AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1464800


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1464800 MtrunA17_Chr3g0119011 92.969 128 8 1 1 127 1 128 1.02e-82 238
Msa1464800 MtrunA17_Chr3g0118991 73.770 61 13 2 68 127 1 59 8.43e-23 84.3
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1464800 AT5G20935.1 79.012 81 17 0 45 125 37 117 4.46e-41 132
Msa1464800 AT5G20935.2 77.083 48 11 0 45 92 37 84 1.89e-19 77.4

Find 42 sgRNAs with CRISPR-Local

Find 120 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
ACTAATGACACTGAAATATT+TGG 0.193807 tig0044637:-1628 Msa1464800:intergenic
CCTTGCCTCAGAGTTAATTC+TGG 0.251411 tig0044637:+1775 Msa1464800:CDS
GATTTGTGGTTTCAATGTTT+TGG 0.261828 tig0044637:-1498 Msa1464800:intergenic
TGGAGCTTCAATGATAATAA+TGG 0.263065 tig0044637:-1725 Msa1464800:intergenic
CGTACTGCCCACACATCTTT+TGG 0.272835 tig0044637:-2229 Msa1464800:intergenic
ACTATACTCAACCAGATCTA+AGG 0.289522 tig0044637:-2296 Msa1464800:intergenic
AAACGTTCAAAGTTGGATAA+AGG 0.314200 tig0044637:+1697 Msa1464800:CDS
ATTGGAACTTATCTTATTGA+TGG 0.358224 tig0044637:+2259 Msa1464800:CDS
CCCAACCAGCAGGTGGCTCT+TGG 0.375234 tig0044637:+2375 Msa1464800:three_prime_UTR
GTTGCAATGTTTCTGATTTG+TGG 0.375721 tig0044637:-1512 Msa1464800:intergenic
GGAGCTTCAATGATAATAAT+GGG 0.378832 tig0044637:-1724 Msa1464800:intergenic
CCAAGAGCCACCTGCTGGTT+GGG 0.395859 tig0044637:-2375 Msa1464800:intergenic
TATGTGTGAGGAAGGATATT+AGG 0.413182 tig0044637:-1422 Msa1464800:intergenic
AACGTTCAAAGTTGGATAAA+GGG 0.431347 tig0044637:+1698 Msa1464800:CDS
ATATTTCAAGCCCTTAGATC+TGG 0.435238 tig0044637:+2285 Msa1464800:CDS
ACACATACACTGCAAATGAT+TGG 0.445934 tig0044637:+1438 Msa1464800:five_prime_UTR
ATATTTCAGTGTCATTAGTA+AGG 0.457947 tig0044637:+1632 Msa1464800:CDS
CTGTTGTTGAACTTTAGAAA+TGG 0.461418 tig0044637:-1583 Msa1464800:intergenic
GCCAAGAGCCACCTGCTGGT+TGG 0.499573 tig0044637:-2376 Msa1464800:intergenic
ATGTCTTTGTCCCTTTCTTG+TGG 0.510900 tig0044637:+1550 Msa1464800:CDS
CTTTGTGATACCACAAGAAA+GGG 0.530774 tig0044637:-1560 Msa1464800:intergenic
GCTTTGTGATACCACAAGAA+AGG 0.545899 tig0044637:-1561 Msa1464800:intergenic
CAAAAGATGTGTGGGCAGTA+CGG 0.550493 tig0044637:+2230 Msa1464800:CDS
AATTCTGGCTTAGTCAAACC+TGG 0.553371 tig0044637:+1790 Msa1464800:CDS
AGTCAAGCAAAATATTACAT+TGG 0.554810 tig0044637:+2433 Msa1464800:three_prime_UTR
CAGAATTAACTCTGAGGCAA+GGG 0.557005 tig0044637:-1774 Msa1464800:intergenic
CTATACTCAACCAGATCTAA+GGG 0.566149 tig0044637:-2295 Msa1464800:intergenic
TGGGCAGTACGGCTCAACAT+TGG 0.579445 tig0044637:+2241 Msa1464800:CDS
TCAAACCTGGTGATGTTGGA+AGG 0.583959 tig0044637:+1803 Msa1464800:CDS
AAGAAAGCCAAAAGATGTGT+GGG 0.587735 tig0044637:+2222 Msa1464800:CDS
CCAGAATTAACTCTGAGGCA+AGG 0.590927 tig0044637:-1775 Msa1464800:intergenic
CAAGAAAGCCAAAAGATGTG+TGG 0.602135 tig0044637:+2221 Msa1464800:CDS
TTAGTCAAACCTGGTGATGT+TGG 0.604419 tig0044637:+1799 Msa1464800:CDS
AAATACCTTCCAACATCACC+AGG 0.606725 tig0044637:-1808 Msa1464800:intergenic
TTTGTTTCCCAACCAGCAGG+TGG 0.609564 tig0044637:+2368 Msa1464800:three_prime_UTR
GTATGCCAAGAGCCACCTGC+TGG 0.623688 tig0044637:-2380 Msa1464800:intergenic
TTGCAGTGTATGTGTGAGGA+AGG 0.631311 tig0044637:-1430 Msa1464800:intergenic
TGAATCAAAAGAGTCATCAG+AGG 0.675313 tig0044637:+1657 Msa1464800:CDS
CTAAGCCAGAATTAACTCTG+AGG 0.700737 tig0044637:-1780 Msa1464800:intergenic
ACAGCTTGAAGTATCAACAA+CGG 0.721755 tig0044637:+1602 Msa1464800:CDS
TCATTTGCAGTGTATGTGTG+AGG 0.727329 tig0044637:-1434 Msa1464800:intergenic
GCTTGAAGTATCAACAACGG+AGG 0.739120 tig0044637:+1605 Msa1464800:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AATGTATAAATGATTTAATT+TGG + tig0044637:2005-2024 Msa1464800:intron 10.0%
!! AATTAATATCATGTATAAAA+TGG + tig0044637:2155-2174 Msa1464800:intron 10.0%
!! AATGTATAAATGATTTAATT+TGG + tig0044637:2005-2024 Msa1464800:intron 10.0%
!! AATTAATATCATGTATAAAA+TGG + tig0044637:2155-2174 Msa1464800:intron 10.0%
!! GTAAATAATTATATATCACT+TGG + tig0044637:2185-2204 Msa1464800:intron 15.0%
!! GTAAATAATTATATATCACT+TGG + tig0044637:2185-2204 Msa1464800:intron 15.0%
!! AATGAAAAACTTAAAAGATG+AGG - tig0044637:1836-1855 Msa1464800:intergenic 20.0%
!! GATTAGATACATAGTAAAAA+AGG - tig0044637:2036-2055 Msa1464800:intergenic 20.0%
!! AATGAAAAACTTAAAAGATG+AGG - tig0044637:1836-1855 Msa1464800:intergenic 20.0%
!! GATTAGATACATAGTAAAAA+AGG - tig0044637:2036-2055 Msa1464800:intergenic 20.0%
!!! TTCAATGTTTTGGAATTTGT+TGG - tig0044637:1491-1510 Msa1464800:intergenic 25.0%
! ACTAATGACACTGAAATATT+TGG - tig0044637:1631-1650 Msa1464800:intergenic 25.0%
!! ATATTTCAGTGTCATTAGTA+AGG + tig0044637:1632-1651 Msa1464800:CDS 25.0%
!! TTACGTGTAGAAATTTTGTA+AGG + tig0044637:2124-2143 Msa1464800:intron 25.0%
! TATCATGTATAAAATGGCAA+TGG + tig0044637:2161-2180 Msa1464800:intron 25.0%
! ATTGGAACTTATCTTATTGA+TGG + tig0044637:2259-2278 Msa1464800:CDS 25.0%
! AGTCAAGCAAAATATTACAT+TGG + tig0044637:2433-2452 Msa1464800:three_prime_UTR 25.0%
!!! TTCAATGTTTTGGAATTTGT+TGG - tig0044637:1491-1510 Msa1464800:intergenic 25.0%
! ACTAATGACACTGAAATATT+TGG - tig0044637:1631-1650 Msa1464800:intergenic 25.0%
!! ATATTTCAGTGTCATTAGTA+AGG + tig0044637:1632-1651 Msa1464800:CDS 25.0%
!! TTACGTGTAGAAATTTTGTA+AGG + tig0044637:2124-2143 Msa1464800:intron 25.0%
! TATCATGTATAAAATGGCAA+TGG + tig0044637:2161-2180 Msa1464800:intron 25.0%
! ATTGGAACTTATCTTATTGA+TGG + tig0044637:2259-2278 Msa1464800:CDS 25.0%
! AGTCAAGCAAAATATTACAT+TGG + tig0044637:2433-2452 Msa1464800:three_prime_UTR 25.0%
!!! GTTTTGGAATTTGTTGGTTA+TGG - tig0044637:1485-1504 Msa1464800:intergenic 30.0%
! GATTTGTGGTTTCAATGTTT+TGG - tig0044637:1501-1520 Msa1464800:intergenic 30.0%
! CTGTTGTTGAACTTTAGAAA+TGG - tig0044637:1586-1605 Msa1464800:intergenic 30.0%
AAACGTTCAAAGTTGGATAA+AGG + tig0044637:1697-1716 Msa1464800:CDS 30.0%
AACGTTCAAAGTTGGATAAA+GGG + tig0044637:1698-1717 Msa1464800:CDS 30.0%
GGAGCTTCAATGATAATAAT+GGG - tig0044637:1727-1746 Msa1464800:intergenic 30.0%
TGGAGCTTCAATGATAATAA+TGG - tig0044637:1728-1747 Msa1464800:intergenic 30.0%
CTTATCCCATTAAATTGGAT+CGG + tig0044637:1947-1966 Msa1464800:intron 30.0%
!!! GTTTTGGAATTTGTTGGTTA+TGG - tig0044637:1485-1504 Msa1464800:intergenic 30.0%
! GATTTGTGGTTTCAATGTTT+TGG - tig0044637:1501-1520 Msa1464800:intergenic 30.0%
! CTGTTGTTGAACTTTAGAAA+TGG - tig0044637:1586-1605 Msa1464800:intergenic 30.0%
AAACGTTCAAAGTTGGATAA+AGG + tig0044637:1697-1716 Msa1464800:CDS 30.0%
AACGTTCAAAGTTGGATAAA+GGG + tig0044637:1698-1717 Msa1464800:CDS 30.0%
GGAGCTTCAATGATAATAAT+GGG - tig0044637:1727-1746 Msa1464800:intergenic 30.0%
TGGAGCTTCAATGATAATAA+TGG - tig0044637:1728-1747 Msa1464800:intergenic 30.0%
CTTATCCCATTAAATTGGAT+CGG + tig0044637:1947-1966 Msa1464800:intron 30.0%
TATGTGTGAGGAAGGATATT+AGG - tig0044637:1425-1444 None:intergenic 35.0%
ACACATACACTGCAAATGAT+TGG + tig0044637:1438-1457 Msa1464800:five_prime_UTR 35.0%
! GTTGCAATGTTTCTGATTTG+TGG - tig0044637:1515-1534 Msa1464800:intergenic 35.0%
CTTTGTGATACCACAAGAAA+GGG - tig0044637:1563-1582 Msa1464800:intergenic 35.0%
! ACAGCTTGAAGTATCAACAA+CGG + tig0044637:1602-1621 Msa1464800:CDS 35.0%
TGAATCAAAAGAGTCATCAG+AGG + tig0044637:1657-1676 Msa1464800:CDS 35.0%
GCTTGAAAAACGTTCAAAGT+TGG + tig0044637:1690-1709 Msa1464800:CDS 35.0%
CAATTTAATGGGATAAGGCT+TGG - tig0044637:1944-1963 Msa1464800:intergenic 35.0%
! CAAGCCTTATCCCATTAAAT+TGG + tig0044637:1942-1961 Msa1464800:intron 35.0%
CGATCCAATTTAATGGGATA+AGG - tig0044637:1949-1968 Msa1464800:intergenic 35.0%
TGTTGCCGATCCAATTTAAT+GGG - tig0044637:1955-1974 Msa1464800:intergenic 35.0%
ATGTTGCCGATCCAATTTAA+TGG - tig0044637:1956-1975 Msa1464800:intergenic 35.0%
AAGAAAGCCAAAAGATGTGT+GGG + tig0044637:2222-2241 Msa1464800:CDS 35.0%
ATATTTCAAGCCCTTAGATC+TGG + tig0044637:2285-2304 Msa1464800:CDS 35.0%
CTATACTCAACCAGATCTAA+GGG - tig0044637:2298-2317 Msa1464800:intergenic 35.0%
ACTATACTCAACCAGATCTA+AGG - tig0044637:2299-2318 Msa1464800:intergenic 35.0%
TATGTGTGAGGAAGGATATT+AGG - tig0044637:1425-1444 Msa1464800:intergenic 35.0%
ACACATACACTGCAAATGAT+TGG + tig0044637:1438-1457 Msa1464800:five_prime_UTR 35.0%
! GTTGCAATGTTTCTGATTTG+TGG - tig0044637:1515-1534 Msa1464800:intergenic 35.0%
CTTTGTGATACCACAAGAAA+GGG - tig0044637:1563-1582 Msa1464800:intergenic 35.0%
! ACAGCTTGAAGTATCAACAA+CGG + tig0044637:1602-1621 Msa1464800:CDS 35.0%
TGAATCAAAAGAGTCATCAG+AGG + tig0044637:1657-1676 Msa1464800:CDS 35.0%
GCTTGAAAAACGTTCAAAGT+TGG + tig0044637:1690-1709 Msa1464800:CDS 35.0%
CAATTTAATGGGATAAGGCT+TGG - tig0044637:1944-1963 Msa1464800:intergenic 35.0%
! CAAGCCTTATCCCATTAAAT+TGG + tig0044637:1942-1961 Msa1464800:intron 35.0%
CGATCCAATTTAATGGGATA+AGG - tig0044637:1949-1968 Msa1464800:intergenic 35.0%
TGTTGCCGATCCAATTTAAT+GGG - tig0044637:1955-1974 Msa1464800:intergenic 35.0%
ATGTTGCCGATCCAATTTAA+TGG - tig0044637:1956-1975 Msa1464800:intergenic 35.0%
AAGAAAGCCAAAAGATGTGT+GGG + tig0044637:2222-2241 Msa1464800:CDS 35.0%
ATATTTCAAGCCCTTAGATC+TGG + tig0044637:2285-2304 Msa1464800:CDS 35.0%
CTATACTCAACCAGATCTAA+GGG - tig0044637:2298-2317 Msa1464800:intergenic 35.0%
ACTATACTCAACCAGATCTA+AGG - tig0044637:2299-2318 Msa1464800:intergenic 35.0%
TCATTTGCAGTGTATGTGTG+AGG - tig0044637:1437-1456 None:intergenic 40.0%
ATGTCTTTGTCCCTTTCTTG+TGG + tig0044637:1550-1569 Msa1464800:CDS 40.0%
GCTTTGTGATACCACAAGAA+AGG - tig0044637:1564-1583 Msa1464800:intergenic 40.0%
!! GCTGCAGTTTTGATCATCTT+TGG - tig0044637:1748-1767 Msa1464800:intergenic 40.0%
!! CAGAATTAACTCTGAGGCAA+GGG - tig0044637:1777-1796 Msa1464800:intergenic 40.0%
CTAAGCCAGAATTAACTCTG+AGG - tig0044637:1783-1802 Msa1464800:intergenic 40.0%
!! AATTCTGGCTTAGTCAAACC+TGG + tig0044637:1790-1809 Msa1464800:CDS 40.0%
! TTAGTCAAACCTGGTGATGT+TGG + tig0044637:1799-1818 Msa1464800:CDS 40.0%
AAATACCTTCCAACATCACC+AGG - tig0044637:1811-1830 Msa1464800:intergenic 40.0%
CAAGAAAGCCAAAAGATGTG+TGG + tig0044637:2221-2240 Msa1464800:CDS 40.0%
!! ATTTTTGTTTCCCAACCAGC+AGG + tig0044637:2365-2384 Msa1464800:three_prime_UTR 40.0%
TCATTTGCAGTGTATGTGTG+AGG - tig0044637:1437-1456 Msa1464800:intergenic 40.0%
ATGTCTTTGTCCCTTTCTTG+TGG + tig0044637:1550-1569 Msa1464800:CDS 40.0%
GCTTTGTGATACCACAAGAA+AGG - tig0044637:1564-1583 Msa1464800:intergenic 40.0%
!! GCTGCAGTTTTGATCATCTT+TGG - tig0044637:1748-1767 Msa1464800:intergenic 40.0%
!! CAGAATTAACTCTGAGGCAA+GGG - tig0044637:1777-1796 Msa1464800:intergenic 40.0%
CTAAGCCAGAATTAACTCTG+AGG - tig0044637:1783-1802 Msa1464800:intergenic 40.0%
!! AATTCTGGCTTAGTCAAACC+TGG + tig0044637:1790-1809 Msa1464800:CDS 40.0%
! TTAGTCAAACCTGGTGATGT+TGG + tig0044637:1799-1818 Msa1464800:CDS 40.0%
AAATACCTTCCAACATCACC+AGG - tig0044637:1811-1830 Msa1464800:intergenic 40.0%
CAAGAAAGCCAAAAGATGTG+TGG + tig0044637:2221-2240 Msa1464800:CDS 40.0%
!! ATTTTTGTTTCCCAACCAGC+AGG + tig0044637:2365-2384 Msa1464800:three_prime_UTR 40.0%
TTGCAGTGTATGTGTGAGGA+AGG - tig0044637:1433-1452 None:intergenic 45.0%
! GCTTGAAGTATCAACAACGG+AGG + tig0044637:1605-1624 Msa1464800:CDS 45.0%
!! CCAGAATTAACTCTGAGGCA+AGG - tig0044637:1778-1797 Msa1464800:intergenic 45.0%
CCTTGCCTCAGAGTTAATTC+TGG + tig0044637:1775-1794 Msa1464800:CDS 45.0%
! TCAAACCTGGTGATGTTGGA+AGG + tig0044637:1803-1822 Msa1464800:CDS 45.0%
CAAAAGATGTGTGGGCAGTA+CGG + tig0044637:2230-2249 Msa1464800:CDS 45.0%
TTGCAGTGTATGTGTGAGGA+AGG - tig0044637:1433-1452 Msa1464800:intergenic 45.0%
! GCTTGAAGTATCAACAACGG+AGG + tig0044637:1605-1624 Msa1464800:CDS 45.0%
!! CCAGAATTAACTCTGAGGCA+AGG - tig0044637:1778-1797 Msa1464800:intergenic 45.0%
CCTTGCCTCAGAGTTAATTC+TGG + tig0044637:1775-1794 Msa1464800:CDS 45.0%
! TCAAACCTGGTGATGTTGGA+AGG + tig0044637:1803-1822 Msa1464800:CDS 45.0%
CAAAAGATGTGTGGGCAGTA+CGG + tig0044637:2230-2249 Msa1464800:CDS 45.0%
! CGTACTGCCCACACATCTTT+TGG - tig0044637:2232-2251 Msa1464800:intergenic 50.0%
TTTGTTTCCCAACCAGCAGG+TGG + tig0044637:2368-2387 Msa1464800:three_prime_UTR 50.0%
! CGTACTGCCCACACATCTTT+TGG - tig0044637:2232-2251 Msa1464800:intergenic 50.0%
TTTGTTTCCCAACCAGCAGG+TGG + tig0044637:2368-2387 Msa1464800:three_prime_UTR 50.0%
TGGGCAGTACGGCTCAACAT+TGG + tig0044637:2241-2260 Msa1464800:CDS 55.0%
TGGGCAGTACGGCTCAACAT+TGG + tig0044637:2241-2260 Msa1464800:CDS 55.0%
! CCAAGAGCCACCTGCTGGTT+GGG - tig0044637:2378-2397 Msa1464800:intergenic 60.0%
GTATGCCAAGAGCCACCTGC+TGG - tig0044637:2383-2402 Msa1464800:intergenic 60.0%
! CCAAGAGCCACCTGCTGGTT+GGG - tig0044637:2378-2397 Msa1464800:intergenic 60.0%
GTATGCCAAGAGCCACCTGC+TGG - tig0044637:2383-2402 Msa1464800:intergenic 60.0%
CCCAACCAGCAGGTGGCTCT+TGG + tig0044637:2375-2394 Msa1464800:three_prime_UTR 65.0%
GCCAAGAGCCACCTGCTGGT+TGG - tig0044637:2379-2398 Msa1464800:intergenic 65.0%
CCCAACCAGCAGGTGGCTCT+TGG + tig0044637:2375-2394 Msa1464800:three_prime_UTR 65.0%
GCCAAGAGCCACCTGCTGGT+TGG - tig0044637:2379-2398 Msa1464800:intergenic 65.0%
Chromosome Type Strat End Strand Name
tig0044637 gene 1360 2508 1360 ID=Msa1464800;Name=Msa1464800
tig0044637 mRNA 1360 2508 1360 ID=Msa1464800-mRNA-1;Parent=Msa1464800;Name=Msa1464800-mRNA-1;_AED=0.00;_eAED=0.00;_QI=190|1|1|1|1|1|2|187|127
tig0044637 exon 1360 1824 1360 ID=Msa1464800-mRNA-1:exon:24583;Parent=Msa1464800-mRNA-1
tig0044637 exon 2213 2508 2213 ID=Msa1464800-mRNA-1:exon:24584;Parent=Msa1464800-mRNA-1
tig0044637 five_prime_UTR 1360 1549 1360 ID=Msa1464800-mRNA-1:five_prime_utr;Parent=Msa1464800-mRNA-1
tig0044637 CDS 1550 1824 1550 ID=Msa1464800-mRNA-1:cds;Parent=Msa1464800-mRNA-1
tig0044637 CDS 2213 2321 2213 ID=Msa1464800-mRNA-1:cds;Parent=Msa1464800-mRNA-1
tig0044637 three_prime_UTR 2322 2508 2322 ID=Msa1464800-mRNA-1:three_prime_utr;Parent=Msa1464800-mRNA-1
Gene Sequence

>Msa1464800

ATGTCTTTGTCCCTTTCTTGTGGTATCACAAAGCCATTTCTAAAGTTCAACAACAGCTTGAAGTATCAACAACGGAGGCCAAATATTTCAGTGTCATTAGTAAGGTGTGAATCAAAAGAGTCATCAGAGGAGAATGAGTTGCTTGAAAAACGTTCAAAGTTGGATAAAGGGTCTCCCATTATTATCATTGAAGCTCCAAAGATGATCAAAACTGCAGCTTCTGTCCCTTGCCTCAGAGTTAATTCTGGCTTAGTCAAACCTGGTGATGTTGGAAGAATTGTTTCAAGAAAGCCAAAAGATGTGTGGGCAGTACGGCTCAACATTGGAACTTATCTTATTGATGGCAAATATTTCAAGCCCTTAGATCTGGTTGAGTATAGTTAG

Protein sequence

>Msa1464800

MSLSLSCGITKPFLKFNNSLKYQQRRPNISVSLVRCESKESSEENELLEKRSKLDKGSPIIIIEAPKMIKTAASVPCLRVNSGLVKPGDVGRIVSRKPKDVWAVRLNIGTYLIDGKYFKPLDLVEYS*