AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1274310


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1274310 MtrunA17_Chr8g0340421 95.855 193 7 1 1 193 3 194 2.26e-135 376
Msa1274310 MtrunA17_Chr2g0331111 66.332 199 58 5 1 193 1 196 1.69e-84 248
Msa1274310 MtrunA17_Chr8g0344381 46.212 132 58 5 59 183 29 154 3.33e-31 111
Msa1274310 MtrunA17_Chr1g0205251 47.778 90 39 3 60 146 2 86 2.60e-23 89.7
Msa1274310 MtrunA17_Chr3g0136441 59.091 66 26 1 57 121 8 73 2.98e-22 87.4
Msa1274310 MtrunA17_Chr5g0394601 43.750 96 45 3 60 152 2 91 1.57e-21 85.1
Msa1274310 MtrunA17_Chr3g0140381 34.211 152 87 4 29 177 4 145 4.69e-19 79.7
Msa1274310 MtrunA17_Chr4g0070371 37.234 94 52 2 60 146 24 117 9.70e-18 76.3
Msa1274310 MtrunA17_Chr4g0070351 40.860 93 50 3 33 121 1 92 1.05e-17 75.5
Msa1274310 MtrunA17_Chr1g0150711 40.217 92 47 2 45 132 1 88 6.64e-16 71.2
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1274310 AT5G25840.1 50.543 184 54 5 33 193 4 173 2.46e-53 168
Msa1274310 AT1G79770.1 52.903 155 59 3 33 187 27 167 1.09e-46 151
Msa1274310 AT4G14819.1 42.727 110 51 3 60 169 2 99 1.54e-23 90.1
Msa1274310 AT2G25780.1 36.774 155 83 4 33 182 7 151 1.97e-22 89.0
Msa1274310 AT3G22540.1 40.449 89 50 1 60 148 2 87 1.80e-21 85.1
Msa1274310 AT1G72510.1 39.706 136 67 7 60 183 33 165 1.08e-20 84.7
Msa1274310 AT1G72510.2 39.706 136 67 7 60 183 33 165 1.08e-20 84.7
Msa1274310 AT1G54095.1 39.706 136 69 5 59 183 14 147 3.52e-19 80.5
Msa1274310 AT5G20670.1 33.582 134 82 3 57 183 19 152 4.49e-19 80.1
Msa1274310 AT2G09970.1 34.058 138 73 7 60 183 33 166 4.22e-16 72.8

Find 40 sgRNAs with CRISPR-Local

Find 45 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GTAACATGGATGGGAAAATT+AGG 0.194429 8_3:-8040691 Msa1274310:CDS
CCTCCTCCTTTCTTGTCCCT+TGG 0.275546 8_3:+8040653 None:intergenic
AAAATAGATAGATAGTTAAT+TGG 0.284549 8_3:+8040562 None:intergenic
TGTGTTAAGTTTAACAAATA+TGG 0.300385 8_3:-8040770 Msa1274310:CDS
GAAAGCTTTGTTGGTTTGTT+TGG 0.348037 8_3:+8041076 None:intergenic
GCTTGTGCTTGAAACAAAAC+TGG 0.379794 8_3:+8040737 None:intergenic
GACAAGAAAGGAGGAGGAGG+AGG 0.400333 8_3:-8040647 Msa1274310:CDS
TCGGAAGTTGAAAGCTTTGT+TGG 0.400947 8_3:+8041067 None:intergenic
TAACATGGATGGGAAAATTA+GGG 0.434099 8_3:-8040690 Msa1274310:CDS
CGACATTTCCTTCGAGCTGA+TGG 0.460178 8_3:-8041023 Msa1274310:CDS
TTGATCTCTCTTGTAAGTGC+TGG 0.461637 8_3:+8040599 None:intergenic
ATTTGTGTGCGGTTTGTGTT+CGG 0.464682 8_3:-8040867 Msa1274310:CDS
ACACTTTGCATCTTCAACTT+CGG 0.466067 8_3:+8040961 None:intergenic
TGTCGGAGACCGTTCTTTGA+AGG 0.474473 8_3:+8041041 None:intergenic
TTAAGTTTAACAAATATGGT+AGG 0.490124 8_3:-8040766 Msa1274310:CDS
AGGGACAAGAAAGGAGGAGG+AGG 0.494514 8_3:-8040650 Msa1274310:CDS
TGTTGTCAAGTTCATTCTCA+AGG 0.519029 8_3:-8041114 Msa1274310:CDS
TAAGTTTAACAAATATGGTA+GGG 0.538103 8_3:-8040765 Msa1274310:CDS
GGAGGCGGTGAAAGAAGAGT+TGG 0.546775 8_3:-8040846 Msa1274310:CDS
GTGCGGTTTGTGTTCGGAGG+CGG 0.552330 8_3:-8040861 Msa1274310:CDS
GACCGTTCTTTGAAGGTGGT+CGG 0.559329 8_3:+8041048 None:intergenic
ATCATGGTTATGGCACCTCA+TGG 0.562684 8_3:-8041145 None:intergenic
CCAAGGGACAAGAAAGGAGG+AGG 0.566147 8_3:-8040653 Msa1274310:CDS
CGGAGACCGTTCTTTGAAGG+TGG 0.567308 8_3:+8041044 None:intergenic
GGGCTAAGTCAATTAGTCCA+AGG 0.570684 8_3:-8040670 Msa1274310:CDS
ATTAGTCCAAGGGACAAGAA+AGG 0.576487 8_3:-8040659 Msa1274310:CDS
ACGAACACGATCTATGTACT+CGG 0.578833 8_3:+8040907 None:intergenic
CGTGTTCGTAACAAGTTCGA+AGG 0.581435 8_3:-8040893 Msa1274310:CDS
ACAAGAAAGGAGGAGGAGGA+GGG 0.591395 8_3:-8040646 Msa1274310:CDS
GGCTAAGTCAATTAGTCCAA+GGG 0.598516 8_3:-8040669 Msa1274310:CDS
TTCCGACCACCTTCAAAGAA+CGG 0.607623 8_3:-8041050 Msa1274310:CDS
CATCAGCTCGAAGGAAATGT+CGG 0.626398 8_3:+8041024 None:intergenic
TCTTCAACTTCGGATATCGA+TGG 0.633325 8_3:+8040971 None:intergenic
TGTGTGCGGTTTGTGTTCGG+AGG 0.638466 8_3:-8040864 Msa1274310:CDS
GTGTTCGTAACAAGTTCGAA+GGG 0.639090 8_3:-8040892 Msa1274310:CDS
TTCGAAGGGAAATTTGTGTG+CGG 0.644656 8_3:-8040878 Msa1274310:CDS
CGAACACGATCTATGTACTC+GGG 0.649900 8_3:+8040908 None:intergenic
GATGCAAAGTGTGAGTGTTG+TGG 0.665594 8_3:-8040950 Msa1274310:CDS
AGTCCAAGGGACAAGAAAGG+AGG 0.666513 8_3:-8040656 Msa1274310:CDS
GACAACAAACATTCTCCATG+AGG 0.716500 8_3:+8041130 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! TGTGTTAAGTTTAACAAATA+TGG - chr8_3:8040943-8040962 Msa1274310:CDS 20.0%
!! TTAAGTTTAACAAATATGGT+AGG - chr8_3:8040947-8040966 Msa1274310:CDS 20.0%
!! TAAGTTTAACAAATATGGTA+GGG - chr8_3:8040948-8040967 Msa1274310:CDS 20.0%
! AATGTTGAAAAAGAGTAACA+TGG - chr8_3:8041008-8041027 Msa1274310:CDS 25.0%
AAAGAAGAGTTGGAGAAAAA+TGG - chr8_3:8040877-8040896 Msa1274310:CDS 30.0%
TTGAAAAAGAGTAACATGGA+TGG - chr8_3:8041012-8041031 Msa1274310:CDS 30.0%
TGAAAAAGAGTAACATGGAT+GGG - chr8_3:8041013-8041032 Msa1274310:CDS 30.0%
TAACATGGATGGGAAAATTA+GGG - chr8_3:8041023-8041042 Msa1274310:CDS 30.0%
TGTTGTCAAGTTCATTCTCA+AGG - chr8_3:8040599-8040618 Msa1274310:CDS 35.0%
!! GAAAGCTTTGTTGGTTTGTT+TGG + chr8_3:8040640-8040659 None:intergenic 35.0%
ACACTTTGCATCTTCAACTT+CGG + chr8_3:8040755-8040774 None:intergenic 35.0%
AAGAGTTGGAGAAAAATGGT+GGG - chr8_3:8040881-8040900 Msa1274310:CDS 35.0%
GTAACATGGATGGGAAAATT+AGG - chr8_3:8041022-8041041 Msa1274310:CDS 35.0%
GACAACAAACATTCTCCATG+AGG + chr8_3:8040586-8040605 None:intergenic 40.0%
! TCGGAAGTTGAAAGCTTTGT+TGG + chr8_3:8040649-8040668 None:intergenic 40.0%
TCTTCAACTTCGGATATCGA+TGG + chr8_3:8040745-8040764 None:intergenic 40.0%
ACGAACACGATCTATGTACT+CGG + chr8_3:8040809-8040828 None:intergenic 40.0%
GTGTTCGTAACAAGTTCGAA+GGG - chr8_3:8040821-8040840 Msa1274310:CDS 40.0%
TTCGAAGGGAAATTTGTGTG+CGG - chr8_3:8040835-8040854 Msa1274310:CDS 40.0%
ATTTGTGTGCGGTTTGTGTT+CGG - chr8_3:8040846-8040865 Msa1274310:CDS 40.0%
GAAGAGTTGGAGAAAAATGG+TGG - chr8_3:8040880-8040899 Msa1274310:CDS 40.0%
GCTTGTGCTTGAAACAAAAC+TGG + chr8_3:8040979-8040998 None:intergenic 40.0%
GGCTAAGTCAATTAGTCCAA+GGG - chr8_3:8041044-8041063 Msa1274310:CDS 40.0%
ATTAGTCCAAGGGACAAGAA+AGG - chr8_3:8041054-8041073 Msa1274310:CDS 40.0%
TTGATCTCTCTTGTAAGTGC+TGG + chr8_3:8041117-8041136 None:intergenic 40.0%
TTCCGACCACCTTCAAAGAA+CGG - chr8_3:8040663-8040682 Msa1274310:CDS 45.0%
CATCAGCTCGAAGGAAATGT+CGG + chr8_3:8040692-8040711 None:intergenic 45.0%
! TTCTTTTGCCATCAGCTCGA+AGG + chr8_3:8040701-8040720 None:intergenic 45.0%
! GATGCAAAGTGTGAGTGTTG+TGG - chr8_3:8040763-8040782 Msa1274310:CDS 45.0%
CGAACACGATCTATGTACTC+GGG + chr8_3:8040808-8040827 None:intergenic 45.0%
CGTGTTCGTAACAAGTTCGA+AGG - chr8_3:8040820-8040839 Msa1274310:CDS 45.0%
GGGCTAAGTCAATTAGTCCA+AGG - chr8_3:8041043-8041062 Msa1274310:CDS 45.0%
! GACCGTTCTTTGAAGGTGGT+CGG + chr8_3:8040668-8040687 None:intergenic 50.0%
TGTCGGAGACCGTTCTTTGA+AGG + chr8_3:8040675-8040694 None:intergenic 50.0%
CGACATTTCCTTCGAGCTGA+TGG - chr8_3:8040690-8040709 Msa1274310:CDS 50.0%
AGTCCAAGGGACAAGAAAGG+AGG - chr8_3:8041057-8041076 Msa1274310:CDS 50.0%
ACAAGAAAGGAGGAGGAGGA+GGG - chr8_3:8041067-8041086 Msa1274310:CDS 50.0%
! CGGAGACCGTTCTTTGAAGG+TGG + chr8_3:8040672-8040691 None:intergenic 55.0%
TGTGTGCGGTTTGTGTTCGG+AGG - chr8_3:8040849-8040868 Msa1274310:CDS 55.0%
GGAGGCGGTGAAAGAAGAGT+TGG - chr8_3:8040867-8040886 Msa1274310:CDS 55.0%
CCTCCTCCTTTCTTGTCCCT+TGG + chr8_3:8041063-8041082 None:intergenic 55.0%
CCAAGGGACAAGAAAGGAGG+AGG - chr8_3:8041060-8041079 Msa1274310:CDS 55.0%
AGGGACAAGAAAGGAGGAGG+AGG - chr8_3:8041063-8041082 Msa1274310:CDS 55.0%
GACAAGAAAGGAGGAGGAGG+AGG - chr8_3:8041066-8041085 Msa1274310:CDS 55.0%
GTGCGGTTTGTGTTCGGAGG+CGG - chr8_3:8040852-8040871 Msa1274310:CDS 60.0%
Chromosome Type Strat End Strand Name
chr8_3 gene 8040577 8041158 8040577 ID=Msa1274310;Name=Msa1274310
chr8_3 mRNA 8040577 8041158 8040577 ID=Msa1274310-mRNA-1;Parent=Msa1274310;Name=Msa1274310-mRNA-1;_AED=0.00;_eAED=0.00;_QI=0|-1|0|1|-1|1|1|0|193
chr8_3 exon 8040577 8041158 8040577 ID=Msa1274310-mRNA-1:exon:3206;Parent=Msa1274310-mRNA-1
chr8_3 CDS 8040577 8041158 8040577 ID=Msa1274310-mRNA-1:cds;Parent=Msa1274310-mRNA-1
Gene Sequence

>Msa1274310

ATGGCACCTCATGGAGAATGTTTGTTGTCAAGTTCATTCTCAAGGAACAACAACAACACACCAAACAAACCAACAAAGCTTTCAACTTCCGACCACCTTCAAAGAACGGTCTCCGACATTTCCTTCGAGCTGATGGCAAAAGAAGCAATCGATAATTTAAAACTACCATCGATATCCGAAGTTGAAGATGCAAAGTGTGAGTGTTGTGGCATGTCTGAAGAGTGCACACCCGAGTACATAGATCGTGTTCGTAACAAGTTCGAAGGGAAATTTGTGTGCGGTTTGTGTTCGGAGGCGGTGAAAGAAGAGTTGGAGAAAAATGGTGGGAAAAAATTAGAAGAAGCTTTAAACACACATATGAATGCATGTGTTAAGTTTAACAAATATGGTAGGGCTTTTCCAGTTTTGTTTCAAGCACAAGCTATGAAAGAAATGTTGAAAAAGAGTAACATGGATGGGAAAATTAGGGCTAAGTCAATTAGTCCAAGGGACAAGAAAGGAGGAGGAGGAGGGCTTGCTCGTAGTACAAGTTGTATTCCAGCACTTACAAGAGAGATCAACAATATCAAAATAGCCAATTAA

Protein sequence

>Msa1274310

MAPHGECLLSSSFSRNNNNTPNKPTKLSTSDHLQRTVSDISFELMAKEAIDNLKLPSISEVEDAKCECCGMSEECTPEYIDRVRNKFEGKFVCGLCSEAVKEELEKNGGKKLEEALNTHMNACVKFNKYGRAFPVLFQAQAMKEMLKKSNMDGKIRAKSISPRDKKGGGGGLARSTSCIPALTREINNIKIAN*