AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1454530


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1454530 MtrunA17_Chr4g0071001 92.126 127 2 3 1 123 1 123 8.97e-78 225
Msa1454530 MtrunA17_Chr3g0135901 54.032 124 42 3 1 123 1 110 1.45e-28 100
Msa1454530 MtrunA17_Chr2g0329951 49.587 121 44 5 3 122 2 106 3.83e-28 99.4
Msa1454530 MtrunA17_Chr8g0342841 51.282 117 42 3 3 119 2 103 9.24e-28 98.2
Msa1454530 MtrunA17_Chr8g0342831 51.282 117 42 3 3 119 2 103 9.24e-28 98.2
Msa1454530 MtrunA17_Chr1g0151181 49.600 125 50 5 1 121 1 116 1.41e-19 77.8
Msa1454530 MtrunA17_Chr7g0269811 54.386 57 25 1 67 123 36 91 1.10e-17 72.0
Msa1454530 MtrunA17_Chr1g0195031 51.923 52 25 0 72 123 55 106 2.11e-16 69.3
Msa1454530 MtrunA17_Chr1g0201581 53.333 60 23 2 69 123 29 88 5.15e-11 55.1
Msa1454530 MtrunA17_Chr7g0271701 55.319 47 20 1 73 119 73 118 9.83e-11 55.1
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1454530 AT2G19460.1 53.906 128 40 6 1 121 1 116 3.63e-34 115
Msa1454530 AT2G19460.2 53.906 128 40 6 1 121 53 168 8.10e-34 115
Msa1454530 AT5G11970.1 52.419 124 38 6 1 123 1 104 1.06e-30 105
Msa1454530 AT3G13910.1 60.294 68 22 2 52 114 30 97 4.03e-19 76.6
Msa1454530 AT3G13910.2 60.294 68 22 2 52 114 30 97 8.52e-19 75.9
Msa1454530 AT3G05725.1 44.872 78 41 2 46 122 47 123 1.51e-17 73.2
Msa1454530 AT3G62640.1 48.077 52 27 0 71 122 59 110 8.56e-15 65.5
Msa1454530 AT2G47480.1 45.902 61 33 0 61 121 48 108 9.84e-15 65.5
Msa1454530 AT1G72720.1 44.565 92 41 4 33 122 42 125 1.63e-14 65.5
Msa1454530 AT4G09890.1 59.459 37 15 0 79 115 39 75 8.89e-11 54.7

Find 22 sgRNAs with CRISPR-Local

Find 29 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TGTTGTTACCAATCTGGTTT+TGG 0.243522 tig0035254:+16632 None:intergenic
CCTTCCATCAGCGTAGGATT+TGG 0.309332 tig0035254:+16756 None:intergenic
TGTTGTTGTTGTTACCAATC+TGG 0.354115 tig0035254:+16626 None:intergenic
GTAAACTCAAAGGCTCTCTT+AGG 0.367994 tig0035254:-16477 Msa1454530:CDS
AAGAAAGGTAAATCCACAAA+TGG 0.395506 tig0035254:-16586 Msa1454530:CDS
TACAAGGTTTATTCTGTTGA+AGG 0.413127 tig0035254:-16499 Msa1454530:CDS
TTTGAAGAAGGTGCAGAGTA+AGG 0.455372 tig0035254:+16718 None:intergenic
TACTCTGCACCTTCTTCAAA+CGG 0.463760 tig0035254:-16715 Msa1454530:CDS
AGATGCAACAGAGTTGTTCA+TGG 0.485910 tig0035254:-16430 Msa1454530:CDS
AACGATGTTAAGTTCAAGAA+AGG 0.501790 tig0035254:-16601 Msa1454530:CDS
CATCCAACCCAAAACCAGAT+TGG 0.504703 tig0035254:-16640 Msa1454530:CDS
ATGCCTCCTCCGTTTGAAGA+AGG 0.518627 tig0035254:+16706 None:intergenic
AGAAAGGTAAATCCACAAAT+GGG 0.520575 tig0035254:-16585 Msa1454530:CDS
CTGCATCCTTCCATCAGCGT+AGG 0.527015 tig0035254:+16750 None:intergenic
GCAACAGAGTTGTTCATGGC+TGG 0.536888 tig0035254:-16426 Msa1454530:CDS
TTTGGATCTGAAATCTTCCA+TGG 0.557041 tig0035254:+16774 None:intergenic
AGATCCAAATCCTACGCTGA+TGG 0.558533 tig0035254:-16760 Msa1454530:CDS
TCTGTTGAAGGTAAACTCAA+AGG 0.562516 tig0035254:-16487 Msa1454530:CDS
GCACCTTCTTCAAACGGAGG+AGG 0.581419 tig0035254:-16709 Msa1454530:CDS
CCAAATCCTACGCTGATGGA+AGG 0.584749 tig0035254:-16756 Msa1454530:CDS
TCAGTGATCCTGAATTGCAG+AGG 0.668157 tig0035254:-16540 Msa1454530:CDS
TCTGCACCTTCTTCAAACGG+AGG 0.687076 tig0035254:-16712 Msa1454530:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
AACGATGTTAAGTTCAAGAA+AGG - tig0035254:16594-16613 Msa1454530:CDS 30.0%
AAGAAAGGTAAATCCACAAA+TGG - tig0035254:16609-16628 Msa1454530:CDS 30.0%
AGAAAGGTAAATCCACAAAT+GGG - tig0035254:16610-16629 Msa1454530:CDS 30.0%
AAAAAGAGTTGCTAGTTACA+AGG - tig0035254:16680-16699 Msa1454530:CDS 30.0%
TACAAGGTTTATTCTGTTGA+AGG - tig0035254:16696-16715 Msa1454530:CDS 30.0%
!!! GTTGTTACCAATCTGGTTTT+GGG + tig0035254:16565-16584 None:intergenic 35.0%
!! TGTTGTTACCAATCTGGTTT+TGG + tig0035254:16566-16585 None:intergenic 35.0%
! TGTTGTTGTTGTTACCAATC+TGG + tig0035254:16572-16591 None:intergenic 35.0%
!!! TTTTGAAGTTGACCCATTTG+TGG + tig0035254:16625-16644 None:intergenic 35.0%
ATGGGTCAACTTCAAAAAGT+TGG - tig0035254:16628-16647 Msa1454530:CDS 35.0%
!!! CTTTTTTTCCTCTGCAATTC+AGG + tig0035254:16666-16685 None:intergenic 35.0%
TCTGTTGAAGGTAAACTCAA+AGG - tig0035254:16708-16727 Msa1454530:CDS 35.0%
!!! CTCTTAGGAAGAGTTTTAAG+TGG - tig0035254:16733-16752 Msa1454530:CDS 35.0%
! TTTGAAGAAGGTGCAGAGTA+AGG + tig0035254:16480-16499 None:intergenic 40.0%
TACTCTGCACCTTCTTCAAA+CGG - tig0035254:16480-16499 Msa1454530:CDS 40.0%
!!! TTACCAATCTGGTTTTGGGT+TGG + tig0035254:16561-16580 None:intergenic 40.0%
GTAAACTCAAAGGCTCTCTT+AGG - tig0035254:16718-16737 Msa1454530:CDS 40.0%
AGATGCAACAGAGTTGTTCA+TGG - tig0035254:16765-16784 Msa1454530:CDS 40.0%
AGATCCAAATCCTACGCTGA+TGG - tig0035254:16435-16454 Msa1454530:CDS 45.0%
!!! GTTTTGGGTTGGATGAACAG+AGG + tig0035254:16550-16569 None:intergenic 45.0%
CATCCAACCCAAAACCAGAT+TGG - tig0035254:16555-16574 Msa1454530:CDS 45.0%
TCAGTGATCCTGAATTGCAG+AGG - tig0035254:16655-16674 Msa1454530:CDS 45.0%
CCTTCCATCAGCGTAGGATT+TGG + tig0035254:16442-16461 None:intergenic 50.0%
CCAAATCCTACGCTGATGGA+AGG - tig0035254:16439-16458 Msa1454530:CDS 50.0%
TCTGCACCTTCTTCAAACGG+AGG - tig0035254:16483-16502 Msa1454530:CDS 50.0%
ATGCCTCCTCCGTTTGAAGA+AGG + tig0035254:16492-16511 None:intergenic 50.0%
GCAACAGAGTTGTTCATGGC+TGG - tig0035254:16769-16788 Msa1454530:CDS 50.0%
CTGCATCCTTCCATCAGCGT+AGG + tig0035254:16448-16467 None:intergenic 55.0%
GCACCTTCTTCAAACGGAGG+AGG - tig0035254:16486-16505 Msa1454530:CDS 55.0%
Chromosome Type Strat End Strand Name
tig0035254 gene 16423 16794 16423 ID=Msa1454530;Name=Msa1454530
tig0035254 mRNA 16423 16794 16423 ID=Msa1454530-mRNA-1;Parent=Msa1454530;Name=Msa1454530-mRNA-1;_AED=0.00;_eAED=0.00;_QI=0|-1|0|1|-1|1|1|0|123
tig0035254 exon 16423 16794 16423 ID=Msa1454530-mRNA-1:exon:19780;Parent=Msa1454530-mRNA-1
tig0035254 CDS 16423 16794 16423 ID=Msa1454530-mRNA-1:cds;Parent=Msa1454530-mRNA-1
Gene Sequence

>Msa1454530

ATGGAAGATTTCAGATCCAAATCCTACGCTGATGGAAGGATGCAGCAAATTGAACCTTACTCTGCACCTTCTTCAAACGGAGGAGGCATGCAAGATCTACGTTGTTACAGCGCTTCTTATGCTTCCTCTGTTCATCCAACCCAAAACCAGATTGGTAACAACAACAACAACAACGATGTTAAGTTCAAGAAAGGTAAATCCACAAATGGGTCAACTTCAAAAAGTTGGAGCTTCAGTGATCCTGAATTGCAGAGGAAAAAAAGAGTTGCTAGTTACAAGGTTTATTCTGTTGAAGGTAAACTCAAAGGCTCTCTTAGGAAGAGTTTTAAGTGGATTAAAGATAGATGCAACAGAGTTGTTCATGGCTGGTAG

Protein sequence

>Msa1454530

MEDFRSKSYADGRMQQIEPYSAPSSNGGGMQDLRCYSASYASSVHPTQNQIGNNNNNNDVKFKKGKSTNGSTSKSWSFSDPELQRKKRVASYKVYSVEGKLKGSLRKSFKWIKDRCNRVVHGW*