AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0516500

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0516500 MtrunA17_Chr3g0127111 93.671 79 4 1 1 78 1 79 9.36e-50 150
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 104 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CCAGGTTTCTTTGAATGCTT+TGG 0.177524 3_4:+68004235 None:intergenic
TTCTTTGAATGCTTTGGGTT+GGG 0.313836 3_4:+68004241 None:intergenic
ATTTGTTTACCTGAAGATAA+AGG 0.340472 3_4:+68004794 None:intergenic
CAGGTTTCTTTGAATGCTTT+GGG 0.352628 3_4:+68004236 None:intergenic
AGGTATTAATAAATAAAGTA+TGG 0.361284 3_4:-68004007 Msa0516500:three_prime_UTR
AAACCAAGAGGATGGCTAAA+AGG 0.364847 3_4:+68004828 None:intergenic
TGATTAGTAATTAGTTGTTA+AGG 0.392811 3_4:+68004196 None:intergenic
TTTCTTTGAATGCTTTGGGT+TGG 0.396872 3_4:+68004240 None:intergenic
TTGTAAAGAAAGTTATTAGT+AGG 0.421064 3_4:+68004659 None:intergenic
TACTAATAACTTTCTTTACA+AGG 0.464774 3_4:-68004657 Msa0516500:intron
TGAGTGTATTGTAACTTATG+AGG 0.474983 3_4:-68004027 Msa0516500:three_prime_UTR
GGTGTTTAACGACCCTTGCC+AGG 0.478184 3_4:+68004217 None:intergenic
TTCATTGCATATACTTGCCA+TGG 0.509554 3_4:-68004870 Msa0516500:exon
ATGAATATAAATGACTTGGC+AGG 0.510347 3_4:+68004935 None:intergenic
CCAAAGCATTCAAAGAAACC+TGG 0.549609 3_4:-68004235 Msa0516500:CDS
AATCGAGCTAGTTTCTTCAC+CGG 0.549992 3_4:-68004060 Msa0516500:three_prime_UTR
TAAAATGAATATAAATGACT+TGG 0.575545 3_4:+68004931 None:intergenic
ATGAATGAAAACCAAGAGGA+TGG 0.580545 3_4:+68004820 None:intergenic
ATACACTCAAGTAGTGGCTC+CGG 0.581091 3_4:+68004041 None:intergenic
GTGTTGGATTATGATGAAGC+AGG 0.583814 3_4:-68004265 Msa0516500:CDS
GCATTCAAAGAAACCTGGCA+AGG 0.596187 3_4:-68004230 Msa0516500:CDS
CATTCAAAGAAACCTGGCAA+GGG 0.630511 3_4:-68004229 Msa0516500:CDS
GTTACAATACACTCAAGTAG+TGG 0.639021 3_4:+68004035 None:intergenic
GAAAATGAATGAAAACCAAG+AGG 0.671422 3_4:+68004816 None:intergenic
ATGGTGTAAAGATGAACTCG+AGG 0.686471 3_4:-68004309 Msa0516500:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! TTTTTTCATATAGTTTTAAA+TGG - chr3_4:68004312-68004331 Msa0516500:CDS 10.0%
!!! TTATTTGTAAACATTATTTT+GGG + chr3_4:68004487-68004506 None:intergenic 10.0%
!!! TTTATTTGTAAACATTATTT+TGG + chr3_4:68004488-68004507 None:intergenic 10.0%
!!! AGATTACAAATTTTTTTTAT+AGG + chr3_4:68004522-68004541 None:intergenic 10.0%
!!! TTTTTTCATATAGTTTTAAA+TGG - chr3_4:68004312-68004331 Msa0516500:CDS 10.0%
!!! TTATTTGTAAACATTATTTT+GGG + chr3_4:68004487-68004506 None:intergenic 10.0%
!!! TTTATTTGTAAACATTATTT+TGG + chr3_4:68004488-68004507 None:intergenic 10.0%
!!! AGATTACAAATTTTTTTTAT+AGG + chr3_4:68004522-68004541 None:intergenic 10.0%
!! TAAAATGAATATAAATGACT+TGG + chr3_4:68004006-68004025 None:intergenic 15.0%
!!! ATTTATTTTTTTGCTCTTTT+AGG - chr3_4:68004221-68004240 Msa0516500:exon 15.0%
!! AGGTATTAATAAATAAAGTA+TGG - chr3_4:68004927-68004946 Msa0516500:five_prime_UTR 15.0%
!! TAAAATGAATATAAATGACT+TGG + chr3_4:68004006-68004025 None:intergenic 15.0%
!!! ATTTATTTTTTTGCTCTTTT+AGG - chr3_4:68004221-68004240 Msa0516500:exon 15.0%
!! AGGTATTAATAAATAAAGTA+TGG - chr3_4:68004927-68004946 Msa0516500:five_prime_UTR 15.0%
!! AAATTCTTACTTGATATAAG+TGG - chr3_4:68004159-68004178 Msa0516500:three_prime_UTR 20.0%
!! TTGTAAAGAAAGTTATTAGT+AGG + chr3_4:68004278-68004297 None:intergenic 20.0%
!! TACTAATAACTTTCTTTACA+AGG - chr3_4:68004277-68004296 Msa0516500:CDS 20.0%
!! CTATATGAAAAAAGATAGTA+AGG + chr3_4:68004305-68004324 None:intergenic 20.0%
!! AAAATTAAGATGAATACAGA+TGG - chr3_4:68004396-68004415 Msa0516500:intron 20.0%
!!! ACATTATTTTGGGATTATAT+GGG + chr3_4:68004477-68004496 None:intergenic 20.0%
!!! AACATTATTTTGGGATTATA+TGG + chr3_4:68004478-68004497 None:intergenic 20.0%
!!! TTTTTAACTAACAAGTACTT+TGG - chr3_4:68004589-68004608 Msa0516500:intron 20.0%
!! TGATTAGTAATTAGTTGTTA+AGG + chr3_4:68004741-68004760 None:intergenic 20.0%
!! AAATTCTTACTTGATATAAG+TGG - chr3_4:68004159-68004178 Msa0516500:three_prime_UTR 20.0%
!! TTGTAAAGAAAGTTATTAGT+AGG + chr3_4:68004278-68004297 None:intergenic 20.0%
!! TACTAATAACTTTCTTTACA+AGG - chr3_4:68004277-68004296 Msa0516500:CDS 20.0%
!! CTATATGAAAAAAGATAGTA+AGG + chr3_4:68004305-68004324 None:intergenic 20.0%
!! AAAATTAAGATGAATACAGA+TGG - chr3_4:68004396-68004415 Msa0516500:intron 20.0%
!!! ACATTATTTTGGGATTATAT+GGG + chr3_4:68004477-68004496 None:intergenic 20.0%
!!! AACATTATTTTGGGATTATA+TGG + chr3_4:68004478-68004497 None:intergenic 20.0%
!!! TTTTTAACTAACAAGTACTT+TGG - chr3_4:68004589-68004608 Msa0516500:intron 20.0%
!! TGATTAGTAATTAGTTGTTA+AGG + chr3_4:68004741-68004760 None:intergenic 20.0%
!! ATTCATTTTCCTTTATCTTC+AGG - chr3_4:68004131-68004150 Msa0516500:three_prime_UTR 25.0%
! ATTTGTTTACCTGAAGATAA+AGG + chr3_4:68004143-68004162 None:intergenic 25.0%
!!! TTTTTTTGCTCTTTTAGGAT+TGG - chr3_4:68004226-68004245 Msa0516500:CDS 25.0%
!! TATGTTCATCTTAAGTATTG+TGG + chr3_4:68004364-68004383 None:intergenic 25.0%
!! ACATGAACAAAACATTTTGA+GGG + chr3_4:68004822-68004841 None:intergenic 25.0%
!! TACATGAACAAAACATTTTG+AGG + chr3_4:68004823-68004842 None:intergenic 25.0%
!!! AAATGTTTTGTTCATGTAAG+AGG - chr3_4:68004825-68004844 Msa0516500:CDS 25.0%
!! ATTCATTTTCCTTTATCTTC+AGG - chr3_4:68004131-68004150 Msa0516500:three_prime_UTR 25.0%
! ATTTGTTTACCTGAAGATAA+AGG + chr3_4:68004143-68004162 None:intergenic 25.0%
!!! TTTTTTTGCTCTTTTAGGAT+TGG - chr3_4:68004226-68004245 Msa0516500:CDS 25.0%
!! TATGTTCATCTTAAGTATTG+TGG + chr3_4:68004364-68004383 None:intergenic 25.0%
!! ACATGAACAAAACATTTTGA+GGG + chr3_4:68004822-68004841 None:intergenic 25.0%
!! TACATGAACAAAACATTTTG+AGG + chr3_4:68004823-68004842 None:intergenic 25.0%
!!! AAATGTTTTGTTCATGTAAG+AGG - chr3_4:68004825-68004844 Msa0516500:CDS 25.0%
! ATGAATATAAATGACTTGGC+AGG + chr3_4:68004002-68004021 None:intergenic 30.0%
!!! TTTTAGCTTCTCATAAAGAG+AGG - chr3_4:68004021-68004040 Msa0516500:three_prime_UTR 30.0%
GAAAATGAATGAAAACCAAG+AGG + chr3_4:68004121-68004140 None:intergenic 30.0%
! AGTACTTTGGTATTGAATGA+AGG - chr3_4:68004602-68004621 Msa0516500:intron 30.0%
! CATGAACAAAACATTTTGAG+GGG + chr3_4:68004821-68004840 None:intergenic 30.0%
TGAGTGTATTGTAACTTATG+AGG - chr3_4:68004907-68004926 Msa0516500:five_prime_UTR 30.0%
! ATGAATATAAATGACTTGGC+AGG + chr3_4:68004002-68004021 None:intergenic 30.0%
!!! TTTTAGCTTCTCATAAAGAG+AGG - chr3_4:68004021-68004040 Msa0516500:three_prime_UTR 30.0%
GAAAATGAATGAAAACCAAG+AGG + chr3_4:68004121-68004140 None:intergenic 30.0%
! AGTACTTTGGTATTGAATGA+AGG - chr3_4:68004602-68004621 Msa0516500:intron 30.0%
! CATGAACAAAACATTTTGAG+GGG + chr3_4:68004821-68004840 None:intergenic 30.0%
TGAGTGTATTGTAACTTATG+AGG - chr3_4:68004907-68004926 Msa0516500:five_prime_UTR 30.0%
TTCATTGCATATACTTGCCA+TGG - chr3_4:68004064-68004083 Msa0516500:three_prime_UTR 35.0%
!!! AGTTTTGACTTTGTGTTCCA+TGG + chr3_4:68004084-68004103 None:intergenic 35.0%
ATGAATGAAAACCAAGAGGA+TGG + chr3_4:68004117-68004136 None:intergenic 35.0%
GGCAAATGCTAATATTTGCT+TGG - chr3_4:68004439-68004458 Msa0516500:intron 35.0%
! CTTTGGTATTGAATGAAGGA+TGG - chr3_4:68004606-68004625 Msa0516500:intron 35.0%
! ATTGTCTCATGCTTTTGTGT+TGG - chr3_4:68004653-68004672 Msa0516500:intron 35.0%
! TTCTTTGAATGCTTTGGGTT+GGG + chr3_4:68004696-68004715 None:intergenic 35.0%
! TTTCTTTGAATGCTTTGGGT+TGG + chr3_4:68004697-68004716 None:intergenic 35.0%
CAGGTTTCTTTGAATGCTTT+GGG + chr3_4:68004701-68004720 None:intergenic 35.0%
GTTACAATACACTCAAGTAG+TGG + chr3_4:68004902-68004921 None:intergenic 35.0%
TTCATTGCATATACTTGCCA+TGG - chr3_4:68004064-68004083 Msa0516500:three_prime_UTR 35.0%
!!! AGTTTTGACTTTGTGTTCCA+TGG + chr3_4:68004084-68004103 None:intergenic 35.0%
ATGAATGAAAACCAAGAGGA+TGG + chr3_4:68004117-68004136 None:intergenic 35.0%
GGCAAATGCTAATATTTGCT+TGG - chr3_4:68004439-68004458 Msa0516500:intron 35.0%
! CTTTGGTATTGAATGAAGGA+TGG - chr3_4:68004606-68004625 Msa0516500:intron 35.0%
! ATTGTCTCATGCTTTTGTGT+TGG - chr3_4:68004653-68004672 Msa0516500:intron 35.0%
! TTCTTTGAATGCTTTGGGTT+GGG + chr3_4:68004696-68004715 None:intergenic 35.0%
! TTTCTTTGAATGCTTTGGGT+TGG + chr3_4:68004697-68004716 None:intergenic 35.0%
CAGGTTTCTTTGAATGCTTT+GGG + chr3_4:68004701-68004720 None:intergenic 35.0%
GTTACAATACACTCAAGTAG+TGG + chr3_4:68004902-68004921 None:intergenic 35.0%
! TTTCCTTTTAGCCATCCTCT+TGG - chr3_4:68004103-68004122 Msa0516500:three_prime_UTR 40.0%
AAACCAAGAGGATGGCTAAA+AGG + chr3_4:68004109-68004128 None:intergenic 40.0%
GAGCTACTACATTCACATTG+AGG - chr3_4:68004418-68004437 Msa0516500:intron 40.0%
ATGGTGTAAAGATGAACTCG+AGG - chr3_4:68004625-68004644 Msa0516500:intron 40.0%
GTGTTGGATTATGATGAAGC+AGG - chr3_4:68004669-68004688 Msa0516500:CDS 40.0%
CCAGGTTTCTTTGAATGCTT+TGG + chr3_4:68004702-68004721 None:intergenic 40.0%
! CCAAAGCATTCAAAGAAACC+TGG - chr3_4:68004699-68004718 Msa0516500:intron 40.0%
CATTCAAAGAAACCTGGCAA+GGG - chr3_4:68004705-68004724 Msa0516500:intron 40.0%
! AATCGAGCTAGTTTCTTCAC+CGG - chr3_4:68004874-68004893 Msa0516500:five_prime_UTR 40.0%
! TTTCCTTTTAGCCATCCTCT+TGG - chr3_4:68004103-68004122 Msa0516500:three_prime_UTR 40.0%
AAACCAAGAGGATGGCTAAA+AGG + chr3_4:68004109-68004128 None:intergenic 40.0%
GAGCTACTACATTCACATTG+AGG - chr3_4:68004418-68004437 Msa0516500:intron 40.0%
ATGGTGTAAAGATGAACTCG+AGG - chr3_4:68004625-68004644 Msa0516500:intron 40.0%
GTGTTGGATTATGATGAAGC+AGG - chr3_4:68004669-68004688 Msa0516500:CDS 40.0%
CCAGGTTTCTTTGAATGCTT+TGG + chr3_4:68004702-68004721 None:intergenic 40.0%
! CCAAAGCATTCAAAGAAACC+TGG - chr3_4:68004699-68004718 Msa0516500:intron 40.0%
CATTCAAAGAAACCTGGCAA+GGG - chr3_4:68004705-68004724 Msa0516500:intron 40.0%
! AATCGAGCTAGTTTCTTCAC+CGG - chr3_4:68004874-68004893 Msa0516500:five_prime_UTR 40.0%
!!! GCTCTTTTAGGATTGGCTGA+AGG - chr3_4:68004233-68004252 Msa0516500:CDS 45.0%
GCATTCAAAGAAACCTGGCA+AGG - chr3_4:68004704-68004723 Msa0516500:intron 45.0%
ATACACTCAAGTAGTGGCTC+CGG + chr3_4:68004896-68004915 None:intergenic 45.0%
!!! GCTCTTTTAGGATTGGCTGA+AGG - chr3_4:68004233-68004252 Msa0516500:CDS 45.0%
GCATTCAAAGAAACCTGGCA+AGG - chr3_4:68004704-68004723 Msa0516500:intron 45.0%
ATACACTCAAGTAGTGGCTC+CGG + chr3_4:68004896-68004915 None:intergenic 45.0%
GGTGTTTAACGACCCTTGCC+AGG + chr3_4:68004720-68004739 None:intergenic 55.0%
GGTGTTTAACGACCCTTGCC+AGG + chr3_4:68004720-68004739 None:intergenic 55.0%
Chromosome Type Strat End Strand Name
chr3_4 gene 68003994 68004962 68003994 ID=Msa0516500;Name=Msa0516500
chr3_4 mRNA 68003994 68004962 68003994 ID=Msa0516500-mRNA-1;Parent=Msa0516500;Name=Msa0516500-mRNA-1;_AED=0.02;_eAED=0.02;_QI=89|1|1|1|1|1|3|228|78
chr3_4 exon 68003994 68004332 68003994 ID=Msa0516500-mRNA-1:exon:17871;Parent=Msa0516500-mRNA-1
chr3_4 exon 68004658 68004713 68004658 ID=Msa0516500-mRNA-1:exon:17870;Parent=Msa0516500-mRNA-1
chr3_4 exon 68004804 68004962 68004804 ID=Msa0516500-mRNA-1:exon:17869;Parent=Msa0516500-mRNA-1
chr3_4 five_prime_UTR 68004874 68004962 68004874 ID=Msa0516500-mRNA-1:five_prime_utr;Parent=Msa0516500-mRNA-1
chr3_4 CDS 68004804 68004873 68004804 ID=Msa0516500-mRNA-1:cds;Parent=Msa0516500-mRNA-1
chr3_4 CDS 68004658 68004713 68004658 ID=Msa0516500-mRNA-1:cds;Parent=Msa0516500-mRNA-1
chr3_4 CDS 68004222 68004332 68004222 ID=Msa0516500-mRNA-1:cds;Parent=Msa0516500-mRNA-1
chr3_4 three_prime_UTR 68003994 68004221 68003994 ID=Msa0516500-mRNA-1:three_prime_utr;Parent=Msa0516500-mRNA-1
Gene Sequence

>Msa0516500

ATGGAACACAAAGTCAAAACTTTCCTTTTAGCCATCCTCTTGGTTTTCATTCATTTTCCTTTATCTTCAGGATTGGCTGAAGGATTCAGAGAAAATATGCATCCTACTAATAACTTTCTTTACAAGGATGGTGTAAAGATGAACTCGAGGAAGCTATTGTCTCATGCTTTTGTGTTGGATTATGATGAAGCAGGACCCAACCCAAAGCATTCAAAGAAACCTGGCAAGGGTCGTTAA
Protein sequence

>Msa0516500

MEHKVKTFLLAILLVFIHFPLSSGLAEGFRENMHPTNNFLYKDGVKMNSRKLLSHAFVLDYDEAGPNPKHSKKPGKGR*