AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0095160


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0095160 MtrunA17_CPg0492821 70.732 82 24 0 1 82 1 82 6.38e-34 112
Msa0095160 MtrunA17_Chr4g0016851 70.732 82 24 0 1 82 1 82 6.38e-34 112
Msa0095160 MtrunA17_Chr4g0015751 70.732 82 24 0 1 82 1 82 6.38e-34 112
Msa0095160 MtrunA17_Chr4g0017011 98.148 54 1 0 1 54 1 54 2.07e-33 111
Msa0095160 MtrunA17_Chr5g0423051 96.296 54 2 0 1 54 1 54 3.52e-32 107
Msa0095160 MtrunA17_Chr4g0016841 61.538 91 21 2 14 104 9 85 4.52e-31 105
Msa0095160 MtrunA17_Chr6g0451331 90.323 31 3 0 24 54 41 71 5.28e-14 61.6
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0095160 ATCG00580.1 70.732 82 24 0 1 82 1 82 1.19e-34 114
Msa0095160 ATCG00560.1 97.297 37 1 0 68 104 2 38 3.75e-19 73.9

Find 27 sgRNAs with CRISPR-Local

Find 50 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GGTTTAGCTTACGATGTATT+TGG 0.244623 1_2:+79014273 Msa0095160:CDS
GTAGCTCTATAATTCGGATT+AGG 0.338134 1_2:-79014535 None:intergenic
ATAACCAACCCGCAATGAAT+AGG 0.348030 1_2:-79014239 None:intergenic
TTATTACCAGTATTCGATAC+TGG 0.348418 1_2:+79014190 Msa0095160:CDS
TATGTGGAGCTCGGCATGTC+TGG 0.349487 1_2:+79014138 Msa0095160:exon
ATACCCTCCCTATTCATTGC+GGG 0.391873 1_2:+79014231 Msa0095160:CDS
TAACCAACCCGCAATGAATA+GGG 0.406851 1_2:-79014238 None:intergenic
TGAATCGTACCAGTCTCTAC+TGG 0.410190 1_2:+79014593 Msa0095160:CDS
CTTTCTGTAAAATACTCGTT+TGG 0.412027 1_2:-79014306 None:intergenic
TGTGTCGTAGCTCTATAATT+CGG 0.415726 1_2:-79014541 None:intergenic
AATAATCCAGTATCGAATAC+TGG 0.423687 1_2:-79014196 None:intergenic
CTCGGCATGTCTGGAAGCAC+AGG 0.508926 1_2:+79014147 Msa0095160:exon
ATTCGGATTAGGTTTATCGT+TGG 0.512045 1_2:-79014524 None:intergenic
GAATCGTACCAGTCTCTACT+GGG 0.515213 1_2:+79014594 Msa0095160:CDS
TTTGACTGTATAAGAATATG+TGG 0.517465 1_2:+79014122 None:intergenic
GGTTGGTTATTTGTCAGCAC+GGG 0.523918 1_2:+79014252 Msa0095160:CDS
TGTAAAATACTCGTTTGGAC+GGG 0.525534 1_2:-79014301 None:intergenic
GTAAAATACTCGTTTGGACG+GGG 0.531710 1_2:-79014300 None:intergenic
GGGTTGGTTATTTGTCAGCA+CGG 0.532372 1_2:+79014251 Msa0095160:CDS
CCTCCCTATTCATTGCGGGT+TGG 0.536548 1_2:+79014235 Msa0095160:CDS
CTGTAAAATACTCGTTTGGA+CGG 0.550313 1_2:-79014302 None:intergenic
TAATAAACCCCAGTAGAGAC+TGG 0.572062 1_2:-79014602 None:intergenic
GTATAAGAATATGTGGAGCT+CGG 0.584815 1_2:+79014129 None:intergenic
TATACCCTCCCTATTCATTG+CGG 0.586067 1_2:+79014230 Msa0095160:CDS
CAACCCGCAATGAATAGGGA+GGG 0.665638 1_2:-79014234 None:intergenic
CCAACCCGCAATGAATAGGG+AGG 0.678708 1_2:-79014235 None:intergenic
AATCGTACCAGTCTCTACTG+GGG 0.711157 1_2:+79014595 Msa0095160:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! TGAATTTAGTAGATCTTTTT+AGG + chr1_2:79014383-79014402 Msa0095160:intron 20.0%
!!! ATTCAACATTTTGTTCATTT+GGG - chr1_2:79014573-79014592 None:intergenic 20.0%
!!! AATTCAACATTTTGTTCATT+TGG - chr1_2:79014574-79014593 None:intergenic 20.0%
! TTATTAATGGAATTCCTTGT+CGG - chr1_2:79014332-79014351 None:intergenic 25.0%
!!! ATTTAGTAGATCTTTTTAGG+AGG + chr1_2:79014386-79014405 Msa0095160:intron 25.0%
! TATTGATCCCAAAAAAAAGA+CGG - chr1_2:79014487-79014506 None:intergenic 25.0%
TTATTACCAGTATTCGATAC+TGG + chr1_2:79014190-79014209 Msa0095160:CDS 30.0%
! AATAATCCAGTATCGAATAC+TGG - chr1_2:79014199-79014218 None:intergenic 30.0%
CTTTCTGTAAAATACTCGTT+TGG - chr1_2:79014309-79014328 None:intergenic 30.0%
CAAGGAATTCCATTAATAAC+TGG + chr1_2:79014333-79014352 Msa0095160:intron 30.0%
GTTGTTCCAAAGAATCAAAA+CGG - chr1_2:79014359-79014378 None:intergenic 30.0%
AACCATCGTACTGTAAAAAT+GGG - chr1_2:79014438-79014457 None:intergenic 30.0%
! GGTTTAGCTTACGATGTATT+TGG + chr1_2:79014273-79014292 Msa0095160:CDS 35.0%
TGTAAAATACTCGTTTGGAC+GGG - chr1_2:79014304-79014323 None:intergenic 35.0%
CTGTAAAATACTCGTTTGGA+CGG - chr1_2:79014305-79014324 None:intergenic 35.0%
! TATTTTACAGAAAGCCGACA+AGG + chr1_2:79014315-79014334 Msa0095160:intron 35.0%
TCAAAACGGCCAGTTATTAA+TGG - chr1_2:79014345-79014364 None:intergenic 35.0%
TCGTACTGTAAAAATGGGAT+AGG - chr1_2:79014433-79014452 None:intergenic 35.0%
!! ATCCCATTTTTACAGTACGA+TGG + chr1_2:79014433-79014452 Msa0095160:intron 35.0%
CAACCATCGTACTGTAAAAA+TGG - chr1_2:79014439-79014458 None:intergenic 35.0%
! CATTTTTACAGTACGATGGT+TGG + chr1_2:79014437-79014456 Msa0095160:intron 35.0%
! ATTCGGATTAGGTTTATCGT+TGG - chr1_2:79014527-79014546 None:intergenic 35.0%
! GTAGCTCTATAATTCGGATT+AGG - chr1_2:79014538-79014557 None:intergenic 35.0%
! TGTGTCGTAGCTCTATAATT+CGG - chr1_2:79014544-79014563 None:intergenic 35.0%
TATACCCTCCCTATTCATTG+CGG + chr1_2:79014230-79014249 Msa0095160:CDS 40.0%
TAACCAACCCGCAATGAATA+GGG - chr1_2:79014241-79014260 None:intergenic 40.0%
ATAACCAACCCGCAATGAAT+AGG - chr1_2:79014242-79014261 None:intergenic 40.0%
GTAAAATACTCGTTTGGACG+GGG - chr1_2:79014303-79014322 None:intergenic 40.0%
!!! AACTGGCCGTTTTGATTCTT+TGG + chr1_2:79014350-79014369 Msa0095160:intron 40.0%
TAGGTCCTATCTATGGTCAT+TGG - chr1_2:79014414-79014433 None:intergenic 40.0%
AATGGGATAGGTCCTATCTA+TGG - chr1_2:79014421-79014440 None:intergenic 40.0%
!!! GTACCCACCGTCTTTTTTTT+GGG + chr1_2:79014477-79014496 Msa0095160:intron 40.0%
GATCCCAAAAAAAAGACGGT+GGG - chr1_2:79014483-79014502 None:intergenic 40.0%
TGATCCCAAAAAAAAGACGG+TGG - chr1_2:79014484-79014503 None:intergenic 40.0%
TAATAAACCCCAGTAGAGAC+TGG - chr1_2:79014605-79014624 None:intergenic 40.0%
ATACCCTCCCTATTCATTGC+GGG + chr1_2:79014231-79014250 Msa0095160:CDS 45.0%
!! GGGTTGGTTATTTGTCAGCA+CGG + chr1_2:79014251-79014270 Msa0095160:CDS 45.0%
! GGTTGGTTATTTGTCAGCAC+GGG + chr1_2:79014252-79014271 Msa0095160:CDS 45.0%
AGGCTCCAATGACCATAGAT+AGG + chr1_2:79014406-79014425 Msa0095160:intron 45.0%
!!! GGTACCCACCGTCTTTTTTT+TGG + chr1_2:79014476-79014495 Msa0095160:intron 45.0%
TGAATCGTACCAGTCTCTAC+TGG + chr1_2:79014593-79014612 Msa0095160:CDS 45.0%
GAATCGTACCAGTCTCTACT+GGG + chr1_2:79014594-79014613 Msa0095160:CDS 45.0%
AATCGTACCAGTCTCTACTG+GGG + chr1_2:79014595-79014614 Msa0095160:CDS 45.0%
CAACCCGCAATGAATAGGGA+GGG - chr1_2:79014237-79014256 None:intergenic 50.0%
! GTACGATGGTTGGCTGTTCA+CGG + chr1_2:79014447-79014466 Msa0095160:intron 50.0%
TATGTGGAGCTCGGCATGTC+TGG + chr1_2:79014138-79014157 Msa0095160:exon 55.0%
CCAACCCGCAATGAATAGGG+AGG - chr1_2:79014238-79014257 None:intergenic 55.0%
CCTCCCTATTCATTGCGGGT+TGG + chr1_2:79014235-79014254 Msa0095160:CDS 55.0%
!! GTTGGCTGTTCACGGACTAG+CGG + chr1_2:79014455-79014474 Msa0095160:intron 55.0%
! CTCGGCATGTCTGGAAGCAC+AGG + chr1_2:79014147-79014166 Msa0095160:exon 60.0%
Chromosome Type Strat End Strand Name
chr1_2 gene 79014136 79014669 79014136 ID=Msa0095160;Name=Msa0095160
chr1_2 mRNA 79014136 79014669 79014136 ID=Msa0095160-mRNA-1;Parent=Msa0095160;Name=Msa0095160-mRNA-1;_AED=0.22;_eAED=0.22;_QI=17|0|0|1|0|0|2|0|104
chr1_2 exon 79014136 79014313 79014136 ID=Msa0095160-mRNA-1:exon:28078;Parent=Msa0095160-mRNA-1
chr1_2 exon 79014519 79014669 79014519 ID=Msa0095160-mRNA-1:exon:28079;Parent=Msa0095160-mRNA-1
chr1_2 five_prime_UTR 79014136 79014152 79014136 ID=Msa0095160-mRNA-1:five_prime_utr;Parent=Msa0095160-mRNA-1
chr1_2 CDS 79014153 79014313 79014153 ID=Msa0095160-mRNA-1:cds;Parent=Msa0095160-mRNA-1
chr1_2 CDS 79014519 79014669 79014519 ID=Msa0095160-mRNA-1:cds;Parent=Msa0095160-mRNA-1
Gene Sequence

>Msa0095160

ATGTCTGGAAGCACAGGAGAACGTTCTTTTGCTGATATTATTACCAGTATTCGATACTGGATTATTCATAGCATTACTATACCCTCCCTATTCATTGCGGGTTGGTTATTTGTCAGCACGGGTTTAGCTTACGATGTATTTGGAAGTCCCCGTCCAAACGATTCATCCAACGATAAACCTAATCCGAATTATAGAGCTACGACACAATCAAACCCAAATGAACAAAATGTTGAATTGAATCGTACCAGTCTCTACTGGGGTTTATTACTCATTTTTGTACTTGCTGTTTTATTTTCAAATTATTTCTTCAAT

Protein sequence

>Msa0095160

MSGSTGERSFADIITSIRYWIIHSITIPSLFIAGWLFVSTGLAYDVFGSPRPNDSSNDKPNPNYRATTQSNPNEQNVELNRTSLYWGLLLIFVLAVLFSNYFFN