AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1086850


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1086850 MtrunA17_CPg0492821 70.732 82 24 0 1 82 1 82 6.38e-34 112
Msa1086850 MtrunA17_Chr4g0016851 70.732 82 24 0 1 82 1 82 6.38e-34 112
Msa1086850 MtrunA17_Chr4g0015751 70.732 82 24 0 1 82 1 82 6.38e-34 112
Msa1086850 MtrunA17_Chr4g0017011 98.148 54 1 0 1 54 1 54 2.07e-33 111
Msa1086850 MtrunA17_Chr5g0423051 96.296 54 2 0 1 54 1 54 3.52e-32 107
Msa1086850 MtrunA17_Chr4g0016841 61.538 91 21 2 14 104 9 85 4.52e-31 105
Msa1086850 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
Msa1086850 ATCG00580.1 70.732 82 24 0 1 82 1 82 1.19e-34 114
Msa1086850 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:+87594463 Msa1086850:CDS
GTAGCTCTATAATTCGGATT+AGG 0.338134 7_2:-87594725 None:intergenic
ATAACCAACCCGCAATGAAT+AGG 0.348030 7_2:-87594429 None:intergenic
TTATTACCAGTATTCGATAC+TGG 0.348418 7_2:+87594380 Msa1086850:CDS
TATGTGGAGCTCGGCATGTC+TGG 0.349487 7_2:+87594328 Msa1086850:exon
ATACCCTCCCTATTCATTGC+GGG 0.391873 7_2:+87594421 Msa1086850:CDS
TAACCAACCCGCAATGAATA+GGG 0.406851 7_2:-87594428 None:intergenic
TGAATCGTACCAGTCTCTAC+TGG 0.410190 7_2:+87594783 Msa1086850:CDS
CTTTCTGTAAAATACTCGTT+TGG 0.412027 7_2:-87594496 None:intergenic
TGTGTCGTAGCTCTATAATT+CGG 0.415726 7_2:-87594731 None:intergenic
AATAATCCAGTATCGAATAC+TGG 0.423687 7_2:-87594386 None:intergenic
CTCGGCATGTCTGGAAGCAC+AGG 0.508926 7_2:+87594337 Msa1086850:exon
ATTCGGATTAGGTTTATCGT+TGG 0.512045 7_2:-87594714 None:intergenic
GAATCGTACCAGTCTCTACT+GGG 0.515213 7_2:+87594784 Msa1086850:CDS
TTTGACTGTATAAGAATATG+TGG 0.517465 7_2:+87594312 None:intergenic
GGTTGGTTATTTGTCAGCAC+GGG 0.523918 7_2:+87594442 Msa1086850:CDS
TGTAAAATACTCGTTTGGAC+GGG 0.525534 7_2:-87594491 None:intergenic
GTAAAATACTCGTTTGGACG+GGG 0.531710 7_2:-87594490 None:intergenic
GGGTTGGTTATTTGTCAGCA+CGG 0.532372 7_2:+87594441 Msa1086850:CDS
CCTCCCTATTCATTGCGGGT+TGG 0.536548 7_2:+87594425 Msa1086850:CDS
CTGTAAAATACTCGTTTGGA+CGG 0.550313 7_2:-87594492 None:intergenic
TAATAAACCCCAGTAGAGAC+TGG 0.572062 7_2:-87594792 None:intergenic
GTATAAGAATATGTGGAGCT+CGG 0.584815 7_2:+87594319 None:intergenic
TATACCCTCCCTATTCATTG+CGG 0.586067 7_2:+87594420 Msa1086850:CDS
CAACCCGCAATGAATAGGGA+GGG 0.665638 7_2:-87594424 None:intergenic
CCAACCCGCAATGAATAGGG+AGG 0.678708 7_2:-87594425 None:intergenic
AATCGTACCAGTCTCTACTG+GGG 0.711157 7_2:+87594785 Msa1086850:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! TGAATTTAGTAGATCTTTTT+AGG + chr7_2:87594573-87594592 Msa1086850:intron 20.0%
!!! ATTCAACATTTTGTTCATTT+GGG - chr7_2:87594763-87594782 None:intergenic 20.0%
!!! AATTCAACATTTTGTTCATT+TGG - chr7_2:87594764-87594783 None:intergenic 20.0%
! TTATTAATGGAATTCCTTGT+CGG - chr7_2:87594522-87594541 None:intergenic 25.0%
!!! ATTTAGTAGATCTTTTTAGG+AGG + chr7_2:87594576-87594595 Msa1086850:intron 25.0%
! TATTGATCCCAAAAAAAAGA+CGG - chr7_2:87594677-87594696 None:intergenic 25.0%
TTATTACCAGTATTCGATAC+TGG + chr7_2:87594380-87594399 Msa1086850:CDS 30.0%
! AATAATCCAGTATCGAATAC+TGG - chr7_2:87594389-87594408 None:intergenic 30.0%
CTTTCTGTAAAATACTCGTT+TGG - chr7_2:87594499-87594518 None:intergenic 30.0%
CAAGGAATTCCATTAATAAC+TGG + chr7_2:87594523-87594542 Msa1086850:intron 30.0%
GTTGTTCCAAAGAATCAAAA+CGG - chr7_2:87594549-87594568 None:intergenic 30.0%
AACCATCGTACTGTAAAAAT+GGG - chr7_2:87594628-87594647 None:intergenic 30.0%
! GGTTTAGCTTACGATGTATT+TGG + chr7_2:87594463-87594482 Msa1086850:CDS 35.0%
TGTAAAATACTCGTTTGGAC+GGG - chr7_2:87594494-87594513 None:intergenic 35.0%
CTGTAAAATACTCGTTTGGA+CGG - chr7_2:87594495-87594514 None:intergenic 35.0%
! TATTTTACAGAAAGCCGACA+AGG + chr7_2:87594505-87594524 Msa1086850:intron 35.0%
TCAAAACGGCCAGTTATTAA+TGG - chr7_2:87594535-87594554 None:intergenic 35.0%
TCGTACTGTAAAAATGGGAT+AGG - chr7_2:87594623-87594642 None:intergenic 35.0%
!! ATCCCATTTTTACAGTACGA+TGG + chr7_2:87594623-87594642 Msa1086850:intron 35.0%
CAACCATCGTACTGTAAAAA+TGG - chr7_2:87594629-87594648 None:intergenic 35.0%
! CATTTTTACAGTACGATGGT+TGG + chr7_2:87594627-87594646 Msa1086850:intron 35.0%
! ATTCGGATTAGGTTTATCGT+TGG - chr7_2:87594717-87594736 None:intergenic 35.0%
! GTAGCTCTATAATTCGGATT+AGG - chr7_2:87594728-87594747 None:intergenic 35.0%
! TGTGTCGTAGCTCTATAATT+CGG - chr7_2:87594734-87594753 None:intergenic 35.0%
TATACCCTCCCTATTCATTG+CGG + chr7_2:87594420-87594439 Msa1086850:CDS 40.0%
TAACCAACCCGCAATGAATA+GGG - chr7_2:87594431-87594450 None:intergenic 40.0%
ATAACCAACCCGCAATGAAT+AGG - chr7_2:87594432-87594451 None:intergenic 40.0%
GTAAAATACTCGTTTGGACG+GGG - chr7_2:87594493-87594512 None:intergenic 40.0%
!!! AACTGGCCGTTTTGATTCTT+TGG + chr7_2:87594540-87594559 Msa1086850:intron 40.0%
TAGGTCCTATCTATGGTCAT+TGG - chr7_2:87594604-87594623 None:intergenic 40.0%
AATGGGATAGGTCCTATCTA+TGG - chr7_2:87594611-87594630 None:intergenic 40.0%
!!! GTACCCACCGTCTTTTTTTT+GGG + chr7_2:87594667-87594686 Msa1086850:intron 40.0%
GATCCCAAAAAAAAGACGGT+GGG - chr7_2:87594673-87594692 None:intergenic 40.0%
TGATCCCAAAAAAAAGACGG+TGG - chr7_2:87594674-87594693 None:intergenic 40.0%
TAATAAACCCCAGTAGAGAC+TGG - chr7_2:87594795-87594814 None:intergenic 40.0%
ATACCCTCCCTATTCATTGC+GGG + chr7_2:87594421-87594440 Msa1086850:CDS 45.0%
!! GGGTTGGTTATTTGTCAGCA+CGG + chr7_2:87594441-87594460 Msa1086850:CDS 45.0%
! GGTTGGTTATTTGTCAGCAC+GGG + chr7_2:87594442-87594461 Msa1086850:CDS 45.0%
AGGCTCCAATGACCATAGAT+AGG + chr7_2:87594596-87594615 Msa1086850:intron 45.0%
!!! GGTACCCACCGTCTTTTTTT+TGG + chr7_2:87594666-87594685 Msa1086850:intron 45.0%
TGAATCGTACCAGTCTCTAC+TGG + chr7_2:87594783-87594802 Msa1086850:CDS 45.0%
GAATCGTACCAGTCTCTACT+GGG + chr7_2:87594784-87594803 Msa1086850:CDS 45.0%
AATCGTACCAGTCTCTACTG+GGG + chr7_2:87594785-87594804 Msa1086850:CDS 45.0%
CAACCCGCAATGAATAGGGA+GGG - chr7_2:87594427-87594446 None:intergenic 50.0%
! GTACGATGGTTGGCTGTTCA+CGG + chr7_2:87594637-87594656 Msa1086850:intron 50.0%
TATGTGGAGCTCGGCATGTC+TGG + chr7_2:87594328-87594347 Msa1086850:exon 55.0%
CCAACCCGCAATGAATAGGG+AGG - chr7_2:87594428-87594447 None:intergenic 55.0%
CCTCCCTATTCATTGCGGGT+TGG + chr7_2:87594425-87594444 Msa1086850:CDS 55.0%
!! GTTGGCTGTTCACGGACTAG+CGG + chr7_2:87594645-87594664 Msa1086850:intron 55.0%
! CTCGGCATGTCTGGAAGCAC+AGG + chr7_2:87594337-87594356 Msa1086850:exon 60.0%
Chromosome Type Strat End Strand Name
chr7_2 gene 87594326 87594859 87594326 ID=Msa1086850;Name=Msa1086850
chr7_2 mRNA 87594326 87594859 87594326 ID=Msa1086850-mRNA-1;Parent=Msa1086850;Name=Msa1086850-mRNA-1;_AED=0.22;_eAED=0.22;_QI=17|0|0|1|0|0|2|0|104
chr7_2 exon 87594326 87594503 87594326 ID=Msa1086850-mRNA-1:exon:23961;Parent=Msa1086850-mRNA-1
chr7_2 exon 87594709 87594859 87594709 ID=Msa1086850-mRNA-1:exon:23962;Parent=Msa1086850-mRNA-1
chr7_2 five_prime_UTR 87594326 87594342 87594326 ID=Msa1086850-mRNA-1:five_prime_utr;Parent=Msa1086850-mRNA-1
chr7_2 CDS 87594343 87594503 87594343 ID=Msa1086850-mRNA-1:cds;Parent=Msa1086850-mRNA-1
chr7_2 CDS 87594709 87594859 87594709 ID=Msa1086850-mRNA-1:cds;Parent=Msa1086850-mRNA-1
Gene Sequence

>Msa1086850

ATGTCTGGAAGCACAGGAGAACGTTCTTTTGCTGATATTATTACCAGTATTCGATACTGGATTATTCATAGCATTACTATACCCTCCCTATTCATTGCGGGTTGGTTATTTGTCAGCACGGGTTTAGCTTACGATGTATTTGGAAGTCCCCGTCCAAACGATTCATCCAACGATAAACCTAATCCGAATTATAGAGCTACGACACAATCAAACCCAAATGAACAAAATGTTGAATTGAATCGTACCAGTCTCTACTGGGGTTTATTACTCATTTTTGTACTTGCTGTTTTATTTTCAAATTATTTCTTCAAT

Protein sequence

>Msa1086850

MSGSTGERSFADIITSIRYWIIHSITIPSLFIAGWLFVSTGLAYDVFGSPRPNDSSNDKPNPNYRATTQSNPNEQNVELNRTSLYWGLLLIFVLAVLFSNYFFN