AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0097570


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0097570 MtrunA17_Chr1g0152341 91.026 156 6 2 1 153 10 160 2.08e-89 257
Msa0097570 MtrunA17_Chr3g0134971 57.516 153 50 5 2 150 13 154 1.21e-47 151
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0097570 AT1G10140.1 46.104 154 74 5 2 147 8 160 9.13e-22 86.3
Msa0097570 AT1G58420.1 43.373 166 76 4 2 150 11 175 3.97e-19 79.7

Find 19 sgRNAs with CRISPR-Local

Find 22 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CAACAGCAGAAATTGAATAA+AGG 0.334932 1_3:-3384200 Msa0097570:CDS
TGTTCACCAATAAGAGCATT+AGG 0.382819 1_3:-3384476 Msa0097570:CDS
AACAGCAGAAATTGAATAAA+GGG 0.389999 1_3:-3384199 Msa0097570:CDS
TCTAGTGTTGAAGGAAAAGT+TGG 0.393697 1_3:-3384119 Msa0097570:CDS
ACAGCATAACTCTTTGATCT+AGG 0.434486 1_3:+3384077 None:intergenic
AAGATCATCAGCATCATTAG+AGG 0.441233 1_3:-3384312 Msa0097570:CDS
TGTGGTCAAAATATGAGTTA+TGG 0.456641 1_3:-3384416 Msa0097570:CDS
CCTTCAACACTAGAATCAAA+AGG 0.478362 1_3:+3384128 None:intergenic
TTTAGTTAATAGAATTGATG+TGG 0.523602 1_3:-3384243 Msa0097570:CDS
AATTTACTAGCAGCATCCAT+TGG 0.526181 1_3:+3384386 None:intergenic
TTACCTAAGTCTAGTAGTGT+TGG 0.528478 1_3:-3384176 Msa0097570:CDS
ATTCCAACACTACTAGACTT+AGG 0.543949 1_3:+3384173 None:intergenic
TAAGTCTAGTAGTGTTGGAA+TGG 0.550381 1_3:-3384171 Msa0097570:CDS
AGATCAAAGAGTTATGCTGT+TGG 0.581741 1_3:-3384074 Msa0097570:CDS
GAGTTATGGAAGTTATCCAA+TGG 0.620886 1_3:-3384402 Msa0097570:CDS
AGATCATCAGCATCATTAGA+GGG 0.626119 1_3:-3384311 Msa0097570:CDS
AGAACCAAAACATGTTTGTG+AGG 0.637515 1_3:-3384505 None:intergenic
TGGAATGGCTAAGATTGATG+AGG 0.704946 1_3:-3384156 Msa0097570:CDS
GTAAGAAGCATAACAAACTG+TGG 0.710541 1_3:-3384434 Msa0097570:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! TTTAGTTAATAGAATTGATG+TGG - chr1_3:3384297-3384316 Msa0097570:CDS 20.0%
! AACAGCAGAAATTGAATAAA+GGG - chr1_3:3384341-3384360 Msa0097570:CDS 25.0%
TGTGGTCAAAATATGAGTTA+TGG - chr1_3:3384124-3384143 Msa0097570:CDS 30.0%
CAACAGCAGAAATTGAATAA+AGG - chr1_3:3384340-3384359 Msa0097570:CDS 30.0%
!! TGTTCACCAATAAGAGCATT+AGG - chr1_3:3384064-3384083 Msa0097570:CDS 35.0%
! GCTTTTCCTAATGCTCTTAT+TGG + chr1_3:3384073-3384092 None:intergenic 35.0%
! GTAAGAAGCATAACAAACTG+TGG - chr1_3:3384106-3384125 Msa0097570:CDS 35.0%
GAGTTATGGAAGTTATCCAA+TGG - chr1_3:3384138-3384157 Msa0097570:CDS 35.0%
AATTTACTAGCAGCATCCAT+TGG + chr1_3:3384157-3384176 None:intergenic 35.0%
AAGATCATCAGCATCATTAG+AGG - chr1_3:3384228-3384247 Msa0097570:CDS 35.0%
AGATCATCAGCATCATTAGA+GGG - chr1_3:3384229-3384248 Msa0097570:CDS 35.0%
!! AAGATTTTGCTGAGCTTGTT+AGG - chr1_3:3384257-3384276 Msa0097570:CDS 35.0%
!!! AGATTTTGCTGAGCTTGTTA+GGG - chr1_3:3384258-3384277 Msa0097570:CDS 35.0%
TTACCTAAGTCTAGTAGTGT+TGG - chr1_3:3384364-3384383 Msa0097570:CDS 35.0%
ATTCCAACACTACTAGACTT+AGG + chr1_3:3384370-3384389 None:intergenic 35.0%
! TAAGTCTAGTAGTGTTGGAA+TGG - chr1_3:3384369-3384388 Msa0097570:CDS 35.0%
CCTTCAACACTAGAATCAAA+AGG + chr1_3:3384415-3384434 None:intergenic 35.0%
!! CCTTTTGATTCTAGTGTTGA+AGG - chr1_3:3384412-3384431 Msa0097570:CDS 35.0%
! TCTAGTGTTGAAGGAAAAGT+TGG - chr1_3:3384421-3384440 Msa0097570:CDS 35.0%
ACAGCATAACTCTTTGATCT+AGG + chr1_3:3384466-3384485 None:intergenic 35.0%
AGATCAAAGAGTTATGCTGT+TGG - chr1_3:3384466-3384485 Msa0097570:CDS 35.0%
TGGAATGGCTAAGATTGATG+AGG - chr1_3:3384384-3384403 Msa0097570:CDS 40.0%
Chromosome Type Strat End Strand Name
chr1_3 gene 3384046 3384516 3384046 ID=Msa0097570;Name=Msa0097570
chr1_3 mRNA 3384046 3384516 3384046 ID=Msa0097570-mRNA-1;Parent=Msa0097570;Name=Msa0097570-mRNA-1;_AED=0.04;_eAED=0.04;_QI=0|-1|0|1|-1|1|1|0|156
chr1_3 exon 3384046 3384516 3384046 ID=Msa0097570-mRNA-1:exon:994;Parent=Msa0097570-mRNA-1
chr1_3 CDS 3384046 3384516 3384046 ID=Msa0097570-mRNA-1:cds;Parent=Msa0097570-mRNA-1
Gene Sequence

>Msa0097570

ATGTTTGTGAGGATCATGTGTTCACCAATAAGAGCATTAGGAAAAGCAAGAGATGCATACGTAAGAAGCATAACAAACTGTGGTCAAAATATGAGTTATGGAAGTTATCCAATGGATGCTGCTAGTAAATTTTCTTTATCAAGAAGTCAAAGTGCAGCAACATCAAGAAGATCATCATCAAGAAGATCATCAGCATCATTAGAGGGTAATGAAGATTTTGCTGAGCTTGTTAGGGCTGCTTCTGCTAGAACTTTAGTTAATAGAATTGATGTGGATTTAGTTCTCAAGCAACAACAACAGCAGAAATTGAATAAAGGGTTACCTAAGTCTAGTAGTGTTGGAATGGCTAAGATTGATGAGGATATGCCTTTTGATTCTAGTGTTGAAGGAAAAGTTGGTTTTGTTGCTGATTCTTATCCTAGATCAAAGAGTTATGCTGTTGGACATAGAAGAAATGTTGTTGCTTTCTGA

Protein sequence

>Msa0097570

MFVRIMCSPIRALGKARDAYVRSITNCGQNMSYGSYPMDAASKFSLSRSQSAATSRRSSSRRSSASLEGNEDFAELVRAASARTLVNRIDVDLVLKQQQQQKLNKGLPKSSSVGMAKIDEDMPFDSSVEGKVGFVADSYPRSKSYAVGHRRNVVAF*