AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0907550

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0907550 MtrunA17_Chr6g0456061 99.500 200 1 0 1 200 1 200 4.59e-147 406
Msa0907550 MtrunA17_Chr7g0220571 64.286 196 58 6 1 189 1 191 5.75e-66 201
Msa0907550 MtrunA17_Chr7g0225661 59.627 161 56 5 9 167 8 161 1.47e-54 172
Msa0907550 MtrunA17_Chr8g0341311 59.375 160 48 5 9 167 8 151 3.62e-54 171
Msa0907550 MtrunA17_Chr4g0035414 52.326 86 38 2 73 158 16 98 1.85e-18 78.6
Msa0907550 MtrunA17_Chr1g0155551 40.196 102 61 0 64 165 4 105 1.47e-17 76.3
Msa0907550 MtrunA17_Chr3g0144941 50.000 80 40 0 79 158 19 98 3.61e-17 75.1
Msa0907550 MtrunA17_Chr4g0054291 36.620 142 66 3 43 162 8 147 1.09e-16 74.3
Msa0907550 MtrunA17_Chr5g0400901 41.509 106 57 1 65 165 31 136 5.50e-13 63.9
Msa0907550 MtrunA17_Chr1g0194681 39.362 94 52 2 65 158 7 95 5.01e-12 61.2
Msa0907550 MtrunA17_Chr8g0378901 34.375 96 63 0 63 158 8 103 7.37e-12 60.8
Msa0907550 MtrunA17_Chr5g0410531 48.438 64 33 0 90 153 310 373 5.49e-11 60.8
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0907550 AT3G30530.1 74.545 110 25 2 65 171 53 162 5.14e-50 160
Msa0907550 AT5G38800.1 61.207 116 38 2 71 186 53 161 1.23e-41 138
Msa0907550 AT5G15830.1 60.909 110 43 0 57 166 41 150 6.01e-39 132
Msa0907550 AT1G13600.1 56.693 127 45 3 71 195 68 186 1.46e-36 126
Msa0907550 AT2G04038.1 64.583 96 34 0 70 165 54 149 4.20e-36 124
Msa0907550 AT1G68880.1 46.316 95 49 1 74 168 33 125 1.57e-21 86.3
Msa0907550 AT1G75390.1 47.423 97 50 1 62 158 14 109 8.84e-19 80.1
Msa0907550 AT5G60830.1 45.192 104 52 2 89 189 70 171 1.80e-17 77.4
Msa0907550 AT1G75390.2 46.237 93 49 1 62 154 14 105 3.63e-16 72.0
Msa0907550 AT2G18160.1 48.611 72 37 0 87 158 28 99 1.91e-15 71.2
Msa0907550 AT3G62420.1 44.304 79 44 0 80 158 15 93 4.80e-15 69.7
Msa0907550 AT4G34590.1 45.946 74 40 0 85 158 22 95 3.41e-13 65.1
Msa0907550 AT2G22850.1 36.522 115 61 3 70 172 106 220 3.57e-11 60.8
Msa0907550 AT2G22850.2 36.522 115 61 3 70 172 106 220 3.57e-11 60.8

Find 30 sgRNAs with CRISPR-Local

Find 34 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
AGCTTTGGTCACAAGTTCTT+TGG 0.273917 6_2:+6211218 Msa0907550:CDS
TTAGGTAATTACCATATAAT+TGG 0.292562 6_2:-6211006 None:intergenic
GGACTAAAAGAAGGGATTAA+AGG 0.295805 6_2:-6211382 None:intergenic
TCAAGTTCAATGGATCTTCT+TGG 0.335013 6_2:+6211451 Msa0907550:CDS
AAATTCTCAAACCAATTATA+TGG 0.356492 6_2:+6210995 Msa0907550:CDS
ATTGTTGATGAGGGGTGTTT+AGG 0.356793 6_2:-6211024 None:intergenic
TCCTCTCATTGATGAGACTA+AGG 0.387624 6_2:-6211123 None:intergenic
AGAAACACCTTGATGAGCTT+TGG 0.415939 6_2:+6211203 Msa0907550:CDS
TCAGCTTAAAGAAGAAGCTT+TGG 0.440839 6_2:+6211321 Msa0907550:CDS
TGTTACTTCTCTTGTTTGCA+TGG 0.445242 6_2:-6210873 None:intergenic
CTGCTTATGCATGATGATTG+TGG 0.470545 6_2:-6211067 None:intergenic
CAATTCCATCTCAAGTTCAA+TGG 0.471344 6_2:+6211441 Msa0907550:CDS
GGTCACAAGTTCTTTGGCTG+AGG 0.486097 6_2:+6211224 Msa0907550:CDS
AGATAAGGTGATGTGTTTGA+TGG 0.498736 6_2:-6210917 None:intergenic
TCATCCAAAGGACTAAAAGA+AGG 0.506277 6_2:-6211391 None:intergenic
GGTTAAGTTTCTCTATAAGC+TGG 0.509495 6_2:-6211258 None:intergenic
GTGACCGACGTGCTGATTCG+CGG 0.510591 6_2:-6211168 None:intergenic
CAAACAAGAGAAGTAACAAC+AGG 0.515554 6_2:+6210878 Msa0907550:CDS
TGTGGACTATAGTTGAAGTC+AGG 0.518116 6_2:-6211049 None:intergenic
AAGATCCATTGAACTTGAGA+TGG 0.525838 6_2:-6211446 None:intergenic
AAGTCAGGAAATTGTTGATG+AGG 0.551877 6_2:-6211034 None:intergenic
CTTGTGACCAAAGCTCATCA+AGG 0.582135 6_2:-6211210 None:intergenic
AGTCAGGAAATTGTTGATGA+GGG 0.582558 6_2:-6211033 None:intergenic
CATCCAAAGGACTAAAAGAA+GGG 0.584492 6_2:-6211390 None:intergenic
CTAAGATATGTATCATCCAA+AGG 0.603956 6_2:-6211403 None:intergenic
TCAATGAGAGGAAACACAGA+AGG 0.630812 6_2:+6211134 Msa0907550:CDS
ACCTTAGTCTCATCAATGAG+AGG 0.631783 6_2:+6211122 Msa0907550:CDS
GATCATGATTCTCAGAAACA+TGG 0.641220 6_2:-6211279 None:intergenic
GTCAGGAAATTGTTGATGAG+GGG 0.693054 6_2:-6211032 None:intergenic
CAAACCGCGAATCAGCACGT+CGG 0.801689 6_2:+6211164 Msa0907550:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! TTGTTATAGTTTTGTAGATA+AGG - chr6_2:6210935-6210954 None:intergenic 20.0%
!!! ATAATTGGTTTGAGAATTTT+TGG - chr6_2:6210994-6211013 None:intergenic 20.0%
!! AAATTCTCAAACCAATTATA+TGG + chr6_2:6210995-6211014 Msa0907550:CDS 20.0%
!! TTAGGTAATTACCATATAAT+TGG - chr6_2:6211009-6211028 None:intergenic 20.0%
!!! GAATTTTTGGAGTTGATATG+AGG - chr6_2:6210981-6211000 None:intergenic 30.0%
CTAAGATATGTATCATCCAA+AGG - chr6_2:6211406-6211425 None:intergenic 30.0%
CAAACAAGAGAAGTAACAAC+AGG + chr6_2:6210878-6210897 Msa0907550:CDS 35.0%
AGATAAGGTGATGTGTTTGA+TGG - chr6_2:6210920-6210939 None:intergenic 35.0%
! AGTCAGGAAATTGTTGATGA+GGG - chr6_2:6211036-6211055 None:intergenic 35.0%
AAGTCAGGAAATTGTTGATG+AGG - chr6_2:6211037-6211056 None:intergenic 35.0%
GGTTAAGTTTCTCTATAAGC+TGG - chr6_2:6211261-6211280 None:intergenic 35.0%
GATCATGATTCTCAGAAACA+TGG - chr6_2:6211282-6211301 None:intergenic 35.0%
TCAGCTTAAAGAAGAAGCTT+TGG + chr6_2:6211321-6211340 Msa0907550:CDS 35.0%
GGACTAAAAGAAGGGATTAA+AGG - chr6_2:6211385-6211404 None:intergenic 35.0%
! AATCCCTTCTTTTAGTCCTT+TGG + chr6_2:6211387-6211406 Msa0907550:CDS 35.0%
CATCCAAAGGACTAAAAGAA+GGG - chr6_2:6211393-6211412 None:intergenic 35.0%
TCATCCAAAGGACTAAAAGA+AGG - chr6_2:6211394-6211413 None:intergenic 35.0%
CAATTCCATCTCAAGTTCAA+TGG + chr6_2:6211441-6211460 Msa0907550:CDS 35.0%
AAGATCCATTGAACTTGAGA+TGG - chr6_2:6211449-6211468 None:intergenic 35.0%
TCAAGTTCAATGGATCTTCT+TGG + chr6_2:6211451-6211470 Msa0907550:CDS 35.0%
!! ATTGTTGATGAGGGGTGTTT+AGG - chr6_2:6211027-6211046 None:intergenic 40.0%
! GTCAGGAAATTGTTGATGAG+GGG - chr6_2:6211035-6211054 None:intergenic 40.0%
! TGTGGACTATAGTTGAAGTC+AGG - chr6_2:6211052-6211071 None:intergenic 40.0%
CTGCTTATGCATGATGATTG+TGG - chr6_2:6211070-6211089 None:intergenic 40.0%
ACCTTAGTCTCATCAATGAG+AGG + chr6_2:6211122-6211141 Msa0907550:CDS 40.0%
TCCTCTCATTGATGAGACTA+AGG - chr6_2:6211126-6211145 None:intergenic 40.0%
TCAATGAGAGGAAACACAGA+AGG + chr6_2:6211134-6211153 Msa0907550:CDS 40.0%
AGAAACACCTTGATGAGCTT+TGG + chr6_2:6211203-6211222 Msa0907550:CDS 40.0%
! AGCTTTGGTCACAAGTTCTT+TGG + chr6_2:6211218-6211237 Msa0907550:CDS 40.0%
CTTGTGACCAAAGCTCATCA+AGG - chr6_2:6211213-6211232 None:intergenic 45.0%
GGTCACAAGTTCTTTGGCTG+AGG + chr6_2:6211224-6211243 Msa0907550:CDS 50.0%
CAAACCGCGAATCAGCACGT+CGG + chr6_2:6211164-6211183 Msa0907550:CDS 55.0%
!! GTGACCGACGTGCTGATTCG+CGG - chr6_2:6211171-6211190 None:intergenic 60.0%
CAGCACGTCGGTCACGCATG+AGG + chr6_2:6211176-6211195 Msa0907550:CDS 65.0%
Chromosome Type Strat End Strand Name
chr6_2 gene 6210875 6211477 6210875 ID=Msa0907550;Name=Msa0907550
chr6_2 mRNA 6210875 6211477 6210875 ID=Msa0907550-mRNA-1;Parent=Msa0907550;Name=Msa0907550-mRNA-1;_AED=0.00;_eAED=0.00;_QI=0|-1|0|1|-1|1|1|0|200
chr6_2 exon 6210875 6211477 6210875 ID=Msa0907550-mRNA-1:exon:1967;Parent=Msa0907550-mRNA-1
chr6_2 CDS 6210875 6211477 6210875 ID=Msa0907550-mRNA-1:cds;Parent=Msa0907550-mRNA-1
Gene Sequence

>Msa0907550

ATGCAAACAAGAGAAGTAACAACAGGACTCAATTACATGCTACCATCAAACACATCACCTTATCTACAAAACTATAACAACATGATTCAAAATAACAACATTTCCTCATATCAACTCCAAAAATTCTCAAACCAATTATATGGTAATTACCTAAACACCCCTCATCAACAATTTCCTGACTTCAACTATAGTCCACAATCATCATGCATAAGCAGCAACTCAACTTCTGATGAAGCAGATGAACAAAACCTTAGTCTCATCAATGAGAGGAAACACAGAAGGATGATATCAAACCGCGAATCAGCACGTCGGTCACGCATGAGGAAGCAGAAACACCTTGATGAGCTTTGGTCACAAGTTCTTTGGCTGAGGAATGAAAATCACCAGCTTATAGAGAAACTTAACCATGTTTCTGAGAATCATGATCAAGTTGTTCAAGAGAATGCTCAGCTTAAAGAAGAAGCTTTGGAACTTCGACAAATGATAAAAGATATGCAGATTCATAGTCCTTTAATCCCTTCTTTTAGTCCTTTGGATGATACATATCTTAGAGATGATTCTTCAAACAATTCCATCTCAAGTTCAATGGATCTTCTTGGCTGA
Protein sequence

>Msa0907550

MQTREVTTGLNYMLPSNTSPYLQNYNNMIQNNNISSYQLQKFSNQLYGNYLNTPHQQFPDFNYSPQSSCISSNSTSDEADEQNLSLINERKHRRMISNRESARRSRMRKQKHLDELWSQVLWLRNENHQLIEKLNHVSENHDQVVQENAQLKEEALELRQMIKDMQIHSPLIPSFSPLDDTYLRDDSSNNSISSSMDLLG*