AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0484690


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0484690 MtrunA17_Chr3g0129411 97.647 85 2 0 1 85 35 119 1.24e-57 172
Msa0484690 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 70 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
ATTAAATAGTGCACAAATTT+TGG 0.112038 3_4:+2199214 Msa0484690:exon
CCATATGGATATGTTAATTT+AGG 0.228692 3_4:-2198761 None:intergenic
TCCTATATATAGACACATTT+TGG 0.251593 3_4:-2198738 None:intergenic
TCCATCCATATTCAAGTAAA+AGG 0.259194 3_4:+2198904 Msa0484690:CDS
CAATTAACCATGTTAGTATC+TGG 0.347082 3_4:+2199403 Msa0484690:three_prime_UTR
ATAAGGTGGTGATAATGTTT+TGG 0.354103 3_4:+2199435 Msa0484690:three_prime_UTR
TGCACTATTTAATTGTGAAT+TGG 0.396593 3_4:-2199204 None:intergenic
GTATCTGGATCTAGAATATA+AGG 0.397126 3_4:+2199418 Msa0484690:three_prime_UTR
GCCAAAATGTGTCTATATAT+AGG 0.397555 3_4:+2198737 Msa0484690:five_prime_UTR
ATTGGTGGTTTCCTTGATGC+TGG 0.439868 3_4:-2199186 None:intergenic
TGTTGACATCCTCACTACTT+TGG 0.458998 3_4:-2199068 None:intergenic
CAACAAAGCTCAACAACATA+AGG 0.461599 3_4:+2199086 Msa0484690:CDS
ACTATTTAATTGTGAATTGG+TGG 0.515565 3_4:-2199201 None:intergenic
CCTAAATTAACATATCCATA+TGG 0.523592 3_4:+2198761 Msa0484690:five_prime_UTR
GACATGTTTAAGCTAAAAGA+AGG 0.527331 3_4:+2199120 Msa0484690:CDS
AAATAGCTATTCTATAGCTA+TGG 0.532562 3_4:+2199280 Msa0484690:three_prime_UTR
TATGGATGGAGAAGAAGCAA+AGG 0.568511 3_4:-2198891 None:intergenic
TGGATTATACTCCAGCATCA+AGG 0.596772 3_4:+2199175 Msa0484690:CDS
AATAAACAACCAAAGTAGTG+AGG 0.645718 3_4:+2199059 Msa0484690:CDS
CAAAGCTCAACAACATAAGG+AGG 0.647677 3_4:+2199089 Msa0484690:CDS
ATGTTTAAGCTAAAAGAAGG+AGG 0.667536 3_4:+2199123 Msa0484690:CDS
AAAGAAGGAGGAGATAACGT+TGG 0.669136 3_4:+2199135 Msa0484690:CDS
TCTAGATCCAGATACTAACA+TGG 0.690048 3_4:-2199410 None:intergenic
TCTGGATCTAGAATATAAGG+TGG 0.701138 3_4:+2199421 Msa0484690:three_prime_UTR
TGATGCTGGAGTATAATCCA+TGG 0.719915 3_4:-2199172 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! TAAAAAAAATATTACAACAT+TGG + chr3_4:2198953-2198972 Msa0484690:intron 10.0%
!! AATTAAACAGAAAATAAAAA+TGG - chr3_4:2198992-2199011 None:intergenic 10.0%
!!! AATTTTTCTTACATTTTTTT+TGG + chr3_4:2199012-2199031 Msa0484690:intron 10.0%
!! TAAAAAAAATATTACAACAT+TGG + chr3_4:2198953-2198972 Msa0484690:intron 10.0%
!! AATTAAACAGAAAATAAAAA+TGG - chr3_4:2198992-2199011 None:intergenic 10.0%
!!! AATTTTTCTTACATTTTTTT+TGG + chr3_4:2199012-2199031 Msa0484690:intron 10.0%
!!! TGTAATATTTTTTTTAGCTA+TGG - chr3_4:2198949-2198968 None:intergenic 15.0%
!!! TGTAATATTTTTTTTAGCTA+TGG - chr3_4:2198949-2198968 None:intergenic 15.0%
!!! AATTGCTTTTAACTTTAAGA+TGG + chr3_4:2198825-2198844 Msa0484690:exon 20.0%
!!! ATTAAATAGTGCACAAATTT+TGG + chr3_4:2199214-2199233 Msa0484690:exon 20.0%
!!! AATTGCTTTTAACTTTAAGA+TGG + chr3_4:2198825-2198844 Msa0484690:exon 20.0%
!!! ATTAAATAGTGCACAAATTT+TGG + chr3_4:2199214-2199233 Msa0484690:exon 20.0%
!! TCCTATATATAGACACATTT+TGG - chr3_4:2198741-2198760 None:intergenic 25.0%
! CCATATGGATATGTTAATTT+AGG - chr3_4:2198764-2198783 None:intergenic 25.0%
! CCTAAATTAACATATCCATA+TGG + chr3_4:2198761-2198780 Msa0484690:five_prime_UTR 25.0%
!! CTTTTTCTGAATATACCATA+TGG - chr3_4:2198779-2198798 None:intergenic 25.0%
! ACTATTTAATTGTGAATTGG+TGG - chr3_4:2199204-2199223 None:intergenic 25.0%
! TGCACTATTTAATTGTGAAT+TGG - chr3_4:2199207-2199226 None:intergenic 25.0%
! AAATAGCTATTCTATAGCTA+TGG + chr3_4:2199280-2199299 Msa0484690:three_prime_UTR 25.0%
!! TCCTATATATAGACACATTT+TGG - chr3_4:2198741-2198760 None:intergenic 25.0%
! CCATATGGATATGTTAATTT+AGG - chr3_4:2198764-2198783 None:intergenic 25.0%
! CCTAAATTAACATATCCATA+TGG + chr3_4:2198761-2198780 Msa0484690:five_prime_UTR 25.0%
!! CTTTTTCTGAATATACCATA+TGG - chr3_4:2198779-2198798 None:intergenic 25.0%
! ACTATTTAATTGTGAATTGG+TGG - chr3_4:2199204-2199223 None:intergenic 25.0%
! TGCACTATTTAATTGTGAAT+TGG - chr3_4:2199207-2199226 None:intergenic 25.0%
! AAATAGCTATTCTATAGCTA+TGG + chr3_4:2199280-2199299 Msa0484690:three_prime_UTR 25.0%
GCCAAAATGTGTCTATATAT+AGG + chr3_4:2198737-2198756 Msa0484690:five_prime_UTR 30.0%
TCCATCCATATTCAAGTAAA+AGG + chr3_4:2198904-2198923 Msa0484690:CDS 30.0%
! ACCTTTTACTTGAATATGGA+TGG - chr3_4:2198908-2198927 None:intergenic 30.0%
! AGGTACCTTTTACTTGAATA+TGG - chr3_4:2198912-2198931 None:intergenic 30.0%
! CTATGGATATTTGAAGCAAA+AGG - chr3_4:2198932-2198951 None:intergenic 30.0%
AATAAACAACCAAAGTAGTG+AGG + chr3_4:2199059-2199078 Msa0484690:CDS 30.0%
GACATGTTTAAGCTAAAAGA+AGG + chr3_4:2199120-2199139 Msa0484690:CDS 30.0%
ATGTTTAAGCTAAAAGAAGG+AGG + chr3_4:2199123-2199142 Msa0484690:CDS 30.0%
CAATTAACCATGTTAGTATC+TGG + chr3_4:2199403-2199422 Msa0484690:three_prime_UTR 30.0%
! GTATCTGGATCTAGAATATA+AGG + chr3_4:2199418-2199437 Msa0484690:three_prime_UTR 30.0%
!! ATAAGGTGGTGATAATGTTT+TGG + chr3_4:2199435-2199454 Msa0484690:three_prime_UTR 30.0%
GCCAAAATGTGTCTATATAT+AGG + chr3_4:2198737-2198756 Msa0484690:five_prime_UTR 30.0%
TCCATCCATATTCAAGTAAA+AGG + chr3_4:2198904-2198923 Msa0484690:CDS 30.0%
! ACCTTTTACTTGAATATGGA+TGG - chr3_4:2198908-2198927 None:intergenic 30.0%
! AGGTACCTTTTACTTGAATA+TGG - chr3_4:2198912-2198931 None:intergenic 30.0%
! CTATGGATATTTGAAGCAAA+AGG - chr3_4:2198932-2198951 None:intergenic 30.0%
AATAAACAACCAAAGTAGTG+AGG + chr3_4:2199059-2199078 Msa0484690:CDS 30.0%
GACATGTTTAAGCTAAAAGA+AGG + chr3_4:2199120-2199139 Msa0484690:CDS 30.0%
ATGTTTAAGCTAAAAGAAGG+AGG + chr3_4:2199123-2199142 Msa0484690:CDS 30.0%
CAATTAACCATGTTAGTATC+TGG + chr3_4:2199403-2199422 Msa0484690:three_prime_UTR 30.0%
! GTATCTGGATCTAGAATATA+AGG + chr3_4:2199418-2199437 Msa0484690:three_prime_UTR 30.0%
!! ATAAGGTGGTGATAATGTTT+TGG + chr3_4:2199435-2199454 Msa0484690:three_prime_UTR 30.0%
CAACAAAGCTCAACAACATA+AGG + chr3_4:2199086-2199105 Msa0484690:CDS 35.0%
TCTAGATCCAGATACTAACA+TGG - chr3_4:2199413-2199432 None:intergenic 35.0%
! TCTGGATCTAGAATATAAGG+TGG + chr3_4:2199421-2199440 Msa0484690:three_prime_UTR 35.0%
CAACAAAGCTCAACAACATA+AGG + chr3_4:2199086-2199105 Msa0484690:CDS 35.0%
TCTAGATCCAGATACTAACA+TGG - chr3_4:2199413-2199432 None:intergenic 35.0%
! TCTGGATCTAGAATATAAGG+TGG + chr3_4:2199421-2199440 Msa0484690:three_prime_UTR 35.0%
TATGGATGGAGAAGAAGCAA+AGG - chr3_4:2198894-2198913 None:intergenic 40.0%
TGTTGACATCCTCACTACTT+TGG - chr3_4:2199071-2199090 None:intergenic 40.0%
CAAAGCTCAACAACATAAGG+AGG + chr3_4:2199089-2199108 Msa0484690:CDS 40.0%
AAAGAAGGAGGAGATAACGT+TGG + chr3_4:2199135-2199154 Msa0484690:CDS 40.0%
!!! TGGTTCTGATGTTTTCACCA+TGG + chr3_4:2199155-2199174 Msa0484690:CDS 40.0%
TGATGCTGGAGTATAATCCA+TGG - chr3_4:2199175-2199194 None:intergenic 40.0%
TGGATTATACTCCAGCATCA+AGG + chr3_4:2199175-2199194 Msa0484690:CDS 40.0%
TATGGATGGAGAAGAAGCAA+AGG - chr3_4:2198894-2198913 None:intergenic 40.0%
TGTTGACATCCTCACTACTT+TGG - chr3_4:2199071-2199090 None:intergenic 40.0%
CAAAGCTCAACAACATAAGG+AGG + chr3_4:2199089-2199108 Msa0484690:CDS 40.0%
AAAGAAGGAGGAGATAACGT+TGG + chr3_4:2199135-2199154 Msa0484690:CDS 40.0%
!!! TGGTTCTGATGTTTTCACCA+TGG + chr3_4:2199155-2199174 Msa0484690:CDS 40.0%
TGATGCTGGAGTATAATCCA+TGG - chr3_4:2199175-2199194 None:intergenic 40.0%
TGGATTATACTCCAGCATCA+AGG + chr3_4:2199175-2199194 Msa0484690:CDS 40.0%
! ATTGGTGGTTTCCTTGATGC+TGG - chr3_4:2199189-2199208 None:intergenic 45.0%
! ATTGGTGGTTTCCTTGATGC+TGG - chr3_4:2199189-2199208 None:intergenic 45.0%
Chromosome Type Strat End Strand Name
chr3_4 gene 2198730 2199473 2198730 ID=Msa0484690;Name=Msa0484690
chr3_4 mRNA 2198730 2199473 2198730 ID=Msa0484690-mRNA-1;Parent=Msa0484690;Name=Msa0484690-mRNA-1;_AED=0.08;_eAED=0.08;_QI=114|1|1|1|1|1|2|255|85
chr3_4 exon 2198730 2198925 2198730 ID=Msa0484690-mRNA-1:exon:748;Parent=Msa0484690-mRNA-1
chr3_4 exon 2199043 2199473 2199043 ID=Msa0484690-mRNA-1:exon:749;Parent=Msa0484690-mRNA-1
chr3_4 five_prime_UTR 2198730 2198843 2198730 ID=Msa0484690-mRNA-1:five_prime_utr;Parent=Msa0484690-mRNA-1
chr3_4 CDS 2198844 2198925 2198844 ID=Msa0484690-mRNA-1:cds;Parent=Msa0484690-mRNA-1
chr3_4 CDS 2199043 2199218 2199043 ID=Msa0484690-mRNA-1:cds;Parent=Msa0484690-mRNA-1
chr3_4 three_prime_UTR 2199219 2199473 2199219 ID=Msa0484690-mRNA-1:three_prime_utr;Parent=Msa0484690-mRNA-1
Gene Sequence

>Msa0484690

ATGGTTGCTTCACAAAACAAACGCATTCTACAAGTGATTGTTGTTCTCCTTTGCTTCTTCTCCATCCATATTCAAGTAAAAGCAAGAGTATTGAAAGAAATAAACAACCAAAGTAGTGAGGATGTCAACAAAGCTCAACAACATAAGGAGGTACATGCTGACATGTTTAAGCTAAAAGAAGGAGGAGATAACGTTGGTTCTGATGTTTTCACCATGGATTATACTCCAGCATCAAGGAAACCACCAATTCACAATTAA

Protein sequence

>Msa0484690

MVASQNKRILQVIVVLLCFFSIHIQVKARVLKEINNQSSEDVNKAQQHKEVHADMFKLKEGGDNVGSDVFTMDYTPASRKPPIHN*