AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1374440


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1374440 MtrunA17_Chr3g0129411 97.647 85 2 0 1 85 35 119 1.24e-57 172
Msa1374440 MtrunA17_Chr8g0383481 52.941 85 32 4 1 85 36 112 9.19e-21 79.0
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 25 sgRNAs with CRISPR-Local

Find 35 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
ATTAAATAGTGCACAAATTT+TGG 0.112038 tig0019487:+100648 Msa1374440:exon
CCATATGGATATGTTAATTT+AGG 0.228692 tig0019487:-100195 None:intergenic
TCCTATATATAGACACATTT+TGG 0.251593 tig0019487:-100172 None:intergenic
TCCATCCATATTCAAGTAAA+AGG 0.259194 tig0019487:+100338 Msa1374440:CDS
CAATTAACCATGTTAGTATC+TGG 0.347082 tig0019487:+100837 Msa1374440:three_prime_UTR
ATAAGGTGGTGATAATGTTT+TGG 0.354103 tig0019487:+100869 Msa1374440:three_prime_UTR
TGCACTATTTAATTGTGAAT+TGG 0.396593 tig0019487:-100638 None:intergenic
GTATCTGGATCTAGAATATA+AGG 0.397126 tig0019487:+100852 Msa1374440:three_prime_UTR
GCCAAAATGTGTCTATATAT+AGG 0.397555 tig0019487:+100171 Msa1374440:five_prime_UTR
ATTGGTGGTTTCCTTGATGC+TGG 0.439868 tig0019487:-100620 None:intergenic
TGTTGACATCCTCACTACTT+TGG 0.458998 tig0019487:-100502 None:intergenic
CAACAAAGCTCAACAACATA+AGG 0.461599 tig0019487:+100520 Msa1374440:CDS
ACTATTTAATTGTGAATTGG+TGG 0.515565 tig0019487:-100635 None:intergenic
CCTAAATTAACATATCCATA+TGG 0.523592 tig0019487:+100195 Msa1374440:five_prime_UTR
GACATGTTTAAGCTAAAAGA+AGG 0.527331 tig0019487:+100554 Msa1374440:CDS
AAATAGCTATTCTATAGCTA+TGG 0.532562 tig0019487:+100714 Msa1374440:three_prime_UTR
TATGGATGGAGAAGAAGCAA+AGG 0.568511 tig0019487:-100325 None:intergenic
TGGATTATACTCCAGCATCA+AGG 0.596772 tig0019487:+100609 Msa1374440:CDS
AATAAACAACCAAAGTAGTG+AGG 0.645718 tig0019487:+100493 Msa1374440:CDS
CAAAGCTCAACAACATAAGG+AGG 0.647677 tig0019487:+100523 Msa1374440:CDS
ATGTTTAAGCTAAAAGAAGG+AGG 0.667536 tig0019487:+100557 Msa1374440:CDS
AAAGAAGGAGGAGATAACGT+TGG 0.669136 tig0019487:+100569 Msa1374440:CDS
TCTAGATCCAGATACTAACA+TGG 0.690048 tig0019487:-100844 None:intergenic
TCTGGATCTAGAATATAAGG+TGG 0.701138 tig0019487:+100855 Msa1374440:three_prime_UTR
TGATGCTGGAGTATAATCCA+TGG 0.719915 tig0019487:-100606 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! TAAAAAAAATATTACAACAT+TGG + tig0019487:100387-100406 Msa1374440:intron 10.0%
!! AATTAAACAGAAAATAAAAA+TGG - tig0019487:100426-100445 None:intergenic 10.0%
!!! AATTTTTCTTACATTTTTTT+TGG + tig0019487:100446-100465 Msa1374440:intron 10.0%
!!! TGTAATATTTTTTTTAGCTA+TGG - tig0019487:100383-100402 None:intergenic 15.0%
!!! AATTGCTTTTAACTTTAAGA+TGG + tig0019487:100259-100278 Msa1374440:exon 20.0%
!!! ATTAAATAGTGCACAAATTT+TGG + tig0019487:100648-100667 Msa1374440:exon 20.0%
!! TCCTATATATAGACACATTT+TGG - tig0019487:100175-100194 None:intergenic 25.0%
! CCATATGGATATGTTAATTT+AGG - tig0019487:100198-100217 None:intergenic 25.0%
! CCTAAATTAACATATCCATA+TGG + tig0019487:100195-100214 Msa1374440:five_prime_UTR 25.0%
!! CTTTTTCTGAATATACCATA+TGG - tig0019487:100213-100232 None:intergenic 25.0%
! ACTATTTAATTGTGAATTGG+TGG - tig0019487:100638-100657 None:intergenic 25.0%
! TGCACTATTTAATTGTGAAT+TGG - tig0019487:100641-100660 None:intergenic 25.0%
! AAATAGCTATTCTATAGCTA+TGG + tig0019487:100714-100733 Msa1374440:three_prime_UTR 25.0%
GCCAAAATGTGTCTATATAT+AGG + tig0019487:100171-100190 Msa1374440:five_prime_UTR 30.0%
TCCATCCATATTCAAGTAAA+AGG + tig0019487:100338-100357 Msa1374440:CDS 30.0%
! ACCTTTTACTTGAATATGGA+TGG - tig0019487:100342-100361 None:intergenic 30.0%
! AGGTACCTTTTACTTGAATA+TGG - tig0019487:100346-100365 None:intergenic 30.0%
! CTATGGATATTTGAAGCAAA+AGG - tig0019487:100366-100385 None:intergenic 30.0%
AATAAACAACCAAAGTAGTG+AGG + tig0019487:100493-100512 Msa1374440:CDS 30.0%
GACATGTTTAAGCTAAAAGA+AGG + tig0019487:100554-100573 Msa1374440:CDS 30.0%
ATGTTTAAGCTAAAAGAAGG+AGG + tig0019487:100557-100576 Msa1374440:CDS 30.0%
CAATTAACCATGTTAGTATC+TGG + tig0019487:100837-100856 Msa1374440:three_prime_UTR 30.0%
! GTATCTGGATCTAGAATATA+AGG + tig0019487:100852-100871 Msa1374440:three_prime_UTR 30.0%
!! ATAAGGTGGTGATAATGTTT+TGG + tig0019487:100869-100888 Msa1374440:three_prime_UTR 30.0%
CAACAAAGCTCAACAACATA+AGG + tig0019487:100520-100539 Msa1374440:CDS 35.0%
TCTAGATCCAGATACTAACA+TGG - tig0019487:100847-100866 None:intergenic 35.0%
! TCTGGATCTAGAATATAAGG+TGG + tig0019487:100855-100874 Msa1374440:three_prime_UTR 35.0%
TATGGATGGAGAAGAAGCAA+AGG - tig0019487:100328-100347 None:intergenic 40.0%
TGTTGACATCCTCACTACTT+TGG - tig0019487:100505-100524 None:intergenic 40.0%
CAAAGCTCAACAACATAAGG+AGG + tig0019487:100523-100542 Msa1374440:CDS 40.0%
AAAGAAGGAGGAGATAACGT+TGG + tig0019487:100569-100588 Msa1374440:CDS 40.0%
!!! TGGTTCTGATGTTTTCACCA+TGG + tig0019487:100589-100608 Msa1374440:CDS 40.0%
TGATGCTGGAGTATAATCCA+TGG - tig0019487:100609-100628 None:intergenic 40.0%
TGGATTATACTCCAGCATCA+AGG + tig0019487:100609-100628 Msa1374440:CDS 40.0%
! ATTGGTGGTTTCCTTGATGC+TGG - tig0019487:100623-100642 None:intergenic 45.0%
Chromosome Type Strat End Strand Name
tig0019487 gene 100164 100907 100164 ID=Msa1374440;Name=Msa1374440
tig0019487 mRNA 100164 100907 100164 ID=Msa1374440-mRNA-1;Parent=Msa1374440;Name=Msa1374440-mRNA-1;_AED=0.08;_eAED=0.08;_QI=114|1|1|1|1|1|2|255|85
tig0019487 exon 100164 100359 100164 ID=Msa1374440-mRNA-1:exon:3916;Parent=Msa1374440-mRNA-1
tig0019487 exon 100477 100907 100477 ID=Msa1374440-mRNA-1:exon:3917;Parent=Msa1374440-mRNA-1
tig0019487 five_prime_UTR 100164 100277 100164 ID=Msa1374440-mRNA-1:five_prime_utr;Parent=Msa1374440-mRNA-1
tig0019487 CDS 100278 100359 100278 ID=Msa1374440-mRNA-1:cds;Parent=Msa1374440-mRNA-1
tig0019487 CDS 100477 100652 100477 ID=Msa1374440-mRNA-1:cds;Parent=Msa1374440-mRNA-1
tig0019487 three_prime_UTR 100653 100907 100653 ID=Msa1374440-mRNA-1:three_prime_utr;Parent=Msa1374440-mRNA-1
Gene Sequence

>Msa1374440

ATGGTTGCTTCACAAAACAAACGCATTCTACAAGTGATTGTTGTTCTCCTTTGCTTCTTCTCCATCCATATTCAAGTAAAAGCAAGAGTATTGAAAGAAATAAACAACCAAAGTAGTGAGGATGTCAACAAAGCTCAACAACATAAGGAGGTACATGCTGACATGTTTAAGCTAAAAGAAGGAGGAGATAACGTTGGTTCTGATGTTTTCACCATGGATTATACTCCAGCATCAAGGAAACCACCAATTCACAATTAA

Protein sequence

>Msa1374440

MVASQNKRILQVIVVLLCFFSIHIQVKARVLKEINNQSSEDVNKAQQHKEVHADMFKLKEGGDNVGSDVFTMDYTPASRKPPIHN*