AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1358790


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1358790 MtrunA17_Chr4g0072111 89.474 114 6 2 1 109 1 113 1.79e-61 186
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1358790 AT5G57345.1 60.870 69 26 1 37 105 40 107 7.56e-21 82.8

Find 31 sgRNAs with CRISPR-Local

Find 74 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CACTTCTTAACCCAACTTTC+AGG 0.253275 tig0016538:-1782 Msa1358790:CDS
AACAATCTTCAACTCCATTA+AGG 0.317786 tig0016538:-1701 Msa1358790:CDS
TGGTATTTGAGGGAGATAGA+AGG 0.318024 tig0016538:-1919 Msa1358790:five_prime_UTR
ACCAATTCTACCACCAGTTT+TGG 0.337468 tig0016538:+1485 Msa1358790:intergenic
GAATTGTTATTGTTGATTCT+TGG 0.352408 tig0016538:+1423 Msa1358790:intergenic
AAGAAGAATGAGAACAAGTT+AGG 0.368246 tig0016538:-1576 Msa1358790:CDS
TCCTGCTGCTCCTGAAAGTT+GGG 0.398618 tig0016538:+1753 Msa1358790:intergenic
GTCCTGCTGCTCCTGAAAGT+TGG 0.414303 tig0016538:+1752 Msa1358790:intergenic
GAATCAACAATAACAATTCC+AGG 0.432239 tig0016538:-1419 Msa1358790:CDS
GATGCATCAGCTGCCAAAAC+TGG 0.451635 tig0016538:-1498 Msa1358790:CDS
AGGAAAAGAGTTGGTATTTG+AGG 0.456509 tig0016538:-1930 None:intergenic
GCCAAAACTGGTGGTAGAAT+TGG 0.463723 tig0016538:-1486 Msa1358790:CDS
GGAAAAGAGTTGGTATTTGA+GGG 0.474287 tig0016538:-1929 None:intergenic
TTGTTGATTCTTGGTGAGGA+AGG 0.491949 tig0016538:+1432 Msa1358790:intergenic
GCTGCTGGTGTGTTAACGTT+TGG 0.494174 tig0016538:-1531 Msa1358790:CDS
GCAATGATTGCAGTGGCTGC+TGG 0.497359 tig0016538:-1546 Msa1358790:CDS
ACCCAACTTTCAGGAGCAGC+AGG 0.521337 tig0016538:-1773 Msa1358790:CDS
CTTTCAGGAGCAGCAGGACG+AGG 0.524478 tig0016538:-1767 Msa1358790:CDS
GAAGTGTTGGTGAAGAGATG+AGG 0.545411 tig0016538:+1780 Msa1358790:intergenic
TGTTGATTCTTGGTGAGGAA+GGG 0.549367 tig0016538:+1433 Msa1358790:intergenic
GCGAGGAGCGGATGATCTGA+AGG 0.565349 tig0016538:+1455 Msa1358790:intergenic
GGAGTTGAAGATTGTTGTTG+TGG 0.590399 tig0016538:+1689 Msa1358790:intergenic
ATTCTTGGTGAGGAAGGGCG+AGG 0.590888 tig0016538:+1438 Msa1358790:intergenic
AAAACTGGTGGTAGAATTGG+TGG 0.598132 tig0016538:-1483 Msa1358790:CDS
AAAGTTGGGTTAAGAAGTGT+TGG 0.609494 tig0016538:+1767 Msa1358790:intergenic
GTTATTGTTGATTCTTGGTG+AGG 0.615397 tig0016538:+1428 Msa1358790:intergenic
GAGGAAGCTTTGCTGCGACA+AGG 0.618200 tig0016538:+1799 Msa1358790:intergenic
TGGTGAGGAAGGGCGAGGAG+CGG 0.629460 tig0016538:+1443 Msa1358790:intergenic
AAAGTTAGCAATGATTGCAG+TGG 0.664147 tig0016538:-1553 Msa1358790:CDS
CAGCAGGACGAGGAAGACTG+TGG 0.702489 tig0016538:-1757 Msa1358790:CDS
GCATCAGCTGCCAAAACTGG+TGG 0.706688 tig0016538:-1495 Msa1358790:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! ATAAACAAATAAGCAAAAAC+AGG - tig0016538:1452-1471 Msa1358790:CDS 20.0%
!! ATAAACAAATAAGCAAAAAC+AGG - tig0016538:1452-1471 Msa1358790:CDS 20.0%
!! TTTTGATGTAGTTACCTTAA+TGG + tig0016538:1661-1680 Msa1358790:intergenic 25.0%
!!! GAATTGTTATTGTTGATTCT+TGG + tig0016538:1906-1925 Msa1358790:intergenic 25.0%
!! TTTTGATGTAGTTACCTTAA+TGG + tig0016538:1661-1680 Msa1358790:intergenic 25.0%
!!! GAATTGTTATTGTTGATTCT+TGG + tig0016538:1906-1925 Msa1358790:intergenic 25.0%
! AAGGAACACATTTTTGATGT+CGG + tig0016538:1511-1530 Msa1358790:intergenic 30.0%
AACAATCTTCAACTCCATTA+AGG - tig0016538:1644-1663 Msa1358790:intron 30.0%
! TTTGCTTTGTTATACTTGCA+TGG - tig0016538:1702-1721 Msa1358790:CDS 30.0%
AAGAAGAATGAGAACAAGTT+AGG - tig0016538:1750-1769 Msa1358790:CDS 30.0%
GAATCAACAATAACAATTCC+AGG - tig0016538:1907-1926 Msa1358790:five_prime_UTR 30.0%
! AAGGAACACATTTTTGATGT+CGG + tig0016538:1511-1530 Msa1358790:intergenic 30.0%
AACAATCTTCAACTCCATTA+AGG - tig0016538:1644-1663 Msa1358790:intron 30.0%
! TTTGCTTTGTTATACTTGCA+TGG - tig0016538:1702-1721 Msa1358790:CDS 30.0%
AAGAAGAATGAGAACAAGTT+AGG - tig0016538:1750-1769 Msa1358790:CDS 30.0%
GAATCAACAATAACAATTCC+AGG - tig0016538:1907-1926 Msa1358790:five_prime_UTR 30.0%
! TCAAATACCAACTCTTTTCC+TGG + tig0016538:1416-1435 None:intergenic 35.0%
!! AGGAAAAGAGTTGGTATTTG+AGG - tig0016538:1415-1434 Msa1358790:CDS 35.0%
!! GGAAAAGAGTTGGTATTTGA+GGG - tig0016538:1416-1435 Msa1358790:CDS 35.0%
! AAAGTTGGGTTAAGAAGTGT+TGG + tig0016538:1562-1581 Msa1358790:intergenic 35.0%
AAAGTTAGCAATGATTGCAG+TGG - tig0016538:1773-1792 Msa1358790:CDS 35.0%
!! GTTATTGTTGATTCTTGGTG+AGG + tig0016538:1901-1920 Msa1358790:intergenic 35.0%
! TCAAATACCAACTCTTTTCC+TGG + tig0016538:1416-1435 Msa1358790:intergenic 35.0%
!! AGGAAAAGAGTTGGTATTTG+AGG - tig0016538:1415-1434 Msa1358790:CDS 35.0%
!! GGAAAAGAGTTGGTATTTGA+GGG - tig0016538:1416-1435 Msa1358790:CDS 35.0%
! AAAGTTGGGTTAAGAAGTGT+TGG + tig0016538:1562-1581 Msa1358790:intergenic 35.0%
AAAGTTAGCAATGATTGCAG+TGG - tig0016538:1773-1792 Msa1358790:CDS 35.0%
!! GTTATTGTTGATTCTTGGTG+AGG + tig0016538:1901-1920 Msa1358790:intergenic 35.0%
TGGTATTTGAGGGAGATAGA+AGG - tig0016538:1426-1445 Msa1358790:CDS 40.0%
CACTTCTTAACCCAACTTTC+AGG - tig0016538:1563-1582 Msa1358790:CDS 40.0%
! GGAGTTGAAGATTGTTGTTG+TGG + tig0016538:1640-1659 Msa1358790:intergenic 40.0%
! ACCAATTCTACCACCAGTTT+TGG + tig0016538:1844-1863 Msa1358790:intergenic 40.0%
AAAACTGGTGGTAGAATTGG+TGG - tig0016538:1843-1862 Msa1358790:five_prime_UTR 40.0%
!! TGTTGATTCTTGGTGAGGAA+GGG + tig0016538:1896-1915 Msa1358790:intergenic 40.0%
!! TTGTTGATTCTTGGTGAGGA+AGG + tig0016538:1897-1916 Msa1358790:intergenic 40.0%
TGGTATTTGAGGGAGATAGA+AGG - tig0016538:1426-1445 Msa1358790:CDS 40.0%
CACTTCTTAACCCAACTTTC+AGG - tig0016538:1563-1582 Msa1358790:CDS 40.0%
! GGAGTTGAAGATTGTTGTTG+TGG + tig0016538:1640-1659 Msa1358790:intergenic 40.0%
! ACCAATTCTACCACCAGTTT+TGG + tig0016538:1844-1863 Msa1358790:intergenic 40.0%
AAAACTGGTGGTAGAATTGG+TGG - tig0016538:1843-1862 Msa1358790:five_prime_UTR 40.0%
!! TGTTGATTCTTGGTGAGGAA+GGG + tig0016538:1896-1915 Msa1358790:intergenic 40.0%
!! TTGTTGATTCTTGGTGAGGA+AGG + tig0016538:1897-1916 Msa1358790:intergenic 40.0%
!! GAAGTGTTGGTGAAGAGATG+AGG + tig0016538:1549-1568 Msa1358790:intergenic 45.0%
GCCAAAACTGGTGGTAGAAT+TGG - tig0016538:1840-1859 Msa1358790:five_prime_UTR 45.0%
!! GAAGTGTTGGTGAAGAGATG+AGG + tig0016538:1549-1568 Msa1358790:intergenic 45.0%
GCCAAAACTGGTGGTAGAAT+TGG - tig0016538:1840-1859 Msa1358790:five_prime_UTR 45.0%
!! CTTAAATATTATATATAAAT+AGG - tig0016538:1727-1746 Msa1358790:CDS 5.0%
!! CTTAAATATTATATATAAAT+AGG - tig0016538:1727-1746 Msa1358790:CDS 5.0%
TCCTGCTGCTCCTGAAAGTT+GGG + tig0016538:1576-1595 Msa1358790:intergenic 50.0%
GCTGCTGGTGTGTTAACGTT+TGG - tig0016538:1795-1814 Msa1358790:CDS 50.0%
GATGCATCAGCTGCCAAAAC+TGG - tig0016538:1828-1847 Msa1358790:exon 50.0%
TCCTGCTGCTCCTGAAAGTT+GGG + tig0016538:1576-1595 Msa1358790:intergenic 50.0%
GCTGCTGGTGTGTTAACGTT+TGG - tig0016538:1795-1814 Msa1358790:CDS 50.0%
GATGCATCAGCTGCCAAAAC+TGG - tig0016538:1828-1847 Msa1358790:exon 50.0%
GAGGAAGCTTTGCTGCGACA+AGG + tig0016538:1530-1549 Msa1358790:intergenic 55.0%
ACCCAACTTTCAGGAGCAGC+AGG - tig0016538:1572-1591 Msa1358790:CDS 55.0%
GTCCTGCTGCTCCTGAAAGT+TGG + tig0016538:1577-1596 Msa1358790:intergenic 55.0%
GCAATGATTGCAGTGGCTGC+TGG - tig0016538:1780-1799 Msa1358790:CDS 55.0%
GCATCAGCTGCCAAAACTGG+TGG - tig0016538:1831-1850 Msa1358790:five_prime_UTR 55.0%
ATTCTTGGTGAGGAAGGGCG+AGG + tig0016538:1891-1910 Msa1358790:intergenic 55.0%
GAGGAAGCTTTGCTGCGACA+AGG + tig0016538:1530-1549 Msa1358790:intergenic 55.0%
ACCCAACTTTCAGGAGCAGC+AGG - tig0016538:1572-1591 Msa1358790:CDS 55.0%
GTCCTGCTGCTCCTGAAAGT+TGG + tig0016538:1577-1596 Msa1358790:intergenic 55.0%
GCAATGATTGCAGTGGCTGC+TGG - tig0016538:1780-1799 Msa1358790:CDS 55.0%
GCATCAGCTGCCAAAACTGG+TGG - tig0016538:1831-1850 Msa1358790:five_prime_UTR 55.0%
ATTCTTGGTGAGGAAGGGCG+AGG + tig0016538:1891-1910 Msa1358790:intergenic 55.0%
CTTTCAGGAGCAGCAGGACG+AGG - tig0016538:1578-1597 Msa1358790:CDS 60.0%
CAGCAGGACGAGGAAGACTG+TGG - tig0016538:1588-1607 Msa1358790:intron 60.0%
GCGAGGAGCGGATGATCTGA+AGG + tig0016538:1874-1893 Msa1358790:intergenic 60.0%
CTTTCAGGAGCAGCAGGACG+AGG - tig0016538:1578-1597 Msa1358790:CDS 60.0%
CAGCAGGACGAGGAAGACTG+TGG - tig0016538:1588-1607 Msa1358790:intron 60.0%
GCGAGGAGCGGATGATCTGA+AGG + tig0016538:1874-1893 Msa1358790:intergenic 60.0%
TGGTGAGGAAGGGCGAGGAG+CGG + tig0016538:1886-1905 Msa1358790:intergenic 65.0%
TGGTGAGGAAGGGCGAGGAG+CGG + tig0016538:1886-1905 Msa1358790:intergenic 65.0%
Chromosome Type Strat End Strand Name
tig0016538 gene 1410 1938 1410 ID=Msa1358790;Name=Msa1358790
tig0016538 mRNA 1410 1938 1410 ID=Msa1358790-mRNA-1;Parent=Msa1358790;Name=Msa1358790-mRNA-1;_AED=0.08;_eAED=0.08;_QI=110|1|1|1|1|1|2|0|112
tig0016538 exon 1410 1599 1410 ID=Msa1358790-mRNA-1:exon:11030;Parent=Msa1358790-mRNA-1
tig0016538 exon 1683 1938 1683 ID=Msa1358790-mRNA-1:exon:11029;Parent=Msa1358790-mRNA-1
tig0016538 five_prime_UTR 1829 1938 1829 ID=Msa1358790-mRNA-1:five_prime_utr;Parent=Msa1358790-mRNA-1
tig0016538 CDS 1683 1828 1683 ID=Msa1358790-mRNA-1:cds;Parent=Msa1358790-mRNA-1
tig0016538 CDS 1410 1599 1410 ID=Msa1358790-mRNA-1:cds;Parent=Msa1358790-mRNA-1
Gene Sequence

>Msa1358790

ATGTGTTCCTTGTCGCAGCAAAGCTTCCTCATCTCTTCACCAACACTTCTTAACCCAACTTTCAGGAGCAGCAGGACGAGGAAGACTGTGGTTGTTGTCTACTGCAGTTGCACACAGCCACAACAACAATCTTCAACTCCATTAAGGAAGAAGAATGAGAACAAGTTAGGAAAGTTAGCAATGATTGCAGTGGCTGCTGGTGTGTTAACGTTTGGATCAGTTCATGATGCATCAGCTGCCAAAACTGGTGGTAGAATTGGTGGTCAGTCCTTCAGATCATCCGCTCCTCGCCCTTCCTCACCAAGAATCAACAATAACAATTCCAGGTATCTAACA

Protein sequence

>Msa1358790

MCSLSQQSFLISSPTLLNPTFRSSRTRKTVVVVYCSCTQPQQQSSTPLRKKNENKLGKLAMIAVAAGVLTFGSVHDASAAKTGGRIGGQSFRSSAPRPSSPRINNNNSRYLT