AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1343770


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1343770 MtrunA17_Chr8g0340421 95.337 193 8 1 1 193 3 194 8.99e-135 375
Msa1343770 MtrunA17_Chr2g0331111 65.829 199 59 5 1 193 1 196 6.29e-84 246
Msa1343770 MtrunA17_Chr8g0344381 46.212 132 58 5 59 183 29 154 5.53e-31 110
Msa1343770 MtrunA17_Chr1g0205251 47.778 90 39 3 60 146 2 86 5.82e-23 89.0
Msa1343770 MtrunA17_Chr3g0136441 59.091 66 26 1 57 121 8 73 7.90e-22 86.3
Msa1343770 MtrunA17_Chr5g0394601 43.750 96 45 3 60 152 2 91 1.85e-21 84.7
Msa1343770 MtrunA17_Chr3g0140381 34.211 152 87 4 29 177 4 145 7.09e-19 79.0
Msa1343770 MtrunA17_Chr4g0070351 40.860 93 50 3 33 121 1 92 1.76e-17 75.1
Msa1343770 MtrunA17_Chr4g0070371 37.234 94 52 2 60 146 24 117 1.79e-17 75.5
Msa1343770 MtrunA17_Chr1g0150711 40.217 92 47 2 45 132 1 88 1.00e-15 70.9
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1343770 AT5G25840.1 50.543 184 54 5 33 193 4 173 3.00e-53 168
Msa1343770 AT1G79770.1 52.903 155 59 3 33 187 27 167 1.18e-46 151
Msa1343770 AT4G14819.1 43.636 110 50 3 60 169 2 99 2.08e-24 92.4
Msa1343770 AT2G25780.1 36.129 155 84 4 33 182 7 151 8.15e-22 87.4
Msa1343770 AT3G22540.1 40.449 89 50 1 60 148 2 87 3.43e-21 84.3
Msa1343770 AT1G72510.1 39.706 136 67 7 60 183 33 165 1.51e-20 84.3
Msa1343770 AT1G72510.2 39.706 136 67 7 60 183 33 165 1.51e-20 84.3
Msa1343770 AT5G20670.1 33.582 134 82 3 57 183 19 152 7.87e-19 79.3
Msa1343770 AT1G54095.1 39.706 136 69 5 59 183 14 147 8.06e-19 79.3
Msa1343770 AT2G09970.1 34.058 138 73 7 60 183 33 166 8.17e-16 72.0

Find 39 sgRNAs with CRISPR-Local

Find 44 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GTAACATGGATGGGAAAATT+AGG 0.194429 tig0006524:+3355 Msa1343770:CDS
CCTCCTCCTTTCTTGTCCCT+TGG 0.275546 tig0006524:-3393 Msa1343770:intergenic
AAAATAGATAGATAGTTAAT+TGG 0.284549 tig0006524:-3484 Msa1343770:intergenic
TGTGTTAAGTTTAACAAATA+TGG 0.300385 tig0006524:+3276 Msa1343770:CDS
GAAAGCTTTGTTGGTTTGTT+TGG 0.348037 tig0006524:-2970 Msa1343770:intergenic
GCTTGTGCTTGAAACAAAAC+TGG 0.379794 tig0006524:-3309 Msa1343770:intergenic
GACAAGAAAGGAGGAGGAGG+AGG 0.400333 tig0006524:+3399 Msa1343770:CDS
TCGGAAGTTGAAAGCTTTGT+TGG 0.400947 tig0006524:-2979 Msa1343770:intergenic
TAACATGGATGGGAAAATTA+GGG 0.434099 tig0006524:+3356 Msa1343770:CDS
CGACATTTCCTTCGAGCTGA+TGG 0.460178 tig0006524:+3023 Msa1343770:CDS
TTGATCTCTCTTGTAAGTGC+TGG 0.461637 tig0006524:-3447 Msa1343770:intergenic
ATTTGTGTGCGGTTTGTGTT+CGG 0.464682 tig0006524:+3179 Msa1343770:CDS
ACACTTTGCATCTTCAACTT+CGG 0.466067 tig0006524:-3085 Msa1343770:intergenic
TGTCGGAGACCGTTCTTTGA+AGG 0.474473 tig0006524:-3005 Msa1343770:intergenic
TTAAGTTTAACAAATATGGT+AGG 0.490124 tig0006524:+3280 Msa1343770:CDS
AGGGACAAGAAAGGAGGAGG+AGG 0.494514 tig0006524:+3396 Msa1343770:CDS
TGTTGTCAAGTTCATTCTCA+AGG 0.519029 tig0006524:+2932 Msa1343770:CDS
TAAGTTTAACAAATATGGTA+GGG 0.538103 tig0006524:+3281 Msa1343770:CDS
GTGCGGTTTGTGTTCGGAGG+CGG 0.552330 tig0006524:+3185 Msa1343770:CDS
GACCGTTCTTTGAAGGTGGT+CGG 0.559329 tig0006524:-2998 None:intergenic
ATCATGGTTATGGCACCTCA+TGG 0.562684 tig0006524:+2901 None:intergenic
CCAAGGGACAAGAAAGGAGG+AGG 0.566147 tig0006524:+3393 Msa1343770:CDS
CGGAGACCGTTCTTTGAAGG+TGG 0.567308 tig0006524:-3002 Msa1343770:intergenic
GGGCTAAGTCAATTAGTCCA+AGG 0.570684 tig0006524:+3376 Msa1343770:CDS
ATTAGTCCAAGGGACAAGAA+AGG 0.576487 tig0006524:+3387 Msa1343770:CDS
ACGAACACGATCTATGTACT+CGG 0.578833 tig0006524:-3139 Msa1343770:intergenic
CGTGTTCGTAACAAGTTCGA+AGG 0.581435 tig0006524:+3153 Msa1343770:CDS
ACAAGAAAGGAGGAGGAGGA+GGG 0.591395 tig0006524:+3400 Msa1343770:CDS
GGCTAAGTCAATTAGTCCAA+GGG 0.598516 tig0006524:+3377 Msa1343770:CDS
TTCCGACCACCTTCAAAGAA+CGG 0.607623 tig0006524:+2996 Msa1343770:CDS
CATCAGCTCGAAGGAAATGT+CGG 0.626398 tig0006524:-3022 Msa1343770:intergenic
TCTTCAACTTCGGATATCGA+TGG 0.633325 tig0006524:-3075 Msa1343770:intergenic
TGTGTGCGGTTTGTGTTCGG+AGG 0.638466 tig0006524:+3182 Msa1343770:CDS
GTGTTCGTAACAAGTTCGAA+GGG 0.639090 tig0006524:+3154 Msa1343770:CDS
TTCGAAGGGAAATTTGTGTG+CGG 0.644656 tig0006524:+3168 Msa1343770:CDS
CGAACACGATCTATGTACTC+GGG 0.649900 tig0006524:-3138 Msa1343770:intergenic
GATGCAAAGTGTGAGTGTTG+TGG 0.665594 tig0006524:+3096 Msa1343770:CDS
AGTCCAAGGGACAAGAAAGG+AGG 0.666513 tig0006524:+3390 Msa1343770:CDS
GACAACAAACATTCTCCATG+AGG 0.716500 tig0006524:-2916 Msa1343760:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! TGTGTTAAGTTTAACAAATA+TGG + tig0006524:3276-3295 Msa1343770:CDS 20.0%
!! TTAAGTTTAACAAATATGGT+AGG + tig0006524:3280-3299 Msa1343770:CDS 20.0%
!! TAAGTTTAACAAATATGGTA+GGG + tig0006524:3281-3300 Msa1343770:CDS 20.0%
! AATGTTGAAAAAGAGTAACA+TGG + tig0006524:3341-3360 Msa1343770:CDS 25.0%
AAAGAAGAGTTCGAGAAAAA+TGG + tig0006524:3210-3229 Msa1343770:CDS 30.0%
TTGAAAAAGAGTAACATGGA+TGG + tig0006524:3345-3364 Msa1343770:CDS 30.0%
TGAAAAAGAGTAACATGGAT+GGG + tig0006524:3346-3365 Msa1343770:CDS 30.0%
TAACATGGATGGGAAAATTA+GGG + tig0006524:3356-3375 Msa1343770:CDS 30.0%
TGTTGTCAAGTTCATTCTCA+AGG + tig0006524:2932-2951 Msa1343770:CDS 35.0%
!! GAAAGCTTTGTTGGTTTGTT+TGG - tig0006524:2973-2992 Msa1343770:intergenic 35.0%
ACACTTTGCATCTTCAACTT+CGG - tig0006524:3088-3107 Msa1343770:intergenic 35.0%
AAGAGTTCGAGAAAAATGGT+GGG + tig0006524:3214-3233 Msa1343770:CDS 35.0%
GTAACATGGATGGGAAAATT+AGG + tig0006524:3355-3374 Msa1343770:CDS 35.0%
GACAACAAACATTCTCCATG+AGG - tig0006524:2919-2938 None:intergenic 40.0%
! TCGGAAGTTGAAAGCTTTGT+TGG - tig0006524:2982-3001 Msa1343770:intergenic 40.0%
TCTTCAACTTCGGATATCGA+TGG - tig0006524:3078-3097 Msa1343770:intergenic 40.0%
ACGAACACGATCTATGTACT+CGG - tig0006524:3142-3161 Msa1343770:intergenic 40.0%
GTGTTCGTAACAAGTTCGAA+GGG + tig0006524:3154-3173 Msa1343770:CDS 40.0%
TTCGAAGGGAAATTTGTGTG+CGG + tig0006524:3168-3187 Msa1343770:CDS 40.0%
ATTTGTGTGCGGTTTGTGTT+CGG + tig0006524:3179-3198 Msa1343770:CDS 40.0%
GAAGAGTTCGAGAAAAATGG+TGG + tig0006524:3213-3232 Msa1343770:CDS 40.0%
GCTTGTGCTTGAAACAAAAC+TGG - tig0006524:3312-3331 Msa1343770:intergenic 40.0%
GGCTAAGTCAATTAGTCCAA+GGG + tig0006524:3377-3396 Msa1343770:CDS 40.0%
ATTAGTCCAAGGGACAAGAA+AGG + tig0006524:3387-3406 Msa1343770:CDS 40.0%
TTGATCTCTCTTGTAAGTGC+TGG - tig0006524:3450-3469 Msa1343770:intergenic 40.0%
TTCCGACCACCTTCAAAGAA+CGG + tig0006524:2996-3015 Msa1343770:CDS 45.0%
CATCAGCTCGAAGGAAATGT+CGG - tig0006524:3025-3044 Msa1343770:intergenic 45.0%
! TTCTTTTGCCATCAGCTCGA+AGG - tig0006524:3034-3053 Msa1343770:intergenic 45.0%
! GATGCAAAGTGTGAGTGTTG+TGG + tig0006524:3096-3115 Msa1343770:CDS 45.0%
CGAACACGATCTATGTACTC+GGG - tig0006524:3141-3160 Msa1343770:intergenic 45.0%
CGTGTTCGTAACAAGTTCGA+AGG + tig0006524:3153-3172 Msa1343770:CDS 45.0%
GGGCTAAGTCAATTAGTCCA+AGG + tig0006524:3376-3395 Msa1343770:CDS 45.0%
! GACCGTTCTTTGAAGGTGGT+CGG - tig0006524:3001-3020 Msa1343770:intergenic 50.0%
TGTCGGAGACCGTTCTTTGA+AGG - tig0006524:3008-3027 Msa1343770:intergenic 50.0%
CGACATTTCCTTCGAGCTGA+TGG + tig0006524:3023-3042 Msa1343770:CDS 50.0%
AGTCCAAGGGACAAGAAAGG+AGG + tig0006524:3390-3409 Msa1343770:CDS 50.0%
ACAAGAAAGGAGGAGGAGGA+GGG + tig0006524:3400-3419 Msa1343770:CDS 50.0%
! CGGAGACCGTTCTTTGAAGG+TGG - tig0006524:3005-3024 Msa1343770:intergenic 55.0%
TGTGTGCGGTTTGTGTTCGG+AGG + tig0006524:3182-3201 Msa1343770:CDS 55.0%
CCTCCTCCTTTCTTGTCCCT+TGG - tig0006524:3396-3415 Msa1343770:intergenic 55.0%
CCAAGGGACAAGAAAGGAGG+AGG + tig0006524:3393-3412 Msa1343770:CDS 55.0%
AGGGACAAGAAAGGAGGAGG+AGG + tig0006524:3396-3415 Msa1343770:CDS 55.0%
GACAAGAAAGGAGGAGGAGG+AGG + tig0006524:3399-3418 Msa1343770:CDS 55.0%
GTGCGGTTTGTGTTCGGAGG+CGG + tig0006524:3185-3204 Msa1343770:CDS 60.0%
Chromosome Type Strat End Strand Name
tig0006524 gene 2910 3491 2910 ID=Msa1343770;Name=Msa1343770
tig0006524 mRNA 2910 3491 2910 ID=Msa1343770-mRNA-1;Parent=Msa1343770;Name=Msa1343770-mRNA-1;_AED=0.00;_eAED=0.00;_QI=0|-1|0|1|-1|1|1|0|193
tig0006524 exon 2910 3491 2910 ID=Msa1343770-mRNA-1:exon:4273;Parent=Msa1343770-mRNA-1
tig0006524 CDS 2910 3491 2910 ID=Msa1343770-mRNA-1:cds;Parent=Msa1343770-mRNA-1
Gene Sequence

>Msa1343770

ATGGCACCTCATGGAGAATGTTTGTTGTCAAGTTCATTCTCAAGGAACAACAACAACACACCAAACAAACCAACAAAGCTTTCAACTTCCGACCACCTTCAAAGAACGGTCTCCGACATTTCCTTCGAGCTGATGGCAAAAGAAGCAATCGATAATTTAAAACTACCATCGATATCCGAAGTTGAAGATGCAAAGTGTGAGTGTTGTGGCATGTCTGAAGAGTGCACACCCGAGTACATAGATCGTGTTCGTAACAAGTTCGAAGGGAAATTTGTGTGCGGTTTGTGTTCGGAGGCGGTGAAAGAAGAGTTCGAGAAAAATGGTGGGAAAAAATTAGAAGAAGCTTTAAACACACATATGAATGCATGTGTTAAGTTTAACAAATATGGTAGGGCTTTTCCAGTTTTGTTTCAAGCACAAGCTATGAAAGAAATGTTGAAAAAGAGTAACATGGATGGGAAAATTAGGGCTAAGTCAATTAGTCCAAGGGACAAGAAAGGAGGAGGAGGAGGGCTTGCTCGTAGTACAAGTTGTATTCCAGCACTTACAAGAGAGATCAACAATATCAAAATAGCCAATTAA

Protein sequence

>Msa1343770

MAPHGECLLSSSFSRNNNNTPNKPTKLSTSDHLQRTVSDISFELMAKEAIDNLKLPSISEVEDAKCECCGMSEECTPEYIDRVRNKFEGKFVCGLCSEAVKEEFEKNGGKKLEEALNTHMNACVKFNKYGRAFPVLFQAQAMKEMLKKSNMDGKIRAKSISPRDKKGGGGGLARSTSCIPALTREINNIKIAN*