AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1115580


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1115580 MtrunA17_Chr7g0246981 93.711 159 10 0 1 159 1 159 2.10e-108 305
Msa1115580 MtrunA17_Chr8g0349971 48.592 142 66 3 1 135 1 142 8.69e-40 134
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1115580 AT4G23890.1 47.368 133 63 3 6 134 7 136 2.88e-32 115

Find 26 sgRNAs with CRISPR-Local

Find 38 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GGGTTTCCTGGTGGTGAAAA+AGG 0.216558 7_3:+63073116 Msa1115580:CDS
TTTATTTCTTCAATAGTAAA+AGG 0.269787 7_3:-63073185 None:intergenic
GGACTATGCAATGGAGAAAA+AGG 0.281632 7_3:+63072936 Msa1115580:CDS
GGGCTAACTGGAGGGTTTCC+TGG 0.314218 7_3:+63073104 Msa1115580:CDS
GCTACTCTTCAAGGAATTCA+TGG 0.329958 7_3:+63072774 Msa1115580:CDS
TCCTTCTCAAAACCATCTTT+AGG 0.343967 7_3:-63073074 None:intergenic
AAGGAAATGATGGGGCTAAC+TGG 0.367060 7_3:+63073092 Msa1115580:CDS
AGAGTTGAACTATGTTGCTT+TGG 0.385186 7_3:-63073228 None:intergenic
GGTGATCTTGGCCTATGAAC+TGG 0.404590 7_3:-63072812 None:intergenic
CAAGTTGATAAAGATGAAAC+AGG 0.427205 7_3:+63072981 Msa1115580:CDS
ATTGCTGCAATTCCTAAAGA+TGG 0.439610 7_3:+63073062 Msa1115580:CDS
CGTGGTTGTAGTTGAGAAGT+TGG 0.442826 7_3:-63072876 None:intergenic
GACTTGAACAAGAGCTGAAA+AGG 0.446004 7_3:+63072958 Msa1115580:CDS
CTCCTACGATCCCAGTTCAT+AGG 0.487970 7_3:+63072801 Msa1115580:CDS
TGAGAGTGAAGTGGTGATCT+TGG 0.497067 7_3:-63072824 None:intergenic
AAAGGTTGAGAAGAATTCCT+AGG 0.555335 7_3:-63073167 None:intergenic
GTGATCTTGGCCTATGAACT+GGG 0.572739 7_3:-63072811 None:intergenic
AAAGTGCAAGAAAACTCAGA+TGG 0.584856 7_3:+63073017 Msa1115580:CDS
AAATGATGGGGCTAACTGGA+GGG 0.586145 7_3:+63073096 Msa1115580:CDS
GGCCTATGAACTGGGATCGT+AGG 0.587300 7_3:-63072803 None:intergenic
GAAATGATGGGGCTAACTGG+AGG 0.588055 7_3:+63073095 Msa1115580:CDS
GGAGGAAGAGGACTATGCAA+TGG 0.605614 7_3:+63072927 Msa1115580:CDS
AAGATTTCATGAGAGTGAAG+TGG 0.619848 7_3:-63072833 None:intergenic
CTAACTGGAGGGTTTCCTGG+TGG 0.624925 7_3:+63073107 Msa1115580:CDS
GGTTGAGAAGAATTCCTAGG+TGG 0.675895 7_3:-63073164 None:intergenic
AGTATGTTGAATTCAGCACG+TGG 0.711591 7_3:-63072894 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! TTTATTTCTTCAATAGTAAA+AGG - chr7_3:63073188-63073207 None:intergenic 15.0%
!! ATTCAACATACTAAAAATGA+TGG + chr7_3:63072905-63072924 Msa1115580:CDS 20.0%
!! TTCAACATACTAAAAATGAT+GGG + chr7_3:63072906-63072925 Msa1115580:CDS 20.0%
! AACATACTAAAAATGATGGG+AGG + chr7_3:63072909-63072928 Msa1115580:CDS 30.0%
!! CAAGTTGATAAAGATGAAAC+AGG + chr7_3:63072981-63073000 Msa1115580:CDS 30.0%
!!! GTTTTCTTGCACTTTTTCAT+TGG - chr7_3:63073012-63073031 None:intergenic 30.0%
AAGATTTCATGAGAGTGAAG+TGG - chr7_3:63072836-63072855 None:intergenic 35.0%
AAAGTGCAAGAAAACTCAGA+TGG + chr7_3:63073017-63073036 Msa1115580:CDS 35.0%
ATTGCTGCAATTCCTAAAGA+TGG + chr7_3:63073062-63073081 Msa1115580:CDS 35.0%
!!! TCCTAAAGATGGTTTTGAGA+AGG + chr7_3:63073073-63073092 Msa1115580:CDS 35.0%
TCCTTCTCAAAACCATCTTT+AGG - chr7_3:63073077-63073096 None:intergenic 35.0%
!!! TGGTTTTGAGAAGGAAATGA+TGG + chr7_3:63073082-63073101 Msa1115580:CDS 35.0%
!!! GGTTTTGAGAAGGAAATGAT+GGG + chr7_3:63073083-63073102 Msa1115580:CDS 35.0%
!!! GTTTTGAGAAGGAAATGATG+GGG + chr7_3:63073084-63073103 Msa1115580:CDS 35.0%
TCATTGAGAAAAATCCACCT+AGG + chr7_3:63073150-63073169 Msa1115580:CDS 35.0%
AAAGGTTGAGAAGAATTCCT+AGG - chr7_3:63073170-63073189 None:intergenic 35.0%
GCTACTCTTCAAGGAATTCA+TGG + chr7_3:63072774-63072793 Msa1115580:CDS 40.0%
AGTATGTTGAATTCAGCACG+TGG - chr7_3:63072897-63072916 None:intergenic 40.0%
! CTAAAAATGATGGGAGGAAG+AGG + chr7_3:63072915-63072934 Msa1115580:CDS 40.0%
GGACTATGCAATGGAGAAAA+AGG + chr7_3:63072936-63072955 Msa1115580:CDS 40.0%
GACTTGAACAAGAGCTGAAA+AGG + chr7_3:63072958-63072977 Msa1115580:CDS 40.0%
!!! GCTGCTTTTGCTACTCTTCA+AGG + chr7_3:63072765-63072784 Msa1115580:CDS 45.0%
GTGATCTTGGCCTATGAACT+GGG - chr7_3:63072814-63072833 None:intergenic 45.0%
TGAGAGTGAAGTGGTGATCT+TGG - chr7_3:63072827-63072846 None:intergenic 45.0%
CGTGGTTGTAGTTGAGAAGT+TGG - chr7_3:63072879-63072898 None:intergenic 45.0%
! AAGGAAATGATGGGGCTAAC+TGG + chr7_3:63073092-63073111 Msa1115580:CDS 45.0%
! AAATGATGGGGCTAACTGGA+GGG + chr7_3:63073096-63073115 Msa1115580:CDS 45.0%
! GGTTTCCTGGTGGTGAAAAA+GGG + chr7_3:63073117-63073136 Msa1115580:CDS 45.0%
!! ATCAACCCTTTTTCACCACC+AGG - chr7_3:63073125-63073144 None:intergenic 45.0%
GGTTGAGAAGAATTCCTAGG+TGG - chr7_3:63073167-63073186 None:intergenic 45.0%
CTCCTACGATCCCAGTTCAT+AGG + chr7_3:63072801-63072820 Msa1115580:CDS 50.0%
GGTGATCTTGGCCTATGAAC+TGG - chr7_3:63072815-63072834 None:intergenic 50.0%
GGAGGAAGAGGACTATGCAA+TGG + chr7_3:63072927-63072946 Msa1115580:CDS 50.0%
! GAAATGATGGGGCTAACTGG+AGG + chr7_3:63073095-63073114 Msa1115580:CDS 50.0%
! GGGTTTCCTGGTGGTGAAAA+AGG + chr7_3:63073116-63073135 Msa1115580:CDS 50.0%
GGCCTATGAACTGGGATCGT+AGG - chr7_3:63072806-63072825 None:intergenic 55.0%
CTAACTGGAGGGTTTCCTGG+TGG + chr7_3:63073107-63073126 Msa1115580:CDS 55.0%
GGGCTAACTGGAGGGTTTCC+TGG + chr7_3:63073104-63073123 Msa1115580:CDS 60.0%
Chromosome Type Strat End Strand Name
chr7_3 gene 63072762 63073241 63072762 ID=Msa1115580;Name=Msa1115580
chr7_3 mRNA 63072762 63073241 63072762 ID=Msa1115580-mRNA-1;Parent=Msa1115580;Name=Msa1115580-mRNA-1;_AED=0.40;_eAED=0.40;_QI=0|-1|0|1|-1|1|1|0|159
chr7_3 exon 63072762 63073241 63072762 ID=Msa1115580-mRNA-1:exon:14634;Parent=Msa1115580-mRNA-1
chr7_3 CDS 63072762 63073241 63072762 ID=Msa1115580-mRNA-1:cds;Parent=Msa1115580-mRNA-1
Gene Sequence

>Msa1115580

ATGGCTGCTTTTGCTACTCTTCAAGGAATTCATGGCTCTCTCCTACGATCCCAGTTCATAGGCCAAGATCACCACTTCACTCTCATGAAATCTTCAACAACACATCACAGAAAACCAACTTCTCAACTACAACCACGTGCTGAATTCAACATACTAAAAATGATGGGAGGAAGAGGACTATGCAATGGAGAAAAAGGACTTGAACAAGAGCTGAAAAGGCAAGTTGATAAAGATGAAACAGGATCATCCAATGAAAAAGTGCAAGAAAACTCAGATGGATCAGAAAAGTTGACTAGTGATATTGCTGCAATTCCTAAAGATGGTTTTGAGAAGGAAATGATGGGGCTAACTGGAGGGTTTCCTGGTGGTGAAAAAGGGTTGATTAAGTTCATTGAGAAAAATCCACCTAGGAATTCTTCTCAACCTTTTACTATTGAAGAAATAAATCAAAGTCTTGTTGAAGAATCCAAAGCAACATAG

Protein sequence

>Msa1115580

MAAFATLQGIHGSLLRSQFIGQDHHFTLMKSSTTHHRKPTSQLQPRAEFNILKMMGGRGLCNGEKGLEQELKRQVDKDETGSSNEKVQENSDGSEKLTSDIAAIPKDGFEKEMMGLTGGFPGGEKGLIKFIEKNPPRNSSQPFTIEEINQSLVEESKAT*