AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0271970


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0271970 MtrunA17_Chr2g0279971 91.139 158 10 1 1 158 1 154 1.93e-95 272
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0271970 AT5G64480.1 37.398 123 71 2 41 157 61 183 1.28e-18 78.6
Msa0271970 AT5G64480.2 37.398 123 71 2 41 157 89 211 2.25e-18 78.6

Find 19 sgRNAs with CRISPR-Local

Find 36 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TAAGAAATTTGAGAAGCTTT+TGG 0.274466 2_3:+3464872 None:intergenic
CTTTGCACGTGCGTTGATTA+TGG 0.282351 2_3:+3465126 None:intergenic
GAATGGGTTTGTTAAGGAAT+TGG 0.313532 2_3:-3464972 Msa0271970:CDS
ATATTCTTCAACCAATTCTT+TGG 0.317932 2_3:+3464916 None:intergenic
TTTGGTGAATGGGTTTGTTA+AGG 0.351101 2_3:-3464978 Msa0271970:CDS
TAAACTCAAATGGAAGGAAA+TGG 0.366100 2_3:-3465020 Msa0271970:CDS
AATGGGTTTGTTAAGGAATT+GGG 0.376515 2_3:-3464971 Msa0271970:CDS
TGGGTTGGTGGAGAGTGTGA+TGG 0.408702 2_3:+3465240 None:intergenic
TGAAGATGAGAAATGGGTTT+TGG 0.409174 2_3:-3464996 Msa0271970:CDS
AAATGGGTGAAGATGAGAAA+TGG 0.422016 2_3:-3465003 Msa0271970:CDS
AAGAAGAAGGTAAACTCAAA+TGG 0.438592 2_3:-3465030 Msa0271970:CDS
GGGTTGGTGGAGAGTGTGAT+GGG 0.453615 2_3:+3465241 None:intergenic
AAACTCAAATGGAAGGAAAT+GGG 0.483778 2_3:-3465019 Msa0271970:CDS
AATGGGTGAAGATGAGAAAT+GGG 0.493388 2_3:-3465002 Msa0271970:CDS
AAACCAATTATACTATCAAA+AGG 0.495506 2_3:+3464839 None:intergenic
GGAGAGATTGTGAAGAACAT+TGG 0.506943 2_3:+3465262 None:intergenic
TTAGAACTCAATGAAGAAGA+AGG 0.536771 2_3:-3465043 Msa0271970:CDS
AGAAGGTAAACTCAAATGGA+AGG 0.589477 2_3:-3465026 Msa0271970:CDS
ATACTATCAAAAGGAAACAA+TGG 0.596338 2_3:+3464848 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! TTTCCTTTTGATAGTATAAT+TGG - chr2_3:3465276-3465295 Msa0271970:CDS 20.0%
!! AAACCAATTATACTATCAAA+AGG + chr2_3:3465282-3465301 None:intergenic 20.0%
! ATATTCTTCAACCAATTCTT+TGG + chr2_3:3465205-3465224 None:intergenic 25.0%
!! TAAGAAATTTGAGAAGCTTT+TGG + chr2_3:3465249-3465268 None:intergenic 25.0%
! ATACTATCAAAAGGAAACAA+TGG + chr2_3:3465273-3465292 None:intergenic 25.0%
TTAGAACTCAATGAAGAAGA+AGG - chr2_3:3465075-3465094 Msa0271970:CDS 30.0%
AAGAAGAAGGTAAACTCAAA+TGG - chr2_3:3465088-3465107 Msa0271970:CDS 30.0%
TAAACTCAAATGGAAGGAAA+TGG - chr2_3:3465098-3465117 Msa0271970:CDS 30.0%
AAACTCAAATGGAAGGAAAT+GGG - chr2_3:3465099-3465118 Msa0271970:CDS 30.0%
!! AATGGGTTTGTTAAGGAATT+GGG - chr2_3:3465147-3465166 Msa0271970:CDS 30.0%
TGAAAAAGCTACCAAAGAAT+TGG - chr2_3:3465191-3465210 Msa0271970:CDS 30.0%
! TGTTGGTGCATGAGATTTTT+GGG + chr2_3:3464915-3464934 None:intergenic 35.0%
! TTGTTGGTGCATGAGATTTT+TGG + chr2_3:3464916-3464935 None:intergenic 35.0%
! GTTGTTGTTGTTGTTGTTGT+TGG + chr2_3:3464932-3464951 None:intergenic 35.0%
AGAAGGTAAACTCAAATGGA+AGG - chr2_3:3465092-3465111 Msa0271970:CDS 35.0%
AAATGGGTGAAGATGAGAAA+TGG - chr2_3:3465115-3465134 Msa0271970:CDS 35.0%
AATGGGTGAAGATGAGAAAT+GGG - chr2_3:3465116-3465135 Msa0271970:CDS 35.0%
!! TGAAGATGAGAAATGGGTTT+TGG - chr2_3:3465122-3465141 Msa0271970:CDS 35.0%
!! AGAAATGGGTTTTGGTGAAT+GGG - chr2_3:3465130-3465149 Msa0271970:CDS 35.0%
!! TTTGGTGAATGGGTTTGTTA+AGG - chr2_3:3465140-3465159 Msa0271970:CDS 35.0%
!! GAATGGGTTTGTTAAGGAAT+TGG - chr2_3:3465146-3465165 Msa0271970:CDS 35.0%
!!! TTGGTAGCTTTTTCAGACAA+AGG + chr2_3:3465186-3465205 None:intergenic 35.0%
! GAAATTTGAGAAGCTTTTGG+AGG + chr2_3:3465246-3465265 None:intergenic 35.0%
GGAGAGATTGTGAAGAACAT+TGG + chr2_3:3464859-3464878 None:intergenic 40.0%
!! TTTTTGGGGGTTTGGGTTTT+GGG + chr2_3:3464900-3464919 None:intergenic 40.0%
!! ATTTTTGGGGGTTTGGGTTT+TGG + chr2_3:3464901-3464920 None:intergenic 40.0%
!! CATGAGATTTTTGGGGGTTT+GGG + chr2_3:3464907-3464926 None:intergenic 40.0%
!! TTGGTGCATGAGATTTTTGG+GGG + chr2_3:3464913-3464932 None:intergenic 40.0%
! GTTGGTGCATGAGATTTTTG+GGG + chr2_3:3464914-3464933 None:intergenic 40.0%
!! GAGAAATGGGTTTTGGTGAA+TGG - chr2_3:3465129-3465148 Msa0271970:CDS 40.0%
!! GCATGAGATTTTTGGGGGTT+TGG + chr2_3:3464908-3464927 None:intergenic 45.0%
!! CTTTGCACGTGCGTTGATTA+TGG + chr2_3:3464995-3465014 None:intergenic 45.0%
!! GGGTTGGTGGAGAGTGTGAT+GGG + chr2_3:3464880-3464899 None:intergenic 55.0%
!! TGGGTTGGTGGAGAGTGTGA+TGG + chr2_3:3464881-3464900 None:intergenic 55.0%
!!! GGGTTTGGGTTTTGGGTTGG+TGG + chr2_3:3464893-3464912 None:intergenic 55.0%
!!! TGGGGGTTTGGGTTTTGGGT+TGG + chr2_3:3464896-3464915 None:intergenic 55.0%
Chromosome Type Strat End Strand Name
chr2_3 gene 3464832 3465308 3464832 ID=Msa0271970;Name=Msa0271970
chr2_3 mRNA 3464832 3465308 3464832 ID=Msa0271970-mRNA-1;Parent=Msa0271970;Name=Msa0271970-mRNA-1;_AED=0.00;_eAED=0.00;_QI=0|-1|0|1|-1|1|1|0|158
chr2_3 exon 3464832 3465308 3464832 ID=Msa0271970-mRNA-1:exon:1730;Parent=Msa0271970-mRNA-1
chr2_3 CDS 3464832 3465308 3464832 ID=Msa0271970-mRNA-1:cds;Parent=Msa0271970-mRNA-1
Gene Sequence

>Msa0271970

ATGGCTCTTCGAATTCAACACATTCCAATGTTCTTCACAATCTCTCCCATCACACTCTCCACCAACCCAAAACCCAAACCCCCAAAAATCTCATGCACCAACAACAACAACAACAACAACAACGATGTATCACTCGCATCAGAGTTTGCAGAAAAAGCATCCATAATCAACGCACGTGCAAAGCAAGCAGAAGAAGCAATGAGAAAGAGCAGAAAGATTGTTTTCAAAGAACTCTGCGAATATTTAGAACTCAATGAAGAAGAAGGTAAACTCAAATGGAAGGAAATGGGTGAAGATGAGAAATGGGTTTTGGTGAATGGGTTTGTTAAGGAATTGGGTCAATTTTTTCATCCTTTGTCTGAAAAAGCTACCAAAGAATTGGTTGAAGAATATTTGCTACAAGAGAATCAGCCTCCAAAAGCTTCTCAAATTTCTTATCCATTGTTTCCTTTTGATAGTATAATTGGTTTTCCATAG

Protein sequence

>Msa0271970

MALRIQHIPMFFTISPITLSTNPKPKPPKISCTNNNNNNNNDVSLASEFAEKASIINARAKQAEEAMRKSRKIVFKELCEYLELNEEEGKLKWKEMGEDEKWVLVNGFVKELGQFFHPLSEKATKELVEEYLLQENQPPKASQISYPLFPFDSIIGFP*