AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0603600


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0603600 MtrunA17_Chr4g0032291 55.833 120 4 1 43 113 46 165 1.35e-35 119
Msa0603600 MtrunA17_Chr4g0032581 51.007 149 21 4 14 113 8 153 1.82e-29 103
Msa0603600 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
Msa0603600 AT2G26975.1 36.735 147 38 4 12 107 1 143 6.70e-18 74.3
Msa0603600 AT5G59030.1 33.871 124 29 3 43 113 45 168 7.73e-12 58.9
Msa0603600 AT3G46900.1 32.203 118 29 3 44 110 34 151 5.68e-11 56.6

Find 39 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_2:-48209014 Msa0603600:intron
ACCCATCATCATGGTGTTAT+TGG 0.242191 4_2:+48209258 None:intergenic
GTTGATGATGATGATGGTTT+TGG 0.274914 4_2:+48209280 None:intergenic
AGAGGTTACTGTGTGGTTAC+AGG 0.278616 4_2:+48209372 None:intergenic
TCTTGTGTAGCAGTGCTATT+AGG 0.286924 4_2:-48208919 Msa0603600:CDS
TGATGCACATGACATTCTTC+TGG 0.295699 4_2:-48209219 Msa0603600:CDS
ATGTAATAAATGTGTATTTA+GGG 0.312526 4_2:+48209404 None:intergenic
TAAGCCTTATCATCATGTTT+TGG 0.336110 4_2:+48208893 None:intergenic
AATGTAATAAATGTGTATTT+AGG 0.339646 4_2:+48209403 None:intergenic
TACTGTGTGGTTACAGGGTT+TGG 0.340111 4_2:+48209378 None:intergenic
CTTTAATTCTCTTCAACAAT+TGG 0.349322 4_2:-48209186 Msa0603600:CDS
GCTGTGCTTGGTCATGCTCT+TGG 0.350764 4_2:-48208947 Msa0603600:CDS
TTGGCTCTTATGTCTTTCAA+TGG 0.387989 4_2:-48208986 Msa0603600:CDS
GTTAGCTTATTTGGTTATGT+TGG 0.388968 4_2:-48209005 Msa0603600:intron
GAAACCAAAACATGATGATA+AGG 0.457740 4_2:-48208897 Msa0603600:CDS
GATGCACATGACATTCTTCT+GGG 0.470744 4_2:-48209218 Msa0603600:CDS
AACCAATAACACCATGATGA+TGG 0.477184 4_2:-48209260 Msa0603600:CDS
CTCTTCAACAATTGGCCTAA+CGG 0.488088 4_2:-48209178 Msa0603600:CDS
ATGCACGGTGGCGGCATGGA+TGG 0.492115 4_2:-48209316 Msa0603600:CDS
AATTGGCCTAACGGTGATAC+CGG 0.503435 4_2:-48209169 Msa0603600:intron
TTATTGGTTGATGATGATGA+TGG 0.527547 4_2:+48209274 None:intergenic
CTCTTCAGATCTCACATCCA+TGG 0.529767 4_2:-48209353 Msa0603600:exon
GAGGTTACTGTGTGGTTACA+GGG 0.531390 4_2:+48209373 None:intergenic
ACCAATAACACCATGATGAT+GGG 0.534019 4_2:-48209259 Msa0603600:CDS
GGTGGTAACATGCACGGTGG+CGG 0.534398 4_2:-48209325 Msa0603600:CDS
GCTCTTATGTCTTTCAATGG+TGG 0.539076 4_2:-48208983 Msa0603600:CDS
GATCTCACATCCATGGATCA+TGG 0.541471 4_2:-48209346 Msa0603600:exon
CATGTTACCACCATGATCCA+TGG 0.570126 4_2:+48209336 None:intergenic
CATCTTATGACCCATCATCA+TGG 0.576922 4_2:+48209249 None:intergenic
CATGGATGTGAGATCTGAAG+AGG 0.588461 4_2:+48209354 None:intergenic
TAACATGCACGGTGGCGGCA+TGG 0.592169 4_2:-48209320 Msa0603600:CDS
ATGATGGGTCATAAGATGCA+CGG 0.627281 4_2:-48209244 Msa0603600:CDS
TACATACCGGTATCACCGTT+AGG 0.669036 4_2:+48209163 None:intergenic
AACAATTAACAAGACAACGG+AGG 0.682394 4_2:+48208863 None:intergenic
ATGCACATGACATTCTTCTG+GGG 0.688076 4_2:-48209217 Msa0603600:CDS
GATCATGGTGGTAACATGCA+CGG 0.714076 4_2:-48209331 Msa0603600:CDS
CTCACATCCATGGATCATGG+TGG 0.733160 4_2:-48209343 Msa0603600:exon
CATGGTGGTAACATGCACGG+TGG 0.787274 4_2:-48209328 Msa0603600:CDS
GATCTGAAGAGGTTACTGTG+TGG 0.856147 4_2:+48209365 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! ATGTAATAAATGTGTATTTA+GGG + chr4_2:48208916-48208935 None:intergenic 15.0%
!! AATGTAATAAATGTGTATTT+AGG + chr4_2:48208917-48208936 None:intergenic 15.0%
! CTTTAATTCTCTTCAACAAT+TGG - chr4_2:48209131-48209150 Msa0603600:intron 25.0%
! TACTTATTGAATTACTCTCA+CGG - chr4_2:48209212-48209231 Msa0603600:CDS 25.0%
!! TTATTGGTTGATGATGATGA+TGG + chr4_2:48209046-48209065 None:intergenic 30.0%
! GTTAGCTTATTTGGTTATGT+TGG - chr4_2:48209312-48209331 Msa0603600:CDS 30.0%
GAAACCAAAACATGATGATA+AGG - chr4_2:48209420-48209439 Msa0603600:five_prime_UTR 30.0%
!! TAAGCCTTATCATCATGTTT+TGG + chr4_2:48209427-48209446 None:intergenic 30.0%
!!! GTTGATGATGATGATGGTTT+TGG + chr4_2:48209040-48209059 None:intergenic 35.0%
AACCAATAACACCATGATGA+TGG - chr4_2:48209057-48209076 Msa0603600:intron 35.0%
ACCAATAACACCATGATGAT+GGG - chr4_2:48209058-48209077 Msa0603600:intron 35.0%
TGATACCGGTATGTATGTAT+TGG - chr4_2:48209162-48209181 Msa0603600:intron 35.0%
!! CAAAAGTGTCTGAAACAAAC+CGG + chr4_2:48209275-48209294 None:intergenic 35.0%
! AGACACTTTTGCATGTTCTT+AGG - chr4_2:48209284-48209303 Msa0603600:CDS 35.0%
! GACACTTTTGCATGTTCTTA+GGG - chr4_2:48209285-48209304 Msa0603600:CDS 35.0%
! TTTTGCATGTTCTTAGGGTT+GGG - chr4_2:48209290-48209309 Msa0603600:CDS 35.0%
! TTGGCTCTTATGTCTTTCAA+TGG - chr4_2:48209331-48209350 Msa0603600:CDS 35.0%
!! TTTCAATGGTGGTGTGTTTT+TGG - chr4_2:48209345-48209364 Msa0603600:exon 35.0%
!!! GATGATGATGATGGTTTTGG+TGG + chr4_2:48209037-48209056 None:intergenic 40.0%
!! ACCCATCATCATGGTGTTAT+TGG + chr4_2:48209062-48209081 None:intergenic 40.0%
CATCTTATGACCCATCATCA+TGG + chr4_2:48209071-48209090 None:intergenic 40.0%
!! ATGATGGGTCATAAGATGCA+CGG - chr4_2:48209073-48209092 Msa0603600:intron 40.0%
TGATGCACATGACATTCTTC+TGG - chr4_2:48209098-48209117 Msa0603600:intron 40.0%
GATGCACATGACATTCTTCT+GGG - chr4_2:48209099-48209118 Msa0603600:intron 40.0%
ATGCACATGACATTCTTCTG+GGG - chr4_2:48209100-48209119 Msa0603600:intron 40.0%
! CTCTTCAACAATTGGCCTAA+CGG - chr4_2:48209139-48209158 Msa0603600:intron 40.0%
CAACGCCAATACATACATAC+CGG + chr4_2:48209170-48209189 None:intergenic 40.0%
GTACAGACATGACGAAAACA+AGG + chr4_2:48209195-48209214 None:intergenic 40.0%
TTGAATTACTCTCACGGACT+CGG - chr4_2:48209218-48209237 Msa0603600:CDS 40.0%
! CTTTTGCATGTTCTTAGGGT+TGG - chr4_2:48209289-48209308 Msa0603600:CDS 40.0%
!! TAGGGTTGGGTTAGCTTATT+TGG - chr4_2:48209303-48209322 Msa0603600:CDS 40.0%
GCTCTTATGTCTTTCAATGG+TGG - chr4_2:48209334-48209353 Msa0603600:CDS 40.0%
! TCTTGTGTAGCAGTGCTATT+AGG - chr4_2:48209398-48209417 Msa0603600:five_prime_UTR 40.0%
TACTGTGTGGTTACAGGGTT+TGG + chr4_2:48208942-48208961 None:intergenic 45.0%
GAGGTTACTGTGTGGTTACA+GGG + chr4_2:48208947-48208966 None:intergenic 45.0%
AGAGGTTACTGTGTGGTTAC+AGG + chr4_2:48208948-48208967 None:intergenic 45.0%
GATCTGAAGAGGTTACTGTG+TGG + chr4_2:48208955-48208974 None:intergenic 45.0%
CATGGATGTGAGATCTGAAG+AGG + chr4_2:48208966-48208985 None:intergenic 45.0%
CTCTTCAGATCTCACATCCA+TGG - chr4_2:48208964-48208983 Msa0603600:CDS 45.0%
GATCTCACATCCATGGATCA+TGG - chr4_2:48208971-48208990 Msa0603600:CDS 45.0%
CATGTTACCACCATGATCCA+TGG + chr4_2:48208984-48209003 None:intergenic 45.0%
GATCATGGTGGTAACATGCA+CGG - chr4_2:48208986-48209005 Msa0603600:CDS 45.0%
! AATTGGCCTAACGGTGATAC+CGG - chr4_2:48209148-48209167 Msa0603600:intron 45.0%
TACATACCGGTATCACCGTT+AGG + chr4_2:48209157-48209176 None:intergenic 45.0%
!!! GTGTTTTTGGTTGCTGTGCT+TGG - chr4_2:48209358-48209377 Msa0603600:five_prime_UTR 45.0%
CTCACATCCATGGATCATGG+TGG - chr4_2:48208974-48208993 Msa0603600:CDS 50.0%
! CGGACTCGGTTCATTAAACC+CGG - chr4_2:48209232-48209251 Msa0603600:CDS 50.0%
GAAACAAACCGGCAGCAACA+TGG + chr4_2:48209264-48209283 None:intergenic 50.0%
CATGGTGGTAACATGCACGG+TGG - chr4_2:48208989-48209008 Msa0603600:CDS 55.0%
GCAGCAACATGGTTCGAACC+GGG + chr4_2:48209253-48209272 None:intergenic 55.0%
GGCAGCAACATGGTTCGAAC+CGG + chr4_2:48209254-48209273 None:intergenic 55.0%
GGTTCGAACCATGTTGCTGC+CGG - chr4_2:48209253-48209272 Msa0603600:CDS 55.0%
GCTGTGCTTGGTCATGCTCT+TGG - chr4_2:48209370-48209389 Msa0603600:five_prime_UTR 55.0%
GGTGGTAACATGCACGGTGG+CGG - chr4_2:48208992-48209011 Msa0603600:CDS 60.0%
! TAACATGCACGGTGGCGGCA+TGG - chr4_2:48208997-48209016 Msa0603600:CDS 60.0%
! ATGCACGGTGGCGGCATGGA+TGG - chr4_2:48209001-48209020 Msa0603600:CDS 65.0%
Chromosome Type Strat End Strand Name
chr4_2 gene 48208868 48209471 48208868 ID=Msa0603600;Name=Msa0603600
chr4_2 mRNA 48208868 48209471 48208868 ID=Msa0603600-mRNA-1;Parent=Msa0603600;Name=Msa0603600-mRNA-1;_AED=0.29;_eAED=0.29;_QI=115|0|0.5|1|0|0|2|0|113
chr4_2 exon 48208868 48209022 48208868 ID=Msa0603600-mRNA-1:exon:11109;Parent=Msa0603600-mRNA-1
chr4_2 exon 48209170 48209471 48209170 ID=Msa0603600-mRNA-1:exon:11108;Parent=Msa0603600-mRNA-1
chr4_2 five_prime_UTR 48209357 48209471 48209357 ID=Msa0603600-mRNA-1:five_prime_utr;Parent=Msa0603600-mRNA-1
chr4_2 CDS 48209170 48209356 48209170 ID=Msa0603600-mRNA-1:cds;Parent=Msa0603600-mRNA-1
chr4_2 CDS 48208868 48209022 48208868 ID=Msa0603600-mRNA-1:cds;Parent=Msa0603600-mRNA-1
Gene Sequence

>Msa0603600

ATGGATCATGGTGGTAACATGCACGGTGGCGGCATGGATGGAATGAACATGCCACCAAAACCATCATCATCATCAACCAATAACACCATGATGATGGGTCATAAGATGCACGGCATGATGCACATGACATTCTTCTGGGGCAAAGATGCTTTAATTCTCTTCAACAATTGGCCTAACGGTGATACCGCTTATTTGGTTATGTTGGCTCTTATGTCTTTCAATGGTGGTGTGTTTTTGGTTGCTGTGCTTGGTCATGCTCTTGGATTCTTCTTGTGTAGCAGTGCTATTAGGAAACCAAAACATGATGATAAGGCTTATGATCTTCCTCCGTTGTCTTGTTAA

Protein sequence

>Msa0603600

MDHGGNMHGGGMDGMNMPPKPSSSSTNNTMMMGHKMHGMMHMTFFWGKDALILFNNWPNGDTAYLVMLALMSFNGGVFLVAVLGHALGFFLCSSAIRKPKHDDKAYDLPPLSC*