AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0311130


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0311130 MtrunA17_Chr2g0279971 91.083 157 11 1 1 157 1 154 3.01e-94 269
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0311130 AT5G64480.1 37.398 123 71 2 40 156 61 183 1.21e-18 78.6
Msa0311130 AT5G64480.2 37.398 123 71 2 40 156 89 211 2.18e-18 78.6

Find 18 sgRNAs with CRISPR-Local

Find 35 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TAAGAAATTTGAGAAGCTTT+TGG 0.274466 2_4:-6023702 None:intergenic
CTTTGCACGTGCGTTGATTA+TGG 0.282351 2_4:-6023448 None:intergenic
GAATGGGTTTGTTAAGGAAT+TGG 0.313532 2_4:+6023602 Msa0311130:CDS
ATATTCTTCAACCAATTCTT+TGG 0.317932 2_4:-6023658 None:intergenic
TTTGGTGAATGGGTTTGTTA+AGG 0.351101 2_4:+6023596 Msa0311130:CDS
TAAACTCAAATGGAAGGAAA+TGG 0.366100 2_4:+6023554 Msa0311130:CDS
AATGGGTTTGTTAAGGAATT+GGG 0.376515 2_4:+6023603 Msa0311130:CDS
TGGGTTGGTGGAGAGTGTGA+TGG 0.408702 2_4:-6023337 None:intergenic
TGAAGATGAGAAATGGGTTT+TGG 0.409174 2_4:+6023578 Msa0311130:CDS
AAATGGGTGAAGATGAGAAA+TGG 0.422016 2_4:+6023571 Msa0311130:CDS
AAGAAGAAGGTAAACTCAAA+TGG 0.438592 2_4:+6023544 Msa0311130:CDS
GGGTTGGTGGAGAGTGTGAT+GGG 0.453615 2_4:-6023336 None:intergenic
AAACTCAAATGGAAGGAAAT+GGG 0.483778 2_4:+6023555 Msa0311130:CDS
AATGGGTGAAGATGAGAAAT+GGG 0.493388 2_4:+6023572 Msa0311130:CDS
AAACCAATTATACTATCAAA+AGG 0.495506 2_4:-6023735 None:intergenic
TTAGAACTCAATGAAGAAGA+AGG 0.536771 2_4:+6023531 Msa0311130:CDS
AGAAGGTAAACTCAAATGGA+AGG 0.589477 2_4:+6023548 Msa0311130:CDS
ATACTATCAAAAGGAAACAA+CGG 0.652071 2_4:-6023726 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! TTTCCTTTTGATAGTATAAT+TGG + chr2_4:6023732-6023751 Msa0311130:CDS 20.0%
!! AAACCAATTATACTATCAAA+AGG - chr2_4:6023738-6023757 None:intergenic 20.0%
! ATATTCTTCAACCAATTCTT+TGG - chr2_4:6023661-6023680 None:intergenic 25.0%
!! TAAGAAATTTGAGAAGCTTT+TGG - chr2_4:6023705-6023724 None:intergenic 25.0%
! ATACTATCAAAAGGAAACAA+CGG - chr2_4:6023729-6023748 None:intergenic 25.0%
TTAGAACTCAATGAAGAAGA+AGG + chr2_4:6023531-6023550 Msa0311130:CDS 30.0%
AAGAAGAAGGTAAACTCAAA+TGG + chr2_4:6023544-6023563 Msa0311130:CDS 30.0%
TAAACTCAAATGGAAGGAAA+TGG + chr2_4:6023554-6023573 Msa0311130:CDS 30.0%
AAACTCAAATGGAAGGAAAT+GGG + chr2_4:6023555-6023574 Msa0311130:CDS 30.0%
!! AATGGGTTTGTTAAGGAATT+GGG + chr2_4:6023603-6023622 Msa0311130:CDS 30.0%
TGAAAAAGCTACCAAAGAAT+TGG + chr2_4:6023647-6023666 Msa0311130:CDS 30.0%
! TGTTGGTGCATGAGATTTTT+GGG - chr2_4:6023374-6023393 None:intergenic 35.0%
! TTGTTGGTGCATGAGATTTT+TGG - chr2_4:6023375-6023394 None:intergenic 35.0%
! GTTGTTGTTGTTGTTGTTGT+TGG - chr2_4:6023391-6023410 None:intergenic 35.0%
AGAAGGTAAACTCAAATGGA+AGG + chr2_4:6023548-6023567 Msa0311130:CDS 35.0%
AAATGGGTGAAGATGAGAAA+TGG + chr2_4:6023571-6023590 Msa0311130:CDS 35.0%
AATGGGTGAAGATGAGAAAT+GGG + chr2_4:6023572-6023591 Msa0311130:CDS 35.0%
!! TGAAGATGAGAAATGGGTTT+TGG + chr2_4:6023578-6023597 Msa0311130:CDS 35.0%
!! AGAAATGGGTTTTGGTGAAT+GGG + chr2_4:6023586-6023605 Msa0311130:CDS 35.0%
!! TTTGGTGAATGGGTTTGTTA+AGG + chr2_4:6023596-6023615 Msa0311130:CDS 35.0%
!! GAATGGGTTTGTTAAGGAAT+TGG + chr2_4:6023602-6023621 Msa0311130:CDS 35.0%
!!! TTGGTAGCTTTTTCAGACAA+AGG - chr2_4:6023642-6023661 None:intergenic 35.0%
! GAAATTTGAGAAGCTTTTGG+AGG - chr2_4:6023702-6023721 None:intergenic 35.0%
!! TTTTTGGGGGTTTGGGTTTT+GGG - chr2_4:6023359-6023378 None:intergenic 40.0%
!! ATTTTTGGGGGTTTGGGTTT+TGG - chr2_4:6023360-6023379 None:intergenic 40.0%
!! CATGAGATTTTTGGGGGTTT+GGG - chr2_4:6023366-6023385 None:intergenic 40.0%
!! TTGGTGCATGAGATTTTTGG+GGG - chr2_4:6023372-6023391 None:intergenic 40.0%
! GTTGGTGCATGAGATTTTTG+GGG - chr2_4:6023373-6023392 None:intergenic 40.0%
!! GAGAAATGGGTTTTGGTGAA+TGG + chr2_4:6023585-6023604 Msa0311130:CDS 40.0%
!! GCATGAGATTTTTGGGGGTT+TGG - chr2_4:6023367-6023386 None:intergenic 45.0%
!! CTTTGCACGTGCGTTGATTA+TGG - chr2_4:6023451-6023470 None:intergenic 45.0%
!! GGGTTGGTGGAGAGTGTGAT+GGG - chr2_4:6023339-6023358 None:intergenic 55.0%
!! TGGGTTGGTGGAGAGTGTGA+TGG - chr2_4:6023340-6023359 None:intergenic 55.0%
!!! GGGTTTGGGTTTTGGGTTGG+TGG - chr2_4:6023352-6023371 None:intergenic 55.0%
!!! TGGGGGTTTGGGTTTTGGGT+TGG - chr2_4:6023355-6023374 None:intergenic 55.0%
Chromosome Type Strat End Strand Name
chr2_4 gene 6023291 6023764 6023291 ID=Msa0311130;Name=Msa0311130
chr2_4 mRNA 6023291 6023764 6023291 ID=Msa0311130-mRNA-1;Parent=Msa0311130;Name=Msa0311130-mRNA-1;_AED=0.00;_eAED=0.00;_QI=0|-1|0|1|-1|1|1|0|157
chr2_4 exon 6023291 6023764 6023291 ID=Msa0311130-mRNA-1:exon:2271;Parent=Msa0311130-mRNA-1
chr2_4 CDS 6023291 6023764 6023291 ID=Msa0311130-mRNA-1:cds;Parent=Msa0311130-mRNA-1
Gene Sequence

>Msa0311130

ATGGCTCTTCGAATTCAACACATTCTAATGTTCTTCACAATCTCTCCCATCACACTCTCCACCAACCCAAAACCCAAACCCCCAAAAATCTCATGCACCAACAACAACAACAACAACAACGATGTATCACTCGCATCAGAGTTTGCAGAAAAAGCATCCATAATCAACGCACGTGCAAAGCAAGCAGAAGAAGCAATGAGAAAGAGCAGAAAGATTGTTTTCAAAGAACTCTGCGAATATTTAGAACTCAATGAAGAAGAAGGTAAACTCAAATGGAAGGAAATGGGTGAAGATGAGAAATGGGTTTTGGTGAATGGGTTTGTTAAGGAATTGGGTCAATTTTTTCATCCTTTGTCTGAAAAAGCTACCAAAGAATTGGTTGAAGAATATTTGCTACAAGAGAATCAGCCTCCAAAAGCTTCTCAAATTTCTTATCCGTTGTTTCCTTTTGATAGTATAATTGGTTTTCCATAG

Protein sequence

>Msa0311130

MALRIQHILMFFTISPITLSTNPKPKPPKISCTNNNNNNNDVSLASEFAEKASIINARAKQAEEAMRKSRKIVFKELCEYLELNEEEGKLKWKEMGEDEKWVLVNGFVKELGQFFHPLSEKATKELVEEYLLQENQPPKASQISYPLFPFDSIIGFP*