AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0829970


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0829970 MtrunA17_Chr5g0394481 94.805 154 4 2 1 151 1 153 5.54e-103 291
Msa0829970 MtrunA17_Chr4g0026331 33.775 151 90 4 1 141 4 154 3.41e-23 89.0
Msa0829970 MtrunA17_Chr2g0321501 38.655 119 71 2 26 142 37 155 1.25e-22 87.8
Msa0829970 MtrunA17_Chr1g0210661 38.095 126 71 4 22 141 29 153 5.90e-20 80.9
Msa0829970 MtrunA17_Chr1g0210631 38.462 104 62 2 40 141 114 217 8.17e-19 79.3
Msa0829970 MtrunA17_Chr2g0277481 31.387 137 86 3 10 141 15 148 1.52e-18 77.0
Msa0829970 MtrunA17_Chr8g0380641 31.852 135 89 2 10 143 16 148 2.69e-18 76.3
Msa0829970 MtrunA17_Chr4g0054691 31.373 102 67 2 49 147 63 164 1.75e-13 64.7
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0829970 AT4G14890.1 81.132 106 20 0 46 151 49 154 4.96e-62 188
Msa0829970 AT2G27510.1 33.758 157 87 5 1 142 1 155 1.38e-22 87.8
Msa0829970 AT1G60950.1 34.532 139 81 6 10 142 14 148 2.15e-18 77.0
Msa0829970 AT5G10000.1 31.387 137 84 2 16 142 12 148 2.45e-16 71.6
Msa0829970 AT1G10960.1 30.435 138 88 4 10 142 14 148 4.33e-15 68.2
Msa0829970 AT1G32550.1 33.333 102 65 2 49 147 58 159 1.33e-13 65.1

Find 37 sgRNAs with CRISPR-Local

Find 36 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GTCCAATGCCTTTGATAATA+TGG 0.193692 5_4:-2938164 None:intergenic
TCGTTCTGATTGTCATATTA+AGG 0.194811 5_4:+2938336 Msa0829970:CDS
TTCTGTCTGAAGAGAGTTAA+GGG 0.376635 5_4:-2937977 None:intergenic
TTTGATAATATGGTTTCATC+AGG 0.398760 5_4:-2938154 None:intergenic
CTGAAAGCTAAATTAGTCAT+TGG 0.415804 5_4:-2938401 None:intergenic
CTTCTGTCTGAAGAGAGTTA+AGG 0.435022 5_4:-2937978 None:intergenic
AGGATAGGGGAGCTTAGTTG+TGG 0.462415 5_4:-2938008 None:intergenic
GAGTTAAGGGTGTAAATTGA+AGG 0.462964 5_4:-2937964 None:intergenic
TTATCAAAGGCATTGGACTC+TGG 0.464183 5_4:+2938169 Msa0829970:CDS
GGATAGGGGAGCTTAGTTGT+GGG 0.466042 5_4:-2938007 None:intergenic
AACCATATTATCAAAGGCAT+TGG 0.476989 5_4:+2938162 Msa0829970:CDS
TGTGTTGAGCTGAGAAGGAT+AGG 0.480320 5_4:-2938023 None:intergenic
ACAAGACCACGCCTTGGTTC+AGG 0.487317 5_4:+2938043 Msa0829970:CDS
ACAATCAGAACGAGGGTAAG+AGG 0.509900 5_4:-2938326 None:intergenic
GTGCCTCATGACTGTAAGCT+TGG 0.510320 5_4:+2938199 Msa0829970:CDS
AGTTAAGGGTGTAAATTGAA+GGG 0.533055 5_4:-2937963 None:intergenic
GTGTTGAGCTGAGAAGGATA+GGG 0.540357 5_4:-2938022 None:intergenic
TGTGAGGTCTTCTTATAAAG+TGG 0.558437 5_4:+2938090 Msa0829970:CDS
TAAAGTGGTGATTGAGCATG+AGG 0.567310 5_4:+2938105 Msa0829970:CDS
TGATGAAACCATATTATCAA+AGG 0.569530 5_4:+2938156 Msa0829970:CDS
GGTCTTGTGTTGAGCTGAGA+AGG 0.574174 5_4:-2938028 None:intergenic
CTCAACACAAGACCACGCCT+TGG 0.584774 5_4:+2938037 Msa0829970:CDS
GTGCCACTGATAAGACGAGC+AGG 0.599960 5_4:-2938238 None:intergenic
TCATATTAAGGTTATAGCAG+AGG 0.608535 5_4:+2938348 Msa0829970:CDS
GGCACAGTTGATCAGAGTGA+TGG 0.619808 5_4:+2938256 Msa0829970:CDS
TGTTGAGCTGAGAAGGATAG+GGG 0.635174 5_4:-2938021 None:intergenic
TGTCCTGCTCGTCTTATCAG+TGG 0.649957 5_4:+2938235 Msa0829970:CDS
AAGCTTACAGTCATGAGGCA+CGG 0.652590 5_4:-2938197 None:intergenic
GATAGGGGAGCTTAGTTGTG+GGG 0.665612 5_4:-2938006 None:intergenic
AGTGATGATGTTGTAGAGCG+TGG 0.677618 5_4:+2938286 Msa0829970:CDS
ACTCCAAGCTTACAGTCATG+AGG 0.678735 5_4:-2938202 None:intergenic
TAATATGACAATCAGAACGA+GGG 0.699912 5_4:-2938333 None:intergenic
CATCACTCACTTTCACTGTG+AGG 0.704299 5_4:+2938074 Msa0829970:CDS
AAAGTGGTGATTGAGCATGA+GGG 0.724790 5_4:+2938106 Msa0829970:CDS
TTAATATGACAATCAGAACG+AGG 0.733351 5_4:-2938334 None:intergenic
ATGAGTGTGAACCTGAACCA+AGG 0.754812 5_4:-2938054 None:intergenic
TGTGAACCTGAACCAAGGCG+TGG 0.759373 5_4:-2938049 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! TTTGATAATATGGTTTCATC+AGG - chr5_4:2938157-2938176 None:intergenic 25.0%
! TGATGAAACCATATTATCAA+AGG + chr5_4:2938156-2938175 Msa0829970:CDS 25.0%
! AGTTAAGGGTGTAAATTGAA+GGG - chr5_4:2937966-2937985 None:intergenic 30.0%
! AACCATATTATCAAAGGCAT+TGG + chr5_4:2938162-2938181 Msa0829970:CDS 30.0%
TAATATGACAATCAGAACGA+GGG - chr5_4:2938336-2938355 None:intergenic 30.0%
TTAATATGACAATCAGAACG+AGG - chr5_4:2938337-2938356 None:intergenic 30.0%
TCGTTCTGATTGTCATATTA+AGG + chr5_4:2938336-2938355 Msa0829970:CDS 30.0%
TCATATTAAGGTTATAGCAG+AGG + chr5_4:2938348-2938367 Msa0829970:CDS 30.0%
! GAGTTAAGGGTGTAAATTGA+AGG - chr5_4:2937967-2937986 None:intergenic 35.0%
TTCTGTCTGAAGAGAGTTAA+GGG - chr5_4:2937980-2937999 None:intergenic 35.0%
TGTGAGGTCTTCTTATAAAG+TGG + chr5_4:2938090-2938109 Msa0829970:CDS 35.0%
! GTCCAATGCCTTTGATAATA+TGG - chr5_4:2938167-2938186 None:intergenic 35.0%
CTTCTGTCTGAAGAGAGTTA+AGG - chr5_4:2937981-2938000 None:intergenic 40.0%
TAAAGTGGTGATTGAGCATG+AGG + chr5_4:2938105-2938124 Msa0829970:CDS 40.0%
AAAGTGGTGATTGAGCATGA+GGG + chr5_4:2938106-2938125 Msa0829970:CDS 40.0%
!! TTATCAAAGGCATTGGACTC+TGG + chr5_4:2938169-2938188 Msa0829970:CDS 40.0%
TGTTGAGCTGAGAAGGATAG+GGG - chr5_4:2938024-2938043 None:intergenic 45.0%
GTGTTGAGCTGAGAAGGATA+GGG - chr5_4:2938025-2938044 None:intergenic 45.0%
TGTGTTGAGCTGAGAAGGAT+AGG - chr5_4:2938026-2938045 None:intergenic 45.0%
ATGAGTGTGAACCTGAACCA+AGG - chr5_4:2938057-2938076 None:intergenic 45.0%
CATCACTCACTTTCACTGTG+AGG + chr5_4:2938074-2938093 Msa0829970:CDS 45.0%
AAGCTTACAGTCATGAGGCA+CGG - chr5_4:2938200-2938219 None:intergenic 45.0%
ACTCCAAGCTTACAGTCATG+AGG - chr5_4:2938205-2938224 None:intergenic 45.0%
! AGTGATGATGTTGTAGAGCG+TGG + chr5_4:2938286-2938305 Msa0829970:CDS 45.0%
ACAATCAGAACGAGGGTAAG+AGG - chr5_4:2938329-2938348 None:intergenic 45.0%
GATAGGGGAGCTTAGTTGTG+GGG - chr5_4:2938009-2938028 None:intergenic 50.0%
GGATAGGGGAGCTTAGTTGT+GGG - chr5_4:2938010-2938029 None:intergenic 50.0%
AGGATAGGGGAGCTTAGTTG+TGG - chr5_4:2938011-2938030 None:intergenic 50.0%
! GGTCTTGTGTTGAGCTGAGA+AGG - chr5_4:2938031-2938050 None:intergenic 50.0%
GTGCCTCATGACTGTAAGCT+TGG + chr5_4:2938199-2938218 Msa0829970:CDS 50.0%
TGTCCTGCTCGTCTTATCAG+TGG + chr5_4:2938235-2938254 Msa0829970:CDS 50.0%
GGCACAGTTGATCAGAGTGA+TGG + chr5_4:2938256-2938275 Msa0829970:CDS 50.0%
CTCAACACAAGACCACGCCT+TGG + chr5_4:2938037-2938056 Msa0829970:CDS 55.0%
ACAAGACCACGCCTTGGTTC+AGG + chr5_4:2938043-2938062 Msa0829970:CDS 55.0%
TGTGAACCTGAACCAAGGCG+TGG - chr5_4:2938052-2938071 None:intergenic 55.0%
! GTGCCACTGATAAGACGAGC+AGG - chr5_4:2938241-2938260 None:intergenic 55.0%
Chromosome Type Strat End Strand Name
chr5_4 gene 2937956 2938411 2937956 ID=Msa0829970;Name=Msa0829970
chr5_4 mRNA 2937956 2938411 2937956 ID=Msa0829970-mRNA-1;Parent=Msa0829970;Name=Msa0829970-mRNA-1;_AED=0.00;_eAED=0.00;_QI=0|-1|0|1|-1|1|1|0|151
chr5_4 exon 2937956 2938411 2937956 ID=Msa0829970-mRNA-1:exon:1034;Parent=Msa0829970-mRNA-1
chr5_4 CDS 2937956 2938411 2937956 ID=Msa0829970-mRNA-1:cds;Parent=Msa0829970-mRNA-1
Gene Sequence

>Msa0829970

ATGGCAACCCTTCAATTTACACCCTTAACTCTCTTCAGACAGAAGAAGCACCCCACAACTAAGCTCCCCTATCCTTCTCAGCTCAACACAAGACCACGCCTTGGTTCAGGTTCACACTCATCACTCACTTTCACTGTGAGGTCTTCTTATAAAGTGGTGATTGAGCATGAGGGCAAGACTACACAGCTTGAAGTTGAACCTGATGAAACCATATTATCAAAGGCATTGGACTCTGGTTTGTCCGTGCCTCATGACTGTAAGCTTGGAGTTTGCATGACTTGTCCTGCTCGTCTTATCAGTGGCACAGTTGATCAGAGTGATGGTATGCTCAGTGATGATGTTGTAGAGCGTGGCTATGCACTCTTGTGTGCCTCTTACCCTCGTTCTGATTGTCATATTAAGGTTATAGCAGAGGATGAGCTACTCTCAATGCAGTTAGCTACAGCCAATGACTAA

Protein sequence

>Msa0829970

MATLQFTPLTLFRQKKHPTTKLPYPSQLNTRPRLGSGSHSSLTFTVRSSYKVVIEHEGKTTQLEVEPDETILSKALDSGLSVPHDCKLGVCMTCPARLISGTVDQSDGMLSDDVVERGYALLCASYPRSDCHIKVIAEDELLSMQLATAND*