AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene39593

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene39593.t1 MTR_4g087160 90.000 200 11 4 1 195 1 196 4.33e-123 346
MS.gene39593.t1 MTR_4g087160 87.000 200 10 5 1 195 1 189 8.54e-115 324
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene39593.t1 AT2G15890 59.884 172 63 3 27 195 35 203 2.19e-65 200
MS.gene39593.t1 AT2G15890 51.479 169 54 3 27 195 35 175 1.31e-49 159

Find 39 sgRNAs with CRISPR-Local

Find 75 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
ATCATTTCATCAGCAGATTT+TGG 0.193138 4.2:-24106319 None:intergenic
TCAAGTTTGGTTCGGCTAAA+AGG 0.273045 4.2:-24105035 None:intergenic
GGTGGTGTAAAATCTTTAAT+AGG 0.274831 4.2:+24106184 MS.gene39593:CDS
TTCTTCTGAATTTATTTCAT+TGG 0.320099 4.2:-24106263 None:intergenic
AATAATGGAAGAAGGAAGTT+TGG 0.327631 4.2:-24104970 None:intergenic
GGAAGTTTGGTTGAAGAAGT+TGG 0.331092 4.2:-24104957 None:intergenic
TCTAGAAGAACAACAAATAA+TGG 0.365979 4.2:-24104985 None:intergenic
AGCCTCTCTATCTCTGCTTT+AGG 0.377284 4.2:-24106148 None:intergenic
ATAATCATCAATCTGTTTCA+TGG 0.378464 4.2:-24106435 None:intergenic
GAGAGGCTGATTATTGAGAT+TGG 0.379912 4.2:+24106163 MS.gene39593:CDS
AAAATCTGAGAAAGATCTCT+TGG 0.387196 4.2:+24105088 MS.gene39593:CDS
CGACTCTGTCAAGTTTGGTT+CGG 0.395191 4.2:-24105043 None:intergenic
CATCAATCTGTTTCATGGTC+TGG 0.409270 4.2:-24106430 None:intergenic
GAAGTTTGGTTGAAGAAGTT+GGG 0.409888 4.2:-24104956 None:intergenic
CGGCTAAAAGGTTCAAGCTT+AGG 0.425055 4.2:-24105023 None:intergenic
TTTAGCGACTCTGTCAAGTT+TGG 0.428057 4.2:-24105048 None:intergenic
TTTGGTAATCCATCTGGTCT+AGG 0.428412 4.2:-24106301 None:intergenic
GTGATGAATCATATAGTTGC+TGG 0.434059 4.2:+24105211 MS.gene39593:CDS
AGCTTAGTATATGATGAATC+AGG 0.449951 4.2:-24106364 None:intergenic
TTGTTTGGTAGATTATTGTT+CGG 0.474583 4.2:+24105179 MS.gene39593:intron
TACTAAGCTTCTTAGATCCA+TGG 0.476278 4.2:+24106378 MS.gene39593:CDS
CAAGCTTAGGAATGAAAGGT+TGG 0.486187 4.2:-24105010 None:intergenic
AAAATCTGCTGATGAAATGA+TGG 0.503481 4.2:+24106321 MS.gene39593:CDS
AAATCTGAGAAAGATCTCTT+GGG 0.506201 4.2:+24105089 MS.gene39593:CDS
TCTTTAATAGGATGTTTACA+TGG 0.524984 4.2:+24106196 MS.gene39593:CDS
TTGGTAATCCATCTGGTCTA+GGG 0.526166 4.2:-24106300 None:intergenic
GGTTCAAGCTTAGGAATGAA+AGG 0.526887 4.2:-24105014 None:intergenic
GATTATTGTTCGGTACTTGA+AGG 0.537788 4.2:+24105189 MS.gene39593:intron
GAACAACAAATAATGGAAGA+AGG 0.539572 4.2:-24104978 None:intergenic
CACCTAAAGCAGAGATAGAG+AGG 0.546613 4.2:+24106146 MS.gene39593:CDS
ACTAAGCTTCTTAGATCCAT+GGG 0.550589 4.2:+24106379 MS.gene39593:CDS
AATGTTTGCCCTAGACCAGA+TGG 0.572937 4.2:+24106292 MS.gene39593:CDS
TTGCGATGAAGAAACAGAGA+AGG 0.583672 4.2:-24104933 None:intergenic
TGAATCATATAGTTGCTGGC+AGG 0.600681 4.2:+24105215 MS.gene39593:CDS
CCATGCAGGTGACTTTCCCA+TGG 0.612938 4.2:-24106395 None:intergenic
GGTGCTTCAGAATACCATGC+AGG 0.623000 4.2:-24106409 None:intergenic
AGGCTGATTATTGAGATTGG+TGG 0.626912 4.2:+24106166 MS.gene39593:CDS
TGCGATGAAGAAACAGAGAA+GGG 0.638715 4.2:-24104932 None:intergenic
CCATGGGAAAGTCACCTGCA+TGG 0.641511 4.2:+24106395 MS.gene39593:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AGACATAAAAAAAAAAAATA+TGG + chr4.2:24105618-24105637 MS.gene39593:intron 10.0%
!! TTTAAAAATAGAAACAAATT+TGG - chr4.2:24105403-24105422 None:intergenic 10.0%
!!! TTATTTATGTTATTTGATTT+TGG + chr4.2:24105147-24105166 MS.gene39593:intron 10.0%
!! AAAATTAAATGAAAAACAAC+AGG - chr4.2:24105299-24105318 None:intergenic 15.0%
!! AATATTTAAGCATAATTAAG+GGG - chr4.2:24106072-24106091 None:intergenic 15.0%
!! GAATATTTAAGCATAATTAA+GGG - chr4.2:24106073-24106092 None:intergenic 15.0%
!! TGAATATTTAAGCATAATTA+AGG - chr4.2:24106074-24106093 None:intergenic 15.0%
!!! ATTCATATTTTTATGTTGAA+AGG - chr4.2:24105598-24105617 None:intergenic 15.0%
!!! ATTTTTAAATTCACAAAGAA+TGG + chr4.2:24105414-24105433 MS.gene39593:intron 15.0%
!!! CAATTTTTTGATGAAAAAAT+AGG + chr4.2:24105816-24105835 MS.gene39593:intron 15.0%
!!! CTATTTTTTCATCAAAAAAT+TGG - chr4.2:24105818-24105837 None:intergenic 15.0%
!! AATCTAACAAAATTTCATGA+TGG - chr4.2:24105879-24105898 None:intergenic 20.0%
!! TAAAACAAGTGAGAAAATTA+AGG + chr4.2:24105533-24105552 MS.gene39593:intron 20.0%
!! TTCTTCTGAATTTATTTCAT+TGG - chr4.2:24106266-24106285 None:intergenic 20.0%
!!! ACTTTCATTTGTTTGTTTTT+TGG + chr4.2:24105942-24105961 MS.gene39593:intron 20.0%
!!! TTTTGGTTTATGATTTTGTT+TGG + chr4.2:24105164-24105183 MS.gene39593:intron 20.0%
! AAATTATATAGCCTGACATT+TGG - chr4.2:24105908-24105927 None:intergenic 25.0%
! ACACGAAATAAGAAAGAAAA+CGG - chr4.2:24105121-24105140 None:intergenic 25.0%
! TAGTCACATATAGTCAAAAT+AGG - chr4.2:24105469-24105488 None:intergenic 25.0%
! TCTAGAAGAACAACAAATAA+TGG - chr4.2:24104988-24105007 None:intergenic 25.0%
! TCTTTAATAGGATGTTTACA+TGG + chr4.2:24106196-24106215 MS.gene39593:CDS 25.0%
! TTGTTTGGTAGATTATTGTT+CGG + chr4.2:24105179-24105198 MS.gene39593:intron 25.0%
!!! TTCTCAGATTTTTCAATCAA+AGG - chr4.2:24105080-24105099 None:intergenic 25.0%
AAAATCTGAGAAAGATCTCT+TGG + chr4.2:24105088-24105107 MS.gene39593:CDS 30.0%
AAAATCTGCTGATGAAATGA+TGG + chr4.2:24106321-24106340 MS.gene39593:CDS 30.0%
AAATCTGAGAAAGATCTCTT+GGG + chr4.2:24105089-24105108 MS.gene39593:CDS 30.0%
ACACAGAAACAGAAATATCA+GGG - chr4.2:24105350-24105369 None:intergenic 30.0%
AGCTTAGTATATGATGAATC+AGG - chr4.2:24106367-24106386 None:intergenic 30.0%
ATGCGTAAACTGAAAAAGAA+TGG + chr4.2:24106229-24106248 MS.gene39593:CDS 30.0%
ATGTGACTATAGATAGAACA+TGG + chr4.2:24105480-24105499 MS.gene39593:intron 30.0%
GAAACAAATTTGGTCAAGAA+AGG - chr4.2:24105393-24105412 None:intergenic 30.0%
GAACATCTGTTTATAGTTGA+AGG - chr4.2:24106025-24106044 None:intergenic 30.0%
GGTGGTGTAAAATCTTTAAT+AGG + chr4.2:24106184-24106203 MS.gene39593:CDS 30.0%
TAGAAACACAAGGAATTCAT+TGG + chr4.2:24106046-24106065 MS.gene39593:intron 30.0%
! AATAATGGAAGAAGGAAGTT+TGG - chr4.2:24104973-24104992 None:intergenic 30.0%
! ATCATTGATGTGTTGATCTT+CGG + chr4.2:24105736-24105755 MS.gene39593:intron 30.0%
! ATCATTTCATCAGCAGATTT+TGG - chr4.2:24106322-24106341 None:intergenic 30.0%
! GAACAACAAATAATGGAAGA+AGG - chr4.2:24104981-24105000 None:intergenic 30.0%
! TCTTCTTTGTTTGAGAGATT+TGG + chr4.2:24105318-24105337 MS.gene39593:intron 30.0%
!! CAGATTTTTCAATCAAAGGA+AGG - chr4.2:24105076-24105095 None:intergenic 30.0%
ACTAAGCTTCTTAGATCCAT+GGG + chr4.2:24106379-24106398 MS.gene39593:CDS 35.0%
ACTCCTTCTGTAAAAGATTG+TGG - chr4.2:24106126-24106145 None:intergenic 35.0%
AGATTTAGAGACCAAATGTC+AGG + chr4.2:24105894-24105913 MS.gene39593:intron 35.0%
AGTCAAAATAGGACATCTCA+TGG - chr4.2:24105458-24105477 None:intergenic 35.0%
CACACAGAAACAGAAATATC+AGG - chr4.2:24105351-24105370 None:intergenic 35.0%
CAGATGTTCTTAGAAACACA+AGG + chr4.2:24106036-24106055 MS.gene39593:intron 35.0%
GAAGTTTGGTTGAAGAAGTT+GGG - chr4.2:24104959-24104978 None:intergenic 35.0%
GATTATTGTTCGGTACTTGA+AGG + chr4.2:24105189-24105208 MS.gene39593:intron 35.0%
GTGATGAATCATATAGTTGC+TGG + chr4.2:24105211-24105230 MS.gene39593:CDS 35.0%
TAAAAGATTGTGGAGAGGAA+TGG - chr4.2:24106116-24106135 None:intergenic 35.0%
TACTAAGCTTCTTAGATCCA+TGG + chr4.2:24106378-24106397 MS.gene39593:CDS 35.0%
TAGTTGAAGGCTAGTACAAT+AGG - chr4.2:24106012-24106031 None:intergenic 35.0%
TTCTGTAAAAGATTGTGGAG+AGG - chr4.2:24106121-24106140 None:intergenic 35.0%
! TCTCCACAATCTTTTACAGA+AGG + chr4.2:24106120-24106139 MS.gene39593:intron 35.0%
AGGCTGATTATTGAGATTGG+TGG + chr4.2:24106166-24106185 MS.gene39593:CDS 40.0%
CAAGCTTAGGAATGAAAGGT+TGG - chr4.2:24105013-24105032 None:intergenic 40.0%
GAGAGGCTGATTATTGAGAT+TGG + chr4.2:24106163-24106182 MS.gene39593:CDS 40.0%
GGAAGTTTGGTTGAAGAAGT+TGG - chr4.2:24104960-24104979 None:intergenic 40.0%
GGTTCAAGCTTAGGAATGAA+AGG - chr4.2:24105017-24105036 None:intergenic 40.0%
TGAATCATATAGTTGCTGGC+AGG + chr4.2:24105215-24105234 MS.gene39593:CDS 40.0%
TGCGATGAAGAAACAGAGAA+GGG - chr4.2:24104935-24104954 None:intergenic 40.0%
TTGCGATGAAGAAACAGAGA+AGG - chr4.2:24104936-24104955 None:intergenic 40.0%
TTTAGCGACTCTGTCAAGTT+TGG - chr4.2:24105051-24105070 None:intergenic 40.0%
! TTGGTAATCCATCTGGTCTA+GGG - chr4.2:24106303-24106322 None:intergenic 40.0%
! TTTGGTAATCCATCTGGTCT+AGG - chr4.2:24106304-24106323 None:intergenic 40.0%
!! GCAGATTTTGGTAATCCATC+TGG - chr4.2:24106310-24106329 None:intergenic 40.0%
!! TCAAGTTTGGTTCGGCTAAA+AGG - chr4.2:24105038-24105057 None:intergenic 40.0%
AATGTTTGCCCTAGACCAGA+TGG + chr4.2:24106292-24106311 MS.gene39593:CDS 45.0%
AGCCTCTCTATCTCTGCTTT+AGG - chr4.2:24106151-24106170 None:intergenic 45.0%
CACCTAAAGCAGAGATAGAG+AGG + chr4.2:24106146-24106165 MS.gene39593:CDS 45.0%
CGACTCTGTCAAGTTTGGTT+CGG - chr4.2:24105046-24105065 None:intergenic 45.0%
CGGCTAAAAGGTTCAAGCTT+AGG - chr4.2:24105026-24105045 None:intergenic 45.0%
GGTGCTTCAGAATACCATGC+AGG - chr4.2:24106412-24106431 None:intergenic 50.0%
CCATGCAGGTGACTTTCCCA+TGG - chr4.2:24106398-24106417 None:intergenic 55.0%
CCATGGGAAAGTCACCTGCA+TGG + chr4.2:24106395-24106414 MS.gene39593:CDS 55.0%


Chromosome Type Strat End Strand Name
chr4.2 gene 24104909 24106450 24104909 ID=MS.gene39593
chr4.2 mRNA 24104909 24106450 24104909 ID=MS.gene39593.t1;Parent=MS.gene39593
chr4.2 exon 24104909 24105110 24104909 ID=MS.gene39593.t1.exon1;Parent=MS.gene39593.t1
chr4.2 CDS 24104909 24105110 24104909 ID=cds.MS.gene39593.t1;Parent=MS.gene39593.t1
chr4.2 exon 24105190 24105263 24105190 ID=MS.gene39593.t1.exon2;Parent=MS.gene39593.t1
chr4.2 CDS 24105190 24105263 24105190 ID=cds.MS.gene39593.t1;Parent=MS.gene39593.t1
chr4.2 exon 24106139 24106450 24106139 ID=MS.gene39593.t1.exon3;Parent=MS.gene39593.t1
chr4.2 CDS 24106139 24106450 24106139 ID=cds.MS.gene39593.t1;Parent=MS.gene39593.t1
Gene Sequence

>MS.gene39593

ATGAATTCAACAACACTACTTCGCCCTTCTCTGTTTCTTCATCGCAACCCAACTTCTTCAACCAAACTTCCTTCTTCCATTATTTGTTGTTCTTCTAGAAACCAACCTTTCATTCCTAAGCTTGAACCTTTTAGCCGAACCAAACTTGACAGAGTCGCTAAAGACCTTCCTTTGATTGAAAAATCTGAGAAAGATCTCTTGGGTGCGTTCCGTTTTCTTTCTTATTTCGTGTAGCAATTTATTTATGTTATTTGATTTTGGTTTATGATTTTGTTTGGTAGATTATTGTTCGGTACTTGAAGGTGATGAATCATATAGTTGCTGGCAGGCTTATTTTGAGCTCAAAGATCTTCAAGTACGTAATCTCTTTCTTCTTCTTTATCTTGTCCTGTTGTTTTTCATTTAATTTTCTTCTTTGTTTGAGAGATTTGGCGTTTTCCCTGATATTTCTGTTTCTGTGTGTTCTGTTTTAGTGTTTTTGCCTTTCTTGACCAAATTTGTTTCTATTTTTAAATTCACAAAGAATGGTTTGTAGAAAACACTAGTCCATGAGATGTCCTATTTTGACTATATGTGACTATAGATAGAACATGGATATTCGTTAATACTTTATTCTAAAGTGAGTAAAACAAGTGAGAAAATTAAGGTTATTGATTTACTACTTATTAGAGATTGATATTAATCTACCTTTCAACATAAAAATATGAATAGACATAAAAAAAAAAAATATGGATCTGTCTTCTCTAAAATCATAGTTAGTAAATAGAGAAAATTAATTGTCGATATTTTAACTATGATAATTTGTTATTCATGTGCATATAATATCAATCATTGATGTGTTGATCTTCGGTTGACATCATTCACTTTATTCTCTAAAGTGATTTGCTTAATTTAGAGTAGTCTGATCCAATTTTTTGATGAAAAAATAGGTGATGCAAGAAAAATGTGATTGAGAATTTTTACTTCGCCATCATGAAATTTTGTTAGATTTAGAGACCAAATGTCAGGCTATATAATTTTTGAAAGTAAATTGACTTTCATTTGTTTGTTTTTTGGCTCAATTTCAATGTGTGACATGTTTTGTTAGAATACATTATTGTCCTATTGTACTAGCCTTCAACTATAAACAGATGTTCTTAGAAACACAAGGAATTCATTGGCCCCTTAATTATGCTTAAATATTCATGAACTTTCATTAACAATTCCATTCCTCTCCACAATCTTTTACAGAAGGAGTCACCTAAAGCAGAGATAGAGAGGCTGATTATTGAGATTGGTGGTGTAAAATCTTTAATAGGATGTTTACATGGAATTGCACTAATGCGTAAACTGAAAAAGAATGGTTTGAATTTAACCAATGAAATAAATTCAGAAGAACAACAAAATGTTTGCCCTAGACCAGATGGATTACCAAAATCTGCTGATGAAATGATGGAAGAAGAGCAAGCAAAAATGCCTGATTCATCATATACTAAGCTTCTTAGATCCATGGGAAAGTCACCTGCATGGTATTCTGAAGCACCAGACCATGAAACAGATTGA
Protein sequence

>MS.gene39593.t1

MNSTTLLRPSLFLHRNPTSSTKLPSSIICCSSRNQPFIPKLEPFSRTKLDRVAKDLPLIEKSEKDLLDYCSVLEGDESYSCWQAYFELKDLQKESPKAEIERLIIEIGGVKSLIGCLHGIALMRKLKKNGLNLTNEINSEEQQNVCPRPDGLPKSADEMMEEEQAKMPDSSYTKLLRSMGKSPAWYSEAPDHETD