AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1086040


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1086040 MtrunA17_CPg0492821 70.732 82 24 0 1 82 1 82 6.38e-34 112
Msa1086040 MtrunA17_Chr4g0016851 70.732 82 24 0 1 82 1 82 6.38e-34 112
Msa1086040 MtrunA17_Chr4g0015751 70.732 82 24 0 1 82 1 82 6.38e-34 112
Msa1086040 MtrunA17_Chr4g0017011 98.148 54 1 0 1 54 1 54 2.07e-33 111
Msa1086040 MtrunA17_Chr5g0423051 96.296 54 2 0 1 54 1 54 3.52e-32 107
Msa1086040 MtrunA17_Chr4g0016841 61.538 91 21 2 14 104 9 85 4.52e-31 105
Msa1086040 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
Msa1086040 ATCG00580.1 70.732 82 24 0 1 82 1 82 1.19e-34 114
Msa1086040 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:+87101764 Msa1086040:CDS
GTAGCTCTATAATTCGGATT+AGG 0.338134 7_2:-87102026 None:intergenic
ATAACCAACCCGCAATGAAT+AGG 0.348030 7_2:-87101730 None:intergenic
TTATTACCAGTATTCGATAC+TGG 0.348418 7_2:+87101681 Msa1086040:CDS
TATGTGGAGCTCGGCATGTC+TGG 0.349487 7_2:+87101629 Msa1086040:exon
ATACCCTCCCTATTCATTGC+GGG 0.391873 7_2:+87101722 Msa1086040:CDS
TAACCAACCCGCAATGAATA+GGG 0.406851 7_2:-87101729 None:intergenic
TGAATCGTACCAGTCTCTAC+TGG 0.410190 7_2:+87102084 Msa1086040:CDS
CTTTCTGTAAAATACTCGTT+TGG 0.412027 7_2:-87101797 None:intergenic
TGTGTCGTAGCTCTATAATT+CGG 0.415726 7_2:-87102032 None:intergenic
AATAATCCAGTATCGAATAC+TGG 0.423687 7_2:-87101687 None:intergenic
CTCGGCATGTCTGGAAGCAC+AGG 0.508926 7_2:+87101638 Msa1086040:exon
ATTCGGATTAGGTTTATCGT+TGG 0.512045 7_2:-87102015 None:intergenic
GAATCGTACCAGTCTCTACT+GGG 0.515213 7_2:+87102085 Msa1086040:CDS
TTTGACTGTATAAGAATATG+TGG 0.517465 7_2:+87101613 None:intergenic
GGTTGGTTATTTGTCAGCAC+GGG 0.523918 7_2:+87101743 Msa1086040:CDS
TGTAAAATACTCGTTTGGAC+GGG 0.525534 7_2:-87101792 None:intergenic
GTAAAATACTCGTTTGGACG+GGG 0.531710 7_2:-87101791 None:intergenic
GGGTTGGTTATTTGTCAGCA+CGG 0.532372 7_2:+87101742 Msa1086040:CDS
CCTCCCTATTCATTGCGGGT+TGG 0.536548 7_2:+87101726 Msa1086040:CDS
CTGTAAAATACTCGTTTGGA+CGG 0.550313 7_2:-87101793 None:intergenic
TAATAAACCCCAGTAGAGAC+TGG 0.572062 7_2:-87102093 None:intergenic
GTATAAGAATATGTGGAGCT+CGG 0.584815 7_2:+87101620 None:intergenic
TATACCCTCCCTATTCATTG+CGG 0.586067 7_2:+87101721 Msa1086040:CDS
CAACCCGCAATGAATAGGGA+GGG 0.665638 7_2:-87101725 None:intergenic
CCAACCCGCAATGAATAGGG+AGG 0.678708 7_2:-87101726 None:intergenic
AATCGTACCAGTCTCTACTG+GGG 0.711157 7_2:+87102086 Msa1086040:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! TGAATTTAGTAGATCTTTTT+AGG + chr7_2:87101874-87101893 Msa1086040:intron 20.0%
!!! ATTCAACATTTTGTTCATTT+GGG - chr7_2:87102064-87102083 None:intergenic 20.0%
!!! AATTCAACATTTTGTTCATT+TGG - chr7_2:87102065-87102084 None:intergenic 20.0%
! TTATTAATGGAATTCCTTGT+CGG - chr7_2:87101823-87101842 None:intergenic 25.0%
!!! ATTTAGTAGATCTTTTTAGG+AGG + chr7_2:87101877-87101896 Msa1086040:intron 25.0%
! TATTGATCCCAAAAAAAAGA+CGG - chr7_2:87101978-87101997 None:intergenic 25.0%
TTATTACCAGTATTCGATAC+TGG + chr7_2:87101681-87101700 Msa1086040:CDS 30.0%
! AATAATCCAGTATCGAATAC+TGG - chr7_2:87101690-87101709 None:intergenic 30.0%
CTTTCTGTAAAATACTCGTT+TGG - chr7_2:87101800-87101819 None:intergenic 30.0%
CAAGGAATTCCATTAATAAC+TGG + chr7_2:87101824-87101843 Msa1086040:intron 30.0%
GTTGTTCCAAAGAATCAAAA+CGG - chr7_2:87101850-87101869 None:intergenic 30.0%
AACCATCGTACTGTAAAAAT+GGG - chr7_2:87101929-87101948 None:intergenic 30.0%
! GGTTTAGCTTACGATGTATT+TGG + chr7_2:87101764-87101783 Msa1086040:CDS 35.0%
TGTAAAATACTCGTTTGGAC+GGG - chr7_2:87101795-87101814 None:intergenic 35.0%
CTGTAAAATACTCGTTTGGA+CGG - chr7_2:87101796-87101815 None:intergenic 35.0%
! TATTTTACAGAAAGCCGACA+AGG + chr7_2:87101806-87101825 Msa1086040:intron 35.0%
TCAAAACGGCCAGTTATTAA+TGG - chr7_2:87101836-87101855 None:intergenic 35.0%
TCGTACTGTAAAAATGGGAT+AGG - chr7_2:87101924-87101943 None:intergenic 35.0%
!! ATCCCATTTTTACAGTACGA+TGG + chr7_2:87101924-87101943 Msa1086040:intron 35.0%
CAACCATCGTACTGTAAAAA+TGG - chr7_2:87101930-87101949 None:intergenic 35.0%
! CATTTTTACAGTACGATGGT+TGG + chr7_2:87101928-87101947 Msa1086040:intron 35.0%
! ATTCGGATTAGGTTTATCGT+TGG - chr7_2:87102018-87102037 None:intergenic 35.0%
! GTAGCTCTATAATTCGGATT+AGG - chr7_2:87102029-87102048 None:intergenic 35.0%
! TGTGTCGTAGCTCTATAATT+CGG - chr7_2:87102035-87102054 None:intergenic 35.0%
TATACCCTCCCTATTCATTG+CGG + chr7_2:87101721-87101740 Msa1086040:CDS 40.0%
TAACCAACCCGCAATGAATA+GGG - chr7_2:87101732-87101751 None:intergenic 40.0%
ATAACCAACCCGCAATGAAT+AGG - chr7_2:87101733-87101752 None:intergenic 40.0%
GTAAAATACTCGTTTGGACG+GGG - chr7_2:87101794-87101813 None:intergenic 40.0%
!!! AACTGGCCGTTTTGATTCTT+TGG + chr7_2:87101841-87101860 Msa1086040:intron 40.0%
TAGGTCCTATCTATGGTCAT+TGG - chr7_2:87101905-87101924 None:intergenic 40.0%
AATGGGATAGGTCCTATCTA+TGG - chr7_2:87101912-87101931 None:intergenic 40.0%
!!! GTACCCACCGTCTTTTTTTT+GGG + chr7_2:87101968-87101987 Msa1086040:intron 40.0%
GATCCCAAAAAAAAGACGGT+GGG - chr7_2:87101974-87101993 None:intergenic 40.0%
TGATCCCAAAAAAAAGACGG+TGG - chr7_2:87101975-87101994 None:intergenic 40.0%
TAATAAACCCCAGTAGAGAC+TGG - chr7_2:87102096-87102115 None:intergenic 40.0%
ATACCCTCCCTATTCATTGC+GGG + chr7_2:87101722-87101741 Msa1086040:CDS 45.0%
!! GGGTTGGTTATTTGTCAGCA+CGG + chr7_2:87101742-87101761 Msa1086040:CDS 45.0%
! GGTTGGTTATTTGTCAGCAC+GGG + chr7_2:87101743-87101762 Msa1086040:CDS 45.0%
AGGCTCCAATGACCATAGAT+AGG + chr7_2:87101897-87101916 Msa1086040:intron 45.0%
!!! GGTACCCACCGTCTTTTTTT+TGG + chr7_2:87101967-87101986 Msa1086040:intron 45.0%
TGAATCGTACCAGTCTCTAC+TGG + chr7_2:87102084-87102103 Msa1086040:CDS 45.0%
GAATCGTACCAGTCTCTACT+GGG + chr7_2:87102085-87102104 Msa1086040:CDS 45.0%
AATCGTACCAGTCTCTACTG+GGG + chr7_2:87102086-87102105 Msa1086040:CDS 45.0%
CAACCCGCAATGAATAGGGA+GGG - chr7_2:87101728-87101747 None:intergenic 50.0%
! GTACGATGGTTGGCTGTTCA+CGG + chr7_2:87101938-87101957 Msa1086040:intron 50.0%
TATGTGGAGCTCGGCATGTC+TGG + chr7_2:87101629-87101648 Msa1086040:exon 55.0%
CCAACCCGCAATGAATAGGG+AGG - chr7_2:87101729-87101748 None:intergenic 55.0%
CCTCCCTATTCATTGCGGGT+TGG + chr7_2:87101726-87101745 Msa1086040:CDS 55.0%
!! GTTGGCTGTTCACGGACTAG+CGG + chr7_2:87101946-87101965 Msa1086040:intron 55.0%
! CTCGGCATGTCTGGAAGCAC+AGG + chr7_2:87101638-87101657 Msa1086040:exon 60.0%
Chromosome Type Strat End Strand Name
chr7_2 gene 87101627 87102160 87101627 ID=Msa1086040;Name=Msa1086040
chr7_2 mRNA 87101627 87102160 87101627 ID=Msa1086040-mRNA-1;Parent=Msa1086040;Name=Msa1086040-mRNA-1;_AED=0.22;_eAED=0.22;_QI=17|0|0|1|0|0|2|0|104
chr7_2 exon 87101627 87101804 87101627 ID=Msa1086040-mRNA-1:exon:23704;Parent=Msa1086040-mRNA-1
chr7_2 exon 87102010 87102160 87102010 ID=Msa1086040-mRNA-1:exon:23705;Parent=Msa1086040-mRNA-1
chr7_2 five_prime_UTR 87101627 87101643 87101627 ID=Msa1086040-mRNA-1:five_prime_utr;Parent=Msa1086040-mRNA-1
chr7_2 CDS 87101644 87101804 87101644 ID=Msa1086040-mRNA-1:cds;Parent=Msa1086040-mRNA-1
chr7_2 CDS 87102010 87102160 87102010 ID=Msa1086040-mRNA-1:cds;Parent=Msa1086040-mRNA-1
Gene Sequence

>Msa1086040

ATGTCTGGAAGCACAGGAGAACGTTCTTTTGCTGATATTATTACCAGTATTCGATACTGGATTATTCATAGCATTACTATACCCTCCCTATTCATTGCGGGTTGGTTATTTGTCAGCACGGGTTTAGCTTACGATGTATTTGGAAGTCCCCGTCCAAACGATTCATCCAACGATAAACCTAATCCGAATTATAGAGCTACGACACAATCAAACCCAAATGAACAAAATGTTGAATTGAATCGTACCAGTCTCTACTGGGGTTTATTACTCATTTTTGTACTTGCTGTTTTATTTTCAAATTATTTCTTCAAT

Protein sequence

>Msa1086040

MSGSTGERSFADIITSIRYWIIHSITIPSLFIAGWLFVSTGLAYDVFGSPRPNDSSNDKPNPNYRATTQSNPNEQNVELNRTSLYWGLLLIFVLAVLFSNYFFN