AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1190820


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1190820 MtrunA17_Chr8g0360121 100.000 63 0 0 1 63 1 63 5.96e-41 127
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1190820 AT3G15353.1 57.576 66 23 2 1 61 1 66 1.04e-17 69.7
Msa1190820 AT3G15353.2 56.923 65 23 2 1 61 1 64 5.29e-17 67.8

Find 19 sgRNAs with CRISPR-Local

Find 66 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CATTTGCATATATTCTTTAA+TGG 0.154703 8_1:+34091454 None:intergenic
TTGTGGCATTCTGTTGTTAC+TGG 0.188780 8_1:-34091310 Msa1190820:three_prime_UTR
AAATGTAATTGCCATGAATT+TGG 0.244815 8_1:-34091436 Msa1190820:three_prime_UTR
ATGAGCTTGACATGTTTGTT+TGG 0.442431 8_1:+34091887 None:intergenic
ATATATTCTTTAATGGCCAC+AGG 0.505243 8_1:+34091461 None:intergenic
TTGCAATCATGCTCAACAGC+TGG 0.507300 8_1:+34091516 None:intergenic
TGTGGCATTCTGTTGTTACT+GGG 0.512610 8_1:-34091309 Msa1190820:three_prime_UTR
CTTCGTCGAGACTGTTGTCA+TGG 0.555720 8_1:-34091544 Msa1190820:CDS
ATTATACAACTGCCATGTTG+TGG 0.564419 8_1:-34091327 Msa1190820:three_prime_UTR
AGAGGAGCACTTACCCGCAC+TGG 0.574771 8_1:+34091836 None:intergenic
GTTGAGCATGATTGCAAGTG+TGG 0.581040 8_1:-34091510 Msa1190820:CDS
TTCAGGAAGGGAAACAACTA+CGG 0.588697 8_1:-34091707 Msa1190820:intron
GCGCTGACAAGAGCCAGTGC+GGG 0.597634 8_1:-34091849 Msa1190820:intron
ACAAACATGTCAAGCTCATG+CGG 0.602184 8_1:-34091883 Msa1190820:exon
TGCGCTGACAAGAGCCAGTG+CGG 0.611618 8_1:-34091850 Msa1190820:CDS
AACAACAGAATGCCACAACA+TGG 0.645156 8_1:+34091315 None:intergenic
ACTTGCACTAACTGCACCTG+TGG 0.650678 8_1:-34091477 Msa1190820:CDS
CCTCTTCTGAGTCTCGACAA+TGG 0.679042 8_1:+34091679 None:intergenic
CCATTGTCGAGACTCAGAAG+AGG 0.690774 8_1:-34091679 Msa1190820:intron

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! CATTTGCATATATTCTTTAA+TGG + chr8_1:34091638-34091657 None:intergenic 20.0%
!! CATTTGCATATATTCTTTAA+TGG + chr8_1:34091638-34091657 None:intergenic 20.0%
!!! AAGGTTGATGTGTATTTTAT+TGG - chr8_1:34091288-34091307 Msa1190820:three_prime_UTR 25.0%
! AAATGTAATTGCCATGAATT+TGG - chr8_1:34091653-34091672 Msa1190820:intron 25.0%
!!! AGATCTTTTTTGAAGTGAAT+TGG + chr8_1:34091930-34091949 None:intergenic 25.0%
!!! AAGGTTGATGTGTATTTTAT+TGG - chr8_1:34091288-34091307 Msa1190820:three_prime_UTR 25.0%
! AAATGTAATTGCCATGAATT+TGG - chr8_1:34091653-34091672 Msa1190820:intron 25.0%
!!! AGATCTTTTTTGAAGTGAAT+TGG + chr8_1:34091930-34091949 None:intergenic 25.0%
TACCATAGCATCATATATGA+GGG + chr8_1:34091362-34091381 None:intergenic 30.0%
ATACCATAGCATCATATATG+AGG + chr8_1:34091363-34091382 None:intergenic 30.0%
TATATGATGCTATGGTATTC+AGG - chr8_1:34091365-34091384 Msa1190820:three_prime_UTR 30.0%
ATATATTCTTTAATGGCCAC+AGG + chr8_1:34091631-34091650 None:intergenic 30.0%
! GTTTTGTATTGCCAAATTCA+TGG + chr8_1:34091667-34091686 None:intergenic 30.0%
TACCATAGCATCATATATGA+GGG + chr8_1:34091362-34091381 None:intergenic 30.0%
ATACCATAGCATCATATATG+AGG + chr8_1:34091363-34091382 None:intergenic 30.0%
TATATGATGCTATGGTATTC+AGG - chr8_1:34091365-34091384 Msa1190820:three_prime_UTR 30.0%
ATATATTCTTTAATGGCCAC+AGG + chr8_1:34091631-34091650 None:intergenic 30.0%
! GTTTTGTATTGCCAAATTCA+TGG + chr8_1:34091667-34091686 None:intergenic 30.0%
ATGAGCTTGACATGTTTGTT+TGG + chr8_1:34091205-34091224 None:intergenic 35.0%
AACCTTACAGTACAAGATAG+AGG + chr8_1:34091274-34091293 None:intergenic 35.0%
ACCATAGCATCATATATGAG+GGG + chr8_1:34091361-34091380 None:intergenic 35.0%
TCGAGGAGTTATTAGAAACA+TGG + chr8_1:34091465-34091484 None:intergenic 35.0%
ATTATACAACTGCCATGTTG+TGG - chr8_1:34091762-34091781 Msa1190820:intron 35.0%
ATGAGCTTGACATGTTTGTT+TGG + chr8_1:34091205-34091224 None:intergenic 35.0%
AACCTTACAGTACAAGATAG+AGG + chr8_1:34091274-34091293 None:intergenic 35.0%
ACCATAGCATCATATATGAG+GGG + chr8_1:34091361-34091380 None:intergenic 35.0%
TCGAGGAGTTATTAGAAACA+TGG + chr8_1:34091465-34091484 None:intergenic 35.0%
ATTATACAACTGCCATGTTG+TGG - chr8_1:34091762-34091781 Msa1190820:intron 35.0%
ACAAACATGTCAAGCTCATG+CGG - chr8_1:34091206-34091225 Msa1190820:three_prime_UTR 40.0%
CTCCTCTATCTTGTACTGTA+AGG - chr8_1:34091269-34091288 Msa1190820:three_prime_UTR 40.0%
TCCCCTCATATATGATGCTA+TGG - chr8_1:34091357-34091376 Msa1190820:three_prime_UTR 40.0%
TGATGCTATGGTATTCAGGA+AGG - chr8_1:34091369-34091388 Msa1190820:three_prime_UTR 40.0%
GATGCTATGGTATTCAGGAA+GGG - chr8_1:34091370-34091389 Msa1190820:three_prime_UTR 40.0%
TTCAGGAAGGGAAACAACTA+CGG - chr8_1:34091382-34091401 Msa1190820:three_prime_UTR 40.0%
AACAACAGAATGCCACAACA+TGG + chr8_1:34091777-34091796 None:intergenic 40.0%
TTGTGGCATTCTGTTGTTAC+TGG - chr8_1:34091779-34091798 Msa1190820:intron 40.0%
TGTGGCATTCTGTTGTTACT+GGG - chr8_1:34091780-34091799 Msa1190820:intron 40.0%
ACAAACATGTCAAGCTCATG+CGG - chr8_1:34091206-34091225 Msa1190820:three_prime_UTR 40.0%
CTCCTCTATCTTGTACTGTA+AGG - chr8_1:34091269-34091288 Msa1190820:three_prime_UTR 40.0%
TCCCCTCATATATGATGCTA+TGG - chr8_1:34091357-34091376 Msa1190820:three_prime_UTR 40.0%
TGATGCTATGGTATTCAGGA+AGG - chr8_1:34091369-34091388 Msa1190820:three_prime_UTR 40.0%
GATGCTATGGTATTCAGGAA+GGG - chr8_1:34091370-34091389 Msa1190820:three_prime_UTR 40.0%
TTCAGGAAGGGAAACAACTA+CGG - chr8_1:34091382-34091401 Msa1190820:three_prime_UTR 40.0%
AACAACAGAATGCCACAACA+TGG + chr8_1:34091777-34091796 None:intergenic 40.0%
TTGTGGCATTCTGTTGTTAC+TGG - chr8_1:34091779-34091798 Msa1190820:intron 40.0%
TGTGGCATTCTGTTGTTACT+GGG - chr8_1:34091780-34091799 Msa1190820:intron 40.0%
TTGCAATCATGCTCAACAGC+TGG + chr8_1:34091576-34091595 None:intergenic 45.0%
GTTGAGCATGATTGCAAGTG+TGG - chr8_1:34091579-34091598 Msa1190820:intron 45.0%
TTGCAATCATGCTCAACAGC+TGG + chr8_1:34091576-34091595 None:intergenic 45.0%
GTTGAGCATGATTGCAAGTG+TGG - chr8_1:34091579-34091598 Msa1190820:intron 45.0%
CCTCTTCTGAGTCTCGACAA+TGG + chr8_1:34091413-34091432 None:intergenic 50.0%
CCATTGTCGAGACTCAGAAG+AGG - chr8_1:34091410-34091429 Msa1190820:three_prime_UTR 50.0%
!! GCTAGCTTTGCATTGAGTCG+AGG + chr8_1:34091482-34091501 None:intergenic 50.0%
CTTCGTCGAGACTGTTGTCA+TGG - chr8_1:34091545-34091564 Msa1190820:CDS 50.0%
ACTTGCACTAACTGCACCTG+TGG - chr8_1:34091612-34091631 Msa1190820:intron 50.0%
CCTCTTCTGAGTCTCGACAA+TGG + chr8_1:34091413-34091432 None:intergenic 50.0%
CCATTGTCGAGACTCAGAAG+AGG - chr8_1:34091410-34091429 Msa1190820:three_prime_UTR 50.0%
!! GCTAGCTTTGCATTGAGTCG+AGG + chr8_1:34091482-34091501 None:intergenic 50.0%
CTTCGTCGAGACTGTTGTCA+TGG - chr8_1:34091545-34091564 Msa1190820:CDS 50.0%
ACTTGCACTAACTGCACCTG+TGG - chr8_1:34091612-34091631 Msa1190820:intron 50.0%
! TGCGCTGACAAGAGCCAGTG+CGG - chr8_1:34091239-34091258 Msa1190820:three_prime_UTR 60.0%
!! AGAGGAGCACTTACCCGCAC+TGG + chr8_1:34091256-34091275 None:intergenic 60.0%
! TGCGCTGACAAGAGCCAGTG+CGG - chr8_1:34091239-34091258 Msa1190820:three_prime_UTR 60.0%
!! AGAGGAGCACTTACCCGCAC+TGG + chr8_1:34091256-34091275 None:intergenic 60.0%
! GCGCTGACAAGAGCCAGTGC+GGG - chr8_1:34091240-34091259 Msa1190820:three_prime_UTR 65.0%
! GCGCTGACAAGAGCCAGTGC+GGG - chr8_1:34091240-34091259 Msa1190820:three_prime_UTR 65.0%
Chromosome Type Strat End Strand Name
chr8_1 gene 34091151 34091960 34091151 ID=Msa1190820;Name=Msa1190820
chr8_1 mRNA 34091151 34091960 34091151 ID=Msa1190820-mRNA-1;Parent=Msa1190820;Name=Msa1190820-mRNA-1;_AED=0.00;_eAED=0.00;_QI=61|1|1|1|1|1|3|319|63
chr8_1 exon 34091151 34091566 34091151 ID=Msa1190820-mRNA-1:exon:11487;Parent=Msa1190820-mRNA-1
chr8_1 exon 34091680 34091724 34091680 ID=Msa1190820-mRNA-1:exon:11486;Parent=Msa1190820-mRNA-1
chr8_1 exon 34091850 34091960 34091850 ID=Msa1190820-mRNA-1:exon:11485;Parent=Msa1190820-mRNA-1
chr8_1 five_prime_UTR 34091900 34091960 34091900 ID=Msa1190820-mRNA-1:five_prime_utr;Parent=Msa1190820-mRNA-1
chr8_1 CDS 34091850 34091899 34091850 ID=Msa1190820-mRNA-1:cds;Parent=Msa1190820-mRNA-1
chr8_1 CDS 34091680 34091724 34091680 ID=Msa1190820-mRNA-1:cds;Parent=Msa1190820-mRNA-1
chr8_1 CDS 34091470 34091566 34091470 ID=Msa1190820-mRNA-1:cds;Parent=Msa1190820-mRNA-1
chr8_1 three_prime_UTR 34091151 34091469 34091151 ID=Msa1190820-mRNA-1:three_prime_utr;Parent=Msa1190820-mRNA-1
Gene Sequence

>Msa1190820

ATGTCAAGCTCATGCGGCAACTGCGACTGCGCTGACAAGAGCCAGTGCGGGAAGGGAAACAACTACGGCATGACCATTGTCGAGACTCAGAAGAGCTTCGTCGAGACTGTTGTCATGGATGCTCCAGCTGTTGAGCATGATTGCAAGTGTGGTTCTAACTGCACTTGCACTAACTGCACCTGTGGCCATTAA

Protein sequence

>Msa1190820

MSSSCGNCDCADKSQCGKGNNYGMTIVETQKSFVETVVMDAPAVEHDCKCGSNCTCTNCTCGH*