AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene29523

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene29523.t1 MTR_5g080880 75.294 255 51 4 1 244 1 254 1.18e-122 352
MS.gene29523.t1 MTR_5g080870 66.935 248 51 5 1 245 1 220 1.99e-101 298
MS.gene29523.t1 MTR_7g063520 38.554 249 126 7 8 244 20 253 8.91e-45 151
MS.gene29523.t1 MTR_4g006560 33.793 145 92 2 104 244 91 235 7.75e-20 85.5
MS.gene29523.t1 MTR_1g013120 27.897 233 152 8 24 244 4 232 6.80e-14 69.3
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene29523.t1 AT3G55605 40.590 271 120 10 1 244 1 257 4.39e-44 149
MS.gene29523.t1 AT5G05990 35.985 264 137 7 5 244 3 258 6.23e-41 141
MS.gene29523.t1 AT2G39795 36.905 252 137 8 6 244 7 249 1.27e-39 137
MS.gene29523.t1 AT5G02050 40.758 211 100 6 55 244 60 266 5.53e-38 134
MS.gene29523.t1 AT2G39790 31.984 247 159 6 1 245 1 240 5.09e-27 104
MS.gene29523.t1 AT1G15870 29.861 144 98 3 104 244 97 240 3.18e-14 70.5
MS.gene29523.t1 AT1G80720 29.747 158 106 4 92 244 31 188 7.02e-12 62.8
MS.gene29523.t1 AT1G80720 29.747 158 106 4 92 244 83 240 1.01e-11 63.2

Find 45 sgRNAs with CRISPR-Local

Find 87 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
AGATCATCAACTATCTTAAA+TGG 0.152055 5.2:-68672712 None:intergenic
TTATCCGCAGCTTGTTTATT+AGG 0.223286 5.2:+68672938 MS.gene29523:CDS
ATCAGTTCATAAGACTTAAA+AGG 0.242549 5.2:+68672737 MS.gene29523:CDS
AAGCACAACAAATTTCTTAC+TGG 0.307443 5.2:+68673429 MS.gene29523:CDS
TAAGAAGGATGGGACCTCTT+TGG 0.326135 5.2:+68672882 MS.gene29523:CDS
CGAAGTCAAGCACTTTCGTT+AGG 0.372011 5.2:+68672225 MS.gene29523:CDS
CAAGCATTCCACTTTCAGTC+AGG 0.380172 5.2:+68672854 MS.gene29523:CDS
ATTACTTGGTGAGGCTGAAT+AGG 0.381828 5.2:+68673479 MS.gene29523:CDS
CTGCGGATAACCATCTCATC+AGG 0.394847 5.2:-68672925 None:intergenic
CTCTTATTTCTAAGTACTTG+TGG 0.408675 5.2:-68673396 None:intergenic
TTCAGTCAGGGTTTCTAAGA+AGG 0.411975 5.2:+68672867 MS.gene29523:CDS
AACAGATTTGTTATTATGAC+TGG 0.418204 5.2:+68672971 MS.gene29523:CDS
AGTAAGAAATTTGTTGTGCT+TGG 0.424406 5.2:-68673427 None:intergenic
CAAGAAAAGTAGAGATTACT+TGG 0.433788 5.2:+68673465 MS.gene29523:CDS
CACAAGTACTTAGAAATAAG+AGG 0.434165 5.2:+68673397 MS.gene29523:CDS
GATCATCAACTATCTTAAAT+GGG 0.461342 5.2:-68672711 None:intergenic
TTAGAAACCCTGACTGAAAG+TGG 0.461666 5.2:-68672862 None:intergenic
CTCGTAGCGGTTGACGGCAG+TGG 0.471104 5.2:-68672309 None:intergenic
AAGAAAAGTCTCATCGGAGT+TGG 0.473820 5.2:-68672384 None:intergenic
GAACATGATAATCATCAAAC+GGG 0.483902 5.2:+68672820 MS.gene29523:CDS
ATCGAAAATCACTTGTGCTC+AGG 0.490320 5.2:+68672418 MS.gene29523:CDS
AGAACATGATAATCATCAAA+CGG 0.497010 5.2:+68672819 MS.gene29523:CDS
AGAAAAGTCTCATCGGAGTT+GGG 0.497268 5.2:-68672383 None:intergenic
GTCAGGGTTTCTAAGAAGGA+TGG 0.501378 5.2:+68672871 MS.gene29523:CDS
TGAACCCTCGTAGCGGTTGA+CGG 0.507166 5.2:-68672315 None:intergenic
AGACTTAAAAGGACTTATCA+AGG 0.514679 5.2:+68672748 MS.gene29523:CDS
ATCTTAAATGGGAAATTGCT+CGG 0.515748 5.2:-68672700 None:intergenic
AGGTGAAGAAATTCATGTTG+AGG 0.546869 5.2:+68672768 MS.gene29523:CDS
AAGCATTCCACTTTCAGTCA+GGG 0.546965 5.2:+68672855 MS.gene29523:CDS
GAAGTCAAGCACTTTCGTTA+GGG 0.555276 5.2:+68672226 MS.gene29523:CDS
TCAGGGTTTCTAAGAAGGAT+GGG 0.578315 5.2:+68672872 MS.gene29523:CDS
TGTTGCTTACCCTGATGAGA+TGG 0.579238 5.2:+68672915 MS.gene29523:CDS
GTTTACAGCGCGGAACTCAT+CGG 0.581714 5.2:-68672444 None:intergenic
CACTGCCGTCAACCGCTACG+AGG 0.581926 5.2:+68672310 MS.gene29523:CDS
AAGTGGAATGCTTGATTGAG+TGG 0.598328 5.2:-68672845 None:intergenic
TAAAGGAAGAAAAGTCTCAT+CGG 0.606140 5.2:-68672390 None:intergenic
AAAGTAGAGATTACTTGGTG+AGG 0.619484 5.2:+68673470 MS.gene29523:CDS
GTTGACGGCAGTGGAAAGCA+CGG 0.620720 5.2:-68672300 None:intergenic
AACACAATTGAACTCCAAAG+AGG 0.630953 5.2:-68672896 None:intergenic
ACTGCCGTCAACCGCTACGA+GGG 0.639281 5.2:+68672311 MS.gene29523:CDS
GATTCCTAATAAACAAGCTG+CGG 0.642181 5.2:-68672942 None:intergenic
TCAGAAGAAAAGTGAAACGT+AGG 0.644962 5.2:-68672344 None:intergenic
AAGTGCTTGACTTCGAACGA+AGG 0.657096 5.2:-68672217 None:intergenic
TGCGGATAACCATCTCATCA+GGG 0.665501 5.2:-68672924 None:intergenic
GAACAAATGAACCCTCGTAG+CGG 0.717050 5.2:-68672322 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! ATCATGAGTTTAATAAATTA+AGG - chr5.2:68672478-68672497 None:intergenic 15.0%
!!! AAATGTTGAAAATTTGATTT+TGG + chr5.2:68672656-68672675 MS.gene29523:intron 15.0%
!! AATTGAAAGTAATACAAACA+AGG - chr5.2:68673295-68673314 None:intergenic 20.0%
!! ATGGTATGAAAATTTGAATT+TGG + chr5.2:68672601-68672620 MS.gene29523:intron 20.0%
!!! AATTTGATTTTGGTTGATAT+AGG + chr5.2:68672666-68672685 MS.gene29523:intron 20.0%
!!! ACATCAGTGATTTTAAATAA+AGG + chr5.2:68673074-68673093 MS.gene29523:intron 20.0%
!!! ATTTGATTTTGGTTGATATA+GGG + chr5.2:68672667-68672686 MS.gene29523:intron 20.0%
!!! ATTTTAAATAAAGGCTATAG+CGG + chr5.2:68673083-68673102 MS.gene29523:intron 20.0%
! AGAACATGATAATCATCAAA+CGG + chr5.2:68672819-68672838 MS.gene29523:CDS 25.0%
! AGATCATCAACTATCTTAAA+TGG - chr5.2:68672715-68672734 None:intergenic 25.0%
! ATCAGTTCATAAGACTTAAA+AGG + chr5.2:68672737-68672756 MS.gene29523:CDS 25.0%
! GATCATCAACTATCTTAAAT+GGG - chr5.2:68672714-68672733 None:intergenic 25.0%
! TATAAGTTCAAAAATGTGTC+TGG - chr5.2:68672542-68672561 None:intergenic 25.0%
! TTAATAAATTAAGGAAGACG+AGG - chr5.2:68672469-68672488 None:intergenic 25.0%
!! ATTTTCATACCATTACGAAA+TGG - chr5.2:68672594-68672613 None:intergenic 25.0%
!! GTGATTTTCGATTCAATTAA+AGG - chr5.2:68672410-68672429 None:intergenic 25.0%
!! TTTTCATACCATTACGAAAT+GGG - chr5.2:68672593-68672612 None:intergenic 25.0%
!!! AACAGATTTGTTATTATGAC+TGG + chr5.2:68672971-68672990 MS.gene29523:CDS 25.0%
AAAAAAGACCCATTTCGTAA+TGG + chr5.2:68672582-68672601 MS.gene29523:intron 30.0%
AAGCACAACAAATTTCTTAC+TGG + chr5.2:68673429-68673448 MS.gene29523:CDS 30.0%
AATCAGAATGAAGTACATAC+TGG - chr5.2:68673005-68673024 None:intergenic 30.0%
AGACTTAAAAGGACTTATCA+AGG + chr5.2:68672748-68672767 MS.gene29523:CDS 30.0%
ATCTTAAATGGGAAATTGCT+CGG - chr5.2:68672703-68672722 None:intergenic 30.0%
ATTGATCAGAAAAACTCAAC+TGG + chr5.2:68672268-68672287 MS.gene29523:CDS 30.0%
CAAGAAAAGTAGAGATTACT+TGG + chr5.2:68673465-68673484 MS.gene29523:CDS 30.0%
CACAAGTACTTAGAAATAAG+AGG + chr5.2:68673397-68673416 MS.gene29523:CDS 30.0%
GAACATGATAATCATCAAAC+GGG + chr5.2:68672820-68672839 MS.gene29523:CDS 30.0%
TAAAGGAAGAAAAGTCTCAT+CGG - chr5.2:68672393-68672412 None:intergenic 30.0%
TGAACTTATACCTTATAAGC+TGG + chr5.2:68672552-68672571 MS.gene29523:intron 30.0%
TTGATCAGAAAAACTCAACT+GGG + chr5.2:68672269-68672288 MS.gene29523:CDS 30.0%
TTTAAGCATACCAGCTTATA+AGG - chr5.2:68672565-68672584 None:intergenic 30.0%
! GTGCATTCAATATTTGAAAC+CGG + chr5.2:68673047-68673066 MS.gene29523:intron 30.0%
! TGCATTCAATATTTGAAACC+GGG + chr5.2:68673048-68673067 MS.gene29523:intron 30.0%
!! AGTAAGAAATTTGTTGTGCT+TGG - chr5.2:68673430-68673449 None:intergenic 30.0%
!! CTCTTATTTCTAAGTACTTG+TGG - chr5.2:68673399-68673418 None:intergenic 30.0%
AACACAATTGAACTCCAAAG+AGG - chr5.2:68672899-68672918 None:intergenic 35.0%
AGGTGAAGAAATTCATGTTG+AGG + chr5.2:68672768-68672787 MS.gene29523:CDS 35.0%
GATTCCTAATAAACAAGCTG+CGG - chr5.2:68672945-68672964 None:intergenic 35.0%
TAAAATCACTGATGTAACCC+CGG - chr5.2:68673069-68673088 None:intergenic 35.0%
TCAGAAGAAAAGTGAAACGT+AGG - chr5.2:68672347-68672366 None:intergenic 35.0%
TCCAAATCCCTGGAAAAAAA+TGG - chr5.2:68673355-68673374 None:intergenic 35.0%
! AAAGTAGAGATTACTTGGTG+AGG + chr5.2:68673470-68673489 MS.gene29523:CDS 35.0%
! AACTACTATTTTCCGCGATT+TGG + chr5.2:68673167-68673186 MS.gene29523:intron 35.0%
! GCATTCAATATTTGAAACCG+GGG + chr5.2:68673049-68673068 MS.gene29523:intron 35.0%
! TTATCCGCAGCTTGTTTATT+AGG + chr5.2:68672938-68672957 MS.gene29523:CDS 35.0%
!!! AGATTCTGCCATTTTTTTCC+AGG + chr5.2:68673344-68673363 MS.gene29523:intron 35.0%
!!! ATTTTGGTTGATATAGGGTG+AGG + chr5.2:68672672-68672691 MS.gene29523:intron 35.0%
!!! GATTCTGCCATTTTTTTCCA+GGG + chr5.2:68673345-68673364 MS.gene29523:intron 35.0%
!!! TGAGGTTTCGAGTTTTGATT+TGG + chr5.2:68672786-68672805 MS.gene29523:CDS 35.0%
!!! TGCAGTTCAGATTGTTGTTT+TGG + chr5.2:68673255-68673274 MS.gene29523:intron 35.0%
AAGAAAAGTCTCATCGGAGT+TGG - chr5.2:68672387-68672406 None:intergenic 40.0%
AAGCATTCCACTTTCAGTCA+GGG + chr5.2:68672855-68672874 MS.gene29523:CDS 40.0%
AAGTGGAATGCTTGATTGAG+TGG - chr5.2:68672848-68672867 None:intergenic 40.0%
AGAAAAGTCTCATCGGAGTT+GGG - chr5.2:68672386-68672405 None:intergenic 40.0%
ATCGAAAATCACTTGTGCTC+AGG + chr5.2:68672418-68672437 MS.gene29523:CDS 40.0%
CCAATCTCAATTCCAAATCG+CGG - chr5.2:68673182-68673201 None:intergenic 40.0%
CCACTATAGCTGCTATGATA+TGG - chr5.2:68673111-68673130 None:intergenic 40.0%
CCATATCATAGCAGCTATAG+TGG + chr5.2:68673108-68673127 MS.gene29523:intron 40.0%
GAAGTCAAGCACTTTCGTTA+GGG + chr5.2:68672226-68672245 MS.gene29523:CDS 40.0%
TTAGAAACCCTGACTGAAAG+TGG - chr5.2:68672865-68672884 None:intergenic 40.0%
! ATTACTTGGTGAGGCTGAAT+AGG + chr5.2:68673479-68673498 MS.gene29523:CDS 40.0%
! CGCGATTTGGAATTGAGATT+GGG + chr5.2:68673180-68673199 MS.gene29523:intron 40.0%
! GATTTGGAATTGAGATTGGG+TGG + chr5.2:68673183-68673202 MS.gene29523:intron 40.0%
! GCTATAGCACTTTTGCATAG+CGG + chr5.2:68673134-68673153 MS.gene29523:intron 40.0%
! TCAGGGTTTCTAAGAAGGAT+GGG + chr5.2:68672872-68672891 MS.gene29523:CDS 40.0%
! TTCAGTCAGGGTTTCTAAGA+AGG + chr5.2:68672867-68672886 MS.gene29523:CDS 40.0%
! TTTTTCCAGGGATTTGGATG+AGG + chr5.2:68673357-68673376 MS.gene29523:intron 40.0%
!!! GCCATTTTTTTCCAGGGATT+TGG + chr5.2:68673351-68673370 MS.gene29523:intron 40.0%
AAGTGCTTGACTTCGAACGA+AGG - chr5.2:68672220-68672239 None:intergenic 45.0%
CAAGCATTCCACTTTCAGTC+AGG + chr5.2:68672854-68672873 MS.gene29523:CDS 45.0%
CGAAGTCAAGCACTTTCGTT+AGG + chr5.2:68672225-68672244 MS.gene29523:CDS 45.0%
GAACAAATGAACCCTCGTAG+CGG - chr5.2:68672325-68672344 None:intergenic 45.0%
GTCTCTACAACAAGCAGTAC+AGG - chr5.2:68673218-68673237 None:intergenic 45.0%
TAAGAAGGATGGGACCTCTT+TGG + chr5.2:68672882-68672901 MS.gene29523:CDS 45.0%
TGCGGATAACCATCTCATCA+GGG - chr5.2:68672927-68672946 None:intergenic 45.0%
! CCGCGATTTGGAATTGAGAT+TGG + chr5.2:68673179-68673198 MS.gene29523:intron 45.0%
! GTCAGGGTTTCTAAGAAGGA+TGG + chr5.2:68672871-68672890 MS.gene29523:CDS 45.0%
! TGTTGCTTACCCTGATGAGA+TGG + chr5.2:68672915-68672934 MS.gene29523:CDS 45.0%
CTGCGGATAACCATCTCATC+AGG - chr5.2:68672928-68672947 None:intergenic 50.0%
GTTTACAGCGCGGAACTCAT+CGG - chr5.2:68672447-68672466 None:intergenic 50.0%
CAACGCCTCATCCAAATCCC+TGG - chr5.2:68673365-68673384 None:intergenic 55.0%
GGAAGACGAGGTTTACAGCG+CGG - chr5.2:68672457-68672476 None:intergenic 55.0%
GTTGACGGCAGTGGAAAGCA+CGG - chr5.2:68672303-68672322 None:intergenic 55.0%
TGAACCCTCGTAGCGGTTGA+CGG - chr5.2:68672318-68672337 None:intergenic 55.0%
ACTGCCGTCAACCGCTACGA+GGG + chr5.2:68672311-68672330 MS.gene29523:CDS 60.0%
CACTGCCGTCAACCGCTACG+AGG + chr5.2:68672310-68672329 MS.gene29523:CDS 65.0%
CTCGTAGCGGTTGACGGCAG+TGG - chr5.2:68672312-68672331 None:intergenic 65.0%


Chromosome Type Strat End Strand Name
chr5.2 gene 68672200 68673525 68672200 ID=MS.gene29523
chr5.2 mRNA 68672200 68673525 68672200 ID=MS.gene29523.t1;Parent=MS.gene29523
chr5.2 exon 68672200 68672460 68672200 ID=MS.gene29523.t1.exon1;Parent=MS.gene29523.t1
chr5.2 CDS 68672200 68672460 68672200 ID=cds.MS.gene29523.t1;Parent=MS.gene29523.t1
chr5.2 exon 68672688 68673004 68672688 ID=MS.gene29523.t1.exon2;Parent=MS.gene29523.t1
chr5.2 CDS 68672688 68673004 68672688 ID=cds.MS.gene29523.t1;Parent=MS.gene29523.t1
chr5.2 exon 68673366 68673525 68673366 ID=MS.gene29523.t1.exon3;Parent=MS.gene29523.t1
chr5.2 CDS 68673366 68673525 68673366 ID=cds.MS.gene29523.t1;Parent=MS.gene29523.t1
Gene Sequence

>MS.gene29523

ATGGCGTTCAATTCAATCCTTCGTTCGAAGTCAAGCACTTTCGTTAGGGCTTTTTCTTCTGCGACTCAATTGATCAGAAAAACTCAACTGGGTCATCGCGCCGTGCTTTCCACTGCCGTCAACCGCTACGAGGGTTCATTTGTTCCTACGTTTCACTTTTCTTCTGAAGCTGTCAAAAACGAACCCAACTCCGATGAGACTTTTCTTCCTTTAATTGAATCGAAAATCACTTGTGCTCAGGAAACCGATGAGTTCCGCGCTGTAAACCTCGTCTTCCTTAATTTATTAAACTCATGATTGTAGTAATAGAAACACTGTTTTTCTTTTTAATTTCATTAGCCAGACACATTTTTGAACTTATACCTTATAAGCTGGTATGCTTAAAAAAGACCCATTTCGTAATGGTATGAAAATTTGAATTTGGTTGTTAATTATGATAATTATTATTATGTTGTGAAATGTTGAAAATTTGATTTTGGTTGATATAGGGTGAGGAAGTTCCGAGCAATTTCCCATTTAAGATAGTTGATGATCTTGATCAGTTCATAAGACTTAAAAGGACTTATCAAGGTGAAGAAATTCATGTTGAGGTTTCGAGTTTTGATTTGGATACTCGTGAAGAACATGATAATCATCAAACGGGTTCCACTCAATCAAGCATTCCACTTTCAGTCAGGGTTTCTAAGAAGGATGGGACCTCTTTGGAGTTCAATTGTGTTGCTTACCCTGATGAGATGGTTATCCGCAGCTTGTTTATTAGGAATCGTGATGAACAGATTTGTTATTATGACTGGCTAGATTTCCAGTATGTACTTCATTCTGATTATTTTATTCTGTTTATAAATATGTGCATTCAATATTTGAAACCGGGGTTACATCAGTGATTTTAAATAAAGGCTATAGCGGTACCATATCATAGCAGCTATAGTGGTGCGCTATAGCACTTTTGCATAGCGGAGTTTGAACAAACTACTATTTTCCGCGATTTGGAATTGAGATTGGGTGGTGTTGCTAACCTGTACTGCTTGTTGTAGAGACATGAAAAATATTGATGTTGCAGTTCAGATTGTTGTTTTGGAGCTTTTTGTAAAACCTTGTTTGTATTACTTTCAATTAATGTTGTAGCTAATACATTGTTTGATTGAGATTCTGCCATTTTTTTCCAGGGATTTGGATGAGGCGTTGCAAAAGTCATTCCACAAGTACTTAGAAATAAGAGGAATCAAACCAAGCACAACAAATTTCTTACTGGAGTACATGATCAGCAAGAAAAGTAGAGATTACTTGGTGAGGCTGAATAGGCTCAAGAATTTCATTAAAGCATGA
Protein sequence

>MS.gene29523.t1

MAFNSILRSKSSTFVRAFSSATQLIRKTQLGHRAVLSTAVNRYEGSFVPTFHFSSEAVKNEPNSDETFLPLIESKITCAQETDEFRAGEEVPSNFPFKIVDDLDQFIRLKRTYQGEEIHVEVSSFDLDTREEHDNHQTGSTQSSIPLSVRVSKKDGTSLEFNCVAYPDEMVIRSLFIRNRDEQICYYDWLDFQDLDEALQKSFHKYLEIRGIKPSTTNFLLEYMISKKSRDYLVRLNRLKNFIKA