AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1423350


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1423350 MtrunA17_Chr7g0235621 98.969 97 1 0 1 97 122 218 1.23e-60 184
Msa1423350 MtrunA17_Chr4g0024941 37.931 87 54 0 5 91 118 204 9.00e-11 55.8
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1423350 AT3G07190.1 67.033 91 30 0 1 91 122 212 6.35e-15 67.4
Msa1423350 AT5G48660.2 67.347 98 31 1 1 97 46 143 1.21e-14 65.1
Msa1423350 AT5G48660.1 67.347 98 31 1 1 97 122 219 3.34e-14 65.5
Msa1423350 AT5G42570.1 39.080 87 53 0 5 91 118 204 1.29e-11 58.5

Find 15 sgRNAs with CRISPR-Local

Find 20 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CTGCTTGAGCCTGAAGATTT+TGG 0.137576 tig0025528:+56368 None:intergenic
AACTCTCTTGTCTTTCTCTT+CGG 0.340250 tig0025528:+56474 None:intergenic
TCTAACAGAAGGTTTGAAAA+AGG 0.345623 tig0025528:-56509 Msa1423350:CDS
GGAAGACAACCAAAATCTTC+AGG 0.401724 tig0025528:-56377 Msa1423350:CDS
CAAAATCTTCAGGCTCAAGC+AGG 0.486517 tig0025528:-56367 Msa1423350:CDS
AAATGTCGAGCTCAAAGAAA+AGG 0.491750 tig0025528:-56581 Msa1423350:CDS
GCTTGAATATGACAGACTCT+TGG 0.508233 tig0025528:-56398 Msa1423350:CDS
GAACTTTCAACTCTAACAGA+AGG 0.533214 tig0025528:-56520 Msa1423350:CDS
AAAGGAGGAGAAAGCTTCCA+AGG 0.549039 tig0025528:-56563 Msa1423350:CDS
GGGAGCTTCAAAAGAAGAAG+TGG 0.560241 tig0025528:-56620 Msa1423350:CDS
GAAAGACAAGAGAGTTGAGA+CGG 0.586053 tig0025528:-56467 Msa1423350:CDS
GCAGGGAGGCATAAGAGTTG+AGG 0.597943 tig0025528:-56349 None:intergenic
AAAATCTTCAGGCTCAAGCA+GGG 0.625078 tig0025528:-56366 Msa1423350:CDS
TGTCGAGCTCAAAGAAAAGG+AGG 0.645126 tig0025528:-56578 Msa1423350:CDS
ATCTTCAGGCTCAAGCAGGG+AGG 0.695143 tig0025528:-56363 Msa1423350:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
TCTAACAGAAGGTTTGAAAA+AGG - tig0025528:56464-56483 Msa1423350:CDS 30.0%
AGGTTTGAAAAAGGTAAAGA+TGG - tig0025528:56473-56492 Msa1423350:CDS 30.0%
!! GCTCGACATTTTCTTTTTTG+AGG + tig0025528:56383-56402 None:intergenic 35.0%
AAATGTCGAGCTCAAAGAAA+AGG - tig0025528:56392-56411 Msa1423350:CDS 35.0%
GAACTTTCAACTCTAACAGA+AGG - tig0025528:56453-56472 Msa1423350:CDS 35.0%
AACTCTCTTGTCTTTCTCTT+CGG + tig0025528:56502-56521 None:intergenic 35.0%
!! GTAAATCTGCAGCTTGTTTT+TGG + tig0025528:56554-56573 None:intergenic 35.0%
!! CTTCAGCTGTTTTATCTCCT+TGG + tig0025528:56430-56449 None:intergenic 40.0%
GAAAGACAAGAGAGTTGAGA+CGG - tig0025528:56506-56525 Msa1423350:CDS 40.0%
!!! ATCTGCAGCTTGTTTTTGGA+GGG + tig0025528:56550-56569 None:intergenic 40.0%
!!! AATCTGCAGCTTGTTTTTGG+AGG + tig0025528:56551-56570 None:intergenic 40.0%
GCTTGAATATGACAGACTCT+TGG - tig0025528:56575-56594 Msa1423350:CDS 40.0%
GGAAGACAACCAAAATCTTC+AGG - tig0025528:56596-56615 Msa1423350:CDS 40.0%
AAAATCTTCAGGCTCAAGCA+GGG - tig0025528:56607-56626 Msa1423350:CDS 40.0%
GGGAGCTTCAAAAGAAGAAG+TGG - tig0025528:56353-56372 Msa1423350:CDS 45.0%
TGTCGAGCTCAAAGAAAAGG+AGG - tig0025528:56395-56414 Msa1423350:CDS 45.0%
AAAGGAGGAGAAAGCTTCCA+AGG - tig0025528:56410-56429 Msa1423350:CDS 45.0%
! CTGCTTGAGCCTGAAGATTT+TGG + tig0025528:56608-56627 None:intergenic 45.0%
CAAAATCTTCAGGCTCAAGC+AGG - tig0025528:56606-56625 Msa1423350:CDS 45.0%
ATCTTCAGGCTCAAGCAGGG+AGG - tig0025528:56610-56629 Msa1423350:CDS 55.0%
Chromosome Type Strat End Strand Name
tig0025528 gene 56351 56644 56351 ID=Msa1423350;Name=Msa1423350
tig0025528 mRNA 56351 56644 56351 ID=Msa1423350-mRNA-1;Parent=Msa1423350;Name=Msa1423350-mRNA-1;_AED=0.12;_eAED=0.12;_QI=0|-1|0|1|-1|1|1|0|97
tig0025528 exon 56351 56644 56351 ID=Msa1423350-mRNA-1:exon:3171;Parent=Msa1423350-mRNA-1
tig0025528 CDS 56351 56644 56351 ID=Msa1423350-mRNA-1:cds;Parent=Msa1423350-mRNA-1
Gene Sequence

>Msa1423350

ATGGGAGCTTCAAAAGAAGAAGTGGAGAACCTCAAAAAAGAAAATGTCGAGCTCAAAGAAAAGGAGGAGAAAGCTTCCAAGGAGATAAAACAGCTGAAGAAAGAACTTTCAACTCTAACAGAAGGTTTGAAAAAGGTAAAGATGGAATCCGAAGAGAAAGACAAGAGAGTTGAGACGGCTGATGCTCATGTTGCTTCCCTCCAAAAACAAGCTGCAGATTTACTGCTTGAATATGACAGACTCTTGGAAGACAACCAAAATCTTCAGGCTCAAGCAGGGAGGCATAAGAGTTGA

Protein sequence

>Msa1423350

MGASKEEVENLKKENVELKEKEEKASKEIKQLKKELSTLTEGLKKVKMESEEKDKRVETADAHVASLQKQAADLLLEYDRLLEDNQNLQAQAGRHKS*