AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1465410


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1465410 MtrunA17_Chr1g0198941 97.059 68 1 1 1 68 1 67 7.74e-36 115
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 21 sgRNAs with CRISPR-Local

Find 28 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
ATGAAACATGCACCATATTA+TGG 0.203774 tig0045213:+3486 None:intergenic
TATTTATGTGCCTTCCTCTT+AGG 0.239565 tig0045213:+3691 None:intergenic
ACCTTGGAGGCTCTAGCTTT+AGG 0.324474 tig0045213:+3745 None:intergenic
AATATGAAGAATCCATAATA+TGG 0.340279 tig0045213:-3498 Msa1465410:three_prime_UTR
AGGAGTAGTCCCACTAGTTT+TGG 0.346620 tig0045213:+3765 None:intergenic
CATGTAAATCCTTGCCAGTT+TGG 0.348500 tig0045213:-3402 Msa1465410:three_prime_UTR
TCTTTCTTGACTTGCCCTGA+TGG 0.433141 tig0045213:+3796 None:intergenic
TCTGGTAGCTCTCAACCATC+AGG 0.435394 tig0045213:-3811 Msa1465410:CDS
TTTCTTTGGTGCTACCTTGG+AGG 0.439933 tig0045213:+3732 None:intergenic
TATCAGTAGTACTATCTGTA+TGG 0.447641 tig0045213:-3457 Msa1465410:three_prime_UTR
GAGAAACCAACTGAGAAATC+TGG 0.453123 tig0045213:-3829 Msa1465410:CDS
GAGCTACCAGATTTCTCAGT+TGG 0.466377 tig0045213:+3823 None:intergenic
AGCAGAAATCTCAGCCTAAG+AGG 0.534590 tig0045213:-3705 Msa1465410:CDS
TCCTAAAGCTAGAGCCTCCA+AGG 0.550929 tig0045213:-3746 Msa1465410:CDS
TTTAAAAGGCCAAACTGGCA+AGG 0.553496 tig0045213:+3393 None:intergenic
GAAATCTCAGCCTAAGAGGA+AGG 0.562849 tig0045213:-3701 Msa1465410:intron
CAAACTGGCAAGGATTTACA+TGG 0.573072 tig0045213:+3403 None:intergenic
GAGCCTGCTGCCAAAACTAG+TGG 0.582011 tig0045213:-3775 Msa1465410:CDS
AGCCTGCTGCCAAAACTAGT+GGG 0.610029 tig0045213:-3774 Msa1465410:CDS
AATGAGACAACATAAGCAAG+TGG 0.629024 tig0045213:+3432 None:intergenic
CTGGTAGCTCTCAACCATCA+GGG 0.637266 tig0045213:-3810 Msa1465410:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! TTACTTGAAAAAATAATTGT+TGG - tig0045213:3669-3688 Msa1465410:intron 15.0%
!! AATATGAAGAATCCATAATA+TGG - tig0045213:3714-3733 Msa1465410:CDS 20.0%
!!! ATCTTTTGATTACTTGTTTC+AGG - tig0045213:3607-3626 Msa1465410:intron 25.0%
!!! TTTTATTTAAAAGGCCAAAC+TGG + tig0045213:3827-3846 None:intergenic 25.0%
ATGAAACATGCACCATATTA+TGG + tig0045213:3729-3748 None:intergenic 30.0%
TATCAGTAGTACTATCTGTA+TGG - tig0045213:3755-3774 Msa1465410:CDS 30.0%
! GATTTCTGCTCAGTTTTCTT+TGG + tig0045213:3497-3516 None:intergenic 35.0%
TATTTATGTGCCTTCCTCTT+AGG + tig0045213:3524-3543 None:intergenic 35.0%
AATGAGACAACATAAGCAAG+TGG + tig0045213:3783-3802 None:intergenic 35.0%
GAGAAACCAACTGAGAAATC+TGG - tig0045213:3383-3402 Msa1465410:three_prime_UTR 40.0%
!!! AGTTTTCTTTGGTGCTACCT+TGG + tig0045213:3486-3505 None:intergenic 40.0%
CAAACTGGCAAGGATTTACA+TGG + tig0045213:3812-3831 None:intergenic 40.0%
CATGTAAATCCTTGCCAGTT+TGG - tig0045213:3810-3829 Msa1465410:CDS 40.0%
TTTAAAAGGCCAAACTGGCA+AGG + tig0045213:3822-3841 None:intergenic 40.0%
GAGCTACCAGATTTCTCAGT+TGG + tig0045213:3392-3411 None:intergenic 45.0%
!! TCTTTCTTGACTTGCCCTGA+TGG + tig0045213:3419-3438 None:intergenic 45.0%
!! AGGAGTAGTCCCACTAGTTT+TGG + tig0045213:3450-3469 None:intergenic 45.0%
!! TTTCTTTGGTGCTACCTTGG+AGG + tig0045213:3483-3502 None:intergenic 45.0%
AGCAGAAATCTCAGCCTAAG+AGG - tig0045213:3507-3526 Msa1465410:three_prime_UTR 45.0%
GAAATCTCAGCCTAAGAGGA+AGG - tig0045213:3511-3530 Msa1465410:three_prime_UTR 45.0%
!!! ATAAGTATATTTTATTTAAA+AGG + tig0045213:3836-3855 None:intergenic 5.0%
TCTGGTAGCTCTCAACCATC+AGG - tig0045213:3401-3420 Msa1465410:three_prime_UTR 50.0%
CTGGTAGCTCTCAACCATCA+GGG - tig0045213:3402-3421 Msa1465410:three_prime_UTR 50.0%
AGCCTGCTGCCAAAACTAGT+GGG - tig0045213:3438-3457 Msa1465410:three_prime_UTR 50.0%
TCCTAAAGCTAGAGCCTCCA+AGG - tig0045213:3466-3485 Msa1465410:three_prime_UTR 50.0%
!! ACCTTGGAGGCTCTAGCTTT+AGG + tig0045213:3470-3489 None:intergenic 50.0%
GAGCCTGCTGCCAAAACTAG+TGG - tig0045213:3437-3456 Msa1465410:three_prime_UTR 55.0%
!!! GTCCCACTAGTTTTGGCAGC+AGG + tig0045213:3443-3462 None:intergenic 55.0%
Chromosome Type Strat End Strand Name
tig0045213 gene 3365 3869 3365 ID=Msa1465410;Name=Msa1465410
tig0045213 mRNA 3365 3869 3365 ID=Msa1465410-mRNA-1;Parent=Msa1465410;Name=Msa1465410-mRNA-1;_AED=0.05;_eAED=0.05;_QI=0|0|0.5|1|1|1|2|202|68
tig0045213 exon 3365 3605 3365 ID=Msa1465410-mRNA-1:exon:24792;Parent=Msa1465410-mRNA-1
tig0045213 exon 3702 3869 3702 ID=Msa1465410-mRNA-1:exon:24791;Parent=Msa1465410-mRNA-1
tig0045213 CDS 3702 3869 3702 ID=Msa1465410-mRNA-1:cds;Parent=Msa1465410-mRNA-1
tig0045213 CDS 3567 3605 3567 ID=Msa1465410-mRNA-1:cds;Parent=Msa1465410-mRNA-1
tig0045213 three_prime_UTR 3365 3566 3365 ID=Msa1465410-mRNA-1:three_prime_utr;Parent=Msa1465410-mRNA-1
Gene Sequence

>Msa1465410

ATGGCATCACTCAAAGCTGAGAAACCAACTGAGAAATCTGGTAGCTCTCAACCATCAGGGCAAGTCAAGAAAGAGCCTGCTGCCAAAACTAGTGGGACTACTCCTAAAGCTAGAGCCTCCAAGGTAGCACCAAAGAAAACTGAGCAGAAATCTCAGCCTAAGAGGAAGGCTAGCAGCATTAAGCAGAAGATAACAAGTGAAACTTAA

Protein sequence

>Msa1465410

MASLKAEKPTEKSGSSQPSGQVKKEPAAKTSGTTPKARASKVAPKKTEQKSQPKRKASSIKQKITSET*