AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0644890


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0644890 MtrunA17_Chr4g0032291 55.833 120 4 1 43 113 46 165 1.35e-35 119
Msa0644890 MtrunA17_Chr4g0032581 51.007 149 21 4 14 113 8 153 1.82e-29 103
Msa0644890 MtrunA17_Chr4g0032571 50.000 138 20 2 12 101 1 137 2.17e-28 100
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0644890 AT2G26975.1 36.735 147 38 4 12 107 1 143 6.70e-18 74.3
Msa0644890 AT5G59030.1 33.871 124 29 3 43 113 45 168 7.73e-12 58.9
Msa0644890 AT3G46900.1 32.203 118 29 3 44 110 34 151 5.68e-11 56.6

Find 38 sgRNAs with CRISPR-Local

Find 56 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TAGGGTTGGGTTAGCTTATT+TGG 0.161485 4_3:-49246748 Msa0644890:intron
AGAGGTTACTGTGTGGTTAC+AGG 0.278616 4_3:+49247106 None:intergenic
TCTTGTGTAGCAGTGCTATT+AGG 0.286924 4_3:-49246653 Msa0644890:CDS
TGATGCACATGACATTCTTC+TGG 0.300847 4_3:-49246953 Msa0644890:CDS
ATGTAATAAATGTGTATTTA+GGG 0.312526 4_3:+49247138 None:intergenic
TAAGCCTTATCATCATGTTT+TGG 0.336110 4_3:+49246627 None:intergenic
AATGTAATAAATGTGTATTT+AGG 0.339646 4_3:+49247137 None:intergenic
TACTGTGTGGTTACAGGGTT+TGG 0.340111 4_3:+49247112 None:intergenic
GTTGATGATGATGATGGTTT+TGG 0.347605 4_3:+49247014 None:intergenic
CTTTAATTCTCTTCAACAAT+TGG 0.349322 4_3:-49246920 Msa0644890:CDS
GCTGTGCTTGGTCATGCTCT+TGG 0.350764 4_3:-49246681 Msa0644890:CDS
TTGGCTCTTATGTCTTTCAA+TGG 0.387989 4_3:-49246720 Msa0644890:CDS
GTTAGCTTATTTGGTTATGT+TGG 0.388968 4_3:-49246739 Msa0644890:intron
GAAACCAAAACATGATGATA+AGG 0.457740 4_3:-49246631 Msa0644890:CDS
GATGCACATGACATTCTTCT+GGG 0.472072 4_3:-49246952 Msa0644890:CDS
AACGAATAACACCATGATGA+TGG 0.472546 4_3:-49246994 Msa0644890:CDS
CTCTTCAACAATTGGCCTAA+CGG 0.488088 4_3:-49246912 Msa0644890:CDS
ATGCACGGTGGCGGCATGGA+TGG 0.492115 4_3:-49247050 Msa0644890:CDS
AATTGGCCTAACGGTGATAC+CGG 0.503435 4_3:-49246903 Msa0644890:intron
CTCTTCAGATCTCACATCCA+TGG 0.529767 4_3:-49247087 Msa0644890:exon
TTATTCGTTGATGATGATGA+TGG 0.530330 4_3:+49247008 None:intergenic
GAGGTTACTGTGTGGTTACA+GGG 0.531390 4_3:+49247107 None:intergenic
GGTGGTAACATGCACGGTGG+CGG 0.534398 4_3:-49247059 Msa0644890:CDS
GCTCTTATGTCTTTCAATGG+TGG 0.539076 4_3:-49246717 Msa0644890:CDS
GATCTCACATCCATGGATCA+TGG 0.541471 4_3:-49247080 Msa0644890:exon
ACGAATAACACCATGATGAT+GGG 0.553848 4_3:-49246993 Msa0644890:CDS
CATGTTACCACCATGATCCA+TGG 0.570126 4_3:+49247070 None:intergenic
CATCTTATGACCCATCATCA+TGG 0.576922 4_3:+49246983 None:intergenic
CATGGATGTGAGATCTGAAG+AGG 0.588461 4_3:+49247088 None:intergenic
TAACATGCACGGTGGCGGCA+TGG 0.592169 4_3:-49247054 Msa0644890:CDS
ATGATGGGTCATAAGATGCA+CGG 0.642320 4_3:-49246978 Msa0644890:CDS
AACAATTAACAAGACAAGGG+AGG 0.655863 4_3:+49246597 None:intergenic
TACATACCGGTATCACCGTT+AGG 0.669036 4_3:+49246897 None:intergenic
ATGCACATGACATTCTTCTG+GGG 0.701142 4_3:-49246951 Msa0644890:CDS
GATCATGGTGGTAACATGCA+CGG 0.714076 4_3:-49247065 Msa0644890:CDS
CTCACATCCATGGATCATGG+TGG 0.733160 4_3:-49247077 Msa0644890:exon
CATGGTGGTAACATGCACGG+TGG 0.787274 4_3:-49247062 Msa0644890:CDS
GATCTGAAGAGGTTACTGTG+TGG 0.856147 4_3:+49247099 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! ATGTAATAAATGTGTATTTA+GGG + chr4_3:49246650-49246669 None:intergenic 15.0%
!! AATGTAATAAATGTGTATTT+AGG + chr4_3:49246651-49246670 None:intergenic 15.0%
! CTTTAATTCTCTTCAACAAT+TGG - chr4_3:49246865-49246884 Msa0644890:intron 25.0%
!! TTATTCGTTGATGATGATGA+TGG + chr4_3:49246780-49246799 None:intergenic 30.0%
! GTTAGCTTATTTGGTTATGT+TGG - chr4_3:49247046-49247065 Msa0644890:CDS 30.0%
GAAACCAAAACATGATGATA+AGG - chr4_3:49247154-49247173 Msa0644890:five_prime_UTR 30.0%
!! TAAGCCTTATCATCATGTTT+TGG + chr4_3:49247161-49247180 None:intergenic 30.0%
!!! GTTGATGATGATGATGGTTT+TGG + chr4_3:49246774-49246793 None:intergenic 35.0%
AACGAATAACACCATGATGA+TGG - chr4_3:49246791-49246810 Msa0644890:intron 35.0%
ACGAATAACACCATGATGAT+GGG - chr4_3:49246792-49246811 Msa0644890:intron 35.0%
TGATACCGGTATGTATGTAT+TGG - chr4_3:49246896-49246915 Msa0644890:intron 35.0%
GTACAGACATGACAAAAACA+AGG + chr4_3:49246929-49246948 None:intergenic 35.0%
!! CAAAAGTGTCTGAAACAAAC+CGG + chr4_3:49247009-49247028 None:intergenic 35.0%
! AGACACTTTTGCATGTTCTT+AGG - chr4_3:49247018-49247037 Msa0644890:CDS 35.0%
! GACACTTTTGCATGTTCTTA+GGG - chr4_3:49247019-49247038 Msa0644890:CDS 35.0%
! TTTTGCATGTTCTTAGGGTT+GGG - chr4_3:49247024-49247043 Msa0644890:CDS 35.0%
! TTGGCTCTTATGTCTTTCAA+TGG - chr4_3:49247065-49247084 Msa0644890:CDS 35.0%
!! TTTCAATGGTGGTGTGTTTT+TGG - chr4_3:49247079-49247098 Msa0644890:exon 35.0%
!!! GATGATGATGATGGTTTTGG+TGG + chr4_3:49246771-49246790 None:intergenic 40.0%
CATCTTATGACCCATCATCA+TGG + chr4_3:49246805-49246824 None:intergenic 40.0%
!! ATGATGGGTCATAAGATGCA+CGG - chr4_3:49246807-49246826 Msa0644890:intron 40.0%
TGATGCACATGACATTCTTC+TGG - chr4_3:49246832-49246851 Msa0644890:intron 40.0%
GATGCACATGACATTCTTCT+GGG - chr4_3:49246833-49246852 Msa0644890:intron 40.0%
ATGCACATGACATTCTTCTG+GGG - chr4_3:49246834-49246853 Msa0644890:intron 40.0%
! CTCTTCAACAATTGGCCTAA+CGG - chr4_3:49246873-49246892 Msa0644890:intron 40.0%
CAACGCCAATACATACATAC+CGG + chr4_3:49246904-49246923 None:intergenic 40.0%
TTGAATTACTCTCCCGTACA+CGG - chr4_3:49246952-49246971 Msa0644890:CDS 40.0%
! CTTTTGCATGTTCTTAGGGT+TGG - chr4_3:49247023-49247042 Msa0644890:CDS 40.0%
!! TAGGGTTGGGTTAGCTTATT+TGG - chr4_3:49247037-49247056 Msa0644890:CDS 40.0%
GCTCTTATGTCTTTCAATGG+TGG - chr4_3:49247068-49247087 Msa0644890:CDS 40.0%
! TCTTGTGTAGCAGTGCTATT+AGG - chr4_3:49247132-49247151 Msa0644890:five_prime_UTR 40.0%
TACTGTGTGGTTACAGGGTT+TGG + chr4_3:49246676-49246695 None:intergenic 45.0%
GAGGTTACTGTGTGGTTACA+GGG + chr4_3:49246681-49246700 None:intergenic 45.0%
AGAGGTTACTGTGTGGTTAC+AGG + chr4_3:49246682-49246701 None:intergenic 45.0%
GATCTGAAGAGGTTACTGTG+TGG + chr4_3:49246689-49246708 None:intergenic 45.0%
CATGGATGTGAGATCTGAAG+AGG + chr4_3:49246700-49246719 None:intergenic 45.0%
CTCTTCAGATCTCACATCCA+TGG - chr4_3:49246698-49246717 Msa0644890:CDS 45.0%
GATCTCACATCCATGGATCA+TGG - chr4_3:49246705-49246724 Msa0644890:CDS 45.0%
CATGTTACCACCATGATCCA+TGG + chr4_3:49246718-49246737 None:intergenic 45.0%
GATCATGGTGGTAACATGCA+CGG - chr4_3:49246720-49246739 Msa0644890:CDS 45.0%
! AATTGGCCTAACGGTGATAC+CGG - chr4_3:49246882-49246901 Msa0644890:intron 45.0%
TACATACCGGTATCACCGTT+AGG + chr4_3:49246891-49246910 None:intergenic 45.0%
GGGTTTAATGAACCGTGTAC+GGG + chr4_3:49246967-49246986 None:intergenic 45.0%
CGGGTTTAATGAACCGTGTA+CGG + chr4_3:49246968-49246987 None:intergenic 45.0%
CGTACACGGTTCATTAAACC+CGG - chr4_3:49246966-49246985 Msa0644890:CDS 45.0%
!!! GTGTTTTTGGTTGCTGTGCT+TGG - chr4_3:49247092-49247111 Msa0644890:five_prime_UTR 45.0%
CTCACATCCATGGATCATGG+TGG - chr4_3:49246708-49246727 Msa0644890:CDS 50.0%
GAAACAAACCGGCAGCAACA+TGG + chr4_3:49246998-49247017 None:intergenic 50.0%
CATGGTGGTAACATGCACGG+TGG - chr4_3:49246723-49246742 Msa0644890:CDS 55.0%
GCAGCAACATGGTTCGAACC+GGG + chr4_3:49246987-49247006 None:intergenic 55.0%
GGCAGCAACATGGTTCGAAC+CGG + chr4_3:49246988-49247007 None:intergenic 55.0%
GGTTCGAACCATGTTGCTGC+CGG - chr4_3:49246987-49247006 Msa0644890:CDS 55.0%
GCTGTGCTTGGTCATGCTCT+TGG - chr4_3:49247104-49247123 Msa0644890:five_prime_UTR 55.0%
GGTGGTAACATGCACGGTGG+CGG - chr4_3:49246726-49246745 Msa0644890:CDS 60.0%
! TAACATGCACGGTGGCGGCA+TGG - chr4_3:49246731-49246750 Msa0644890:CDS 60.0%
! ATGCACGGTGGCGGCATGGA+TGG - chr4_3:49246735-49246754 Msa0644890:CDS 65.0%
Chromosome Type Strat End Strand Name
chr4_3 gene 49246602 49247205 49246602 ID=Msa0644890;Name=Msa0644890
chr4_3 mRNA 49246602 49247205 49246602 ID=Msa0644890-mRNA-1;Parent=Msa0644890;Name=Msa0644890-mRNA-1;_AED=0.28;_eAED=0.29;_QI=115|0|0.5|1|0|0.5|2|0|113
chr4_3 exon 49246602 49246756 49246602 ID=Msa0644890-mRNA-1:exon:11744;Parent=Msa0644890-mRNA-1
chr4_3 exon 49246904 49247205 49246904 ID=Msa0644890-mRNA-1:exon:11743;Parent=Msa0644890-mRNA-1
chr4_3 five_prime_UTR 49247091 49247205 49247091 ID=Msa0644890-mRNA-1:five_prime_utr;Parent=Msa0644890-mRNA-1
chr4_3 CDS 49246904 49247090 49246904 ID=Msa0644890-mRNA-1:cds;Parent=Msa0644890-mRNA-1
chr4_3 CDS 49246602 49246756 49246602 ID=Msa0644890-mRNA-1:cds;Parent=Msa0644890-mRNA-1
Gene Sequence

>Msa0644890

ATGGATCATGGTGGTAACATGCACGGTGGCGGCATGGATGGAATGAACATGCCACCAAAACCATCATCATCATCAACGAATAACACCATGATGATGGGTCATAAGATGCACGGTATGATGCACATGACATTCTTCTGGGGCAAAGATGCTTTAATTCTCTTCAACAATTGGCCTAACGGTGATACCGCTTATTTGGTTATGTTGGCTCTTATGTCTTTCAATGGTGGTGTGTTTTTGGTTGCTGTGCTTGGTCATGCTCTTGGATTCTTCTTGTGTAGCAGTGCTATTAGGAAACCAAAACATGATGATAAGGCTTATGATCTTCCTCCCTTGTCTTGTTAA

Protein sequence

>Msa0644890

MDHGGNMHGGGMDGMNMPPKPSSSSTNNTMMMGHKMHGMMHMTFFWGKDALILFNNWPNGDTAYLVMLALMSFNGGVFLVAVLGHALGFFLCSSAIRKPKHDDKAYDLPPLSC*