AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0793590


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0793590 MtrunA17_Chr5g0394481 94.805 154 4 2 1 151 1 153 2.04e-103 292
Msa0793590 MtrunA17_Chr2g0321501 34.416 154 83 4 7 142 2 155 5.19e-23 88.6
Msa0793590 MtrunA17_Chr4g0026331 33.113 151 91 4 1 141 4 154 2.01e-22 87.0
Msa0793590 MtrunA17_Chr1g0210661 37.302 126 72 4 22 141 29 153 2.91e-19 79.0
Msa0793590 MtrunA17_Chr1g0210631 39.286 112 57 3 41 141 106 217 1.12e-18 79.0
Msa0793590 MtrunA17_Chr2g0277481 31.387 137 86 3 10 141 15 148 2.03e-18 76.6
Msa0793590 MtrunA17_Chr8g0380641 34.400 125 77 2 20 143 28 148 6.07e-18 75.5
Msa0793590 MtrunA17_Chr4g0054691 32.759 116 71 3 33 147 55 164 2.25e-14 67.0
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0793590 AT4G14890.1 81.132 106 20 0 46 151 49 154 5.66e-62 187
Msa0793590 AT2G27510.1 34.395 157 86 5 1 142 1 155 4.41e-23 89.4
Msa0793590 AT1G60950.1 34.532 139 81 6 10 142 14 148 2.82e-18 76.6
Msa0793590 AT5G10000.1 32.847 137 82 3 16 142 12 148 1.70e-16 72.0
Msa0793590 AT1G10960.1 30.435 138 88 4 10 142 14 148 4.98e-15 68.2
Msa0793590 AT1G32550.1 31.915 141 88 4 9 147 25 159 4.80e-14 66.2

Find 38 sgRNAs with CRISPR-Local

Find 37 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GTCCAATGCCTTTGATAATA+TGG 0.193692 5_3:+5537741 None:intergenic
TCGTTCTGATTGTCATATTA+AGG 0.194811 5_3:-5537569 Msa0793590:CDS
TTCTGTCTGAAGAGAGTTAA+GGG 0.376635 5_3:+5537928 None:intergenic
TTTGATAATATGGTTTCATC+AGG 0.398760 5_3:+5537751 None:intergenic
CTGAAAGCTAAATTAGTCAT+TGG 0.415804 5_3:+5537504 None:intergenic
CTTCTGTCTGAAGAGAGTTA+AGG 0.435022 5_3:+5537927 None:intergenic
AGGATAGGGGAGCTTAGTTG+TGG 0.462415 5_3:+5537897 None:intergenic
GAGTTAAGGGTGTAAATTGA+AGG 0.462964 5_3:+5537941 None:intergenic
TTATCAAAGGCATTGGACTC+TGG 0.464183 5_3:-5537736 Msa0793590:CDS
GGATAGGGGAGCTTAGTTGT+GGG 0.466042 5_3:+5537898 None:intergenic
AACCATATTATCAAAGGCAT+TGG 0.476989 5_3:-5537743 Msa0793590:CDS
TGTGTTGAGCTGAGAAGGAT+AGG 0.480320 5_3:+5537882 None:intergenic
ACAAGACCACGCCTTGGTTC+AGG 0.487317 5_3:-5537862 Msa0793590:CDS
TGTGAAGTCTTCTTATAAAG+TGG 0.499881 5_3:-5537815 Msa0793590:CDS
ACAATCAGAACGAGGGTAAG+AGG 0.509900 5_3:+5537579 None:intergenic
GTGCCTCATGACTGTAAGCT+TGG 0.510320 5_3:-5537706 Msa0793590:CDS
AGTTAAGGGTGTAAATTGAA+GGG 0.533055 5_3:+5537942 None:intergenic
GTGTTGAGCTGAGAAGGATA+GGG 0.540357 5_3:+5537883 None:intergenic
TAAAGTGGTGATTGAGCATG+AGG 0.567310 5_3:-5537800 Msa0793590:CDS
TGATGAAACCATATTATCAA+AGG 0.569530 5_3:-5537749 Msa0793590:CDS
GGTCTTGTGTTGAGCTGAGA+AGG 0.574174 5_3:+5537877 None:intergenic
CTCAACACAAGACCACGCCT+TGG 0.584774 5_3:-5537868 Msa0793590:CDS
GTGCCACTGATAAGACGAGC+AGG 0.599960 5_3:+5537667 None:intergenic
TCATATTAAGGTTATAGCAG+AGG 0.608535 5_3:-5537557 Msa0793590:CDS
TCACAGTGAAAGTGAGTGAT+GGG 0.611048 5_3:+5537833 None:intergenic
GGCACAGTTGATCAGAGTGA+TGG 0.619808 5_3:-5537649 Msa0793590:CDS
TTCACAGTGAAAGTGAGTGA+TGG 0.627712 5_3:+5537832 None:intergenic
TGTTGAGCTGAGAAGGATAG+GGG 0.635174 5_3:+5537884 None:intergenic
TGTCCTGCTCGTCTTATCAG+TGG 0.649957 5_3:-5537670 Msa0793590:CDS
AAGCTTACAGTCATGAGGCA+CGG 0.652590 5_3:+5537708 None:intergenic
GATAGGGGAGCTTAGTTGTG+GGG 0.665612 5_3:+5537899 None:intergenic
AGTGATGATGTTGTAGAGCG+TGG 0.677618 5_3:-5537619 Msa0793590:CDS
ACTCCAAGCTTACAGTCATG+AGG 0.678735 5_3:+5537703 None:intergenic
TAATATGACAATCAGAACGA+GGG 0.699912 5_3:+5537572 None:intergenic
AAAGTGGTGATTGAGCATGA+GGG 0.724790 5_3:-5537799 Msa0793590:CDS
TGTGAACCTGAACCAAGGCG+TGG 0.725548 5_3:+5537856 None:intergenic
TTAATATGACAATCAGAACG+AGG 0.733351 5_3:+5537571 None:intergenic
ATGGGTGTGAACCTGAACCA+AGG 0.761073 5_3:+5537851 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! TTTGATAATATGGTTTCATC+AGG + chr5_3:5537717-5537736 None:intergenic 25.0%
! TGATGAAACCATATTATCAA+AGG - chr5_3:5537716-5537735 Msa0793590:CDS 25.0%
! AGTTAAGGGTGTAAATTGAA+GGG + chr5_3:5537526-5537545 None:intergenic 30.0%
TGTGAAGTCTTCTTATAAAG+TGG - chr5_3:5537650-5537669 Msa0793590:CDS 30.0%
! AACCATATTATCAAAGGCAT+TGG - chr5_3:5537722-5537741 Msa0793590:CDS 30.0%
TAATATGACAATCAGAACGA+GGG + chr5_3:5537896-5537915 None:intergenic 30.0%
TTAATATGACAATCAGAACG+AGG + chr5_3:5537897-5537916 None:intergenic 30.0%
TCGTTCTGATTGTCATATTA+AGG - chr5_3:5537896-5537915 Msa0793590:CDS 30.0%
TCATATTAAGGTTATAGCAG+AGG - chr5_3:5537908-5537927 Msa0793590:CDS 30.0%
! GAGTTAAGGGTGTAAATTGA+AGG + chr5_3:5537527-5537546 None:intergenic 35.0%
TTCTGTCTGAAGAGAGTTAA+GGG + chr5_3:5537540-5537559 None:intergenic 35.0%
! GTCCAATGCCTTTGATAATA+TGG + chr5_3:5537727-5537746 None:intergenic 35.0%
CTTCTGTCTGAAGAGAGTTA+AGG + chr5_3:5537541-5537560 None:intergenic 40.0%
TCACAGTGAAAGTGAGTGAT+GGG + chr5_3:5537635-5537654 None:intergenic 40.0%
TTCACAGTGAAAGTGAGTGA+TGG + chr5_3:5537636-5537655 None:intergenic 40.0%
TAAAGTGGTGATTGAGCATG+AGG - chr5_3:5537665-5537684 Msa0793590:CDS 40.0%
AAAGTGGTGATTGAGCATGA+GGG - chr5_3:5537666-5537685 Msa0793590:CDS 40.0%
!! TTATCAAAGGCATTGGACTC+TGG - chr5_3:5537729-5537748 Msa0793590:CDS 40.0%
TGTTGAGCTGAGAAGGATAG+GGG + chr5_3:5537584-5537603 None:intergenic 45.0%
GTGTTGAGCTGAGAAGGATA+GGG + chr5_3:5537585-5537604 None:intergenic 45.0%
TGTGTTGAGCTGAGAAGGAT+AGG + chr5_3:5537586-5537605 None:intergenic 45.0%
AAGCTTACAGTCATGAGGCA+CGG + chr5_3:5537760-5537779 None:intergenic 45.0%
ACTCCAAGCTTACAGTCATG+AGG + chr5_3:5537765-5537784 None:intergenic 45.0%
! AGTGATGATGTTGTAGAGCG+TGG - chr5_3:5537846-5537865 Msa0793590:CDS 45.0%
ACAATCAGAACGAGGGTAAG+AGG + chr5_3:5537889-5537908 None:intergenic 45.0%
GATAGGGGAGCTTAGTTGTG+GGG + chr5_3:5537569-5537588 None:intergenic 50.0%
GGATAGGGGAGCTTAGTTGT+GGG + chr5_3:5537570-5537589 None:intergenic 50.0%
AGGATAGGGGAGCTTAGTTG+TGG + chr5_3:5537571-5537590 None:intergenic 50.0%
! GGTCTTGTGTTGAGCTGAGA+AGG + chr5_3:5537591-5537610 None:intergenic 50.0%
ATGGGTGTGAACCTGAACCA+AGG + chr5_3:5537617-5537636 None:intergenic 50.0%
GTGCCTCATGACTGTAAGCT+TGG - chr5_3:5537759-5537778 Msa0793590:CDS 50.0%
TGTCCTGCTCGTCTTATCAG+TGG - chr5_3:5537795-5537814 Msa0793590:CDS 50.0%
GGCACAGTTGATCAGAGTGA+TGG - chr5_3:5537816-5537835 Msa0793590:CDS 50.0%
CTCAACACAAGACCACGCCT+TGG - chr5_3:5537597-5537616 Msa0793590:CDS 55.0%
ACAAGACCACGCCTTGGTTC+AGG - chr5_3:5537603-5537622 Msa0793590:CDS 55.0%
TGTGAACCTGAACCAAGGCG+TGG + chr5_3:5537612-5537631 None:intergenic 55.0%
! GTGCCACTGATAAGACGAGC+AGG + chr5_3:5537801-5537820 None:intergenic 55.0%
Chromosome Type Strat End Strand Name
chr5_3 gene 5537516 5537971 5537516 ID=Msa0793590;Name=Msa0793590
chr5_3 mRNA 5537516 5537971 5537516 ID=Msa0793590-mRNA-1;Parent=Msa0793590;Name=Msa0793590-mRNA-1;_AED=0.00;_eAED=0.00;_QI=0|-1|0|1|-1|1|1|0|151
chr5_3 exon 5537516 5537971 5537516 ID=Msa0793590-mRNA-1:exon:2178;Parent=Msa0793590-mRNA-1
chr5_3 CDS 5537516 5537971 5537516 ID=Msa0793590-mRNA-1:cds;Parent=Msa0793590-mRNA-1
Gene Sequence

>Msa0793590

ATGGCAACCCTTCAATTTACACCCTTAACTCTCTTCAGACAGAAGAAGCACCCCACAACTAAGCTCCCCTATCCTTCTCAGCTCAACACAAGACCACGCCTTGGTTCAGGTTCACACCCATCACTCACTTTCACTGTGAAGTCTTCTTATAAAGTGGTGATTGAGCATGAGGGCAAGACTACACAGCTTGAAGTTGAACCTGATGAAACCATATTATCAAAGGCATTGGACTCTGGTTTGTCCGTGCCTCATGACTGTAAGCTTGGAGTTTGCATGACTTGTCCTGCTCGTCTTATCAGTGGCACAGTTGATCAGAGTGATGGTATGCTCAGTGATGATGTTGTAGAGCGTGGCTATGCACTCTTGTGTGCCTCTTACCCTCGTTCTGATTGTCATATTAAGGTTATAGCAGAGGATGAGCTACTCTCAATGCAGTTAGCTACAGCCAATGACTAA

Protein sequence

>Msa0793590

MATLQFTPLTLFRQKKHPTTKLPYPSQLNTRPRLGSGSHPSLTFTVKSSYKVVIEHEGKTTQLEVEPDETILSKALDSGLSVPHDCKLGVCMTCPARLISGTVDQSDGMLSDDVVERGYALLCASYPRSDCHIKVIAEDELLSMQLATAND*