AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1233500


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1233500 MtrunA17_Chr8g0342841 92.593 108 4 1 1 108 1 104 5.47e-68 199
Msa1233500 MtrunA17_Chr8g0342831 92.593 108 4 1 1 108 1 104 5.47e-68 199
Msa1233500 MtrunA17_Chr2g0329951 66.667 108 28 5 1 106 1 102 5.27e-39 126
Msa1233500 MtrunA17_Chr4g0071001 53.390 118 42 3 2 107 3 119 4.57e-31 106
Msa1233500 MtrunA17_Chr3g0135901 55.238 105 42 2 4 107 6 106 2.58e-21 81.3
Msa1233500 MtrunA17_Chr7g0269811 65.217 46 16 0 62 107 42 87 4.84e-17 70.1
Msa1233500 MtrunA17_Chr1g0195031 56.250 48 21 0 60 107 55 102 3.53e-16 68.2
Msa1233500 MtrunA17_Chr1g0151181 41.837 98 48 2 11 102 15 109 1.98e-13 61.6
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1233500 AT5G11970.1 45.192 104 48 2 4 107 6 100 6.42e-22 83.2
Msa1233500 AT2G19460.1 43.860 114 54 4 2 107 3 114 1.13e-21 82.8
Msa1233500 AT2G19460.2 43.860 114 54 4 2 107 55 166 2.80e-21 83.2
Msa1233500 AT3G13910.1 59.016 61 22 1 47 104 39 99 5.02e-16 68.2
Msa1233500 AT3G13910.2 56.250 64 25 1 47 107 39 102 6.41e-16 68.2
Msa1233500 AT1G72720.1 38.095 126 58 6 3 108 2 127 2.10e-13 62.0
Msa1233500 AT3G05725.1 56.522 46 19 1 62 107 76 120 1.15e-11 57.4
Msa1233500 AT2G47480.1 44.068 59 33 0 49 107 48 106 2.07e-11 56.6

Find 10 sgRNAs with CRISPR-Local

Find 17 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CAATCAATTATCACCATAAT+TGG 0.252461 8_2:+10301421 None:intergenic
CTCAGATCTTGCATGCTTGA+TGG 0.267870 8_2:+10301663 None:intergenic
ACTTTGATCCTTGCATGATT+TGG 0.271027 8_2:+10301722 None:intergenic
AGAACACGTGCAGCCAATTA+TGG 0.311974 8_2:-10301434 Msa1233500:CDS
CAGAGAAAGAAAAGAGTAGC+TGG 0.442245 8_2:-10301522 Msa1233500:CDS
TTGCAGATTGAAAGCTATAG+TGG 0.472998 8_2:-10301699 Msa1233500:CDS
TATAAAGTATATGATGTTGA+AGG 0.535495 8_2:-10301498 Msa1233500:CDS
AGTTATAGTACAAATTATGC+TGG 0.558009 8_2:-10301639 Msa1233500:CDS
CAGATTGAAAGCTATAGTGG+TGG 0.602253 8_2:-10301696 Msa1233500:CDS
ATTCAGATCCAAATCATGCA+AGG 0.617513 8_2:-10301730 Msa1233500:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! GAAAAAAGTAAAAGTAAATT+TGG - chr8_2:10301581-10301600 Msa1233500:CDS 15.0%
!! TATAAAGTATATGATGTTGA+AGG - chr8_2:10301668-10301687 Msa1233500:CDS 20.0%
! AGTTATAGTACAAATTATGC+TGG - chr8_2:10301527-10301546 Msa1233500:CDS 25.0%
! ATGTTGAAGGAAAAATGAAA+GGG - chr8_2:10301681-10301700 Msa1233500:CDS 25.0%
!! ATCTGCTTTTGATCAAAACA+AGG - chr8_2:10301556-10301575 Msa1233500:CDS 30.0%
GATGTTGAAGGAAAAATGAA+AGG - chr8_2:10301680-10301699 Msa1233500:CDS 30.0%
!! GGTCTTTTAAGAAGAGTTTA+AGG - chr8_2:10301702-10301721 Msa1233500:CDS 30.0%
!! CTTTTAAGAAGAGTTTAAGG+TGG - chr8_2:10301705-10301724 Msa1233500:CDS 30.0%
ATTCAGATCCAAATCATGCA+AGG - chr8_2:10301436-10301455 Msa1233500:CDS 35.0%
ACTTTGATCCTTGCATGATT+TGG + chr8_2:10301447-10301466 None:intergenic 35.0%
TTGCAGATTGAAAGCTATAG+TGG - chr8_2:10301467-10301486 Msa1233500:CDS 35.0%
! TTGGCAAAGCATCAAAAAGT+TGG - chr8_2:10301600-10301619 Msa1233500:CDS 35.0%
CAGATTGAAAGCTATAGTGG+TGG - chr8_2:10301470-10301489 Msa1233500:CDS 40.0%
! CTTTTCTTTCTCTGCAACTC+TGG + chr8_2:10301638-10301657 None:intergenic 40.0%
CAGAGAAAGAAAAGAGTAGC+TGG - chr8_2:10301644-10301663 Msa1233500:CDS 40.0%
CTCAGATCTTGCATGCTTGA+TGG + chr8_2:10301506-10301525 None:intergenic 45.0%
AGAACACGTGCAGCCAATTA+TGG - chr8_2:10301732-10301751 Msa1233500:CDS 45.0%
Chromosome Type Strat End Strand Name
chr8_2 gene 10301431 10301757 10301431 ID=Msa1233500;Name=Msa1233500
chr8_2 mRNA 10301431 10301757 10301431 ID=Msa1233500-mRNA-1;Parent=Msa1233500;Name=Msa1233500-mRNA-1;_AED=0.15;_eAED=0.17;_QI=0|-1|0|1|-1|1|1|0|108
chr8_2 exon 10301431 10301757 10301431 ID=Msa1233500-mRNA-1:exon:4079;Parent=Msa1233500-mRNA-1
chr8_2 CDS 10301431 10301757 10301431 ID=Msa1233500-mRNA-1:cds;Parent=Msa1233500-mRNA-1
Gene Sequence

>Msa1233500

ATGGAATTCAGATCCAAATCATGCAAGGATCAAAGTTTGCAGATTGAAAGCTATAGTGGTGGAAGAGTAGCTCCATCAAGCATGCAAGATCTGAGAAGTTATAGTACAAATTATGCTGGTAATTCATCTGCTTTTGATCAAAACAAGGTAGAAAAAAGTAAAAGTAAATTTGGCAAAGCATCAAAAAGTTGGAGCTTCAATGATCCAGAGTTGCAGAGAAAGAAAAGAGTAGCTGGATATAAAGTATATGATGTTGAAGGAAAAATGAAAGGGTCTTTTAAGAAGAGTTTAAGGTGGATCAAGAACACGTGCAGCCAATTATGGTGA

Protein sequence

>Msa1233500

MEFRSKSCKDQSLQIESYSGGRVAPSSMQDLRSYSTNYAGNSSAFDQNKVEKSKSKFGKASKSWSFNDPELQRKKRVAGYKVYDVEGKMKGSFKKSLRWIKNTCSQLW*