AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0936270


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0936270 MtrunA17_Chr4g0062381 98.214 56 1 0 1 56 267 322 1.11e-32 113
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0936270 AT1G74070.1 80.357 56 11 0 1 56 258 313 4.67e-27 99.4

Find 11 sgRNAs with CRISPR-Local

Find 19 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GTAATGACAACTTTGGAATA+AGG 0.264096 6_3:+6943643 None:intergenic
TGTTATACTCACCTAAAATA+TGG 0.299921 6_3:+6943882 None:intergenic
TAATGACAACTTTGGAATAA+GGG 0.342912 6_3:+6943644 None:intergenic
AACAGGGTGGCGAAGCTTAT+AGG 0.358689 6_3:-6943706 Msa0936270:intron
ACAGTTTGTAATGACAACTT+TGG 0.444850 6_3:+6943636 None:intergenic
AGGGCTGTTGTTGCAGAAAG+AGG 0.493060 6_3:-6943676 Msa0936270:CDS
GGTTGTACAGAAGATTAGTC+AGG 0.532433 6_3:-6943934 Msa0936270:CDS
AAAGTTGTCATTACAAACTG+TGG 0.597691 6_3:-6943634 Msa0936270:CDS
CGAAGCTTATAGGAGACAAG+AGG 0.623848 6_3:-6943696 Msa0936270:CDS
GAAGCTTATAGGAGACAAGA+GGG 0.659815 6_3:-6943695 Msa0936270:CDS
TGACAACTTTGGAATAAGGG+CGG 0.673460 6_3:+6943647 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! ATACAAATGATTAATAAACA+GGG + chr6_3:6943820-6943839 None:intergenic 15.0%
!! AATACAAATGATTAATAAAC+AGG + chr6_3:6943821-6943840 None:intergenic 15.0%
!!! TATATTTTTATATAACAGGG+TGG - chr6_3:6943841-6943860 Msa0936270:intron 20.0%
! TGTTATACTCACCTAAAATA+TGG + chr6_3:6943681-6943700 None:intergenic 25.0%
!!! TAATGACAACTTTGGAATAA+GGG + chr6_3:6943919-6943938 None:intergenic 25.0%
! GATATTGTCACTGACTAAAA+TGG + chr6_3:6943717-6943736 None:intergenic 30.0%
!! GTAATGACAACTTTGGAATA+AGG + chr6_3:6943920-6943939 None:intergenic 30.0%
ACAGTTTGTAATGACAACTT+TGG + chr6_3:6943927-6943946 None:intergenic 30.0%
AAAGTTGTCATTACAAACTG+TGG - chr6_3:6943926-6943945 Msa0936270:CDS 30.0%
CTGTTTCAAACTTGTCATGT+TGG + chr6_3:6943747-6943766 None:intergenic 35.0%
! GGTTGTACAGAAGATTAGTC+AGG - chr6_3:6943626-6943645 Msa0936270:CDS 40.0%
! ACACGAGCTCTCCATATTTT+AGG - chr6_3:6943667-6943686 Msa0936270:CDS 40.0%
GAAGCTTATAGGAGACAAGA+GGG - chr6_3:6943865-6943884 Msa0936270:intron 40.0%
!! TGACAACTTTGGAATAAGGG+CGG + chr6_3:6943916-6943935 None:intergenic 40.0%
CGAAGCTTATAGGAGACAAG+AGG - chr6_3:6943864-6943883 Msa0936270:intron 45.0%
!!! TATTTATATTTTTATATAAC+AGG - chr6_3:6943837-6943856 Msa0936270:intron 5.0%
!!! ATTTATATTTTTATATAACA+GGG - chr6_3:6943838-6943857 Msa0936270:intron 5.0%
AACAGGGTGGCGAAGCTTAT+AGG - chr6_3:6943854-6943873 Msa0936270:intron 50.0%
AGGGCTGTTGTTGCAGAAAG+AGG - chr6_3:6943884-6943903 Msa0936270:intron 50.0%
Chromosome Type Strat End Strand Name
chr6_3 gene 6943621 6943961 6943621 ID=Msa0936270;Name=Msa0936270
chr6_3 mRNA 6943621 6943961 6943621 ID=Msa0936270-mRNA-1;Parent=Msa0936270;Name=Msa0936270-mRNA-1;_AED=0.48;_eAED=0.48;_QI=0|0|0|1|1|1|2|0|56
chr6_3 exon 6943894 6943961 6943894 ID=Msa0936270-mRNA-1:exon:2279;Parent=Msa0936270-mRNA-1
chr6_3 exon 6943621 6943723 6943621 ID=Msa0936270-mRNA-1:exon:2278;Parent=Msa0936270-mRNA-1
chr6_3 CDS 6943894 6943961 6943894 ID=Msa0936270-mRNA-1:cds;Parent=Msa0936270-mRNA-1
chr6_3 CDS 6943621 6943723 6943621 ID=Msa0936270-mRNA-1:cds;Parent=Msa0936270-mRNA-1
Gene Sequence

>Msa0936270

ATGGAGGTTGTACAGAAGATTAGTCAGGTAAAAACTGTACAAGAGAACACGAGCTCTCCATATTTTAGGGTGGCGAAGCTTATAGGAGACAAGAGGGCTGTTGTTGCAGAAAGAGGATTCAACCGCCCTTATTCCAAAGTTGTCATTACAAACTGTGGTGTAATACAGTAG

Protein sequence

>Msa0936270

MEVVQKISQVKTVQENTSSPYFRVAKLIGDKRAVVAERGFNRPYSKVVITNCGVIQ*