AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0803890


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0803890 MtrunA17_Chr5g0411641 100.000 85 0 0 1 85 1 85 2.12e-57 171
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0803890 AT2G22640.1 90.588 85 8 0 1 85 1 85 7.13e-53 159

Find 28 sgRNAs with CRISPR-Local

Find 74 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GTTCTTGATTGCCTATTTAT+TGG 0.171334 5_3:-19339042 Msa0803890:three_prime_UTR
AAAATCTTTAAAAGCACTTA+TGG 0.245901 5_3:-19338907 Msa0803890:three_prime_UTR
CATTGGTTTATTTGCAAATT+CGG 0.278022 5_3:-19339000 Msa0803890:three_prime_UTR
TTCTTGATTGCCTATTTATT+GGG 0.282570 5_3:-19339041 Msa0803890:three_prime_UTR
CTATTTATTGGGTTATTAGA+TGG 0.316505 5_3:-19339030 Msa0803890:three_prime_UTR
CATCTAATAACCCAATAAAT+AGG 0.321197 5_3:+19339031 None:intergenic
TGATGTATTGGAACGTCGTT+TGG 0.348132 5_3:-19339284 Msa0803890:CDS
CCACCAGCACGTGCCATTGA+TGG 0.365965 5_3:+19339572 None:intergenic
GAAGAAATTGAGTACCGAAT+TGG 0.367198 5_3:+19339441 None:intergenic
GAATCGCTGTTCAAGCTGAT+TGG 0.386107 5_3:-19339526 Msa0803890:CDS
TTCGATTTCCTTGTCCAATT+CGG 0.396293 5_3:-19339455 Msa0803890:intron
CTAACTCTCGTTTACTTCTC+AGG 0.398070 5_3:+19339661 None:intergenic
GAATGAGAAGCTTGATGTAT+TGG 0.424872 5_3:-19339296 Msa0803890:CDS
TATTAGATGGTTTAATGCAT+TGG 0.431631 5_3:-19339017 Msa0803890:three_prime_UTR
AATCGCTGTTCAAGCTGATT+GGG 0.456401 5_3:-19339525 Msa0803890:CDS
GTCTAGATTATACATTATAT+AGG 0.465793 5_3:+19339152 None:intergenic
AGTTCAAGTTGGCAATGCTT+CGG 0.492873 5_3:-19339251 Msa0803890:CDS
AGCAAAATCAAAATCTACAT+TGG 0.503801 5_3:-19339613 Msa0803890:five_prime_UTR
AAATCAAAGAATTCCATCAA+TGG 0.510384 5_3:-19339585 Msa0803890:exon
AGAAGTAAACGAGAGTTAGT+TGG 0.515439 5_3:-19339657 Msa0803890:five_prime_UTR
GAATTACTTGAAGTTCAAGT+TGG 0.523303 5_3:-19339262 Msa0803890:CDS
ATTATACATTATATAGGTGG+TGG 0.532369 5_3:+19339158 None:intergenic
ATTCCATCAATGGCACGTGC+TGG 0.544732 5_3:-19339575 Msa0803890:exon
CCATCAATGGCACGTGCTGG+TGG 0.566134 5_3:-19339572 Msa0803890:exon
TATATAATGTATAATCTAGA+CGG 0.607083 5_3:-19339150 Msa0803890:three_prime_UTR
ATCACAAACGCAGTTAACGT+TGG 0.620945 5_3:-19339548 Msa0803890:CDS
ATTGAGTACCGAATTGGACA+AGG 0.623936 5_3:+19339447 None:intergenic
TAGATTATACATTATATAGG+TGG 0.625836 5_3:+19339155 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! AATCTTATATCTTTTTTTGA+TGG - chr5_3:19339229-19339248 Msa0803890:CDS 15.0%
!!! ATCTTATATCTTTTTTTGAT+GGG - chr5_3:19339230-19339249 Msa0803890:CDS 15.0%
!! TATATAATGTATAATCTAGA+CGG - chr5_3:19339454-19339473 Msa0803890:intron 15.0%
!!! TTAAAGATTTTTACTCAAAT+TGG + chr5_3:19339688-19339707 None:intergenic 15.0%
!!! AATCTTATATCTTTTTTTGA+TGG - chr5_3:19339229-19339248 Msa0803890:CDS 15.0%
!!! ATCTTATATCTTTTTTTGAT+GGG - chr5_3:19339230-19339249 Msa0803890:CDS 15.0%
!! TATATAATGTATAATCTAGA+CGG - chr5_3:19339454-19339473 Msa0803890:intron 15.0%
!!! TTAAAGATTTTTACTCAAAT+TGG + chr5_3:19339688-19339707 None:intergenic 15.0%
!! ATATAAGATTTCAACTAACA+AGG + chr5_3:19339219-19339238 None:intergenic 20.0%
!!! TGTTATTTTTGTTATTTCAG+AGG - chr5_3:19339257-19339276 Msa0803890:CDS 20.0%
!! TAGATTATACATTATATAGG+TGG + chr5_3:19339452-19339471 None:intergenic 20.0%
!! GTCTAGATTATACATTATAT+AGG + chr5_3:19339455-19339474 None:intergenic 20.0%
!!! AAAATCTTTAAAAGCACTTA+TGG - chr5_3:19339697-19339716 Msa0803890:five_prime_UTR 20.0%
!! ATATAAGATTTCAACTAACA+AGG + chr5_3:19339219-19339238 None:intergenic 20.0%
!!! TGTTATTTTTGTTATTTCAG+AGG - chr5_3:19339257-19339276 Msa0803890:CDS 20.0%
!! TAGATTATACATTATATAGG+TGG + chr5_3:19339452-19339471 None:intergenic 20.0%
!! GTCTAGATTATACATTATAT+AGG + chr5_3:19339455-19339474 None:intergenic 20.0%
!!! AAAATCTTTAAAAGCACTTA+TGG - chr5_3:19339697-19339716 Msa0803890:five_prime_UTR 20.0%
! AGCAAAATCAAAATCTACAT+TGG - chr5_3:19338991-19339010 Msa0803890:three_prime_UTR 25.0%
! AAATCAAAGAATTCCATCAA+TGG - chr5_3:19339019-19339038 Msa0803890:three_prime_UTR 25.0%
! ATTATACATTATATAGGTGG+TGG + chr5_3:19339449-19339468 None:intergenic 25.0%
! TTCTTGATTGCCTATTTATT+GGG - chr5_3:19339563-19339582 Msa0803890:CDS 25.0%
! CATCTAATAACCCAATAAAT+AGG + chr5_3:19339576-19339595 None:intergenic 25.0%
! CTATTTATTGGGTTATTAGA+TGG - chr5_3:19339574-19339593 Msa0803890:exon 25.0%
! TATTAGATGGTTTAATGCAT+TGG - chr5_3:19339587-19339606 Msa0803890:exon 25.0%
!!! CATTGGTTTATTTGCAAATT+CGG - chr5_3:19339604-19339623 Msa0803890:five_prime_UTR 25.0%
! AGCAAAATCAAAATCTACAT+TGG - chr5_3:19338991-19339010 Msa0803890:three_prime_UTR 25.0%
! AAATCAAAGAATTCCATCAA+TGG - chr5_3:19339019-19339038 Msa0803890:three_prime_UTR 25.0%
! ATTATACATTATATAGGTGG+TGG + chr5_3:19339449-19339468 None:intergenic 25.0%
! TTCTTGATTGCCTATTTATT+GGG - chr5_3:19339563-19339582 Msa0803890:CDS 25.0%
! CATCTAATAACCCAATAAAT+AGG + chr5_3:19339576-19339595 None:intergenic 25.0%
! CTATTTATTGGGTTATTAGA+TGG - chr5_3:19339574-19339593 Msa0803890:exon 25.0%
! TATTAGATGGTTTAATGCAT+TGG - chr5_3:19339587-19339606 Msa0803890:exon 25.0%
!!! CATTGGTTTATTTGCAAATT+CGG - chr5_3:19339604-19339623 Msa0803890:five_prime_UTR 25.0%
! AGGACTTTTTGTTCTACTTT+TGG + chr5_3:19338926-19338945 None:intergenic 30.0%
TTTCAACTAACAAGGCAAAA+GGG + chr5_3:19339211-19339230 None:intergenic 30.0%
ATTTCAACTAACAAGGCAAA+AGG + chr5_3:19339212-19339231 None:intergenic 30.0%
GAATTACTTGAAGTTCAAGT+TGG - chr5_3:19339342-19339361 Msa0803890:intron 30.0%
GTTCTTGATTGCCTATTTAT+TGG - chr5_3:19339562-19339581 Msa0803890:CDS 30.0%
! AGGACTTTTTGTTCTACTTT+TGG + chr5_3:19338926-19338945 None:intergenic 30.0%
TTTCAACTAACAAGGCAAAA+GGG + chr5_3:19339211-19339230 None:intergenic 30.0%
ATTTCAACTAACAAGGCAAA+AGG + chr5_3:19339212-19339231 None:intergenic 30.0%
GAATTACTTGAAGTTCAAGT+TGG - chr5_3:19339342-19339361 Msa0803890:intron 30.0%
GTTCTTGATTGCCTATTTAT+TGG - chr5_3:19339562-19339581 Msa0803890:CDS 30.0%
AGAAGTAAACGAGAGTTAGT+TGG - chr5_3:19338947-19338966 Msa0803890:three_prime_UTR 35.0%
TTCGATTTCCTTGTCCAATT+CGG - chr5_3:19339149-19339168 Msa0803890:three_prime_UTR 35.0%
!! GAAGAAATTGAGTACCGAAT+TGG + chr5_3:19339166-19339185 None:intergenic 35.0%
GAATGAGAAGCTTGATGTAT+TGG - chr5_3:19339308-19339327 Msa0803890:CDS 35.0%
! CATCAAGTTGCAAAAAGAGA+AGG + chr5_3:19339384-19339403 None:intergenic 35.0%
AGAAGTAAACGAGAGTTAGT+TGG - chr5_3:19338947-19338966 Msa0803890:three_prime_UTR 35.0%
TTCGATTTCCTTGTCCAATT+CGG - chr5_3:19339149-19339168 Msa0803890:three_prime_UTR 35.0%
!! GAAGAAATTGAGTACCGAAT+TGG + chr5_3:19339166-19339185 None:intergenic 35.0%
GAATGAGAAGCTTGATGTAT+TGG - chr5_3:19339308-19339327 Msa0803890:CDS 35.0%
! CATCAAGTTGCAAAAAGAGA+AGG + chr5_3:19339384-19339403 None:intergenic 35.0%
CTAACTCTCGTTTACTTCTC+AGG + chr5_3:19338946-19338965 None:intergenic 40.0%
ATCACAAACGCAGTTAACGT+TGG - chr5_3:19339056-19339075 Msa0803890:three_prime_UTR 40.0%
AATCGCTGTTCAAGCTGATT+GGG - chr5_3:19339079-19339098 Msa0803890:three_prime_UTR 40.0%
!! ATTGAGTACCGAATTGGACA+AGG + chr5_3:19339160-19339179 None:intergenic 40.0%
TGATGTATTGGAACGTCGTT+TGG - chr5_3:19339320-19339339 Msa0803890:CDS 40.0%
!! AGTTCAAGTTGGCAATGCTT+CGG - chr5_3:19339353-19339372 Msa0803890:intron 40.0%
CTAACTCTCGTTTACTTCTC+AGG + chr5_3:19338946-19338965 None:intergenic 40.0%
ATCACAAACGCAGTTAACGT+TGG - chr5_3:19339056-19339075 Msa0803890:three_prime_UTR 40.0%
AATCGCTGTTCAAGCTGATT+GGG - chr5_3:19339079-19339098 Msa0803890:three_prime_UTR 40.0%
!! ATTGAGTACCGAATTGGACA+AGG + chr5_3:19339160-19339179 None:intergenic 40.0%
TGATGTATTGGAACGTCGTT+TGG - chr5_3:19339320-19339339 Msa0803890:CDS 40.0%
!! AGTTCAAGTTGGCAATGCTT+CGG - chr5_3:19339353-19339372 Msa0803890:intron 40.0%
GAATCGCTGTTCAAGCTGAT+TGG - chr5_3:19339078-19339097 Msa0803890:three_prime_UTR 45.0%
GAATCGCTGTTCAAGCTGAT+TGG - chr5_3:19339078-19339097 Msa0803890:three_prime_UTR 45.0%
ATTCCATCAATGGCACGTGC+TGG - chr5_3:19339029-19339048 Msa0803890:three_prime_UTR 50.0%
ATTCCATCAATGGCACGTGC+TGG - chr5_3:19339029-19339048 Msa0803890:three_prime_UTR 50.0%
! CCACCAGCACGTGCCATTGA+TGG + chr5_3:19339035-19339054 None:intergenic 60.0%
CCATCAATGGCACGTGCTGG+TGG - chr5_3:19339032-19339051 Msa0803890:three_prime_UTR 60.0%
! CCACCAGCACGTGCCATTGA+TGG + chr5_3:19339035-19339054 None:intergenic 60.0%
CCATCAATGGCACGTGCTGG+TGG - chr5_3:19339032-19339051 Msa0803890:three_prime_UTR 60.0%
Chromosome Type Strat End Strand Name
chr5_3 gene 19338885 19339741 19338885 ID=Msa0803890;Name=Msa0803890
chr5_3 mRNA 19338885 19339741 19338885 ID=Msa0803890-mRNA-1;Parent=Msa0803890;Name=Msa0803890-mRNA-1;_AED=0.00;_eAED=0.00;_QI=153|1|1|1|1|1|2|340|85
chr5_3 exon 19338885 19339349 19338885 ID=Msa0803890-mRNA-1:exon:7936;Parent=Msa0803890-mRNA-1
chr5_3 exon 19339456 19339741 19339456 ID=Msa0803890-mRNA-1:exon:7935;Parent=Msa0803890-mRNA-1
chr5_3 five_prime_UTR 19339589 19339741 19339589 ID=Msa0803890-mRNA-1:five_prime_utr;Parent=Msa0803890-mRNA-1
chr5_3 CDS 19339456 19339588 19339456 ID=Msa0803890-mRNA-1:cds;Parent=Msa0803890-mRNA-1
chr5_3 CDS 19339225 19339349 19339225 ID=Msa0803890-mRNA-1:cds;Parent=Msa0803890-mRNA-1
chr5_3 three_prime_UTR 19338885 19339224 19338885 ID=Msa0803890-mRNA-1:three_prime_utr;Parent=Msa0803890-mRNA-1
Gene Sequence

>Msa0803890

ATGGCACGTGCTGGTGGAATCACAAACGCAGTTAACGTTGGAATCGCTGTTCAAGCTGATTGGGAAAATCGTGAATTCATCTCTCACATTTCTCTCAATGTTCGTCGTCTCTTCGATTTCCTTGTCCAATTCGAGGCTACAACAAAGAGTAAATTAGCTTCATTGAATGAGAAGCTTGATGTATTGGAACGTCGTTTGGAATTACTTGAAGTTCAAGTTGGCAATGCTTCGGCAAATCCTTCTCTTTTTGCAACTTGA

Protein sequence

>Msa0803890

MARAGGITNAVNVGIAVQADWENREFISHISLNVRRLFDFLVQFEATTKSKLASLNEKLDVLERRLELLEVQVGNASANPSLFAT*