AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0747600

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0747600 MtrunA17_Chr4g0019481 83.761 117 18 1 1 116 1 117 5.95e-61 182
Msa0747600 MtrunA17_Chr4g0019471 74.809 131 18 2 1 116 1 131 1.85e-56 171
Msa0747600 MtrunA17_Chr4g0019551 76.068 117 27 1 1 116 1 117 8.18e-46 144
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 17 sgRNAs with CRISPR-Local

Find 28 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TCTGGTTCAGGCTGGTTATT+TGG 0.175696 5_2:+268893 None:intergenic
TCTCATTCATCTGGTGTATA+AGG 0.203991 5_2:+268692 None:intergenic
CTTGATTCTAATATATAATC+TGG 0.305373 5_2:+268932 None:intergenic
CTCATTCATCTGGTGTATAA+GGG 0.375685 5_2:+268693 None:intergenic
TCAGGCTGGTTATTTGGTGG+TGG 0.452210 5_2:+268899 None:intergenic
TTGAGGTCGAAAGCTTGAAC+AGG 0.493044 5_2:+268719 None:intergenic
GGAGGCTGGTTCAAGTCAAA+TGG 0.506887 5_2:+268740 None:intergenic
GGTTCAGGCTGGTTATTTGG+TGG 0.509510 5_2:+268896 None:intergenic
CGAAAGCTTGAACAGGAGGC+TGG 0.520977 5_2:+268726 None:intergenic
AAGTCAAATGGTTGCACATG+TGG 0.522527 5_2:+268752 None:intergenic
AATGGTTGCACATGTGGAGG+TGG 0.555990 5_2:+268758 None:intergenic
ACTGTTAAAGCTTCTCGAGA+TGG 0.587984 5_2:+268977 None:intergenic
CTGGTGTATAAGGGAGATTG+AGG 0.611261 5_2:+268702 None:intergenic
AGGTCGAAAGCTTGAACAGG+AGG 0.614849 5_2:+268722 None:intergenic
ATATTAGAATCAAGTAAACA+AGG 0.665430 5_2:-268923 Msa0747600:CDS
TCAAATGGTTGCACATGTGG+AGG 0.671560 5_2:+268755 None:intergenic
TCAAAGCTAGAATTCTTATG+CGG 0.715209 5_2:-269019 Msa0747600:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! CTTGATTCTAATATATAATC+TGG + chr5_2:268787-268806 None:intergenic 20.0%
!! ATATTAGAATCAAGTAAACA+AGG - chr5_2:268793-268812 Msa0747600:CDS 20.0%
TCAAAGCTAGAATTCTTATG+CGG - chr5_2:268697-268716 Msa0747600:CDS 30.0%
! TGTTCAACATTTTGTGGTTG+AGG + chr5_2:268859-268878 None:intergenic 35.0%
!! GGTTGATGTTCAACATTTTG+TGG + chr5_2:268865-268884 None:intergenic 35.0%
! TGATGTTCAACATTTTGTGG+TGG + chr5_2:268862-268881 None:intergenic 35.0%
!! GGTTGATGTTCAACATTTTG+TGG + chr5_2:268865-268884 None:intergenic 35.0%
ACTGTTAAAGCTTCTCGAGA+TGG + chr5_2:268742-268761 None:intergenic 40.0%
AAGTCAAATGGTTGCACATG+TGG + chr5_2:268967-268986 None:intergenic 40.0%
! TCTGGTTCAGGCTGGTTATT+TGG + chr5_2:268826-268845 None:intergenic 45.0%
!! TCAACATTTTGTGGTGGAGC+TGG + chr5_2:268898-268917 None:intergenic 45.0%
TCAAATGGTTGCACATGTGG+AGG + chr5_2:268964-268983 None:intergenic 45.0%
TTGAGGTCGAAAGCTTGAAC+AGG + chr5_2:269000-269019 None:intergenic 45.0%
CTGGTGTATAAGGGAGATTG+AGG + chr5_2:269017-269036 None:intergenic 45.0%
! TCAGGCTGGTTATTTGGTGG+TGG + chr5_2:268820-268839 None:intergenic 50.0%
! GGTTCAGGCTGGTTATTTGG+TGG + chr5_2:268823-268842 None:intergenic 50.0%
!!! GAGCATTTTCTGGTTCAGGC+TGG + chr5_2:268834-268853 None:intergenic 50.0%
!!! GGCTGAGCATTTTCTGGTTC+AGG + chr5_2:268838-268857 None:intergenic 50.0%
! GGTTGAGGCTGAGCATTTTC+TGG + chr5_2:268844-268863 None:intergenic 50.0%
! TGTGGAGGTGGTGCATTTTG+TGG + chr5_2:268949-268968 None:intergenic 50.0%
AATGGTTGCACATGTGGAGG+TGG + chr5_2:268961-268980 None:intergenic 50.0%
! GGAGGCTGGTTCAAGTCAAA+TGG + chr5_2:268979-268998 None:intergenic 50.0%
AGGTCGAAAGCTTGAACAGG+AGG + chr5_2:268997-269016 None:intergenic 50.0%
! GGTGGAGCTGGTGCATTTTG+TGG + chr5_2:268886-268905 None:intergenic 55.0%
! GGTGGAGCTGGTGCATTTTG+TGG + chr5_2:268886-268905 None:intergenic 55.0%
!! GGTGCATTTTGTGGTGGAGC+TGG + chr5_2:268940-268959 None:intergenic 55.0%
! GGAGGTGGTGCATTTTGTGG+TGG + chr5_2:268946-268965 None:intergenic 55.0%
CGAAAGCTTGAACAGGAGGC+TGG + chr5_2:268993-269012 None:intergenic 55.0%
Chromosome Type Strat End Strand Name
chr5_2 gene 268694 269044 268694 ID=Msa0747600;Name=Msa0747600
chr5_2 mRNA 268694 269044 268694 ID=Msa0747600-mRNA-1;Parent=Msa0747600;Name=Msa0747600-mRNA-1;_AED=0.00;_eAED=0.00;_QI=0|-1|0|1|-1|1|1|0|116
chr5_2 exon 268694 269044 268694 ID=Msa0747600-mRNA-1:exon:22;Parent=Msa0747600-mRNA-1
chr5_2 CDS 268694 269044 268694 ID=Msa0747600-mRNA-1:cds;Parent=Msa0747600-mRNA-1
Gene Sequence

>Msa0747600

ATGTCAAAGCTAGAATTCTTATGCGGTGAATGTGACACAATGTTTCCATCTCGAGAAGCTTTAACAGTGCATGTTATCGAAGAACATCATCCAGATTATATATTAGAATCAAGTAAACAAGGTCCACCACCAAATAACCAGCCTGAACCAGAAAATGCTCAGCCTCAACCACAAAATGTTGAACATCAACCACAAAATGCACCAGCTCCACCACAAAATGTTGAACATCAACCACAAAATGCACCAGCTCCACCACAAAATGCACCACCTCCACATGTGCAACCATTTGACTTGAACCAGCCTCCTGTTCAAGCTTTCGACCTCAATCTCCCTTATACACCAGATGAATGA
Protein sequence

>Msa0747600

MSKLEFLCGECDTMFPSREALTVHVIEEHHPDYILESSKQGPPPNNQPEPENAQPQPQNVEHQPQNAPAPPQNVEHQPQNAPAPPQNAPPPHVQPFDLNQPPVQAFDLNLPYTPDE*