AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0344260


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0344260 MtrunA17_Chr8g0355631 100.000 37 0 0 1 37 35 71 2.22e-20 74.7
Msa0344260 MtrunA17_Chr4g0015761 100.000 37 0 0 1 37 35 71 2.56e-20 74.7
Msa0344260 MtrunA17_CPg0492811 100.000 37 0 0 1 37 35 71 2.56e-20 74.7
Msa0344260 MtrunA17_Chr4g0016861 100.000 35 0 0 1 35 1 35 9.96e-19 70.1
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0344260 ATCG00600.1 97.222 36 1 0 1 36 1 36 2.23e-18 69.3

Find 14 sgRNAs with CRISPR-Local

Find 20 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
ATGATTGAAGTTTCTCTATT+TGG 0.115333 3_1:-2738365 Msa0344260:CDS
TCATGTCAATTGCCAATTCT+TGG 0.245809 3_1:-2738469 Msa0344260:five_prime_UTR
AATAATCCAGCCAAAGTAAT+AGG 0.315680 3_1:+2738323 None:intergenic
AAACTTCAATCATTTGAGTT+TGG 0.328054 3_1:+2738375 None:intergenic
CTAATTCCTATTACTTTGGC+TGG 0.352028 3_1:-2738329 Msa0344260:CDS
TCTCTATTTGGAATCGTGTT+AGG 0.358426 3_1:-2738353 Msa0344260:CDS
AGGTCTAATTCCTATTACTT+TGG 0.388074 3_1:-2738333 Msa0344260:CDS
ATCATTTGAGTTTGGTTGAA+AGG 0.406278 3_1:+2738383 None:intergenic
GAATCTCAATGACCAAGAAT+TGG 0.414372 3_1:+2738457 None:intergenic
AATTGGCAATTGACATGATA+AGG 0.448909 3_1:+2738474 None:intergenic
TTCTTGGTCATTGAGATTCA+CGG 0.471290 3_1:-2738453 Msa0344260:intron
ATATCGACGTGGTGATCAGT+TGG 0.572503 3_1:-2738282 Msa0344260:CDS
TTTGGCTGGATTATTTGTAA+CGG 0.592623 3_1:-2738315 Msa0344260:CDS
GCATATTTACAATATCGACG+TGG 0.789819 3_1:-2738293 Msa0344260:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AAACTTCAATCATTTGAGTT+TGG + chr3_1:2738381-2738400 None:intergenic 25.0%
! ATGATTGAAGTTTCTCTATT+TGG - chr3_1:2738388-2738407 Msa0344260:five_prime_UTR 25.0%
AATTGGCAATTGACATGATA+AGG + chr3_1:2738282-2738301 None:intergenic 30.0%
TCAATACAGATTCCTATTGA+AGG - chr3_1:2738323-2738342 Msa0344260:CDS 30.0%
GGTAATATCTATCCTTCAAT+AGG + chr3_1:2738338-2738357 None:intergenic 30.0%
TGGTTGAAAGGAAAAAAAGT+GGG + chr3_1:2738361-2738380 None:intergenic 30.0%
TTGGTTGAAAGGAAAAAAAG+TGG + chr3_1:2738362-2738381 None:intergenic 30.0%
! ATCATTTGAGTTTGGTTGAA+AGG + chr3_1:2738373-2738392 None:intergenic 30.0%
AGGTCTAATTCCTATTACTT+TGG - chr3_1:2738420-2738439 Msa0344260:intron 30.0%
AATAATCCAGCCAAAGTAAT+AGG + chr3_1:2738433-2738452 None:intergenic 30.0%
TTTGGCTGGATTATTTGTAA+CGG - chr3_1:2738438-2738457 Msa0344260:intron 30.0%
TCATGTCAATTGCCAATTCT+TGG - chr3_1:2738284-2738303 Msa0344260:CDS 35.0%
GAATCTCAATGACCAAGAAT+TGG + chr3_1:2738299-2738318 None:intergenic 35.0%
TTCTTGGTCATTGAGATTCA+CGG - chr3_1:2738300-2738319 Msa0344260:CDS 35.0%
GTTGAAAGGAAAAAAAGTGG+GGG + chr3_1:2738359-2738378 None:intergenic 35.0%
GGTTGAAAGGAAAAAAAGTG+GGG + chr3_1:2738360-2738379 None:intergenic 35.0%
! TCTCTATTTGGAATCGTGTT+AGG - chr3_1:2738400-2738419 Msa0344260:five_prime_UTR 35.0%
CTAATTCCTATTACTTTGGC+TGG - chr3_1:2738424-2738443 Msa0344260:intron 35.0%
GCATATTTACAATATCGACG+TGG - chr3_1:2738460-2738479 Msa0344260:five_prime_UTR 35.0%
ATATCGACGTGGTGATCAGT+TGG - chr3_1:2738471-2738490 Msa0344260:five_prime_UTR 45.0%
Chromosome Type Strat End Strand Name
chr3_1 gene 2738277 2738498 2738277 ID=Msa0344260;Name=Msa0344260
chr3_1 mRNA 2738277 2738498 2738277 ID=Msa0344260-mRNA-1;Parent=Msa0344260;Name=Msa0344260-mRNA-1;_AED=0.41;_eAED=0.67;_QI=83|0|0|1|0|0|2|0|37
chr3_1 exon 2738454 2738498 2738454 ID=Msa0344260-mRNA-1:exon:896;Parent=Msa0344260-mRNA-1
chr3_1 exon 2738277 2738425 2738277 ID=Msa0344260-mRNA-1:exon:895;Parent=Msa0344260-mRNA-1
chr3_1 five_prime_UTR 2738454 2738498 2738454 ID=Msa0344260-mRNA-1:five_prime_utr;Parent=Msa0344260-mRNA-1
chr3_1 five_prime_UTR 2738388 2738425 2738388 ID=Msa0344260-mRNA-1:five_prime_utr;Parent=Msa0344260-mRNA-1
chr3_1 CDS 2738277 2738387 2738277 ID=Msa0344260-mRNA-1:cds;Parent=Msa0344260-mRNA-1
Gene Sequence

>Msa0344260

ATGATTGAAGTTTCTCTATTTGGAATCGTGTTAGGTCTAATTCCTATTACTTTGGCTGGATTATTTGTAACGGCATATTTACAATATCGACGTGGTGATCAGTTGGATATT

Protein sequence

>Msa0344260

MIEVSLFGIVLGLIPITLAGLFVTAYLQYRRGDQLDI