AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene65680

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene65680.t1 MTR_5g056450 91.667 144 12 0 1 144 15 158 4.11e-87 251
MS.gene65680.t1 MTR_1g041455 57.233 159 45 5 2 144 16 167 7.83e-52 162
MS.gene65680.t1 MTR_1g048880 45.513 156 54 7 2 144 16 153 8.48e-26 95.9
MS.gene65680.t1 MTR_1g075780 34.667 150 75 5 4 144 10 145 1.93e-13 63.5
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 27 sgRNAs with CRISPR-Local

Find 41 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GAAAATTGATTTCATTGATT+TGG 0.224195 5.2:+48407949 MS.gene65680:CDS
CATTTGAAGATTCTCCTTCT+AGG 0.234818 5.2:-48407883 None:intergenic
GGCCGAATCACCGTTGGTTT+TGG 0.304502 5.2:-48407779 None:intergenic
AAATCCAATGGATTAACATC+TGG 0.363954 5.2:-48407992 None:intergenic
TGCTTCGATTGGTAAGCATT+TGG 0.404776 5.2:-48407860 None:intergenic
AACCAAAACCAACGGTGATT+CGG 0.418396 5.2:+48407777 MS.gene65680:CDS
TGAATAAAGCTTTCTGATTG+TGG 0.433760 5.2:-48407684 None:intergenic
TACCAATCGAAGCACCTAGA+AGG 0.448280 5.2:+48407869 MS.gene65680:CDS
CTCCTTCTAGGTGCTTCGAT+TGG 0.488901 5.2:-48407871 None:intergenic
GAAGGAGAATCTTCAAATGA+TGG 0.491518 5.2:+48407887 MS.gene65680:CDS
TAACCCAGATGTTAATCCAT+TGG 0.496678 5.2:+48407988 MS.gene65680:CDS
AATCCAATGGATTAACATCT+GGG 0.500492 5.2:-48407991 None:intergenic
ATCTTCAAATGATGGTACTA+AGG 0.506473 5.2:+48407895 MS.gene65680:CDS
GGCTGAGGCCGAATCACCGT+TGG 0.513154 5.2:-48407785 None:intergenic
AAAGGGTTTCTGCTTGGCTG+AGG 0.532206 5.2:-48407800 None:intergenic
TTCGATTGGTAAGCATTTGG+TGG 0.535435 5.2:-48407857 None:intergenic
TGCAACATCATCACCATGGC+TGG 0.552771 5.2:+48407539 None:intergenic
AATCAGAAAGCTTTATTCAA+CGG 0.559288 5.2:+48407688 MS.gene65680:CDS
AGCTTAAGTGATAAATCCAA+TGG 0.575565 5.2:-48408004 None:intergenic
CAATGTTTGCCACCACATGA+TGG 0.576640 5.2:+48407743 MS.gene65680:CDS
AACTCACATCGAGTCTCACA+TGG 0.586787 5.2:+48407649 MS.gene65680:CDS
ATTACTAAACTCACCAGCCA+TGG 0.594645 5.2:-48407552 None:intergenic
TCATGTGGTGGCAAACATTG+AGG 0.597472 5.2:-48407740 None:intergenic
GCATTTGCCGATAACCAACA+TGG 0.630189 5.2:-48407829 None:intergenic
TGTGGTGGCAAACATTGAGG+AGG 0.673338 5.2:-48407737 None:intergenic
GTCTCACATGGAGTACGAAG+AGG 0.675983 5.2:+48407661 MS.gene65680:CDS
AAAATCTTGCCATCATGTGG+TGG 0.685328 5.2:-48407752 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! ATGAAATCAATTTTCTTGAT+AGG - chr5.2:48407944-48407963 None:intergenic 20.0%
!!! GAAAATTGATTTCATTGATT+TGG + chr5.2:48407949-48407968 MS.gene65680:CDS 20.0%
!!! AATCAGAAAGCTTTATTCAA+CGG + chr5.2:48407688-48407707 MS.gene65680:CDS 25.0%
AGCTTAAGTGATAAATCCAA+TGG - chr5.2:48408007-48408026 None:intergenic 30.0%
ATCTTCAAATGATGGTACTA+AGG + chr5.2:48407895-48407914 MS.gene65680:CDS 30.0%
CTGGTGAGTTTAGTAATATT+AGG + chr5.2:48407558-48407577 MS.gene65680:intron 30.0%
TGAATAAAGCTTTCTGATTG+TGG - chr5.2:48407687-48407706 None:intergenic 30.0%
TTTGAGTGTTTGTGAAAAAG+CGG - chr5.2:48407622-48407641 None:intergenic 30.0%
!! AAATCCAATGGATTAACATC+TGG - chr5.2:48407995-48408014 None:intergenic 30.0%
!! AATCCAATGGATTAACATCT+GGG - chr5.2:48407994-48408013 None:intergenic 30.0%
!! GATTTTTCAACCAAAACCAA+CGG + chr5.2:48407769-48407788 MS.gene65680:CDS 30.0%
ATGATGTGTCAAACTTGGTA+GGG + chr5.2:48407582-48407601 MS.gene65680:intron 35.0%
CATTTGAAGATTCTCCTTCT+AGG - chr5.2:48407886-48407905 None:intergenic 35.0%
GAAGGAGAATCTTCAAATGA+TGG + chr5.2:48407887-48407906 MS.gene65680:CDS 35.0%
TAACCCAGATGTTAATCCAT+TGG + chr5.2:48407988-48408007 MS.gene65680:CDS 35.0%
TGAAAAATCTTGCCATCATG+TGG - chr5.2:48407758-48407777 None:intergenic 35.0%
! GAGGAGGAAATTGTCTTTTA+GGG - chr5.2:48407724-48407743 None:intergenic 35.0%
! TGAGGAGGAAATTGTCTTTT+AGG - chr5.2:48407725-48407744 None:intergenic 35.0%
AAAATCTTGCCATCATGTGG+TGG - chr5.2:48407755-48407774 None:intergenic 40.0%
AACCAAAACCAACGGTGATT+CGG + chr5.2:48407777-48407796 MS.gene65680:CDS 40.0%
AACCAACATGGCCGAAAAAA+GGG - chr5.2:48407820-48407839 None:intergenic 40.0%
CATGATGTGTCAAACTTGGT+AGG + chr5.2:48407581-48407600 MS.gene65680:intron 40.0%
TAACCAACATGGCCGAAAAA+AGG - chr5.2:48407821-48407840 None:intergenic 40.0%
TAGGCATGATGTGTCAAACT+TGG + chr5.2:48407577-48407596 MS.gene65680:intron 40.0%
TGCTTCGATTGGTAAGCATT+TGG - chr5.2:48407863-48407882 None:intergenic 40.0%
TTCGATTGGTAAGCATTTGG+TGG - chr5.2:48407860-48407879 None:intergenic 40.0%
!! TTTTCGGCCATGTTGGTTAT+CGG + chr5.2:48407822-48407841 MS.gene65680:CDS 40.0%
!!! CCAAGCAGAAACCCTTTTTT+CGG + chr5.2:48407806-48407825 MS.gene65680:CDS 40.0%
AACTCACATCGAGTCTCACA+TGG + chr5.2:48407649-48407668 MS.gene65680:CDS 45.0%
CAATGTTTGCCACCACATGA+TGG + chr5.2:48407743-48407762 MS.gene65680:CDS 45.0%
CCGAAAAAAGGGTTTCTGCT+TGG - chr5.2:48407809-48407828 None:intergenic 45.0%
GCATTTGCCGATAACCAACA+TGG - chr5.2:48407832-48407851 None:intergenic 45.0%
TCATGTGGTGGCAAACATTG+AGG - chr5.2:48407743-48407762 None:intergenic 45.0%
! TACCAATCGAAGCACCTAGA+AGG + chr5.2:48407869-48407888 MS.gene65680:CDS 45.0%
!!! AACCCTTTTTTCGGCCATGT+TGG + chr5.2:48407815-48407834 MS.gene65680:CDS 45.0%
AAAGGGTTTCTGCTTGGCTG+AGG - chr5.2:48407803-48407822 None:intergenic 50.0%
CTCCTTCTAGGTGCTTCGAT+TGG - chr5.2:48407874-48407893 None:intergenic 50.0%
GTCTCACATGGAGTACGAAG+AGG + chr5.2:48407661-48407680 MS.gene65680:CDS 50.0%
TGTGGTGGCAAACATTGAGG+AGG - chr5.2:48407740-48407759 None:intergenic 50.0%
!!! GGCCGAATCACCGTTGGTTT+TGG - chr5.2:48407782-48407801 None:intergenic 55.0%
GGCTGAGGCCGAATCACCGT+TGG - chr5.2:48407788-48407807 None:intergenic 65.0%


Chromosome Type Strat End Strand Name
chr5.2 gene 48407554 48408030 48407554 ID=MS.gene65680
chr5.2 mRNA 48407554 48408030 48407554 ID=MS.gene65680.t1;Parent=MS.gene65680
chr5.2 exon 48407554 48407560 48407554 ID=MS.gene65680.t1.exon1;Parent=MS.gene65680.t1
chr5.2 CDS 48407554 48407560 48407554 ID=cds.MS.gene65680.t1;Parent=MS.gene65680.t1
chr5.2 exon 48407603 48408030 48407603 ID=MS.gene65680.t1.exon2;Parent=MS.gene65680.t1
chr5.2 CDS 48407603 48408030 48407603 ID=cds.MS.gene65680.t1;Parent=MS.gene65680.t1
Gene Sequence

>MS.gene65680

ATGGCTGGTGAGTTTAGTAATATTAGGCATGATGTGTCAAACTTGGTAGGGTGTAAATATTGCAACCGCTTTTTCACAAACACTCAAACACTCGTAACTCACATCGAGTCTCACATGGAGTACGAAGAGGCCACAATCAGAAAGCTTTATTCAACGGAGCGTATCAACCCTAAAAGACAATTTCCTCCTCAATGTTTGCCACCACATGATGGCAAGATTTTTCAACCAAAACCAACGGTGATTCGGCCTCAGCCAAGCAGAAACCCTTTTTTCGGCCATGTTGGTTATCGGCAAATGCAACTTCCACCAAATGCTTACCAATCGAAGCACCTAGAAGGAGAATCTTCAAATGATGGTACTAAGGCATATATCAAGCAGCTTGAGAAACCTATCAAGAAAATTGATTTCATTGATTTGGTTAATAATGATGATGATAACCCAGATGTTAATCCATTGGATTTATCACTTAAGCTCTAG
Protein sequence

>MS.gene65680.t1

MAGCKYCNRFFTNTQTLVTHIESHMEYEEATIRKLYSTERINPKRQFPPQCLPPHDGKIFQPKPTVIRPQPSRNPFFGHVGYRQMQLPPNAYQSKHLEGESSNDGTKAYIKQLEKPIKKIDFIDLVNNDDDNPDVNPLDLSLKL