AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0426330


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0426330 MtrunA17_Chr3g0128301 94.444 162 7 1 1 160 291 452 5.82e-98 290
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0426330 AT1G18010.1 67.949 156 46 1 1 152 293 448 1.08e-68 215
Msa0426330 AT1G18000.1 67.949 156 46 1 1 152 293 448 1.08e-68 215

Find 40 sgRNAs with CRISPR-Local

Find 124 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CTGTTCTTGGATCTATTATA+TGG 0.213344 3_2:-76715412 Msa0426330:CDS
ATTAGTGTGGTTGCTGTTCT+TGG 0.242665 3_2:-76715425 Msa0426330:CDS
AGATGCCATGTTTCAGAGTA+TGG 0.258685 3_2:-76715276 Msa0426330:CDS
TGTTTCAGAGTATGGTTTAC+TGG 0.266519 3_2:-76715268 Msa0426330:CDS
TGTTCTTGGATCTATTATAT+GGG 0.338310 3_2:-76715411 Msa0426330:CDS
AGGTACACAGGATTCTATAA+AGG 0.355926 3_2:-76714825 Msa0426330:CDS
AGTATGGTTTACTGGTCTAT+TGG 0.363404 3_2:-76715260 Msa0426330:CDS
AATTGGGATTGGTTACACTA+TGG 0.364274 3_2:-76715489 Msa0426330:CDS
ACATAAACATGGCAAGGTCT+TGG 0.373279 3_2:-76715363 Msa0426330:CDS
TATTGGGGAGCACAAATGAT+AGG 0.383645 3_2:-76715515 None:intergenic
TTCACAATCAACTGTGTCAT+TGG 0.386175 3_2:+76714747 None:intergenic
TGACACAGTTGATTGTGAAT+TGG 0.408150 3_2:-76714743 Msa0426330:CDS
GCACAAATGATAGGGTCAAT+TGG 0.413131 3_2:-76715506 Msa0426330:exon
TAGAAAGAAAAGAGGAATTG+TGG 0.430494 3_2:-76715450 Msa0426330:CDS
TTACTGGTCTATTGGAGCAT+TGG 0.434243 3_2:-76715252 Msa0426330:CDS
TTTGTAAATAATATAATGGA+TGG 0.438919 3_2:-76714561 Msa0426330:three_prime_UTR
CACAAATGATAGGGTCAATT+GGG 0.440466 3_2:-76715505 Msa0426330:exon
TTTAAGAGTAGAAAGAAAAG+AGG 0.440838 3_2:-76715458 Msa0426330:CDS
AGAAAGAAAAGAGGAATTGT+GGG 0.444597 3_2:-76715449 Msa0426330:CDS
GACACAGTTGATTGTGAATT+GGG 0.445991 3_2:-76714742 Msa0426330:CDS
ACTAAGCTATCCGTTATTGT+TGG 0.457774 3_2:-76714709 Msa0426330:CDS
GGTACACAGGATTCTATAAA+GGG 0.462985 3_2:-76714824 Msa0426330:CDS
TATTATATGGGGTGGTGCAT+TGG 0.473668 3_2:-76715399 Msa0426330:CDS
ATCATTAAAACCAACAATAA+CGG 0.482912 3_2:+76714699 None:intergenic
ATGATAGGGTCAATTGGGAT+TGG 0.495144 3_2:-76715500 Msa0426330:CDS
ATTGGGGAGCACAAATGATA+GGG 0.533554 3_2:-76715514 Msa0426330:exon
TTGTAAATAATATAATGGAT+GGG 0.536565 3_2:-76714560 Msa0426330:three_prime_UTR
ATGACTCTGAAGTTCTTAGC+AGG 0.541389 3_2:-76715226 Msa0426330:intron
TATAAAGGGATACAAAGTGC+GGG 0.551438 3_2:-76714810 Msa0426330:CDS
GTTCTTGGATCTATTATATG+GGG 0.579371 3_2:-76715410 Msa0426330:CDS
CTTGGATCTATTATATGGGG+TGG 0.589106 3_2:-76715407 Msa0426330:CDS
GATTAAACATAAACATGGCA+AGG 0.600741 3_2:-76715369 Msa0426330:CDS
TTGGACTTACACAGGTACAC+AGG 0.625881 3_2:-76714837 Msa0426330:intron
AGGAATTGTGGGAATTAGTG+TGG 0.626228 3_2:-76715438 Msa0426330:CDS
ATAAAGGGATACAAAGTGCG+GGG 0.639763 3_2:-76714809 Msa0426330:CDS
AATCAGATTAAACATAAACA+TGG 0.664350 3_2:-76715374 Msa0426330:CDS
CTATAAAGGGATACAAAGTG+CGG 0.672233 3_2:-76714811 Msa0426330:CDS
GTAAACCATACTCTGAAACA+TGG 0.672850 3_2:+76715271 None:intergenic
TAAAGGGATACAAAGTGCGG+GGG 0.692575 3_2:-76714808 Msa0426330:CDS
TGTGAAAGAGGACAATAACG+AGG 0.786049 3_2:-76714670 Msa0426330:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! AGTTTTTGTAAATAATATAA+TGG - chr3_2:76715506-76715525 Msa0426330:exon 10.0%
!!! AGTTTTTGTAAATAATATAA+TGG - chr3_2:76715506-76715525 Msa0426330:exon 10.0%
!! AAAGAAAAATACAAAACAAA+AGG + chr3_2:76714766-76714785 None:intergenic 15.0%
!!! TTTGTTTTGTATTTTTCTTT+TGG - chr3_2:76714766-76714785 Msa0426330:CDS 15.0%
!!! TTGTTTTGTATTTTTCTTTT+GGG - chr3_2:76714767-76714786 Msa0426330:CDS 15.0%
!!! TTTGTAAATAATATAATGGA+TGG - chr3_2:76715510-76715529 Msa0426330:exon 15.0%
!!! TTGTAAATAATATAATGGAT+GGG - chr3_2:76715511-76715530 Msa0426330:exon 15.0%
!! AAAGAAAAATACAAAACAAA+AGG + chr3_2:76714766-76714785 None:intergenic 15.0%
!!! TTTGTTTTGTATTTTTCTTT+TGG - chr3_2:76714766-76714785 Msa0426330:CDS 15.0%
!!! TTGTTTTGTATTTTTCTTTT+GGG - chr3_2:76714767-76714786 Msa0426330:CDS 15.0%
!!! TTTGTAAATAATATAATGGA+TGG - chr3_2:76715510-76715529 Msa0426330:exon 15.0%
!! AATCAGATTAAACATAAACA+TGG - chr3_2:76714697-76714716 Msa0426330:CDS 20.0%
!! AGAAACTTCAAGAAAATATT+TGG - chr3_2:76715019-76715038 Msa0426330:intron 20.0%
!! AATAATCCACAAAAAAATAC+TGG + chr3_2:76715085-76715104 None:intergenic 20.0%
!!! TAATTTGTAGTTTTAGTGAT+TGG - chr3_2:76715142-76715161 Msa0426330:intron 20.0%
!! ATCATTAAAACCAACAATAA+CGG + chr3_2:76715375-76715394 None:intergenic 20.0%
!!! ATTGTTGGTTTTAATGATTT+TGG - chr3_2:76715377-76715396 Msa0426330:CDS 20.0%
!!! TGTAAATAATATAATGGATG+GGG - chr3_2:76715512-76715531 Msa0426330:exon 20.0%
!! AATCAGATTAAACATAAACA+TGG - chr3_2:76714697-76714716 Msa0426330:CDS 20.0%
!! AGAAACTTCAAGAAAATATT+TGG - chr3_2:76715019-76715038 Msa0426330:intron 20.0%
!! AATAATCCACAAAAAAATAC+TGG + chr3_2:76715085-76715104 None:intergenic 20.0%
!!! TAATTTGTAGTTTTAGTGAT+TGG - chr3_2:76715142-76715161 Msa0426330:intron 20.0%
!! ATCATTAAAACCAACAATAA+CGG + chr3_2:76715375-76715394 None:intergenic 20.0%
!!! ATTGTTGGTTTTAATGATTT+TGG - chr3_2:76715377-76715396 Msa0426330:CDS 20.0%
! TTTAAGAGTAGAAAGAAAAG+AGG - chr3_2:76714613-76714632 Msa0426330:three_prime_UTR 25.0%
! TGTTCTTGGATCTATTATAT+GGG - chr3_2:76714660-76714679 Msa0426330:CDS 25.0%
! TTAACTATTCCATTTGTTCT+TGG - chr3_2:76714904-76714923 Msa0426330:intron 25.0%
!!! TATCAACCAGTATTTTTTTG+TGG - chr3_2:76715076-76715095 Msa0426330:intron 25.0%
! TTTCCAAATTTCAACTATCA+GGG + chr3_2:76715185-76715204 None:intergenic 25.0%
! ATTTCCAAATTTCAACTATC+AGG + chr3_2:76715186-76715205 None:intergenic 25.0%
!!! GTAAATAATATAATGGATGG+GGG - chr3_2:76715513-76715532 Msa0426330:exon 25.0%
!!! TAAATAATATAATGGATGGG+GGG - chr3_2:76715514-76715533 Msa0426330:exon 25.0%
! TTTAAGAGTAGAAAGAAAAG+AGG - chr3_2:76714613-76714632 Msa0426330:three_prime_UTR 25.0%
! TGTTCTTGGATCTATTATAT+GGG - chr3_2:76714660-76714679 Msa0426330:CDS 25.0%
! TTAACTATTCCATTTGTTCT+TGG - chr3_2:76714904-76714923 Msa0426330:intron 25.0%
!!! TATCAACCAGTATTTTTTTG+TGG - chr3_2:76715076-76715095 Msa0426330:intron 25.0%
! TTTCCAAATTTCAACTATCA+GGG + chr3_2:76715185-76715204 None:intergenic 25.0%
! ATTTCCAAATTTCAACTATC+AGG + chr3_2:76715186-76715205 None:intergenic 25.0%
TAGAAAGAAAAGAGGAATTG+TGG - chr3_2:76714621-76714640 Msa0426330:three_prime_UTR 30.0%
AGAAAGAAAAGAGGAATTGT+GGG - chr3_2:76714622-76714641 Msa0426330:three_prime_UTR 30.0%
CTGTTCTTGGATCTATTATA+TGG - chr3_2:76714659-76714678 Msa0426330:CDS 30.0%
GTTCTTGGATCTATTATATG+GGG - chr3_2:76714661-76714680 Msa0426330:CDS 30.0%
GATTAAACATAAACATGGCA+AGG - chr3_2:76714702-76714721 Msa0426330:CDS 30.0%
AAAATGCAACCAAGAACAAA+TGG + chr3_2:76714916-76714935 None:intergenic 30.0%
TTAGTGATTGGCATTTCATT+TGG - chr3_2:76715154-76715173 Msa0426330:intron 30.0%
TATCCCTGATAGTTGAAATT+TGG - chr3_2:76715179-76715198 Msa0426330:intron 30.0%
!!! AATGATTTTGGTTGTGAAAG+AGG - chr3_2:76715389-76715408 Msa0426330:CDS 30.0%
TAGAAAGAAAAGAGGAATTG+TGG - chr3_2:76714621-76714640 Msa0426330:three_prime_UTR 30.0%
AGAAAGAAAAGAGGAATTGT+GGG - chr3_2:76714622-76714641 Msa0426330:three_prime_UTR 30.0%
CTGTTCTTGGATCTATTATA+TGG - chr3_2:76714659-76714678 Msa0426330:CDS 30.0%
GTTCTTGGATCTATTATATG+GGG - chr3_2:76714661-76714680 Msa0426330:CDS 30.0%
GATTAAACATAAACATGGCA+AGG - chr3_2:76714702-76714721 Msa0426330:CDS 30.0%
AAAATGCAACCAAGAACAAA+TGG + chr3_2:76714916-76714935 None:intergenic 30.0%
TTAGTGATTGGCATTTCATT+TGG - chr3_2:76715154-76715173 Msa0426330:intron 30.0%
TATCCCTGATAGTTGAAATT+TGG - chr3_2:76715179-76715198 Msa0426330:intron 30.0%
!!! AATGATTTTGGTTGTGAAAG+AGG - chr3_2:76715389-76715408 Msa0426330:CDS 30.0%
CACAAATGATAGGGTCAATT+GGG - chr3_2:76714566-76714585 Msa0426330:three_prime_UTR 35.0%
!! AATTGGGATTGGTTACACTA+TGG - chr3_2:76714582-76714601 Msa0426330:three_prime_UTR 35.0%
!! GTAAACCATACTCTGAAACA+TGG + chr3_2:76714803-76714822 None:intergenic 35.0%
TGTTTCAGAGTATGGTTTAC+TGG - chr3_2:76714803-76714822 Msa0426330:CDS 35.0%
! AGTATGGTTTACTGGTCTAT+TGG - chr3_2:76714811-76714830 Msa0426330:CDS 35.0%
CTACTGCTAGTACTAATGTT+TGG - chr3_2:76715215-76715234 Msa0426330:intron 35.0%
ACTAATGTTTGGACTTACAC+AGG - chr3_2:76715226-76715245 Msa0426330:intron 35.0%
AGGTACACAGGATTCTATAA+AGG - chr3_2:76715246-76715265 Msa0426330:CDS 35.0%
GGTACACAGGATTCTATAAA+GGG - chr3_2:76715247-76715266 Msa0426330:CDS 35.0%
CTATAAAGGGATACAAAGTG+CGG - chr3_2:76715260-76715279 Msa0426330:CDS 35.0%
TATAAAGGGATACAAAGTGC+GGG - chr3_2:76715261-76715280 Msa0426330:CDS 35.0%
TTCACAATCAACTGTGTCAT+TGG + chr3_2:76715327-76715346 None:intergenic 35.0%
TGACACAGTTGATTGTGAAT+TGG - chr3_2:76715328-76715347 Msa0426330:CDS 35.0%
GACACAGTTGATTGTGAATT+GGG - chr3_2:76715329-76715348 Msa0426330:CDS 35.0%
ACTAAGCTATCCGTTATTGT+TGG - chr3_2:76715362-76715381 Msa0426330:CDS 35.0%
CACAAATGATAGGGTCAATT+GGG - chr3_2:76714566-76714585 Msa0426330:three_prime_UTR 35.0%
!! AATTGGGATTGGTTACACTA+TGG - chr3_2:76714582-76714601 Msa0426330:three_prime_UTR 35.0%
!! GTAAACCATACTCTGAAACA+TGG + chr3_2:76714803-76714822 None:intergenic 35.0%
TGTTTCAGAGTATGGTTTAC+TGG - chr3_2:76714803-76714822 Msa0426330:CDS 35.0%
! AGTATGGTTTACTGGTCTAT+TGG - chr3_2:76714811-76714830 Msa0426330:CDS 35.0%
CTACTGCTAGTACTAATGTT+TGG - chr3_2:76715215-76715234 Msa0426330:intron 35.0%
ACTAATGTTTGGACTTACAC+AGG - chr3_2:76715226-76715245 Msa0426330:intron 35.0%
AGGTACACAGGATTCTATAA+AGG - chr3_2:76715246-76715265 Msa0426330:CDS 35.0%
GGTACACAGGATTCTATAAA+GGG - chr3_2:76715247-76715266 Msa0426330:CDS 35.0%
CTATAAAGGGATACAAAGTG+CGG - chr3_2:76715260-76715279 Msa0426330:CDS 35.0%
TATAAAGGGATACAAAGTGC+GGG - chr3_2:76715261-76715280 Msa0426330:CDS 35.0%
TTCACAATCAACTGTGTCAT+TGG + chr3_2:76715327-76715346 None:intergenic 35.0%
TGACACAGTTGATTGTGAAT+TGG - chr3_2:76715328-76715347 Msa0426330:CDS 35.0%
GACACAGTTGATTGTGAATT+GGG - chr3_2:76715329-76715348 Msa0426330:CDS 35.0%
ACTAAGCTATCCGTTATTGT+TGG - chr3_2:76715362-76715381 Msa0426330:CDS 35.0%
GCACAAATGATAGGGTCAAT+TGG - chr3_2:76714565-76714584 Msa0426330:three_prime_UTR 40.0%
ATGATAGGGTCAATTGGGAT+TGG - chr3_2:76714571-76714590 Msa0426330:three_prime_UTR 40.0%
AGGAATTGTGGGAATTAGTG+TGG - chr3_2:76714633-76714652 Msa0426330:three_prime_UTR 40.0%
! ATTAGTGTGGTTGCTGTTCT+TGG - chr3_2:76714646-76714665 Msa0426330:exon 40.0%
CTTGGATCTATTATATGGGG+TGG - chr3_2:76714664-76714683 Msa0426330:CDS 40.0%
TATTATATGGGGTGGTGCAT+TGG - chr3_2:76714672-76714691 Msa0426330:CDS 40.0%
ACATAAACATGGCAAGGTCT+TGG - chr3_2:76714708-76714727 Msa0426330:CDS 40.0%
! TGGCAAGGTCTTGGATTTTA+AGG - chr3_2:76714717-76714736 Msa0426330:CDS 40.0%
!! GTCTTGGATTTTAAGGAGTC+TGG - chr3_2:76714724-76714743 Msa0426330:CDS 40.0%
AGATGCCATGTTTCAGAGTA+TGG - chr3_2:76714795-76714814 Msa0426330:CDS 40.0%
! TTACTGGTCTATTGGAGCAT+TGG - chr3_2:76714819-76714838 Msa0426330:CDS 40.0%
!! ATGACTCTGAAGTTCTTAGC+AGG - chr3_2:76714845-76714864 Msa0426330:intron 40.0%
ATAAAGGGATACAAAGTGCG+GGG - chr3_2:76715262-76715281 Msa0426330:CDS 40.0%
TGTGAAAGAGGACAATAACG+AGG - chr3_2:76715401-76715420 Msa0426330:CDS 40.0%
GCACAAATGATAGGGTCAAT+TGG - chr3_2:76714565-76714584 Msa0426330:three_prime_UTR 40.0%
ATGATAGGGTCAATTGGGAT+TGG - chr3_2:76714571-76714590 Msa0426330:three_prime_UTR 40.0%
AGGAATTGTGGGAATTAGTG+TGG - chr3_2:76714633-76714652 Msa0426330:three_prime_UTR 40.0%
! ATTAGTGTGGTTGCTGTTCT+TGG - chr3_2:76714646-76714665 Msa0426330:exon 40.0%
CTTGGATCTATTATATGGGG+TGG - chr3_2:76714664-76714683 Msa0426330:CDS 40.0%
TATTATATGGGGTGGTGCAT+TGG - chr3_2:76714672-76714691 Msa0426330:CDS 40.0%
ACATAAACATGGCAAGGTCT+TGG - chr3_2:76714708-76714727 Msa0426330:CDS 40.0%
! TGGCAAGGTCTTGGATTTTA+AGG - chr3_2:76714717-76714736 Msa0426330:CDS 40.0%
!! GTCTTGGATTTTAAGGAGTC+TGG - chr3_2:76714724-76714743 Msa0426330:CDS 40.0%
AGATGCCATGTTTCAGAGTA+TGG - chr3_2:76714795-76714814 Msa0426330:CDS 40.0%
! TTACTGGTCTATTGGAGCAT+TGG - chr3_2:76714819-76714838 Msa0426330:CDS 40.0%
!! ATGACTCTGAAGTTCTTAGC+AGG - chr3_2:76714845-76714864 Msa0426330:intron 40.0%
ATAAAGGGATACAAAGTGCG+GGG - chr3_2:76715262-76715281 Msa0426330:CDS 40.0%
TGTGAAAGAGGACAATAACG+AGG - chr3_2:76715401-76715420 Msa0426330:CDS 40.0%
!!! GAGTCTGGTTCTGATTTTGC+TGG - chr3_2:76714739-76714758 Msa0426330:CDS 45.0%
TTGGACTTACACAGGTACAC+AGG - chr3_2:76715234-76715253 Msa0426330:CDS 45.0%
TAAAGGGATACAAAGTGCGG+GGG - chr3_2:76715263-76715282 Msa0426330:CDS 45.0%
!!! GAGTCTGGTTCTGATTTTGC+TGG - chr3_2:76714739-76714758 Msa0426330:CDS 45.0%
TTGGACTTACACAGGTACAC+AGG - chr3_2:76715234-76715253 Msa0426330:CDS 45.0%
TAAAGGGATACAAAGTGCGG+GGG - chr3_2:76715263-76715282 Msa0426330:CDS 45.0%
!!! ATTAAAAAAATATTATGTTT+TGG + chr3_2:76714995-76715014 None:intergenic 5.0%
!!! ATTAAAAAAATATTATGTTT+TGG + chr3_2:76714995-76715014 None:intergenic 5.0%
GTGCGGGGGCTGCAGTTGCA+TGG - chr3_2:76715277-76715296 Msa0426330:CDS 70.0%
GTGCGGGGGCTGCAGTTGCA+TGG - chr3_2:76715277-76715296 Msa0426330:CDS 70.0%
Chromosome Type Strat End Strand Name
chr3_2 gene 76714560 76715533 76714560 ID=Msa0426330;Name=Msa0426330
chr3_2 mRNA 76714560 76715533 76714560 ID=Msa0426330-mRNA-1;Parent=Msa0426330;Name=Msa0426330-mRNA-1;_AED=0.37;_eAED=0.37;_QI=11|1|1|1|1|1|2|99|160
chr3_2 exon 76714560 76714845 76714560 ID=Msa0426330-mRNA-1:exon:19922;Parent=Msa0426330-mRNA-1
chr3_2 exon 76715227 76715533 76715227 ID=Msa0426330-mRNA-1:exon:19921;Parent=Msa0426330-mRNA-1
chr3_2 five_prime_UTR 76715523 76715533 76715523 ID=Msa0426330-mRNA-1:five_prime_utr;Parent=Msa0426330-mRNA-1
chr3_2 CDS 76715227 76715522 76715227 ID=Msa0426330-mRNA-1:cds;Parent=Msa0426330-mRNA-1
chr3_2 CDS 76714659 76714845 76714659 ID=Msa0426330-mRNA-1:cds;Parent=Msa0426330-mRNA-1
chr3_2 three_prime_UTR 76714560 76714658 76714560 ID=Msa0426330-mRNA-1:three_prime_utr;Parent=Msa0426330-mRNA-1
Gene Sequence

>Msa0426330

ATGATAGGGTCAATTGGGATTGGTTACACTATGGATTTCAGTTTTAAGAGTAGAAAGAAAAGAGGAATTGTGGGAATTAGTGTGGTTGCTGTTCTTGGATCTATTATATGGGGTGGTGCATTGGCTAATCAGATTAAACATAAACATGGCAAGGTCTTGGATTTTAAGGAGTCTGGTTCTGATTTTGCTGGTCCTTTTGTTTTGTATTTTTCTTTTGGGCTGTTAGATGCCATGTTTCAGAGTATGGTTTACTGGTCTATTGGAGCATTGGCTAATGACTCTGAAGTTCTTAGCAGGTACACAGGATTCTATAAAGGGATACAAAGTGCGGGGGCTGCAGTTGCATGGCAAATTGATAATCACAATGTATCTCCAATGACACAGTTGATTGTGAATTGGGTGCTCACTACACTAAGCTATCCGTTATTGTTGGTTTTAATGATTTTGGTTGTGAAAGAGGACAATAACGAGGAAGAGAAATGA

Protein sequence

>Msa0426330

MIGSIGIGYTMDFSFKSRKKRGIVGISVVAVLGSIIWGGALANQIKHKHGKVLDFKESGSDFAGPFVLYFSFGLLDAMFQSMVYWSIGALANDSEVLSRYTGFYKGIQSAGAAVAWQIDNHNVSPMTQLIVNWVLTTLSYPLLLVLMILVVKEDNNEEEK*