4:9138833-9138852 Msa0488980:CDS 40.0%
TGAATCTGGTCATGTATTGG+AGG + chr3_4:9138925-9138944 Msa0488980:CDS 40.0%
TGTATTGGAGGAACACATGA+AGG + chr3_4:9138937-9138956 Msa0488980:CDS 40.0%
GAGTGTGTCTCATTTGTAAC+AGG + chr3_4:9138219-9138238 Msa0488980:CDS 40.0%
! GATTGGTAGTTTGGCATAGT+GGG - chr3_4:9138285-9138304 None:intergenic 40.0%
! AGGTACTTGGTTGTTGATTG+GGG - chr3_4:9138318-9138337 None:intergenic 40.0%
! CAGGTACTTGGTTGTTGATT+GGG - chr3_4:9138319-9138338 None:intergenic 40.0%
TCAGGTACTTGGTTGTTGAT+TGG - chr3_4:9138320-9138339 None:intergenic 40.0%
! GATAGAGTGAGTTGGATGTT+TGG - chr3_4:9138360-9138379 None:intergenic 40.0%
GATGTAGAGATAGAGTGAGT+TGG - chr3_4:9138368-9138387 None:intergenic 40.0%
AAATGTACCCCGTCAAACTT+TGG + chr3_4:9138455-9138474 Msa0488980:CDS 40.0%
ATTCCTACCAAAGTTTGACG+GGG - chr3_4:9138465-9138484 None:intergenic 40.0%
TCTTATCCAACAAACCCAAC+TGG + chr3_4:9138497-9138516 Msa0488980:CDS 40.0%
! CTTTTTCCAGTTGGGTTTGT+TGG - chr3_4:9138506-9138525 None:intergenic 40.0%
TCAGCCATATGAAACTGTCT+TGG - chr3_4:9138542-9138561 None:intergenic 40.0%
ATAGAAGCTGCTGAAACACT+AGG + chr3_4:9138647-9138666 Msa0488980:CDS 40.0%
TTGGACATGAAGAGATCCAT+AGG + chr3_4:9138804-9138823 Msa0488980:CDS 40.0%
AACAATCTAGCAGGAGAGAT+TGG + chr3_4:9138833-9138852 Msa0488980:CDS 40.0%
TGAATCTGGTCATGTATTGG+AGG + chr3_4:9138925-9138944 Msa0488980:CDS 40.0%
TGTATTGGAGGAACACATGA+AGG + chr3_4:9138937-9138956 Msa0488980:CDS 40.0%
!! TCCAATGGAAAAGCTTTGGG+AGG + chr3_4:9138248-9138267 Msa0488980:CDS 45.0%
! TCCTCCCAAAGCTTTTCCAT+TGG - chr3_4:9138252-9138271 None:intergenic 45.0%
! GGATTGGTAGTTTGGCATAG+TGG - chr3_4:9138286-9138305 None:intergenic 45.0%
!!! ATTGGGGGTTTTGGATGGAT+TGG - chr3_4:9138302-9138321 None:intergenic 45.0%
!!! TGTTGATTGGGGGTTTTGGA+TGG - chr3_4:9138307-9138326 None:intergenic 45.0%
!! TGGTTGTTGATTGGGGGTTT+TGG - chr3_4:9138311-9138330 None:intergenic 45.0%
! GGTACTTGGTTGTTGATTGG+GGG - chr3_4:9138317-9138336 None:intergenic 45.0%
CAGCTGAGTATTCAGGTACT+TGG - chr3_4:9138331-9138350 None:intergenic 45.0%
ACCTGAATACTCAGCTGAGT+TGG + chr3_4:9138334-9138353 Msa0488980:CDS 45.0%
!! TCCAATGGAAAAGCTTTGGG+AGG + chr3_4:9138248-9138267 Msa0488980:CDS 45.0%
! TCCTCCCAAAGCTTTTCCAT+TGG - chr3_4:9138252-9138271 None:intergenic 45.0%
! GGATTGGTAGTTTGGCATAG+TGG - chr3_4:9138286-9138305 None:intergenic 45.0%
!!! ATTGGGGGTTTTGGATGGAT+TGG - chr3_4:9138302-9138321 None:intergenic 45.0%
!!! TGTTGATTGGGGGTTTTGGA+TGG - chr3_4:9138307-9138326 None:intergenic 45.0%
!! TGGTTGTTGATTGGGGGTTT+TGG - chr3_4:9138311-9138330 None:intergenic 45.0%
! GGTACTTGGTTGTTGATTGG+GGG - chr3_4:9138317-9138336 None:intergenic 45.0%
CAGCTGAGTATTCAGGTACT+TGG - chr3_4:9138331-9138350 None:intergenic 45.0%
ACCTGAATACTCAGCTGAGT+TGG + chr3_4:9138334-9138353 Msa0488980:CDS 45.0%
GCCAACTCAGCTGAGTATTC+AGG - chr3_4:9138338-9138357 None:intergenic 50.0%
GTACCCCGTCAAACTTTGGT+AGG + chr3_4:9138459-9138478 Msa0488980:CDS 50.0%
GCAGGAGAGATTGGTAGAAG+TGG + chr3_4:9138842-9138861 Msa0488980:CDS 50.0%
GCCAACTCAGCTGAGTATTC+AGG - chr3_4:9138338-9138357 None:intergenic 50.0%
GTACCCCGTCAAACTTTGGT+AGG + chr3_4:9138459-9138478 Msa0488980:CDS 50.0%
GCAGGAGAGATTGGTAGAAG+TGG + chr3_4:9138842-9138861 Msa0488980:CDS 50.0%
Chromosome Type Strat End Strand Name
chr3_4 gene 9138203 9138994 9138203 ID=Msa0488980;Name=Msa0488980
chr3_4 mRNA 9138203 9138994 9138203 ID=Msa0488980-mRNA-1;Parent=Msa0488980;Name=Msa0488980-mRNA-1;_AED=0.00;_eAED=0.00;_QI=0|-1|0|1|-1|1|1|0|263
chr3_4 exon 9138203 9138994 9138203 ID=Msa0488980-mRNA-1:exon:3000;Parent=Msa0488980-mRNA-1
chr3_4 CDS 9138203 9138994 9138203 ID=Msa0488980-mRNA-1:cds;Parent=Msa0488980-mRNA-1
Gene Sequence

>Msa0488980

ATGGAGAACAATGGTAGAGTGTGTCTCATTTGTAACAGGTCATTTTCCAATGGAAAAGCTTTGGGAGGACATATGAAATCCCACTATGCCAAACTACCAATCCATCCAAAACCCCCAATCAACAACCAAGTACCTGAATACTCAGCTGAGTTGGCCAAACATCCAACTCACTCTATCTCTACATCTTCACCATCAATTGTTAATCCAAGAAATAACCCAACAAACAATCCTCAATCTTTGAAAGTGAAATTCAAATGTACCCCGTCAAACTTTGGTAGGAATAATGTGTTTCAGTCTTATCCAACAAACCCAACTGGAAAAAGATCAAAACGCAAACCAAGACAGTTTCATATGGCTGAAGAAAGAGAAGAGAATACACAATTTAACATGGCTGAAGAAAAAGAAGATAATACACAATTACAATCAGCGTATAGTGATTTGGATATAGAAGCTGCTGAAACACTAGGTGTTATTCTTAAGAATGAATGGAAACAAATTGAGGACAAATACTACACTGAGAAGAAAAAAGCAAGTGAAAATGGAAACACCGTGTTTGAGTGTGATATTTGTCATGAAGTGTTTCAATCTGGCAAAGATCTTTTTGGACATGAAGAGATCCATAGGAAAACTAACAATCTAGCAGGAGAGATTGGTAGAAGTGGAAACATATATGATGTCGTAAATGAAAAAGTGCATAAGTGCGAATATTGCTTTGACATCTTTGAATCTGGTCATGTATTGGAGGAACACATGAAGGTACACCTATACAATTATTATGATTCTGACCCATAG

Protein sequence

>Msa0488980

MENNGRVCLICNRSFSNGKALGGHMKSHYAKLPIHPKPPINNQVPEYSAELAKHPTHSISTSSPSIVNPRNNPTNNPQSLKVKFKCTPSNFGRNNVFQSYPTNPTGKRSKRKPRQFHMAEEREENTQFNMAEEKEDNTQLQSAYSDLDIEAAETLGVILKNEWKQIEDKYYTEKKKASENGNTVFECDICHEVFQSGKDLFGHEEIHRKTNNLAGEIGRSGNIYDVVNEKVHKCEYCFDIFESGHVLEEHMKVHLYNYYDSDP*