AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1066430

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1066430 MtrunA17_Chr7g0246981 93.125 160 10 1 1 160 1 159 6.58e-107 301
Msa1066430 MtrunA17_Chr8g0349971 50.000 142 65 3 1 136 1 142 1.78e-41 139
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1066430 AT4G23890.1 45.324 139 66 4 2 135 3 136 1.82e-30 111

Find 22 sgRNAs with CRISPR-Local

Find 37 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GGGTTTCCTGGTGGTGAAAA+AGG 0.216558 7_2:+60476998 Msa1066430:CDS
TTTCTTTCTTCAATAGTAAA+AGG 0.267304 7_2:-60477067 None:intergenic
GGACTATGCAATGGAGAAAA+AGG 0.281632 7_2:+60476818 Msa1066430:CDS
TCCTTCTCAAAACCATCTTT+TGG 0.284985 7_2:-60476956 None:intergenic
GGGCTAACTGGAGGGTTTCC+TGG 0.314218 7_2:+60476986 Msa1066430:CDS
GCTACTCTTCAAGGCCTTCA+TGG 0.325932 7_2:+60476653 Msa1066430:CDS
AAGGAAATGATGGGGCTAAC+TGG 0.367060 7_2:+60476974 Msa1066430:CDS
AGAGTTGAACTATGTTGCTT+TGG 0.385186 7_2:-60477110 None:intergenic
ATTGCTGCAATTCCAAAAGA+TGG 0.433035 7_2:+60476944 Msa1066430:CDS
CTTCTACGATCTCAGTTCAT+AGG 0.439511 7_2:+60476680 Msa1066430:CDS
CGTGGTTGTAGTTGAGAAGC+TGG 0.452047 7_2:-60476758 None:intergenic
ATCGTAGAAGAGAGCCATGA+AGG 0.526335 7_2:-60476667 None:intergenic
GACTTGAACAAGAGCTGAAG+AGG 0.548181 7_2:+60476840 Msa1066430:CDS
AAAGGTTGAGAAGAATTCCT+AGG 0.555335 7_2:-60477049 None:intergenic
GAGGGAAGTGATGATGATCT+TGG 0.577411 7_2:-60476703 None:intergenic
AAAGTGCAAGAAAACTCAGA+TGG 0.584856 7_2:+60476899 Msa1066430:CDS
AAATGATGGGGCTAACTGGA+GGG 0.586145 7_2:+60476978 Msa1066430:CDS
GAAATGATGGGGCTAACTGG+AGG 0.588055 7_2:+60476977 Msa1066430:CDS
GGAGGAAGAGGACTATGCAA+TGG 0.605614 7_2:+60476809 Msa1066430:CDS
CTAACTGGAGGGTTTCCTGG+TGG 0.624925 7_2:+60476989 Msa1066430:CDS
GGTTGAGAAGAATTCCTAGG+TGG 0.675895 7_2:-60477046 None:intergenic
AGTATGTTGAATTCAGCACG+TGG 0.711591 7_2:-60476776 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! ATTCAACATACTAAAAATGA+TGG + chr7_2:60476787-60476806 Msa1066430:CDS 20.0%
!! TTCAACATACTAAAAATGAT+GGG + chr7_2:60476788-60476807 Msa1066430:CDS 20.0%
!! TTTCTTTCTTCAATAGTAAA+AGG - chr7_2:60477070-60477089 None:intergenic 20.0%
! AACATACTAAAAATGATGGG+AGG + chr7_2:60476791-60476810 Msa1066430:CDS 30.0%
! GTTTCTTTTGCTACTCTTCA+AGG + chr7_2:60476644-60476663 Msa1066430:CDS 35.0%
! TTGTGGAAGTTTTTGTGAGA+GGG - chr7_2:60476724-60476743 None:intergenic 35.0%
! GTTTTCTTGCACTTTCTCAT+TGG - chr7_2:60476894-60476913 None:intergenic 35.0%
AAAGTGCAAGAAAACTCAGA+TGG + chr7_2:60476899-60476918 Msa1066430:CDS 35.0%
ATTGCTGCAATTCCAAAAGA+TGG + chr7_2:60476944-60476963 Msa1066430:CDS 35.0%
!!! TCCAAAAGATGGTTTTGAGA+AGG + chr7_2:60476955-60476974 Msa1066430:CDS 35.0%
! TCCTTCTCAAAACCATCTTT+TGG - chr7_2:60476959-60476978 None:intergenic 35.0%
!!! TGGTTTTGAGAAGGAAATGA+TGG + chr7_2:60476964-60476983 Msa1066430:CDS 35.0%
!!! GGTTTTGAGAAGGAAATGAT+GGG + chr7_2:60476965-60476984 Msa1066430:CDS 35.0%
!!! GTTTTGAGAAGGAAATGATG+GGG + chr7_2:60476966-60476985 Msa1066430:CDS 35.0%
TCATTGAGAAAAATCCACCT+AGG + chr7_2:60477032-60477051 Msa1066430:CDS 35.0%
AAAGGTTGAGAAGAATTCCT+AGG - chr7_2:60477052-60477071 None:intergenic 35.0%
CTTCTACGATCTCAGTTCAT+AGG + chr7_2:60476680-60476699 Msa1066430:CDS 40.0%
! GTTGTGGAAGTTTTTGTGAG+AGG - chr7_2:60476725-60476744 None:intergenic 40.0%
! TGGTTTTCTGTGATGTGTTG+TGG - chr7_2:60476741-60476760 None:intergenic 40.0%
AGTATGTTGAATTCAGCACG+TGG - chr7_2:60476779-60476798 None:intergenic 40.0%
! CTAAAAATGATGGGAGGAAG+AGG + chr7_2:60476797-60476816 Msa1066430:CDS 40.0%
GGACTATGCAATGGAGAAAA+AGG + chr7_2:60476818-60476837 Msa1066430:CDS 40.0%
ATCGTAGAAGAGAGCCATGA+AGG - chr7_2:60476670-60476689 None:intergenic 45.0%
! GAGGGAAGTGATGATGATCT+TGG - chr7_2:60476706-60476725 None:intergenic 45.0%
GACTTGAACAAGAGCTGAAG+AGG + chr7_2:60476840-60476859 Msa1066430:CDS 45.0%
! AAGGAAATGATGGGGCTAAC+TGG + chr7_2:60476974-60476993 Msa1066430:CDS 45.0%
! AAATGATGGGGCTAACTGGA+GGG + chr7_2:60476978-60476997 Msa1066430:CDS 45.0%
! GGTTTCCTGGTGGTGAAAAA+GGG + chr7_2:60476999-60477018 Msa1066430:CDS 45.0%
!! ATCAACCCTTTTTCACCACC+AGG - chr7_2:60477007-60477026 None:intergenic 45.0%
GGTTGAGAAGAATTCCTAGG+TGG - chr7_2:60477049-60477068 None:intergenic 45.0%
GCTACTCTTCAAGGCCTTCA+TGG + chr7_2:60476653-60476672 Msa1066430:CDS 50.0%
CGTGGTTGTAGTTGAGAAGC+TGG - chr7_2:60476761-60476780 None:intergenic 50.0%
GGAGGAAGAGGACTATGCAA+TGG + chr7_2:60476809-60476828 Msa1066430:CDS 50.0%
! GAAATGATGGGGCTAACTGG+AGG + chr7_2:60476977-60476996 Msa1066430:CDS 50.0%
! GGGTTTCCTGGTGGTGAAAA+AGG + chr7_2:60476998-60477017 Msa1066430:CDS 50.0%
CTAACTGGAGGGTTTCCTGG+TGG + chr7_2:60476989-60477008 Msa1066430:CDS 55.0%
GGGCTAACTGGAGGGTTTCC+TGG + chr7_2:60476986-60477005 Msa1066430:CDS 60.0%
Chromosome Type Strat End Strand Name
chr7_2 gene 60476641 60477123 60476641 ID=Msa1066430;Name=Msa1066430
chr7_2 mRNA 60476641 60477123 60476641 ID=Msa1066430-mRNA-1;Parent=Msa1066430;Name=Msa1066430-mRNA-1;_AED=0.41;_eAED=0.41;_QI=0|-1|0|1|-1|1|1|0|160
chr7_2 exon 60476641 60477123 60476641 ID=Msa1066430-mRNA-1:exon:11868;Parent=Msa1066430-mRNA-1
chr7_2 CDS 60476641 60477123 60476641 ID=Msa1066430-mRNA-1:cds;Parent=Msa1066430-mRNA-1
Gene Sequence

>Msa1066430

ATGGTTTCTTTTGCTACTCTTCAAGGCCTTCATGGCTCTCTTCTACGATCTCAGTTCATAGGCCAAGATCATCATCACTTCCCTCTCACAAAAACTTCCACAACACATCACAGAAAACCAGCTTCTCAACTACAACCACGTGCTGAATTCAACATACTAAAAATGATGGGAGGAAGAGGACTATGCAATGGAGAAAAAGGACTTGAACAAGAGCTGAAGAGGCAAGTTGATAAAGATGAAACAGCATCATCCAATGAGAAAGTGCAAGAAAACTCAGATGGATCAGAAAAGTTGACTAGTGATATTGCTGCAATTCCAAAAGATGGTTTTGAGAAGGAAATGATGGGGCTAACTGGAGGGTTTCCTGGTGGTGAAAAAGGGTTGATTAAGTTCATTGAGAAAAATCCACCTAGGAATTCTTCTCAACCTTTTACTATTGAAGAAAGAAATCAAAGTCTTGTTGAAGAATCCAAAGCAACATAG
Protein sequence

>Msa1066430

MVSFATLQGLHGSLLRSQFIGQDHHHFPLTKTSTTHHRKPASQLQPRAEFNILKMMGGRGLCNGEKGLEQELKRQVDKDETASSNEKVQENSDGSEKLTSDIAAIPKDGFEKEMMGLTGGFPGGEKGLIKFIEKNPPRNSSQPFTIEERNQSLVEESKAT*