AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0825350

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0825350 MtrunA17_Chr5g0447061 58.537 123 49 2 1 122 1 122 2.30e-49 153
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 24 sgRNAs with CRISPR-Local

Find 37 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GTTATATTCCTTCTTGCTTC+TGG 0.212854 5_3:+65110302 None:intergenic
ATCAAGGAGGAGTTGGAAAT+TGG 0.290061 5_3:-65110415 Msa0825350:CDS
TTTGTTCCACCACAAAATTA+TGG 0.333981 5_3:-65110233 Msa0825350:CDS
TTTCTTTAGGCTATTACTCA+TGG 0.421485 5_3:-65109938 Msa0825350:intron
AAGAACCTGTGGTTTGTCTC+AGG 0.425780 5_3:+65110344 None:intergenic
CACCACAAAATTATGGAGCT+TGG 0.430852 5_3:-65110226 Msa0825350:CDS
TGTTGGTGCGGTAACGGTCT+CGG 0.455039 5_3:+65109842 None:intergenic
AATCACCAGGGAGCTCTTCA+AGG 0.457956 5_3:+65110264 None:intergenic
TTCTTTAGGCTATTACTCAT+GGG 0.494106 5_3:-65109937 Msa0825350:intron
CATATCTGTTGGTGCGGTAA+CGG 0.499015 5_3:+65109836 None:intergenic
ATGGCAAATCAAGGAGGAGT+TGG 0.501152 5_3:-65110422 Msa0825350:CDS
CTGAAACTCTCAAGAACCTG+TGG 0.518744 5_3:+65110333 None:intergenic
CTAGAGAGATTGTGTTGACG+AGG 0.558612 5_3:-65109879 Msa0825350:CDS
ACAAATTGCTCGAAATCACC+AGG 0.563161 5_3:+65110251 None:intergenic
AACCTGTGGTTTGTCTCAGG+TGG 0.578043 5_3:+65110347 None:intergenic
ACCGCACCAACAGATATGCT+TGG 0.580278 5_3:-65109831 Msa0825350:CDS
CACTACCTTGAAGAGCTCCC+TGG 0.582630 5_3:-65110269 Msa0825350:CDS
GTTCATCCAAGCATATCTGT+TGG 0.609345 5_3:+65109825 None:intergenic
TCCAAGCATATCTGTTGGTG+CGG 0.624491 5_3:+65109830 None:intergenic
TTTACGGCCGAAAATGGACG+CGG 0.649194 5_3:-65109906 Msa0825350:CDS
TGGAGCTTGGAGTAATGATG+AGG 0.655946 5_3:-65110213 Msa0825350:CDS
TTCCACCTGAGACAAACCAC+AGG 0.670730 5_3:-65110349 Msa0825350:CDS
TTCACAATGGCAAATCAAGG+AGG 0.686222 5_3:-65110428 None:intergenic
CAAATTGCTCGAAATCACCA+GGG 0.727892 5_3:+65110252 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! TATTTTAATGAAAAATAACA+TGG + chr5_3:65110169-65110188 None:intergenic 10.0%
!!! AACATATTTTAATCAAGAAA+AGG + chr5_3:65110146-65110165 None:intergenic 15.0%
!!! TAATGTTTTCTATTTTCTTT+AGG - chr5_3:65110290-65110309 Msa0825350:CDS 15.0%
!!! TCTTTGGTTTTTTTTTTTGA+AGG - chr5_3:65110091-65110110 Msa0825350:intron 20.0%
!!! AACATGTTTTAATCAAGAAA+AGG + chr5_3:65110247-65110266 None:intergenic 20.0%
! TCATTAAAACATGTGTTCTT+TGG - chr5_3:65110075-65110094 Msa0825350:intron 25.0%
! TCATTAAAATATGCGTTCTT+TGG - chr5_3:65110178-65110197 Msa0825350:intron 25.0%
! AAATTTTTCCAGAAGCAAGA+AGG - chr5_3:65109931-65109950 Msa0825350:CDS 30.0%
TTTGTTCCACCACAAAATTA+TGG - chr5_3:65110008-65110027 Msa0825350:intron 30.0%
TTTCTTTAGGCTATTACTCA+TGG - chr5_3:65110303-65110322 Msa0825350:CDS 30.0%
TTCTTTAGGCTATTACTCAT+GGG - chr5_3:65110304-65110323 Msa0825350:CDS 30.0%
GTTATATTCCTTCTTGCTTC+TGG + chr5_3:65109942-65109961 None:intergenic 35.0%
!!! GTTCTTTGGTTTTTTGTCGA+AGG - chr5_3:65110192-65110211 Msa0825350:intron 35.0%
! CTCATGGGATTGAGATTTTA+CGG - chr5_3:65110319-65110338 Msa0825350:CDS 35.0%
ATCAAGGAGGAGTTGGAAAT+TGG - chr5_3:65109826-65109845 Msa0825350:CDS 40.0%
CAAATTGCTCGAAATCACCA+GGG + chr5_3:65109992-65110011 None:intergenic 40.0%
ACAAATTGCTCGAAATCACC+AGG + chr5_3:65109993-65110012 None:intergenic 40.0%
! CAAGCTCCATAATTTTGTGG+TGG + chr5_3:65110017-65110036 None:intergenic 40.0%
CACCACAAAATTATGGAGCT+TGG - chr5_3:65110015-65110034 Msa0825350:intron 40.0%
! CTCCAAGCTCCATAATTTTG+TGG + chr5_3:65110020-65110039 None:intergenic 40.0%
! TGAGATTTTACGGCCGAAAA+TGG - chr5_3:65110329-65110348 Msa0825350:CDS 40.0%
! TAGAAATCCGCGTCCATTTT+CGG + chr5_3:65110345-65110364 None:intergenic 40.0%
GTTCATCCAAGCATATCTGT+TGG + chr5_3:65110419-65110438 None:intergenic 40.0%
ATGGCAAATCAAGGAGGAGT+TGG - chr5_3:65109819-65109838 Msa0825350:CDS 45.0%
! AAGAACCTGTGGTTTGTCTC+AGG + chr5_3:65109900-65109919 None:intergenic 45.0%
CTGAAACTCTCAAGAACCTG+TGG + chr5_3:65109911-65109930 None:intergenic 45.0%
TGGAGCTTGGAGTAATGATG+AGG - chr5_3:65110028-65110047 Msa0825350:intron 45.0%
! CTAGAGAGATTGTGTTGACG+AGG - chr5_3:65110362-65110381 Msa0825350:CDS 45.0%
CATATCTGTTGGTGCGGTAA+CGG + chr5_3:65110408-65110427 None:intergenic 45.0%
TCCAAGCATATCTGTTGGTG+CGG + chr5_3:65110414-65110433 None:intergenic 45.0%
TTCCACCTGAGACAAACCAC+AGG - chr5_3:65109892-65109911 Msa0825350:CDS 50.0%
! AACCTGTGGTTTGTCTCAGG+TGG + chr5_3:65109897-65109916 None:intergenic 50.0%
AATCACCAGGGAGCTCTTCA+AGG + chr5_3:65109980-65109999 None:intergenic 50.0%
TTTACGGCCGAAAATGGACG+CGG - chr5_3:65110335-65110354 Msa0825350:CDS 50.0%
ACCGCACCAACAGATATGCT+TGG - chr5_3:65110410-65110429 Msa0825350:CDS 50.0%
CACTACCTTGAAGAGCTCCC+TGG - chr5_3:65109972-65109991 Msa0825350:intron 55.0%
! TGTTGGTGCGGTAACGGTCT+CGG + chr5_3:65110402-65110421 None:intergenic 55.0%
Chromosome Type Strat End Strand Name
chr5_3 gene 65109819 65110444 65109819 ID=Msa0825350;Name=Msa0825350
chr5_3 mRNA 65109819 65110444 65109819 ID=Msa0825350-mRNA-1;Parent=Msa0825350;Name=Msa0825350-mRNA-1;_AED=0.00;_eAED=0.01;_QI=0|0|0|1|1|1|2|0|122
chr5_3 exon 65110209 65110444 65110209 ID=Msa0825350-mRNA-1:exon:20393;Parent=Msa0825350-mRNA-1
chr5_3 exon 65109819 65109951 65109819 ID=Msa0825350-mRNA-1:exon:20392;Parent=Msa0825350-mRNA-1
chr5_3 CDS 65110209 65110444 65110209 ID=Msa0825350-mRNA-1:cds;Parent=Msa0825350-mRNA-1
chr5_3 CDS 65109819 65109951 65109819 ID=Msa0825350-mRNA-1:cds;Parent=Msa0825350-mRNA-1
Gene Sequence

>Msa0825350

ATGGCAAATCAAGGAGGAGTTGGAAATTGGAACGTAGATGATACATTGATGCTTAGACAAGCAATGATAATATTTCCACCTGAGACAAACCACAGGTTCTTGAGAGTTTCAGAAATTTTTCCAGAAGCAAGAAGGAATATAACTCTTTTGCAACACTACCTTGAAGAGCTCCCTGGTGATTTCGAGCAATTTGTTCCACCACAAAATTATGGAGCTTGGAGTAATGATGAGGATCAGCTATTACTCATGGGATTGAGATTTTACGGCCGAAAATGGACGCGGATTTCTAGAGAGATTGTGTTGACGAGGAACGCATCGCAATGCCGAGACCGTTACCGCACCAACAGATATGCTTGGATGAACTTTTAG
Protein sequence

>Msa0825350

MANQGGVGNWNVDDTLMLRQAMIIFPPETNHRFLRVSEIFPEARRNITLLQHYLEELPGDFEQFVPPQNYGAWSNDEDQLLLMGLRFYGRKWTRISREIVLTRNASQCRDRYRTNRYAWMNF*