AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0336030


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0336030 MtrunA17_Chr2g0321711 95.506 89 4 0 1 89 1 89 5.75e-52 168
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0336030 AT5G22320.2 65.169 89 31 0 1 89 1 89 5.07e-34 121
Msa0336030 AT5G22320.1 65.169 89 31 0 1 89 1 89 6.57e-34 120

Find 18 sgRNAs with CRISPR-Local

Find 39 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CTTAGCCAGCTTCAATAAAT+TGG 0.169541 2_4:-55303052 Msa0336030:CDS
TTCCTCACTGCACTCATTCA+AGG 0.388703 2_4:+55303280 None:intergenic
GGAGAATAAATTAGAAAGCT+TGG 0.390492 2_4:-55302848 Msa0336030:CDS
GAAAGCTTGGAAGGAATTCA+AGG 0.449690 2_4:-55302835 Msa0336030:CDS
TTTGAAGTGGTTATCAGTTG+TGG 0.468829 2_4:-55302869 Msa0336030:CDS
TGAAGACTGGAAATTGAACT+TGG 0.471828 2_4:+55303203 None:intergenic
GTATGGTGTAAAAGGGATTG+AGG 0.475885 2_4:-55302903 Msa0336030:intron
TATGGTGTAAAAGGGATTGA+GGG 0.493320 2_4:-55302902 Msa0336030:intron
ACTGGAAATTGAACTTGGAT+TGG 0.499943 2_4:+55303208 None:intergenic
GGAAATTGAACTTGGATTGG+CGG 0.520167 2_4:+55303211 None:intergenic
AATAAATTAGAAAGCTTGGA+AGG 0.526330 2_4:-55302844 Msa0336030:CDS
GCTGTCGTTCAATACTTGCT+CGG 0.536067 2_4:+55303238 None:intergenic
CAATAATCTCACTTCACTTG+AGG 0.539721 2_4:-55303010 Msa0336030:intron
CGGAAAGAGCTTTGTGAGTG+AGG 0.545351 2_4:+55303180 None:intergenic
TTTGTGAGTGAGGTGAAGAC+TGG 0.573523 2_4:+55303190 None:intergenic
TTTATATTAACAAAGCAGCT+AGG 0.575771 2_4:+55302789 None:intergenic
GGGCATGTGTTAATTTGAAG+TGG 0.617171 2_4:-55302882 Msa0336030:CDS
TGCCTTGAATGAGTGCAGTG+AGG 0.768971 2_4:-55303282 Msa0336030:five_prime_UTR

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! AAAAAAGTTAAGATTTTTTA+GGG + chr2_4:55302982-55303001 None:intergenic 10.0%
!!! AAAAAAAGTTAAGATTTTTT+AGG + chr2_4:55302983-55303002 None:intergenic 10.0%
!! TTGAAAGTTATGAAAAAAAT+TGG - chr2_4:55303124-55303143 Msa0336030:intron 15.0%
!!! TTTTTAGGGTTTTAACAAAA+GGG + chr2_4:55302968-55302987 None:intergenic 20.0%
!!! TTTTTTAGGGTTTTAACAAA+AGG + chr2_4:55302969-55302988 None:intergenic 20.0%
!! TATGAAAAAAATTGGAACTT+TGG - chr2_4:55303132-55303151 Msa0336030:intron 20.0%
!!! TTGATTGTATTTTGTATGTA+TGG - chr2_4:55303163-55303182 Msa0336030:intron 20.0%
!!! TTTTAGGGTTTTAACAAAAG+GGG + chr2_4:55302967-55302986 None:intergenic 25.0%
!! TTTTGTATGTATGGTGTAAA+AGG - chr2_4:55303172-55303191 Msa0336030:intron 25.0%
! TTTGTATGTATGGTGTAAAA+GGG - chr2_4:55303173-55303192 Msa0336030:intron 25.0%
! AATAAATTAGAAAGCTTGGA+AGG - chr2_4:55303239-55303258 Msa0336030:CDS 25.0%
! TTTATATTAACAAAGCAGCT+AGG + chr2_4:55303297-55303316 None:intergenic 25.0%
TTAATCTTTGTTCATTTCCC+AGG - chr2_4:55303001-55303020 Msa0336030:intron 30.0%
! CTTTTCCAATTTATTGAAGC+TGG + chr2_4:55303039-55303058 None:intergenic 30.0%
GGAGAATAAATTAGAAAGCT+TGG - chr2_4:55303235-55303254 Msa0336030:CDS 30.0%
ACTGGAAATTGAACTTGGAT+TGG + chr2_4:55302878-55302897 None:intergenic 35.0%
TGAAGACTGGAAATTGAACT+TGG + chr2_4:55302883-55302902 None:intergenic 35.0%
GGTTTAGAGAAAAGAAAAGG+GGG + chr2_4:55302946-55302965 None:intergenic 35.0%
GGGTTTAGAGAAAAGAAAAG+GGG + chr2_4:55302947-55302966 None:intergenic 35.0%
GGGGTTTAGAGAAAAGAAAA+GGG + chr2_4:55302948-55302967 None:intergenic 35.0%
AGGGGTTTAGAGAAAAGAAA+AGG + chr2_4:55302949-55302968 None:intergenic 35.0%
CTTAGCCAGCTTCAATAAAT+TGG - chr2_4:55303031-55303050 Msa0336030:CDS 35.0%
CAATAATCTCACTTCACTTG+AGG - chr2_4:55303073-55303092 Msa0336030:intron 35.0%
TATGGTGTAAAAGGGATTGA+GGG - chr2_4:55303181-55303200 Msa0336030:CDS 35.0%
! TTTGAAGTGGTTATCAGTTG+TGG - chr2_4:55303214-55303233 Msa0336030:CDS 35.0%
! GGAAATTGAACTTGGATTGG+CGG + chr2_4:55302875-55302894 None:intergenic 40.0%
TTAGAGAAAAGAAAAGGGGG+TGG + chr2_4:55302943-55302962 None:intergenic 40.0%
GTATGGTGTAAAAGGGATTG+AGG - chr2_4:55303180-55303199 Msa0336030:CDS 40.0%
! GGGCATGTGTTAATTTGAAG+TGG - chr2_4:55303201-55303220 Msa0336030:CDS 40.0%
GAAAGCTTGGAAGGAATTCA+AGG - chr2_4:55303248-55303267 Msa0336030:CDS 40.0%
TTCCTCACTGCACTCATTCA+AGG + chr2_4:55302806-55302825 None:intergenic 45.0%
GCTGTCGTTCAATACTTGCT+CGG + chr2_4:55302848-55302867 None:intergenic 45.0%
TTTGTGAGTGAGGTGAAGAC+TGG + chr2_4:55302896-55302915 None:intergenic 45.0%
GGGTGGAAAGAAGGTTACAT+CGG + chr2_4:55302926-55302945 None:intergenic 45.0%
AAGAAAAGGGGGTGGAAAGA+AGG + chr2_4:55302935-55302954 None:intergenic 45.0%
TGCCTTGAATGAGTGCAGTG+AGG - chr2_4:55302801-55302820 Msa0336030:exon 50.0%
! CGGAAAGAGCTTTGTGAGTG+AGG + chr2_4:55302906-55302925 None:intergenic 50.0%
GCTGGCTAAGCATGATACCT+GGG + chr2_4:55303021-55303040 None:intergenic 50.0%
AGCTGGCTAAGCATGATACC+TGG + chr2_4:55303022-55303041 None:intergenic 50.0%
Chromosome Type Strat End Strand Name
chr2_4 gene 55302782 55303323 55302782 ID=Msa0336030;Name=Msa0336030
chr2_4 mRNA 55302782 55303323 55302782 ID=Msa0336030-mRNA-1;Parent=Msa0336030;Name=Msa0336030-mRNA-1;_AED=0.00;_eAED=0.00;_QI=47|1|1|1|1|1|3|25|91
chr2_4 exon 55302782 55302911 55302782 ID=Msa0336030-mRNA-1:exon:16776;Parent=Msa0336030-mRNA-1
chr2_4 exon 55303011 55303082 55303011 ID=Msa0336030-mRNA-1:exon:16775;Parent=Msa0336030-mRNA-1
chr2_4 exon 55303178 55303323 55303178 ID=Msa0336030-mRNA-1:exon:16774;Parent=Msa0336030-mRNA-1
chr2_4 five_prime_UTR 55303277 55303323 55303277 ID=Msa0336030-mRNA-1:five_prime_utr;Parent=Msa0336030-mRNA-1
chr2_4 CDS 55303178 55303276 55303178 ID=Msa0336030-mRNA-1:cds;Parent=Msa0336030-mRNA-1
chr2_4 CDS 55303011 55303082 55303011 ID=Msa0336030-mRNA-1:cds;Parent=Msa0336030-mRNA-1
chr2_4 CDS 55302807 55302911 55302807 ID=Msa0336030-mRNA-1:cds;Parent=Msa0336030-mRNA-1
chr2_4 three_prime_UTR 55302782 55302806 55302782 ID=Msa0336030-mRNA-1:three_prime_utr;Parent=Msa0336030-mRNA-1
Gene Sequence

>Msa0336030

ATGACTCGTTTGAGCTCCGAGCAAGTATTGAACGACAGCAATGCCGCCAATCCAAGTTCAATTTCCAGTCTTCACCTCACTCACAAAGCTCTTTCCGATGTATCATGCTTAGCCAGCTTCAATAAATTGGAAAAGCTTGATCTAAAATTCAATAATCTCACTTCACTTGAGGGATTGAGGGCATGTGTTAATTTGAAGTGGTTATCAGTTGTGGAGAATAAATTAGAAAGCTTGGAAGGAATTCAAGGACTTACTAAGCTTACTGTAAGTACCTAG

Protein sequence

>Msa0336030

MTRLSSEQVLNDSNAANPSSISSLHLTHKALSDVSCLASFNKLEKLDLKFNNLTSLEGLRACVNLKWLSVVENKLESLEGIQGLTKLTVST*