AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1269400


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1269400 MtrunA17_Chr7g0229301 97.512 201 5 0 1 201 1 201 1.37e-143 398
Msa1269400 MtrunA17_Chr6g0454441 97.512 201 5 0 1 201 1 201 1.37e-143 398
Msa1269400 MtrunA17_Chr4g0016451 97.512 201 5 0 1 201 1 201 1.37e-143 398
Msa1269400 MtrunA17_Chr6g0466281 97.512 201 5 0 1 201 1 201 1.37e-143 398
Msa1269400 MtrunA17_CPg0493311 97.512 201 5 0 1 201 1 201 1.37e-143 398
Msa1269400 MtrunA17_Chr7g0229661 84.080 201 13 1 1 201 1 182 1.89e-115 327
Msa1269400 MtrunA17_Chr4g0015291 97.436 156 4 0 1 156 1 156 3.32e-108 307
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1269400 ATCG00380.1 88.060 201 24 0 1 201 1 201 2.12e-126 355

Find 33 sgRNAs with CRISPR-Local

Find 43 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
ATCAAATAATAGATAGTAAA+TGG 0.189787 8_3:-2549654 Msa1269400:CDS
GATTGACTAATCCTTTATAT+TGG 0.284280 8_3:+2549674 None:intergenic
CTTGATCCATTCCAATATAA+AGG 0.291752 8_3:-2549685 Msa1269400:CDS
CTTAAATACGTTCGTATCGC+TGG 0.342652 8_3:-2549985 Msa1269400:CDS
ACAATTACTTGAAATGCGTT+TGG 0.359489 8_3:-2549929 Msa1269400:CDS
TTTGAAAATTAATGAATTGC+TGG 0.365999 8_3:-2549626 Msa1269400:CDS
ATGGATTGGCAATTCTTCGC+GGG 0.450528 8_3:+2549714 None:intergenic
TACCAGGACTAACTAGTAAA+CGG 0.463029 8_3:-2550128 Msa1269400:CDS
TGAGGTTTGCAACGATAACT+TGG 0.468099 8_3:+2549805 None:intergenic
ACTAATCCTTTATATTGGAA+TGG 0.475526 8_3:+2549679 None:intergenic
GTCTGTGGTTAACTAATTGA+CGG 0.477609 8_3:+2549860 None:intergenic
TCAAATAATAGATAGTAAAT+GGG 0.487910 8_3:-2549653 Msa1269400:CDS
ATAATAGATAGTAAATGGGT+TGG 0.504615 8_3:-2549649 Msa1269400:CDS
CTAAGTTCGCTTCCAACTGT+AGG 0.508663 8_3:+2550105 None:intergenic
GGATCAAGAGTCAAATGGAT+TGG 0.511159 8_3:+2549700 None:intergenic
GGAAAAGCGAAAGGTTCAAC+CGG 0.516182 8_3:-2549964 Msa1269400:CDS
TCTGTGGTTAACTAATTGAC+GGG 0.521261 8_3:+2549861 None:intergenic
GGCCGTTTACTAGTTAGTCC+TGG 0.527000 8_3:+2550126 None:intergenic
AATGGATTGGCAATTCTTCG+CGG 0.545268 8_3:+2549713 None:intergenic
TCAAGATATTATTACAGCGA+AGG 0.559737 8_3:-2549785 Msa1269400:CDS
TTCGCTGTAATAATATCTTG+AGG 0.560954 8_3:+2549787 None:intergenic
TAATTGTAGTAAAACTTGAC+CGG 0.568250 8_3:+2549945 None:intergenic
ACTAGTAAACGGCCTACAGT+TGG 0.568372 8_3:-2550117 Msa1269400:CDS
CAAGATATTATTACAGCGAA+GGG 0.569002 8_3:-2549784 Msa1269400:CDS
TTAACTAATTGACGGGCTTG+AGG 0.581554 8_3:+2549868 None:intergenic
GGAATGGATCAAGAGTCAAA+TGG 0.582974 8_3:+2549695 None:intergenic
GATTGGCAATTCTTCGCGGG+GGG 0.584547 8_3:+2549717 None:intergenic
TGGATTGGCAATTCTTCGCG+GGG 0.610754 8_3:+2549715 None:intergenic
TGTTTATGTCACGTTACAGA+GGG 0.632465 8_3:-2550185 None:intergenic
GTGTTTATGTCACGTTACAG+AGG 0.633128 8_3:-2550186 None:intergenic
CGTATCGCTGGAAAAGCGAA+AGG 0.633501 8_3:-2549973 Msa1269400:CDS
CATTAACTAAAACATGTCTG+TGG 0.663264 8_3:+2549845 None:intergenic
GGATTGGCAATTCTTCGCGG+GGG 0.681198 8_3:+2549716 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! ATCAAATAATAGATAGTAAA+TGG - chr8_3:2550123-2550142 Msa1269400:CDS 15.0%
!! TCAAATAATAGATAGTAAAT+GGG - chr8_3:2550124-2550143 Msa1269400:CDS 15.0%
!! TTTGAAAATTAATGAATTGC+TGG - chr8_3:2550151-2550170 Msa1269400:CDS 20.0%
!! CAAAAATTGCGTTTTCATTA+TGG - chr8_3:2549750-2549769 Msa1269400:CDS 25.0%
! TAATTGTAGTAAAACTTGAC+CGG + chr8_3:2549835-2549854 None:intergenic 25.0%
!!! GATAACATACTTTTTCGATT+GGG - chr8_3:2549870-2549889 Msa1269400:CDS 25.0%
! ACTAATCCTTTATATTGGAA+TGG + chr8_3:2550101-2550120 None:intergenic 25.0%
! GATTGACTAATCCTTTATAT+TGG + chr8_3:2550106-2550125 None:intergenic 25.0%
! ATAATAGATAGTAAATGGGT+TGG - chr8_3:2550128-2550147 Msa1269400:CDS 25.0%
TTTCAAAAAAATACGTCGTC+TGG - chr8_3:2549620-2549639 Msa1269400:CDS 30.0%
TTCAAAAAAATACGTCGTCT+GGG - chr8_3:2549621-2549640 Msa1269400:CDS 30.0%
ACAATTACTTGAAATGCGTT+TGG - chr8_3:2549848-2549867 Msa1269400:CDS 30.0%
!!! GGATAACATACTTTTTCGAT+TGG - chr8_3:2549869-2549888 Msa1269400:CDS 30.0%
CATTAACTAAAACATGTCTG+TGG + chr8_3:2549935-2549954 None:intergenic 30.0%
!!! CACAGACATGTTTTAGTTAA+TGG - chr8_3:2549933-2549952 Msa1269400:CDS 30.0%
TTCGCTGTAATAATATCTTG+AGG + chr8_3:2549993-2550012 None:intergenic 30.0%
TCAAGATATTATTACAGCGA+AGG - chr8_3:2549992-2550011 Msa1269400:CDS 30.0%
CAAGATATTATTACAGCGAA+GGG - chr8_3:2549993-2550012 Msa1269400:CDS 30.0%
CTTGATCCATTCCAATATAA+AGG - chr8_3:2550092-2550111 Msa1269400:CDS 30.0%
!!! CGACGTATTTTTTTGAAACG+AGG + chr8_3:2549618-2549637 None:intergenic 35.0%
TCAAAAAAATACGTCGTCTG+GGG - chr8_3:2549622-2549641 Msa1269400:CDS 35.0%
TACCAGGACTAACTAGTAAA+CGG - chr8_3:2549649-2549668 Msa1269400:CDS 35.0%
!!! CATACTTTTTCGATTGGGTA+TGG - chr8_3:2549875-2549894 Msa1269400:CDS 35.0%
TCTGTGGTTAACTAATTGAC+GGG + chr8_3:2549919-2549938 None:intergenic 35.0%
GTCTGTGGTTAACTAATTGA+CGG + chr8_3:2549920-2549939 None:intergenic 35.0%
CAAAAAAATACGTCGTCTGG+GGG - chr8_3:2549623-2549642 Msa1269400:CDS 40.0%
!!! ATTTTTTACTCGAGCGCGAT+TGG + chr8_3:2549701-2549720 None:intergenic 40.0%
CTTAAATACGTTCGTATCGC+TGG - chr8_3:2549792-2549811 Msa1269400:CDS 40.0%
!! TTAACTAATTGACGGGCTTG+AGG + chr8_3:2549912-2549931 None:intergenic 40.0%
TGAGGTTTGCAACGATAACT+TGG + chr8_3:2549975-2549994 None:intergenic 40.0%
!! AATGGATTGGCAATTCTTCG+CGG + chr8_3:2550067-2550086 None:intergenic 40.0%
GGATCAAGAGTCAAATGGAT+TGG + chr8_3:2550080-2550099 None:intergenic 40.0%
GGAATGGATCAAGAGTCAAA+TGG + chr8_3:2550085-2550104 None:intergenic 40.0%
ACTAGTAAACGGCCTACAGT+TGG - chr8_3:2549660-2549679 Msa1269400:CDS 45.0%
CTAAGTTCGCTTCCAACTGT+AGG + chr8_3:2549675-2549694 None:intergenic 45.0%
GGAAAAGCGAAAGGTTCAAC+CGG - chr8_3:2549813-2549832 Msa1269400:CDS 45.0%
!! ATGGATTGGCAATTCTTCGC+GGG + chr8_3:2550066-2550085 None:intergenic 45.0%
GGCCGTTTACTAGTTAGTCC+TGG + chr8_3:2549654-2549673 None:intergenic 50.0%
CGTATCGCTGGAAAAGCGAA+AGG - chr8_3:2549804-2549823 Msa1269400:CDS 50.0%
!! TGGATTGGCAATTCTTCGCG+GGG + chr8_3:2550065-2550084 None:intergenic 50.0%
GATTGGCAATTCTTCGCGGG+GGG + chr8_3:2550063-2550082 None:intergenic 55.0%
! GGATTGGCAATTCTTCGCGG+GGG + chr8_3:2550064-2550083 None:intergenic 55.0%
CGTCGTCTGGGGGCTTTACC+AGG - chr8_3:2549633-2549652 Msa1269400:CDS 65.0%
Chromosome Type Strat End Strand Name
chr8_3 gene 2549597 2550202 2549597 ID=Msa1269400;Name=Msa1269400
chr8_3 mRNA 2549597 2550202 2549597 ID=Msa1269400-mRNA-1;Parent=Msa1269400;Name=Msa1269400-mRNA-1;_AED=0.00;_eAED=0.00;_QI=0|-1|0|1|-1|1|1|0|201
chr8_3 exon 2549597 2550202 2549597 ID=Msa1269400-mRNA-1:exon:811;Parent=Msa1269400-mRNA-1
chr8_3 CDS 2549597 2550202 2549597 ID=Msa1269400-mRNA-1:cds;Parent=Msa1269400-mRNA-1
Gene Sequence

>Msa1269400

ATGTCACGTTACAGAGGGCCTCGTTTCAAAAAAATACGTCGTCTGGGGGCTTTACCAGGACTAACTAGTAAACGGCCTACAGTTGGAAGCGAACTTAGAAACCAATCGCGCTCGAGTAAAAAATCTCAATATCGTATTCGTTTAGAAGAAAAACAAAAATTGCGTTTTCATTATGGTCTTACAGAACGACAATTGCTTAAATACGTTCGTATCGCTGGAAAAGCGAAAGGTTCAACCGGTCAAGTTTTACTACAATTACTTGAAATGCGTTTGGATAACATACTTTTTCGATTGGGTATGGCTTCGACTATTCCTCAAGCCCGTCAATTAGTTAACCACAGACATGTTTTAGTTAATGGTCGTATAGTAGATATACCAAGTTATCGTTGCAAACCTCAAGATATTATTACAGCGAAGGGTGAACAAAAATCTAGAACTCTGATTCAAAATTCTCTTGAATCAGCCCCCCGCGAAGAATTGCCAATCCATTTGACTCTTGATCCATTCCAATATAAAGGATTAGTCAATCAAATAATAGATAGTAAATGGGTTGGTTTGAAAATTAATGAATTGCTGGTTGTAGAATATTATTCTCGTCAGACTTAA

Protein sequence

>Msa1269400

MSRYRGPRFKKIRRLGALPGLTSKRPTVGSELRNQSRSSKKSQYRIRLEEKQKLRFHYGLTERQLLKYVRIAGKAKGSTGQVLLQLLEMRLDNILFRLGMASTIPQARQLVNHRHVLVNGRIVDIPSYRCKPQDIITAKGEQKSRTLIQNSLESAPREELPIHLTLDPFQYKGLVNQIIDSKWVGLKINELLVVEYYSRQT*