AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1086500


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1086500 MtrunA17_CPg0492821 70.732 82 24 0 1 82 1 82 6.38e-34 112
Msa1086500 MtrunA17_Chr4g0016851 70.732 82 24 0 1 82 1 82 6.38e-34 112
Msa1086500 MtrunA17_Chr4g0015751 70.732 82 24 0 1 82 1 82 6.38e-34 112
Msa1086500 MtrunA17_Chr4g0017011 98.148 54 1 0 1 54 1 54 2.07e-33 111
Msa1086500 MtrunA17_Chr5g0423051 96.296 54 2 0 1 54 1 54 3.52e-32 107
Msa1086500 MtrunA17_Chr4g0016841 61.538 91 21 2 14 104 9 85 4.52e-31 105
Msa1086500 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
Msa1086500 ATCG00580.1 70.732 82 24 0 1 82 1 82 1.19e-34 114
Msa1086500 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:-87423680 Msa1086500:CDS
GTAGCTCTATAATTCGGATT+AGG 0.338134 7_2:+87423418 None:intergenic
ATAACCAACCCGCAATGAAT+AGG 0.348030 7_2:+87423714 None:intergenic
TTATTACCAGTATTCGATAC+TGG 0.348418 7_2:-87423763 Msa1086500:CDS
TATGTGGAGCTCGGCATGTC+TGG 0.349487 7_2:-87423815 Msa1086500:exon
ATACCCTCCCTATTCATTGC+GGG 0.391873 7_2:-87423722 Msa1086500:CDS
TAACCAACCCGCAATGAATA+GGG 0.406851 7_2:+87423715 None:intergenic
TGAATCGTACCAGTCTCTAC+TGG 0.410190 7_2:-87423360 Msa1086500:CDS
CTTTCTGTAAAATACTCGTT+TGG 0.412027 7_2:+87423647 None:intergenic
TGTGTCGTAGCTCTATAATT+CGG 0.415726 7_2:+87423412 None:intergenic
AATAATCCAGTATCGAATAC+TGG 0.423687 7_2:+87423757 None:intergenic
CTCGGCATGTCTGGAAGCAC+AGG 0.508926 7_2:-87423806 Msa1086500:exon
ATTCGGATTAGGTTTATCGT+TGG 0.512045 7_2:+87423429 None:intergenic
GAATCGTACCAGTCTCTACT+GGG 0.515213 7_2:-87423359 Msa1086500:CDS
TTTGACTGTATAAGAATATG+TGG 0.517465 7_2:-87423831 None:intergenic
GGTTGGTTATTTGTCAGCAC+GGG 0.523918 7_2:-87423701 Msa1086500:CDS
TGTAAAATACTCGTTTGGAC+GGG 0.525534 7_2:+87423652 None:intergenic
GTAAAATACTCGTTTGGACG+GGG 0.531710 7_2:+87423653 None:intergenic
GGGTTGGTTATTTGTCAGCA+CGG 0.532372 7_2:-87423702 Msa1086500:CDS
CCTCCCTATTCATTGCGGGT+TGG 0.536548 7_2:-87423718 Msa1086500:CDS
CTGTAAAATACTCGTTTGGA+CGG 0.550313 7_2:+87423651 None:intergenic
TAATAAACCCCAGTAGAGAC+TGG 0.572062 7_2:+87423351 None:intergenic
GTATAAGAATATGTGGAGCT+CGG 0.584815 7_2:-87423824 None:intergenic
TATACCCTCCCTATTCATTG+CGG 0.586067 7_2:-87423723 Msa1086500:CDS
CAACCCGCAATGAATAGGGA+GGG 0.665638 7_2:+87423719 None:intergenic
CCAACCCGCAATGAATAGGG+AGG 0.678708 7_2:+87423718 None:intergenic
AATCGTACCAGTCTCTACTG+GGG 0.711157 7_2:-87423358 Msa1086500:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! TGAATTTAGTAGATCTTTTT+AGG - chr7_2:87423553-87423572 Msa1086500:intron 20.0%
!!! ATTCAACATTTTGTTCATTT+GGG + chr7_2:87423743-87423762 None:intergenic 20.0%
!!! AATTCAACATTTTGTTCATT+TGG + chr7_2:87423744-87423763 None:intergenic 20.0%
! TTATTAATGGAATTCCTTGT+CGG + chr7_2:87423502-87423521 None:intergenic 25.0%
!!! ATTTAGTAGATCTTTTTAGG+AGG - chr7_2:87423556-87423575 Msa1086500:intron 25.0%
! TATTGATCCCAAAAAAAAGA+CGG + chr7_2:87423657-87423676 None:intergenic 25.0%
TTATTACCAGTATTCGATAC+TGG - chr7_2:87423360-87423379 Msa1086500:CDS 30.0%
! AATAATCCAGTATCGAATAC+TGG + chr7_2:87423369-87423388 None:intergenic 30.0%
CTTTCTGTAAAATACTCGTT+TGG + chr7_2:87423479-87423498 None:intergenic 30.0%
CAAGGAATTCCATTAATAAC+TGG - chr7_2:87423503-87423522 Msa1086500:intron 30.0%
GTTGTTCCAAAGAATCAAAA+CGG + chr7_2:87423529-87423548 None:intergenic 30.0%
AACCATCGTACTGTAAAAAT+GGG + chr7_2:87423608-87423627 None:intergenic 30.0%
! GGTTTAGCTTACGATGTATT+TGG - chr7_2:87423443-87423462 Msa1086500:intron 35.0%
TGTAAAATACTCGTTTGGAC+GGG + chr7_2:87423474-87423493 None:intergenic 35.0%
CTGTAAAATACTCGTTTGGA+CGG + chr7_2:87423475-87423494 None:intergenic 35.0%
! TATTTTACAGAAAGCCGACA+AGG - chr7_2:87423485-87423504 Msa1086500:intron 35.0%
TCAAAACGGCCAGTTATTAA+TGG + chr7_2:87423515-87423534 None:intergenic 35.0%
TCGTACTGTAAAAATGGGAT+AGG + chr7_2:87423603-87423622 None:intergenic 35.0%
!! ATCCCATTTTTACAGTACGA+TGG - chr7_2:87423603-87423622 Msa1086500:intron 35.0%
CAACCATCGTACTGTAAAAA+TGG + chr7_2:87423609-87423628 None:intergenic 35.0%
! CATTTTTACAGTACGATGGT+TGG - chr7_2:87423607-87423626 Msa1086500:intron 35.0%
! ATTCGGATTAGGTTTATCGT+TGG + chr7_2:87423697-87423716 None:intergenic 35.0%
! GTAGCTCTATAATTCGGATT+AGG + chr7_2:87423708-87423727 None:intergenic 35.0%
! TGTGTCGTAGCTCTATAATT+CGG + chr7_2:87423714-87423733 None:intergenic 35.0%
TATACCCTCCCTATTCATTG+CGG - chr7_2:87423400-87423419 Msa1086500:CDS 40.0%
TAACCAACCCGCAATGAATA+GGG + chr7_2:87423411-87423430 None:intergenic 40.0%
ATAACCAACCCGCAATGAAT+AGG + chr7_2:87423412-87423431 None:intergenic 40.0%
GTAAAATACTCGTTTGGACG+GGG + chr7_2:87423473-87423492 None:intergenic 40.0%
!!! AACTGGCCGTTTTGATTCTT+TGG - chr7_2:87423520-87423539 Msa1086500:intron 40.0%
TAGGTCCTATCTATGGTCAT+TGG + chr7_2:87423584-87423603 None:intergenic 40.0%
AATGGGATAGGTCCTATCTA+TGG + chr7_2:87423591-87423610 None:intergenic 40.0%
!!! GTACCCACCGTCTTTTTTTT+GGG - chr7_2:87423647-87423666 Msa1086500:intron 40.0%
GATCCCAAAAAAAAGACGGT+GGG + chr7_2:87423653-87423672 None:intergenic 40.0%
TGATCCCAAAAAAAAGACGG+TGG + chr7_2:87423654-87423673 None:intergenic 40.0%
TAATAAACCCCAGTAGAGAC+TGG + chr7_2:87423775-87423794 None:intergenic 40.0%
ATACCCTCCCTATTCATTGC+GGG - chr7_2:87423401-87423420 Msa1086500:CDS 45.0%
!! GGGTTGGTTATTTGTCAGCA+CGG - chr7_2:87423421-87423440 Msa1086500:CDS 45.0%
! GGTTGGTTATTTGTCAGCAC+GGG - chr7_2:87423422-87423441 Msa1086500:CDS 45.0%
AGGCTCCAATGACCATAGAT+AGG - chr7_2:87423576-87423595 Msa1086500:intron 45.0%
!!! GGTACCCACCGTCTTTTTTT+TGG - chr7_2:87423646-87423665 Msa1086500:intron 45.0%
TGAATCGTACCAGTCTCTAC+TGG - chr7_2:87423763-87423782 Msa1086500:CDS 45.0%
GAATCGTACCAGTCTCTACT+GGG - chr7_2:87423764-87423783 Msa1086500:CDS 45.0%
AATCGTACCAGTCTCTACTG+GGG - chr7_2:87423765-87423784 Msa1086500:CDS 45.0%
CAACCCGCAATGAATAGGGA+GGG + chr7_2:87423407-87423426 None:intergenic 50.0%
! GTACGATGGTTGGCTGTTCA+CGG - chr7_2:87423617-87423636 Msa1086500:intron 50.0%
TATGTGGAGCTCGGCATGTC+TGG - chr7_2:87423308-87423327 Msa1086500:CDS 55.0%
CCAACCCGCAATGAATAGGG+AGG + chr7_2:87423408-87423427 None:intergenic 55.0%
CCTCCCTATTCATTGCGGGT+TGG - chr7_2:87423405-87423424 Msa1086500:CDS 55.0%
!! GTTGGCTGTTCACGGACTAG+CGG - chr7_2:87423625-87423644 Msa1086500:intron 55.0%
! CTCGGCATGTCTGGAAGCAC+AGG - chr7_2:87423317-87423336 Msa1086500:CDS 60.0%
Chromosome Type Strat End Strand Name
chr7_2 gene 87423306 87423839 87423306 ID=Msa1086500;Name=Msa1086500
chr7_2 mRNA 87423306 87423839 87423306 ID=Msa1086500-mRNA-1;Parent=Msa1086500;Name=Msa1086500-mRNA-1;_AED=0.22;_eAED=0.22;_QI=17|0|0|1|0|0|2|0|104
chr7_2 exon 87423662 87423839 87423662 ID=Msa1086500-mRNA-1:exon:23842;Parent=Msa1086500-mRNA-1
chr7_2 exon 87423306 87423456 87423306 ID=Msa1086500-mRNA-1:exon:23841;Parent=Msa1086500-mRNA-1
chr7_2 five_prime_UTR 87423823 87423839 87423823 ID=Msa1086500-mRNA-1:five_prime_utr;Parent=Msa1086500-mRNA-1
chr7_2 CDS 87423662 87423822 87423662 ID=Msa1086500-mRNA-1:cds;Parent=Msa1086500-mRNA-1
chr7_2 CDS 87423306 87423456 87423306 ID=Msa1086500-mRNA-1:cds;Parent=Msa1086500-mRNA-1
Gene Sequence

>Msa1086500

ATGTCTGGAAGCACAGGAGAACGTTCTTTTGCTGATATTATTACCAGTATTCGATACTGGATTATTCATAGCATTACTATACCCTCCCTATTCATTGCGGGTTGGTTATTTGTCAGCACGGGTTTAGCTTACGATGTATTTGGAAGTCCCCGTCCAAACGATTCATCCAACGATAAACCTAATCCGAATTATAGAGCTACGACACAATCAAACCCAAATGAACAAAATGTTGAATTGAATCGTACCAGTCTCTACTGGGGTTTATTACTCATTTTTGTACTTGCTGTTTTATTTTCAAATTATTTCTTCAAT

Protein sequence

>Msa1086500

MSGSTGERSFADIITSIRYWIIHSITIPSLFIAGWLFVSTGLAYDVFGSPRPNDSSNDKPNPNYRATTQSNPNEQNVELNRTSLYWGLLLIFVLAVLFSNYFFN