AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1454900

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1454900 MtrunA17_Chr2g0322651 95.556 135 6 0 1 135 1 135 6.89e-90 256
Msa1454900 MtrunA17_Chr4g0024531 40.541 148 69 6 1 134 1 143 3.15e-19 78.2
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 28 sgRNAs with CRISPR-Local

Find 30 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
AATTACTACCTATAGCTTTA+TGG 0.181508 tig0035522:-1858 None:intergenic
ATGCTATCTTCTCTCCTTGA+TGG 0.225457 tig0035522:-1554 None:intergenic
CATATTGTGCTGATGATATT+TGG 0.253195 tig0035522:-1487 None:intergenic
TCTTCTCTCCTTGATGGTTT+AGG 0.273383 tig0035522:-1548 None:intergenic
TGGTGTTAAGAATACTTCTT+TGG 0.346243 tig0035522:+1718 Msa1454900:CDS
CTTCTACAAATGGGATTATG+AGG 0.369074 tig0035522:+1633 Msa1454900:CDS
GATGGTAATTCTTCTACAAA+TGG 0.380283 tig0035522:+1623 Msa1454900:CDS
AAAATACAAGATGGTAATAA+AGG 0.383448 tig0035522:+1596 Msa1454900:CDS
TGAGCAAGGAAGAGTTGAAA+AGG 0.433978 tig0035522:+1669 Msa1454900:CDS
GGATCACTCCATAAAGCTAT+AGG 0.447618 tig0035522:+1850 Msa1454900:CDS
AGCTTTATGGAGTGATCCTC+AGG 0.453586 tig0035522:-1845 None:intergenic
ATGGTAATTCTTCTACAAAT+GGG 0.455241 tig0035522:+1624 Msa1454900:CDS
TGTTAAGAATACTTCTTTGG+AGG 0.491214 tig0035522:+1721 Msa1454900:CDS
AGAAGATAGCATGAAGAAGA+AGG 0.497833 tig0035522:+1565 Msa1454900:CDS
AGGGTTGAAGAAATTGATGA+TGG 0.510389 tig0035522:+1785 Msa1454900:CDS
ATAGCATGAAGAAGAAGGTA+AGG 0.516436 tig0035522:+1570 Msa1454900:CDS
AGCAATAAGAACATTGAGAA+TGG 0.527142 tig0035522:+1698 Msa1454900:CDS
GATGGTAATAAAGGAAGTGA+TGG 0.535398 tig0035522:+1605 Msa1454900:CDS
GATTAAGCTAGTTGTGAGCA+AGG 0.543965 tig0035522:+1655 Msa1454900:CDS
GGTTGAAGAAATTGATGATG+GGG 0.548126 tig0035522:+1787 Msa1454900:CDS
GAGCAAGGAAGAGTTGAAAA+GGG 0.552525 tig0035522:+1670 Msa1454900:CDS
GGGTTGAAGAAATTGATGAT+GGG 0.553313 tig0035522:+1786 Msa1454900:CDS
TCAGGAATACTATCTAAAGC+TGG 0.566598 tig0035522:-1827 None:intergenic
GTTGAAGAAATTGATGATGG+GGG 0.576047 tig0035522:+1788 Msa1454900:CDS
AAAGAAAGTTGAGAAGATGA+AGG 0.577557 tig0035522:+1523 Msa1454900:CDS
TGAAGGCACCTAAACCATCA+AGG 0.604079 tig0035522:+1540 Msa1454900:CDS
GTAAGGTTCAAAATACAAGA+TGG 0.613431 tig0035522:+1587 Msa1454900:CDS
AGCTTTAGATAGTATTCCTG+AGG 0.616536 tig0035522:+1829 Msa1454900:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AAAATACAAGATGGTAATAA+AGG + tig0035522:1596-1615 Msa1454900:CDS 20.0%
! ATGGTAATTCTTCTACAAAT+GGG + tig0035522:1624-1643 Msa1454900:CDS 25.0%
! CATATTGTGCTGATGATATT+TGG - tig0035522:1490-1509 None:intergenic 30.0%
AAAGAAAGTTGAGAAGATGA+AGG + tig0035522:1523-1542 Msa1454900:CDS 30.0%
GTAAGGTTCAAAATACAAGA+TGG + tig0035522:1587-1606 Msa1454900:CDS 30.0%
GATGGTAATTCTTCTACAAA+TGG + tig0035522:1623-1642 Msa1454900:CDS 30.0%
AGCAATAAGAACATTGAGAA+TGG + tig0035522:1698-1717 Msa1454900:CDS 30.0%
! TGGTGTTAAGAATACTTCTT+TGG + tig0035522:1718-1737 Msa1454900:CDS 30.0%
TGTTAAGAATACTTCTTTGG+AGG + tig0035522:1721-1740 Msa1454900:CDS 30.0%
! TGAAAGAAAAAAGTGTGTCT+AGG + tig0035522:1765-1784 Msa1454900:CDS 30.0%
! GAAAGAAAAAAGTGTGTCTA+GGG + tig0035522:1766-1785 Msa1454900:CDS 30.0%
AGAAGATAGCATGAAGAAGA+AGG + tig0035522:1565-1584 Msa1454900:CDS 35.0%
ATAGCATGAAGAAGAAGGTA+AGG + tig0035522:1570-1589 Msa1454900:CDS 35.0%
GATGGTAATAAAGGAAGTGA+TGG + tig0035522:1605-1624 Msa1454900:CDS 35.0%
CTTCTACAAATGGGATTATG+AGG + tig0035522:1633-1652 Msa1454900:CDS 35.0%
AGGGTTGAAGAAATTGATGA+TGG + tig0035522:1785-1804 Msa1454900:CDS 35.0%
! GGGTTGAAGAAATTGATGAT+GGG + tig0035522:1786-1805 Msa1454900:CDS 35.0%
!! GGTTGAAGAAATTGATGATG+GGG + tig0035522:1787-1806 Msa1454900:CDS 35.0%
!! GTTGAAGAAATTGATGATGG+GGG + tig0035522:1788-1807 Msa1454900:CDS 35.0%
! TCAGGAATACTATCTAAAGC+TGG - tig0035522:1830-1849 None:intergenic 35.0%
!! AGCTTTAGATAGTATTCCTG+AGG + tig0035522:1829-1848 Msa1454900:CDS 35.0%
! TCTTCTCTCCTTGATGGTTT+AGG - tig0035522:1551-1570 None:intergenic 40.0%
ATGCTATCTTCTCTCCTTGA+TGG - tig0035522:1557-1576 None:intergenic 40.0%
GATTAAGCTAGTTGTGAGCA+AGG + tig0035522:1655-1674 Msa1454900:CDS 40.0%
TGAGCAAGGAAGAGTTGAAA+AGG + tig0035522:1669-1688 Msa1454900:CDS 40.0%
GAGCAAGGAAGAGTTGAAAA+GGG + tig0035522:1670-1689 Msa1454900:CDS 40.0%
! ATGATGGGGGATTAGATTCT+TGG + tig0035522:1801-1820 Msa1454900:CDS 40.0%
!! TGAAGGCACCTAAACCATCA+AGG + tig0035522:1540-1559 Msa1454900:CDS 45.0%
ATGGGGGATTAGATTCTTGG+AGG + tig0035522:1804-1823 Msa1454900:CDS 45.0%
! AGCTTTATGGAGTGATCCTC+AGG - tig0035522:1848-1867 None:intergenic 45.0%
Chromosome Type Strat End Strand Name
tig0035522 gene 1464 1871 1464 ID=Msa1454900;Name=Msa1454900
tig0035522 mRNA 1464 1871 1464 ID=Msa1454900-mRNA-1;Parent=Msa1454900;Name=Msa1454900-mRNA-1;_AED=0.00;_eAED=0.00;_QI=0|-1|0|1|-1|1|1|0|135
tig0035522 exon 1464 1871 1464 ID=Msa1454900-mRNA-1:exon:20005;Parent=Msa1454900-mRNA-1
tig0035522 CDS 1464 1871 1464 ID=Msa1454900-mRNA-1:cds;Parent=Msa1454900-mRNA-1
Gene Sequence

>Msa1454900

ATGGGAAACTGCATTAGAAAAAACCAAATATCATCAGCACAATATGAGAATGAAGAAATAAAGAAAGTTGAGAAGATGAAGGCACCTAAACCATCAAGGAGAGAAGATAGCATGAAGAAGAAGGTAAGGTTCAAAATACAAGATGGTAATAAAGGAAGTGATGGTAATTCTTCTACAAATGGGATTATGAGGATTAAGCTAGTTGTGAGCAAGGAAGAGTTGAAAAGGGTGTTGAGCAATAAGAACATTGAGAATGGTGTTAAGAATACTTCTTTGGAGGAATTGCTAAAAGATATGAAGTTGAAAGAAAAAAGTGTGTCTAGGGTTGAAGAAATTGATGATGGGGGATTAGATTCTTGGAGGCCAGCTTTAGATAGTATTCCTGAGGATCACTCCATAAAGCTATAG
Protein sequence

>Msa1454900

MGNCIRKNQISSAQYENEEIKKVEKMKAPKPSRREDSMKKKVRFKIQDGNKGSDGNSSTNGIMRIKLVVSKEELKRVLSNKNIENGVKNTSLEELLKDMKLKEKSVSRVEEIDDGGLDSWRPALDSIPEDHSIKL*