AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1436300

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1436300 MtrunA17_Chr6g0452671 76.923 156 17 3 2 156 65 202 1.75e-77 229
Msa1436300 MtrunA17_Chr6g0452661 38.342 193 80 6 2 169 64 242 6.79e-26 99.4
Msa1436300 MtrunA17_Chr5g0439111 36.957 184 75 7 4 161 66 234 1.57e-21 87.8
Msa1436300 MtrunA17_Chr4g0055441 42.400 125 45 4 2 126 57 154 1.69e-19 80.5
Msa1436300 MtrunA17_Chr6g0452691 45.918 98 43 2 3 97 65 155 6.37e-18 77.0
Msa1436300 MtrunA17_Chr6g0449311 51.685 89 38 2 2 88 28 113 4.67e-14 65.9
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 27 sgRNAs with CRISPR-Local

Find 40 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
ATTCCATTGTGAAGAATTAT+TGG 0.152750 tig0027907:-29812 Msa1436300:CDS
AAACTTTGAAACTAATTCTA+TGG 0.254760 tig0027907:-29914 Msa1436300:CDS
CAAAATTTGTACTACCATTA+AGG 0.279065 tig0027907:+29788 Msa1436300:intergenic
GAAGAATTATTGGACCTTAA+TGG 0.283903 tig0027907:-29802 Msa1436300:CDS
GATGTTATTATGATGTATTA+TGG 0.406805 tig0027907:-30141 Msa1436300:CDS
ACATCAAGACATCCACCAAC+AGG 0.415425 tig0027907:+30159 Msa1436300:intergenic
ATTCTTACTAGATCATTGTA+AGG 0.440710 tig0027907:-30079 Msa1436300:CDS
GGGATGTCATAATAAGAATT+CGG 0.449186 tig0027907:+29973 Msa1436300:intergenic
ACAATGATCAATTGATAAGT+AGG 0.452504 tig0027907:+30023 Msa1436300:intergenic
GGAACTCGAGTGCTACTAGA+AGG 0.478886 tig0027907:+29994 Msa1436300:intergenic
TCCTTGTGTTACCATCAAGT+TGG 0.488291 tig0027907:+29837 Msa1436300:intergenic
CGTGCTCAATTCCCTGTTGG+TGG 0.544713 tig0027907:-30171 Msa1436300:CDS
GTTATACAATTGATCGGTGG+TGG 0.566006 tig0027907:-29880 Msa1436300:CDS
CTAATTCTATGGATGCAACA+AGG 0.571579 tig0027907:-29903 Msa1436300:CDS
GGTCCAATAATTCTTCACAA+TGG 0.586783 tig0027907:+29809 Msa1436300:intergenic
CAATGATCAATTGATAAGTA+GGG 0.590328 tig0027907:+30024 Msa1436300:intergenic
ACAAGGGTTATACAATTGAT+CGG 0.617732 tig0027907:-29886 Msa1436300:CDS
TAATTCTATGGATGCAACAA+GGG 0.625530 tig0027907:-29902 Msa1436300:CDS
ATGCGTGCTCAATTCCCTGT+TGG 0.627603 tig0027907:-30174 Msa1436300:CDS
GATCGGTGGTGGCAATGCAA+TGG 0.634656 tig0027907:-29869 Msa1436300:CDS
TCGAGTGCTACTAGAAGGAG+CGG 0.637892 tig0027907:+29999 Msa1436300:intergenic
GGGTTAATAGTAACATTACG+AGG 0.645055 tig0027907:+29952 Msa1436300:intergenic
CATCAAGACATCCACCAACA+GGG 0.653135 tig0027907:+30160 Msa1436300:intergenic
TGCTGATAAAGTAGTAACTG+AGG 0.661688 tig0027907:-29737 Msa1436300:intron
GGTTAATAGTAACATTACGA+GGG 0.671173 tig0027907:+29953 Msa1436300:intergenic
TCCAACTTGATGGTAACACA+AGG 0.676070 tig0027907:-29838 Msa1436300:CDS
AGGGTTATACAATTGATCGG+TGG 0.726517 tig0027907:-29883 Msa1436300:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! ATTTTAATTATTATTATTTT+TGG - tig0027907:30048-30067 Msa1436300:CDS 0.0%
!!! TTTTAATTATTATTATTTTT+GGG - tig0027907:30049-30068 Msa1436300:CDS 0.0%
!!! TAGTACAAATTTTGATTTAA+GGG - tig0027907:29965-29984 Msa1436300:CDS 15.0%
!! TAAAGATATGTAATTAATGA+AGG + tig0027907:30167-30186 Msa1436300:intergenic 15.0%
!! TACATATCTTTAATCAATAT+AGG - tig0027907:30175-30194 Msa1436300:CDS 15.0%
!! GATGTTATTATGATGTATTA+TGG - tig0027907:29603-29622 Msa1436300:intron 20.0%
!!! ATTAGTTTCAAAGTTTTGTT+TGG + tig0027907:29826-29845 Msa1436300:intergenic 20.0%
!!! AAACTTTGAAACTAATTCTA+TGG - tig0027907:29830-29849 Msa1436300:CDS 20.0%
!!! GTAGTACAAATTTTGATTTA+AGG - tig0027907:29964-29983 Msa1436300:CDS 20.0%
! ATTCTTACTAGATCATTGTA+AGG - tig0027907:29665-29684 Msa1436300:intron 25.0%
! CAATGATCAATTGATAAGTA+GGG + tig0027907:29723-29742 Msa1436300:intergenic 25.0%
! ACAATGATCAATTGATAAGT+AGG + tig0027907:29724-29743 Msa1436300:intergenic 25.0%
!!! AGTTTTGTTTGGTATCAATT+GGG + tig0027907:29815-29834 Msa1436300:intergenic 25.0%
!!! AAGTTTTGTTTGGTATCAAT+TGG + tig0027907:29816-29835 Msa1436300:intergenic 25.0%
! ATTCCATTGTGAAGAATTAT+TGG - tig0027907:29932-29951 Msa1436300:CDS 25.0%
! CAAAATTTGTACTACCATTA+AGG + tig0027907:29959-29978 Msa1436300:intergenic 25.0%
!!! AAATTTTGATTTAAGGGAAG+AGG - tig0027907:29971-29990 Msa1436300:CDS 25.0%
!!! CAAGATTTTGTTGTTGCAAA+GGG + tig0027907:29698-29717 Msa1436300:intergenic 30.0%
!!! TCAAGATTTTGTTGTTGCAA+AGG + tig0027907:29699-29718 Msa1436300:intergenic 30.0%
GGGATGTCATAATAAGAATT+CGG + tig0027907:29774-29793 Msa1436300:intergenic 30.0%
GGTTAATAGTAACATTACGA+GGG + tig0027907:29794-29813 Msa1436300:intergenic 30.0%
TAATTCTATGGATGCAACAA+GGG - tig0027907:29842-29861 Msa1436300:CDS 30.0%
ACAAGGGTTATACAATTGAT+CGG - tig0027907:29858-29877 Msa1436300:CDS 30.0%
GAAGAATTATTGGACCTTAA+TGG - tig0027907:29942-29961 Msa1436300:CDS 30.0%
GGGTTAATAGTAACATTACG+AGG + tig0027907:29795-29814 Msa1436300:intergenic 35.0%
CTAATTCTATGGATGCAACA+AGG - tig0027907:29841-29860 Msa1436300:CDS 35.0%
GGAAGAAAAATCCAACTTGA+TGG - tig0027907:29896-29915 Msa1436300:CDS 35.0%
GGTCCAATAATTCTTCACAA+TGG + tig0027907:29938-29957 Msa1436300:intergenic 35.0%
TGCTGATAAAGTAGTAACTG+AGG - tig0027907:30007-30026 Msa1436300:CDS 35.0%
AGGGTTATACAATTGATCGG+TGG - tig0027907:29861-29880 Msa1436300:CDS 40.0%
GTTATACAATTGATCGGTGG+TGG - tig0027907:29864-29883 Msa1436300:CDS 40.0%
! TCCAACTTGATGGTAACACA+AGG - tig0027907:29906-29925 Msa1436300:CDS 40.0%
TCCTTGTGTTACCATCAAGT+TGG + tig0027907:29910-29929 Msa1436300:intergenic 40.0%
CATCAAGACATCCACCAACA+GGG + tig0027907:29587-29606 Msa1436300:intergenic 45.0%
ACATCAAGACATCCACCAAC+AGG + tig0027907:29588-29607 Msa1436300:intergenic 45.0%
ATGCGTGCTCAATTCCCTGT+TGG - tig0027907:29570-29589 Msa1436300:intron 50.0%
! TCGAGTGCTACTAGAAGGAG+CGG + tig0027907:29748-29767 Msa1436300:intergenic 50.0%
! GGAACTCGAGTGCTACTAGA+AGG + tig0027907:29753-29772 Msa1436300:intergenic 50.0%
CGTGCTCAATTCCCTGTTGG+TGG - tig0027907:29573-29592 Msa1436300:intron 55.0%
! GATCGGTGGTGGCAATGCAA+TGG - tig0027907:29875-29894 Msa1436300:CDS 55.0%
Chromosome Type Strat End Strand Name
tig0027907 gene 29531 30235 29531 ID=Msa1436300;Name=Msa1436300
tig0027907 mRNA 29531 30235 29531 ID=Msa1436300-mRNA-1;Parent=Msa1436300;Name=Msa1436300-mRNA-1;_AED=0.19;_eAED=0.19;_QI=0|0|0|0.5|1|1|2|0|178
tig0027907 exon 29738 30235 29738 ID=Msa1436300-mRNA-1:exon:10176;Parent=Msa1436300-mRNA-1
tig0027907 exon 29531 29569 29531 ID=Msa1436300-mRNA-1:exon:10175;Parent=Msa1436300-mRNA-1
tig0027907 CDS 29738 30235 29738 ID=Msa1436300-mRNA-1:cds;Parent=Msa1436300-mRNA-1
tig0027907 CDS 29531 29569 29531 ID=Msa1436300-mRNA-1:cds;Parent=Msa1436300-mRNA-1
Gene Sequence

>Msa1436300

ATGAATGAAGCAATGAAATCAATTATTTTTGAGTCAGATATGCGTGCTCAATTCCCTGTTGGTGGATGTCTTGATGTTATTATGATGTATTATGGTATGATCAAACACTCTGAGCAAGAACTAAATTCTGTTAAATTCTTACTAGATCATTGTAAGGTAAATTACCCTTTGCAACAACAAAATCTTGAACCCTACTTATCAATTGATCATTGTTCCGCTCCTTCTAGTAGCACTCGAGTTCCGAATTCTTATTATGACATCCCTCGTAATGTTACTATTAACCCAATTGATACCAAACAAAACTTTGAAACTAATTCTATGGATGCAACAAGGGTTATACAATTGATCGGTGGTGGCAATGCAATGGAAGAAAAATCCAACTTGATGGTAACACAAGGATTATTCCATTGTGAAGAATTATTGGACCTTAATGGTAGTACAAATTTTGATTTAAGGGAAGAGGAGAAAATATCAGATGCTGATAAAGTAGTAACTGAGGTTTATAATTGTATTCAATATTCTGCATTTGTTTCATGA
Protein sequence

>Msa1436300

MNEAMKSIIFESDMRAQFPVGGCLDVIMMYYGMIKHSEQELNSVKFLLDHCKVNYPLQQQNLEPYLSIDHCSAPSSSTRVPNSYYDIPRNVTINPIDTKQNFETNSMDATRVIQLIGGGNAMEEKSNLMVTQGLFHCEELLDLNGSTNFDLREEEKISDADKVVTEVYNCIQYSAFVS*