AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1394120


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1394120 MtrunA17_CPg0492821 70.732 82 24 0 1 82 1 82 6.38e-34 112
Msa1394120 MtrunA17_Chr4g0016851 70.732 82 24 0 1 82 1 82 6.38e-34 112
Msa1394120 MtrunA17_Chr4g0015751 70.732 82 24 0 1 82 1 82 6.38e-34 112
Msa1394120 MtrunA17_Chr4g0017011 98.148 54 1 0 1 54 1 54 2.07e-33 111
Msa1394120 MtrunA17_Chr5g0423051 96.296 54 2 0 1 54 1 54 3.52e-32 107
Msa1394120 MtrunA17_Chr4g0016841 61.538 91 21 2 14 104 9 85 4.52e-31 105
Msa1394120 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
Msa1394120 ATCG00580.1 70.732 82 24 0 1 82 1 82 1.19e-34 114
Msa1394120 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 tig0021785:+56457 Msa1394120:CDS
GTAGCTCTATAATTCGGATT+AGG 0.338134 tig0021785:-56719 None:intergenic
ATAACCAACCCGCAATGAAT+AGG 0.348030 tig0021785:-56423 None:intergenic
TTATTACCAGTATTCGATAC+TGG 0.348418 tig0021785:+56374 Msa1394120:CDS
TATGTGGAGCTCGGCATGTC+TGG 0.349487 tig0021785:+56322 Msa1394120:exon
ATACCCTCCCTATTCATTGC+GGG 0.391873 tig0021785:+56415 Msa1394120:CDS
TAACCAACCCGCAATGAATA+GGG 0.406851 tig0021785:-56422 None:intergenic
TGAATCGTACCAGTCTCTAC+TGG 0.410190 tig0021785:+56777 Msa1394120:CDS
CTTTCTGTAAAATACTCGTT+TGG 0.412027 tig0021785:-56490 None:intergenic
TGTGTCGTAGCTCTATAATT+CGG 0.415726 tig0021785:-56725 None:intergenic
AATAATCCAGTATCGAATAC+TGG 0.423687 tig0021785:-56380 None:intergenic
CTCGGCATGTCTGGAAGCAC+AGG 0.508926 tig0021785:+56331 Msa1394120:exon
ATTCGGATTAGGTTTATCGT+TGG 0.512045 tig0021785:-56708 None:intergenic
GAATCGTACCAGTCTCTACT+GGG 0.515213 tig0021785:+56778 Msa1394120:CDS
TTTGACTGTATAAGAATATG+TGG 0.517465 tig0021785:+56306 None:intergenic
GGTTGGTTATTTGTCAGCAC+GGG 0.523918 tig0021785:+56436 Msa1394120:CDS
TGTAAAATACTCGTTTGGAC+GGG 0.525534 tig0021785:-56485 None:intergenic
GTAAAATACTCGTTTGGACG+GGG 0.531710 tig0021785:-56484 None:intergenic
GGGTTGGTTATTTGTCAGCA+CGG 0.532372 tig0021785:+56435 Msa1394120:CDS
CCTCCCTATTCATTGCGGGT+TGG 0.536548 tig0021785:+56419 Msa1394120:CDS
CTGTAAAATACTCGTTTGGA+CGG 0.550313 tig0021785:-56486 None:intergenic
TAATAAACCCCAGTAGAGAC+TGG 0.572062 tig0021785:-56786 None:intergenic
GTATAAGAATATGTGGAGCT+CGG 0.584815 tig0021785:+56313 None:intergenic
TATACCCTCCCTATTCATTG+CGG 0.586067 tig0021785:+56414 Msa1394120:CDS
CAACCCGCAATGAATAGGGA+GGG 0.665638 tig0021785:-56418 None:intergenic
CCAACCCGCAATGAATAGGG+AGG 0.678708 tig0021785:-56419 None:intergenic
AATCGTACCAGTCTCTACTG+GGG 0.711157 tig0021785:+56779 Msa1394120:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! TGAATTTAGTAGATCTTTTT+AGG + tig0021785:56567-56586 Msa1394120:intron 20.0%
!!! ATTCAACATTTTGTTCATTT+GGG - tig0021785:56757-56776 None:intergenic 20.0%
!!! AATTCAACATTTTGTTCATT+TGG - tig0021785:56758-56777 None:intergenic 20.0%
! TTATTAATGGAATTCCTTGT+CGG - tig0021785:56516-56535 None:intergenic 25.0%
!!! ATTTAGTAGATCTTTTTAGG+AGG + tig0021785:56570-56589 Msa1394120:intron 25.0%
! TATTGATCCCAAAAAAAAGA+CGG - tig0021785:56671-56690 None:intergenic 25.0%
TTATTACCAGTATTCGATAC+TGG + tig0021785:56374-56393 Msa1394120:CDS 30.0%
! AATAATCCAGTATCGAATAC+TGG - tig0021785:56383-56402 None:intergenic 30.0%
CTTTCTGTAAAATACTCGTT+TGG - tig0021785:56493-56512 None:intergenic 30.0%
CAAGGAATTCCATTAATAAC+TGG + tig0021785:56517-56536 Msa1394120:intron 30.0%
GTTGTTCCAAAGAATCAAAA+CGG - tig0021785:56543-56562 None:intergenic 30.0%
AACCATCGTACTGTAAAAAT+GGG - tig0021785:56622-56641 None:intergenic 30.0%
! GGTTTAGCTTACGATGTATT+TGG + tig0021785:56457-56476 Msa1394120:CDS 35.0%
TGTAAAATACTCGTTTGGAC+GGG - tig0021785:56488-56507 None:intergenic 35.0%
CTGTAAAATACTCGTTTGGA+CGG - tig0021785:56489-56508 None:intergenic 35.0%
! TATTTTACAGAAAGCCGACA+AGG + tig0021785:56499-56518 Msa1394120:intron 35.0%
TCAAAACGGCCAGTTATTAA+TGG - tig0021785:56529-56548 None:intergenic 35.0%
TCGTACTGTAAAAATGGGAT+AGG - tig0021785:56617-56636 None:intergenic 35.0%
!! ATCCCATTTTTACAGTACGA+TGG + tig0021785:56617-56636 Msa1394120:intron 35.0%
CAACCATCGTACTGTAAAAA+TGG - tig0021785:56623-56642 None:intergenic 35.0%
! CATTTTTACAGTACGATGGT+TGG + tig0021785:56621-56640 Msa1394120:intron 35.0%
! ATTCGGATTAGGTTTATCGT+TGG - tig0021785:56711-56730 None:intergenic 35.0%
! GTAGCTCTATAATTCGGATT+AGG - tig0021785:56722-56741 None:intergenic 35.0%
! TGTGTCGTAGCTCTATAATT+CGG - tig0021785:56728-56747 None:intergenic 35.0%
TATACCCTCCCTATTCATTG+CGG + tig0021785:56414-56433 Msa1394120:CDS 40.0%
TAACCAACCCGCAATGAATA+GGG - tig0021785:56425-56444 None:intergenic 40.0%
ATAACCAACCCGCAATGAAT+AGG - tig0021785:56426-56445 None:intergenic 40.0%
GTAAAATACTCGTTTGGACG+GGG - tig0021785:56487-56506 None:intergenic 40.0%
!!! AACTGGCCGTTTTGATTCTT+TGG + tig0021785:56534-56553 Msa1394120:intron 40.0%
TAGGTCCTATCTATGGTCAT+TGG - tig0021785:56598-56617 None:intergenic 40.0%
AATGGGATAGGTCCTATCTA+TGG - tig0021785:56605-56624 None:intergenic 40.0%
!!! GTACCCACCGTCTTTTTTTT+GGG + tig0021785:56661-56680 Msa1394120:intron 40.0%
GATCCCAAAAAAAAGACGGT+GGG - tig0021785:56667-56686 None:intergenic 40.0%
TGATCCCAAAAAAAAGACGG+TGG - tig0021785:56668-56687 None:intergenic 40.0%
TAATAAACCCCAGTAGAGAC+TGG - tig0021785:56789-56808 None:intergenic 40.0%
ATACCCTCCCTATTCATTGC+GGG + tig0021785:56415-56434 Msa1394120:CDS 45.0%
!! GGGTTGGTTATTTGTCAGCA+CGG + tig0021785:56435-56454 Msa1394120:CDS 45.0%
! GGTTGGTTATTTGTCAGCAC+GGG + tig0021785:56436-56455 Msa1394120:CDS 45.0%
AGGCTCCAATGACCATAGAT+AGG + tig0021785:56590-56609 Msa1394120:intron 45.0%
!!! GGTACCCACCGTCTTTTTTT+TGG + tig0021785:56660-56679 Msa1394120:intron 45.0%
TGAATCGTACCAGTCTCTAC+TGG + tig0021785:56777-56796 Msa1394120:CDS 45.0%
GAATCGTACCAGTCTCTACT+GGG + tig0021785:56778-56797 Msa1394120:CDS 45.0%
AATCGTACCAGTCTCTACTG+GGG + tig0021785:56779-56798 Msa1394120:CDS 45.0%
CAACCCGCAATGAATAGGGA+GGG - tig0021785:56421-56440 None:intergenic 50.0%
! GTACGATGGTTGGCTGTTCA+CGG + tig0021785:56631-56650 Msa1394120:intron 50.0%
TATGTGGAGCTCGGCATGTC+TGG + tig0021785:56322-56341 Msa1394120:exon 55.0%
CCAACCCGCAATGAATAGGG+AGG - tig0021785:56422-56441 None:intergenic 55.0%
CCTCCCTATTCATTGCGGGT+TGG + tig0021785:56419-56438 Msa1394120:CDS 55.0%
!! GTTGGCTGTTCACGGACTAG+CGG + tig0021785:56639-56658 Msa1394120:intron 55.0%
! CTCGGCATGTCTGGAAGCAC+AGG + tig0021785:56331-56350 Msa1394120:exon 60.0%
Chromosome Type Strat End Strand Name
tig0021785 gene 56320 56853 56320 ID=Msa1394120;Name=Msa1394120
tig0021785 mRNA 56320 56853 56320 ID=Msa1394120-mRNA-1;Parent=Msa1394120;Name=Msa1394120-mRNA-1;_AED=0.22;_eAED=0.22;_QI=17|0|0|1|0|0|2|0|104
tig0021785 exon 56320 56497 56320 ID=Msa1394120-mRNA-1:exon:14242;Parent=Msa1394120-mRNA-1
tig0021785 exon 56703 56853 56703 ID=Msa1394120-mRNA-1:exon:14243;Parent=Msa1394120-mRNA-1
tig0021785 five_prime_UTR 56320 56336 56320 ID=Msa1394120-mRNA-1:five_prime_utr;Parent=Msa1394120-mRNA-1
tig0021785 CDS 56337 56497 56337 ID=Msa1394120-mRNA-1:cds;Parent=Msa1394120-mRNA-1
tig0021785 CDS 56703 56853 56703 ID=Msa1394120-mRNA-1:cds;Parent=Msa1394120-mRNA-1
Gene Sequence

>Msa1394120

ATGTCTGGAAGCACAGGAGAACGTTCTTTTGCTGATATTATTACCAGTATTCGATACTGGATTATTCATAGCATTACTATACCCTCCCTATTCATTGCGGGTTGGTTATTTGTCAGCACGGGTTTAGCTTACGATGTATTTGGAAGTCCCCGTCCAAACGATTCATCCAACGATAAACCTAATCCGAATTATAGAGCTACGACACAATCAAACCCAAATGAACAAAATGTTGAATTGAATCGTACCAGTCTCTACTGGGGTTTATTACTCATTTTTGTACTTGCTGTTTTATTTTCAAATTATTTCTTCAAT

Protein sequence

>Msa1394120

MSGSTGERSFADIITSIRYWIIHSITIPSLFIAGWLFVSTGLAYDVFGSPRPNDSSNDKPNPNYRATTQSNPNEQNVELNRTSLYWGLLLIFVLAVLFSNYFFN