AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0188150


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0188150 MtrunA17_Chr2g0293221 92.035 113 9 0 1 113 1 113 9.05e-72 219
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0188150 AT1G19980.1 33.333 105 62 2 14 114 9 109 9.75e-14 66.6

Find 16 sgRNAs with CRISPR-Local

Find 39 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TTCTGATATTAAACGTTATA+AGG 0.239982 2_1:+3289159 Msa0188150:CDS
TCTACGGCGTTTGAAGGTTT+TGG 0.295363 2_1:-3288995 None:intergenic
AATCTGTAGAGCGTGGAAAT+TGG 0.346900 2_1:+3289017 Msa0188150:CDS
GGTTCAGATGATGAAGAATC+AGG 0.362544 2_1:+3289060 Msa0188150:CDS
ATCTGTAGAGCGTGGAAATT+GGG 0.376472 2_1:+3289018 Msa0188150:CDS
CGCATCGTGTGATGCAGAAT+AGG 0.438445 2_1:-3288959 None:intergenic
ACAGATTCTACGGCGTTTGA+AGG 0.453164 2_1:-3289001 None:intergenic
AGCTAAGGCTGATTTGATGA+TGG 0.458362 2_1:+3289336 Msa0188150:CDS
TGATGTTTGAAGAGAAGAAA+CGG 0.503982 2_1:+3289302 Msa0188150:CDS
GCTAAGGCTGATTTGATGAT+GGG 0.535120 2_1:+3289337 Msa0188150:CDS
TCCACGCTCTACAGATTCTA+CGG 0.536952 2_1:-3289011 None:intergenic
ACGGTTGCTTGAAGAAGCTA+AGG 0.550968 2_1:+3289321 Msa0188150:CDS
AAAATTGCAGAATCAACGCT+GGG 0.563347 2_1:+3289135 Msa0188150:CDS
TAAAATTGCAGAATCAACGC+TGG 0.563506 2_1:+3289134 Msa0188150:CDS
TTATAAGGATCAAATTACTC+AGG 0.623873 2_1:+3289174 Msa0188150:CDS
GCCGTAGAATCTGTAGAGCG+TGG 0.627881 2_1:+3289010 Msa0188150:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! TTTCATGTTTTTTTATTAAT+TGG + chr2_1:3289416-3289435 Msa0188150:intron 10.0%
!!! AAAAAGAATGGTTTTTTTAA+TGG + chr2_1:3289245-3289264 Msa0188150:intron 15.0%
!!! AAAAGAATGGTTTTTTTAAT+GGG + chr2_1:3289246-3289265 Msa0188150:intron 15.0%
!! TAAAAAAACATGAAAGAAAA+AGG - chr2_1:3289411-3289430 None:intergenic 15.0%
!!! ATGTTTTTTTATTAATTGGT+TGG + chr2_1:3289420-3289439 Msa0188150:intron 15.0%
!! TTCTGATATTAAACGTTATA+AGG + chr2_1:3289159-3289178 Msa0188150:CDS 20.0%
!!! TATTCAACAATTTCAGTTTT+AGG + chr2_1:3289199-3289218 Msa0188150:intron 20.0%
!!! ATTCAACAATTTCAGTTTTA+GGG + chr2_1:3289200-3289219 Msa0188150:intron 20.0%
!!! TTTTGTTGTTGAAAAAAGAA+TGG + chr2_1:3289233-3289252 Msa0188150:intron 20.0%
!!! AGAATCTTCTATTTTGAAAT+GGG + chr2_1:3289372-3289391 Msa0188150:CDS 20.0%
!!! TAATTGGTTGGTTTTTAAAT+AGG + chr2_1:3289432-3289451 Msa0188150:intron 20.0%
! TTATAAGGATCAAATTACTC+AGG + chr2_1:3289174-3289193 Msa0188150:CDS 25.0%
!!! GAGAATCTTCTATTTTGAAA+TGG + chr2_1:3289371-3289390 Msa0188150:CDS 25.0%
!!! TTCTATTTTGAAATGGGTTT+TGG + chr2_1:3289378-3289397 Msa0188150:CDS 25.0%
!!! TCTATTTTGAAATGGGTTTT+GGG + chr2_1:3289379-3289398 Msa0188150:CDS 25.0%
! TTCTATAACCCAAAATCAAA+GGG - chr2_1:3289475-3289494 None:intergenic 25.0%
! TTTCTATAACCCAAAATCAA+AGG - chr2_1:3289476-3289495 None:intergenic 25.0%
GGAAAAAATATTCAGCACTT+TGG + chr2_1:3289039-3289058 Msa0188150:CDS 30.0%
TGATGTTTGAAGAGAAGAAA+CGG + chr2_1:3289302-3289321 Msa0188150:CDS 30.0%
!!! TGGTTGGTTTTTAAATAGGT+TGG + chr2_1:3289436-3289455 Msa0188150:intron 30.0%
!!! GGTTGGTTTTTAAATAGGTT+GGG + chr2_1:3289437-3289456 Msa0188150:intron 30.0%
!! TAAATAGGTTGGGTTTTTGA+TGG + chr2_1:3289447-3289466 Msa0188150:intron 30.0%
!! AAATAGGTTGGGTTTTTGAT+GGG + chr2_1:3289448-3289467 Msa0188150:intron 30.0%
!!! TGTCTTGTTGTTTTTGTTCT+TGG + chr2_1:3289531-3289550 Msa0188150:CDS 30.0%
TAAAATTGCAGAATCAACGC+TGG + chr2_1:3289134-3289153 Msa0188150:CDS 35.0%
AAAATTGCAGAATCAACGCT+GGG + chr2_1:3289135-3289154 Msa0188150:CDS 35.0%
AATCTGTAGAGCGTGGAAAT+TGG + chr2_1:3289017-3289036 Msa0188150:CDS 40.0%
ATCTGTAGAGCGTGGAAATT+GGG + chr2_1:3289018-3289037 Msa0188150:CDS 40.0%
GGTTCAGATGATGAAGAATC+AGG + chr2_1:3289060-3289079 Msa0188150:CDS 40.0%
!! AGCTAAGGCTGATTTGATGA+TGG + chr2_1:3289336-3289355 Msa0188150:CDS 40.0%
!! GCTAAGGCTGATTTGATGAT+GGG + chr2_1:3289337-3289356 Msa0188150:CDS 40.0%
!! TTGATGGGTCCCTTTGATTT+TGG + chr2_1:3289463-3289482 Msa0188150:intron 40.0%
!! TGATGGGTCCCTTTGATTTT+GGG + chr2_1:3289464-3289483 Msa0188150:intron 40.0%
! TCTACGGCGTTTGAAGGTTT+TGG - chr2_1:3288998-3289017 None:intergenic 45.0%
ACAGATTCTACGGCGTTTGA+AGG - chr2_1:3289004-3289023 None:intergenic 45.0%
TCCACGCTCTACAGATTCTA+CGG - chr2_1:3289014-3289033 None:intergenic 45.0%
ACGGTTGCTTGAAGAAGCTA+AGG + chr2_1:3289321-3289340 Msa0188150:CDS 45.0%
CGCATCGTGTGATGCAGAAT+AGG - chr2_1:3288962-3288981 None:intergenic 50.0%
GCCGTAGAATCTGTAGAGCG+TGG + chr2_1:3289010-3289029 Msa0188150:CDS 55.0%
Chromosome Type Strat End Strand Name
chr2_1 gene 3288884 3289567 3288884 ID=Msa0188150;Name=Msa0188150
chr2_1 mRNA 3288884 3289567 3288884 ID=Msa0188150-mRNA-1;Parent=Msa0188150;Name=Msa0188150-mRNA-1;_AED=0.06;_eAED=0.06;_QI=93|0.5|0.33|0.66|1|1|3|0|124
chr2_1 exon 3288884 3289195 3288884 ID=Msa0188150-mRNA-1:exon:1395;Parent=Msa0188150-mRNA-1
chr2_1 exon 3289289 3289400 3289289 ID=Msa0188150-mRNA-1:exon:1396;Parent=Msa0188150-mRNA-1
chr2_1 exon 3289524 3289567 3289524 ID=Msa0188150-mRNA-1:exon:1397;Parent=Msa0188150-mRNA-1
chr2_1 five_prime_UTR 3288884 3288976 3288884 ID=Msa0188150-mRNA-1:five_prime_utr;Parent=Msa0188150-mRNA-1
chr2_1 CDS 3288977 3289195 3288977 ID=Msa0188150-mRNA-1:cds;Parent=Msa0188150-mRNA-1
chr2_1 CDS 3289289 3289400 3289289 ID=Msa0188150-mRNA-1:cds;Parent=Msa0188150-mRNA-1
chr2_1 CDS 3289524 3289567 3289524 ID=Msa0188150-mRNA-1:cds;Parent=Msa0188150-mRNA-1
Gene Sequence

>Msa0188150

ATGCGTAAATCGAAAAAACCAAAACCTTCAAACGCCGTAGAATCTGTAGAGCGTGGAAATTGGGAAAAAATATTCAGCACTTTGGTTCAGATGATGAAGAATCAGGAAAAGCAACTTCAATCATTCGCTGATCAACAGAACTTTCTACAAGATCGCTTAAAATTGCAGAATCAACGCTGGGCTTCTGATATTAAACGTTATAAGGATCAAATTACTCAGATGAAGACGTTTTTGATGTTTGAAGAGAAGAAACGGTTGCTTGAAGAAGCTAAGGCTGATTTGATGATGGGTTCTAAGCATAGAGAATCTTCTATTTTGAAATGGGTTTTGGATGAATCTGTCTTGTTGTTTTTGTTCTTGGTGTTAGATTCTTAA

Protein sequence

>Msa0188150

MRKSKKPKPSNAVESVERGNWEKIFSTLVQMMKNQEKQLQSFADQQNFLQDRLKLQNQRWASDIKRYKDQITQMKTFLMFEEKKRLLEEAKADLMMGSKHRESSILKWVLDESVLLFLFLVLDS*