AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1139050


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1139050 MtrunA17_Chr5g0410931 99.160 119 1 0 1 119 1 119 1.34e-82 238
Msa1139050 MtrunA17_Chr5g0410951 99.160 119 1 0 1 119 1 119 1.34e-82 238
Msa1139050 MtrunA17_Chr8g0383851 99.160 119 1 0 1 119 1 119 1.34e-82 238
Msa1139050 MtrunA17_Chr8g0383781 99.160 119 1 0 1 119 1 119 1.34e-82 238
Msa1139050 MtrunA17_Chr8g0390361 99.160 119 1 0 1 119 1 119 1.34e-82 238
Msa1139050 MtrunA17_Chr2g0295191 99.160 119 1 0 1 119 1 119 1.34e-82 238
Msa1139050 MtrunA17_Chr7g0237661 99.160 119 1 0 1 119 1 119 1.34e-82 238
Msa1139050 MtrunA17_Chr4g0033041 99.160 119 1 0 1 119 1 119 1.34e-82 238
Msa1139050 MtrunA17_Chr7g0218971 99.160 119 1 0 1 119 1 119 1.34e-82 238
Msa1139050 MtrunA17_Chr4g0046301 99.160 119 1 0 1 119 1 119 1.34e-82 238
Msa1139050 MtrunA17_Chr8g0364801 99.160 119 1 0 1 119 1 119 1.34e-82 238
Msa1139050 MtrunA17_Chr4g0054151 95.798 119 5 0 1 119 4 122 1.66e-79 231
Msa1139050 MtrunA17_Chr4g0054161 95.798 119 5 0 1 119 1 119 2.11e-79 230
Msa1139050 MtrunA17_Chr8g0363741 95.798 119 5 0 1 119 1 119 2.11e-79 230
Msa1139050 MtrunA17_Chr1g0156021 95.798 119 5 0 1 119 1 119 2.11e-79 230
Msa1139050 MtrunA17_Chr8g0388121 94.958 119 6 0 1 119 1 119 7.54e-79 229
Msa1139050 MtrunA17_Chr2g0319141 89.076 119 13 0 1 119 1 119 8.63e-75 218
Msa1139050 MtrunA17_Chr2g0319151 89.076 119 13 0 1 119 1 119 8.63e-75 218
Msa1139050 MtrunA17_Chr2g0319131 82.946 129 12 1 1 119 1 129 7.89e-69 204
Msa1139050 MtrunA17_Chr2g0319121 82.500 120 19 2 1 119 1 119 4.85e-63 189
Msa1139050 MtrunA17_Chr7g0218961 87.368 95 12 0 25 119 2 96 1.13e-55 169
Msa1139050 MtrunA17_Chr7g0222991 65.546 119 40 1 1 119 10 127 6.46e-46 145
Msa1139050 MtrunA17_Chr5g0407311 66.379 116 36 2 1 116 1 113 2.94e-44 140
Msa1139050 MtrunA17_Chr7g0240791 98.485 66 1 0 1 66 1 66 2.68e-40 132
Msa1139050 MtrunA17_Chr7g0223001 56.780 118 37 3 3 119 27 131 6.17e-34 115
Msa1139050 MtrunA17_Chr8g0347231 54.762 84 37 1 37 119 28 111 3.52e-23 87.8
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1139050 AT1G09200.1 98.319 119 2 0 1 119 1 119 6.91e-82 237
Msa1139050 AT5G65360.1 98.319 119 2 0 1 119 1 119 6.91e-82 237
Msa1139050 AT5G10390.1 98.319 119 2 0 1 119 1 119 6.91e-82 237
Msa1139050 AT5G10400.1 98.319 119 2 0 1 119 1 119 6.91e-82 237
Msa1139050 AT3G27360.1 98.319 119 2 0 1 119 1 119 6.91e-82 237
Msa1139050 AT4G40030.3 95.798 119 5 0 1 119 1 119 2.92e-79 230
Msa1139050 AT4G40030.1 95.798 119 5 0 1 119 1 119 2.92e-79 230
Msa1139050 AT4G40030.4 95.798 119 5 0 1 119 1 119 2.92e-79 230
Msa1139050 AT5G10980.1 95.798 119 5 0 1 119 1 119 2.92e-79 230
Msa1139050 AT4G40040.2 95.798 119 5 0 1 119 1 119 2.92e-79 230
Msa1139050 AT4G40040.3 95.798 119 5 0 1 119 1 119 2.92e-79 230
Msa1139050 AT4G40040.1 95.798 119 5 0 1 119 1 119 2.92e-79 230
Msa1139050 AT4G40030.2 95.798 119 5 0 1 119 29 147 5.69e-79 230
Msa1139050 AT5G65350.1 94.118 119 7 0 1 119 1 119 3.84e-78 228
Msa1139050 AT1G13370.1 93.277 119 8 0 1 119 1 119 4.79e-76 222
Msa1139050 AT1G75600.1 92.437 119 9 0 1 119 1 119 8.66e-76 221
Msa1139050 AT1G19890.1 88.333 120 13 1 1 119 1 120 1.89e-71 210
Msa1139050 AT5G12910.1 68.908 119 32 2 1 119 1 114 1.34e-54 167
Msa1139050 AT1G01370.2 54.082 98 42 2 24 119 63 159 1.04e-24 93.6
Msa1139050 AT1G01370.1 54.082 98 42 2 24 119 63 159 1.04e-24 93.6
Msa1139050 AT1G01370.4 54.082 98 42 2 24 119 63 159 1.04e-24 93.6
Msa1139050 AT1G01370.3 54.082 98 42 2 24 119 63 159 1.04e-24 93.6

Find 30 sgRNAs with CRISPR-Local

Find 40 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TTTACTACTTCGATAGTATT+TGG 0.190676 7_4:-9078016 None:intergenic
TCGTGAAGTGCGACTGTTCC+TGG 0.230897 7_4:-9077767 None:intergenic
CGATTTCACGAACCAATCTT+TGG 0.247437 7_4:-9077841 None:intergenic
TTCTTCACTCCTCCGGTTGC+CGG 0.280449 7_4:-9077728 None:intergenic
GAAACTTCCATTCCAAAGAT+TGG 0.376853 7_4:+9077829 Msa1139050:CDS
GCTGCTGAAGCGTATCTTGT+TGG 0.377871 7_4:+9077923 Msa1139050:CDS
TTGCCACTAGGCAGTAGATT+TGG 0.378898 7_4:+9078122 Msa1139050:intron
TTTCCGTGGGGCTTTGCCGC+CGG 0.416326 7_4:-9077672 None:intergenic
AGAAAATCAGCTCCGGCAAC+CGG 0.420148 7_4:+9077716 Msa1139050:CDS
AGAGCACCGAGCTTCTCATT+AGG 0.438663 7_4:+9077807 Msa1139050:CDS
TGGTGGCGAGTTGTTTCCGT+GGG 0.469293 7_4:-9077685 None:intergenic
GTGTGGCTTCTTCACTCCTC+CGG 0.469362 7_4:-9077735 None:intergenic
GAGAGTTACTGATAGATCTC+TGG 0.496343 7_4:+9077985 Msa1139050:CDS
CCGTGGGGCTTTGCCGCCGG+TGG 0.499508 7_4:-9077669 None:intergenic
TCACGAACCAATCTTTGGAA+TGG 0.535409 7_4:-9077836 None:intergenic
AGCCGCAAGAAAATCAGCTC+CGG 0.539637 7_4:+9077709 Msa1139050:CDS
ATTGGTTCGTGAAATCGCTC+AGG 0.553548 7_4:+9077847 Msa1139050:CDS
CCACCGGCGGCAAAGCCCCA+CGG 0.566992 7_4:+9077669 Msa1139050:CDS
TTCAGCAGCTTCTTGAAGAG+CGG 0.568476 7_4:-9077909 None:intergenic
TTGGTGGCGAGTTGTTTCCG+TGG 0.577381 7_4:-9077686 None:intergenic
CGGTGCTCTTCTGATACTTG+CGG 0.587237 7_4:-9077793 None:intergenic
CAAACAGCACGAAAATCCAC+CGG 0.613909 7_4:+9077653 Msa1139050:CDS
AAATCAGCTCCGGCAACCGG+AGG 0.628601 7_4:+9077719 Msa1139050:CDS
AAGTTTCCTAATGAGAAGCT+CGG 0.631897 7_4:-9077813 None:intergenic
AAGCCACACAGATTCCGTCC+AGG 0.632383 7_4:+9077749 Msa1139050:CDS
ACTACTCTGAAATCGAAGAT+CGG 0.637960 7_4:-9077879 None:intergenic
GAAGTGCGACTGTTCCTGGA+CGG 0.665827 7_4:-9077763 None:intergenic
GTTCCTGGACGGAATCTGTG+TGG 0.677012 7_4:-9077752 None:intergenic
ACAGCACGAAAATCCACCGG+CGG 0.704457 7_4:+9077656 Msa1139050:CDS
GGTGGCGAGTTGTTTCCGTG+GGG 0.739791 7_4:-9077684 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! TTCAATTGCGTTATAAAATT+AGG + chr7_4:9078077-9078096 Msa1139050:intron 20.0%
! TTTACTACTTCGATAGTATT+TGG - chr7_4:9078019-9078038 None:intergenic 25.0%
!!! GTTTATTTTATTTTGCCACT+AGG + chr7_4:9078110-9078129 Msa1139050:intron 25.0%
AAGTTTCCTAATGAGAAGCT+CGG - chr7_4:9077816-9077835 None:intergenic 35.0%
GAAACTTCCATTCCAAAGAT+TGG + chr7_4:9077829-9077848 Msa1139050:CDS 35.0%
!! ACTACTCTGAAATCGAAGAT+CGG - chr7_4:9077882-9077901 None:intergenic 35.0%
AAGTTAAAAACAGTCCTCGT+GGG - chr7_4:9078051-9078070 None:intergenic 35.0%
!!! GGATTTTCGTGCTGTTTGTT+TGG - chr7_4:9077651-9077670 None:intergenic 40.0%
! TCACGAACCAATCTTTGGAA+TGG - chr7_4:9077839-9077858 None:intergenic 40.0%
CGATTTCACGAACCAATCTT+TGG - chr7_4:9077844-9077863 None:intergenic 40.0%
GAGAGTTACTGATAGATCTC+TGG + chr7_4:9077985-9078004 Msa1139050:CDS 40.0%
GTAAAAATATCGATCCCACG+AGG + chr7_4:9078034-9078053 Msa1139050:intron 40.0%
GAAGTTAAAAACAGTCCTCG+TGG - chr7_4:9078052-9078071 None:intergenic 40.0%
AAACCAAATCTACTGCCTAG+TGG - chr7_4:9078128-9078147 None:intergenic 40.0%
CAAACAGCACGAAAATCCAC+CGG + chr7_4:9077653-9077672 Msa1139050:CDS 45.0%
!! TGATTTTCTTGCGGCTTTGG+TGG - chr7_4:9077705-9077724 None:intergenic 45.0%
!! AGCTGATTTTCTTGCGGCTT+TGG - chr7_4:9077708-9077727 None:intergenic 45.0%
!! ATTGGTTCGTGAAATCGCTC+AGG + chr7_4:9077847-9077866 Msa1139050:CDS 45.0%
TTCAGCAGCTTCTTGAAGAG+CGG - chr7_4:9077912-9077931 None:intergenic 45.0%
TTGCCACTAGGCAGTAGATT+TGG + chr7_4:9078122-9078141 Msa1139050:intron 45.0%
AGCCGCAAGAAAATCAGCTC+CGG + chr7_4:9077709-9077728 Msa1139050:CDS 50.0%
!! TGCCGGAGCTGATTTTCTTG+CGG - chr7_4:9077714-9077733 None:intergenic 50.0%
AGAAAATCAGCTCCGGCAAC+CGG + chr7_4:9077716-9077735 Msa1139050:CDS 50.0%
CGGTGCTCTTCTGATACTTG+CGG - chr7_4:9077796-9077815 None:intergenic 50.0%
!! AGAGCACCGAGCTTCTCATT+AGG + chr7_4:9077807-9077826 Msa1139050:CDS 50.0%
GCTGCTGAAGCGTATCTTGT+TGG + chr7_4:9077923-9077942 Msa1139050:CDS 50.0%
ACAGCACGAAAATCCACCGG+CGG + chr7_4:9077656-9077675 Msa1139050:CDS 55.0%
! TGGTGGCGAGTTGTTTCCGT+GGG - chr7_4:9077688-9077707 None:intergenic 55.0%
!! TTGGTGGCGAGTTGTTTCCG+TGG - chr7_4:9077689-9077708 None:intergenic 55.0%
TTCTTCACTCCTCCGGTTGC+CGG - chr7_4:9077731-9077750 None:intergenic 55.0%
GTGTGGCTTCTTCACTCCTC+CGG - chr7_4:9077738-9077757 None:intergenic 55.0%
AAGCCACACAGATTCCGTCC+AGG + chr7_4:9077749-9077768 Msa1139050:CDS 55.0%
GTTCCTGGACGGAATCTGTG+TGG - chr7_4:9077755-9077774 None:intergenic 55.0%
GAAGTGCGACTGTTCCTGGA+CGG - chr7_4:9077766-9077785 None:intergenic 55.0%
TCGTGAAGTGCGACTGTTCC+TGG - chr7_4:9077770-9077789 None:intergenic 55.0%
! GGTGGCGAGTTGTTTCCGTG+GGG - chr7_4:9077687-9077706 None:intergenic 60.0%
AAATCAGCTCCGGCAACCGG+AGG + chr7_4:9077719-9077738 Msa1139050:CDS 60.0%
TTTCCGTGGGGCTTTGCCGC+CGG - chr7_4:9077675-9077694 None:intergenic 65.0%
CCACCGGCGGCAAAGCCCCA+CGG + chr7_4:9077669-9077688 Msa1139050:CDS 75.0%
! CCGTGGGGCTTTGCCGCCGG+TGG - chr7_4:9077672-9077691 None:intergenic 80.0%
Chromosome Type Strat End Strand Name
chr7_4 gene 9077638 9078149 9077638 ID=Msa1139050;Name=Msa1139050
chr7_4 mRNA 9077638 9078149 9077638 ID=Msa1139050-mRNA-1;Parent=Msa1139050;Name=Msa1139050-mRNA-1;_AED=0.29;_eAED=0.29;_QI=0|0|0|0.5|1|1|2|0|136
chr7_4 exon 9077638 9078030 9077638 ID=Msa1139050-mRNA-1:exon:2398;Parent=Msa1139050-mRNA-1
chr7_4 exon 9078132 9078149 9078132 ID=Msa1139050-mRNA-1:exon:2399;Parent=Msa1139050-mRNA-1
chr7_4 CDS 9077638 9078030 9077638 ID=Msa1139050-mRNA-1:cds;Parent=Msa1139050-mRNA-1
chr7_4 CDS 9078132 9078149 9078132 ID=Msa1139050-mRNA-1:cds;Parent=Msa1139050-mRNA-1
Gene Sequence

>Msa1139050

ATGGCACGTACCAAACAAACAGCACGAAAATCCACCGGCGGCAAAGCCCCACGGAAACAACTCGCCACCAAAGCCGCAAGAAAATCAGCTCCGGCAACCGGAGGAGTGAAGAAGCCACACAGATTCCGTCCAGGAACAGTCGCACTTCACGAGATCCGCAAGTATCAGAAGAGCACCGAGCTTCTCATTAGGAAACTTCCATTCCAAAGATTGGTTCGTGAAATCGCTCAGGATTTCAAAACCGATCTTCGATTTCAGAGTAGTGCTGTTTCCGCTCTTCAAGAAGCTGCTGAAGCGTATCTTGTTGGATTGTTTGAAGATACGAATCTTTGTGCTATTCATGCTAAGAGAGTTACTGATAGATCTCTGGCAAGTGCACCAAATACTATCGAAGCAGTAGATTTGGTTTGA

Protein sequence

>Msa1139050

MARTKQTARKSTGGKAPRKQLATKAARKSAPATGGVKKPHRFRPGTVALHEIRKYQKSTELLIRKLPFQRLVREIAQDFKTDLRFQSSAVSALQEAAEAYLVGLFEDTNLCAIHAKRVTDRSLASAPNTIEAVDLV*