AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene002460

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene002460.t1 MTR_2g013920 87.582 153 18 1 1 152 1 153 1.99e-93 268
MS.gene002460.t1 MTR_2g090440 42.208 154 87 1 6 157 12 165 3.01e-37 127
MS.gene002460.t1 MTR_2g090480 39.744 156 90 2 6 157 12 167 2.84e-35 122
MS.gene002460.t1 MTR_2g090425 42.038 157 86 2 6 157 12 168 2.94e-35 125
MS.gene002460.t1 MTR_4g078350 44.375 160 73 6 3 152 7 160 1.86e-32 115
MS.gene002460.t1 MTR_2g090500 35.385 130 84 0 28 157 49 178 3.99e-25 96.7
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene002460.t1 AT4G20970 42.236 161 82 4 3 152 7 167 1.46e-36 125

Find 26 sgRNAs with CRISPR-Local

Find 33 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TTAGAGGTTGTTCTAATAAC+TGG 0.223327 2.1:-71095706 MS.gene002460:CDS
AAAATTAAGATACAACAAAT+TGG 0.306857 2.1:-71095736 MS.gene002460:CDS
TTTCTATTCATATTCACATT+TGG 0.306963 2.1:+71095784 None:intergenic
ACAAATTGGTTTAGTCTTAG+AGG 0.319445 2.1:-71095722 MS.gene002460:CDS
TCTGCCTCATCAAACTTCTA+AGG 0.344529 2.1:-71096131 MS.gene002460:intron
CTGTCAACTCTTGATGAACT+AGG 0.359161 2.1:+71096217 None:intergenic
TATTGTCAATGCAAGTTATA+AGG 0.360092 2.1:-71095623 MS.gene002460:CDS
GGTTGTTCTAATAACTGGAT+TGG 0.435753 2.1:-71095701 MS.gene002460:CDS
TTTCCATTCAATACATTGCC+AGG 0.438842 2.1:-71095584 MS.gene002460:CDS
CTTCGTGTTCTTCATGAAGA+AGG 0.454763 2.1:-71095652 MS.gene002460:CDS
TTACCTGGCAATGTATTGAA+TGG 0.496250 2.1:+71095581 None:intergenic
GAAAAGAAGAACTTTCTACT+AGG 0.532951 2.1:-71095817 MS.gene002460:CDS
TGTCAACTCTTGATGAACTA+GGG 0.540967 2.1:+71096218 None:intergenic
GATCAACTTGGAGAAAATGA+AGG 0.550998 2.1:-71095839 MS.gene002460:CDS
CTAGTTCATCAAGAGTTGAC+AGG 0.559038 2.1:-71096216 MS.gene002460:CDS
GTAACAATTTATGATTTACC+TGG 0.575321 2.1:+71095566 None:intergenic
ACTTTCTACTAGGAATTCAA+AGG 0.595040 2.1:-71095807 MS.gene002460:CDS
AAAGAAATTACAGATCAACT+TGG 0.602314 2.1:-71095851 MS.gene002460:CDS
GAGACCTTAGAAGTTTGATG+AGG 0.624740 2.1:+71096127 None:intergenic
ATGAATAGAAACAAGAACAT+GGG 0.625623 2.1:-71095772 MS.gene002460:CDS
TATGAATAGAAACAAGAACA+TGG 0.630359 2.1:-71095773 MS.gene002460:CDS
TCTGATGCAGGCGATTTCAG+CGG 0.655278 2.1:-71095905 MS.gene002460:intron
GCAGAAATGAGTTGAGCTTG+TGG 0.677546 2.1:+71096149 None:intergenic
CTTCTTCATGAAGAACACGA+AGG 0.679799 2.1:+71095653 None:intergenic
GAAATGAGTTGAGCTTGTGG+CGG 0.691957 2.1:+71096152 None:intergenic
TTCAGCGGCAGATCAGCTCG+AGG 0.698732 2.1:-71095890 MS.gene002460:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AAAATTAAGATACAACAAAT+TGG - chr2.1:71096045-71096064 MS.gene002460:intron 15.0%
!!! ATTTGTTGTATCTTAATTTT+TGG + chr2.1:71096045-71096064 None:intergenic 15.0%
!! ATGTTAGTATTGTTAGTATT+TGG - chr2.1:71095837-71095856 MS.gene002460:CDS 20.0%
!! GAAAAAAATAGAATTAGTGA+CGG - chr2.1:71095738-71095757 MS.gene002460:CDS 20.0%
!! TTTCTATTCATATTCACATT+TGG + chr2.1:71096000-71096019 None:intergenic 20.0%
!!! TAATTTAATTTATCTGATGC+AGG - chr2.1:71095864-71095883 MS.gene002460:CDS 20.0%
! AAAGAAATTACAGATCAACT+TGG - chr2.1:71095930-71095949 MS.gene002460:intron 25.0%
! ATGAATAGAAACAAGAACAT+GGG - chr2.1:71096009-71096028 MS.gene002460:intron 25.0%
! GTAACAATTTATGATTTACC+TGG + chr2.1:71096218-71096237 None:intergenic 25.0%
! TATGAATAGAAACAAGAACA+TGG - chr2.1:71096008-71096027 MS.gene002460:intron 25.0%
! TATTGTCAATGCAAGTTATA+AGG - chr2.1:71096158-71096177 MS.gene002460:CDS 25.0%
!! ATTTCTTCTTTTGCTTTCAA+TGG + chr2.1:71095595-71095614 None:intergenic 25.0%
ACTTTCTACTAGGAATTCAA+AGG - chr2.1:71095974-71095993 MS.gene002460:intron 30.0%
GAAAAGAAGAACTTTCTACT+AGG - chr2.1:71095964-71095983 MS.gene002460:intron 30.0%
TTAGAGGTTGTTCTAATAAC+TGG - chr2.1:71096075-71096094 MS.gene002460:intron 30.0%
!! ACAAATTGGTTTAGTCTTAG+AGG - chr2.1:71096059-71096078 MS.gene002460:intron 30.0%
!!! GTCACTATGTTTTAAAACGA+CGG - chr2.1:71095814-71095833 MS.gene002460:CDS 30.0%
CTAAGAGAAGAAGAGAGTAA+AGG + chr2.1:71095689-71095708 None:intergenic 35.0%
GATCAACTTGGAGAAAATGA+AGG - chr2.1:71095942-71095961 MS.gene002460:intron 35.0%
GGTTGTTCTAATAACTGGAT+TGG - chr2.1:71096080-71096099 MS.gene002460:intron 35.0%
TGTCAACTCTTGATGAACTA+GGG + chr2.1:71095566-71095585 None:intergenic 35.0%
TTACCTGGCAATGTATTGAA+TGG + chr2.1:71096203-71096222 None:intergenic 35.0%
TTTCCATTCAATACATTGCC+AGG - chr2.1:71096197-71096216 MS.gene002460:CDS 35.0%
CTAGTTCATCAAGAGTTGAC+AGG - chr2.1:71095565-71095584 MS.gene002460:CDS 40.0%
CTGTCAACTCTTGATGAACT+AGG + chr2.1:71095567-71095586 None:intergenic 40.0%
CTTCGTGTTCTTCATGAAGA+AGG - chr2.1:71096129-71096148 MS.gene002460:intron 40.0%
CTTCTTCATGAAGAACACGA+AGG + chr2.1:71096131-71096150 None:intergenic 40.0%
GAGACCTTAGAAGTTTGATG+AGG + chr2.1:71095657-71095676 None:intergenic 40.0%
TCTGCCTCATCAAACTTCTA+AGG - chr2.1:71095650-71095669 MS.gene002460:CDS 40.0%
! GAAATGAGTTGAGCTTGTGG+CGG + chr2.1:71095632-71095651 None:intergenic 45.0%
! GCAGAAATGAGTTGAGCTTG+TGG + chr2.1:71095635-71095654 None:intergenic 45.0%
TCTGATGCAGGCGATTTCAG+CGG - chr2.1:71095876-71095895 MS.gene002460:CDS 50.0%
TTCAGCGGCAGATCAGCTCG+AGG - chr2.1:71095891-71095910 MS.gene002460:CDS 60.0%


Chromosome Type Strat End Strand Name
chr2.1 gene 71095552 71096251 71095552 ID=MS.gene002460
chr2.1 mRNA 71095552 71096251 71095552 ID=MS.gene002460.t1;Parent=MS.gene002460
chr2.1 exon 71096132 71096251 71096132 ID=MS.gene002460.t1.exon1;Parent=MS.gene002460.t1
chr2.1 CDS 71096132 71096251 71096132 ID=cds.MS.gene002460.t1;Parent=MS.gene002460.t1
chr2.1 exon 71095552 71095917 71095552 ID=MS.gene002460.t1.exon2;Parent=MS.gene002460.t1
chr2.1 CDS 71095552 71095917 71095552 ID=cds.MS.gene002460.t1;Parent=MS.gene002460.t1
Gene Sequence

>MS.gene002460

ATGGAGAATAACCCTAGTTCATCAAGAGTTGACAGGAAATCCATTGAAAGCAAAAGAAGAAATCAAATGAAAGCTCTCCGCCACAAGCTCAACTCATTTCTGCCTCATCAAACTTCTAAGGTCTCTCTTAATTTCCTTTACTCTCTTCTTCTCTTAGATGCTTAGTCAATTATATGAATTATACTAGAAAAAAATAGAATTAGTGACGGAAAAAATAAAATTCGTTACAAGTAATTAGAAATGTTCTCTTCTTAAATTTTATGTCACTATGTTTTAAAACGACGGATGTTAGTATTGTTAGTATTTGGTCACTAATTTAATTTATCTGATGCAGGCGATTTCAGCGGCAGATCAGCTCGAGGAAGCAACAAACTACATAAAGAAATTACAGATCAACTTGGAGAAAATGAAGGAAAAGAAGAACTTTCTACTAGGAATTCAAAGGCCAAATGTGAATATGAATAGAAACAAGAACATGGGATTAAAGACTCCAAAAATTAAGATACAACAAATTGGTTTAGTCTTAGAGGTTGTTCTAATAACTGGATTGGATTCTCAGTTTTTGTTCAATGAAATCCTTCGTGTTCTTCATGAAGAAGGAGTTGATATTGTCAATGCAAGTTATAAGGTCAATGAAGATTCAGTTTTCCATTCAATACATTGCCAGGTAAATCATAAATTGTTACTTAATTTCCTTTAA
Protein sequence

>MS.gene002460.t1

MENNPSSSRVDRKSIESKRRNQMKALRHKLNSFLPHQTSKAISAADQLEEATNYIKKLQINLEKMKEKKNFLLGIQRPNVNMNRNKNMGLKTPKIKIQQIGLVLEVVLITGLDSQFLFNEILRVLHEEGVDIVNASYKVNEDSVFHSIHCQVNHKLLLNFL