AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0284600


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0284600 MtrunA17_Chr2g0324011 30.128 156 85 2 22 154 5 159 2.01e-12 63.5
Msa0284600 MtrunA17_Chr7g0258861 26.667 150 87 1 24 150 7 156 3.07e-12 62.8
Msa0284600 MtrunA17_Chr6g0451441 29.299 157 89 4 18 153 75 230 3.16e-12 63.2
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 21 sgRNAs with CRISPR-Local

Find 132 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TCCTTATCATCCGTCTTATT+TGG 0.253463 2_3:+22815204 None:intergenic
TTTAATTCATCATCGCAATT+TGG 0.259676 2_3:+22815390 None:intergenic
AGTTCACAAAAGCTTATTAC+AGG 0.312085 2_3:-22814992 Msa0284600:CDS
TCAAATACTTGTCCAATCTT+AGG 0.341635 2_3:+22815366 None:intergenic
CTTAGAAACGGTCTCTTCAT+AGG 0.411850 2_3:+22815036 None:intergenic
CTATGAAGAGACCGTTTCTA+AGG 0.416138 2_3:-22815035 Msa0284600:CDS
GATGAATTAAAGCCTAAGAT+TGG 0.441758 2_3:-22815378 Msa0284600:CDS
GCCAAATAAGACGGATGATA+AGG 0.447708 2_3:-22815205 Msa0284600:CDS
ACATTTCGTTTGCTCGAAAG+AGG 0.495450 2_3:-22815235 Msa0284600:CDS
TTCCTTGCAGACCTTAGAAA+CGG 0.510667 2_3:+22815024 None:intergenic
ACTTATTAAAAGAACAGTGT+GGG 0.551687 2_3:-22814930 Msa0284600:CDS
GGGTTATTTGCCAAATAAGA+CGG 0.573634 2_3:-22815214 Msa0284600:CDS
TGGACAAGTATTTGATACGT+TGG 0.575442 2_3:-22815358 Msa0284600:CDS
GTGAAGCAAGTGGATGTGTA+TGG 0.586364 2_3:+22815058 None:intergenic
CTTATTAAAAGAACAGTGTG+GGG 0.593050 2_3:-22814929 Msa0284600:CDS
GTATTTGATACGTTGGCAGA+AGG 0.595265 2_3:-22815351 Msa0284600:CDS
CATTTCGTTTGCTCGAAAGA+GGG 0.599887 2_3:-22815234 Msa0284600:CDS
GACCGTTTCTAAGGTCTGCA+AGG 0.602665 2_3:-22815026 Msa0284600:CDS
CACTTATTAAAAGAACAGTG+TGG 0.629235 2_3:-22814931 Msa0284600:CDS
CTCTTCATAGGTGAAGCAAG+TGG 0.639442 2_3:+22815048 None:intergenic
TTATTAAAAGAACAGTGTGG+GGG 0.706691 2_3:-22814928 Msa0284600:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! ACATATATTAATATATAAAG+TGG + chr2_3:22815116-22815135 None:intergenic 10.0%
!! TCTTCAATAAAATAATATAA+AGG + chr2_3:22815513-22815532 None:intergenic 10.0%
!! ACATATATTAATATATAAAG+TGG + chr2_3:22815116-22815135 None:intergenic 10.0%
!! TCTTCAATAAAATAATATAA+AGG + chr2_3:22815513-22815532 None:intergenic 10.0%
!! AAACAATTATAATATACCTG+AGG + chr2_3:22814954-22814973 None:intergenic 20.0%
!! AAAAAAAACAACTATCTCTT+AGG + chr2_3:22814993-22815012 None:intergenic 20.0%
!!! TTTTTTCCCTAATTTTTTGT+TGG - chr2_3:22815007-22815026 Msa0284600:CDS 20.0%
!! ATAGAACCAACAAAAAATTA+GGG + chr2_3:22815016-22815035 None:intergenic 20.0%
!! AATAGAACCAACAAAAAATT+AGG + chr2_3:22815017-22815036 None:intergenic 20.0%
!!! TTATGTTTTGTTCTTTTTTG+AGG - chr2_3:22815090-22815109 Msa0284600:CDS 20.0%
!!! TATATACATGATTAGTTCAA+GGG + chr2_3:22815240-22815259 None:intergenic 20.0%
!!! ATATATACATGATTAGTTCA+AGG + chr2_3:22815241-22815260 None:intergenic 20.0%
!! AGGATTAAACAAAGAATTAA+AGG + chr2_3:22815472-22815491 None:intergenic 20.0%
!! GGAAAACAGAATAAAAAAAA+AGG + chr2_3:22815492-22815511 None:intergenic 20.0%
!! AAACAATTATAATATACCTG+AGG + chr2_3:22814954-22814973 None:intergenic 20.0%
!! AAAAAAAACAACTATCTCTT+AGG + chr2_3:22814993-22815012 None:intergenic 20.0%
!!! TTTTTTCCCTAATTTTTTGT+TGG - chr2_3:22815007-22815026 Msa0284600:CDS 20.0%
!! ATAGAACCAACAAAAAATTA+GGG + chr2_3:22815016-22815035 None:intergenic 20.0%
!! AATAGAACCAACAAAAAATT+AGG + chr2_3:22815017-22815036 None:intergenic 20.0%
!!! TTATGTTTTGTTCTTTTTTG+AGG - chr2_3:22815090-22815109 Msa0284600:CDS 20.0%
!!! TATATACATGATTAGTTCAA+GGG + chr2_3:22815240-22815259 None:intergenic 20.0%
!!! ATATATACATGATTAGTTCA+AGG + chr2_3:22815241-22815260 None:intergenic 20.0%
!! AGGATTAAACAAAGAATTAA+AGG + chr2_3:22815472-22815491 None:intergenic 20.0%
!! GGAAAACAGAATAAAAAAAA+AGG + chr2_3:22815492-22815511 None:intergenic 20.0%
! TTATTATCATTATGAGCACA+TGG - chr2_3:22815333-22815352 Msa0284600:CDS 25.0%
!!! TAATGTTGACTTCTAATTTG+TGG - chr2_3:22815389-22815408 Msa0284600:CDS 25.0%
! TTTAATTCATCATCGCAATT+TGG + chr2_3:22815572-22815591 None:intergenic 25.0%
!! TCATCGACTATAGATAAAAA+CGG - chr2_3:22815686-22815705 Msa0284600:intron 25.0%
!!! ATGCAAATGTTGTTTTCAAA+TGG - chr2_3:22815837-22815856 Msa0284600:intron 25.0%
!!! TGCAAATGTTGTTTTCAAAT+GGG - chr2_3:22815838-22815857 Msa0284600:intron 25.0%
! ACTTATTAAAAGAACAGTGT+GGG - chr2_3:22816029-22816048 Msa0284600:CDS 25.0%
! TTATTATCATTATGAGCACA+TGG - chr2_3:22815333-22815352 Msa0284600:CDS 25.0%
!!! TAATGTTGACTTCTAATTTG+TGG - chr2_3:22815389-22815408 Msa0284600:CDS 25.0%
! TTTAATTCATCATCGCAATT+TGG + chr2_3:22815572-22815591 None:intergenic 25.0%
!! TCATCGACTATAGATAAAAA+CGG - chr2_3:22815686-22815705 Msa0284600:intron 25.0%
!!! ATGCAAATGTTGTTTTCAAA+TGG - chr2_3:22815837-22815856 Msa0284600:intron 25.0%
!!! TGCAAATGTTGTTTTCAAAT+GGG - chr2_3:22815838-22815857 Msa0284600:intron 25.0%
! ACTTATTAAAAGAACAGTGT+GGG - chr2_3:22816029-22816048 Msa0284600:CDS 25.0%
!!! AACTAGTTTTCAAATTCCTC+AGG - chr2_3:22814935-22814954 Msa0284600:CDS 30.0%
TCTTGTTCATTAATGTCTAC+AGG + chr2_3:22815162-22815181 None:intergenic 30.0%
TCTCTAATATGCAGAAAGAT+TGG + chr2_3:22815209-22815228 None:intergenic 30.0%
!! ATGAGATTGACTTTCACTTT+TGG + chr2_3:22815281-22815300 None:intergenic 30.0%
!!! TTTTTAAGATTGTTGTCCAG+TGG - chr2_3:22815436-22815455 Msa0284600:intron 30.0%
GATGAATTAAAGCCTAAGAT+TGG - chr2_3:22815581-22815600 Msa0284600:intron 30.0%
TCAAATACTTGTCCAATCTT+AGG + chr2_3:22815596-22815615 None:intergenic 30.0%
!!! AAATGTTGTTTTCAAATGGG+TGG - chr2_3:22815841-22815860 Msa0284600:intron 30.0%
!!! AATGTTGTTTTCAAATGGGT+GGG - chr2_3:22815842-22815861 Msa0284600:intron 30.0%
AGTTCACAAAAGCTTATTAC+AGG - chr2_3:22815967-22815986 Msa0284600:intron 30.0%
! CTGTTCTTTTAATAAGTGGA+AGG + chr2_3:22816026-22816045 None:intergenic 30.0%
! CACACTGTTCTTTTAATAAG+TGG + chr2_3:22816030-22816049 None:intergenic 30.0%
CACTTATTAAAAGAACAGTG+TGG - chr2_3:22816028-22816047 Msa0284600:CDS 30.0%
CTTATTAAAAGAACAGTGTG+GGG - chr2_3:22816030-22816049 Msa0284600:CDS 30.0%
TTATTAAAAGAACAGTGTGG+GGG - chr2_3:22816031-22816050 Msa0284600:CDS 30.0%
!!! AACTAGTTTTCAAATTCCTC+AGG - chr2_3:22814935-22814954 Msa0284600:CDS 30.0%
TCTTGTTCATTAATGTCTAC+AGG + chr2_3:22815162-22815181 None:intergenic 30.0%
TCTCTAATATGCAGAAAGAT+TGG + chr2_3:22815209-22815228 None:intergenic 30.0%
!! ATGAGATTGACTTTCACTTT+TGG + chr2_3:22815281-22815300 None:intergenic 30.0%
!!! TTTTTAAGATTGTTGTCCAG+TGG - chr2_3:22815436-22815455 Msa0284600:intron 30.0%
GATGAATTAAAGCCTAAGAT+TGG - chr2_3:22815581-22815600 Msa0284600:intron 30.0%
TCAAATACTTGTCCAATCTT+AGG + chr2_3:22815596-22815615 None:intergenic 30.0%
!!! AAATGTTGTTTTCAAATGGG+TGG - chr2_3:22815841-22815860 Msa0284600:intron 30.0%
!!! AATGTTGTTTTCAAATGGGT+GGG - chr2_3:22815842-22815861 Msa0284600:intron 30.0%
AGTTCACAAAAGCTTATTAC+AGG - chr2_3:22815967-22815986 Msa0284600:intron 30.0%
! CTGTTCTTTTAATAAGTGGA+AGG + chr2_3:22816026-22816045 None:intergenic 30.0%
! CACACTGTTCTTTTAATAAG+TGG + chr2_3:22816030-22816049 None:intergenic 30.0%
CACTTATTAAAAGAACAGTG+TGG - chr2_3:22816028-22816047 Msa0284600:CDS 30.0%
CTTATTAAAAGAACAGTGTG+GGG - chr2_3:22816030-22816049 Msa0284600:CDS 30.0%
TTATTAAAAGAACAGTGTGG+GGG - chr2_3:22816031-22816050 Msa0284600:CDS 30.0%
!! TTGTTGGTTCTATTGTTGTC+CGG - chr2_3:22815023-22815042 Msa0284600:CDS 35.0%
GTTCATTAATGTCTACAGGT+TGG + chr2_3:22815158-22815177 None:intergenic 35.0%
!! CACGAGATAAGTTTTATCGT+TGG + chr2_3:22815361-22815380 None:intergenic 35.0%
TGGACAAGTATTTGATACGT+TGG - chr2_3:22815601-22815620 Msa0284600:intron 35.0%
GGGTTATTTGCCAAATAAGA+CGG - chr2_3:22815745-22815764 Msa0284600:intron 35.0%
! TCCTTATCATCCGTCTTATT+TGG + chr2_3:22815758-22815777 None:intergenic 35.0%
TGTCAAGGTTAGAAGAAGAA+GGG - chr2_3:22815793-22815812 Msa0284600:intron 35.0%
!!! ATGTTGTTTTCAAATGGGTG+GGG - chr2_3:22815843-22815862 Msa0284600:intron 35.0%
!! TTGTTGGTTCTATTGTTGTC+CGG - chr2_3:22815023-22815042 Msa0284600:CDS 35.0%
GTTCATTAATGTCTACAGGT+TGG + chr2_3:22815158-22815177 None:intergenic 35.0%
!! CACGAGATAAGTTTTATCGT+TGG + chr2_3:22815361-22815380 None:intergenic 35.0%
TGGACAAGTATTTGATACGT+TGG - chr2_3:22815601-22815620 Msa0284600:intron 35.0%
GGGTTATTTGCCAAATAAGA+CGG - chr2_3:22815745-22815764 Msa0284600:intron 35.0%
! TCCTTATCATCCGTCTTATT+TGG + chr2_3:22815758-22815777 None:intergenic 35.0%
TGTCAAGGTTAGAAGAAGAA+GGG - chr2_3:22815793-22815812 Msa0284600:intron 35.0%
!!! ATGTTGTTTTCAAATGGGTG+GGG - chr2_3:22815843-22815862 Msa0284600:intron 35.0%
CAACAAGCAAATAGAACCAC+CGG + chr2_3:22815045-22815064 None:intergenic 40.0%
!!! TTTCACTTTTGGCTTCTCAC+TGG + chr2_3:22815270-22815289 None:intergenic 40.0%
TAAAGGATCATCAGAACCAC+TGG + chr2_3:22815455-22815474 None:intergenic 40.0%
GTATTTGATACGTTGGCAGA+AGG - chr2_3:22815608-22815627 Msa0284600:intron 40.0%
GAAAAATACGCAGTCTCTGT+CGG - chr2_3:22815644-22815663 Msa0284600:intron 40.0%
ACATTTCGTTTGCTCGAAAG+AGG - chr2_3:22815724-22815743 Msa0284600:intron 40.0%
CATTTCGTTTGCTCGAAAGA+GGG - chr2_3:22815725-22815744 Msa0284600:intron 40.0%
GCCAAATAAGACGGATGATA+AGG - chr2_3:22815754-22815773 Msa0284600:intron 40.0%
GCAAAGTGAATCTACTGTCA+AGG - chr2_3:22815778-22815797 Msa0284600:intron 40.0%
CTGTCAAGGTTAGAAGAAGA+AGG - chr2_3:22815792-22815811 Msa0284600:intron 40.0%
! AGAAGGGCTTTAACAAGAGA+AGG - chr2_3:22815809-22815828 Msa0284600:intron 40.0%
!!! TGTTGTTTTCAAATGGGTGG+GGG - chr2_3:22815844-22815863 Msa0284600:intron 40.0%
CTTAGAAACGGTCTCTTCAT+AGG + chr2_3:22815926-22815945 None:intergenic 40.0%
CTATGAAGAGACCGTTTCTA+AGG - chr2_3:22815924-22815943 Msa0284600:intron 40.0%
TTCCTTGCAGACCTTAGAAA+CGG + chr2_3:22815938-22815957 None:intergenic 40.0%
CAACAAGCAAATAGAACCAC+CGG + chr2_3:22815045-22815064 None:intergenic 40.0%
!!! TTTCACTTTTGGCTTCTCAC+TGG + chr2_3:22815270-22815289 None:intergenic 40.0%
TAAAGGATCATCAGAACCAC+TGG + chr2_3:22815455-22815474 None:intergenic 40.0%
GTATTTGATACGTTGGCAGA+AGG - chr2_3:22815608-22815627 Msa0284600:intron 40.0%
GAAAAATACGCAGTCTCTGT+CGG - chr2_3:22815644-22815663 Msa0284600:intron 40.0%
ACATTTCGTTTGCTCGAAAG+AGG - chr2_3:22815724-22815743 Msa0284600:intron 40.0%
CATTTCGTTTGCTCGAAAGA+GGG - chr2_3:22815725-22815744 Msa0284600:intron 40.0%
GCCAAATAAGACGGATGATA+AGG - chr2_3:22815754-22815773 Msa0284600:intron 40.0%
GCAAAGTGAATCTACTGTCA+AGG - chr2_3:22815778-22815797 Msa0284600:intron 40.0%
CTGTCAAGGTTAGAAGAAGA+AGG - chr2_3:22815792-22815811 Msa0284600:intron 40.0%
! AGAAGGGCTTTAACAAGAGA+AGG - chr2_3:22815809-22815828 Msa0284600:intron 40.0%
!!! TGTTGTTTTCAAATGGGTGG+GGG - chr2_3:22815844-22815863 Msa0284600:intron 40.0%
CTTAGAAACGGTCTCTTCAT+AGG + chr2_3:22815926-22815945 None:intergenic 40.0%
CTATGAAGAGACCGTTTCTA+AGG - chr2_3:22815924-22815943 Msa0284600:intron 40.0%
TTCCTTGCAGACCTTAGAAA+CGG + chr2_3:22815938-22815957 None:intergenic 40.0%
!! TTGGTTCTATTGTTGTCCGG+TGG - chr2_3:22815026-22815045 Msa0284600:CDS 45.0%
! CGGTGGTTCTATTTGCTTGT+TGG - chr2_3:22815043-22815062 Msa0284600:CDS 45.0%
ATAAAAACGGCGTGAAGCGT+TGG - chr2_3:22815699-22815718 Msa0284600:intron 45.0%
GTGAAGCAAGTGGATGTGTA+TGG + chr2_3:22815904-22815923 None:intergenic 45.0%
CTCTTCATAGGTGAAGCAAG+TGG + chr2_3:22815914-22815933 None:intergenic 45.0%
!! TTGGTTCTATTGTTGTCCGG+TGG - chr2_3:22815026-22815045 Msa0284600:CDS 45.0%
! CGGTGGTTCTATTTGCTTGT+TGG - chr2_3:22815043-22815062 Msa0284600:CDS 45.0%
ATAAAAACGGCGTGAAGCGT+TGG - chr2_3:22815699-22815718 Msa0284600:intron 45.0%
GTGAAGCAAGTGGATGTGTA+TGG + chr2_3:22815904-22815923 None:intergenic 45.0%
CTCTTCATAGGTGAAGCAAG+TGG + chr2_3:22815914-22815933 None:intergenic 45.0%
!! TTTATATATTAATATATGTT+AGG - chr2_3:22815117-22815136 Msa0284600:intron 5.0%
!!! ATATTTATTTTGTTAATTTT+AGG - chr2_3:22815532-22815551 Msa0284600:intron 5.0%
!! TTTATATATTAATATATGTT+AGG - chr2_3:22815117-22815136 Msa0284600:intron 5.0%
!!! ATATTTATTTTGTTAATTTT+AGG - chr2_3:22815532-22815551 Msa0284600:intron 5.0%
! GTTTTCAAATGGGTGGGGGA+AGG - chr2_3:22815848-22815867 Msa0284600:intron 50.0%
!! GACCGTTTCTAAGGTCTGCA+AGG - chr2_3:22815933-22815952 Msa0284600:intron 50.0%
! GTTTTCAAATGGGTGGGGGA+AGG - chr2_3:22815848-22815867 Msa0284600:intron 50.0%
!! GACCGTTTCTAAGGTCTGCA+AGG - chr2_3:22815933-22815952 Msa0284600:intron 50.0%
Chromosome Type Strat End Strand Name
chr2_3 gene 22814918 22816063 22814918 ID=Msa0284600;Name=Msa0284600
chr2_3 mRNA 22814918 22816063 22814918 ID=Msa0284600-mRNA-1;Parent=Msa0284600;Name=Msa0284600-mRNA-1;_AED=0.19;_eAED=0.19;_QI=0|0|0|1|0.5|0.33|3|0|154
chr2_3 exon 22816025 22816063 22816025 ID=Msa0284600-mRNA-1:exon:8843;Parent=Msa0284600-mRNA-1
chr2_3 exon 22815199 22815427 22815199 ID=Msa0284600-mRNA-1:exon:8842;Parent=Msa0284600-mRNA-1
chr2_3 exon 22814918 22815111 22814918 ID=Msa0284600-mRNA-1:exon:8841;Parent=Msa0284600-mRNA-1
chr2_3 CDS 22816025 22816063 22816025 ID=Msa0284600-mRNA-1:cds;Parent=Msa0284600-mRNA-1
chr2_3 CDS 22815199 22815427 22815199 ID=Msa0284600-mRNA-1:cds;Parent=Msa0284600-mRNA-1
chr2_3 CDS 22814918 22815111 22814918 ID=Msa0284600-mRNA-1:cds;Parent=Msa0284600-mRNA-1
Gene Sequence

>Msa0284600

ATGGACAAAGATACATCAACTAGTTTTCAAATTCCTCAGGAATATGAATGTGTGCCAAATTGCGATGATGAATTAAAGCCTAAGATTGGACAAGTATTTGATACGTTGGCAGAAGGTAAAAAATTTTACGAAAAATACGCAGTCTCTGTCGGATTTAGTGTGCGTTCATCATCATCGACTATAGATAAAAACGGCGTGAAGCGTTGGAAACATTTCGTTTGCTCGAAAGAGGGTTATTTGCCAAATAAGACGGATGATAAGGAGCAAAGTAAGTATGAGATAGCTCGATTTCATGAAAGCCATACACATCCACTTGCTTCACCTATGAAGAGACCGTTTCTAAGGTCTGCAAGGAAAGTGAATTTAGTTCACAAAAGCTTATTACAGGCATGTAGTAGAGCAAATATTAGAACTTCAAAAACCTTCCACTTATTAAAAGAACAGTGTGGGGGTTATGAAAAT

Protein sequence

>Msa0284600

MDKDTSTSFQIPQEYECVPNCDDELKPKIGQVFDTLAEGKKFYEKYAVSVGFSVRSSSSTIDKNGVKRWKHFVCSKEGYLPNKTDDKEQSKYEIARFHESHTHPLASPMKRPFLRSARKVNLVHKSLLQACSRANIRTSKTFHLLKEQCGGYEN