AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0626140

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0626140 MtrunA17_Chr4g0002211 91.089 202 18 0 1 202 49 250 9.15e-123 347
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 52 sgRNAs with CRISPR-Local

Find 61 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
ATGAGGTTGGAGAAAATATC+AGG 0.281886 4_3:+5511369 Msa0626140:CDS
TTCGGTGAAACCGTCGCATT+TGG 0.282536 4_3:-5510884 None:intergenic
CGCACCCTTCTTGCAATTCA+AGG 0.341656 4_3:-5511452 None:intergenic
GCGAAATGGAGAAGAGAGTT+AGG 0.346518 4_3:+5511186 Msa0626140:CDS
TTGTTATTGTTCTCCGGTGC+CGG 0.383054 4_3:-5511108 None:intergenic
TGGCTGCTGCGACGTCGTTT+TGG 0.398824 4_3:+5511295 Msa0626140:CDS
TTCCTCTTGTTATTGTTCTC+CGG 0.408628 4_3:-5511114 None:intergenic
AACAAGAGGAAGAAGATGAT+TGG 0.414945 4_3:+5511126 Msa0626140:CDS
CGAAATGGAGAAGAGAGTTA+GGG 0.429114 4_3:+5511187 Msa0626140:CDS
CGGAGGAGATATTTGCGAAA+TGG 0.441862 4_3:+5511172 Msa0626140:CDS
ACAAGAGGAAGAAGATGATT+GGG 0.446433 4_3:+5511127 Msa0626140:CDS
TTCCGGTGAGCAAGAGCGGC+AGG 0.464761 4_3:-5510950 None:intergenic
GTCGCAGCAGCCACCTTCAC+CGG 0.482296 4_3:-5511285 None:intergenic
AGTGCCGGAGATATGAATTT+CGG 0.485587 4_3:-5510902 None:intergenic
GAGAACGTGGAAGTTACTTC+CGG 0.494776 4_3:+5511266 Msa0626140:CDS
GTGGCTAAAATAAGCTTAGC+TGG 0.495492 4_3:-5511396 None:intergenic
TTCACCGAAATTCATATCTC+CGG 0.509514 4_3:+5510898 Msa0626140:CDS
GTGTCGAAATTTGATGAGGT+TGG 0.526675 4_3:+5511356 Msa0626140:CDS
GCCACACGATCACCGTTCAC+CGG 0.535889 4_3:-5511219 None:intergenic
AACCTGCCGCTCTTGCTCAC+CGG 0.536391 4_3:+5510948 Msa0626140:CDS
CGATGATACATCTCCGGCAC+CGG 0.539008 4_3:+5511095 Msa0626140:CDS
GAACGGTGATCGTGTGGCGG+TGG 0.541705 4_3:+5511224 Msa0626140:CDS
TGAGGTTGGAGAAAATATCA+GGG 0.543347 4_3:+5511370 Msa0626140:CDS
TCGTGTGGCGGTGGAAGCTA+TGG 0.543504 4_3:+5511233 Msa0626140:CDS
ACGGTGGTGTAGTGTAGTGC+CGG 0.554858 4_3:-5510917 None:intergenic
AACACCTTGAATTGCAAGAA+GGG 0.556767 4_3:+5511448 Msa0626140:CDS
TCACCGGAAAATCATTCCTC+CGG 0.557681 4_3:+5510964 Msa0626140:CDS
TGAAAGTGTTGGATCGGTGG+CGG 0.559970 4_3:+5511152 Msa0626140:CDS
AAGTGTTGGATCGGTGGCGG+AGG 0.560614 4_3:+5511155 Msa0626140:CDS
AGATTGAGAACTCGCCTCAC+CGG 0.561454 4_3:-5510983 None:intergenic
GACTGAAAGTGTTGGATCGG+TGG 0.563595 4_3:+5511149 Msa0626140:CDS
TCCGGTGAACGGTGATCGTG+TGG 0.570131 4_3:+5511218 Msa0626140:CDS
CAACACCTTGAATTGCAAGA+AGG 0.572050 4_3:+5511447 Msa0626140:CDS
GTGGAAGTTACTTCCGGTGA+AGG 0.577957 4_3:+5511272 Msa0626140:CDS
ATGATTGGGACTGAAAGTGT+TGG 0.593930 4_3:+5511141 Msa0626140:CDS
TGTTACCGATGATACATCTC+CGG 0.594095 4_3:+5511089 Msa0626140:CDS
GAAGTTACTTCCGGTGAAGG+TGG 0.596707 4_3:+5511275 Msa0626140:CDS
ATCTTGTGCTCCAAATGCGA+CGG 0.602290 4_3:+5510874 None:intergenic
AGCGGCAGGTTGATGAGAGA+CGG 0.602586 4_3:-5510936 None:intergenic
CACCGGAGAACAATAACAAG+AGG 0.613856 4_3:+5511112 Msa0626140:CDS
CCACGTGTCGAAATTTGATG+AGG 0.617602 4_3:+5511352 Msa0626140:CDS
TGGGACTGAAAGTGTTGGAT+CGG 0.630097 4_3:+5511146 Msa0626140:CDS
CCTCATCAAATTTCGACACG+TGG 0.641370 4_3:-5511352 None:intergenic
TGTGGCGGTGGAAGCTATGG+CGG 0.643579 4_3:+5511236 Msa0626140:CDS
TTGAGAACTCGCCTCACCGG+AGG 0.643923 4_3:-5510980 None:intergenic
CGGTGCCGGAGATGTATCAT+CGG 0.645343 4_3:-5511094 None:intergenic
GGTGAACGGTGATCGTGTGG+CGG 0.678941 4_3:+5511221 Msa0626140:CDS
GGAAAATCATTCCTCCGGTG+AGG 0.685941 4_3:+5510969 Msa0626140:CDS
ACGTGCGAGTTTCACATGTG+TGG 0.691088 4_3:-5511415 None:intergenic
GGCAGGTTGATGAGAGACGG+TGG 0.691500 4_3:-5510933 None:intergenic
TGGCGGTGTGTATGAGAACG+TGG 0.692845 4_3:+5511253 Msa0626140:CDS
GAGGTTGGAGAAAATATCAG+GGG 0.723090 4_3:+5511371 Msa0626140:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
TTCACCGAAATTCATATCTC+CGG + chr4_3:5510898-5510917 Msa0626140:CDS 35.0%
!! TTCCTCTTGTTATTGTTCTC+CGG - chr4_3:5511117-5511136 None:intergenic 35.0%
AACAAGAGGAAGAAGATGAT+TGG + chr4_3:5511126-5511145 Msa0626140:CDS 35.0%
ACAAGAGGAAGAAGATGATT+GGG + chr4_3:5511127-5511146 Msa0626140:CDS 35.0%
! AGAGTTAGGGTTAGATTTTC+CGG + chr4_3:5511200-5511219 Msa0626140:CDS 35.0%
ATGAGGTTGGAGAAAATATC+AGG + chr4_3:5511369-5511388 Msa0626140:CDS 35.0%
TGAGGTTGGAGAAAATATCA+GGG + chr4_3:5511370-5511389 Msa0626140:CDS 35.0%
AACACCTTGAATTGCAAGAA+GGG + chr4_3:5511448-5511467 Msa0626140:CDS 35.0%
! AGTGCCGGAGATATGAATTT+CGG - chr4_3:5510905-5510924 None:intergenic 40.0%
TGTTACCGATGATACATCTC+CGG + chr4_3:5511089-5511108 Msa0626140:CDS 40.0%
! ATGATTGGGACTGAAAGTGT+TGG + chr4_3:5511141-5511160 Msa0626140:CDS 40.0%
CGAAATGGAGAAGAGAGTTA+GGG + chr4_3:5511187-5511206 Msa0626140:CDS 40.0%
! TGGTTGGGGTTAAGATTTTG+TGG + chr4_3:5511315-5511334 Msa0626140:CDS 40.0%
! GGTTGGGGTTAAGATTTTGT+GGG + chr4_3:5511316-5511335 Msa0626140:CDS 40.0%
! GTTGGGGTTAAGATTTTGTG+GGG + chr4_3:5511317-5511336 Msa0626140:CDS 40.0%
GTGTCGAAATTTGATGAGGT+TGG + chr4_3:5511356-5511375 Msa0626140:CDS 40.0%
GAGGTTGGAGAAAATATCAG+GGG + chr4_3:5511371-5511390 Msa0626140:CDS 40.0%
GTGGCTAAAATAAGCTTAGC+TGG - chr4_3:5511399-5511418 None:intergenic 40.0%
CAACACCTTGAATTGCAAGA+AGG + chr4_3:5511447-5511466 Msa0626140:CDS 40.0%
TCACCGGAAAATCATTCCTC+CGG + chr4_3:5510964-5510983 Msa0626140:CDS 45.0%
! TCACCGGAGGAATGATTTTC+CGG - chr4_3:5510970-5510989 None:intergenic 45.0%
! TTGTTATTGTTCTCCGGTGC+CGG - chr4_3:5511111-5511130 None:intergenic 45.0%
CACCGGAGAACAATAACAAG+AGG + chr4_3:5511112-5511131 Msa0626140:CDS 45.0%
!! TGGGACTGAAAGTGTTGGAT+CGG + chr4_3:5511146-5511165 Msa0626140:CDS 45.0%
CGGAGGAGATATTTGCGAAA+TGG + chr4_3:5511172-5511191 Msa0626140:CDS 45.0%
GCGAAATGGAGAAGAGAGTT+AGG + chr4_3:5511186-5511205 Msa0626140:CDS 45.0%
! GGGTTAGATTTTCCGGTGAA+CGG + chr4_3:5511207-5511226 Msa0626140:CDS 45.0%
GAGAACGTGGAAGTTACTTC+CGG + chr4_3:5511266-5511285 Msa0626140:CDS 45.0%
CCTCATCAAATTTCGACACG+TGG - chr4_3:5511355-5511374 None:intergenic 45.0%
CCACGTGTCGAAATTTGATG+AGG + chr4_3:5511352-5511371 Msa0626140:CDS 45.0%
TTCGGTGAAACCGTCGCATT+TGG - chr4_3:5510887-5510906 None:intergenic 50.0%
! GATTTTCCGGTGAGCAAGAG+CGG - chr4_3:5510957-5510976 None:intergenic 50.0%
GGAAAATCATTCCTCCGGTG+AGG + chr4_3:5510969-5510988 Msa0626140:CDS 50.0%
AGATTGAGAACTCGCCTCAC+CGG - chr4_3:5510986-5511005 None:intergenic 50.0%
!! GACTGAAAGTGTTGGATCGG+TGG + chr4_3:5511149-5511168 Msa0626140:CDS 50.0%
!! TGAAAGTGTTGGATCGGTGG+CGG + chr4_3:5511152-5511171 Msa0626140:CDS 50.0%
GTGGAAGTTACTTCCGGTGA+AGG + chr4_3:5511272-5511291 Msa0626140:CDS 50.0%
GAAGTTACTTCCGGTGAAGG+TGG + chr4_3:5511275-5511294 Msa0626140:CDS 50.0%
ACGTGCGAGTTTCACATGTG+TGG - chr4_3:5511418-5511437 None:intergenic 50.0%
CGCACCCTTCTTGCAATTCA+AGG - chr4_3:5511455-5511474 None:intergenic 50.0%
ACGGTGGTGTAGTGTAGTGC+CGG - chr4_3:5510920-5510939 None:intergenic 55.0%
!! AGCGGCAGGTTGATGAGAGA+CGG - chr4_3:5510939-5510958 None:intergenic 55.0%
! CGGTGCCGGAGATGTATCAT+CGG - chr4_3:5511097-5511116 None:intergenic 55.0%
CGATGATACATCTCCGGCAC+CGG + chr4_3:5511095-5511114 Msa0626140:CDS 55.0%
TGGCGGTGTGTATGAGAACG+TGG + chr4_3:5511253-5511272 Msa0626140:CDS 55.0%
!! TGCTGCGACGTCGTTTTGGT+TGG + chr4_3:5511299-5511318 Msa0626140:CDS 55.0%
!!! GCTGCGACGTCGTTTTGGTT+GGG + chr4_3:5511300-5511319 Msa0626140:CDS 55.0%
!!! CTGCGACGTCGTTTTGGTTG+GGG + chr4_3:5511301-5511320 Msa0626140:CDS 55.0%
!! GGCAGGTTGATGAGAGACGG+TGG - chr4_3:5510936-5510955 None:intergenic 60.0%
AACCTGCCGCTCTTGCTCAC+CGG + chr4_3:5510948-5510967 Msa0626140:CDS 60.0%
TTGAGAACTCGCCTCACCGG+AGG - chr4_3:5510983-5511002 None:intergenic 60.0%
!! AAGTGTTGGATCGGTGGCGG+AGG + chr4_3:5511155-5511174 Msa0626140:CDS 60.0%
TCCGGTGAACGGTGATCGTG+TGG + chr4_3:5511218-5511237 Msa0626140:CDS 60.0%
GCCACACGATCACCGTTCAC+CGG - chr4_3:5511222-5511241 None:intergenic 60.0%
GGTGAACGGTGATCGTGTGG+CGG + chr4_3:5511221-5511240 Msa0626140:CDS 60.0%
TCGTGTGGCGGTGGAAGCTA+TGG + chr4_3:5511233-5511252 Msa0626140:CDS 60.0%
TGTGGCGGTGGAAGCTATGG+CGG + chr4_3:5511236-5511255 Msa0626140:CDS 60.0%
! TGGCTGCTGCGACGTCGTTT+TGG + chr4_3:5511295-5511314 Msa0626140:CDS 60.0%
TTCCGGTGAGCAAGAGCGGC+AGG - chr4_3:5510953-5510972 None:intergenic 65.0%
GAACGGTGATCGTGTGGCGG+TGG + chr4_3:5511224-5511243 Msa0626140:CDS 65.0%
GTCGCAGCAGCCACCTTCAC+CGG - chr4_3:5511288-5511307 None:intergenic 65.0%
Chromosome Type Strat End Strand Name
chr4_3 gene 5510877 5511485 5510877 ID=Msa0626140;Name=Msa0626140
chr4_3 mRNA 5510877 5511485 5510877 ID=Msa0626140-mRNA-1;Parent=Msa0626140;Name=Msa0626140-mRNA-1;_AED=0.01;_eAED=0.01;_QI=0|-1|0|1|-1|1|1|0|202
chr4_3 exon 5510877 5511485 5510877 ID=Msa0626140-mRNA-1:exon:1527;Parent=Msa0626140-mRNA-1
chr4_3 CDS 5510877 5511485 5510877 ID=Msa0626140-mRNA-1:cds;Parent=Msa0626140-mRNA-1
Gene Sequence

>Msa0626140

TTGTGCTCCAAATGCGACGGTTTCACCGAAATTCATATCTCCGGCACTACACTACACCACCGTCTCTCATCAACCTGCCGCTCTTGCTCACCGGAAAATCATTCCTCCGGTGAGGCGAGTTCTCAATCTTCTTCATCTTGCGAGTCTTGCGTTACAGAAAAGAAGAAAACAAAATCTCGAAAGATAATGAAGAGTTTTACAATTTCGAATTCTGTTACCGATGATACATCTCCGGCACCGGAGAACAATAACAAGAGGAAGAAGATGATTGGGACTGAAAGTGTTGGATCGGTGGCGGAGGAGATATTTGCGAAATGGAGAAGAGAGTTAGGGTTAGATTTTCCGGTGAACGGTGATCGTGTGGCGGTGGAAGCTATGGCGGTGTGTATGAGAACGTGGAAGTTACTTCCGGTGAAGGTGGCTGCTGCGACGTCGTTTTGGTTGGGGTTAAGATTTTGTGGGGACAATAGTTTTGCCACGTGTCGAAATTTGATGAGGTTGGAGAAAATATCAGGGGTGCCAGCTAAGCTTATTTTAGCCACACATGTGAAACTCGCACGTGTCTTTACTCAACACCTTGAATTGCAAGAAGGGTGCGATGAGTCCTAA
Protein sequence

>Msa0626140

LCSKCDGFTEIHISGTTLHHRLSSTCRSCSPENHSSGEASSQSSSSCESCVTEKKKTKSRKIMKSFTISNSVTDDTSPAPENNNKRKKMIGTESVGSVAEEIFAKWRRELGLDFPVNGDRVAVEAMAVCMRTWKLLPVKVAAATSFWLGLRFCGDNSFATCRNLMRLEKISGVPAKLILATHVKLARVFTQHLELQEGCDES*