AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1342260

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1342260 MtrunA17_Chr1g0151471 70.093 107 28 2 9 114 1 104 7.55e-44 139
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 23 sgRNAs with CRISPR-Local

Find 35 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
ACTCTCATTCTTGGATATTT+TGG 0.094277 tig0005326:+4805 Msa1342260:intergenic
GAATGAGAGTAAGCAATATT+TGG 0.256438 tig0005326:-4792 Msa1342260:CDS
ATATTGCTTACTCTCATTCT+TGG 0.259098 tig0005326:+4796 Msa1342260:intergenic
TTGAGTATCAAGACCCTTAT+CGG 0.292091 tig0005326:+4521 Msa1342260:intergenic
TTGTTACGTACTCTCTTTCT+TGG 0.325832 tig0005326:+4937 Msa1342260:intergenic
ATACAAATACTACTTCTCTT+TGG 0.332697 tig0005326:-4741 Msa1342260:CDS
GAAACTTGGGTATTCGTATT+CGG 0.394103 tig0005326:+4831 Msa1342260:intergenic
TCTTGATACTCAAAAGGAAA+AGG 0.439670 tig0005326:-4511 Msa1342260:CDS
TTTCCTCTTCCCTTCTTCGT+CGG 0.486411 tig0005326:+4547 Msa1342260:intergenic
ACTCAAAAGGAAAAGGGAAA+TGG 0.486925 tig0005326:-4504 Msa1342260:CDS
CAAATACTACTTCTCTTTGG+AGG 0.495243 tig0005326:-4738 Msa1342260:CDS
TAAGGGTCTTGATACTCAAA+AGG 0.499945 tig0005326:-4517 Msa1342260:CDS
CTTGATACTCAAAAGGAAAA+GGG 0.500087 tig0005326:-4510 Msa1342260:CDS
TCTTTGGAGGAGTGATCCTA+CGG 0.509509 tig0005326:-4725 Msa1342260:CDS
ATGTGGACTCCGACGAAGAA+GGG 0.537059 tig0005326:-4556 Msa1342260:CDS
GAGTGATCCTACGGGTTCCA+AGG 0.561497 tig0005326:-4716 Msa1342260:intron
CTTTGGAGGAGTGATCCTAC+GGG 0.578542 tig0005326:-4724 Msa1342260:CDS
CATGTGGACTCCGACGAAGA+AGG 0.582374 tig0005326:-4557 Msa1342260:CDS
TGTATCGCAATCGAAACAAA+CGG 0.590406 tig0005326:+4759 Msa1342260:intergenic
ACTCCGACGAAGAAGGGAAG+AGG 0.605566 tig0005326:-4550 Msa1342260:CDS
TGGCGAAAGCTCATCATCTG+AGG 0.622295 tig0005326:-4484 Msa1342260:CDS
CAGTGGTTGTGTAACGCATG+TGG 0.661654 tig0005326:-4573 Msa1342260:CDS
CTAATTACCTTGGAACCCGT+AGG 0.693638 tig0005326:+4709 Msa1342250:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! AGTAGTTTTCATTTTCTTTT+TGG + tig0005326:4582-4601 Msa1338260:intergenic 20.0%
!! ATAGTTAACAAGAAATATGT+TGG - tig0005326:4836-4855 Msa1342260:CDS 20.0%
!!! GATATTTTGGTTTGAAACTT+GGG + tig0005326:4619-4638 Msa1338260:intergenic 25.0%
! ATACAAATACTACTTCTCTT+TGG - tig0005326:4693-4712 Msa1342260:intron 25.0%
!!! CTACTATCAACTTTAACTTT+TGG - tig0005326:4761-4780 Msa1342260:CDS 25.0%
!! CTTCTTCTTCTTCTTTGTTT+TGG + tig0005326:4537-4556 Msa1338260:intergenic 30.0%
!!! GGATATTTTGGTTTGAAACT+TGG + tig0005326:4620-4639 Msa1338260:intergenic 30.0%
! ACTCTCATTCTTGGATATTT+TGG + tig0005326:4632-4651 Msa1338260:intergenic 30.0%
ATATTGCTTACTCTCATTCT+TGG + tig0005326:4641-4660 Msa1338260:intergenic 30.0%
GAATGAGAGTAAGCAATATT+TGG - tig0005326:4642-4661 Msa1342260:intron 30.0%
AAGAGATGAACTAATTACCT+TGG + tig0005326:4738-4757 Msa1342260:intergenic 30.0%
TCTTGATACTCAAAAGGAAA+AGG - tig0005326:4923-4942 Msa1342260:CDS 30.0%
CTTGATACTCAAAAGGAAAA+GGG - tig0005326:4924-4943 Msa1342260:CDS 30.0%
TTGTTACGTACTCTCTTTCT+TGG + tig0005326:4500-4519 Msa1338260:intergenic 35.0%
!!! TTCTTTGTTTTGGCTGGAAT+TGG + tig0005326:4527-4546 Msa1338260:intergenic 35.0%
!!! TTCTTCTTCTTTGTTTTGGC+TGG + tig0005326:4533-4552 Msa1338260:intergenic 35.0%
GAAACTTGGGTATTCGTATT+CGG + tig0005326:4606-4625 Msa1338260:intergenic 35.0%
TGTATCGCAATCGAAACAAA+CGG + tig0005326:4678-4697 Msa1342260:intergenic 35.0%
CAAATACTACTTCTCTTTGG+AGG - tig0005326:4696-4715 Msa1342260:intron 35.0%
TTGAGTATCAAGACCCTTAT+CGG + tig0005326:4916-4935 Msa1342260:intergenic 35.0%
TAAGGGTCTTGATACTCAAA+AGG - tig0005326:4917-4936 Msa1342260:CDS 35.0%
ACTCAAAAGGAAAAGGGAAA+TGG - tig0005326:4930-4949 Msa1342260:CDS 35.0%
CAAGAAATATGTTGGTGCAG+TGG - tig0005326:4844-4863 Msa1342260:CDS 40.0%
GAAGAGGAAAAAGCCGATAA+GGG - tig0005326:4900-4919 Msa1342260:CDS 40.0%
! TCTTTGGAGGAGTGATCCTA+CGG - tig0005326:4709-4728 Msa1342260:intron 45.0%
CTAATTACCTTGGAACCCGT+AGG + tig0005326:4728-4747 Msa1342260:intergenic 45.0%
TTTCCTCTTCCCTTCTTCGT+CGG + tig0005326:4890-4909 Msa1342260:intergenic 45.0%
GGAAGAGGAAAAAGCCGATA+AGG - tig0005326:4899-4918 Msa1342260:CDS 45.0%
! CTTTGGAGGAGTGATCCTAC+GGG - tig0005326:4710-4729 Msa1342260:intron 50.0%
CAGTGGTTGTGTAACGCATG+TGG - tig0005326:4861-4880 Msa1342260:CDS 50.0%
ATGTGGACTCCGACGAAGAA+GGG - tig0005326:4878-4897 Msa1342260:CDS 50.0%
TGGCGAAAGCTCATCATCTG+AGG - tig0005326:4950-4969 Msa1342260:CDS 50.0%
GAGTGATCCTACGGGTTCCA+AGG - tig0005326:4718-4737 Msa1342260:CDS 55.0%
CATGTGGACTCCGACGAAGA+AGG - tig0005326:4877-4896 Msa1342260:CDS 55.0%
ACTCCGACGAAGAAGGGAAG+AGG - tig0005326:4884-4903 Msa1342260:CDS 55.0%
Chromosome Type Strat End Strand Name
tig0005326 gene 4467 4989 4467 ID=Msa1342260;Name=Msa1342260
tig0005326 mRNA 4467 4989 4467 ID=Msa1342260-mRNA-1;Parent=Msa1342260;Name=Msa1342260-mRNA-1;_AED=0.14;_eAED=0.14;_QI=0|0|0|1|1|1|2|0|132
tig0005326 exon 4717 4989 4717 ID=Msa1342260-mRNA-1:exon:3530;Parent=Msa1342260-mRNA-1
tig0005326 exon 4467 4592 4467 ID=Msa1342260-mRNA-1:exon:3529;Parent=Msa1342260-mRNA-1
tig0005326 CDS 4717 4989 4717 ID=Msa1342260-mRNA-1:cds;Parent=Msa1342260-mRNA-1
tig0005326 CDS 4467 4592 4467 ID=Msa1342260-mRNA-1:cds;Parent=Msa1342260-mRNA-1
Gene Sequence

>Msa1342260

ATGGTGAGTTCAATTTACAAACATATATTACCAAGAAAGAGAGTACGTAACAATGATCCAATTCCAGCCAAAACAAAGAAGAAGAAGAAGAAGAAAACTTCTGCTAGTGCTGCCAAAAAGAAAATGAAAACTACTACCGAATACGAATACCCAAGTTTCAAACCAAAATATCCAAGAATGAGAGTAAGCAATATTTGGTTAACAACTACCGTTTGTTTCGATTGCGATACAAATACTACTTCTCTTTGGAGGAGTGATCCTACGGGTTCCAAGTGGTTGTGTAACGCATGTGGACTCCGACGAAGAAGGGAAGAGGAAAAAGCCGATAAGGGTCTTGATACTCAAAAGGAAAAGGGAAATGGCGAAAGCTCATCATCTGAGGATGTGAAGAAGTTTTAA
Protein sequence

>Msa1342260

MVSSIYKHILPRKRVRNNDPIPAKTKKKKKKKTSASAAKKKMKTTTEYEYPSFKPKYPRMRVSNIWLTTTVCFDCDTNTTSLWRSDPTGSKWLCNACGLRRRREEEKADKGLDTQKEKGNGESSSSEDVKKF*