AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0190400


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0190400 MtrunA17_Chr2g0279971 91.720 157 10 1 1 157 1 154 1.22e-95 273
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0190400 AT5G64480.1 37.398 123 71 2 40 156 61 183 1.27e-18 78.6
Msa0190400 AT5G64480.2 37.398 123 71 2 40 156 89 211 2.18e-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_1:-5914501 None:intergenic
CTTTGCACGTGCGTTGATTA+TGG 0.282351 2_1:-5914247 None:intergenic
GAATGGGTTTGTTAAGGAAT+TGG 0.313532 2_1:+5914401 Msa0190400:CDS
ATATTCTTCAACCAATTCTT+TGG 0.317932 2_1:-5914457 None:intergenic
TTTGGTGAATGGGTTTGTTA+AGG 0.351101 2_1:+5914395 Msa0190400:CDS
TAAACTCAAATGGAAGGAAA+TGG 0.366100 2_1:+5914353 Msa0190400:CDS
AATGGGTTTGTTAAGGAATT+GGG 0.376515 2_1:+5914402 Msa0190400:CDS
TGGGTTGGTGGAGAGTGTGA+TGG 0.408702 2_1:-5914136 None:intergenic
TGAAGATGAGAAATGGGTTT+TGG 0.409174 2_1:+5914377 Msa0190400:CDS
AAATGGGTGAAGATGAGAAA+TGG 0.422016 2_1:+5914370 Msa0190400:CDS
AAGAAGAAGGTAAACTCAAA+TGG 0.438592 2_1:+5914343 Msa0190400:CDS
GGGTTGGTGGAGAGTGTGAT+GGG 0.453615 2_1:-5914135 None:intergenic
AAACTCAAATGGAAGGAAAT+GGG 0.483778 2_1:+5914354 Msa0190400:CDS
AATGGGTGAAGATGAGAAAT+GGG 0.493388 2_1:+5914371 Msa0190400:CDS
AAACCAATTATACTATCAAA+AGG 0.495506 2_1:-5914534 None:intergenic
GGAGAGATTGTGAAGAACAT+TGG 0.506943 2_1:-5914114 None:intergenic
TTAGAACTCAATGAAGAAGA+AGG 0.536771 2_1:+5914330 Msa0190400:CDS
AGAAGGTAAACTCAAATGGA+AGG 0.589477 2_1:+5914347 Msa0190400:CDS
ATACTATCAAAAGGAAACAA+CGG 0.652071 2_1:-5914525 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! TTTCCTTTTGATAGTATAAT+TGG + chr2_1:5914531-5914550 Msa0190400:CDS 20.0%
!! AAACCAATTATACTATCAAA+AGG - chr2_1:5914537-5914556 None:intergenic 20.0%
! ATATTCTTCAACCAATTCTT+TGG - chr2_1:5914460-5914479 None:intergenic 25.0%
!! TAAGAAATTTGAGAAGCTTT+TGG - chr2_1:5914504-5914523 None:intergenic 25.0%
! ATACTATCAAAAGGAAACAA+CGG - chr2_1:5914528-5914547 None:intergenic 25.0%
TTAGAACTCAATGAAGAAGA+AGG + chr2_1:5914330-5914349 Msa0190400:CDS 30.0%
AAGAAGAAGGTAAACTCAAA+TGG + chr2_1:5914343-5914362 Msa0190400:CDS 30.0%
TAAACTCAAATGGAAGGAAA+TGG + chr2_1:5914353-5914372 Msa0190400:CDS 30.0%
AAACTCAAATGGAAGGAAAT+GGG + chr2_1:5914354-5914373 Msa0190400:CDS 30.0%
!! AATGGGTTTGTTAAGGAATT+GGG + chr2_1:5914402-5914421 Msa0190400:CDS 30.0%
TGAAAAAGCTACCAAAGAAT+TGG + chr2_1:5914446-5914465 Msa0190400:CDS 30.0%
! TGTTGGTGCATGAGATTTTT+GGG - chr2_1:5914173-5914192 None:intergenic 35.0%
! TTGTTGGTGCATGAGATTTT+TGG - chr2_1:5914174-5914193 None:intergenic 35.0%
! GTTGTTGTTGTTGTTGTTGT+TGG - chr2_1:5914190-5914209 None:intergenic 35.0%
AGAAGGTAAACTCAAATGGA+AGG + chr2_1:5914347-5914366 Msa0190400:CDS 35.0%
AAATGGGTGAAGATGAGAAA+TGG + chr2_1:5914370-5914389 Msa0190400:CDS 35.0%
AATGGGTGAAGATGAGAAAT+GGG + chr2_1:5914371-5914390 Msa0190400:CDS 35.0%
!! TGAAGATGAGAAATGGGTTT+TGG + chr2_1:5914377-5914396 Msa0190400:CDS 35.0%
!! AGAAATGGGTTTTGGTGAAT+GGG + chr2_1:5914385-5914404 Msa0190400:CDS 35.0%
!! TTTGGTGAATGGGTTTGTTA+AGG + chr2_1:5914395-5914414 Msa0190400:CDS 35.0%
!! GAATGGGTTTGTTAAGGAAT+TGG + chr2_1:5914401-5914420 Msa0190400:CDS 35.0%
!!! TTGGTAGCTTTTTCAGACAA+AGG - chr2_1:5914441-5914460 None:intergenic 35.0%
! GAAATTTGAGAAGCTTTTGG+AGG - chr2_1:5914501-5914520 None:intergenic 35.0%
GGAGAGATTGTGAAGAACAT+TGG - chr2_1:5914117-5914136 None:intergenic 40.0%
!! TTTTTGGGGGTTTGGGTTTT+GGG - chr2_1:5914158-5914177 None:intergenic 40.0%
!! ATTTTTGGGGGTTTGGGTTT+TGG - chr2_1:5914159-5914178 None:intergenic 40.0%
!! CATGAGATTTTTGGGGGTTT+GGG - chr2_1:5914165-5914184 None:intergenic 40.0%
!! TTGGTGCATGAGATTTTTGG+GGG - chr2_1:5914171-5914190 None:intergenic 40.0%
! GTTGGTGCATGAGATTTTTG+GGG - chr2_1:5914172-5914191 None:intergenic 40.0%
!! GAGAAATGGGTTTTGGTGAA+TGG + chr2_1:5914384-5914403 Msa0190400:CDS 40.0%
!! GCATGAGATTTTTGGGGGTT+TGG - chr2_1:5914166-5914185 None:intergenic 45.0%
!! CTTTGCACGTGCGTTGATTA+TGG - chr2_1:5914250-5914269 None:intergenic 45.0%
!! GGGTTGGTGGAGAGTGTGAT+GGG - chr2_1:5914138-5914157 None:intergenic 55.0%
!! TGGGTTGGTGGAGAGTGTGA+TGG - chr2_1:5914139-5914158 None:intergenic 55.0%
!!! GGGTTTGGGTTTTGGGTTGG+TGG - chr2_1:5914151-5914170 None:intergenic 55.0%
!!! TGGGGGTTTGGGTTTTGGGT+TGG - chr2_1:5914154-5914173 None:intergenic 55.0%
Chromosome Type Strat End Strand Name
chr2_1 gene 5914090 5914563 5914090 ID=Msa0190400;Name=Msa0190400
chr2_1 mRNA 5914090 5914563 5914090 ID=Msa0190400-mRNA-1;Parent=Msa0190400;Name=Msa0190400-mRNA-1;_AED=0.00;_eAED=0.00;_QI=0|-1|0|1|-1|1|1|0|157
chr2_1 exon 5914090 5914563 5914090 ID=Msa0190400-mRNA-1:exon:2653;Parent=Msa0190400-mRNA-1
chr2_1 CDS 5914090 5914563 5914090 ID=Msa0190400-mRNA-1:cds;Parent=Msa0190400-mRNA-1
Gene Sequence

>Msa0190400

ATGGCTCTTCGAATTCAACACATTCCAATGTTCTTCACAATCTCTCCCATCACACTCTCCACCAACCCAAAACCCAAACCCCCAAAAATCTCATGCACCAACAACAACAACAACAACAACGATGTATCACTCGCATCAGAGTTTGCAGAAAAAGCATCCATAATCAACGCACGTGCAAAGCAAGCAGAAGAAGCAATGAGAAAGAGCAGAAAGATTGTTTTCAAAGAACTCTGCGAATATTTAGAACTCAATGAAGAAGAAGGTAAACTCAAATGGAAGGAAATGGGTGAAGATGAGAAATGGGTTTTGGTGAATGGGTTTGTTAAGGAATTGGGTCAATTTTTTCATCCTTTGTCTGAAAAAGCTACCAAAGAATTGGTTGAAGAATATTTGCTACAAGAGAATCAGCCTCCAAAAGCTTCTCAAATTTCTTATCCGTTGTTTCCTTTTGATAGTATAATTGGTTTTCCATAG

Protein sequence

>Msa0190400

MALRIQHIPMFFTISPITLSTNPKPKPPKISCTNNNNNNNDVSLASEFAEKASIINARAKQAEEAMRKSRKIVFKELCEYLELNEEEGKLKWKEMGEDEKWVLVNGFVKELGQFFHPLSEKATKELVEEYLLQENQPPKASQISYPLFPFDSIIGFP*