AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1395570


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1395570 MtrunA17_Chr7g0249081 97.015 134 4 0 1 134 124 257 6.06e-96 276
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1395570 AT1G79790.1 61.538 130 50 0 1 130 113 242 1.31e-57 179
Msa1395570 AT1G79790.2 51.613 155 50 1 1 130 113 267 7.33e-52 165
Msa1395570 AT1G79790.4 51.351 148 47 1 8 130 1 148 4.15e-50 157

Find 27 sgRNAs with CRISPR-Local

Find 129 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TTTCGTTTACACGGTGAAAA+AGG 0.177329 tig0021957:+2320 Msa1395570:three_prime_UTR
GATGGTTTAAGTCTATATTT+TGG 0.243049 tig0021957:+2406 Msa1395570:three_prime_UTR
ATCTATCAAAATATTTATCT+TGG 0.276589 tig0021957:+1586 Msa1395570:CDS
TTTCACCGTGTAAACGAAAT+TGG 0.283521 tig0021957:-2316 None:intergenic
TAATTGAGATTTAAAAGAAT+TGG 0.334473 tig0021957:+2431 Msa1395570:three_prime_UTR
CTTAAAACTTGTATGAGAAA+TGG 0.339472 tig0021957:+1373 Msa1395570:CDS
TCTATGAAAATACAATATTC+TGG 0.343770 tig0021957:-1867 None:intergenic
AATGGGTATTCATACATAGA+AGG 0.378988 tig0021957:+1391 Msa1395570:CDS
ACCGGATACTGAATTCTATA+AGG 0.381928 tig0021957:+1818 Msa1395570:CDS
ACAATATACAATTAAGAATC+TGG 0.398877 tig0021957:-2349 None:intergenic
TTAAAACTTGTATGAGAAAT+GGG 0.400962 tig0021957:+1374 Msa1395570:CDS
TTTATTGTGTTTCAGGAAAG+AGG 0.415252 tig0021957:+1793 Msa1395570:intron
TCCTTATAGAATTCAGTATC+CGG 0.443431 tig0021957:-1819 None:intergenic
GCGCGAAGAACTGTCATTGA+TGG 0.454275 tig0021957:+2234 Msa1395570:CDS
TGCAGGCAGCAGCTGAAGTT+GGG 0.455154 tig0021957:+2176 Msa1395570:CDS
GTGCAGGCAGCAGCTGAAGT+TGG 0.459723 tig0021957:+2175 Msa1395570:CDS
AGCAGCTGAAGTTGGGATCA+AGG 0.467596 tig0021957:+2183 Msa1395570:CDS
CGCGAAGAACTGTCATTGAT+GGG 0.472416 tig0021957:+2235 Msa1395570:CDS
ATTGAGCTTTGTTAAAATGA+TGG 0.477570 tig0021957:+2388 Msa1395570:three_prime_UTR
AATTCTATAAGGAAGTTGTC+AGG 0.516039 tig0021957:+1829 Msa1395570:CDS
ATGGGTATTCATACATAGAA+GGG 0.518947 tig0021957:+1392 Msa1395570:CDS
TGTTTCAGGAAAGAGGAAAC+CGG 0.520264 tig0021957:+1800 Msa1395570:intron
ATACACCAATTTCGTTTACA+CGG 0.566029 tig0021957:+2311 Msa1395570:three_prime_UTR
GCAGCTGAAGTTGGGATCAA+GGG 0.568479 tig0021957:+2184 Msa1395570:CDS
GCGAAGAACTGTCATTGATG+GGG 0.637374 tig0021957:+2236 Msa1395570:CDS
TGGGTATTCATACATAGAAG+GGG 0.656968 tig0021957:+1393 Msa1395570:CDS
CGAAGAACTGTCATTGATGG+GGG 0.683926 tig0021957:+2237 Msa1395570:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! ATCTATCAAAATATTTATCT+TGG + tig0021957:1586-1605 Msa1395570:CDS 15.0%
!! TTATGATATTATATCCTAAT+TGG + tig0021957:1682-1701 Msa1395570:intron 15.0%
!! TAATTGAGATTTAAAAGAAT+TGG + tig0021957:2431-2450 Msa1395570:three_prime_UTR 15.0%
!! ATCTATCAAAATATTTATCT+TGG + tig0021957:1586-1605 Msa1395570:CDS 15.0%
!! TTATGATATTATATCCTAAT+TGG + tig0021957:1682-1701 Msa1395570:intron 15.0%
!! TAATTGAGATTTAAAAGAAT+TGG + tig0021957:2431-2450 Msa1395570:three_prime_UTR 15.0%
!! TTAAAACTTGTATGAGAAAT+GGG + tig0021957:1374-1393 Msa1395570:CDS 20.0%
!!! CTCAAAGTTATTTTTCTTTA+AGG - tig0021957:1437-1456 None:intergenic 20.0%
!!! CTTTTACTAATTATCCTATA+TGG + tig0021957:1464-1483 Msa1395570:CDS 20.0%
!!! AATTCATTTTCTTACCATAT+AGG - tig0021957:1481-1500 None:intergenic 20.0%
!!! ATGATGAGTTCTTTTTTTTT+CGG - tig0021957:1709-1728 None:intergenic 20.0%
!! AAAAAGAACTCATCATTTAA+AGG + tig0021957:1713-1732 Msa1395570:intron 20.0%
!! TCTATGAAAATACAATATTC+TGG - tig0021957:1870-1889 None:intergenic 20.0%
!! ATAAATTGTAAGTGATATCA+TGG - tig0021957:1942-1961 None:intergenic 20.0%
!!! ATTTCATTTGAATTTGCTAA+TGG + tig0021957:2081-2100 Msa1395570:intron 20.0%
!! TTATGATAAACTACTTTGAT+AGG - tig0021957:2111-2130 None:intergenic 20.0%
!! TATCAAAGTAGTTTATCATA+AGG + tig0021957:2110-2129 Msa1395570:intron 20.0%
!! ACAATATACAATTAAGAATC+TGG - tig0021957:2352-2371 None:intergenic 20.0%
!! TTAAAACTTGTATGAGAAAT+GGG + tig0021957:1374-1393 Msa1395570:CDS 20.0%
!!! CTCAAAGTTATTTTTCTTTA+AGG - tig0021957:1437-1456 None:intergenic 20.0%
!!! CTTTTACTAATTATCCTATA+TGG + tig0021957:1464-1483 Msa1395570:CDS 20.0%
!!! AATTCATTTTCTTACCATAT+AGG - tig0021957:1481-1500 None:intergenic 20.0%
!!! ATGATGAGTTCTTTTTTTTT+CGG - tig0021957:1709-1728 None:intergenic 20.0%
!! AAAAAGAACTCATCATTTAA+AGG + tig0021957:1713-1732 Msa1395570:intron 20.0%
!! TCTATGAAAATACAATATTC+TGG - tig0021957:1870-1889 None:intergenic 20.0%
!! ATAAATTGTAAGTGATATCA+TGG - tig0021957:1942-1961 None:intergenic 20.0%
!!! ATTTCATTTGAATTTGCTAA+TGG + tig0021957:2081-2100 Msa1395570:intron 20.0%
!! TTATGATAAACTACTTTGAT+AGG - tig0021957:2111-2130 None:intergenic 20.0%
!! TATCAAAGTAGTTTATCATA+AGG + tig0021957:2110-2129 Msa1395570:intron 20.0%
!! ACAATATACAATTAAGAATC+TGG - tig0021957:2352-2371 None:intergenic 20.0%
!! CATTTCTCATACAAGTTTTA+AGG - tig0021957:1375-1394 None:intergenic 25.0%
! CTTAAAACTTGTATGAGAAA+TGG + tig0021957:1373-1392 Msa1395570:CDS 25.0%
!! GAATTTTCTATTGCAATATC+TGG + tig0021957:1496-1515 Msa1395570:intron 25.0%
!! TACGTAATATTTTGTACTGT+AGG + tig0021957:1538-1557 Msa1395570:intron 25.0%
!! AAATGGCTCTATAATATTCA+AGG - tig0021957:1774-1793 None:intergenic 25.0%
! TTCCTGAAACACAATAAAAA+TGG - tig0021957:1791-1810 None:intergenic 25.0%
!! ATTGTATTTTCATAGATGAC+AGG + tig0021957:1874-1893 Msa1395570:CDS 25.0%
! TATATAGTTATTGTCTTCTC+AGG + tig0021957:2143-2162 Msa1395570:intron 25.0%
!!! ATTGAGCTTTGTTAAAATGA+TGG + tig0021957:2388-2407 Msa1395570:three_prime_UTR 25.0%
!! GATGGTTTAAGTCTATATTT+TGG + tig0021957:2406-2425 Msa1395570:three_prime_UTR 25.0%
!! CATTTCTCATACAAGTTTTA+AGG - tig0021957:1375-1394 None:intergenic 25.0%
! CTTAAAACTTGTATGAGAAA+TGG + tig0021957:1373-1392 Msa1395570:CDS 25.0%
!! GAATTTTCTATTGCAATATC+TGG + tig0021957:1496-1515 Msa1395570:intron 25.0%
!! TACGTAATATTTTGTACTGT+AGG + tig0021957:1538-1557 Msa1395570:intron 25.0%
!! AAATGGCTCTATAATATTCA+AGG - tig0021957:1774-1793 None:intergenic 25.0%
! TTCCTGAAACACAATAAAAA+TGG - tig0021957:1791-1810 None:intergenic 25.0%
!! ATTGTATTTTCATAGATGAC+AGG + tig0021957:1874-1893 Msa1395570:CDS 25.0%
! TATATAGTTATTGTCTTCTC+AGG + tig0021957:2143-2162 Msa1395570:intron 25.0%
!!! ATTGAGCTTTGTTAAAATGA+TGG + tig0021957:2388-2407 Msa1395570:three_prime_UTR 25.0%
!! GATGGTTTAAGTCTATATTT+TGG + tig0021957:2406-2425 Msa1395570:three_prime_UTR 25.0%
AATGGGTATTCATACATAGA+AGG + tig0021957:1391-1410 Msa1395570:CDS 30.0%
ATGGGTATTCATACATAGAA+GGG + tig0021957:1392-1411 Msa1395570:CDS 30.0%
AAAAAGCTGATGAACACAAA+AGG - tig0021957:1656-1675 None:intergenic 30.0%
!!! CTTTTTTTTTCGGTCCAATT+AGG - tig0021957:1699-1718 None:intergenic 30.0%
ATATTCAAGGTTTCCATGAA+AGG - tig0021957:1761-1780 None:intergenic 30.0%
!!! AGCCATTTTTATTGTGTTTC+AGG + tig0021957:1786-1805 Msa1395570:intron 30.0%
TTTATTGTGTTTCAGGAAAG+AGG + tig0021957:1793-1812 Msa1395570:intron 30.0%
TCCTTATAGAATTCAGTATC+CGG - tig0021957:1822-1841 None:intergenic 30.0%
AATTCTATAAGGAAGTTGTC+AGG + tig0021957:1829-1848 Msa1395570:CDS 30.0%
GATAAACTACTTTGATAGGT+TGG - tig0021957:2107-2126 None:intergenic 30.0%
ATACACCAATTTCGTTTACA+CGG + tig0021957:2311-2330 Msa1395570:three_prime_UTR 30.0%
AATGGGTATTCATACATAGA+AGG + tig0021957:1391-1410 Msa1395570:CDS 30.0%
ATGGGTATTCATACATAGAA+GGG + tig0021957:1392-1411 Msa1395570:CDS 30.0%
AAAAAGCTGATGAACACAAA+AGG - tig0021957:1656-1675 None:intergenic 30.0%
!!! CTTTTTTTTTCGGTCCAATT+AGG - tig0021957:1699-1718 None:intergenic 30.0%
ATATTCAAGGTTTCCATGAA+AGG - tig0021957:1761-1780 None:intergenic 30.0%
!!! AGCCATTTTTATTGTGTTTC+AGG + tig0021957:1786-1805 Msa1395570:intron 30.0%
TTTATTGTGTTTCAGGAAAG+AGG + tig0021957:1793-1812 Msa1395570:intron 30.0%
TCCTTATAGAATTCAGTATC+CGG - tig0021957:1822-1841 None:intergenic 30.0%
AATTCTATAAGGAAGTTGTC+AGG + tig0021957:1829-1848 Msa1395570:CDS 30.0%
GATAAACTACTTTGATAGGT+TGG - tig0021957:2107-2126 None:intergenic 30.0%
ATACACCAATTTCGTTTACA+CGG + tig0021957:2311-2330 Msa1395570:three_prime_UTR 30.0%
TGGGTATTCATACATAGAAG+GGG + tig0021957:1393-1412 Msa1395570:CDS 35.0%
!!! AATATCTGGTTTGCTTTTCG+TGG + tig0021957:1510-1529 Msa1395570:intron 35.0%
ACCGGATACTGAATTCTATA+AGG + tig0021957:1818-1837 Msa1395570:CDS 35.0%
ATGCTTATGTACTAGCATCT+TGG + tig0021957:1993-2012 Msa1395570:intron 35.0%
ATGAGGGAGAGATTTACATT+GGG - tig0021957:2021-2040 None:intergenic 35.0%
TTTCACCGTGTAAACGAAAT+TGG - tig0021957:2319-2338 None:intergenic 35.0%
TTTCGTTTACACGGTGAAAA+AGG + tig0021957:2320-2339 Msa1395570:three_prime_UTR 35.0%
TTCGTTTACACGGTGAAAAA+GGG + tig0021957:2321-2340 Msa1395570:three_prime_UTR 35.0%
TGGGTATTCATACATAGAAG+GGG + tig0021957:1393-1412 Msa1395570:CDS 35.0%
!!! AATATCTGGTTTGCTTTTCG+TGG + tig0021957:1510-1529 Msa1395570:intron 35.0%
ACCGGATACTGAATTCTATA+AGG + tig0021957:1818-1837 Msa1395570:CDS 35.0%
ATGCTTATGTACTAGCATCT+TGG + tig0021957:1993-2012 Msa1395570:intron 35.0%
ATGAGGGAGAGATTTACATT+GGG - tig0021957:2021-2040 None:intergenic 35.0%
TTTCACCGTGTAAACGAAAT+TGG - tig0021957:2319-2338 None:intergenic 35.0%
TTTCGTTTACACGGTGAAAA+AGG + tig0021957:2320-2339 Msa1395570:three_prime_UTR 35.0%
TTCGTTTACACGGTGAAAAA+GGG + tig0021957:2321-2340 Msa1395570:three_prime_UTR 35.0%
!! ACGTTTTGTTCGTGTACACT+TGG + tig0021957:1609-1628 Msa1395570:CDS 40.0%
TTTGTTCGTGTACACTTGGT+AGG + tig0021957:1613-1632 Msa1395570:intron 40.0%
ACACTCAGACTATCCTTTCA+TGG + tig0021957:1745-1764 Msa1395570:intron 40.0%
TGTTTCAGGAAAGAGGAAAC+CGG + tig0021957:1800-1819 Msa1395570:intron 40.0%
GATGAGGGAGAGATTTACAT+TGG - tig0021957:2022-2041 None:intergenic 40.0%
! TATGTCTGCTGCTTGATTAG+AGG - tig0021957:2053-2072 None:intergenic 40.0%
!!! CAAGTTTTAAGGCCTGTCAT+TGG - tig0021957:1364-1383 None:intergenic 40.0%
!! ACGTTTTGTTCGTGTACACT+TGG + tig0021957:1609-1628 Msa1395570:CDS 40.0%
TTTGTTCGTGTACACTTGGT+AGG + tig0021957:1613-1632 Msa1395570:intron 40.0%
ACACTCAGACTATCCTTTCA+TGG + tig0021957:1745-1764 Msa1395570:intron 40.0%
TGTTTCAGGAAAGAGGAAAC+CGG + tig0021957:1800-1819 Msa1395570:intron 40.0%
GATGAGGGAGAGATTTACAT+TGG - tig0021957:2022-2041 None:intergenic 40.0%
! TATGTCTGCTGCTTGATTAG+AGG - tig0021957:2053-2072 None:intergenic 40.0%
TCTCAGGCCAAAAAATGTGC+AGG + tig0021957:2159-2178 Msa1395570:intron 45.0%
CGCGAAGAACTGTCATTGAT+GGG + tig0021957:2235-2254 Msa1395570:CDS 45.0%
GCGAAGAACTGTCATTGATG+GGG + tig0021957:2236-2255 Msa1395570:CDS 45.0%
CGAAGAACTGTCATTGATGG+GGG + tig0021957:2237-2256 Msa1395570:CDS 45.0%
TCTCAGGCCAAAAAATGTGC+AGG + tig0021957:2159-2178 Msa1395570:intron 45.0%
CGCGAAGAACTGTCATTGAT+GGG + tig0021957:2235-2254 Msa1395570:CDS 45.0%
GCGAAGAACTGTCATTGATG+GGG + tig0021957:2236-2255 Msa1395570:CDS 45.0%
CGAAGAACTGTCATTGATGG+GGG + tig0021957:2237-2256 Msa1395570:CDS 45.0%
TGCTTGATTAGAGGTGACGC+GGG - tig0021957:2044-2063 None:intergenic 50.0%
CTGCTTGATTAGAGGTGACG+CGG - tig0021957:2045-2064 None:intergenic 50.0%
!!! GCTGCTGCCTGCACATTTTT+TGG - tig0021957:2169-2188 None:intergenic 50.0%
AGCAGCTGAAGTTGGGATCA+AGG + tig0021957:2183-2202 Msa1395570:CDS 50.0%
GCAGCTGAAGTTGGGATCAA+GGG + tig0021957:2184-2203 Msa1395570:CDS 50.0%
GCGCGAAGAACTGTCATTGA+TGG + tig0021957:2234-2253 Msa1395570:CDS 50.0%
TGCTTGATTAGAGGTGACGC+GGG - tig0021957:2044-2063 None:intergenic 50.0%
CTGCTTGATTAGAGGTGACG+CGG - tig0021957:2045-2064 None:intergenic 50.0%
!!! GCTGCTGCCTGCACATTTTT+TGG - tig0021957:2169-2188 None:intergenic 50.0%
AGCAGCTGAAGTTGGGATCA+AGG + tig0021957:2183-2202 Msa1395570:CDS 50.0%
GCAGCTGAAGTTGGGATCAA+GGG + tig0021957:2184-2203 Msa1395570:CDS 50.0%
GCGCGAAGAACTGTCATTGA+TGG + tig0021957:2234-2253 Msa1395570:CDS 50.0%
TTAGAGGTGACGCGGGATGA+GGG - tig0021957:2037-2056 None:intergenic 55.0%
ATTAGAGGTGACGCGGGATG+AGG - tig0021957:2038-2057 None:intergenic 55.0%
TGCAGGCAGCAGCTGAAGTT+GGG + tig0021957:2176-2195 Msa1395570:CDS 55.0%
TTAGAGGTGACGCGGGATGA+GGG - tig0021957:2037-2056 None:intergenic 55.0%
ATTAGAGGTGACGCGGGATG+AGG - tig0021957:2038-2057 None:intergenic 55.0%
TGCAGGCAGCAGCTGAAGTT+GGG + tig0021957:2176-2195 Msa1395570:CDS 55.0%
GTGCAGGCAGCAGCTGAAGT+TGG + tig0021957:2175-2194 Msa1395570:CDS 60.0%
GTGCAGGCAGCAGCTGAAGT+TGG + tig0021957:2175-2194 Msa1395570:CDS 60.0%
Chromosome Type Strat End Strand Name
tig0021957 gene 1364 2476 1364 ID=Msa1395570;Name=Msa1395570
tig0021957 mRNA 1364 2476 1364 ID=Msa1395570-mRNA-1;Parent=Msa1395570;Name=Msa1395570-mRNA-1;_AED=0.16;_eAED=0.16;_QI=0|0.66|0.5|1|1|1|4|188|134
tig0021957 exon 1364 1485 1364 ID=Msa1395570-mRNA-1:exon:14972;Parent=Msa1395570-mRNA-1
tig0021957 exon 1560 1630 1560 ID=Msa1395570-mRNA-1:exon:14973;Parent=Msa1395570-mRNA-1
tig0021957 exon 1808 1895 1808 ID=Msa1395570-mRNA-1:exon:14974;Parent=Msa1395570-mRNA-1
tig0021957 exon 2165 2476 2165 ID=Msa1395570-mRNA-1:exon:14975;Parent=Msa1395570-mRNA-1
tig0021957 CDS 1364 1485 1364 ID=Msa1395570-mRNA-1:cds;Parent=Msa1395570-mRNA-1
tig0021957 CDS 1560 1630 1560 ID=Msa1395570-mRNA-1:cds;Parent=Msa1395570-mRNA-1
tig0021957 CDS 1808 1895 1808 ID=Msa1395570-mRNA-1:cds;Parent=Msa1395570-mRNA-1
tig0021957 CDS 2165 2288 2165 ID=Msa1395570-mRNA-1:cds;Parent=Msa1395570-mRNA-1
tig0021957 three_prime_UTR 2289 2476 2289 ID=Msa1395570-mRNA-1:three_prime_utr;Parent=Msa1395570-mRNA-1
Gene Sequence

>Msa1395570

ATGACAGGCCTTAAAACTTGTATGAGAAATGGGTATTCATACATAGAAGGGGTTGAACAATTGCTTCTTGCCTTAAAGAAAAATAACTTTGAGATGCATGCTTTTACTAATTATCCTATATGGTATCAGTTGATCGAAGACAAGTTAAATCTATCAAAATATTTATCTTGGACGTTTTGTTCGTGTACACTTGGAAAGAGGAAACCGGATACTGAATTCTATAAGGAAGTTGTCAGGCATCTTGAAGTTGATCCAGAATATTGTATTTTCATAGATGACAGGCCAAAAAATGTGCAGGCAGCAGCTGAAGTTGGGATCAAGGGTGTACATTTCAAGAATGTCGATTTACTGCGCGAAGAACTGTCATTGATGGGGGTTGACATTTCAACTGATGAAGATCAATAG

Protein sequence

>Msa1395570

MTGLKTCMRNGYSYIEGVEQLLLALKKNNFEMHAFTNYPIWYQLIEDKLNLSKYLSWTFCSCTLGKRKPDTEFYKEVVRHLEVDPEYCIFIDDRPKNVQAAAEVGIKGVHFKNVDLLREELSLMGVDISTDEDQ*