AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1409600


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1409600 MtrunA17_Chr3g0111071 75.000 136 32 2 1 135 1 135 1.91e-71 210
Msa1409600 MtrunA17_Chr3g0111081 75.000 136 32 2 1 135 1 135 1.50e-70 207
Msa1409600 MtrunA17_Chr3g0111131 61.538 130 43 3 1 125 1 128 1.19e-48 152
Msa1409600 MtrunA17_Chr3g0111351 56.391 133 54 3 1 130 9 140 2.26e-45 144
Msa1409600 MtrunA17_Chr3g0111241 55.970 134 47 5 1 130 1 126 2.86e-40 131
Msa1409600 MtrunA17_Chr3g0111281 51.825 137 58 4 1 130 1 136 1.28e-39 129
Msa1409600 MtrunA17_Chr3g0111111 53.521 142 48 5 1 130 1 136 9.97e-39 127
Msa1409600 MtrunA17_Chr3g0104571 53.030 132 58 4 1 129 1 131 2.36e-35 119
Msa1409600 MtrunA17_Chr3g0111261 50.000 140 52 5 1 130 1 132 2.47e-35 119
Msa1409600 MtrunA17_Chr3g0111191 54.701 117 46 3 1 110 1 117 8.28e-33 112
Msa1409600 MtrunA17_Chr6g0464071 49.254 134 60 5 1 130 1 130 9.20e-32 109
Msa1409600 MtrunA17_Chr6g0456951 48.936 141 61 8 1 134 1 137 4.13e-31 108
Msa1409600 MtrunA17_Chr7g0232011 45.865 133 64 5 1 131 1 127 4.80e-30 105
Msa1409600 MtrunA17_Chr7g0236791 45.588 136 66 5 1 130 1 134 1.21e-28 102
Msa1409600 MtrunA17_Chr3g0111221 50.893 112 50 3 22 130 1 110 1.02e-27 99.0
Msa1409600 MtrunA17_Chr7g0236801 44.118 136 69 4 1 130 1 135 1.13e-27 99.4
Msa1409600 MtrunA17_Chr3g0111311 56.383 94 37 3 22 113 1 92 5.39e-27 96.3
Msa1409600 MtrunA17_Chr3g0090571 40.000 150 68 5 1 130 1 148 7.56e-27 97.8
Msa1409600 MtrunA17_Chr4g0012121 44.800 125 55 5 17 130 18 139 4.80e-25 92.8
Msa1409600 MtrunA17_Chr6g0468621 42.222 135 70 5 1 131 1 131 2.29e-24 90.9
Msa1409600 MtrunA17_Chr6g0468601 40.000 135 76 4 1 131 1 134 1.18e-23 89.4
Msa1409600 MtrunA17_Chr1g0153591 43.548 124 53 4 1 120 1 111 2.36e-23 87.8
Msa1409600 MtrunA17_Chr8g0359071 43.925 107 55 3 11 114 12 116 2.29e-22 85.9
Msa1409600 MtrunA17_Chr3g0111711 51.923 104 42 5 1 97 1 103 2.65e-22 85.1
Msa1409600 MtrunA17_Chr8g0344771 40.517 116 64 4 22 134 1 114 8.08e-21 81.6
Msa1409600 MtrunA17_Chr8g0344791 44.828 87 47 1 44 129 25 111 1.00e-19 78.6
Msa1409600 MtrunA17_Chr7g0225821 37.705 122 72 2 1 118 1 122 1.15e-19 78.6
Msa1409600 MtrunA17_Chr3g0111201 72.549 51 13 1 80 130 3 52 6.04e-19 74.7
Msa1409600 MtrunA17_Chr6g0456991 61.538 52 20 0 63 114 48 99 7.72e-19 76.3
Msa1409600 MtrunA17_Chr8g0344801 42.857 91 52 0 44 134 9 99 6.24e-18 73.6
Msa1409600 MtrunA17_Chr7g0231991 42.520 127 54 6 22 130 1 126 2.39e-17 72.8
Msa1409600 MtrunA17_Chr8g0357331 41.772 79 44 1 53 131 8 84 1.64e-14 64.7
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 23 sgRNAs with CRISPR-Local

Find 30 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CTTAATTCTGATATCAAATA+TGG 0.247187 tig0023528:-27545 Msa1409600:CDS
CTCCTTCTACTTTGTTCATT+GGG 0.296363 tig0023528:+27765 None:intergenic
GCTGTCTTTCTTGAATTTAG+AGG 0.344386 tig0023528:+27469 None:intergenic
TTTCTTGAATTTAGAGGTAA+TGG 0.350169 tig0023528:+27475 None:intergenic
TCTCCTTCTACTTTGTTCAT+TGG 0.362323 tig0023528:+27764 None:intergenic
AATTTATTCTATTGAAAAGA+AGG 0.426982 tig0023528:-27645 Msa1409600:CDS
TTCCCAATGAACAAAGTAGA+AGG 0.432028 tig0023528:-27767 Msa1409600:CDS
CTATGAGACATACATAAGTT+AGG 0.445121 tig0023528:+27611 None:intergenic
GACAGCTTCTTGAAGATGCT+TGG 0.451362 tig0023528:-27452 Msa1409600:CDS
GACATTACATATTGTGAAGA+TGG 0.462660 tig0023528:-27719 Msa1409600:CDS
TCATAGCGATTGCACAAAGA+AGG 0.499424 tig0023528:-27594 Msa1409600:CDS
AAAGTAGAAGGAGACTGTAC+GGG 0.562543 tig0023528:-27755 Msa1409600:CDS
ACATATCAATATTAATTAAG+CGG 0.565489 tig0023528:+27424 None:intergenic
ACATATTGTGAAGATGGTTG+TGG 0.567653 tig0023528:-27713 Msa1409600:CDS
CAAAGTAGAAGGAGACTGTA+CGG 0.574901 tig0023528:-27756 Msa1409600:CDS
GATTGCACAAAGAAGGGTAG+TGG 0.585178 tig0023528:-27587 Msa1409600:CDS
GCAAGTAAGAAGACAACGAA+AGG 0.597344 tig0023528:+27969 None:intergenic
CATAGCGATTGCACAAAGAA+GGG 0.599166 tig0023528:-27593 Msa1409600:CDS
AGCAGAAGACGCATACAAGA+TGG 0.599466 tig0023528:-27498 Msa1409600:CDS
TATCAATATTAATTAAGCGG+TGG 0.649392 tig0023528:+27427 None:intergenic
GTCTTCTGCTTCAGTGACAG+AGG 0.660768 tig0023528:+27511 None:intergenic
AAGTAGAAGGAGACTGTACG+GGG 0.665862 tig0023528:-27754 Msa1409600:CDS
AGTAGAAGGAGACTGTACGG+GGG 0.832627 tig0023528:-27753 Msa1409600:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! TCTTTTCAATAGAATAAATT+GGG + tig0023528:27784-27803 None:intergenic 15.0%
!!! TTCTTTTCAATAGAATAAAT+TGG + tig0023528:27785-27804 None:intergenic 15.0%
!! AATTTATTCTATTGAAAAGA+AGG - tig0023528:27784-27803 Msa1409600:intron 15.0%
!! CTTAATTCTGATATCAAATA+TGG - tig0023528:27884-27903 Msa1409600:intron 20.0%
! AAAGATGGCTAAAATACAAA+AGG + tig0023528:27503-27522 None:intergenic 25.0%
!! TTGCGATGTCATATATTTTA+TGG - tig0023528:27739-27758 Msa1409600:CDS 25.0%
!! TGCGATGTCATATATTTTAT+GGG - tig0023528:27740-27759 Msa1409600:CDS 25.0%
! TTTCTTGAATTTAGAGGTAA+TGG + tig0023528:27957-27976 None:intergenic 25.0%
AATGCATCATATGACAAAGA+TGG + tig0023528:27518-27537 None:intergenic 30.0%
AAGCTCATTAGAAATTAGCT+TGG - tig0023528:27561-27580 Msa1409600:CDS 30.0%
GACATTACATATTGTGAAGA+TGG - tig0023528:27710-27729 Msa1409600:CDS 30.0%
! GATGTCATATATTTTATGGG+TGG - tig0023528:27743-27762 Msa1409600:CDS 30.0%
! ATATATTTTATGGGTGGTGA+AGG - tig0023528:27749-27768 Msa1409600:CDS 30.0%
CTATGAGACATACATAAGTT+AGG + tig0023528:27821-27840 None:intergenic 30.0%
TTCCCAATGAACAAAGTAGA+AGG - tig0023528:27662-27681 Msa1409600:CDS 35.0%
CTCCTTCTACTTTGTTCATT+GGG + tig0023528:27667-27686 None:intergenic 35.0%
TCTCCTTCTACTTTGTTCAT+TGG + tig0023528:27668-27687 None:intergenic 35.0%
ACATATTGTGAAGATGGTTG+TGG - tig0023528:27716-27735 Msa1409600:CDS 35.0%
GCTGTCTTTCTTGAATTTAG+AGG + tig0023528:27963-27982 None:intergenic 35.0%
GCAAGTAAGAAGACAACGAA+AGG + tig0023528:27463-27482 None:intergenic 40.0%
CAAAGTAGAAGGAGACTGTA+CGG - tig0023528:27673-27692 Msa1409600:CDS 40.0%
AAAGTAGAAGGAGACTGTAC+GGG - tig0023528:27674-27693 Msa1409600:CDS 40.0%
TCATAGCGATTGCACAAAGA+AGG - tig0023528:27835-27854 Msa1409600:intron 40.0%
CATAGCGATTGCACAAAGAA+GGG - tig0023528:27836-27855 Msa1409600:intron 40.0%
AAGTAGAAGGAGACTGTACG+GGG - tig0023528:27675-27694 Msa1409600:CDS 45.0%
GATTGCACAAAGAAGGGTAG+TGG - tig0023528:27842-27861 Msa1409600:intron 45.0%
AGCAGAAGACGCATACAAGA+TGG - tig0023528:27931-27950 Msa1409600:intron 45.0%
GACAGCTTCTTGAAGATGCT+TGG - tig0023528:27977-27996 Msa1409600:CDS 45.0%
AGTAGAAGGAGACTGTACGG+GGG - tig0023528:27676-27695 Msa1409600:CDS 50.0%
GTCTTCTGCTTCAGTGACAG+AGG + tig0023528:27921-27940 None:intergenic 50.0%
Chromosome Type Strat End Strand Name
tig0023528 gene 27439 28012 27439 ID=Msa1409600;Name=Msa1409600
tig0023528 mRNA 27439 28012 27439 ID=Msa1409600-mRNA-1;Parent=Msa1409600;Name=Msa1409600-mRNA-1;_AED=0.10;_eAED=0.10;_QI=0|0|0|1|1|1|2|0|135
tig0023528 exon 27961 28012 27961 ID=Msa1409600-mRNA-1:exon:26110;Parent=Msa1409600-mRNA-1
tig0023528 exon 27439 27794 27439 ID=Msa1409600-mRNA-1:exon:26109;Parent=Msa1409600-mRNA-1
tig0023528 CDS 27961 28012 27961 ID=Msa1409600-mRNA-1:cds;Parent=Msa1409600-mRNA-1
tig0023528 CDS 27439 27794 27439 ID=Msa1409600-mRNA-1:cds;Parent=Msa1409600-mRNA-1
Gene Sequence

>Msa1409600

ATGGCTTCTGTTAAGCTTGCTCCTTTCGTTGTCTTCTTACTTGCTGCATTCTTAATGTTCCCAATGAACAAAGTAGAAGGAGACTGTACGGGGGTGTATTGCGACGACATTACATATTGTGAAGATGGTTGTGGTTGCGATGTCATATATTTTATGGGTGGTGAAGGCATTTGTCTCCCAATTTATTCTATTGAAAAGAAGGTTGAAGAAAATCCTAACTTATGTATGTCTCATAGCGATTGCACAAAGAAGGGTAGTGGAAATTTCTGTGCTCGTCATCTTAATTCTGATATCAAATATGGCTTCTGTTTTGCCTCTGTCACTGAAGCAGAAGACGCATACAAGATGGCCATTACCTCTAAATTCAAGAAAGACAGCTTCTTGAAGATGCTTGGCACCACCGCTTAA

Protein sequence

>Msa1409600

MASVKLAPFVVFLLAAFLMFPMNKVEGDCTGVYCDDITYCEDGCGCDVIYFMGGEGICLPIYSIEKKVEENPNLCMSHSDCTKKGSGNFCARHLNSDIKYGFCFASVTEAEDAYKMAITSKFKKDSFLKMLGTTA*