AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0669320


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 16 sgRNAs with CRISPR-Local

Find 22 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
ACTCTCCAGGTTATTCTGTT+TGG 0.333707 4_4:-10990824 Msa0669320:CDS
GCCTTCTGTCAAAGCCTCTT+TGG 0.337451 4_4:+10990597 None:intergenic
CTCTTTCAAGCTAACATTCA+AGG 0.379882 4_4:+10990754 None:intergenic
GAAGAGACTTGTGGTTTAGA+TGG 0.445560 4_4:-10990906 Msa0669320:CDS
CTTGAATGTTAGCTTGAAAG+AGG 0.463175 4_4:-10990753 Msa0669320:intron
AAGTCAAAGAAGCTCCCAAC+AGG 0.484404 4_4:+10990623 None:intergenic
TTCTTTGACTTCTTCCAAAG+AGG 0.487396 4_4:-10990611 Msa0669320:CDS
TCCAAAGAGGCTTTGACAGA+AGG 0.490100 4_4:-10990598 Msa0669320:CDS
AAAGTGTTGCAAAACTCTCC+AGG 0.494048 4_4:-10990837 Msa0669320:intron
ATAACATATAGAAGCTAAGT+AGG 0.495419 4_4:-10990562 Msa0669320:exon
TGTCAGGCACTGAACCTGTT+GGG 0.500227 4_4:-10990637 Msa0669320:intron
GACTGAGAAATGAAGCTACA+TGG 0.549979 4_4:-10990939 None:intergenic
GTGTCAGGCACTGAACCTGT+TGG 0.602440 4_4:-10990638 Msa0669320:intron
AGTTACCAAACAGAATAACC+TGG 0.622731 4_4:+10990819 None:intergenic
GAGGCTTTGACAGAAGGCAA+AGG 0.649959 4_4:-10990592 Msa0669320:CDS
GTTTGGTAACTCATACGACT+CGG 0.650990 4_4:-10990807 Msa0669320:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
! ATAACATATAGAAGCTAAGT+AGG - chr4_4:10990927-10990946 Msa0669320:CDS 25.0%
! TGGCAAAGTTTGTTTATGAT+AGG - chr4_4:10990798-10990817 Msa0669320:CDS 30.0%
AATCATCTCTATATAGTGTC+AGG - chr4_4:10990836-10990855 Msa0669320:CDS 30.0%
!! GATTTTAGTGAAGAGACTTG+TGG - chr4_4:10990574-10990593 Msa0669320:CDS 35.0%
AGATGGTCTTTCTGTTAAGA+TGG - chr4_4:10990600-10990619 Msa0669320:CDS 35.0%
GATGGTCTTTCTGTTAAGAT+GGG - chr4_4:10990601-10990620 Msa0669320:CDS 35.0%
ATGGTCTTTCTGTTAAGATG+GGG - chr4_4:10990602-10990621 Msa0669320:CDS 35.0%
AGTTACCAAACAGAATAACC+TGG + chr4_4:10990673-10990692 None:intergenic 35.0%
CTCTTTCAAGCTAACATTCA+AGG + chr4_4:10990738-10990757 None:intergenic 35.0%
! CTTGAATGTTAGCTTGAAAG+AGG - chr4_4:10990736-10990755 Msa0669320:intron 35.0%
! TTCTTTGACTTCTTCCAAAG+AGG - chr4_4:10990878-10990897 Msa0669320:intron 35.0%
GAAGAGACTTGTGGTTTAGA+TGG - chr4_4:10990583-10990602 Msa0669320:CDS 40.0%
!! AAAGTGTTGCAAAACTCTCC+AGG - chr4_4:10990652-10990671 Msa0669320:intron 40.0%
ACTCTCCAGGTTATTCTGTT+TGG - chr4_4:10990665-10990684 Msa0669320:intron 40.0%
! GTTTGGTAACTCATACGACT+CGG - chr4_4:10990682-10990701 Msa0669320:intron 40.0%
AAGTCAAAGAAGCTCCCAAC+AGG + chr4_4:10990869-10990888 None:intergenic 45.0%
! TCCAAAGAGGCTTTGACAGA+AGG - chr4_4:10990891-10990910 Msa0669320:intron 45.0%
!!! TTTTTTATTCAATTTTTTTA+TGG - chr4_4:10990778-10990797 Msa0669320:CDS 5.0%
!! TGTCAGGCACTGAACCTGTT+GGG - chr4_4:10990852-10990871 Msa0669320:intron 50.0%
GCCTTCTGTCAAAGCCTCTT+TGG + chr4_4:10990895-10990914 None:intergenic 50.0%
! GAGGCTTTGACAGAAGGCAA+AGG - chr4_4:10990897-10990916 Msa0669320:intron 50.0%
!! GTGTCAGGCACTGAACCTGT+TGG - chr4_4:10990851-10990870 Msa0669320:intron 55.0%
Chromosome Type Strat End Strand Name
chr4_4 gene 10990559 10990952 10990559 ID=Msa0669320;Name=Msa0669320
chr4_4 mRNA 10990559 10990952 10990559 ID=Msa0669320-mRNA-1;Parent=Msa0669320;Name=Msa0669320-mRNA-1;_AED=0.47;_eAED=0.47;_QI=0|0.5|0.33|1|0.5|0.33|3|8|80
chr4_4 exon 10990559 10990653 10990559 ID=Msa0669320-mRNA-1:exon:3330;Parent=Msa0669320-mRNA-1
chr4_4 exon 10990754 10990855 10990754 ID=Msa0669320-mRNA-1:exon:3329;Parent=Msa0669320-mRNA-1
chr4_4 exon 10990899 10990952 10990899 ID=Msa0669320-mRNA-1:exon:3328;Parent=Msa0669320-mRNA-1
chr4_4 CDS 10990899 10990952 10990899 ID=Msa0669320-mRNA-1:cds;Parent=Msa0669320-mRNA-1
chr4_4 CDS 10990754 10990855 10990754 ID=Msa0669320-mRNA-1:cds;Parent=Msa0669320-mRNA-1
chr4_4 CDS 10990567 10990653 10990567 ID=Msa0669320-mRNA-1:cds;Parent=Msa0669320-mRNA-1
chr4_4 three_prime_UTR 10990559 10990566 10990559 ID=Msa0669320-mRNA-1:three_prime_utr;Parent=Msa0669320-mRNA-1
Gene Sequence

>Msa0669320

ATGAAGCTACATGGAGATTTTAGTGAAGAGACTTGTGGTTTAGATGGTCTTTCTTGTTGCAAAACTCTCCAGGTTATTCTGTTTGGTAACTCATACGACTCGGACACAAACTTTAACAAGTTGACACAAGTGTCCTTGAATGTTAGCTTGAAAGAGGCACTGAACCTGTTGGGAGCTTCTTTGACTTCTTCCAAAGAGGCTTTGACAGAAGGCAAAGGAAGAAGAATAACATATAGAAGCTAA

Protein sequence

>Msa0669320

MKLHGDFSEETCGLDGLSCCKTLQVILFGNSYDSDTNFNKLTQVSLNVSLKEALNLLGASLTSSKEALTEGKGRRITYRS*