AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene68273

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene68273.t1 MTR_4g039380 78.632 117 17 2 1 109 1 117 4.32e-54 164
MS.gene68273.t1 MTR_4g039340 70.229 131 17 2 1 109 1 131 6.00e-52 160
MS.gene68273.t1 MTR_4g039640 78.632 117 17 2 1 109 1 117 2.97e-48 150
MS.gene68273.t1 MTR_4g039400 41.818 110 35 2 1 109 1 82 2.20e-11 55.5
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 16 sgRNAs with CRISPR-Local

Find 23 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TCTGGTTCAGGCTGGTTATT+TGG 0.175696 4.3:+61376857 None:intergenic
TCTCATTCATCTGGTGTATA+AGG 0.203991 4.3:+61376677 None:intergenic
CTAGATTCTAATATATAATC+TGG 0.344499 4.3:+61376896 None:intergenic
CTCATTCATCTGGTGTATAA+GGG 0.375685 4.3:+61376678 None:intergenic
TCAGGCTGGTTATTTGGTGG+TGG 0.452210 4.3:+61376863 None:intergenic
TTGAGGTCGAAAGCTTGAAC+AGG 0.493044 4.3:+61376704 None:intergenic
GGAGGCTGGTTCAAGTCAAA+TGG 0.506887 4.3:+61376725 None:intergenic
GGTTCAGGCTGGTTATTTGG+TGG 0.509510 4.3:+61376860 None:intergenic
CGAAAGCTTGAACAGGAGGC+TGG 0.520977 4.3:+61376711 None:intergenic
AAGTCAAATGGTTGCACATG+TGG 0.522527 4.3:+61376737 None:intergenic
AATGGTTGCACATGTGGAGG+TGG 0.555990 4.3:+61376743 None:intergenic
ACTGCTAAAGCTTCTCGAGA+TGG 0.596385 4.3:+61376941 None:intergenic
CTGGTGTATAAGGGAGATTG+AGG 0.611261 4.3:+61376687 None:intergenic
AGGTCGAAAGCTTGAACAGG+AGG 0.614849 4.3:+61376707 None:intergenic
ATATTAGAATCTAGTAAACA+AGG 0.648272 4.3:-61376887 MS.gene68273:CDS
TCAAATGGTTGCACATGTGG+AGG 0.671560 4.3:+61376740 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! ATATTAGAATCTAGTAAACA+AGG - chr4.3:61376778-61376797 MS.gene68273:CDS 20.0%
!! CTAGATTCTAATATATAATC+TGG + chr4.3:61376772-61376791 None:intergenic 20.0%
! TGATGTTCAACATTTTGTGG+TGG + chr4.3:61376847-61376866 None:intergenic 35.0%
! TGTTCAACATTTTGTGGTTG+AGG + chr4.3:61376844-61376863 None:intergenic 35.0%
!! GGTTGATGTTCAACATTTTG+TGG + chr4.3:61376850-61376869 None:intergenic 35.0%
AAGTCAAATGGTTGCACATG+TGG + chr4.3:61376931-61376950 None:intergenic 40.0%
ACTGCTAAAGCTTCTCGAGA+TGG + chr4.3:61376727-61376746 None:intergenic 45.0%
CTGGTGTATAAGGGAGATTG+AGG + chr4.3:61376981-61377000 None:intergenic 45.0%
TCAAATGGTTGCACATGTGG+AGG + chr4.3:61376928-61376947 None:intergenic 45.0%
TTGAGGTCGAAAGCTTGAAC+AGG + chr4.3:61376964-61376983 None:intergenic 45.0%
! TCTGGTTCAGGCTGGTTATT+TGG + chr4.3:61376811-61376830 None:intergenic 45.0%
!! TCAACATTTTGTGGTGGAGC+TGG + chr4.3:61376883-61376902 None:intergenic 45.0%
AATGGTTGCACATGTGGAGG+TGG + chr4.3:61376925-61376944 None:intergenic 50.0%
AGGTCGAAAGCTTGAACAGG+AGG + chr4.3:61376961-61376980 None:intergenic 50.0%
! GGAGGCTGGTTCAAGTCAAA+TGG + chr4.3:61376943-61376962 None:intergenic 50.0%
! GGTTCAGGCTGGTTATTTGG+TGG + chr4.3:61376808-61376827 None:intergenic 50.0%
! GGTTGAGGCTGAGCATTTTC+TGG + chr4.3:61376829-61376848 None:intergenic 50.0%
! TCAGGCTGGTTATTTGGTGG+TGG + chr4.3:61376805-61376824 None:intergenic 50.0%
! TGTGGAGGTGGTGCATTTTG+TGG + chr4.3:61376913-61376932 None:intergenic 50.0%
!!! GAGCATTTTCTGGTTCAGGC+TGG + chr4.3:61376819-61376838 None:intergenic 50.0%
!!! GGCTGAGCATTTTCTGGTTC+AGG + chr4.3:61376823-61376842 None:intergenic 50.0%
CGAAAGCTTGAACAGGAGGC+TGG + chr4.3:61376957-61376976 None:intergenic 55.0%
! GGTGGAGCTGGTGCATTTTG+TGG + chr4.3:61376871-61376890 None:intergenic 55.0%


Chromosome Type Strat End Strand Name
chr4.3 gene 61376679 61377008 61376679 ID=MS.gene68273
chr4.3 mRNA 61376679 61377008 61376679 ID=MS.gene68273.t1;Parent=MS.gene68273
chr4.3 exon 61376679 61377008 61376679 ID=MS.gene68273.t1.exon1;Parent=MS.gene68273.t1
chr4.3 CDS 61376679 61377008 61376679 ID=cds.MS.gene68273.t1;Parent=MS.gene68273.t1
Gene Sequence

>MS.gene68273

ATGTCAAAGCAAGAATTCTTATGCAGTGAATGTGACACAATGTTTCCATCTCGAGAAGCTTTAGCAGTGCATGTTATCGAAGAACATCATCCAGATTATATATTAGAATCTAGTAAACAAGGTCCACCACCAAATAACCAGCCTGAACCAGAAAATGCTCAGCCTCAACCACAAAATGTTGAACATCAACCACAAAATGCACCAGCTCCACCACAAAATGTTGAACATCAACCACAAAATGCACCACCTCCACATGTGCAACCATTTGACTTGAACCAGCCTCCTGTTCAAGCTTTCGACCTCAATCTCCCTTATACACCAGATGAATGA
Protein sequence

>MS.gene68273.t1

MSKQEFLCSECDTMFPSREALAVHVIEEHHPDYILESSKQGPPPNNQPEPENAQPQPQNVEHQPQNAPAPPQNVEHQPQNAPPPHVQPFDLNQPPVQAFDLNLPYTPDE