AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0582830


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0582830 MtrunA17_Chr4g0015681 96.667 60 2 0 1 60 1 60 7.64e-35 113
Msa0582830 MtrunA17_CPg0492901 96.667 60 2 0 1 60 1 60 7.64e-35 113
Msa0582830 MtrunA17_Chr4g0016771 96.667 60 2 0 1 60 1 60 7.64e-35 113
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0582830 ATCG00070.1 76.667 60 14 0 1 60 1 60 3.76e-26 92.0
Msa0582830 ATCG00080.1 97.222 36 1 0 62 97 1 36 2.92e-19 73.9

Find 6 sgRNAs with CRISPR-Local

Find 30 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TATGCTTAATATCTTTAGCT+TGG 0.440922 4_2:-1254995 Msa0582830:CDS
ACTGGCATAAAATCTACAAT+TGG 0.453871 4_2:+1254892 None:intergenic
AATGATCCAGGACGTAATCC+TGG 0.474800 4_2:-1254345 Msa0582830:CDS
GGATTCCTATCTAATGATCC+AGG 0.536202 4_2:-1254357 Msa0582830:CDS
TCACGTCCAGGATTACGTCC+TGG 0.548081 4_2:+1254339 None:intergenic
TACGTCCTGGATCATTAGAT+AGG 0.581605 4_2:+1254352 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! ATTCCAAATATTAAAATTTT+TGG - chr4_2:1254621-1254640 Msa0582830:intron 10.0%
!!! TATCCAAAAATTTTAATATT+TGG + chr4_2:1254627-1254646 None:intergenic 10.0%
!! ATTTCAAAAAAAAAAAACTT+AGG + chr4_2:1254778-1254797 None:intergenic 10.0%
!!! AATTTTAATATTTGGAATCA+AGG + chr4_2:1254619-1254638 None:intergenic 15.0%
!!! CGTTTTTTTTTTAATTATCT+TGG - chr4_2:1254873-1254892 Msa0582830:CDS 15.0%
!! GAAAAAACTACTTGAATAAA+GGG + chr4_2:1254378-1254397 None:intergenic 20.0%
!! AGAAAAAACTACTTGAATAA+AGG + chr4_2:1254379-1254398 None:intergenic 20.0%
!!! TTATTCAAGTAGTTTTTTCT+TGG - chr4_2:1254379-1254398 Msa0582830:CDS 20.0%
!! TGAAAATTCTATTATTCGAT+TGG - chr4_2:1254665-1254684 Msa0582830:intron 20.0%
!!! TGTGGATATGAAAAAAATTT+TGG - chr4_2:1254716-1254735 Msa0582830:intron 20.0%
!! TCTTATAAACTTAGTATCAA+AGG - chr4_2:1254807-1254826 Msa0582830:intron 20.0%
!!! TTTTTCTCTTAGCTTTTGTT+TGG - chr4_2:1254471-1254490 Msa0582830:intron 25.0%
!!! TTTGTTTCTCTTTTCATCTT+CGG - chr4_2:1254948-1254967 Msa0582830:CDS 25.0%
! AATTGGATTCAAAAAAGCGT+AGG + chr4_2:1254420-1254439 None:intergenic 30.0%
ACTGGCATAAAATCTACAAT+TGG + chr4_2:1254437-1254456 None:intergenic 30.0%
!! AAAAAGAGTAAGGGTATTAC+TGG + chr4_2:1254455-1254474 None:intergenic 30.0%
GCTAAGAGAAAAAAGAGTAA+GGG + chr4_2:1254464-1254483 None:intergenic 30.0%
AGCTAAGAGAAAAAAGAGTA+AGG + chr4_2:1254465-1254484 None:intergenic 30.0%
!! AATCAAGATCTAGGTATTGG+TGG + chr4_2:1254697-1254716 None:intergenic 35.0%
CACAATCAAGATCTAGGTAT+TGG + chr4_2:1254700-1254719 None:intergenic 35.0%
CAATACCTAGATCTTGATTG+TGG - chr4_2:1254698-1254717 Msa0582830:intron 35.0%
CATATCCACAATCAAGATCT+AGG + chr4_2:1254706-1254725 None:intergenic 35.0%
GAGAATCTATTCTCTTTCTC+TGG - chr4_2:1254850-1254869 Msa0582830:CDS 35.0%
! TTCAAAAAAGCGTAGGCTTC+AGG + chr4_2:1254413-1254432 None:intergenic 40.0%
GGATTCCTATCTAATGATCC+AGG - chr4_2:1254969-1254988 Msa0582830:CDS 40.0%
TACGTCCTGGATCATTAGAT+AGG + chr4_2:1254977-1254996 None:intergenic 40.0%
!! CAAGATCTAGGTATTGGTGG+TGG + chr4_2:1254694-1254713 None:intergenic 45.0%
AATGATCCAGGACGTAATCC+TGG - chr4_2:1254981-1255000 Msa0582830:CDS 45.0%
!!! AATAAATTCTTAATTTTTTT+CGG + chr4_2:1254542-1254561 None:intergenic 5.0%
TCACGTCCAGGATTACGTCC+TGG + chr4_2:1254990-1255009 None:intergenic 55.0%
Chromosome Type Strat End Strand Name
chr4_2 gene 1254332 1255016 1254332 ID=Msa0582830;Name=Msa0582830
chr4_2 mRNA 1254332 1255016 1254332 ID=Msa0582830-mRNA-1;Parent=Msa0582830;Name=Msa0582830-mRNA-1;_AED=0.46;_eAED=0.46;_QI=0|0|0|1|0|0|2|0|97
chr4_2 exon 1254842 1255016 1254842 ID=Msa0582830-mRNA-1:exon:301;Parent=Msa0582830-mRNA-1
chr4_2 exon 1254332 1254450 1254332 ID=Msa0582830-mRNA-1:exon:300;Parent=Msa0582830-mRNA-1
chr4_2 CDS 1254842 1255016 1254842 ID=Msa0582830-mRNA-1:cds;Parent=Msa0582830-mRNA-1
chr4_2 CDS 1254332 1254450 1254332 ID=Msa0582830-mRNA-1:cds;Parent=Msa0582830-mRNA-1
Gene Sequence

>Msa0582830

ATGCTTAATATCTTTAGCTTGGTCTGTATTTGTATTGACTCTGCCCTTTATTCAAGTAGTTTTTTCTTGGCAAAATTACCTGAAGCCTACGCTTTTTTGAATCCAATTGTAGATTTTATGCCAGTAATACCCTTACTCTTTTTTCTCTTAGCTTTTGTTTGGCAAGCTGCTGTAAATTTTGTAATGCTTACTCTAAAACTATTTGTTTACACGATAGTGATATTCTTTGTTTCTCTTTTCATCTTCGGATTCCTATCTAATGATCCAGGACGTAATCCTGGACGTGAAGAATAA

Protein sequence

>Msa0582830

MLNIFSLVCICIDSALYSSSFFLAKLPEAYAFLNPIVDFMPVIPLLFFLLAFVWQAAVNFVMLTLKLFVYTIVIFFVSLFIFGFLSNDPGRNPGREE*