AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0011040


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0011040 MtrunA17_Chr1g0159601 93.365 211 13 1 1 211 46 255 6.64e-146 406
Msa0011040 MtrunA17_Chr1g0159611 78.676 136 29 0 1 136 46 181 4.52e-75 236
Msa0011040 MtrunA17_Chr8g0380681 45.536 224 102 6 4 209 2 223 8.86e-53 182
Msa0011040 MtrunA17_Chr8g0380681 39.000 200 109 6 18 205 691 889 8.50e-37 136
Msa0011040 MtrunA17_Chr2g0277731 43.750 208 108 4 9 209 12 217 4.70e-51 174
Msa0011040 MtrunA17_Chr4g0039131 42.969 128 70 2 86 211 1 127 6.56e-31 110
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0011040 AT1G11050.1 42.708 192 103 4 25 210 26 216 2.39e-38 140

Find 36 sgRNAs with CRISPR-Local

Find 39 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CAATCTCTTCTTAGTCTCTT+TGG 0.194083 1_1:+16710403 Msa0011040:CDS
GTTGGTATTGTGAATCATTT+TGG 0.240330 1_1:+16710802 Msa0011040:CDS
GAAAGAGTGAAGTTTCTTTC+AGG 0.244676 1_1:-16710444 None:intergenic
CAGAAGGAGTAGCTATGATA+AGG 0.380662 1_1:-16710282 None:intergenic
TTGTAAAGGTGATTTGAAAT+CGG 0.388227 1_1:+16710669 Msa0011040:CDS
CAACAATGTTGTGTGTCAAT+TGG 0.393976 1_1:-16710379 None:intergenic
TGTGTCAATTGGGTCTCTGC+AGG 0.430262 1_1:-16710368 None:intergenic
CTTCTTAGTCTCTTTGGCAT+AGG 0.437265 1_1:+16710409 Msa0011040:CDS
CTTTACAAGAAGTGTCTAAA+GGG 0.447705 1_1:-16710654 None:intergenic
TAAGGGTGAAGAGGAGGAGA+AGG 0.460180 1_1:-16710264 None:intergenic
CCTTTAGACACTTCTTGTAA+AGG 0.468879 1_1:+16710655 Msa0011040:CDS
AACAATGTTGTGTGTCAATT+GGG 0.477153 1_1:-16710378 None:intergenic
TGCAGCACGTGCACTAATGC+TGG 0.478276 1_1:+16710700 Msa0011040:CDS
GTATCACAAACATCAAAGAT+TGG 0.490764 1_1:+16710608 Msa0011040:CDS
CTATGATAAGGGTGAAGAGG+AGG 0.492847 1_1:-16710270 None:intergenic
CCTTTACAAGAAGTGTCTAA+AGG 0.505136 1_1:-16710655 None:intergenic
TAGCTATGATAAGGGTGAAG+AGG 0.511716 1_1:-16710273 None:intergenic
GCTACAGCTAGTTGTATACT+TGG 0.511927 1_1:+16710838 Msa0011040:CDS
AGAAGGAGTAGCTATGATAA+GGG 0.514017 1_1:-16710281 None:intergenic
TTATTTCTCATCTTCTAAGC+GGG 0.515185 1_1:-16710864 None:intergenic
ATTGAGTTGTGGAAACAAGA+AGG 0.531475 1_1:-16710553 None:intergenic
TGACAAATTGAATTGAGTTG+TGG 0.533475 1_1:-16710564 None:intergenic
TTCTGCAGTATCATGTCCTA+TGG 0.534711 1_1:+16710306 Msa0011040:CDS
AAGAAGGGACTAACGAAGGT+TGG 0.536160 1_1:-16710537 None:intergenic
TCAACATAGCTGAGATCCAT+AGG 0.544235 1_1:-16710322 None:intergenic
ACAAACAACTCAAGCTGCGC+AGG 0.551790 1_1:+16710586 Msa0011040:CDS
AGTATACAACTAGCTGTAGC+AGG 0.563837 1_1:-16710835 None:intergenic
CTAGCTGTAGCAGGATCTGT+AGG 0.582604 1_1:-16710826 None:intergenic
TTGAGTTGTGGAAACAAGAA+GGG 0.597711 1_1:-16710552 None:intergenic
CTATGTTGAGACCTTTCCAT+GGG 0.598491 1_1:+16710336 Msa0011040:CDS
CTGCAGGTTGATGTGTCCCA+TGG 0.599274 1_1:-16710352 None:intergenic
CATGATACTGCAGAAGCAGA+AGG 0.601540 1_1:-16710298 None:intergenic
GGTTGATGTGTCCCATGGAA+AGG 0.611152 1_1:-16710347 None:intergenic
GCTATGTTGAGACCTTTCCA+TGG 0.614762 1_1:+16710335 Msa0011040:CDS
TTTATTTCTCATCTTCTAAG+CGG 0.636465 1_1:-16710865 None:intergenic
AAACAAGAAGGGACTAACGA+AGG 0.740560 1_1:-16710541 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! ATTTTAAAGTGTTTTTATTA+GGG - chr1_1:16710474-16710493 None:intergenic 10.0%
!!! GATTTTAAAGTGTTTTTATT+AGG - chr1_1:16710475-16710494 None:intergenic 15.0%
!! TTGTAAAGGTGATTTGAAAT+CGG + chr1_1:16710669-16710688 Msa0011040:CDS 25.0%
!!! TTTTCAGTTTTATATGCTGT+TGG + chr1_1:16710784-16710803 Msa0011040:CDS 25.0%
AACAATGTTGTGTGTCAATT+GGG - chr1_1:16710381-16710400 None:intergenic 30.0%
! TGACAAATTGAATTGAGTTG+TGG - chr1_1:16710567-16710586 None:intergenic 30.0%
GTATCACAAACATCAAAGAT+TGG + chr1_1:16710608-16710627 Msa0011040:CDS 30.0%
AAAGATTGGAAGCAAAAAGT+TGG + chr1_1:16710622-16710641 Msa0011040:CDS 30.0%
!! CTTTACAAGAAGTGTCTAAA+GGG - chr1_1:16710657-16710676 None:intergenic 30.0%
!!! AAGCACTTAGTTGCATTTTT+TGG - chr1_1:16710760-16710779 None:intergenic 30.0%
! GTTGGTATTGTGAATCATTT+TGG + chr1_1:16710802-16710821 Msa0011040:CDS 30.0%
AGAAGGAGTAGCTATGATAA+GGG - chr1_1:16710284-16710303 None:intergenic 35.0%
CAACAATGTTGTGTGTCAAT+TGG - chr1_1:16710382-16710401 None:intergenic 35.0%
CAATCTCTTCTTAGTCTCTT+TGG + chr1_1:16710403-16710422 Msa0011040:CDS 35.0%
GAAAGAGTGAAGTTTCTTTC+AGG - chr1_1:16710447-16710466 None:intergenic 35.0%
! TTGAGTTGTGGAAACAAGAA+GGG - chr1_1:16710555-16710574 None:intergenic 35.0%
! ATTGAGTTGTGGAAACAAGA+AGG - chr1_1:16710556-16710575 None:intergenic 35.0%
!! CCTTTACAAGAAGTGTCTAA+AGG - chr1_1:16710658-16710677 None:intergenic 35.0%
CCTTTAGACACTTCTTGTAA+AGG + chr1_1:16710655-16710674 Msa0011040:CDS 35.0%
TAGCTATGATAAGGGTGAAG+AGG - chr1_1:16710276-16710295 None:intergenic 40.0%
CAGAAGGAGTAGCTATGATA+AGG - chr1_1:16710285-16710304 None:intergenic 40.0%
TTCTGCAGTATCATGTCCTA+TGG + chr1_1:16710306-16710325 Msa0011040:CDS 40.0%
TCAACATAGCTGAGATCCAT+AGG - chr1_1:16710325-16710344 None:intergenic 40.0%
CTATGTTGAGACCTTTCCAT+GGG + chr1_1:16710336-16710355 Msa0011040:CDS 40.0%
CTTCTTAGTCTCTTTGGCAT+AGG + chr1_1:16710409-16710428 Msa0011040:CDS 40.0%
AAACAAGAAGGGACTAACGA+AGG - chr1_1:16710544-16710563 None:intergenic 40.0%
AGTATACAACTAGCTGTAGC+AGG - chr1_1:16710838-16710857 None:intergenic 40.0%
GCTACAGCTAGTTGTATACT+TGG + chr1_1:16710838-16710857 Msa0011040:CDS 40.0%
CTATGATAAGGGTGAAGAGG+AGG - chr1_1:16710273-16710292 None:intergenic 45.0%
CATGATACTGCAGAAGCAGA+AGG - chr1_1:16710301-16710320 None:intergenic 45.0%
GCTATGTTGAGACCTTTCCA+TGG + chr1_1:16710335-16710354 Msa0011040:CDS 45.0%
AAGAAGGGACTAACGAAGGT+TGG - chr1_1:16710540-16710559 None:intergenic 45.0%
TAAGGGTGAAGAGGAGGAGA+AGG - chr1_1:16710267-16710286 None:intergenic 50.0%
! GGTTGATGTGTCCCATGGAA+AGG - chr1_1:16710350-16710369 None:intergenic 50.0%
TGTGTCAATTGGGTCTCTGC+AGG - chr1_1:16710371-16710390 None:intergenic 50.0%
ACAAACAACTCAAGCTGCGC+AGG + chr1_1:16710586-16710605 Msa0011040:CDS 50.0%
CTAGCTGTAGCAGGATCTGT+AGG - chr1_1:16710829-16710848 None:intergenic 50.0%
!! CTGCAGGTTGATGTGTCCCA+TGG - chr1_1:16710355-16710374 None:intergenic 55.0%
TGCAGCACGTGCACTAATGC+TGG + chr1_1:16710700-16710719 Msa0011040:CDS 55.0%
Chromosome Type Strat End Strand Name
chr1_1 gene 16710244 16710879 16710244 ID=Msa0011040;Name=Msa0011040
chr1_1 mRNA 16710244 16710879 16710244 ID=Msa0011040-mRNA-1;Parent=Msa0011040;Name=Msa0011040-mRNA-1;_AED=0.37;_eAED=0.37;_QI=0|-1|0|1|-1|1|1|0|211
chr1_1 exon 16710244 16710879 16710244 ID=Msa0011040-mRNA-1:exon:6061;Parent=Msa0011040-mRNA-1
chr1_1 CDS 16710244 16710879 16710244 ID=Msa0011040-mRNA-1:cds;Parent=Msa0011040-mRNA-1
Gene Sequence

>Msa0011040

ATGGATAACAAAGCAGTGTTCCTTCTCCTCCTCTTCACCCTTATCATAGCTACTCCTTCTGCTTCTGCAGTATCATGTCCTATGGATCTCAGCTATGTTGAGACCTTTCCATGGGACACATCAACCTGCAGAGACCCAATTGACACACAACATTGTTGTCAATCTCTTCTTAGTCTCTTTGGCATAGGACTTGCAAAACACCTGAAAGAAACTTCACTCTTTCAACTCCCTAATAAAAACACTTTAAAATCTTGCTTACAAGATTTCAAACTCAAACTTTCATGCTTAAAGATCCAACCTTCGTTAGTCCCTTCTTGTTTCCACAACTCAATTCAATTTGTCACAAACAACTCAAGCTGCGCAGGTATCACAAACATCAAAGATTGGAAGCAAAAAGTTGGTAGAATTAGCCCTTTAGACACTTCTTGTAAAGGTGATTTGAAATCGGACACTAGTTGCAGCACGTGCACTAATGCTGGTTTCAAAGTCACTTCTCAGCTTACAAGTATTGATCCAAAAAATGCAACTAAGTGCTTTTTCTTTTCAGTTTTATATGCTGTTGGTATTGTGAATCATTTTGGTCCTACAGATCCTGCTACAGCTAGTTGTATACTTGGTATCCCGCTTAGAAGATGA

Protein sequence

>Msa0011040

MDNKAVFLLLLFTLIIATPSASAVSCPMDLSYVETFPWDTSTCRDPIDTQHCCQSLLSLFGIGLAKHLKETSLFQLPNKNTLKSCLQDFKLKLSCLKIQPSLVPSCFHNSIQFVTNNSSCAGITNIKDWKQKVGRISPLDTSCKGDLKSDTSCSTCTNAGFKVTSQLTSIDPKNATKCFFFSVLYAVGIVNHFGPTDPATASCILGIPLRR*