AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0562440


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 11 sgRNAs with CRISPR-Local

Find 92 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
AAATAGCTTGGGAAAGATTT+TGG 0.183974 4_1:-62343150 Msa0562440:three_prime_UTR
CCAAGCTTCAGTGTTGAATT+TGG 0.200983 4_1:+62343553 None:intergenic
ACAAATAAAACCTTCAGATA+TGG 0.380222 4_1:+62343881 None:intergenic
TTGCAGGTATTAAAATAGCT+TGG 0.399623 4_1:-62343162 Msa0562440:intron
TGCAGGTATTAAAATAGCTT+GGG 0.409624 4_1:-62343161 Msa0562440:intron
ACTAGGTACCTTGGCATACT+AGG 0.422735 4_1:-62343906 Msa0562440:CDS
TTCTAAATATAAAACTTACT+AGG 0.496684 4_1:-62343923 Msa0562440:CDS
CCAAATTCAACACTGAAGCT+TGG 0.509377 4_1:-62343553 Msa0562440:CDS
ATAAAACTTACTAGGTACCT+TGG 0.519048 4_1:-62343915 Msa0562440:CDS
ATACTAGGTGCCATATCTGA+AGG 0.590859 4_1:-62343891 Msa0562440:CDS
ATATGGCACCTAGTATGCCA+AGG 0.670496 4_1:+62343898 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! TTTATTTGTCATTTTAATTA+TGG - chr4_1:62343194-62343213 Msa0562440:intron 10.0%
!!! ACTTTTAGATTAAAAAATAT+AGG - chr4_1:62343792-62343811 Msa0562440:intron 10.0%
!!! TTTATTTGTCATTTTAATTA+TGG - chr4_1:62343194-62343213 Msa0562440:intron 10.0%
!!! ACTTTTAGATTAAAAAATAT+AGG - chr4_1:62343792-62343811 Msa0562440:intron 10.0%
!! TTCTAAATATAAAACTTACT+AGG - chr4_1:62343138-62343157 Msa0562440:three_prime_UTR 15.0%
!! TTCTAAATATAAAACTTACT+AGG - chr4_1:62343138-62343157 Msa0562440:three_prime_UTR 15.0%
!!! CTTTCATTATCTATTTTTGT+AGG - chr4_1:62343466-62343485 Msa0562440:intron 20.0%
!!! GATAATTATTTTCTATCTGT+TGG - chr4_1:62343671-62343690 Msa0562440:intron 20.0%
!!! CTTTCATTATCTATTTTTGT+AGG - chr4_1:62343466-62343485 Msa0562440:intron 20.0%
!!! GATAATTATTTTCTATCTGT+TGG - chr4_1:62343671-62343690 Msa0562440:intron 20.0%
! ACAAATAAAACCTTCAGATA+TGG + chr4_1:62343183-62343202 None:intergenic 25.0%
!!! ATTTTAATTATGGTCAGTCT+GGG - chr4_1:62343204-62343223 Msa0562440:intron 25.0%
! GAAGAATCATAAAACAATCA+TGG + chr4_1:62343305-62343324 None:intergenic 25.0%
! TATCAAATTGTAATTGCCTT+TGG + chr4_1:62343374-62343393 None:intergenic 25.0%
!!! ATCTATTTTTGTAGGTTGAA+TGG - chr4_1:62343474-62343493 Msa0562440:intron 25.0%
!! GAAAGAAAAAAGGTACAATT+AGG - chr4_1:62343553-62343572 Msa0562440:CDS 25.0%
!! CTTGTAAGTTTCTTTAAAGA+TGG + chr4_1:62343608-62343627 None:intergenic 25.0%
! ACACATTACTAATTTGAAAG+GGG + chr4_1:62343743-62343762 None:intergenic 25.0%
! GACACATTACTAATTTGAAA+GGG + chr4_1:62343744-62343763 None:intergenic 25.0%
! CAAAAGTAATAAGCAAATTG+CGG + chr4_1:62343766-62343785 None:intergenic 25.0%
! ACAAATAAAACCTTCAGATA+TGG + chr4_1:62343183-62343202 None:intergenic 25.0%
!!! ATTTTAATTATGGTCAGTCT+GGG - chr4_1:62343204-62343223 Msa0562440:intron 25.0%
! GAAGAATCATAAAACAATCA+TGG + chr4_1:62343305-62343324 None:intergenic 25.0%
! TATCAAATTGTAATTGCCTT+TGG + chr4_1:62343374-62343393 None:intergenic 25.0%
!!! ATCTATTTTTGTAGGTTGAA+TGG - chr4_1:62343474-62343493 Msa0562440:intron 25.0%
!! GAAAGAAAAAAGGTACAATT+AGG - chr4_1:62343553-62343572 Msa0562440:CDS 25.0%
!! CTTGTAAGTTTCTTTAAAGA+TGG + chr4_1:62343608-62343627 None:intergenic 25.0%
! ACACATTACTAATTTGAAAG+GGG + chr4_1:62343743-62343762 None:intergenic 25.0%
! GACACATTACTAATTTGAAA+GGG + chr4_1:62343744-62343763 None:intergenic 25.0%
! CAAAAGTAATAAGCAAATTG+CGG + chr4_1:62343766-62343785 None:intergenic 25.0%
ATAAAACTTACTAGGTACCT+TGG - chr4_1:62343146-62343165 Msa0562440:three_prime_UTR 30.0%
!!! CATTTTAATTATGGTCAGTC+TGG - chr4_1:62343203-62343222 Msa0562440:intron 30.0%
!!! CATTTTCTGGTTTCTTTATC+TGG - chr4_1:62343237-62343256 Msa0562440:intron 30.0%
ATTGAGCATGGTTGTATATA+GGG - chr4_1:62343272-62343291 Msa0562440:intron 30.0%
TGGTCATTATTTAGCAAGAA+TGG + chr4_1:62343354-62343373 None:intergenic 30.0%
TCTTGCTAAATAATGACCAA+AGG - chr4_1:62343355-62343374 Msa0562440:intron 30.0%
! TACGCAAGTTGAAAGAAAAA+AGG - chr4_1:62343543-62343562 Msa0562440:CDS 30.0%
CACATTACTAATTTGAAAGG+GGG + chr4_1:62343742-62343761 None:intergenic 30.0%
GGACACATTACTAATTTGAA+AGG + chr4_1:62343745-62343764 None:intergenic 30.0%
!! CGCAATTTGCTTATTACTTT+TGG - chr4_1:62343764-62343783 Msa0562440:intron 30.0%
TTGCAGGTATTAAAATAGCT+TGG - chr4_1:62343899-62343918 Msa0562440:CDS 30.0%
TGCAGGTATTAAAATAGCTT+GGG - chr4_1:62343900-62343919 Msa0562440:CDS 30.0%
! AAATAGCTTGGGAAAGATTT+TGG - chr4_1:62343911-62343930 Msa0562440:CDS 30.0%
!!! AAAGATTTTGGTTGTGGTTA+TGG - chr4_1:62343923-62343942 Msa0562440:CDS 30.0%
ATAAAACTTACTAGGTACCT+TGG - chr4_1:62343146-62343165 Msa0562440:three_prime_UTR 30.0%
!!! CATTTTAATTATGGTCAGTC+TGG - chr4_1:62343203-62343222 Msa0562440:intron 30.0%
!!! CATTTTCTGGTTTCTTTATC+TGG - chr4_1:62343237-62343256 Msa0562440:intron 30.0%
ATTGAGCATGGTTGTATATA+GGG - chr4_1:62343272-62343291 Msa0562440:intron 30.0%
TGGTCATTATTTAGCAAGAA+TGG + chr4_1:62343354-62343373 None:intergenic 30.0%
TCTTGCTAAATAATGACCAA+AGG - chr4_1:62343355-62343374 Msa0562440:intron 30.0%
! TACGCAAGTTGAAAGAAAAA+AGG - chr4_1:62343543-62343562 Msa0562440:CDS 30.0%
CACATTACTAATTTGAAAGG+GGG + chr4_1:62343742-62343761 None:intergenic 30.0%
GGACACATTACTAATTTGAA+AGG + chr4_1:62343745-62343764 None:intergenic 30.0%
!! CGCAATTTGCTTATTACTTT+TGG - chr4_1:62343764-62343783 Msa0562440:intron 30.0%
TTGCAGGTATTAAAATAGCT+TGG - chr4_1:62343899-62343918 Msa0562440:CDS 30.0%
TGCAGGTATTAAAATAGCTT+GGG - chr4_1:62343900-62343919 Msa0562440:CDS 30.0%
! AAATAGCTTGGGAAAGATTT+TGG - chr4_1:62343911-62343930 Msa0562440:CDS 30.0%
!!! AAAGATTTTGGTTGTGGTTA+TGG - chr4_1:62343923-62343942 Msa0562440:CDS 30.0%
CATTGAGCATGGTTGTATAT+AGG - chr4_1:62343271-62343290 Msa0562440:intron 35.0%
TGGAAATAACATGCTATCAC+AGG + chr4_1:62343334-62343353 None:intergenic 35.0%
! GTGAGTCTTTGAATTGACTT+AGG + chr4_1:62343701-62343720 None:intergenic 35.0%
AATTGTTGCTCAACAATGAG+TGG - chr4_1:62343858-62343877 Msa0562440:CDS 35.0%
CATTGAGCATGGTTGTATAT+AGG - chr4_1:62343271-62343290 Msa0562440:intron 35.0%
TGGAAATAACATGCTATCAC+AGG + chr4_1:62343334-62343353 None:intergenic 35.0%
! GTGAGTCTTTGAATTGACTT+AGG + chr4_1:62343701-62343720 None:intergenic 35.0%
AATTGTTGCTCAACAATGAG+TGG - chr4_1:62343858-62343877 Msa0562440:CDS 35.0%
! ATACTAGGTGCCATATCTGA+AGG - chr4_1:62343170-62343189 Msa0562440:intron 40.0%
! GGGTAAGTTGCTTCATTTTC+TGG - chr4_1:62343224-62343243 Msa0562440:intron 40.0%
!! TTGCTTTGAAGCATTGAGCA+TGG - chr4_1:62343260-62343279 Msa0562440:intron 40.0%
ATGGTTGTATATAGGGTGGT+TGG - chr4_1:62343279-62343298 Msa0562440:intron 40.0%
! CCAAGCTTCAGTGTTGAATT+TGG + chr4_1:62343511-62343530 None:intergenic 40.0%
CCAAATTCAACACTGAAGCT+TGG - chr4_1:62343508-62343527 Msa0562440:intron 40.0%
ACAATGAGTGGTTGTGGTTA+TGG - chr4_1:62343870-62343889 Msa0562440:CDS 40.0%
! GTGGTTATGGTATCTTTTGC+AGG - chr4_1:62343883-62343902 Msa0562440:CDS 40.0%
!!! CTTGGGAAAGATTTTGGTTG+TGG - chr4_1:62343917-62343936 Msa0562440:CDS 40.0%
! ATACTAGGTGCCATATCTGA+AGG - chr4_1:62343170-62343189 Msa0562440:intron 40.0%
! GGGTAAGTTGCTTCATTTTC+TGG - chr4_1:62343224-62343243 Msa0562440:intron 40.0%
!! TTGCTTTGAAGCATTGAGCA+TGG - chr4_1:62343260-62343279 Msa0562440:intron 40.0%
ATGGTTGTATATAGGGTGGT+TGG - chr4_1:62343279-62343298 Msa0562440:intron 40.0%
! CCAAGCTTCAGTGTTGAATT+TGG + chr4_1:62343511-62343530 None:intergenic 40.0%
CCAAATTCAACACTGAAGCT+TGG - chr4_1:62343508-62343527 Msa0562440:intron 40.0%
ACAATGAGTGGTTGTGGTTA+TGG - chr4_1:62343870-62343889 Msa0562440:CDS 40.0%
! GTGGTTATGGTATCTTTTGC+AGG - chr4_1:62343883-62343902 Msa0562440:CDS 40.0%
!!! CTTGGGAAAGATTTTGGTTG+TGG - chr4_1:62343917-62343936 Msa0562440:CDS 40.0%
ACTAGGTACCTTGGCATACT+AGG - chr4_1:62343155-62343174 Msa0562440:three_prime_UTR 45.0%
ATATGGCACCTAGTATGCCA+AGG + chr4_1:62343166-62343185 None:intergenic 45.0%
GAGCATGGTTGTATATAGGG+TGG - chr4_1:62343275-62343294 Msa0562440:intron 45.0%
TGCTCAACAATGAGTGGTTG+TGG - chr4_1:62343864-62343883 Msa0562440:CDS 45.0%
ACTAGGTACCTTGGCATACT+AGG - chr4_1:62343155-62343174 Msa0562440:three_prime_UTR 45.0%
ATATGGCACCTAGTATGCCA+AGG + chr4_1:62343166-62343185 None:intergenic 45.0%
GAGCATGGTTGTATATAGGG+TGG - chr4_1:62343275-62343294 Msa0562440:intron 45.0%
TGCTCAACAATGAGTGGTTG+TGG - chr4_1:62343864-62343883 Msa0562440:CDS 45.0%
Chromosome Type Strat End Strand Name
chr4_1 gene 62343116 62343967 62343116 ID=Msa0562440;Name=Msa0562440
chr4_1 mRNA 62343116 62343967 62343116 ID=Msa0562440-mRNA-1;Parent=Msa0562440;Name=Msa0562440-mRNA-1;_AED=0.43;_eAED=0.43;_QI=0|0.5|0.66|1|0.5|0.33|3|73|58
chr4_1 exon 62343116 62343178 62343116 ID=Msa0562440-mRNA-1:exon:19709;Parent=Msa0562440-mRNA-1
chr4_1 exon 62343519 62343595 62343519 ID=Msa0562440-mRNA-1:exon:19708;Parent=Msa0562440-mRNA-1
chr4_1 exon 62343858 62343967 62343858 ID=Msa0562440-mRNA-1:exon:19707;Parent=Msa0562440-mRNA-1
chr4_1 CDS 62343858 62343967 62343858 ID=Msa0562440-mRNA-1:cds;Parent=Msa0562440-mRNA-1
chr4_1 CDS 62343529 62343595 62343529 ID=Msa0562440-mRNA-1:cds;Parent=Msa0562440-mRNA-1
chr4_1 three_prime_UTR 62343519 62343528 62343519 ID=Msa0562440-mRNA-1:three_prime_utr;Parent=Msa0562440-mRNA-1
chr4_1 three_prime_UTR 62343116 62343178 62343116 ID=Msa0562440-mRNA-1:three_prime_utr;Parent=Msa0562440-mRNA-1
Gene Sequence

>Msa0562440

ATGGAAGATGCAATAGCTCTCATTCTAAATATAAAACTTACTAGGTACCTTGGCATACTAGGTGCCATATCTGAAGGTTTTATTTGTCATTTTAATTATGGTCAGTCTGGGTTGAATGGTTTTGCAATAGCCAAATTCAACACTGAAGCTTGGAAGAAAAATGATTACGCAAGTTGA

Protein sequence

>Msa0562440

MEDAIALILNIKLTRYLGILGAISEGFICHFNYGQSGLNGFAIAKFNTEAWKKNDYAS*