AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1348890


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1348890 MtrunA17_Chr4g0005821 97.826 92 2 0 1 92 597 688 2.40e-58 189
Msa1348890 MtrunA17_Chr7g0241611 68.235 85 27 0 1 85 603 687 1.15e-35 127
Msa1348890 MtrunA17_Chr7g0259681 65.217 92 30 1 1 92 545 634 9.64e-34 121
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1348890 AT3G09100.2 69.136 81 25 0 1 81 588 668 3.72e-33 120
Msa1348890 AT5G01290.1 64.198 81 29 0 1 81 573 653 4.99e-30 111
Msa1348890 AT5G28210.1 54.795 73 33 0 8 80 541 613 2.88e-21 86.7

Find 49 sgRNAs with CRISPR-Local

Find 114 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
ATTGGATTTGGCTATATATT+TGG 0.139270 tig0010575:+2266 Msa1348890:three_prime_UTR
CCCACCAGTGAAATAATTTA+AGG 0.144290 tig0010575:-2165 Msa1348890:intergenic
TGTCTGCTTCTGGTATTTAT+TGG 0.225810 tig0010575:+2248 Msa1348890:three_prime_UTR
CTTCTGGTATTTATTGGATT+TGG 0.247314 tig0010575:+2254 Msa1348890:three_prime_UTR
CTGTAGTTGTCTAGATCAAT+AGG 0.277033 tig0010575:+2377 Msa1348890:three_prime_UTR
TAACCATTGGTGTCTGCTTC+TGG 0.303633 tig0010575:+2238 Msa1348890:three_prime_UTR
CTGTAAGTATTAAACTCATT+TGG 0.310885 tig0010575:-1881 Msa1348890:intergenic
TCTATGTATGTGATGAATAT+TGG 0.315742 tig0010575:+2516 Msa1348890:three_prime_UTR
GTGATTCGTTGTGGTTAGAT+AGG 0.323605 tig0010575:+2131 Msa1348890:exon
AGATCAATAGGGTTAGGTTT+AGG 0.374635 tig0010575:+2389 Msa1348890:three_prime_UTR
TGTTTGTAGGGTAGAAGATC+AGG 0.375622 tig0010575:+2197 Msa1348890:three_prime_UTR
ATCTAGACAACTACAGGAAA+TGG 0.381374 tig0010575:-2370 Msa1348890:intergenic
GAAAGATCATCGAGTGTTCT+TGG 0.390585 tig0010575:+1804 Msa1348890:CDS
GTGATTATAAATTATTCAAA+TGG 0.397526 tig0010575:+2446 Msa1348890:three_prime_UTR
TTTGCAAGAATATCCATTCC+AGG 0.413098 tig0010575:-1838 Msa1348890:intergenic
TTGTCTAGATCAATAGGGTT+AGG 0.424051 tig0010575:+2383 Msa1348890:three_prime_UTR
AATGCCTTAAATTATTTCAC+TGG 0.432603 tig0010575:+2161 Msa1348890:three_prime_UTR
TGCTGTCAAGTCACAGAGAA+TGG 0.448086 tig0010575:-2591 Msa1348890:intergenic
AAAGATCATCGAGTGTTCTT+GGG 0.450552 tig0010575:+1805 Msa1348890:CDS
TGAATATTAATTTAACTACT+AGG 0.455263 tig0010575:+2558 Msa1348890:three_prime_UTR
GAAAATTCTAACCAATGTAC+TGG 0.470626 tig0010575:-2495 Msa1348890:intergenic
AGGTTGCTTATGTAATTAGT+TGG 0.477860 tig0010575:+2300 Msa1348890:three_prime_UTR
CTAATTACATAAGCAACCTT+AGG 0.479770 tig0010575:-2296 Msa1348890:intergenic
GCCTTAAATTATTTCACTGG+TGG 0.481047 tig0010575:+2164 Msa1348890:three_prime_UTR
GATCTTTCCTGAATAAAATG+AGG 0.485887 tig0010575:-1789 Msa1348890:intergenic
TGGGAGAATGAGATGTTTGT+AGG 0.486998 tig0010575:+2184 Msa1348890:three_prime_UTR
GAATCACCTTCGCTGCTTTG+CGG 0.489232 tig0010575:-2115 Msa1348890:intergenic
TGTAGTTGTCTAGATCAATA+GGG 0.492453 tig0010575:+2378 Msa1348890:three_prime_UTR
ATGAAATTTGTGACGCAACT+CGG 0.504231 tig0010575:-2340 Msa1348890:intergenic
CCTTAAATTATTTCACTGGT+GGG 0.508594 tig0010575:+2165 Msa1348890:three_prime_UTR
CATAAGCAACCTTAGGATGA+TGG 0.518880 tig0010575:-2289 Msa1348890:intergenic
CTCATGCCGCAAAGCAGCGA+AGG 0.526270 tig0010575:+2109 Msa1348890:CDS
TGAGTTTAATACTTACAGAA+AGG 0.527213 tig0010575:+1886 Msa1348890:CDS
GCCTTCCCATGTATGCGGAC+AGG 0.528594 tig0010575:+2055 Msa1348890:CDS
CTATTGATCTAGACAACTAC+AGG 0.530585 tig0010575:-2376 Msa1348890:intergenic
TATATTTGGCCATCATCCTA+AGG 0.530710 tig0010575:+2280 Msa1348890:three_prime_UTR
TGATTCGTTGTGGTTAGATA+GGG 0.530949 tig0010575:+2132 Msa1348890:exon
AGAATCAAGTTCCAGTACAT+TGG 0.540413 tig0010575:+2484 Msa1348890:three_prime_UTR
AACTCGGCAGCACTGCTGCA+AGG 0.544386 tig0010575:-2324 Msa1348890:intergenic
ACATAAACATATGTAACCAT+TGG 0.547919 tig0010575:+2225 Msa1348890:three_prime_UTR
TCCTGTCCGCATACATGGGA+AGG 0.564771 tig0010575:-2056 Msa1348890:intergenic
GTCAAGTCACAGAGAATGGA+AGG 0.565175 tig0010575:-2587 Msa1348890:intergenic
ATCTTTCCTGAATAAAATGA+GGG 0.576935 tig0010575:-1788 Msa1348890:intergenic
GGGAGAATGAGATGTTTGTA+GGG 0.614069 tig0010575:+2185 Msa1348890:three_prime_UTR
TTTATCCTGTCCGCATACAT+GGG 0.615995 tig0010575:-2060 Msa1348890:intergenic
GCAGCGAAGGTGATTCGTTG+TGG 0.625865 tig0010575:+2122 Msa1348890:exon
ATACCAGAAGCAGACACCAA+TGG 0.662343 tig0010575:-2241 Msa1348890:intergenic
AATTCGCCTTCCCATGTATG+CGG 0.681083 tig0010575:+2050 Msa1348890:CDS
CATAAAAGACAACATCACAG+AGG 0.751598 tig0010575:+1999 Msa1348890:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! GTGATTATAAATTATTCAAA+TGG + tig0010575:2446-2465 Msa1348890:three_prime_UTR 15.0%
!! TGAATATTAATTTAACTACT+AGG + tig0010575:2558-2577 Msa1348890:three_prime_UTR 15.0%
!! GTGATTATAAATTATTCAAA+TGG + tig0010575:2446-2465 Msa1348890:three_prime_UTR 15.0%
!! TGAATATTAATTTAACTACT+AGG + tig0010575:2558-2577 Msa1348890:three_prime_UTR 15.0%
!! GATGAAAGAAACTAAAAATT+GGG - tig0010575:1925-1944 Msa1348890:intergenic 20.0%
!! AGATGAAAGAAACTAAAAAT+TGG - tig0010575:1926-1945 Msa1348890:intergenic 20.0%
!!! AGCCATTTACTTAATTTTAT+AGG + tig0010575:1966-1985 Msa1348890:intron 20.0%
!! CACCTATAAAATTAAGTAAA+TGG - tig0010575:1971-1990 Msa1348890:intergenic 20.0%
!! GATGAAAGAAACTAAAAATT+GGG - tig0010575:1925-1944 Msa1348890:intergenic 20.0%
!! AGATGAAAGAAACTAAAAAT+TGG - tig0010575:1926-1945 Msa1348890:intergenic 20.0%
!!! AGCCATTTACTTAATTTTAT+AGG + tig0010575:1966-1985 Msa1348890:intron 20.0%
!! CACCTATAAAATTAAGTAAA+TGG - tig0010575:1971-1990 Msa1348890:intergenic 20.0%
! ATCTTTCCTGAATAAAATGA+GGG - tig0010575:1791-1810 Msa1348890:intergenic 25.0%
! CTGTAAGTATTAAACTCATT+TGG - tig0010575:1884-1903 Msa1348890:intergenic 25.0%
! TGAGTTTAATACTTACAGAA+AGG + tig0010575:1886-1905 Msa1348890:CDS 25.0%
! TAAAAATTGGGAGTTAGTAT+TGG - tig0010575:1913-1932 Msa1348890:intergenic 25.0%
! TTCATCTCTAAATATGTACT+TGG + tig0010575:1939-1958 Msa1348890:intron 25.0%
! AATGCCTTAAATTATTTCAC+TGG + tig0010575:2161-2180 Msa1348890:three_prime_UTR 25.0%
! ACATAAACATATGTAACCAT+TGG + tig0010575:2225-2244 Msa1348890:three_prime_UTR 25.0%
! ATTGGATTTGGCTATATATT+TGG + tig0010575:2266-2285 Msa1348890:three_prime_UTR 25.0%
! TCTATGTATGTGATGAATAT+TGG + tig0010575:2516-2535 Msa1348890:three_prime_UTR 25.0%
! ATCTTTCCTGAATAAAATGA+GGG - tig0010575:1791-1810 Msa1348890:intergenic 25.0%
! CTGTAAGTATTAAACTCATT+TGG - tig0010575:1884-1903 Msa1348890:intergenic 25.0%
! TGAGTTTAATACTTACAGAA+AGG + tig0010575:1886-1905 Msa1348890:CDS 25.0%
! TAAAAATTGGGAGTTAGTAT+TGG - tig0010575:1913-1932 Msa1348890:intergenic 25.0%
! TTCATCTCTAAATATGTACT+TGG + tig0010575:1939-1958 Msa1348890:intron 25.0%
! AATGCCTTAAATTATTTCAC+TGG + tig0010575:2161-2180 Msa1348890:three_prime_UTR 25.0%
! ACATAAACATATGTAACCAT+TGG + tig0010575:2225-2244 Msa1348890:three_prime_UTR 25.0%
! ATTGGATTTGGCTATATATT+TGG + tig0010575:2266-2285 Msa1348890:three_prime_UTR 25.0%
! TCTATGTATGTGATGAATAT+TGG + tig0010575:2516-2535 Msa1348890:three_prime_UTR 25.0%
GATCTTTCCTGAATAAAATG+AGG - tig0010575:1792-1811 Msa1348890:intergenic 30.0%
CCTTAAATTATTTCACTGGT+GGG + tig0010575:2165-2184 Msa1348890:three_prime_UTR 30.0%
CTTCTGGTATTTATTGGATT+TGG + tig0010575:2254-2273 Msa1348890:three_prime_UTR 30.0%
CTAATTACATAAGCAACCTT+AGG - tig0010575:2299-2318 Msa1348890:intergenic 30.0%
AGGTTGCTTATGTAATTAGT+TGG + tig0010575:2300-2319 Msa1348890:three_prime_UTR 30.0%
TGTAGTTGTCTAGATCAATA+GGG + tig0010575:2378-2397 Msa1348890:three_prime_UTR 30.0%
GAAAATTCTAACCAATGTAC+TGG - tig0010575:2498-2517 Msa1348890:intergenic 30.0%
GATCTTTCCTGAATAAAATG+AGG - tig0010575:1792-1811 Msa1348890:intergenic 30.0%
CCTTAAATTATTTCACTGGT+GGG + tig0010575:2165-2184 Msa1348890:three_prime_UTR 30.0%
CTTCTGGTATTTATTGGATT+TGG + tig0010575:2254-2273 Msa1348890:three_prime_UTR 30.0%
CTAATTACATAAGCAACCTT+AGG - tig0010575:2299-2318 Msa1348890:intergenic 30.0%
AGGTTGCTTATGTAATTAGT+TGG + tig0010575:2300-2319 Msa1348890:three_prime_UTR 30.0%
TGTAGTTGTCTAGATCAATA+GGG + tig0010575:2378-2397 Msa1348890:three_prime_UTR 30.0%
GAAAATTCTAACCAATGTAC+TGG - tig0010575:2498-2517 Msa1348890:intergenic 30.0%
! ACAGAACCCTCATTTTATTC+AGG + tig0010575:1782-1801 Msa1348890:CDS 35.0%
AAAGATCATCGAGTGTTCTT+GGG + tig0010575:1805-1824 Msa1348890:CDS 35.0%
!! TTCTTGGGATTTTGATAACC+TGG + tig0010575:1820-1839 Msa1348890:CDS 35.0%
TTTGCAAGAATATCCATTCC+AGG - tig0010575:1841-1860 Msa1348890:intergenic 35.0%
CATAAAAGACAACATCACAG+AGG + tig0010575:1999-2018 Msa1348890:CDS 35.0%
TGATTCGTTGTGGTTAGATA+GGG + tig0010575:2132-2151 Msa1348890:exon 35.0%
GCCTTAAATTATTTCACTGG+TGG + tig0010575:2164-2183 Msa1348890:three_prime_UTR 35.0%
CCCACCAGTGAAATAATTTA+AGG - tig0010575:2168-2187 Msa1348890:intergenic 35.0%
TGTCTGCTTCTGGTATTTAT+TGG + tig0010575:2248-2267 Msa1348890:three_prime_UTR 35.0%
TATATTTGGCCATCATCCTA+AGG + tig0010575:2280-2299 Msa1348890:three_prime_UTR 35.0%
ATGAAATTTGTGACGCAACT+CGG - tig0010575:2343-2362 Msa1348890:intergenic 35.0%
ATCTAGACAACTACAGGAAA+TGG - tig0010575:2373-2392 Msa1348890:intergenic 35.0%
CTATTGATCTAGACAACTAC+AGG - tig0010575:2379-2398 Msa1348890:intergenic 35.0%
CTGTAGTTGTCTAGATCAAT+AGG + tig0010575:2377-2396 Msa1348890:three_prime_UTR 35.0%
TTGTCTAGATCAATAGGGTT+AGG + tig0010575:2383-2402 Msa1348890:three_prime_UTR 35.0%
AGATCAATAGGGTTAGGTTT+AGG + tig0010575:2389-2408 Msa1348890:three_prime_UTR 35.0%
AGAATCAAGTTCCAGTACAT+TGG + tig0010575:2484-2503 Msa1348890:three_prime_UTR 35.0%
! ACAGAACCCTCATTTTATTC+AGG + tig0010575:1782-1801 Msa1348890:CDS 35.0%
AAAGATCATCGAGTGTTCTT+GGG + tig0010575:1805-1824 Msa1348890:CDS 35.0%
!! TTCTTGGGATTTTGATAACC+TGG + tig0010575:1820-1839 Msa1348890:CDS 35.0%
TTTGCAAGAATATCCATTCC+AGG - tig0010575:1841-1860 Msa1348890:intergenic 35.0%
CATAAAAGACAACATCACAG+AGG + tig0010575:1999-2018 Msa1348890:CDS 35.0%
TGATTCGTTGTGGTTAGATA+GGG + tig0010575:2132-2151 Msa1348890:exon 35.0%
GCCTTAAATTATTTCACTGG+TGG + tig0010575:2164-2183 Msa1348890:three_prime_UTR 35.0%
CCCACCAGTGAAATAATTTA+AGG - tig0010575:2168-2187 Msa1348890:intergenic 35.0%
TGTCTGCTTCTGGTATTTAT+TGG + tig0010575:2248-2267 Msa1348890:three_prime_UTR 35.0%
TATATTTGGCCATCATCCTA+AGG + tig0010575:2280-2299 Msa1348890:three_prime_UTR 35.0%
ATGAAATTTGTGACGCAACT+CGG - tig0010575:2343-2362 Msa1348890:intergenic 35.0%
ATCTAGACAACTACAGGAAA+TGG - tig0010575:2373-2392 Msa1348890:intergenic 35.0%
CTATTGATCTAGACAACTAC+AGG - tig0010575:2379-2398 Msa1348890:intergenic 35.0%
CTGTAGTTGTCTAGATCAAT+AGG + tig0010575:2377-2396 Msa1348890:three_prime_UTR 35.0%
TTGTCTAGATCAATAGGGTT+AGG + tig0010575:2383-2402 Msa1348890:three_prime_UTR 35.0%
AGATCAATAGGGTTAGGTTT+AGG + tig0010575:2389-2408 Msa1348890:three_prime_UTR 35.0%
AGAATCAAGTTCCAGTACAT+TGG + tig0010575:2484-2503 Msa1348890:three_prime_UTR 35.0%
GAAAGATCATCGAGTGTTCT+TGG + tig0010575:1804-1823 Msa1348890:CDS 40.0%
!! GGGATTTTGATAACCTGGAA+TGG + tig0010575:1825-1844 Msa1348890:CDS 40.0%
TTTATCCTGTCCGCATACAT+GGG - tig0010575:2063-2082 Msa1348890:intergenic 40.0%
! TTTTATCCTGTCCGCATACA+TGG - tig0010575:2064-2083 Msa1348890:intergenic 40.0%
GTGATTCGTTGTGGTTAGAT+AGG + tig0010575:2131-2150 Msa1348890:exon 40.0%
TGGGAGAATGAGATGTTTGT+AGG + tig0010575:2184-2203 Msa1348890:three_prime_UTR 40.0%
GGGAGAATGAGATGTTTGTA+GGG + tig0010575:2185-2204 Msa1348890:three_prime_UTR 40.0%
TGTTTGTAGGGTAGAAGATC+AGG + tig0010575:2197-2216 Msa1348890:three_prime_UTR 40.0%
CATAAGCAACCTTAGGATGA+TGG - tig0010575:2292-2311 Msa1348890:intergenic 40.0%
GAAAGATCATCGAGTGTTCT+TGG + tig0010575:1804-1823 Msa1348890:CDS 40.0%
!! GGGATTTTGATAACCTGGAA+TGG + tig0010575:1825-1844 Msa1348890:CDS 40.0%
TTTATCCTGTCCGCATACAT+GGG - tig0010575:2063-2082 Msa1348890:intergenic 40.0%
! TTTTATCCTGTCCGCATACA+TGG - tig0010575:2064-2083 Msa1348890:intergenic 40.0%
GTGATTCGTTGTGGTTAGAT+AGG + tig0010575:2131-2150 Msa1348890:exon 40.0%
TGGGAGAATGAGATGTTTGT+AGG + tig0010575:2184-2203 Msa1348890:three_prime_UTR 40.0%
GGGAGAATGAGATGTTTGTA+GGG + tig0010575:2185-2204 Msa1348890:three_prime_UTR 40.0%
TGTTTGTAGGGTAGAAGATC+AGG + tig0010575:2197-2216 Msa1348890:three_prime_UTR 40.0%
CATAAGCAACCTTAGGATGA+TGG - tig0010575:2292-2311 Msa1348890:intergenic 40.0%
AATTCGCCTTCCCATGTATG+CGG + tig0010575:2050-2069 Msa1348890:CDS 45.0%
! TAACCATTGGTGTCTGCTTC+TGG + tig0010575:2238-2257 Msa1348890:three_prime_UTR 45.0%
ATACCAGAAGCAGACACCAA+TGG - tig0010575:2244-2263 Msa1348890:intergenic 45.0%
AATTCGCCTTCCCATGTATG+CGG + tig0010575:2050-2069 Msa1348890:CDS 45.0%
! TAACCATTGGTGTCTGCTTC+TGG + tig0010575:2238-2257 Msa1348890:three_prime_UTR 45.0%
ATACCAGAAGCAGACACCAA+TGG - tig0010575:2244-2263 Msa1348890:intergenic 45.0%
! GAATCACCTTCGCTGCTTTG+CGG - tig0010575:2118-2137 Msa1348890:intergenic 50.0%
! GAATCACCTTCGCTGCTTTG+CGG - tig0010575:2118-2137 Msa1348890:intergenic 50.0%
TCCTGTCCGCATACATGGGA+AGG - tig0010575:2059-2078 Msa1348890:intergenic 55.0%
GCAGCGAAGGTGATTCGTTG+TGG + tig0010575:2122-2141 Msa1348890:exon 55.0%
TCCTGTCCGCATACATGGGA+AGG - tig0010575:2059-2078 Msa1348890:intergenic 55.0%
GCAGCGAAGGTGATTCGTTG+TGG + tig0010575:2122-2141 Msa1348890:exon 55.0%
GCCTTCCCATGTATGCGGAC+AGG + tig0010575:2055-2074 Msa1348890:CDS 60.0%
CTCATGCCGCAAAGCAGCGA+AGG + tig0010575:2109-2128 Msa1348890:CDS 60.0%
AACTCGGCAGCACTGCTGCA+AGG - tig0010575:2327-2346 Msa1348890:intergenic 60.0%
GCCTTCCCATGTATGCGGAC+AGG + tig0010575:2055-2074 Msa1348890:CDS 60.0%
CTCATGCCGCAAAGCAGCGA+AGG + tig0010575:2109-2128 Msa1348890:CDS 60.0%
AACTCGGCAGCACTGCTGCA+AGG - tig0010575:2327-2346 Msa1348890:intergenic 60.0%
Chromosome Type Strat End Strand Name
tig0010575 gene 1776 2601 1776 ID=Msa1348890;Name=Msa1348890
tig0010575 mRNA 1776 2601 1776 ID=Msa1348890-mRNA-1;Parent=Msa1348890;Name=Msa1348890-mRNA-1;_AED=0.00;_eAED=0.00;_QI=0|1|0.5|1|1|1|2|467|92
tig0010575 exon 1776 1907 1776 ID=Msa1348890-mRNA-1:exon:6642;Parent=Msa1348890-mRNA-1
tig0010575 exon 1988 2601 1988 ID=Msa1348890-mRNA-1:exon:6643;Parent=Msa1348890-mRNA-1
tig0010575 CDS 1776 1907 1776 ID=Msa1348890-mRNA-1:cds;Parent=Msa1348890-mRNA-1
tig0010575 CDS 1988 2134 1988 ID=Msa1348890-mRNA-1:cds;Parent=Msa1348890-mRNA-1
tig0010575 three_prime_UTR 2135 2601 2135 ID=Msa1348890-mRNA-1:three_prime_utr;Parent=Msa1348890-mRNA-1
Gene Sequence

>Msa1348890

GATGGCACAGAACCCTCATTTTATTCAGGAAAGATCATCGAGTGTTCTTGGGATTTTGATAACCTGGAATGGATATTCTTGCAAATTAGAACAGATAAATCAACTCCAAATGAGTTTAATACTTACAGAAAGGTGATGCAAAGCATAAAAGACAACATCACAGAGGAAGACTTGTTGAATGAAATAAATGAGATAATTCGCCTTCCCATGTATGCGGACAGGATAAAAAGTGATAGTAAAGCAAATCAGATTGCTCATGCCGCAAAGCAGCGAAGGTGA

Protein sequence

>Msa1348890

DGTEPSFYSGKIIECSWDFDNLEWIFLQIRTDKSTPNEFNTYRKVMQSIKDNITEEDLLNEINEIIRLPMYADRIKSDSKANQIAHAAKQRR*