AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0975220


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0975220 MtrunA17_Chr6g0454081 95.455 44 1 1 1 44 1 43 6.87e-24 87.8
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0975220 AT3G29280.2 80.000 30 6 0 15 44 24 53 7.98e-11 54.7
Msa0975220 AT3G29280.1 80.000 30 6 0 15 44 24 53 8.05e-11 54.7

Find 12 sgRNAs with CRISPR-Local

Find 29 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TTCATTCAGTTTCTTTCTCT+TGG 0.254546 6_4:-8913564 Msa0975220:intron
CTCCCTCATTCTACTTGTTA+TGG 0.271409 6_4:-8913898 Msa0975220:CDS
TCTACTTGTTATGGTCTTCA+TGG 0.293845 6_4:-8913889 Msa0975220:CDS
CTTCCAAACGGTTCAATCTC+AGG 0.427063 6_4:-8913934 Msa0975220:CDS
TTGGCTTTGAACTCATGATT+AGG 0.440913 6_4:+8913531 None:intergenic
TGTTATGGTCTTCATGGCAT+TGG 0.465210 6_4:-8913883 Msa0975220:intron
TGTCCTGAGATTGAACCGTT+TGG 0.473850 6_4:+8913931 None:intergenic
TCAATAGCATTACTTCCAAA+CGG 0.548406 6_4:-8913946 Msa0975220:CDS
CAAGAAGAAACAACAATGGA+AGG 0.568539 6_4:-8913976 Msa0975220:CDS
AGACCATAACAAGTAGAATG+AGG 0.576147 6_4:+8913895 None:intergenic
GACCATAACAAGTAGAATGA+GGG 0.584413 6_4:+8913896 None:intergenic
ACAACAAGAAGAAACAACAA+TGG 0.624163 6_4:-8913980 Msa0975220:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AATGAAAAATGAAAATTAGA+GGG + chr6_4:8913591-8913610 None:intergenic 15.0%
!! AAATGAAAAATGAAAATTAG+AGG + chr6_4:8913592-8913611 None:intergenic 15.0%
!!! ATGCAATTTTAAGTTAAAAA+AGG - chr6_4:8913937-8913956 Msa0975220:CDS 15.0%
!!! TTTTTCTTTTGAGAAAGTTA+AGG - chr6_4:8913823-8913842 Msa0975220:intron 20.0%
!!! ATTTTGTTGAAAATCTGAAA+TGG - chr6_4:8913871-8913890 Msa0975220:intron 20.0%
!!! TTTTGTTGAAAATCTGAAAT+GGG - chr6_4:8913872-8913891 Msa0975220:intron 20.0%
!!! AAAAGGTTTTTTTTTTGTGA+TGG - chr6_4:8913954-8913973 Msa0975220:CDS 20.0%
!!! AAAGGTTTTTTTTTTGTGAT+GGG - chr6_4:8913955-8913974 Msa0975220:CDS 20.0%
!!! GCAAAAAAATGATCTTTTTT+AGG - chr6_4:8913993-8914012 Msa0975220:CDS 20.0%
!! TAAAACACAAATTAGGTTTA+GGG + chr6_4:8914031-8914050 None:intergenic 20.0%
! TTTCATCTGAATGTAATAGA+AGG + chr6_4:8913615-8913634 None:intergenic 25.0%
!!! AAGATCATTTTTTTGCAACA+GGG + chr6_4:8913989-8914008 None:intergenic 25.0%
!!! AAAGATCATTTTTTTGCAAC+AGG + chr6_4:8913990-8914009 None:intergenic 25.0%
! CTAAAACACAAATTAGGTTT+AGG + chr6_4:8914032-8914051 None:intergenic 25.0%
! ATGAAGCTAAAACACAAATT+AGG + chr6_4:8914038-8914057 None:intergenic 25.0%
ACAACAAGAAGAAACAACAA+TGG - chr6_4:8913642-8913661 Msa0975220:intron 30.0%
TCAATAGCATTACTTCCAAA+CGG - chr6_4:8913676-8913695 Msa0975220:intron 30.0%
TCATGCTTTGACATTGTTTA+AGG - chr6_4:8913788-8913807 Msa0975220:intron 30.0%
TTCATTCAGTTTCTTTCTCT+TGG - chr6_4:8914058-8914077 Msa0975220:intron 30.0%
CAAGAAGAAACAACAATGGA+AGG - chr6_4:8913646-8913665 Msa0975220:intron 35.0%
GACCATAACAAGTAGAATGA+GGG + chr6_4:8913729-8913748 None:intergenic 35.0%
AGACCATAACAAGTAGAATG+AGG + chr6_4:8913730-8913749 None:intergenic 35.0%
!! TCTACTTGTTATGGTCTTCA+TGG - chr6_4:8913733-8913752 Msa0975220:intron 35.0%
!! TTGGCTTTGAACTCATGATT+AGG + chr6_4:8914094-8914113 None:intergenic 35.0%
GAGTGTGATTGAATGAAGTG+AGG + chr6_4:8913542-8913561 None:intergenic 40.0%
! CTCCCTCATTCTACTTGTTA+TGG - chr6_4:8913724-8913743 Msa0975220:intron 40.0%
TGTTATGGTCTTCATGGCAT+TGG - chr6_4:8913739-8913758 Msa0975220:intron 40.0%
CTTCCAAACGGTTCAATCTC+AGG - chr6_4:8913688-8913707 Msa0975220:intron 45.0%
TGTCCTGAGATTGAACCGTT+TGG + chr6_4:8913694-8913713 None:intergenic 45.0%
Chromosome Type Strat End Strand Name
chr6_4 gene 8913521 8914123 8913521 ID=Msa0975220;Name=Msa0975220
chr6_4 mRNA 8913521 8914123 8913521 ID=Msa0975220-mRNA-1;Parent=Msa0975220;Name=Msa0975220-mRNA-1;_AED=0.30;_eAED=0.30;_QI=0|0|0|0.25|1|1|4|0|66
chr6_4 exon 8914120 8914123 8914120 ID=Msa0975220-mRNA-1:exon:3215;Parent=Msa0975220-mRNA-1
chr6_4 exon 8913884 8914015 8913884 ID=Msa0975220-mRNA-1:exon:3214;Parent=Msa0975220-mRNA-1
chr6_4 exon 8913797 8913804 8913797 ID=Msa0975220-mRNA-1:exon:3213;Parent=Msa0975220-mRNA-1
chr6_4 exon 8913521 8913577 8913521 ID=Msa0975220-mRNA-1:exon:3212;Parent=Msa0975220-mRNA-1
chr6_4 CDS 8914120 8914123 8914120 ID=Msa0975220-mRNA-1:cds;Parent=Msa0975220-mRNA-1
chr6_4 CDS 8913884 8914015 8913884 ID=Msa0975220-mRNA-1:cds;Parent=Msa0975220-mRNA-1
chr6_4 CDS 8913797 8913804 8913797 ID=Msa0975220-mRNA-1:cds;Parent=Msa0975220-mRNA-1
chr6_4 CDS 8913521 8913577 8913521 ID=Msa0975220-mRNA-1:cds;Parent=Msa0975220-mRNA-1
Gene Sequence

>Msa0975220

ATGGATGAAACAGAACAACAACAAGAAGAAACAACAATGGAAGGAGTAGCATCAATAGCATTACTTCCAAACGGTTCAATCTCAGGACACTTTATTCATCTCCCTCATTCTACTTGTTATGGTCTTCATGGCATTGTTAAGGTTTTTCTTTCTCTTGGTCTCATTCTGCCTAATCATGAGTTCAAAGCCAACCTCTGCTAA

Protein sequence

>Msa0975220

MDETEQQQEETTMEGVASIALLPNGSISGHFIHLPHSTCYGLHGIVKVFLSLGLILPNHEFKANLC*