AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0933100


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 9 sgRNAs with CRISPR-Local

Find 114 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CAGAGGTGGAAGAGCATTGT+TGG 0.392371 6_3:-1617436 Msa0933100:CDS
AAGAGCATTGTTGGTTTCAG+TGG 0.499187 6_3:-1617427 Msa0933100:CDS
AAGAACATTGTTGATTTCAG+TGG 0.510674 6_3:-1616443 Msa0933100:CDS
TCTCGTCAAAACCGTGGAAG+AGG 0.517503 6_3:-1617736 Msa0933100:intron
GAGAGAGAGTGAATCAGAAG+AGG 0.523266 6_3:+1617793 None:intergenic
AGCATTGTTGGTTTCAGTGG+AGG 0.538384 6_3:-1617424 Msa0933100:CDS
AAATCAAATATTGAAATCAA+CGG 0.594348 6_3:-1617904 None:intergenic
TTCCTCTCTCGTCAAAACCG+TGG 0.622333 6_3:-1617742 Msa0933100:CDS
AAGAATCCGAACCTCTTCCA+CGG 0.634242 6_3:+1617725 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AATCAATTTACCTTTATATT+GGG + chr6_3:1617412-1617431 None:intergenic 15.0%
!! AAATCAATTTACCTTTATAT+TGG + chr6_3:1617413-1617432 None:intergenic 15.0%
!! AATAAGCTGAAAAAAATTTA+TGG - chr6_3:1617552-1617571 Msa0933100:intron 15.0%
!! AATCAATTTACCTTTATATT+GGG + chr6_3:1617412-1617431 None:intergenic 15.0%
!! AAATCAATTTACCTTTATAT+TGG + chr6_3:1617413-1617432 None:intergenic 15.0%
!! AATAAGCTGAAAAAAATTTA+TGG - chr6_3:1617552-1617571 Msa0933100:intron 15.0%
!!! ATTTTGTTGAATGTTAGTTT+GGG - chr6_3:1616917-1616936 Msa0933100:intron 20.0%
!!! ATTTTGTTGAATGTTAGTTT+GGG - chr6_3:1616917-1616936 Msa0933100:intron 20.0%
!! GATTTTGTTGAATGTTAGTT+TGG - chr6_3:1616916-1616935 Msa0933100:intron 25.0%
!! AAATTTTGTGTTTGAATGCT+AGG - chr6_3:1616952-1616971 Msa0933100:intron 25.0%
!! AATTTTGTGTTTGAATGCTA+GGG - chr6_3:1616953-1616972 Msa0933100:intron 25.0%
! ATAAGCTGAAAACAACTTAT+TGG - chr6_3:1617048-1617067 Msa0933100:intron 25.0%
!! AATTTTCTGTGTTCAGTTTT+AGG - chr6_3:1617123-1617142 Msa0933100:intron 25.0%
!!! TAAGCTATTTCTATTGTGAA+AGG - chr6_3:1617223-1617242 Msa0933100:intron 25.0%
!! AGTTATATGTTGTTTGCATA+AGG - chr6_3:1617439-1617458 Msa0933100:intron 25.0%
! ATGGTTATGATTTCTATCTT+TGG - chr6_3:1617689-1617708 Msa0933100:intron 25.0%
!! GATTTTGTTGAATGTTAGTT+TGG - chr6_3:1616916-1616935 Msa0933100:intron 25.0%
!! AAATTTTGTGTTTGAATGCT+AGG - chr6_3:1616952-1616971 Msa0933100:intron 25.0%
!! AATTTTGTGTTTGAATGCTA+GGG - chr6_3:1616953-1616972 Msa0933100:intron 25.0%
! ATAAGCTGAAAACAACTTAT+TGG - chr6_3:1617048-1617067 Msa0933100:intron 25.0%
!! AATTTTCTGTGTTCAGTTTT+AGG - chr6_3:1617123-1617142 Msa0933100:intron 25.0%
!!! TAAGCTATTTCTATTGTGAA+AGG - chr6_3:1617223-1617242 Msa0933100:intron 25.0%
!! AGTTATATGTTGTTTGCATA+AGG - chr6_3:1617439-1617458 Msa0933100:intron 25.0%
! ATGGTTATGATTTCTATCTT+TGG - chr6_3:1617689-1617708 Msa0933100:intron 25.0%
!!! TTTTTTTGTGTTTGATGCAG+AGG - chr6_3:1616843-1616862 Msa0933100:intron 30.0%
TTGAGTTTATCCATTAGCAT+AGG + chr6_3:1617627-1617646 None:intergenic 30.0%
!! TTTCTATCTTTGGTGTTTCA+AGG - chr6_3:1617699-1617718 Msa0933100:intron 30.0%
!!! TTTTTTTGTGTTTGATGCAG+AGG - chr6_3:1616843-1616862 Msa0933100:intron 30.0%
!! AAGAACATTGTTGATTTCAG+TGG - chr6_3:1617853-1617872 Msa0933100:CDS 30.0%
!!! TTTTTTTGTGTTTGATGCAG+AGG - chr6_3:1616843-1616862 Msa0933100:intron 30.0%
TTGAGTTTATCCATTAGCAT+AGG + chr6_3:1617627-1617646 None:intergenic 30.0%
!! TTTCTATCTTTGGTGTTTCA+AGG - chr6_3:1617699-1617718 Msa0933100:intron 30.0%
!!! TTTTTTTGTGTTTGATGCAG+AGG - chr6_3:1616843-1616862 Msa0933100:intron 30.0%
!! AAGAACATTGTTGATTTCAG+TGG - chr6_3:1617853-1617872 Msa0933100:CDS 30.0%
!!! TTTTTTCGTGTTTGATGCAG+TGG - chr6_3:1616690-1616709 Msa0933100:intron 35.0%
!!! AAGAGCATTTTCGATTTCAG+TGG - chr6_3:1616716-1616735 Msa0933100:intron 35.0%
!!! GTTCAGTTTTAGGTGATGTA+TGG - chr6_3:1617133-1617152 Msa0933100:intron 35.0%
TATATTGGGACTGTTTGGAT+TGG + chr6_3:1617398-1617417 None:intergenic 35.0%
TCCAAACAGTCCCAATATAA+AGG - chr6_3:1617399-1617418 Msa0933100:intron 35.0%
ACCTTTATATTGGGACTGTT+TGG + chr6_3:1617403-1617422 None:intergenic 35.0%
!! GCTGTTTTCATTAGCTATCT+TGG - chr6_3:1617517-1617536 Msa0933100:intron 35.0%
ACAATCCAAACAAACCCTTA+CGG - chr6_3:1617653-1617672 Msa0933100:intron 35.0%
TATATCCAAACATGCCGTAA+GGG + chr6_3:1617670-1617689 None:intergenic 35.0%
ATATATCCAAACATGCCGTA+AGG + chr6_3:1617671-1617690 None:intergenic 35.0%
TTACGGCATGTTTGGATATA+TGG - chr6_3:1617670-1617689 Msa0933100:intron 35.0%
AAAAGAAATCCTTGTGTGTG+TGG - chr6_3:1617731-1617750 Msa0933100:intron 35.0%
!!! TTTTTTCGTGTTTGATGCAG+TGG - chr6_3:1616690-1616709 Msa0933100:intron 35.0%
!!! AAGAGCATTTTCGATTTCAG+TGG - chr6_3:1616716-1616735 Msa0933100:intron 35.0%
!!! GTTCAGTTTTAGGTGATGTA+TGG - chr6_3:1617133-1617152 Msa0933100:intron 35.0%
TATATTGGGACTGTTTGGAT+TGG + chr6_3:1617398-1617417 None:intergenic 35.0%
TCCAAACAGTCCCAATATAA+AGG - chr6_3:1617399-1617418 Msa0933100:intron 35.0%
ACCTTTATATTGGGACTGTT+TGG + chr6_3:1617403-1617422 None:intergenic 35.0%
!! GCTGTTTTCATTAGCTATCT+TGG - chr6_3:1617517-1617536 Msa0933100:intron 35.0%
ACAATCCAAACAAACCCTTA+CGG - chr6_3:1617653-1617672 Msa0933100:intron 35.0%
TATATCCAAACATGCCGTAA+GGG + chr6_3:1617670-1617689 None:intergenic 35.0%
ATATATCCAAACATGCCGTA+AGG + chr6_3:1617671-1617690 None:intergenic 35.0%
TTACGGCATGTTTGGATATA+TGG - chr6_3:1617670-1617689 Msa0933100:intron 35.0%
AAAAGAAATCCTTGTGTGTG+TGG - chr6_3:1617731-1617750 Msa0933100:intron 35.0%
TTCCACGAATTTCTACCTTC+GGG + chr6_3:1616749-1616768 None:intergenic 40.0%
CTTCCACGAATTTCTACCTT+CGG + chr6_3:1616750-1616769 None:intergenic 40.0%
! TTTTGTGTTTGATGCAGAGG+TGG - chr6_3:1616846-1616865 Msa0933100:intron 40.0%
!! AAGAGCATTGTTGGTTTCAG+TGG - chr6_3:1616869-1616888 Msa0933100:intron 40.0%
! GGGTTTAGTGTTTTGTGTTG+TGG - chr6_3:1616973-1616992 Msa0933100:intron 40.0%
TCCATTAGCATAGGTTGTGT+GGG + chr6_3:1617618-1617637 None:intergenic 40.0%
ATCCATTAGCATAGGTTGTG+TGG + chr6_3:1617619-1617638 None:intergenic 40.0%
! TTTTGTGTTTGATGCAGAGG+TGG - chr6_3:1616846-1616865 Msa0933100:intron 40.0%
!! TTCAGTGGAGATTTTGACGA+AGG - chr6_3:1617868-1617887 Msa0933100:CDS 40.0%
TTCCACGAATTTCTACCTTC+GGG + chr6_3:1616749-1616768 None:intergenic 40.0%
CTTCCACGAATTTCTACCTT+CGG + chr6_3:1616750-1616769 None:intergenic 40.0%
! TTTTGTGTTTGATGCAGAGG+TGG - chr6_3:1616846-1616865 Msa0933100:intron 40.0%
!! AAGAGCATTGTTGGTTTCAG+TGG - chr6_3:1616869-1616888 Msa0933100:intron 40.0%
! GGGTTTAGTGTTTTGTGTTG+TGG - chr6_3:1616973-1616992 Msa0933100:intron 40.0%
TCCATTAGCATAGGTTGTGT+GGG + chr6_3:1617618-1617637 None:intergenic 40.0%
ATCCATTAGCATAGGTTGTG+TGG + chr6_3:1617619-1617638 None:intergenic 40.0%
! TTTTGTGTTTGATGCAGAGG+TGG - chr6_3:1616846-1616865 Msa0933100:intron 40.0%
!! TTCAGTGGAGATTTTGACGA+AGG - chr6_3:1617868-1617887 Msa0933100:CDS 40.0%
GAGAGAGAGTGAATCAGAAG+AGG + chr6_3:1616506-1616525 None:intergenic 45.0%
TCAAAACCGTGGAAGAGGTT+CGG - chr6_3:1616565-1616584 Msa0933100:intron 45.0%
AAGAATCCGAACCTCTTCCA+CGG + chr6_3:1616574-1616593 None:intergenic 45.0%
! TTCAGTGGAGATTTTCCCGA+AGG - chr6_3:1616731-1616750 Msa0933100:intron 45.0%
TTCCCGAAGGTAGAAATTCG+TGG - chr6_3:1616744-1616763 Msa0933100:intron 45.0%
!! AGCATTGTTGGTTTCAGTGG+AGG - chr6_3:1616872-1616891 Msa0933100:intron 45.0%
!! TTCAGTGGAGGTTTTGACGA+AGG - chr6_3:1616884-1616903 Msa0933100:intron 45.0%
TAGGTTGTGTGGGACTGTTT+AGG + chr6_3:1617608-1617627 None:intergenic 45.0%
TCCCACACAACCTATGCTAA+TGG - chr6_3:1617614-1617633 Msa0933100:intron 45.0%
! ACATGCCGTAAGGGTTTGTT+TGG + chr6_3:1617661-1617680 None:intergenic 45.0%
ACAAACCCTTACGGCATGTT+TGG - chr6_3:1617662-1617681 Msa0933100:intron 45.0%
AAATCCTTGTGTGTGTGGCA+TGG - chr6_3:1617736-1617755 Msa0933100:intron 45.0%
AATCCTTGTGTGTGTGGCAT+GGG - chr6_3:1617737-1617756 Msa0933100:CDS 45.0%
GAGAGAGAGTGAATCAGAAG+AGG + chr6_3:1616506-1616525 None:intergenic 45.0%
TCAAAACCGTGGAAGAGGTT+CGG - chr6_3:1616565-1616584 Msa0933100:intron 45.0%
AAGAATCCGAACCTCTTCCA+CGG + chr6_3:1616574-1616593 None:intergenic 45.0%
! TTCAGTGGAGATTTTCCCGA+AGG - chr6_3:1616731-1616750 Msa0933100:intron 45.0%
TTCCCGAAGGTAGAAATTCG+TGG - chr6_3:1616744-1616763 Msa0933100:intron 45.0%
!! AGCATTGTTGGTTTCAGTGG+AGG - chr6_3:1616872-1616891 Msa0933100:intron 45.0%
!! TTCAGTGGAGGTTTTGACGA+AGG - chr6_3:1616884-1616903 Msa0933100:intron 45.0%
TAGGTTGTGTGGGACTGTTT+AGG + chr6_3:1617608-1617627 None:intergenic 45.0%
TCCCACACAACCTATGCTAA+TGG - chr6_3:1617614-1617633 Msa0933100:intron 45.0%
! ACATGCCGTAAGGGTTTGTT+TGG + chr6_3:1617661-1617680 None:intergenic 45.0%
ACAAACCCTTACGGCATGTT+TGG - chr6_3:1617662-1617681 Msa0933100:intron 45.0%
AAATCCTTGTGTGTGTGGCA+TGG - chr6_3:1617736-1617755 Msa0933100:intron 45.0%
AATCCTTGTGTGTGTGGCAT+GGG - chr6_3:1617737-1617756 Msa0933100:CDS 45.0%
TTCCTCTCTCGTCAAAACCG+TGG - chr6_3:1616554-1616573 Msa0933100:intron 50.0%
!! TTCCACGGTTTTGACGAGAG+AGG + chr6_3:1616559-1616578 None:intergenic 50.0%
TCTCGTCAAAACCGTGGAAG+AGG - chr6_3:1616560-1616579 Msa0933100:intron 50.0%
!! CAGAGGTGGAAGAGCATTGT+TGG - chr6_3:1616860-1616879 Msa0933100:intron 50.0%
ATCCTTGTGTGTGTGGCATG+GGG - chr6_3:1617738-1617757 Msa0933100:CDS 50.0%
TTCCTCTCTCGTCAAAACCG+TGG - chr6_3:1616554-1616573 Msa0933100:intron 50.0%
!! TTCCACGGTTTTGACGAGAG+AGG + chr6_3:1616559-1616578 None:intergenic 50.0%
TCTCGTCAAAACCGTGGAAG+AGG - chr6_3:1616560-1616579 Msa0933100:intron 50.0%
!! CAGAGGTGGAAGAGCATTGT+TGG - chr6_3:1616860-1616879 Msa0933100:intron 50.0%
ATCCTTGTGTGTGTGGCATG+GGG - chr6_3:1617738-1617757 Msa0933100:CDS 50.0%
AGCCCCATGCCACACACACA+AGG + chr6_3:1617743-1617762 None:intergenic 60.0%
AGCCCCATGCCACACACACA+AGG + chr6_3:1617743-1617762 None:intergenic 60.0%
Chromosome Type Strat End Strand Name
chr6_3 gene 1616406 1617912 1616406 ID=Msa0933100;Name=Msa0933100
chr6_3 mRNA 1616406 1617912 1616406 ID=Msa0933100-mRNA-1;Parent=Msa0933100;Name=Msa0933100-mRNA-1;_AED=0.14;_eAED=0.14;_QI=0|0.5|0.66|1|1|1|3|12|90
chr6_3 exon 1616406 1616471 1616406 ID=Msa0933100-mRNA-1:exon:666;Parent=Msa0933100-mRNA-1
chr6_3 exon 1617413 1617455 1617413 ID=Msa0933100-mRNA-1:exon:665;Parent=Msa0933100-mRNA-1
chr6_3 exon 1617737 1617912 1617737 ID=Msa0933100-mRNA-1:exon:664;Parent=Msa0933100-mRNA-1
chr6_3 CDS 1617737 1617912 1617737 ID=Msa0933100-mRNA-1:cds;Parent=Msa0933100-mRNA-1
chr6_3 CDS 1617413 1617455 1617413 ID=Msa0933100-mRNA-1:cds;Parent=Msa0933100-mRNA-1
chr6_3 CDS 1616418 1616471 1616418 ID=Msa0933100-mRNA-1:cds;Parent=Msa0933100-mRNA-1
chr6_3 three_prime_UTR 1616406 1616417 1616406 ID=Msa0933100-mRNA-1:three_prime_utr;Parent=Msa0933100-mRNA-1
Gene Sequence

>Msa0933100

AATCAACGGTTCAGATCTCTCTATCTCAGCGAGTGTGTGAACGTTGCTGAGTTCACTCAGCGCGTGAACAAAACTCGTTCTTCTTCGTCGTCTTCTTCCTCTTCTGATTCACTCTCTCTCATTCTTCGTTTTCTTCTTCGTTTTCATCTTCCTCTCTCGTCAAAACCGTGGAAGAGAGGTGGAAGAGCATTGTTGGTTTCAGTGGAGGTTTTGACGAAGAGGTGGAAGAACATTGTTGATTTCAGTGGAGATTTTGACGAAGGTAGAATTTAG

Protein sequence

>Msa0933100

NQRFRSLYLSECVNVAEFTQRVNKTRSSSSSSSSSDSLSLILRFLLRFHLPLSSKPWKRGGRALLVSVEVLTKRWKNIVDFSGDFDEGRI*