AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0205510


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0205510 MtrunA17_Chr3g0133201 88.696 115 10 1 5 116 617 731 1.51e-65 211
Msa0205510 MtrunA17_Chr1g0211421 54.098 61 28 0 19 79 348 408 3.71e-18 78.6
Msa0205510 MtrunA17_Chr2g0325981 39.773 88 45 1 19 106 325 404 3.38e-14 67.4
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0205510 AT5G10940.2 69.565 115 32 1 5 116 614 728 1.97e-50 170
Msa0205510 AT5G10940.1 69.565 115 32 1 5 116 617 731 2.24e-50 170
Msa0205510 AT4G38480.2 46.053 76 38 1 19 91 290 365 1.47e-16 74.3
Msa0205510 AT4G38480.1 46.053 76 38 1 19 91 323 398 1.80e-16 74.3
Msa0205510 AT4G35140.1 52.459 61 29 0 19 79 347 407 3.18e-16 73.6
Msa0205510 AT4G35140.2 52.459 61 29 0 19 79 347 407 4.16e-16 73.2
Msa0205510 AT3G45620.2 47.458 59 31 0 19 77 368 426 4.91e-14 67.4
Msa0205510 AT3G45620.1 47.458 59 31 0 19 77 334 392 5.10e-14 67.0

Find 26 sgRNAs with CRISPR-Local

Find 46 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CTTCTCACTTGTATATTTAT+AGG 0.167874 2_1:-32427205 Msa0205510:CDS
ATGATGGCAGATGGTTTATT+TGG 0.174052 2_1:-32427159 Msa0205510:CDS
AACAAAAGTTATCCCGTAAT+AGG 0.237900 2_1:-32426761 Msa0205510:CDS
CCCAACACATCACCAGTTTC+TGG 0.324612 2_1:+32426801 None:intergenic
TGATGGCAGATGGTTTATTT+GGG 0.402572 2_1:-32427158 Msa0205510:CDS
ACAAAAGTTATCCCGTAATA+GGG 0.403715 2_1:-32426760 Msa0205510:CDS
CAGCATTGAATCCCTATTAC+GGG 0.403849 2_1:+32426749 None:intergenic
ACAGCATTGAATCCCTATTA+CGG 0.407538 2_1:+32426748 None:intergenic
TCTGTAGCTGGTGGTTCTGC+AGG 0.414277 2_1:-32426825 Msa0205510:CDS
CCTGTTGCATCTTCTGTAGC+TGG 0.440848 2_1:-32426837 Msa0205510:CDS
TGGGATTGATAACACGATAA+AGG 0.444355 2_1:-32426958 Msa0205510:intron
GTTGCCACAACAAAATCAAA+TGG 0.472347 2_1:+32426984 None:intergenic
TGGTGATGTGTTGGGTGCTA+TGG 0.474086 2_1:-32426793 Msa0205510:CDS
TTTATTTGGGAAAAGCGAAC+TGG 0.476711 2_1:-32427145 Msa0205510:CDS
GTTGCCAGCGGTAGCGATGA+TGG 0.491901 2_1:-32427175 Msa0205510:CDS
GGTTCTGCAGGACCAGAAAC+TGG 0.510294 2_1:-32426813 Msa0205510:CDS
TTGCTGAGTGGCGATGAATC+TGG 0.510859 2_1:-32427109 Msa0205510:intron
CCAGCTACAGAAGATGCAAC+AGG 0.527365 2_1:+32426837 None:intergenic
GAAGATGCAACAGGAGCACT+TGG 0.539197 2_1:+32426846 None:intergenic
CCAGAAACTGGTGATGTGTT+GGG 0.549316 2_1:-32426801 Msa0205510:CDS
ACCAGAAACTGGTGATGTGT+TGG 0.557320 2_1:-32426802 Msa0205510:CDS
TCTGCCATCATCGCTACCGC+TGG 0.558595 2_1:+32427171 None:intergenic
GCGGTAGCGATGATGGCAGA+TGG 0.626278 2_1:-32427168 Msa0205510:CDS
GTTGCATCTTCTGTAGCTGG+TGG 0.634469 2_1:-32426834 Msa0205510:CDS
ATAGGTGAATATGTTGCCAG+CGG 0.668912 2_1:-32427187 Msa0205510:CDS
AGACTCATGAAATTGCTGAG+TGG 0.779389 2_1:-32427121 Msa0205510:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! CAAAATAAAAATTGCAAATA+TGG + chr2_1:32426754-32426773 None:intergenic 15.0%
!! ATCATTATTCTATGATGTAT+TGG - chr2_1:32427051-32427070 Msa0205510:intron 20.0%
!! TCATTATTCTATGATGTATT+GGG - chr2_1:32427052-32427071 Msa0205510:intron 20.0%
! CTTCTCACTTGTATATTTAT+AGG - chr2_1:32426776-32426795 Msa0205510:CDS 25.0%
!! ACATTGTTTTCCTATGATTT+TGG - chr2_1:32426897-32426916 Msa0205510:intron 25.0%
!! CATTGTTTTCCTATGATTTT+GGG - chr2_1:32426898-32426917 Msa0205510:intron 25.0%
! CATTATTCTATGATGTATTG+GGG - chr2_1:32427053-32427072 Msa0205510:intron 25.0%
CTTCAAAATCCCAAAATCAT+AGG + chr2_1:32426910-32426929 None:intergenic 30.0%
!! TCATCCATTTGATTTTGTTG+TGG - chr2_1:32426993-32427012 Msa0205510:CDS 30.0%
AACAAAAGTTATCCCGTAAT+AGG - chr2_1:32427220-32427239 Msa0205510:CDS 30.0%
ACAAAAGTTATCCCGTAATA+GGG - chr2_1:32427221-32427240 Msa0205510:CDS 30.0%
ATGATGGCAGATGGTTTATT+TGG - chr2_1:32426822-32426841 Msa0205510:CDS 35.0%
TGATGGCAGATGGTTTATTT+GGG - chr2_1:32426823-32426842 Msa0205510:CDS 35.0%
TTTATTTGGGAAAAGCGAAC+TGG - chr2_1:32426836-32426855 Msa0205510:CDS 35.0%
AGCTTCAGATAACAGTACAA+GGG + chr2_1:32426937-32426956 None:intergenic 35.0%
TAGCTTCAGATAACAGTACA+AGG + chr2_1:32426938-32426957 None:intergenic 35.0%
TGTACGCAATTTACAACTGT+AGG + chr2_1:32426970-32426989 None:intergenic 35.0%
GTTGCCACAACAAAATCAAA+TGG + chr2_1:32427000-32427019 None:intergenic 35.0%
!! ATTTTGTTGTGGCAACAAGT+GGG - chr2_1:32427004-32427023 Msa0205510:CDS 35.0%
! TGGGATTGATAACACGATAA+AGG - chr2_1:32427023-32427042 Msa0205510:intron 35.0%
!!! GTGATGGATTTTCCTAGATA+TGG - chr2_1:32427109-32427128 Msa0205510:intron 35.0%
! ACAGCATTGAATCCCTATTA+CGG + chr2_1:32427236-32427255 None:intergenic 35.0%
ATAGGTGAATATGTTGCCAG+CGG - chr2_1:32426794-32426813 Msa0205510:CDS 40.0%
AGACTCATGAAATTGCTGAG+TGG - chr2_1:32426860-32426879 Msa0205510:intron 40.0%
TTCAGATAACAGTACAAGGG+GGG + chr2_1:32426934-32426953 None:intergenic 40.0%
CTTCAGATAACAGTACAAGG+GGG + chr2_1:32426935-32426954 None:intergenic 40.0%
GCTTCAGATAACAGTACAAG+GGG + chr2_1:32426936-32426955 None:intergenic 40.0%
!! GATTTTGTTGTGGCAACAAG+TGG - chr2_1:32427003-32427022 Msa0205510:CDS 40.0%
!! TTTCAATCTCTGAAGCTGTC+TGG - chr2_1:32427087-32427106 Msa0205510:intron 40.0%
! CAGCATTGAATCCCTATTAC+GGG + chr2_1:32427235-32427254 None:intergenic 40.0%
AGCACTTGGAGTCCATATCT+AGG + chr2_1:32427124-32427143 None:intergenic 45.0%
! ACCAGAAACTGGTGATGTGT+TGG - chr2_1:32427179-32427198 Msa0205510:CDS 45.0%
! CCAGAAACTGGTGATGTGTT+GGG - chr2_1:32427180-32427199 Msa0205510:CDS 45.0%
TTGCTGAGTGGCGATGAATC+TGG - chr2_1:32426872-32426891 Msa0205510:intron 50.0%
!! TCTCTGAAGCTGTCTGGTGA+TGG - chr2_1:32427093-32427112 Msa0205510:intron 50.0%
!! GAAGATGCAACAGGAGCACT+TGG + chr2_1:32427138-32427157 None:intergenic 50.0%
CCAGCTACAGAAGATGCAAC+AGG + chr2_1:32427147-32427166 None:intergenic 50.0%
CCTGTTGCATCTTCTGTAGC+TGG - chr2_1:32427144-32427163 Msa0205510:CDS 50.0%
GTTGCATCTTCTGTAGCTGG+TGG - chr2_1:32427147-32427166 Msa0205510:CDS 50.0%
CCCAACACATCACCAGTTTC+TGG + chr2_1:32427183-32427202 None:intergenic 50.0%
! TGGTGATGTGTTGGGTGCTA+TGG - chr2_1:32427188-32427207 Msa0205510:CDS 50.0%
! TCTGTAGCTGGTGGTTCTGC+AGG - chr2_1:32427156-32427175 Msa0205510:CDS 55.0%
GGTTCTGCAGGACCAGAAAC+TGG - chr2_1:32427168-32427187 Msa0205510:CDS 55.0%
GTTGCCAGCGGTAGCGATGA+TGG - chr2_1:32426806-32426825 Msa0205510:CDS 60.0%
TCTGCCATCATCGCTACCGC+TGG + chr2_1:32426813-32426832 None:intergenic 60.0%
! GCGGTAGCGATGATGGCAGA+TGG - chr2_1:32426813-32426832 Msa0205510:CDS 60.0%
Chromosome Type Strat End Strand Name
chr2_1 gene 32426746 32427257 32426746 ID=Msa0205510;Name=Msa0205510
chr2_1 mRNA 32426746 32427257 32426746 ID=Msa0205510-mRNA-1;Parent=Msa0205510;Name=Msa0205510-mRNA-1;_AED=0.07;_eAED=0.07;_QI=0|1|0.33|1|1|1|3|0|116
chr2_1 exon 32427110 32427257 32427110 ID=Msa0205510-mRNA-1:exon:11323;Parent=Msa0205510-mRNA-1
chr2_1 exon 32426959 32427029 32426959 ID=Msa0205510-mRNA-1:exon:11322;Parent=Msa0205510-mRNA-1
chr2_1 exon 32426746 32426877 32426746 ID=Msa0205510-mRNA-1:exon:11321;Parent=Msa0205510-mRNA-1
chr2_1 CDS 32427110 32427257 32427110 ID=Msa0205510-mRNA-1:cds;Parent=Msa0205510-mRNA-1
chr2_1 CDS 32426959 32427029 32426959 ID=Msa0205510-mRNA-1:cds;Parent=Msa0205510-mRNA-1
chr2_1 CDS 32426746 32426877 32426746 ID=Msa0205510-mRNA-1:cds;Parent=Msa0205510-mRNA-1
Gene Sequence

>Msa0205510

TTGGTCCATATTTGCAATTTTTATTTTGAACTTCTCACTTGTATATTTATAGGTGAATATGTTGCCAGCGGTAGCGATGATGGCAGATGGTTTATTTGGGAAAAGCGAACTGGAAGACTCATGAAATTGCTGAGTGGCGATGAATCTGTTGTAAATTGCGTACAATGTCATCCATTTGATTTTGTTGTGGCAACAAGTGGGATTGATAACACGATAAAGATATGGACTCCAAGTGCTCCTGTTGCATCTTCTGTAGCTGGTGGTTCTGCAGGACCAGAAACTGGTGATGTGTTGGGTGCTATGGAGAACAATCAACAAAAGTTATCCCGTAATAGGGATTCAATGCTGTAA

Protein sequence

>Msa0205510

LVHICNFYFELLTCIFIGEYVASGSDDGRWFIWEKRTGRLMKLLSGDESVVNCVQCHPFDFVVATSGIDNTIKIWTPSAPVASSVAGGSAGPETGDVLGAMENNQQKLSRNRDSML*