AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene73991

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene73991.t1 MTR_4g039380 73.504 117 17 2 1 103 1 117 8.89e-49 151
MS.gene73991.t1 MTR_4g039640 76.923 117 13 2 1 103 1 117 1.04e-48 150
MS.gene73991.t1 MTR_4g039340 65.649 131 17 2 1 103 1 131 5.03e-46 144
MS.gene73991.t1 MTR_4g039400 49.515 103 31 1 1 103 1 82 9.16e-16 66.6
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 18 sgRNAs with CRISPR-Local

Find 22 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TCTCATTCATCTGGTGTATA+AGG 0.184471 4.1:+59390623 None:intergenic
TGTGGTTGAGGCTGATTATT+TGG 0.247122 4.1:+59390785 None:intergenic
CTCGATTCTAATATTAAATC+TGG 0.264896 4.1:+59390824 None:intergenic
CTCATTCATCTGGTGTATAA+GGG 0.356164 4.1:+59390624 None:intergenic
AGGTCGAAAGCGCGAACATT+AGG 0.356569 4.1:+59390653 None:intergenic
GGAGGTTGGTTCAAATCAAA+TGG 0.432622 4.1:+59390674 None:intergenic
CTGGTGTATAAGGGATATTA+AGG 0.496508 4.1:+59390633 None:intergenic
TGAGGCTGATTATTTGGTGG+TGG 0.505165 4.1:+59390791 None:intergenic
AAATCAAATGGTTGCACGCG+TGG 0.532950 4.1:+59390686 None:intergenic
AAGCGCGAACATTAGGAGGT+TGG 0.540533 4.1:+59390660 None:intergenic
TCGAAAGCGCGAACATTAGG+AGG 0.542553 4.1:+59390656 None:intergenic
ACTGCTAAAGCTTGTGGAGA+TGG 0.545041 4.1:+59390869 None:intergenic
AATGGTTGCACGCGTGGAGG+TGG 0.556418 4.1:+59390692 None:intergenic
ACATGCACTGCTAAAGCTTG+TGG 0.565788 4.1:+59390863 None:intergenic
GGTTGAGGCTGATTATTTGG+TGG 0.570406 4.1:+59390788 None:intergenic
TCAAATGGTTGCACGCGTGG+AGG 0.626989 4.1:+59390689 None:intergenic
GCATCAACCACAAAATGCAC+CGG 0.637007 4.1:-59390753 MS.gene73991:CDS
ATATTAGAATCGAGTAAACA+AGG 0.646902 4.1:-59390815 MS.gene73991:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
! ATATTAGAATCGAGTAAACA+AGG - chr4.1:59390724-59390743 MS.gene73991:CDS 25.0%
! CTCGATTCTAATATTAAATC+TGG + chr4.1:59390718-59390737 None:intergenic 25.0%
CTGGTGTATAAGGGATATTA+AGG + chr4.1:59390909-59390928 None:intergenic 35.0%
TGTGGTTGAGGCTGATTATT+TGG + chr4.1:59390757-59390776 None:intergenic 40.0%
! GGAGGTTGGTTCAAATCAAA+TGG + chr4.1:59390868-59390887 None:intergenic 40.0%
! TGCTCATCATTTTGTGGTTG+AGG + chr4.1:59390769-59390788 None:intergenic 40.0%
!! GGTTGATGCTCATCATTTTG+TGG + chr4.1:59390775-59390794 None:intergenic 40.0%
!! GGTTGATGTTCAGCATTTTG+TGG + chr4.1:59390817-59390836 None:intergenic 40.0%
AAATCAAATGGTTGCACGCG+TGG + chr4.1:59390856-59390875 None:intergenic 45.0%
ACATGCACTGCTAAAGCTTG+TGG + chr4.1:59390679-59390698 None:intergenic 45.0%
ACTGCTAAAGCTTGTGGAGA+TGG + chr4.1:59390673-59390692 None:intergenic 45.0%
GCATCAACCACAAAATGCAC+CGG - chr4.1:59390786-59390805 MS.gene73991:CDS 45.0%
GGTTGAGGCTGATTATTTGG+TGG + chr4.1:59390754-59390773 None:intergenic 45.0%
! TCAGCATTTTGTGGTAGAGC+CGG + chr4.1:59390808-59390827 None:intergenic 45.0%
! TGAGGCTGATTATTTGGTGG+TGG + chr4.1:59390751-59390770 None:intergenic 45.0%
AAGCGCGAACATTAGGAGGT+TGG + chr4.1:59390882-59390901 None:intergenic 50.0%
! AGGTCGAAAGCGCGAACATT+AGG + chr4.1:59390889-59390908 None:intergenic 50.0%
! TCGAAAGCGCGAACATTAGG+AGG + chr4.1:59390886-59390905 None:intergenic 50.0%
TCAAATGGTTGCACGCGTGG+AGG + chr4.1:59390853-59390872 None:intergenic 55.0%
! CGTGGAGGTGGTGCATTTTG+TGG + chr4.1:59390838-59390857 None:intergenic 55.0%
! GGTAGAGCCGGTGCATTTTG+TGG + chr4.1:59390796-59390815 None:intergenic 55.0%
AATGGTTGCACGCGTGGAGG+TGG + chr4.1:59390850-59390869 None:intergenic 60.0%


Chromosome Type Strat End Strand Name
chr4.1 gene 59390625 59390936 59390625 ID=MS.gene73991
chr4.1 mRNA 59390625 59390936 59390625 ID=MS.gene73991.t1;Parent=MS.gene73991
chr4.1 exon 59390625 59390936 59390625 ID=MS.gene73991.t1.exon1;Parent=MS.gene73991.t1
chr4.1 CDS 59390625 59390936 59390625 ID=cds.MS.gene73991.t1;Parent=MS.gene73991.t1
Gene Sequence

>MS.gene73991

ATGTCAAAGCTAGAATTCTTATGCAGTGAATGTGACACAATGTTTCCATCTCCACAAGCTTTAGCAGTGCATGTTATCGAAGAACATCATCCAGATTTAATATTAGAATCGAGTAAACAAGGTCCACCACCAAATAATCAGCCTCAACCACAAAATGATGAGCATCAACCACAAAATGCACCGGCTCTACCACAAAATGCTGAACATCAACCACAAAATGCACCACCTCCACGCGTGCAACCATTTGATTTGAACCAACCTCCTAATGTTCGCGCTTTCGACCTTAATATCCCTTATACACCAGATGAATGA
Protein sequence

>MS.gene73991.t1

MSKLEFLCSECDTMFPSPQALAVHVIEEHHPDLILESSKQGPPPNNQPQPQNDEHQPQNAPALPQNAEHQPQNAPPPRVQPFDLNQPPNVRAFDLNIPYTPDE