AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0048380


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0048380 MtrunA17_Chr1g0159601 93.365 211 13 1 1 211 46 255 6.64e-146 406
Msa0048380 MtrunA17_Chr1g0159611 78.676 136 29 0 1 136 46 181 4.52e-75 236
Msa0048380 MtrunA17_Chr8g0380681 45.536 224 102 6 4 209 2 223 8.86e-53 182
Msa0048380 MtrunA17_Chr8g0380681 39.000 200 109 6 18 205 691 889 8.50e-37 136
Msa0048380 MtrunA17_Chr2g0277731 43.750 208 108 4 9 209 12 217 4.70e-51 174
Msa0048380 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
Msa0048380 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_2:+679906 Msa0048380:CDS
GTTGGTATTGTGAATCATTT+TGG 0.240330 1_2:+680305 Msa0048380:CDS
GAAAGAGTGAAGTTTCTTTC+AGG 0.244676 1_2:-679947 None:intergenic
CAGAAGGAGTAGCTATGATA+AGG 0.380662 1_2:-679785 None:intergenic
TTGTAAAGGTGATTTGAAAT+CGG 0.388227 1_2:+680172 Msa0048380:CDS
CAACAATGTTGTGTGTCAAT+TGG 0.393976 1_2:-679882 None:intergenic
TGTGTCAATTGGGTCTCTGC+AGG 0.430262 1_2:-679871 None:intergenic
CTTCTTAGTCTCTTTGGCAT+AGG 0.437265 1_2:+679912 Msa0048380:CDS
CTTTACAAGAAGTGTCTAAA+GGG 0.447705 1_2:-680157 None:intergenic
TAAGGGTGAAGAGGAGGAGA+AGG 0.460180 1_2:-679767 None:intergenic
CCTTTAGACACTTCTTGTAA+AGG 0.468879 1_2:+680158 Msa0048380:CDS
AACAATGTTGTGTGTCAATT+GGG 0.477153 1_2:-679881 None:intergenic
TGCAGCACGTGCACTAATGC+TGG 0.478276 1_2:+680203 Msa0048380:CDS
GTATCACAAACATCAAAGAT+TGG 0.490764 1_2:+680111 Msa0048380:CDS
CTATGATAAGGGTGAAGAGG+AGG 0.492847 1_2:-679773 None:intergenic
CCTTTACAAGAAGTGTCTAA+AGG 0.505136 1_2:-680158 None:intergenic
TAGCTATGATAAGGGTGAAG+AGG 0.511716 1_2:-679776 None:intergenic
GCTACAGCTAGTTGTATACT+TGG 0.511927 1_2:+680341 Msa0048380:CDS
AGAAGGAGTAGCTATGATAA+GGG 0.514017 1_2:-679784 None:intergenic
TTATTTCTCATCTTCTAAGC+GGG 0.515185 1_2:-680367 None:intergenic
ATTGAGTTGTGGAAACAAGA+AGG 0.531475 1_2:-680056 None:intergenic
TGACAAATTGAATTGAGTTG+TGG 0.533475 1_2:-680067 None:intergenic
TTCTGCAGTATCATGTCCTA+TGG 0.534711 1_2:+679809 Msa0048380:CDS
AAGAAGGGACTAACGAAGGT+TGG 0.536160 1_2:-680040 None:intergenic
TCAACATAGCTGAGATCCAT+AGG 0.544235 1_2:-679825 None:intergenic
ACAAACAACTCAAGCTGCGC+AGG 0.551790 1_2:+680089 Msa0048380:CDS
AGTATACAACTAGCTGTAGC+AGG 0.563837 1_2:-680338 None:intergenic
CTAGCTGTAGCAGGATCTGT+AGG 0.582604 1_2:-680329 None:intergenic
TTGAGTTGTGGAAACAAGAA+GGG 0.597711 1_2:-680055 None:intergenic
CTATGTTGAGACCTTTCCAT+GGG 0.598491 1_2:+679839 Msa0048380:CDS
CTGCAGGTTGATGTGTCCCA+TGG 0.599274 1_2:-679855 None:intergenic
CATGATACTGCAGAAGCAGA+AGG 0.601540 1_2:-679801 None:intergenic
GGTTGATGTGTCCCATGGAA+AGG 0.611152 1_2:-679850 None:intergenic
GCTATGTTGAGACCTTTCCA+TGG 0.614762 1_2:+679838 Msa0048380:CDS
TTTATTTCTCATCTTCTAAG+CGG 0.636465 1_2:-680368 None:intergenic
AAACAAGAAGGGACTAACGA+AGG 0.740560 1_2:-680044 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! ATTTTAAAGTGTTTTTATTA+GGG - chr1_2:679977-679996 None:intergenic 10.0%
!!! GATTTTAAAGTGTTTTTATT+AGG - chr1_2:679978-679997 None:intergenic 15.0%
!! TTGTAAAGGTGATTTGAAAT+CGG + chr1_2:680172-680191 Msa0048380:CDS 25.0%
!!! TTTTCAGTTTTATATGCTGT+TGG + chr1_2:680287-680306 Msa0048380:CDS 25.0%
AACAATGTTGTGTGTCAATT+GGG - chr1_2:679884-679903 None:intergenic 30.0%
! TGACAAATTGAATTGAGTTG+TGG - chr1_2:680070-680089 None:intergenic 30.0%
GTATCACAAACATCAAAGAT+TGG + chr1_2:680111-680130 Msa0048380:CDS 30.0%
AAAGATTGGAAGCAAAAAGT+TGG + chr1_2:680125-680144 Msa0048380:CDS 30.0%
!! CTTTACAAGAAGTGTCTAAA+GGG - chr1_2:680160-680179 None:intergenic 30.0%
!!! AAGCACTTAGTTGCATTTTT+TGG - chr1_2:680263-680282 None:intergenic 30.0%
! GTTGGTATTGTGAATCATTT+TGG + chr1_2:680305-680324 Msa0048380:CDS 30.0%
AGAAGGAGTAGCTATGATAA+GGG - chr1_2:679787-679806 None:intergenic 35.0%
CAACAATGTTGTGTGTCAAT+TGG - chr1_2:679885-679904 None:intergenic 35.0%
CAATCTCTTCTTAGTCTCTT+TGG + chr1_2:679906-679925 Msa0048380:CDS 35.0%
GAAAGAGTGAAGTTTCTTTC+AGG - chr1_2:679950-679969 None:intergenic 35.0%
! TTGAGTTGTGGAAACAAGAA+GGG - chr1_2:680058-680077 None:intergenic 35.0%
! ATTGAGTTGTGGAAACAAGA+AGG - chr1_2:680059-680078 None:intergenic 35.0%
!! CCTTTACAAGAAGTGTCTAA+AGG - chr1_2:680161-680180 None:intergenic 35.0%
CCTTTAGACACTTCTTGTAA+AGG + chr1_2:680158-680177 Msa0048380:CDS 35.0%
TAGCTATGATAAGGGTGAAG+AGG - chr1_2:679779-679798 None:intergenic 40.0%
CAGAAGGAGTAGCTATGATA+AGG - chr1_2:679788-679807 None:intergenic 40.0%
TTCTGCAGTATCATGTCCTA+TGG + chr1_2:679809-679828 Msa0048380:CDS 40.0%
TCAACATAGCTGAGATCCAT+AGG - chr1_2:679828-679847 None:intergenic 40.0%
CTATGTTGAGACCTTTCCAT+GGG + chr1_2:679839-679858 Msa0048380:CDS 40.0%
CTTCTTAGTCTCTTTGGCAT+AGG + chr1_2:679912-679931 Msa0048380:CDS 40.0%
AAACAAGAAGGGACTAACGA+AGG - chr1_2:680047-680066 None:intergenic 40.0%
AGTATACAACTAGCTGTAGC+AGG - chr1_2:680341-680360 None:intergenic 40.0%
GCTACAGCTAGTTGTATACT+TGG + chr1_2:680341-680360 Msa0048380:CDS 40.0%
CTATGATAAGGGTGAAGAGG+AGG - chr1_2:679776-679795 None:intergenic 45.0%
CATGATACTGCAGAAGCAGA+AGG - chr1_2:679804-679823 None:intergenic 45.0%
GCTATGTTGAGACCTTTCCA+TGG + chr1_2:679838-679857 Msa0048380:CDS 45.0%
AAGAAGGGACTAACGAAGGT+TGG - chr1_2:680043-680062 None:intergenic 45.0%
TAAGGGTGAAGAGGAGGAGA+AGG - chr1_2:679770-679789 None:intergenic 50.0%
! GGTTGATGTGTCCCATGGAA+AGG - chr1_2:679853-679872 None:intergenic 50.0%
TGTGTCAATTGGGTCTCTGC+AGG - chr1_2:679874-679893 None:intergenic 50.0%
ACAAACAACTCAAGCTGCGC+AGG + chr1_2:680089-680108 Msa0048380:CDS 50.0%
CTAGCTGTAGCAGGATCTGT+AGG - chr1_2:680332-680351 None:intergenic 50.0%
!! CTGCAGGTTGATGTGTCCCA+TGG - chr1_2:679858-679877 None:intergenic 55.0%
TGCAGCACGTGCACTAATGC+TGG + chr1_2:680203-680222 Msa0048380:CDS 55.0%
Chromosome Type Strat End Strand Name
chr1_2 gene 679747 680382 679747 ID=Msa0048380;Name=Msa0048380
chr1_2 mRNA 679747 680382 679747 ID=Msa0048380-mRNA-1;Parent=Msa0048380;Name=Msa0048380-mRNA-1;_AED=0.37;_eAED=0.37;_QI=0|-1|0|1|-1|1|1|0|211
chr1_2 exon 679747 680382 679747 ID=Msa0048380-mRNA-1:exon:123;Parent=Msa0048380-mRNA-1
chr1_2 CDS 679747 680382 679747 ID=Msa0048380-mRNA-1:cds;Parent=Msa0048380-mRNA-1
Gene Sequence

>Msa0048380

ATGGATAACAAAGCAGTGTTCCTTCTCCTCCTCTTCACCCTTATCATAGCTACTCCTTCTGCTTCTGCAGTATCATGTCCTATGGATCTCAGCTATGTTGAGACCTTTCCATGGGACACATCAACCTGCAGAGACCCAATTGACACACAACATTGTTGTCAATCTCTTCTTAGTCTCTTTGGCATAGGACTTGCAAAACACCTGAAAGAAACTTCACTCTTTCAACTCCCTAATAAAAACACTTTAAAATCTTGCTTACAAGATTTCAAACTCAAACTTTCATGCTTAAAGATCCAACCTTCGTTAGTCCCTTCTTGTTTCCACAACTCAATTCAATTTGTCACAAACAACTCAAGCTGCGCAGGTATCACAAACATCAAAGATTGGAAGCAAAAAGTTGGTAGAATTAGCCCTTTAGACACTTCTTGTAAAGGTGATTTGAAATCGGACACTAGTTGCAGCACGTGCACTAATGCTGGTTTCAAAGTCACTTCTCAGCTTACAAGTATTGATCCAAAAAATGCAACTAAGTGCTTTTTCTTTTCAGTTTTATATGCTGTTGGTATTGTGAATCATTTTGGTCCTACAGATCCTGCTACAGCTAGTTGTATACTTGGTATCCCGCTTAGAAGATGA

Protein sequence

>Msa0048380

MDNKAVFLLLLFTLIIATPSASAVSCPMDLSYVETFPWDTSTCRDPIDTQHCCQSLLSLFGIGLAKHLKETSLFQLPNKNTLKSCLQDFKLKLSCLKIQPSLVPSCFHNSIQFVTNNSSCAGITNIKDWKQKVGRISPLDTSCKGDLKSDTSCSTCTNAGFKVTSQLTSIDPKNATKCFFFSVLYAVGIVNHFGPTDPATASCILGIPLRR*