AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1363830

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1363830 MtrunA17_Chr8g0387971 95.455 176 5 2 1 174 1 175 2.82e-120 337
Msa1363830 MtrunA17_Chr5g0396791 49.714 175 80 5 4 174 21 191 2.47e-40 134
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1363830 AT5G41810.2 43.750 176 78 5 10 174 114 279 4.11e-29 108
Msa1363830 AT5G41810.1 43.750 176 78 5 10 174 123 288 6.06e-29 108
Msa1363830 AT1G64340.1 37.419 155 73 6 10 163 123 254 3.11e-18 79.7
Msa1363830 AT1G64340.2 37.419 155 73 6 10 163 119 250 3.22e-18 79.7

Find 29 sgRNAs with CRISPR-Local

Find 30 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
AAACGTTGTTCTTGATCTTT+TGG 0.226095 tig0018089:+33619 None:intergenic
TAGCTATAGCTGAATCAATT+TGG 0.287046 tig0018089:+33872 None:intergenic
ATCTCAAAATCAGGAAGTTC+AGG 0.333477 tig0018089:+33544 None:intergenic
GCTAGAAGAATTAACCTTGT+TGG 0.344850 tig0018089:+33672 None:intergenic
GTCATCTTCTGAGAGGTTTA+CGG 0.370763 tig0018089:-33482 Msa1363830:CDS
CTGACGAAGTTACTTATATC+CGG 0.400755 tig0018089:+33508 None:intergenic
ACTTATATCCGGCGAAAGTC+CGG 0.402895 tig0018089:+33519 None:intergenic
TCAAGAACAACGTTTGTGTA+TGG 0.416995 tig0018089:-33611 Msa1363830:CDS
CTTGTTGGATTTATTGCCAC+TGG 0.431380 tig0018089:+33687 None:intergenic
AGTCCGGCAATCTCAAAATC+AGG 0.448554 tig0018089:+33535 None:intergenic
TGAGGCATGGAATGTGTTCT+TGG 0.456511 tig0018089:+33844 None:intergenic
GTTGAGGTTGAACTTGAAGT+TGG 0.459084 tig0018089:+33803 None:intergenic
GGAATGGTTGATAGAAGAAT+AGG 0.460811 tig0018089:+33565 None:intergenic
TGAGATTGCCGGACTTTCGC+CGG 0.483557 tig0018089:-33527 Msa1363830:CDS
TTGGTATTTCGTGTGCTTGA+GGG 0.498308 tig0018089:-33447 None:intergenic
ATTGGTATTTCGTGTGCTTG+AGG 0.539169 tig0018089:-33448 None:intergenic
GTTGTTGATCACAAGAGAAG+AGG 0.552835 tig0018089:+33768 None:intergenic
AAAATCAGGAAGTTCAGGAA+TGG 0.592926 tig0018089:+33549 None:intergenic
AAGAGTACAAAGTGGGATTG+TGG 0.599534 tig0018089:-33937 Msa1363830:CDS
TTGATCACAAGAGAAGAGGT+TGG 0.601610 tig0018089:+33772 None:intergenic
TTTACGGCAACAGCTAACAT+TGG 0.623145 tig0018089:-33466 Msa1363830:CDS
TCAGAAAGTCATCTTCTGAG+AGG 0.624842 tig0018089:-33489 Msa1363830:CDS
ACGTTGTGGTAAATGAGGCA+TGG 0.640259 tig0018089:+33831 None:intergenic
CAGTGGCAATAAATCCAACA+AGG 0.642893 tig0018089:-33686 Msa1363830:CDS
ATATTCAAAGAGTACAAAGT+GGG 0.644274 tig0018089:-33944 Msa1363830:CDS
AATATTCAAAGAGTACAAAG+TGG 0.650414 tig0018089:-33945 Msa1363830:CDS
AGTGTACGTTGTGGTAAATG+AGG 0.664152 tig0018089:+33826 None:intergenic
GAGGTTGGCTCATGATGTTG+AGG 0.689173 tig0018089:+33787 None:intergenic
TGAAGTTGGAGTGTACGTTG+TGG 0.776294 tig0018089:+33817 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AATATTCAAAGAGTACAAAG+TGG - tig0018089:33457-33476 Msa1363830:CDS 25.0%
!! ATATTCAAAGAGTACAAAGT+GGG - tig0018089:33458-33477 Msa1363830:CDS 25.0%
TAGCTATAGCTGAATCAATT+TGG + tig0018089:33533-33552 None:intergenic 30.0%
! AAACGTTGTTCTTGATCTTT+TGG + tig0018089:33786-33805 None:intergenic 30.0%
! AAAGCGAAGAAGCTTTTGAA+AGG + tig0018089:33685-33704 None:intergenic 35.0%
GCTAGAAGAATTAACCTTGT+TGG + tig0018089:33733-33752 None:intergenic 35.0%
TCAAGAACAACGTTTGTGTA+TGG - tig0018089:33791-33810 Msa1363830:CDS 35.0%
!! GGAATGGTTGATAGAAGAAT+AGG + tig0018089:33840-33859 None:intergenic 35.0%
AAAATCAGGAAGTTCAGGAA+TGG + tig0018089:33856-33875 None:intergenic 35.0%
ATCTCAAAATCAGGAAGTTC+AGG + tig0018089:33861-33880 None:intergenic 35.0%
CTGACGAAGTTACTTATATC+CGG + tig0018089:33897-33916 None:intergenic 35.0%
! AAGAGTACAAAGTGGGATTG+TGG - tig0018089:33465-33484 Msa1363830:CDS 40.0%
AGTGTACGTTGTGGTAAATG+AGG + tig0018089:33579-33598 None:intergenic 40.0%
GTTGAGGTTGAACTTGAAGT+TGG + tig0018089:33602-33621 None:intergenic 40.0%
TTGATCACAAGAGAAGAGGT+TGG + tig0018089:33633-33652 None:intergenic 40.0%
GTTGTTGATCACAAGAGAAG+AGG + tig0018089:33637-33656 None:intergenic 40.0%
CTTGTTGGATTTATTGCCAC+TGG + tig0018089:33718-33737 None:intergenic 40.0%
CAGTGGCAATAAATCCAACA+AGG - tig0018089:33716-33735 Msa1363830:CDS 40.0%
!!! CTTCCTGATTTTGAGATTGC+CGG - tig0018089:33864-33883 Msa1363830:CDS 40.0%
TCAGAAAGTCATCTTCTGAG+AGG - tig0018089:33913-33932 Msa1363830:CDS 40.0%
! GTCATCTTCTGAGAGGTTTA+CGG - tig0018089:33920-33939 Msa1363830:CDS 40.0%
TTTACGGCAACAGCTAACAT+TGG - tig0018089:33936-33955 Msa1363830:CDS 40.0%
TGAGGCATGGAATGTGTTCT+TGG + tig0018089:33561-33580 None:intergenic 45.0%
ACGTTGTGGTAAATGAGGCA+TGG + tig0018089:33574-33593 None:intergenic 45.0%
TGAAGTTGGAGTGTACGTTG+TGG + tig0018089:33588-33607 None:intergenic 45.0%
!!! CGCTTTGTTTTCAAGTCCAG+TGG - tig0018089:33699-33718 Msa1363830:CDS 45.0%
AGTCCGGCAATCTCAAAATC+AGG + tig0018089:33870-33889 None:intergenic 45.0%
ACTTATATCCGGCGAAAGTC+CGG + tig0018089:33886-33905 None:intergenic 45.0%
! GAGGTTGGCTCATGATGTTG+AGG + tig0018089:33618-33637 None:intergenic 50.0%
TGAGATTGCCGGACTTTCGC+CGG - tig0018089:33875-33894 Msa1363830:CDS 55.0%
Chromosome Type Strat End Strand Name
tig0018089 gene 33450 33974 33450 ID=Msa1363830;Name=Msa1363830
tig0018089 mRNA 33450 33974 33450 ID=Msa1363830-mRNA-1;Parent=Msa1363830;Name=Msa1363830-mRNA-1;_AED=0.02;_eAED=0.02;_QI=0|-1|0|1|-1|1|1|0|174
tig0018089 exon 33450 33974 33450 ID=Msa1363830-mRNA-1:exon:13715;Parent=Msa1363830-mRNA-1
tig0018089 CDS 33450 33974 33450 ID=Msa1363830-mRNA-1:cds;Parent=Msa1363830-mRNA-1
Gene Sequence

>Msa1363830

ATGGAGAAATATTCAAAGAGTACAAAGTGGGATTGTGGTAGCACTCTATATGACTCATACGAACTAAACTCATTCAAACGCCAAATTGATTCAGCTATAGCTAACTCACCAAGAACACATTCCATGCCTCATTTACCACAACGTACACTCCAACTTCAAGTTCAACCTCAACATCATGAGCCAACCTCTTCTCTTGTGATCAACAACAAGTCAACTTTCAAGATCTCTCGTACCTTTCAAAAGCTTCTTCGCTTTGTTTTCAAGTCCAGTGGCAATAAATCCAACAAGGTTAATTCTTCTAGCAGCTCATATAGCAATAGTTTTCGATCATATCCAAAAGATCAAGAACAACGTTTGTGTATGGTTTATGACAAATATGAGTCAGAGCCTATTCTTCTATCAACCATTCCTGAACTTCCTGATTTTGAGATTGCCGGACTTTCGCCGGATATAAGTAACTTCGTCAGAAAGTCATCTTCTGAGAGGTTTACGGCAACAGCTAACATTGGTATTTCGTGTGCTTGA
Protein sequence

>Msa1363830

MEKYSKSTKWDCGSTLYDSYELNSFKRQIDSAIANSPRTHSMPHLPQRTLQLQVQPQHHEPTSSLVINNKSTFKISRTFQKLLRFVFKSSGNKSNKVNSSSSSYSNSFRSYPKDQEQRLCMVYDKYESEPILLSTIPELPDFEIAGLSPDISNFVRKSSSERFTATANIGISCA*