AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1086650


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1086650 MtrunA17_CPg0492821 70.732 82 24 0 1 82 1 82 6.38e-34 112
Msa1086650 MtrunA17_Chr4g0016851 70.732 82 24 0 1 82 1 82 6.38e-34 112
Msa1086650 MtrunA17_Chr4g0015751 70.732 82 24 0 1 82 1 82 6.38e-34 112
Msa1086650 MtrunA17_Chr4g0017011 98.148 54 1 0 1 54 1 54 2.07e-33 111
Msa1086650 MtrunA17_Chr5g0423051 96.296 54 2 0 1 54 1 54 3.52e-32 107
Msa1086650 MtrunA17_Chr4g0016841 61.538 91 21 2 14 104 9 85 4.52e-31 105
Msa1086650 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
Msa1086650 ATCG00580.1 70.732 82 24 0 1 82 1 82 1.19e-34 114
Msa1086650 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 7_2:+87494291 Msa1086650:CDS
GTAGCTCTATAATTCGGATT+AGG 0.338134 7_2:-87494553 None:intergenic
ATAACCAACCCGCAATGAAT+AGG 0.348030 7_2:-87494257 None:intergenic
TTATTACCAGTATTCGATAC+TGG 0.348418 7_2:+87494208 Msa1086650:CDS
TATGTGGAGCTCGGCATGTC+TGG 0.349487 7_2:+87494156 Msa1086650:exon
ATACCCTCCCTATTCATTGC+GGG 0.391873 7_2:+87494249 Msa1086650:CDS
TAACCAACCCGCAATGAATA+GGG 0.406851 7_2:-87494256 None:intergenic
TGAATCGTACCAGTCTCTAC+TGG 0.410190 7_2:+87494611 Msa1086650:CDS
CTTTCTGTAAAATACTCGTT+TGG 0.412027 7_2:-87494324 None:intergenic
TGTGTCGTAGCTCTATAATT+CGG 0.415726 7_2:-87494559 None:intergenic
AATAATCCAGTATCGAATAC+TGG 0.423687 7_2:-87494214 None:intergenic
CTCGGCATGTCTGGAAGCAC+AGG 0.508926 7_2:+87494165 Msa1086650:exon
ATTCGGATTAGGTTTATCGT+TGG 0.512045 7_2:-87494542 None:intergenic
GAATCGTACCAGTCTCTACT+GGG 0.515213 7_2:+87494612 Msa1086650:CDS
TTTGACTGTATAAGAATATG+TGG 0.517465 7_2:+87494140 None:intergenic
GGTTGGTTATTTGTCAGCAC+GGG 0.523918 7_2:+87494270 Msa1086650:CDS
TGTAAAATACTCGTTTGGAC+GGG 0.525534 7_2:-87494319 None:intergenic
GTAAAATACTCGTTTGGACG+GGG 0.531710 7_2:-87494318 None:intergenic
GGGTTGGTTATTTGTCAGCA+CGG 0.532372 7_2:+87494269 Msa1086650:CDS
CCTCCCTATTCATTGCGGGT+TGG 0.536548 7_2:+87494253 Msa1086650:CDS
CTGTAAAATACTCGTTTGGA+CGG 0.550313 7_2:-87494320 None:intergenic
TAATAAACCCCAGTAGAGAC+TGG 0.572062 7_2:-87494620 None:intergenic
GTATAAGAATATGTGGAGCT+CGG 0.584815 7_2:+87494147 None:intergenic
TATACCCTCCCTATTCATTG+CGG 0.586067 7_2:+87494248 Msa1086650:CDS
CAACCCGCAATGAATAGGGA+GGG 0.665638 7_2:-87494252 None:intergenic
CCAACCCGCAATGAATAGGG+AGG 0.678708 7_2:-87494253 None:intergenic
AATCGTACCAGTCTCTACTG+GGG 0.711157 7_2:+87494613 Msa1086650:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! TGAATTTAGTAGATCTTTTT+AGG + chr7_2:87494401-87494420 Msa1086650:intron 20.0%
!!! ATTCAACATTTTGTTCATTT+GGG - chr7_2:87494591-87494610 None:intergenic 20.0%
!!! AATTCAACATTTTGTTCATT+TGG - chr7_2:87494592-87494611 None:intergenic 20.0%
! TTATTAATGGAATTCCTTGT+CGG - chr7_2:87494350-87494369 None:intergenic 25.0%
!!! ATTTAGTAGATCTTTTTAGG+AGG + chr7_2:87494404-87494423 Msa1086650:intron 25.0%
! TATTGATCCCAAAAAAAAGA+CGG - chr7_2:87494505-87494524 None:intergenic 25.0%
TTATTACCAGTATTCGATAC+TGG + chr7_2:87494208-87494227 Msa1086650:CDS 30.0%
! AATAATCCAGTATCGAATAC+TGG - chr7_2:87494217-87494236 None:intergenic 30.0%
CTTTCTGTAAAATACTCGTT+TGG - chr7_2:87494327-87494346 None:intergenic 30.0%
CAAGGAATTCCATTAATAAC+TGG + chr7_2:87494351-87494370 Msa1086650:intron 30.0%
GTTGTTCCAAAGAATCAAAA+CGG - chr7_2:87494377-87494396 None:intergenic 30.0%
AACCATCGTACTGTAAAAAT+GGG - chr7_2:87494456-87494475 None:intergenic 30.0%
! GGTTTAGCTTACGATGTATT+TGG + chr7_2:87494291-87494310 Msa1086650:CDS 35.0%
TGTAAAATACTCGTTTGGAC+GGG - chr7_2:87494322-87494341 None:intergenic 35.0%
CTGTAAAATACTCGTTTGGA+CGG - chr7_2:87494323-87494342 None:intergenic 35.0%
! TATTTTACAGAAAGCCGACA+AGG + chr7_2:87494333-87494352 Msa1086650:intron 35.0%
TCAAAACGGCCAGTTATTAA+TGG - chr7_2:87494363-87494382 None:intergenic 35.0%
TCGTACTGTAAAAATGGGAT+AGG - chr7_2:87494451-87494470 None:intergenic 35.0%
!! ATCCCATTTTTACAGTACGA+TGG + chr7_2:87494451-87494470 Msa1086650:intron 35.0%
CAACCATCGTACTGTAAAAA+TGG - chr7_2:87494457-87494476 None:intergenic 35.0%
! CATTTTTACAGTACGATGGT+TGG + chr7_2:87494455-87494474 Msa1086650:intron 35.0%
! ATTCGGATTAGGTTTATCGT+TGG - chr7_2:87494545-87494564 None:intergenic 35.0%
! GTAGCTCTATAATTCGGATT+AGG - chr7_2:87494556-87494575 None:intergenic 35.0%
! TGTGTCGTAGCTCTATAATT+CGG - chr7_2:87494562-87494581 None:intergenic 35.0%
TATACCCTCCCTATTCATTG+CGG + chr7_2:87494248-87494267 Msa1086650:CDS 40.0%
TAACCAACCCGCAATGAATA+GGG - chr7_2:87494259-87494278 None:intergenic 40.0%
ATAACCAACCCGCAATGAAT+AGG - chr7_2:87494260-87494279 None:intergenic 40.0%
GTAAAATACTCGTTTGGACG+GGG - chr7_2:87494321-87494340 None:intergenic 40.0%
!!! AACTGGCCGTTTTGATTCTT+TGG + chr7_2:87494368-87494387 Msa1086650:intron 40.0%
TAGGTCCTATCTATGGTCAT+TGG - chr7_2:87494432-87494451 None:intergenic 40.0%
AATGGGATAGGTCCTATCTA+TGG - chr7_2:87494439-87494458 None:intergenic 40.0%
!!! GTACCCACCGTCTTTTTTTT+GGG + chr7_2:87494495-87494514 Msa1086650:intron 40.0%
GATCCCAAAAAAAAGACGGT+GGG - chr7_2:87494501-87494520 None:intergenic 40.0%
TGATCCCAAAAAAAAGACGG+TGG - chr7_2:87494502-87494521 None:intergenic 40.0%
TAATAAACCCCAGTAGAGAC+TGG - chr7_2:87494623-87494642 None:intergenic 40.0%
ATACCCTCCCTATTCATTGC+GGG + chr7_2:87494249-87494268 Msa1086650:CDS 45.0%
!! GGGTTGGTTATTTGTCAGCA+CGG + chr7_2:87494269-87494288 Msa1086650:CDS 45.0%
! GGTTGGTTATTTGTCAGCAC+GGG + chr7_2:87494270-87494289 Msa1086650:CDS 45.0%
AGGCTCCAATGACCATAGAT+AGG + chr7_2:87494424-87494443 Msa1086650:intron 45.0%
!!! GGTACCCACCGTCTTTTTTT+TGG + chr7_2:87494494-87494513 Msa1086650:intron 45.0%
TGAATCGTACCAGTCTCTAC+TGG + chr7_2:87494611-87494630 Msa1086650:CDS 45.0%
GAATCGTACCAGTCTCTACT+GGG + chr7_2:87494612-87494631 Msa1086650:CDS 45.0%
AATCGTACCAGTCTCTACTG+GGG + chr7_2:87494613-87494632 Msa1086650:CDS 45.0%
CAACCCGCAATGAATAGGGA+GGG - chr7_2:87494255-87494274 None:intergenic 50.0%
! GTACGATGGTTGGCTGTTCA+CGG + chr7_2:87494465-87494484 Msa1086650:intron 50.0%
TATGTGGAGCTCGGCATGTC+TGG + chr7_2:87494156-87494175 Msa1086650:exon 55.0%
CCAACCCGCAATGAATAGGG+AGG - chr7_2:87494256-87494275 None:intergenic 55.0%
CCTCCCTATTCATTGCGGGT+TGG + chr7_2:87494253-87494272 Msa1086650:CDS 55.0%
!! GTTGGCTGTTCACGGACTAG+CGG + chr7_2:87494473-87494492 Msa1086650:intron 55.0%
! CTCGGCATGTCTGGAAGCAC+AGG + chr7_2:87494165-87494184 Msa1086650:exon 60.0%
Chromosome Type Strat End Strand Name
chr7_2 gene 87494154 87494687 87494154 ID=Msa1086650;Name=Msa1086650
chr7_2 mRNA 87494154 87494687 87494154 ID=Msa1086650-mRNA-1;Parent=Msa1086650;Name=Msa1086650-mRNA-1;_AED=0.22;_eAED=0.22;_QI=17|0|0|1|0|0|2|0|104
chr7_2 exon 87494154 87494331 87494154 ID=Msa1086650-mRNA-1:exon:23907;Parent=Msa1086650-mRNA-1
chr7_2 exon 87494537 87494687 87494537 ID=Msa1086650-mRNA-1:exon:23908;Parent=Msa1086650-mRNA-1
chr7_2 five_prime_UTR 87494154 87494170 87494154 ID=Msa1086650-mRNA-1:five_prime_utr;Parent=Msa1086650-mRNA-1
chr7_2 CDS 87494171 87494331 87494171 ID=Msa1086650-mRNA-1:cds;Parent=Msa1086650-mRNA-1
chr7_2 CDS 87494537 87494687 87494537 ID=Msa1086650-mRNA-1:cds;Parent=Msa1086650-mRNA-1
Gene Sequence

>Msa1086650

ATGTCTGGAAGCACAGGAGAACGTTCTTTTGCTGATATTATTACCAGTATTCGATACTGGATTATTCATAGCATTACTATACCCTCCCTATTCATTGCGGGTTGGTTATTTGTCAGCACGGGTTTAGCTTACGATGTATTTGGAAGTCCCCGTCCAAACGATTCATCCAACGATAAACCTAATCCGAATTATAGAGCTACGACACAATCAAACCCAAATGAACAAAATGTTGAATTGAATCGTACCAGTCTCTACTGGGGTTTATTACTCATTTTTGTACTTGCTGTTTTATTTTCAAATTATTTCTTCAAT

Protein sequence

>Msa1086650

MSGSTGERSFADIITSIRYWIIHSITIPSLFIAGWLFVSTGLAYDVFGSPRPNDSSNDKPNPNYRATTQSNPNEQNVELNRTSLYWGLLLIFVLAVLFSNYFFN