AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1356240


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1356240 MtrunA17_Chr3g0120531 85.217 115 16 1 1 114 1 115 1.27e-58 176
Msa1356240 MtrunA17_Chr3g0120541 70.588 119 26 3 1 114 1 115 2.97e-49 152
Msa1356240 MtrunA17_Chr3g0120551 58.824 119 42 3 1 114 1 117 2.75e-38 124
Msa1356240 MtrunA17_Chr2g0290831 51.351 74 36 0 3 76 2 75 2.17e-20 78.2
Msa1356240 MtrunA17_Chr5g0438551 43.609 133 51 5 4 113 2 133 2.65e-20 79.7
Msa1356240 MtrunA17_Chr6g0483521 50.000 62 31 0 3 64 2 63 6.29e-16 70.5
Msa1356240 MtrunA17_Chr6g0483511 51.613 62 30 0 3 64 2 63 5.63e-15 67.4
Msa1356240 MtrunA17_Chr6g0483581 45.205 73 40 0 3 75 2 74 1.31e-14 67.0
Msa1356240 MtrunA17_Chr6g0483561 44.286 70 39 0 3 72 2 71 6.34e-14 65.1
Msa1356240 MtrunA17_Chr6g0469651 50.704 71 30 4 4 73 2 68 5.53e-12 58.2
Msa1356240 MtrunA17_Chr6g0469571 44.928 69 35 2 5 73 3 68 4.11e-11 55.8
Msa1356240 MtrunA17_Chr6g0469551 44.928 69 35 2 5 73 3 68 5.36e-11 55.5
Msa1356240 MtrunA17_Chr6g0469541 36.036 111 58 7 4 107 2 106 5.38e-11 55.1
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1356240 AT3G20180.3 43.617 94 52 1 3 96 2 94 4.49e-18 73.9
Msa1356240 AT5G48290.1 49.398 83 39 1 3 82 2 84 1.10e-17 74.7
Msa1356240 AT3G20180.2 47.059 85 43 1 3 85 21 105 1.53e-17 73.2
Msa1356240 AT3G07600.1 44.872 78 43 0 3 80 2 79 3.63e-17 72.8
Msa1356240 AT3G20180.4 42.391 92 52 1 5 96 2 92 8.37e-17 70.9
Msa1356240 AT3G20180.1 42.697 89 50 1 8 96 3 90 1.81e-16 69.7
Msa1356240 AT5G48290.3 40.777 103 38 2 3 82 2 104 6.50e-14 65.1
Msa1356240 AT1G55775.1 34.821 112 69 2 2 113 3 110 1.60e-13 62.8
Msa1356240 AT5G48290.2 47.297 74 36 1 12 82 1 74 4.18e-13 62.4
Msa1356240 AT4G05030.2 45.333 75 40 1 1 75 1 74 2.00e-12 58.5
Msa1356240 AT4G05030.1 43.056 72 41 0 4 75 36 107 1.19e-11 57.4

Find 29 sgRNAs with CRISPR-Local

Find 98 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
AAGATTGCAGTTGGAGTTTC+AGG 0.157536 tig0015546:-7287 Msa1356240:intron
TTTATATCTCATAAGTATTA+TGG 0.216328 tig0015546:-7762 Msa1356240:exon
ACACAAGGCCATGCCATAAT+TGG 0.269055 tig0015546:+6997 None:intergenic
ACTTATGAGATATAAATAAA+TGG 0.288883 tig0015546:+7769 None:intergenic
ATTAGAAGAAGCTTTGTTTC+CGG 0.305912 tig0015546:+7792 None:intergenic
AACTGCAATCTTCATGGCTT+TGG 0.309449 tig0015546:+7298 None:intergenic
AAAGAAAGAAGAACCAATTA+TGG 0.328215 tig0015546:-7010 Msa1356240:CDS
ATGGCATGGCCTTGTGTAAC+TGG 0.358016 tig0015546:-6991 Msa1356240:CDS
AACTCCAACTGCAATCTTCA+TGG 0.358381 tig0015546:+7292 None:intergenic
GAAATTCTGTCATGCAGAAT+TGG 0.360093 tig0015546:-7064 Msa1356240:CDS
ACTTTAATAATACACCATTC+CGG 0.451555 tig0015546:-7811 None:intergenic
CTTATCTCACACACAGGGAC+AGG 0.478978 tig0015546:+6955 None:intergenic
AAGGATCAACTAGAAGTAAT+CGG 0.481199 tig0015546:-7129 Msa1356240:CDS
CTGTCCCTGTGTGTGAGATA+AGG 0.485521 tig0015546:-6954 Msa1356240:CDS
TATTGATGACATTCACATGA+TGG 0.492268 tig0015546:+6915 None:intergenic
TGTCCCTGTGTGTGAGATAA+GGG 0.495058 tig0015546:-6953 Msa1356240:CDS
TCTCATAAGTATTATGGCTA+AGG 0.519265 tig0015546:-7756 Msa1356240:intron
GTGGAAAGTGCAGCAATACA+AGG 0.533044 tig0015546:-7159 Msa1356240:CDS
GCAGCAAAAGATAGTGATCA+AGG 0.536634 tig0015546:-7348 Msa1356240:intron
AAGAAGCTTTGTTTCCGGAA+TGG 0.538643 tig0015546:+7797 None:intergenic
CACACAGGGACAGGGTAATG+AGG 0.564551 tig0015546:+6964 None:intergenic
AAAGCCATGAAGATTGCAGT+TGG 0.583776 tig0015546:-7296 Msa1356240:CDS
CATGCAGAATTGGTGAGTGT+TGG 0.620675 tig0015546:-7054 Msa1356240:CDS
AGCAATACAAGGAGATAGCA+AGG 0.620845 tig0015546:-7148 Msa1356240:CDS
AAGAAGAACCAATTATGGCA+TGG 0.625011 tig0015546:-7005 Msa1356240:CDS
TCGTCCCTTATCTCACACAC+AGG 0.651929 tig0015546:+6949 None:intergenic
TTATCTCACACACAGGGACA+GGG 0.661020 tig0015546:+6956 None:intergenic
CGTCCCTTATCTCACACACA+GGG 0.689018 tig0015546:+6950 None:intergenic
TGAGGATAACCAGTTACACA+AGG 0.713738 tig0015546:+6982 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! ATAGTATATATATTGAATAA+AGG + tig0015546:7051-7070 None:intergenic 10.0%
!! TTTGAATTAAAAATGATTAA+TGG + tig0015546:7496-7515 None:intergenic 10.0%
!! ATAGTATATATATTGAATAA+AGG + tig0015546:7051-7070 None:intergenic 10.0%
!! TTTGAATTAAAAATGATTAA+TGG + tig0015546:7496-7515 None:intergenic 10.0%
!! ACTTATGAGATATAAATAAA+TGG + tig0015546:6967-6986 None:intergenic 15.0%
!! TTTATATCTCATAAGTATTA+TGG - tig0015546:6971-6990 Msa1356240:CDS 15.0%
!!! TAATCCTTTTTTGAAATTTT+TGG + tig0015546:7258-7277 None:intergenic 15.0%
!! ACTTATGAGATATAAATAAA+TGG + tig0015546:6967-6986 None:intergenic 15.0%
!! TTTATATCTCATAAGTATTA+TGG - tig0015546:6971-6990 Msa1356240:CDS 15.0%
!!! TAATCCTTTTTTGAAATTTT+TGG + tig0015546:7258-7277 None:intergenic 15.0%
!! GTATATATATTGAATAAAGG+AGG + tig0015546:7048-7067 None:intergenic 20.0%
!! GTATATATATTGAATAAAGG+AGG + tig0015546:7048-7067 None:intergenic 20.0%
! TCCACCAAAAATTTCAAAAA+AGG - tig0015546:7251-7270 Msa1356240:intron 25.0%
!!! TCCTTTTTTGAAATTTTTGG+TGG + tig0015546:7255-7274 None:intergenic 25.0%
! TAGTTTGGATAATTAAGCTA+TGG + tig0015546:7531-7550 None:intergenic 25.0%
!!! ATTTTTGGACATGATTAGTT+TGG + tig0015546:7546-7565 None:intergenic 25.0%
! AATCATGTCCAAAAATATTC+AGG - tig0015546:7550-7569 Msa1356240:intron 25.0%
! AAAGAAAGAAGAACCAATTA+TGG - tig0015546:7723-7742 Msa1356240:intron 25.0%
! TCCACCAAAAATTTCAAAAA+AGG - tig0015546:7251-7270 Msa1356240:intron 25.0%
!!! TCCTTTTTTGAAATTTTTGG+TGG + tig0015546:7255-7274 None:intergenic 25.0%
! TAGTTTGGATAATTAAGCTA+TGG + tig0015546:7531-7550 None:intergenic 25.0%
!!! ATTTTTGGACATGATTAGTT+TGG + tig0015546:7546-7565 None:intergenic 25.0%
! AATCATGTCCAAAAATATTC+AGG - tig0015546:7550-7569 Msa1356240:intron 25.0%
! AAAGAAAGAAGAACCAATTA+TGG - tig0015546:7723-7742 Msa1356240:intron 25.0%
!! ATTAGAAGAAGCTTTGTTTC+CGG + tig0015546:6944-6963 None:intergenic 30.0%
TCTCATAAGTATTATGGCTA+AGG - tig0015546:6977-6996 Msa1356240:CDS 30.0%
!!! TCACACTACTTTTTTTTAGC+AGG + tig0015546:7020-7039 None:intergenic 30.0%
TATATTGAATAAAGGAGGTC+AGG + tig0015546:7043-7062 None:intergenic 30.0%
! TTTCCACTCCTGAATATTTT+TGG + tig0015546:7561-7580 None:intergenic 30.0%
AAGGATCAACTAGAAGTAAT+CGG - tig0015546:7604-7623 Msa1356240:intron 30.0%
!! ATTAGAAGAAGCTTTGTTTC+CGG + tig0015546:6944-6963 None:intergenic 30.0%
TCTCATAAGTATTATGGCTA+AGG - tig0015546:6977-6996 Msa1356240:CDS 30.0%
!!! TCACACTACTTTTTTTTAGC+AGG + tig0015546:7020-7039 None:intergenic 30.0%
TATATTGAATAAAGGAGGTC+AGG + tig0015546:7043-7062 None:intergenic 30.0%
! TTTCCACTCCTGAATATTTT+TGG + tig0015546:7561-7580 None:intergenic 30.0%
AAGGATCAACTAGAAGTAAT+CGG - tig0015546:7604-7623 Msa1356240:intron 30.0%
ATCCTTTGCTTGAAATTGAG+AGG - tig0015546:7129-7148 Msa1356240:CDS 35.0%
TCCTTTGCTTGAAATTGAGA+GGG - tig0015546:7130-7149 Msa1356240:CDS 35.0%
TTGAAATTGAGAGGGAAAGA+GGG - tig0015546:7138-7157 Msa1356240:CDS 35.0%
TGTCCAAAAATATTCAGGAG+TGG - tig0015546:7555-7574 Msa1356240:intron 35.0%
!! TAGCAGTTTTGTGAGTCTAA+CGG + tig0015546:7644-7663 None:intergenic 35.0%
GAAATTCTGTCATGCAGAAT+TGG - tig0015546:7669-7688 Msa1356240:intron 35.0%
TGGTGAAGTGAAAAAGAAAG+AGG - tig0015546:7699-7718 Msa1356240:intron 35.0%
AAGAAGAACCAATTATGGCA+TGG - tig0015546:7728-7747 Msa1356240:intron 35.0%
ATCCTTTGCTTGAAATTGAG+AGG - tig0015546:7129-7148 Msa1356240:CDS 35.0%
TCCTTTGCTTGAAATTGAGA+GGG - tig0015546:7130-7149 Msa1356240:CDS 35.0%
TTGAAATTGAGAGGGAAAGA+GGG - tig0015546:7138-7157 Msa1356240:CDS 35.0%
TGTCCAAAAATATTCAGGAG+TGG - tig0015546:7555-7574 Msa1356240:intron 35.0%
!! TAGCAGTTTTGTGAGTCTAA+CGG + tig0015546:7644-7663 None:intergenic 35.0%
GAAATTCTGTCATGCAGAAT+TGG - tig0015546:7669-7688 Msa1356240:intron 35.0%
TGGTGAAGTGAAAAAGAAAG+AGG - tig0015546:7699-7718 Msa1356240:intron 35.0%
AAGAAGAACCAATTATGGCA+TGG - tig0015546:7728-7747 Msa1356240:intron 35.0%
!! AAGAAGCTTTGTTTCCGGAA+TGG + tig0015546:6939-6958 None:intergenic 40.0%
TCCCTCTCAATTTCAAGCAA+AGG + tig0015546:7134-7153 None:intergenic 40.0%
CTTGAAATTGAGAGGGAAAG+AGG - tig0015546:7137-7156 Msa1356240:CDS 40.0%
GCAGCAAAAGATAGTGATCA+AGG - tig0015546:7385-7404 Msa1356240:intron 40.0%
CAATGCACAGCCAAAAATCA+AGG - tig0015546:7411-7430 Msa1356240:intron 40.0%
!!! TGGCTTTGGACCTTGATTTT+TGG + tig0015546:7424-7443 None:intergenic 40.0%
AACTGCAATCTTCATGGCTT+TGG + tig0015546:7438-7457 None:intergenic 40.0%
AAAGCCATGAAGATTGCAGT+TGG - tig0015546:7437-7456 Msa1356240:intron 40.0%
AACTCCAACTGCAATCTTCA+TGG + tig0015546:7444-7463 None:intergenic 40.0%
AAGATTGCAGTTGGAGTTTC+AGG - tig0015546:7446-7465 Msa1356240:intron 40.0%
AGCAATACAAGGAGATAGCA+AGG - tig0015546:7585-7604 Msa1356240:intron 40.0%
TGAGGATAACCAGTTACACA+AGG + tig0015546:7754-7773 None:intergenic 40.0%
!! AAGAAGCTTTGTTTCCGGAA+TGG + tig0015546:6939-6958 None:intergenic 40.0%
TCCCTCTCAATTTCAAGCAA+AGG + tig0015546:7134-7153 None:intergenic 40.0%
CTTGAAATTGAGAGGGAAAG+AGG - tig0015546:7137-7156 Msa1356240:CDS 40.0%
GCAGCAAAAGATAGTGATCA+AGG - tig0015546:7385-7404 Msa1356240:intron 40.0%
CAATGCACAGCCAAAAATCA+AGG - tig0015546:7411-7430 Msa1356240:intron 40.0%
!!! TGGCTTTGGACCTTGATTTT+TGG + tig0015546:7424-7443 None:intergenic 40.0%
AACTGCAATCTTCATGGCTT+TGG + tig0015546:7438-7457 None:intergenic 40.0%
AAAGCCATGAAGATTGCAGT+TGG - tig0015546:7437-7456 Msa1356240:intron 40.0%
AACTCCAACTGCAATCTTCA+TGG + tig0015546:7444-7463 None:intergenic 40.0%
AAGATTGCAGTTGGAGTTTC+AGG - tig0015546:7446-7465 Msa1356240:intron 40.0%
AGCAATACAAGGAGATAGCA+AGG - tig0015546:7585-7604 Msa1356240:intron 40.0%
TGAGGATAACCAGTTACACA+AGG + tig0015546:7754-7773 None:intergenic 40.0%
! GTGGAAAGTGCAGCAATACA+AGG - tig0015546:7574-7593 Msa1356240:intron 45.0%
CATGCAGAATTGGTGAGTGT+TGG - tig0015546:7679-7698 Msa1356240:intron 45.0%
ACACAAGGCCATGCCATAAT+TGG + tig0015546:7739-7758 None:intergenic 45.0%
TTATCTCACACACAGGGACA+GGG + tig0015546:7780-7799 None:intergenic 45.0%
TGTCCCTGTGTGTGAGATAA+GGG - tig0015546:7780-7799 Msa1356240:five_prime_UTR 45.0%
! GTGGAAAGTGCAGCAATACA+AGG - tig0015546:7574-7593 Msa1356240:intron 45.0%
CATGCAGAATTGGTGAGTGT+TGG - tig0015546:7679-7698 Msa1356240:intron 45.0%
ACACAAGGCCATGCCATAAT+TGG + tig0015546:7739-7758 None:intergenic 45.0%
TTATCTCACACACAGGGACA+GGG + tig0015546:7780-7799 None:intergenic 45.0%
TGTCCCTGTGTGTGAGATAA+GGG - tig0015546:7780-7799 Msa1356240:five_prime_UTR 45.0%
!! ATGGCATGGCCTTGTGTAAC+TGG - tig0015546:7742-7761 Msa1356240:intron 50.0%
CTTATCTCACACACAGGGAC+AGG + tig0015546:7781-7800 None:intergenic 50.0%
CTGTCCCTGTGTGTGAGATA+AGG - tig0015546:7779-7798 Msa1356240:five_prime_UTR 50.0%
CGTCCCTTATCTCACACACA+GGG + tig0015546:7786-7805 None:intergenic 50.0%
TCGTCCCTTATCTCACACAC+AGG + tig0015546:7787-7806 None:intergenic 50.0%
!! ATGGCATGGCCTTGTGTAAC+TGG - tig0015546:7742-7761 Msa1356240:intron 50.0%
CTTATCTCACACACAGGGAC+AGG + tig0015546:7781-7800 None:intergenic 50.0%
CTGTCCCTGTGTGTGAGATA+AGG - tig0015546:7779-7798 Msa1356240:five_prime_UTR 50.0%
CGTCCCTTATCTCACACACA+GGG + tig0015546:7786-7805 None:intergenic 50.0%
TCGTCCCTTATCTCACACAC+AGG + tig0015546:7787-7806 None:intergenic 50.0%
CACACAGGGACAGGGTAATG+AGG + tig0015546:7772-7791 None:intergenic 55.0%
CACACAGGGACAGGGTAATG+AGG + tig0015546:7772-7791 None:intergenic 55.0%
Chromosome Type Strat End Strand Name
tig0015546 gene 6927 7828 6927 ID=Msa1356240;Name=Msa1356240
tig0015546 mRNA 6927 7828 6927 ID=Msa1356240-mRNA-1;Parent=Msa1356240;Name=Msa1356240-mRNA-1;_AED=0.33;_eAED=0.33;_QI=63|1|0.66|1|1|1|3|0|114
tig0015546 exon 6927 7183 6927 ID=Msa1356240-mRNA-1:exon:9820;Parent=Msa1356240-mRNA-1
tig0015546 exon 7288 7366 7288 ID=Msa1356240-mRNA-1:exon:9819;Parent=Msa1356240-mRNA-1
tig0015546 exon 7757 7828 7757 ID=Msa1356240-mRNA-1:exon:9818;Parent=Msa1356240-mRNA-1
tig0015546 five_prime_UTR 7766 7828 7766 ID=Msa1356240-mRNA-1:five_prime_utr;Parent=Msa1356240-mRNA-1
tig0015546 CDS 7757 7765 7757 ID=Msa1356240-mRNA-1:cds;Parent=Msa1356240-mRNA-1
tig0015546 CDS 7288 7366 7288 ID=Msa1356240-mRNA-1:cds;Parent=Msa1356240-mRNA-1
tig0015546 CDS 6927 7183 6927 ID=Msa1356240-mRNA-1:cds;Parent=Msa1356240-mRNA-1
Gene Sequence

>Msa1356240

ATGGCTAAGCAAAAGATAGTGATCAAGGTGTCAATGCACAGCCAAAAATCAAGGTCCAAAGCCATGAAGATTGCAGTTGGAGTTTCAGGAGTGGAAAGTGCAGCAATACAAGGAGATAGCAAGGATCAACTAGAAGTAATCGGCGAACAAATAGACTCCGTTAGACTCACAAAACTGCTAAGAAAGAAATTCTGTCATGCAGAATTGGTGAGTGTTGGTGAAGTGAAAAAGAAAGAGGAAAAGAAAGAAGAACCAATTATGGCATGGCCTTGTGTAACTGGTTATCCTCATTACCCTGTCCCTGTGTGTGAGATAAGGGACGACTCTTCTTGTTCCATCATGTGA

Protein sequence

>Msa1356240

MAKQKIVIKVSMHSQKSRSKAMKIAVGVSGVESAAIQGDSKDQLEVIGEQIDSVRLTKLLRKKFCHAELVSVGEVKKKEEKKEEPIMAWPCVTGYPHYPVPVCEIRDDSSCSIM*