AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0071510

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0071510 MtrunA17_Chr1g0177991 99.130 115 0 1 1 115 1 114 6.52e-79 227
Msa0071510 MtrunA17_Chr7g0267071 70.175 114 18 4 1 113 1 99 3.20e-41 131
Msa0071510 MtrunA17_Chr4g0025941 43.220 118 47 5 1 115 1 101 4.68e-17 70.5
Msa0071510 MtrunA17_Chr2g0321761 46.341 82 28 2 34 113 6 73 5.48e-15 64.7
Msa0071510 MtrunA17_Chr2g0321781 51.786 56 26 1 54 109 56 110 6.34e-14 62.8
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0071510 AT5G06270.1 74.766 107 21 2 1 107 1 101 1.01e-36 121
Msa0071510 AT5G06270.2 74.766 107 21 2 1 107 1 101 1.01e-36 121
Msa0071510 AT3G11600.1 61.468 109 26 3 1 107 1 95 3.57e-36 120
Msa0071510 AT5G22270.1 58.140 43 17 1 71 112 48 90 2.65e-11 55.8

Find 29 sgRNAs with CRISPR-Local

Find 31 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
AGAAGCCACTTCCATGGTTT+TGG 0.236114 1_2:+43457776 Msa0071510:CDS
GCTGGTTGTTTCCATCTTCT+TGG 0.237222 1_2:-43457731 None:intergenic
AAAACCATGGAAGTGGCTTC+TGG 0.299603 1_2:-43457774 None:intergenic
TTAAGTTTCAAGTCAAGTTT+TGG 0.305467 1_2:-43457600 None:intergenic
ATGCACTTAATTCCTCCTTT+TGG 0.306716 1_2:-43457907 None:intergenic
AAACCATGGAAGTGGCTTCT+GGG 0.413561 1_2:-43457773 None:intergenic
AAAACAATGAGTCGAAGAAA+TGG 0.423682 1_2:+43457570 None:intergenic
GACACTGTTGCTGATCTTGT+TGG 0.430360 1_2:-43457666 None:intergenic
ACTCTTCTGTGGTCAACCCT+TGG 0.466923 1_2:-43457633 None:intergenic
ATCTTCTTGGTTTAGCTCAG+TGG 0.472861 1_2:-43457718 None:intergenic
ATGAAAACAACAACTCCAAA+AGG 0.488003 1_2:+43457892 Msa0071510:CDS
TGTTAGAGTATCTCTGCTGC+TGG 0.501808 1_2:-43457749 None:intergenic
CTTCTGTGGTCAACCCTTGG+TGG 0.502015 1_2:-43457630 None:intergenic
GGTCAACCCTTGGTGGTGAT+AGG 0.515699 1_2:-43457623 None:intergenic
TGGACACACATGAACTTGGT+GGG 0.533512 1_2:-43457698 None:intergenic
CATGAACTTGGTGGGGATGT+AGG 0.536181 1_2:-43457690 None:intergenic
GTGGACACACATGAACTTGG+TGG 0.541612 1_2:-43457699 None:intergenic
ACTGAGCTAAACCAAGAAGA+TGG 0.545142 1_2:+43457720 Msa0071510:CDS
TCAGTGGACACACATGAACT+TGG 0.547065 1_2:-43457702 None:intergenic
ACCAACCAAAACCATGGAAG+TGG 0.557850 1_2:-43457781 None:intergenic
CAGCCCAGAAGCCACTTCCA+TGG 0.578825 1_2:+43457770 Msa0071510:CDS
GTGATGACTCAACTCTTCTG+TGG 0.595889 1_2:-43457644 None:intergenic
ATGAGTCGAAGAAATGGAAG+TGG 0.602019 1_2:+43457576 Msa0071510:CDS
AGGACAACCAACCAAAACCA+TGG 0.614893 1_2:-43457787 None:intergenic
AACTTAACCTATCACCACCA+AGG 0.641567 1_2:+43457616 Msa0071510:CDS
ACTTAACCTATCACCACCAA+GGG 0.643165 1_2:+43457617 Msa0071510:CDS
AAAACAACAACTCCAAAAGG+AGG 0.657059 1_2:+43457895 Msa0071510:CDS
GGACACACATGAACTTGGTG+GGG 0.692537 1_2:-43457697 None:intergenic
ATGACATACATAAGACAACG+AGG 0.800120 1_2:-43457807 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! TTAAGTTTCAAGTCAAGTTT+TGG - chr1_2:43457603-43457622 None:intergenic 25.0%
! AAACAGTGCTTTTGCATTTA+GGG - chr1_2:43457857-43457876 None:intergenic 30.0%
! AAAACAGTGCTTTTGCATTT+AGG - chr1_2:43457858-43457877 None:intergenic 30.0%
ATGAAAACAACAACTCCAAA+AGG + chr1_2:43457892-43457911 Msa0071510:CDS 30.0%
ATGACATACATAAGACAACG+AGG - chr1_2:43457810-43457829 None:intergenic 35.0%
AAAACAACAACTCCAAAAGG+AGG + chr1_2:43457895-43457914 Msa0071510:CDS 35.0%
ATGAGTCGAAGAAATGGAAG+TGG + chr1_2:43457576-43457595 Msa0071510:CDS 40.0%
AACTTAACCTATCACCACCA+AGG + chr1_2:43457616-43457635 Msa0071510:CDS 40.0%
ACTTAACCTATCACCACCAA+GGG + chr1_2:43457617-43457636 Msa0071510:CDS 40.0%
! ATCTTCTTGGTTTAGCTCAG+TGG - chr1_2:43457721-43457740 None:intergenic 40.0%
ACTGAGCTAAACCAAGAAGA+TGG + chr1_2:43457720-43457739 Msa0071510:CDS 40.0%
!! CTTTTGCATTTAGGGCACTT+TGG - chr1_2:43457849-43457868 None:intergenic 40.0%
GTGATGACTCAACTCTTCTG+TGG - chr1_2:43457647-43457666 None:intergenic 45.0%
GACACTGTTGCTGATCTTGT+TGG - chr1_2:43457669-43457688 None:intergenic 45.0%
TGGACACACATGAACTTGGT+GGG - chr1_2:43457701-43457720 None:intergenic 45.0%
TCAGTGGACACACATGAACT+TGG - chr1_2:43457705-43457724 None:intergenic 45.0%
! GCTGGTTGTTTCCATCTTCT+TGG - chr1_2:43457734-43457753 None:intergenic 45.0%
! TGTTAGAGTATCTCTGCTGC+TGG - chr1_2:43457752-43457771 None:intergenic 45.0%
AAACCATGGAAGTGGCTTCT+GGG - chr1_2:43457776-43457795 None:intergenic 45.0%
AAAACCATGGAAGTGGCTTC+TGG - chr1_2:43457777-43457796 None:intergenic 45.0%
! AGAAGCCACTTCCATGGTTT+TGG + chr1_2:43457776-43457795 Msa0071510:CDS 45.0%
ACCAACCAAAACCATGGAAG+TGG - chr1_2:43457784-43457803 None:intergenic 45.0%
AGGACAACCAACCAAAACCA+TGG - chr1_2:43457790-43457809 None:intergenic 45.0%
ACTCTTCTGTGGTCAACCCT+TGG - chr1_2:43457636-43457655 None:intergenic 50.0%
! CATGAACTTGGTGGGGATGT+AGG - chr1_2:43457693-43457712 None:intergenic 50.0%
! GGACACACATGAACTTGGTG+GGG - chr1_2:43457700-43457719 None:intergenic 50.0%
GTGGACACACATGAACTTGG+TGG - chr1_2:43457702-43457721 None:intergenic 50.0%
!!! GCCACTTCCATGGTTTTGGT+TGG + chr1_2:43457780-43457799 Msa0071510:CDS 50.0%
!! GGTCAACCCTTGGTGGTGAT+AGG - chr1_2:43457626-43457645 None:intergenic 55.0%
CTTCTGTGGTCAACCCTTGG+TGG - chr1_2:43457633-43457652 None:intergenic 55.0%
CAGCCCAGAAGCCACTTCCA+TGG + chr1_2:43457770-43457789 Msa0071510:CDS 60.0%
Chromosome Type Strat End Strand Name
chr1_2 gene 43457576 43457923 43457576 ID=Msa0071510;Name=Msa0071510
chr1_2 mRNA 43457576 43457923 43457576 ID=Msa0071510-mRNA-1;Parent=Msa0071510;Name=Msa0071510-mRNA-1;_AED=0.44;_eAED=0.45;_QI=0|-1|0|1|-1|1|1|0|115
chr1_2 exon 43457576 43457923 43457576 ID=Msa0071510-mRNA-1:exon:13112;Parent=Msa0071510-mRNA-1
chr1_2 CDS 43457576 43457923 43457576 ID=Msa0071510-mRNA-1:cds;Parent=Msa0071510-mRNA-1
Gene Sequence

>Msa0071510

ATGAGTCGAAGAAATGGAAGTGGTCCAAAACTTGACTTGAAACTTAACCTATCACCACCAAGGGTTGACCACAGAAGAGTTGAGTCATCACCAACAAGATCAGCAACAGTGTCACCTACATCCCCACCAAGTTCATGTGTGTCCACTGAGCTAAACCAAGAAGATGGAAACAACCAGCAGCAGAGATACTCTAACAGCCCAGAAGCCACTTCCATGGTTTTGGTTGGTTGTCCTCGTTGTCTTATGTATGTCATGCTTTCTGAAGATGATCCAAAGTGCCCTAAATGCAAAAGCACTGTTTTACTTGATTTTCATCATGAAAACAACAACTCCAAAAGGAGGAATTAA
Protein sequence

>Msa0071510

MSRRNGSGPKLDLKLNLSPPRVDHRRVESSPTRSATVSPTSPPSSCVSTELNQEDGNNQQQRYSNSPEATSMVLVGCPRCLMYVMLSEDDPKCPKCKSTVLLDFHHENNNSKRRN*