AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0431690


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0431690 MtrunA17_Chr3g0136441 94.068 118 7 0 1 118 1 118 1.70e-81 234
Msa0431690 MtrunA17_Chr1g0150711 51.240 121 52 2 5 118 10 130 2.05e-36 121
Msa0431690 MtrunA17_Chr8g0344381 54.082 98 43 1 6 101 25 122 1.56e-34 117
Msa0431690 MtrunA17_Chr4g0070351 53.398 103 46 1 5 105 24 126 1.67e-32 110
Msa0431690 MtrunA17_Chr4g0070371 48.182 110 51 3 10 115 23 130 1.20e-27 99.4
Msa0431690 MtrunA17_Chr5g0394601 47.297 74 38 1 10 82 1 74 1.32e-22 85.1
Msa0431690 MtrunA17_Chr2g0331111 52.778 72 33 1 1 72 52 122 2.14e-21 84.3
Msa0431690 MtrunA17_Chr8g0340421 57.143 63 26 1 11 73 62 123 8.87e-21 82.8
Msa0431690 MtrunA17_Chr3g0140381 36.111 108 68 1 11 117 36 143 4.67e-20 79.7
Msa0431690 MtrunA17_Chr1g0205251 45.946 74 38 2 10 81 1 74 1.10e-19 78.2
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0431690 AT1G72510.1 53.271 107 47 2 1 105 24 129 7.04e-35 118
Msa0431690 AT1G72510.2 53.271 107 47 2 1 105 24 129 7.04e-35 118
Msa0431690 AT2G09970.1 47.170 106 52 3 3 105 26 130 7.96e-28 100
Msa0431690 AT5G20670.1 47.959 98 46 3 12 106 23 118 3.44e-23 88.2
Msa0431690 AT1G54095.1 45.192 104 52 3 1 101 6 107 8.35e-21 82.0
Msa0431690 AT4G14819.1 36.697 109 62 3 10 118 1 102 2.93e-19 76.6
Msa0431690 AT3G22540.1 38.462 91 51 3 10 99 1 87 5.43e-18 73.6
Msa0431690 AT1G79770.1 43.434 99 48 3 6 100 46 140 5.63e-16 70.1
Msa0431690 AT5G25840.1 42.391 92 38 3 3 82 34 122 4.08e-14 65.1
Msa0431690 AT2G25780.1 38.202 89 51 3 15 100 39 126 1.52e-12 60.8

Find 27 sgRNAs with CRISPR-Local

Find 29 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
AAATCAACCGTAGGTTTATT+AGG 0.246906 3_2:+83710906 None:intergenic
CTCCATCGTCGCCGCGATTT+CGG 0.325788 3_2:+83711139 None:intergenic
TACCTGGGTCGTTGGATTTG+TGG 0.383506 3_2:-83711038 Msa0431690:CDS
ACCTGGGTCGTTGGATTTGT+GGG 0.391134 3_2:-83711037 Msa0431690:CDS
GTGCTACTGTTGCGGCTTAA+CGG 0.404880 3_2:-83711102 Msa0431690:CDS
AAACTCAAAGGTTGTTTCCT+CGG 0.484002 3_2:+83710840 None:intergenic
CCATGTTCGTGAGAAATACC+TGG 0.494919 3_2:-83711054 Msa0431690:CDS
GCCGCAACAGTAGCACTTCA+CGG 0.509628 3_2:+83711109 None:intergenic
GTTGGTAGATCGCATAGATA+AGG 0.511238 3_2:-83710810 None:intergenic
GTGAGAAATACCTGGGTCGT+TGG 0.543743 3_2:-83711046 Msa0431690:CDS
GTGTTGATTAAGAGCTTCAT+CGG 0.550067 3_2:+83710959 None:intergenic
AATCGCGGCGACGATGGAGG+TGG 0.568346 3_2:-83711135 Msa0431690:CDS
AACCGAAATCGCGGCGACGA+TGG 0.593316 3_2:-83711141 Msa0431690:CDS
AAGTCCTCCTAATAAACCTA+CGG 0.601557 3_2:-83710913 Msa0431690:CDS
TCAACCGTAGGTTTATTAGG+AGG 0.609122 3_2:+83710909 None:intergenic
CCAGGTATTTCTCACGAACA+TGG 0.611108 3_2:+83711054 None:intergenic
TTCGGTCTTTGGATTCTCCG+AGG 0.613420 3_2:-83710857 Msa0431690:CDS
CGAAATCGCGGCGACGATGG+AGG 0.613691 3_2:-83711138 Msa0431690:CDS
GATTTGTGGGCTATGTGCAG+AGG 0.630857 3_2:-83711024 Msa0431690:CDS
GCCCACAAATCCAACGACCC+AGG 0.634250 3_2:+83711036 None:intergenic
CCAACCGTTCGAAAACTCAA+AGG 0.637318 3_2:+83710828 None:intergenic
GCAAGAATCAAATCAACCGT+AGG 0.641034 3_2:+83710897 None:intergenic
CATGTTCGTGAGAAATACCT+GGG 0.642264 3_2:-83711053 Msa0431690:CDS
GCCGTGAAGTGCTACTGTTG+CGG 0.673482 3_2:-83711110 Msa0431690:CDS
CTACTGTTGCGGCTTAACGG+AGG 0.677501 3_2:-83711099 Msa0431690:CDS
GATGGCTTTAACCGAAATCG+CGG 0.678355 3_2:-83711150 Msa0431690:CDS
CGAACATGGTCAATATACGA+CGG 0.745897 3_2:+83711068 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
AAATCAACCGTAGGTTTATT+AGG + chr3_2:83711058-83711077 None:intergenic 30.0%
! CTGTGAAACATCTTCTTTTT+CGG - chr3_2:83711086-83711105 Msa0431690:CDS 30.0%
!! GTGTTGATTAAGAGCTTCAT+CGG + chr3_2:83711005-83711024 None:intergenic 35.0%
AAGTCCTCCTAATAAACCTA+CGG - chr3_2:83711048-83711067 Msa0431690:CDS 35.0%
!!! ACATCTTCTTTTTCGGTCTT+TGG - chr3_2:83711093-83711112 Msa0431690:CDS 35.0%
! AAACTCAAAGGTTGTTTCCT+CGG + chr3_2:83711124-83711143 None:intergenic 35.0%
!! ACAACCTTTGAGTTTTCGAA+CGG - chr3_2:83711129-83711148 Msa0431690:CDS 35.0%
CGAACATGGTCAATATACGA+CGG + chr3_2:83710896-83710915 None:intergenic 40.0%
CATGTTCGTGAGAAATACCT+GGG - chr3_2:83710908-83710927 Msa0431690:CDS 40.0%
TCAACCGTAGGTTTATTAGG+AGG + chr3_2:83711055-83711074 None:intergenic 40.0%
GCAAGAATCAAATCAACCGT+AGG + chr3_2:83711067-83711086 None:intergenic 40.0%
CCAGGTATTTCTCACGAACA+TGG + chr3_2:83710910-83710929 None:intergenic 45.0%
CCATGTTCGTGAGAAATACC+TGG - chr3_2:83710907-83710926 Msa0431690:CDS 45.0%
CCAACCGTTCGAAAACTCAA+AGG + chr3_2:83711136-83711155 None:intergenic 45.0%
!! CCTTTGAGTTTTCGAACGGT+TGG - chr3_2:83711133-83711152 Msa0431690:CDS 45.0%
! GTGCTACTGTTGCGGCTTAA+CGG - chr3_2:83710859-83710878 Msa0431690:CDS 50.0%
GTGAGAAATACCTGGGTCGT+TGG - chr3_2:83710915-83710934 Msa0431690:CDS 50.0%
TACCTGGGTCGTTGGATTTG+TGG - chr3_2:83710923-83710942 Msa0431690:CDS 50.0%
ACCTGGGTCGTTGGATTTGT+GGG - chr3_2:83710924-83710943 Msa0431690:CDS 50.0%
! GATTTGTGGGCTATGTGCAG+AGG - chr3_2:83710937-83710956 Msa0431690:CDS 50.0%
TTCGGTCTTTGGATTCTCCG+AGG - chr3_2:83711104-83711123 Msa0431690:CDS 50.0%
! GCCGTGAAGTGCTACTGTTG+CGG - chr3_2:83710851-83710870 Msa0431690:CDS 55.0%
GCCGCAACAGTAGCACTTCA+CGG + chr3_2:83710855-83710874 None:intergenic 55.0%
CTACTGTTGCGGCTTAACGG+AGG - chr3_2:83710862-83710881 Msa0431690:CDS 55.0%
AACCGAAATCGCGGCGACGA+TGG - chr3_2:83710820-83710839 Msa0431690:CDS 60.0%
CTCCATCGTCGCCGCGATTT+CGG + chr3_2:83710825-83710844 None:intergenic 60.0%
GCCCACAAATCCAACGACCC+AGG + chr3_2:83710928-83710947 None:intergenic 60.0%
CGAAATCGCGGCGACGATGG+AGG - chr3_2:83710823-83710842 Msa0431690:CDS 65.0%
AATCGCGGCGACGATGGAGG+TGG - chr3_2:83710826-83710845 Msa0431690:CDS 65.0%
Chromosome Type Strat End Strand Name
chr3_2 gene 83710812 83711171 83710812 ID=Msa0431690;Name=Msa0431690
chr3_2 mRNA 83710812 83711171 83710812 ID=Msa0431690-mRNA-1;Parent=Msa0431690;Name=Msa0431690-mRNA-1;_AED=0.23;_eAED=0.23;_QI=0|-1|0|1|-1|1|1|0|119
chr3_2 exon 83710812 83711171 83710812 ID=Msa0431690-mRNA-1:exon:23543;Parent=Msa0431690-mRNA-1
chr3_2 CDS 83710812 83711171 83710812 ID=Msa0431690-mRNA-1:cds;Parent=Msa0431690-mRNA-1
Gene Sequence

>Msa0431690

ATGGCTTTAACCGAAATCGCGGCGACGATGGAGGTGGTAGCCGTGAAGTGCTACTGTTGCGGCTTAACGGAGGAGTGCACTCCGTCGTATATTGACCATGTTCGTGAGAAATACCTGGGTCGTTGGATTTGTGGGCTATGTGCAGAGGCAGTGAAAGAAGAAGCTTTGAAATCGAAGAGAGATATTAGCACCGATGAAGCTCTTAATCAACACATGAATTTCAGAACTTTAACATCAAGTCCTCCTAATAAACCTACGGTTGATTTGATTCTTGCTGTGAAACATCTTCTTTTTCGGTCTTTGGATTCTCCGAGGAAACAACCTTTGAGTTTTCGAACGGTTGGTAGATCGCATAGATAA

Protein sequence

>Msa0431690

MALTEIAATMEVVAVKCYCCGLTEECTPSYIDHVREKYLGRWICGLCAEAVKEEALKSKRDISTDEALNQHMNFRTLTSSPPNKPTVDLILAVKHLLFRSLDSPRKQPLSFRTVGRSHR*