AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0146020


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 15 sgRNAs with CRISPR-Local

Find 72 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
ATGCATCTCTATTTATTGTT+TGG 0.317320 1_4:+5739178 Msa0146020:CDS
GGAAGATTGATTTGCCTGAT+TGG 0.385899 1_4:+5739199 Msa0146020:CDS
AAGTTCCTGTAAATCATCTT+CGG 0.390419 1_4:-5739302 None:intergenic
GAAATCTGGGCACATCAAAA+AGG 0.398298 1_4:+5738513 None:intergenic
CACAAGAAAAGAAGCCAATC+AGG 0.406069 1_4:-5739213 None:intergenic
CAAGCTGCAAACTCAAATAA+TGG 0.416111 1_4:+5738546 Msa0146020:CDS
AGTTCCTGTAAATCATCTTC+GGG 0.445174 1_4:-5739301 None:intergenic
TGTAACGCTGTGTATAGAAT+CGG 0.514058 1_4:-5739261 None:intergenic
TGTAAATCATCTTCGGGACA+AGG 0.544700 1_4:-5739295 None:intergenic
CGCTGTGTATAGAATCGGAC+TGG 0.547628 1_4:-5739256 None:intergenic
TGTGTTACAGTATCAATGAC+AGG 0.550272 1_4:+5739232 Msa0146020:CDS
AATCACCAAACCTTCAGAGT+TGG 0.552065 1_4:-5738573 None:intergenic
TAATGGCGAACCAACTCTGA+AGG 0.587421 1_4:+5738563 Msa0146020:CDS
GTAAATCATCTTCGGGACAA+GGG 0.622918 1_4:-5739294 None:intergenic
TAATTTATGGAAGTTAACAA+CGG 0.656179 1_4:+5738869 Msa0146020:intron

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! AATTTGTGATTGAAAATTTT+AGG + chr1_4:5738976-5738995 Msa0146020:intron 15.0%
!!! TTGAATTTATTGATTTCTTA+AGG + chr1_4:5739058-5739077 Msa0146020:intron 15.0%
!!! AATTTGTGATTGAAAATTTT+AGG + chr1_4:5738976-5738995 Msa0146020:intron 15.0%
!!! TTGAATTTATTGATTTCTTA+AGG + chr1_4:5739058-5739077 Msa0146020:intron 15.0%
!! TAATGAAAGAGTCAATTTAA+GGG - chr1_4:5738640-5738659 None:intergenic 20.0%
!! ATAATGAAAGAGTCAATTTA+AGG - chr1_4:5738641-5738660 None:intergenic 20.0%
!!! TTTTGCCTTTTTTTTATTTG+TGG + chr1_4:5738721-5738740 Msa0146020:intron 20.0%
!!! TTGTTTAGCTTTGTAATTTA+TGG + chr1_4:5738856-5738875 Msa0146020:intron 20.0%
!! TAATTTATGGAAGTTAACAA+CGG + chr1_4:5738869-5738888 Msa0146020:intron 20.0%
!!! ATTTTAGGACTAATTGAATT+TGG + chr1_4:5738991-5739010 Msa0146020:intron 20.0%
!! AAATTCAATCTAAATCAAAC+AGG - chr1_4:5739046-5739065 None:intergenic 20.0%
!! TAATGAAAGAGTCAATTTAA+GGG - chr1_4:5738640-5738659 None:intergenic 20.0%
!! ATAATGAAAGAGTCAATTTA+AGG - chr1_4:5738641-5738660 None:intergenic 20.0%
!!! TTTTGCCTTTTTTTTATTTG+TGG + chr1_4:5738721-5738740 Msa0146020:intron 20.0%
!!! TTGTTTAGCTTTGTAATTTA+TGG + chr1_4:5738856-5738875 Msa0146020:intron 20.0%
!! TAATTTATGGAAGTTAACAA+CGG + chr1_4:5738869-5738888 Msa0146020:intron 20.0%
!!! ATTTTAGGACTAATTGAATT+TGG + chr1_4:5738991-5739010 Msa0146020:intron 20.0%
!! AAATTCAATCTAAATCAAAC+AGG - chr1_4:5739046-5739065 None:intergenic 20.0%
! AAGAATTGCTGAAAATAAAG+TGG - chr1_4:5738606-5738625 None:intergenic 25.0%
! ATGAGTGACGTATAAAAATA+TGG - chr1_4:5738695-5738714 None:intergenic 25.0%
! TGCATCCACAAATAAAAAAA+AGG - chr1_4:5738729-5738748 None:intergenic 25.0%
!!! TTGTCTGTTGTTTTACATTT+AGG + chr1_4:5738780-5738799 Msa0146020:intron 25.0%
!!! TTCTTAAGGTATTGTAGATT+AGG + chr1_4:5739072-5739091 Msa0146020:intron 25.0%
! TGATATATGTTAACTGAGAA+AGG + chr1_4:5739122-5739141 Msa0146020:intron 25.0%
! ATGCATCTCTATTTATTGTT+TGG + chr1_4:5739178-5739197 Msa0146020:CDS 25.0%
! AAGAATTGCTGAAAATAAAG+TGG - chr1_4:5738606-5738625 None:intergenic 25.0%
! ATGAGTGACGTATAAAAATA+TGG - chr1_4:5738695-5738714 None:intergenic 25.0%
! TGCATCCACAAATAAAAAAA+AGG - chr1_4:5738729-5738748 None:intergenic 25.0%
!!! TTGTCTGTTGTTTTACATTT+AGG + chr1_4:5738780-5738799 Msa0146020:intron 25.0%
!!! TTCTTAAGGTATTGTAGATT+AGG + chr1_4:5739072-5739091 Msa0146020:intron 25.0%
! TGATATATGTTAACTGAGAA+AGG + chr1_4:5739122-5739141 Msa0146020:intron 25.0%
! ATGCATCTCTATTTATTGTT+TGG + chr1_4:5739178-5739197 Msa0146020:CDS 25.0%
!!! TTTTTTATTTGTGGATGCAG+TGG + chr1_4:5738730-5738749 Msa0146020:intron 30.0%
TTGTAGTTATTCTGTCCATT+CGG + chr1_4:5738823-5738842 Msa0146020:intron 30.0%
GAACACATCAATATACTTAC+AGG + chr1_4:5738930-5738949 Msa0146020:intron 30.0%
!!! TTTTTTATTTGTGGATGCAG+TGG + chr1_4:5738730-5738749 Msa0146020:intron 30.0%
TTGTAGTTATTCTGTCCATT+CGG + chr1_4:5738823-5738842 Msa0146020:intron 30.0%
GAACACATCAATATACTTAC+AGG + chr1_4:5738930-5738949 Msa0146020:intron 30.0%
CAAGCTGCAAACTCAAATAA+TGG + chr1_4:5738546-5738565 Msa0146020:CDS 35.0%
AACAAAGTTGCATAACCGAA+TGG - chr1_4:5738841-5738860 None:intergenic 35.0%
ATTGATGTGTTCGATACAGT+AGG - chr1_4:5738922-5738941 None:intergenic 35.0%
TCACAAATTCAAATCAGTCC+AGG - chr1_4:5738965-5738984 None:intergenic 35.0%
TGTGTTACAGTATCAATGAC+AGG + chr1_4:5739232-5739251 Msa0146020:CDS 35.0%
TGTAACGCTGTGTATAGAAT+CGG - chr1_4:5739264-5739283 None:intergenic 35.0%
CAAGCTGCAAACTCAAATAA+TGG + chr1_4:5738546-5738565 Msa0146020:CDS 35.0%
AACAAAGTTGCATAACCGAA+TGG - chr1_4:5738841-5738860 None:intergenic 35.0%
ATTGATGTGTTCGATACAGT+AGG - chr1_4:5738922-5738941 None:intergenic 35.0%
TCACAAATTCAAATCAGTCC+AGG - chr1_4:5738965-5738984 None:intergenic 35.0%
TGTGTTACAGTATCAATGAC+AGG + chr1_4:5739232-5739251 Msa0146020:CDS 35.0%
TGTAACGCTGTGTATAGAAT+CGG - chr1_4:5739264-5739283 None:intergenic 35.0%
AATCACCAAACCTTCAGAGT+TGG - chr1_4:5738576-5738595 None:intergenic 40.0%
!! GGAAGATTGATTTGCCTGAT+TGG + chr1_4:5739199-5739218 Msa0146020:CDS 40.0%
CACAAGAAAAGAAGCCAATC+AGG - chr1_4:5739216-5739235 None:intergenic 40.0%
AATCACCAAACCTTCAGAGT+TGG - chr1_4:5738576-5738595 None:intergenic 40.0%
!! GGAAGATTGATTTGCCTGAT+TGG + chr1_4:5739199-5739218 Msa0146020:CDS 40.0%
CACAAGAAAAGAAGCCAATC+AGG - chr1_4:5739216-5739235 None:intergenic 40.0%
TAATGGCGAACCAACTCTGA+AGG + chr1_4:5738563-5738582 Msa0146020:CDS 45.0%
ACTTACAGGCAAACATGACC+TGG + chr1_4:5738944-5738963 Msa0146020:intron 45.0%
TAATGGCGAACCAACTCTGA+AGG + chr1_4:5738563-5738582 Msa0146020:CDS 45.0%
ACTTACAGGCAAACATGACC+TGG + chr1_4:5738944-5738963 Msa0146020:intron 45.0%
! GCGAACCAACTCTGAAGGTT+TGG + chr1_4:5738568-5738587 Msa0146020:intron 50.0%
TTTGTGGATGCAGTGGCAGA+TGG + chr1_4:5738737-5738756 Msa0146020:intron 50.0%
TTGTGGATGCAGTGGCAGAT+GGG + chr1_4:5738738-5738757 Msa0146020:intron 50.0%
CGCTGTGTATAGAATCGGAC+TGG - chr1_4:5739259-5739278 None:intergenic 50.0%
TTCCCTTGTCCCGAAGATGA+GGG + chr1_4:5739292-5739311 Msa0146020:CDS 50.0%
! GCGAACCAACTCTGAAGGTT+TGG + chr1_4:5738568-5738587 Msa0146020:intron 50.0%
TTTGTGGATGCAGTGGCAGA+TGG + chr1_4:5738737-5738756 Msa0146020:intron 50.0%
TTGTGGATGCAGTGGCAGAT+GGG + chr1_4:5738738-5738757 Msa0146020:intron 50.0%
CGCTGTGTATAGAATCGGAC+TGG - chr1_4:5739259-5739278 None:intergenic 50.0%
!! ATGCAGTGGCAGATGGGTTG+AGG + chr1_4:5738744-5738763 Msa0146020:intron 55.0%
CTTCCCTTGTCCCGAAGATG+AGG + chr1_4:5739291-5739310 Msa0146020:CDS 55.0%
!! ATGCAGTGGCAGATGGGTTG+AGG + chr1_4:5738744-5738763 Msa0146020:intron 55.0%
Chromosome Type Strat End Strand Name
chr1_4 gene 5738520 5739311 5738520 ID=Msa0146020;Name=Msa0146020
chr1_4 mRNA 5738520 5739311 5738520 ID=Msa0146020-mRNA-1;Parent=Msa0146020;Name=Msa0146020-mRNA-1;_AED=0.42;_eAED=0.82;_QI=17|0|0.33|1|0|0|3|0|65
chr1_4 exon 5738520 5738584 5738520 ID=Msa0146020-mRNA-1:exon:2429;Parent=Msa0146020-mRNA-1
chr1_4 exon 5738882 5738890 5738882 ID=Msa0146020-mRNA-1:exon:2430;Parent=Msa0146020-mRNA-1
chr1_4 exon 5739171 5739311 5739171 ID=Msa0146020-mRNA-1:exon:2431;Parent=Msa0146020-mRNA-1
chr1_4 five_prime_UTR 5738520 5738536 5738520 ID=Msa0146020-mRNA-1:five_prime_utr;Parent=Msa0146020-mRNA-1
chr1_4 CDS 5738537 5738584 5738537 ID=Msa0146020-mRNA-1:cds;Parent=Msa0146020-mRNA-1
chr1_4 CDS 5738882 5738890 5738882 ID=Msa0146020-mRNA-1:cds;Parent=Msa0146020-mRNA-1
chr1_4 CDS 5739171 5739311 5739171 ID=Msa0146020-mRNA-1:cds;Parent=Msa0146020-mRNA-1
Gene Sequence

>Msa0146020

ATGTCAAAGCAAGCTGCAAACTCAAATAATGGCGAACCAACTCTGAAGTTAACAACGAATGAAAATGCATCTCTATTTATTGTTTGGAAGATTGATTTGCCTGATTGGCTTCTTTTCTTGTGTTACAGTATCAATGACAGGTCCAGTCCGATTCTATACACAGCGTTACACAACATGCTTCCCTTGTCCCGAAGATGA

Protein sequence

>Msa0146020

MSKQAANSNNGEPTLKLTTNENASLFIVWKIDLPDWLLFLCYSINDRSSPILYTALHNMLPLSRR*