AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1213400

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1213400 MtrunA17_Chr7g0225661 35.714 126 66 3 79 200 55 169 8.17e-17 75.5
Msa1213400 MtrunA17_Chr8g0341311 36.364 121 62 3 84 200 50 159 1.24e-16 74.7
Msa1213400 MtrunA17_Chr7g0220571 42.342 111 60 1 73 179 52 162 1.03e-15 72.4
Msa1213400 MtrunA17_Chr6g0456061 41.441 111 60 1 76 181 57 167 1.22e-15 72.4
Msa1213400 MtrunA17_Chr5g0400901 36.232 138 71 6 73 202 27 155 1.20e-12 63.5
Msa1213400 MtrunA17_Chr4g0035414 35.000 120 65 3 93 199 16 135 2.44e-12 62.4
Msa1213400 MtrunA17_Chr1g0194681 31.624 117 73 1 84 193 7 123 9.10e-12 60.8
Msa1213400 MtrunA17_Chr3g0144941 36.275 102 55 2 93 184 16 117 1.35e-11 60.5
Msa1213400 MtrunA17_Chr4g0054291 29.870 154 86 5 25 172 6 143 3.97e-11 59.7
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1213400 AT5G60830.1 54.118 85 39 0 102 186 69 153 1.40e-21 88.6
Msa1213400 AT5G38800.1 41.667 96 54 1 86 179 52 147 6.80e-18 78.2
Msa1213400 AT3G30530.1 43.000 100 57 0 82 181 59 158 7.70e-18 78.2
Msa1213400 AT1G13600.1 42.105 95 50 1 90 179 67 161 3.32e-16 74.3
Msa1213400 AT5G15830.1 36.937 111 64 1 92 196 56 166 1.80e-14 69.3
Msa1213400 AT2G04038.1 40.426 94 50 1 92 179 56 149 1.70e-13 66.2
Msa1213400 AT2G18160.1 33.043 115 70 1 90 197 17 131 7.81e-12 62.0
Msa1213400 AT1G75390.1 40.566 106 55 2 82 179 11 116 1.39e-11 61.2

Find 58 sgRNAs with CRISPR-Local

Find 65 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TTGAGTTCATGATGGGTTTC+TGG 0.068192 8_1:-73526146 Msa1213390:intron
CAACAAAATGCTCAACTTAA+AGG 0.201570 8_1:+73526546 Msa1213400:CDS
CCAACAAGTAAATGATCTTT+TGG 0.211603 8_1:-73526503 Msa1213390:intron
ATGAGTTGGGAGAAGATTTA+TGG 0.268120 8_1:-73526305 Msa1213390:intron
AGCCTGCAAAACCTGGAAAA+TGG 0.302202 8_1:+73526168 Msa1213400:CDS
CCAAAAGATCATTTACTTGT+TGG 0.311300 8_1:+73526503 Msa1213400:CDS
GTGAGGTATACCAACATTTC+CGG 0.334411 8_1:-73526616 Msa1213390:intron
TGAGTTCATGATGGGTTTCT+GGG 0.383025 8_1:-73526145 Msa1213390:intron
TTTATGGTCTGGAATTTGAA+TGG 0.416953 8_1:-73526289 Msa1213390:intron
GAACTCAAGCCTGCAAAACC+TGG 0.431180 8_1:+73526161 Msa1213400:CDS
TTGGGAGAAGATTTATGGTC+TGG 0.437689 8_1:-73526300 Msa1213390:intron
CGGAAGCATAGGGTACTTCA+TGG 0.438301 8_1:-73526092 Msa1213390:intron
TTGCAGGCTTGAGTTCATGA+TGG 0.445548 8_1:-73526154 Msa1213390:intron
GTTACTGTTTGATGATGAGT+TGG 0.446587 8_1:-73526319 Msa1213390:intron
TGAAGCTGGGAGTAGTGAAA+TGG 0.452683 8_1:-73526243 Msa1213390:intron
TTATGGTCTGGAATTTGAAT+GGG 0.454968 8_1:-73526288 Msa1213390:intron
TTCATGATGGGTTTCTGGGT+TGG 0.465026 8_1:-73526141 Msa1213390:intron
AGCGGTACTATCTACTTTGT+TGG 0.466162 8_1:+73526587 Msa1213400:CDS
TGCAGGCTTGAGTTCATGAT+GGG 0.472548 8_1:-73526153 Msa1213390:intron
ATAGGAAAGGTACTGTATTA+CGG 0.473575 8_1:-73526112 Msa1213390:intron
TTGATGATCGAAAGAAGAAA+AGG 0.480340 8_1:+73526370 Msa1213400:CDS
AGACGAGTTGAAAGGTTGGC+TGG 0.483172 8_1:-73526657 Msa1213390:intron
TGTCGTTAGAGAGGTGAAGC+TGG 0.483487 8_1:-73526257 Msa1213390:intron
ACCCATCTGTATCCATCTCA+AGG 0.506932 8_1:+73526207 Msa1213400:CDS
CTACTCAAAATCGCTATGCT+CGG 0.512535 8_1:-73526700 Msa1213390:intron
TCTACTTTGTTGGTTACGAC+CGG 0.517483 8_1:+73526597 Msa1213400:CDS
TACTCAAAATCGCTATGCTC+GGG 0.518651 8_1:-73526699 Msa1213390:intron
TTACTGTTTGATGATGAGTT+GGG 0.525916 8_1:-73526318 Msa1213390:intron
ATTGATGGTTCAGCGCCTGC+AGG 0.527456 8_1:-73526476 Msa1213390:intron
AGGTTGGCTGGGAAGCCACT+AGG 0.529008 8_1:-73526645 Msa1213390:intron
ATGGGTTTCTGGGTTGGAGA+AGG 0.532216 8_1:-73526135 Msa1213390:intron
GATACAGATGGGTCAAAGAA+TGG 0.534656 8_1:-73526197 Msa1213390:intron
GTACTGTATTACGGAAGCAT+AGG 0.535976 8_1:-73526103 Msa1213390:intron
CTGGGAAGCCACTAGGGATG+TGG 0.538645 8_1:-73526638 Msa1213390:intron
TTTCTGGGTTGGAGAAGGAT+AGG 0.544788 8_1:-73526130 Msa1213390:intron
GTATCAAGTGAATCACCTGC+AGG 0.567327 8_1:+73526461 Msa1213400:CDS
ATATCATGTAAACCTTGAGA+TGG 0.573761 8_1:-73526219 Msa1213390:intron
TCAAACAGTAACAACAACTC+TGG 0.574952 8_1:+73526330 Msa1213400:CDS
GTCGTTAGAGAGGTGAAGCT+GGG 0.575441 8_1:-73526256 Msa1213390:intron
GACGAGTTGAAAGGTTGGCT+GGG 0.575767 8_1:-73526656 Msa1213390:intron
AACCTTGAGATGGATACAGA+TGG 0.576394 8_1:-73526209 Msa1213390:intron
TACTGTATTACGGAAGCATA+GGG 0.578817 8_1:-73526102 Msa1213390:intron
TTGAAACTAGACGAGTTGAA+AGG 0.584520 8_1:-73526665 Msa1213390:intron
GGTTGGCTGGGAAGCCACTA+GGG 0.587937 8_1:-73526644 Msa1213390:intron
TTGGTTACGACCGGAAATGT+TGG 0.596096 8_1:+73526606 Msa1213400:CDS
AACTAGACGAGTTGAAAGGT+TGG 0.596375 8_1:-73526661 Msa1213390:intron
AGATAGTACCGCTTGAAGAG+AGG 0.597446 8_1:-73526577 Msa1213390:intron
CAAAACCTGGAAAATGGAGA+AGG 0.605645 8_1:+73526174 Msa1213400:CDS
CAAAGTTTCCTCTCTTCAAG+CGG 0.609354 8_1:+73526569 Msa1213400:CDS
CAACAACTCTGGTAAAGCAA+AGG 0.613348 8_1:+73526341 Msa1213400:CDS
GGTGATTCACTTGATACCAC+AGG 0.615500 8_1:-73526455 Msa1213390:intron
ACCTTGAGATGGATACAGAT+GGG 0.616103 8_1:-73526208 Msa1213390:intron
CTAACAGAGAATCTGCTCGT+CGG 0.675721 8_1:+73526400 Msa1213400:CDS
AGAGATGGTACGCAATGACG+AGG 0.676375 8_1:+73526065 None:intergenic
ATACCTCACCACATCCCTAG+TGG 0.679014 8_1:+73526630 Msa1213400:CDS
AGCAGCGAATTGAAGTCCTG+TGG 0.703639 8_1:+73526439 Msa1213400:CDS
AAGCCACTAGGGATGTGGTG+AGG 0.721984 8_1:-73526633 Msa1213390:intron
GGGTTGGAGAAGGATAGGAA+AGG 0.730828 8_1:-73526125 Msa1213390:intron

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! CAACAAGTAAATGATCTTTT+GGG - chr8_1:73526505-73526524 Msa1213390:intron 25.0%
!! ATAGGAAAGGTACTGTATTA+CGG - chr8_1:73526115-73526134 Msa1213390:intron 30.0%
ATATCATGTAAACCTTGAGA+TGG - chr8_1:73526222-73526241 Msa1213390:intron 30.0%
! TTATGGTCTGGAATTTGAAT+GGG - chr8_1:73526291-73526310 Msa1213390:intron 30.0%
! TTTATGGTCTGGAATTTGAA+TGG - chr8_1:73526292-73526311 Msa1213390:intron 30.0%
!! TTACTGTTTGATGATGAGTT+GGG - chr8_1:73526321-73526340 Msa1213390:intron 30.0%
! TTTTCTTCTTTCGATCATCA+AGG - chr8_1:73526371-73526390 Msa1213390:intron 30.0%
! TTGATGATCGAAAGAAGAAA+AGG + chr8_1:73526370-73526389 Msa1213400:CDS 30.0%
! CCAACAAGTAAATGATCTTT+TGG - chr8_1:73526506-73526525 Msa1213390:intron 30.0%
CCAAAAGATCATTTACTTGT+TGG + chr8_1:73526503-73526522 Msa1213400:CDS 30.0%
!! CATTTTGTTGGTTGATTAGT+TGG - chr8_1:73526536-73526555 Msa1213390:intron 30.0%
!!! CTTTAAGTTGAGCATTTTGT+TGG - chr8_1:73526548-73526567 Msa1213390:intron 30.0%
CAACAAAATGCTCAACTTAA+AGG + chr8_1:73526546-73526565 Msa1213400:CDS 30.0%
! TACTGTATTACGGAAGCATA+GGG - chr8_1:73526105-73526124 Msa1213390:intron 35.0%
! ATGAGTTGGGAGAAGATTTA+TGG - chr8_1:73526308-73526327 Msa1213390:intron 35.0%
!! GTTACTGTTTGATGATGAGT+TGG - chr8_1:73526322-73526341 Msa1213390:intron 35.0%
TCAAACAGTAACAACAACTC+TGG + chr8_1:73526330-73526349 Msa1213400:CDS 35.0%
!!! TGATCTTTTGGGACAATTGA+TGG - chr8_1:73526494-73526513 Msa1213390:intron 35.0%
! TTGAAACTAGACGAGTTGAA+AGG - chr8_1:73526668-73526687 Msa1213390:intron 35.0%
! GTACTGTATTACGGAAGCAT+AGG - chr8_1:73526106-73526125 Msa1213390:intron 40.0%
!! TGAGTTCATGATGGGTTTCT+GGG - chr8_1:73526148-73526167 Msa1213390:intron 40.0%
!! TTGAGTTCATGATGGGTTTC+TGG - chr8_1:73526149-73526168 Msa1213390:intron 40.0%
CAAAACCTGGAAAATGGAGA+AGG + chr8_1:73526174-73526193 Msa1213400:CDS 40.0%
GATACAGATGGGTCAAAGAA+TGG - chr8_1:73526200-73526219 Msa1213390:intron 40.0%
ACCTTGAGATGGATACAGAT+GGG - chr8_1:73526211-73526230 Msa1213390:intron 40.0%
AACCTTGAGATGGATACAGA+TGG - chr8_1:73526212-73526231 Msa1213390:intron 40.0%
TTGGGAGAAGATTTATGGTC+TGG - chr8_1:73526303-73526322 Msa1213390:intron 40.0%
CAACAACTCTGGTAAAGCAA+AGG + chr8_1:73526341-73526360 Msa1213400:CDS 40.0%
CAAAGTTTCCTCTCTTCAAG+CGG + chr8_1:73526569-73526588 Msa1213400:CDS 40.0%
AGCGGTACTATCTACTTTGT+TGG + chr8_1:73526587-73526606 Msa1213400:CDS 40.0%
! TCTACTTTGTTGGTTACGAC+CGG + chr8_1:73526597-73526616 Msa1213400:CDS 40.0%
GTGAGGTATACCAACATTTC+CGG - chr8_1:73526619-73526638 Msa1213390:intron 40.0%
! AACTAGACGAGTTGAAAGGT+TGG - chr8_1:73526664-73526683 Msa1213390:intron 40.0%
TACTCAAAATCGCTATGCTC+GGG - chr8_1:73526702-73526721 Msa1213390:intron 40.0%
CTACTCAAAATCGCTATGCT+CGG - chr8_1:73526703-73526722 Msa1213390:intron 40.0%
! TTTCTGGGTTGGAGAAGGAT+AGG - chr8_1:73526133-73526152 Msa1213390:intron 45.0%
!! TTCATGATGGGTTTCTGGGT+TGG - chr8_1:73526144-73526163 Msa1213390:intron 45.0%
TGCAGGCTTGAGTTCATGAT+GGG - chr8_1:73526156-73526175 Msa1213390:intron 45.0%
TTGCAGGCTTGAGTTCATGA+TGG - chr8_1:73526157-73526176 Msa1213390:intron 45.0%
AGCCTGCAAAACCTGGAAAA+TGG + chr8_1:73526168-73526187 Msa1213400:CDS 45.0%
! CTCCATTTTCCAGGTTTTGC+AGG - chr8_1:73526173-73526192 Msa1213390:intron 45.0%
! AATGGCCTTCTCCATTTTCC+AGG - chr8_1:73526182-73526201 Msa1213390:intron 45.0%
ACCCATCTGTATCCATCTCA+AGG + chr8_1:73526207-73526226 Msa1213400:CDS 45.0%
TGAAGCTGGGAGTAGTGAAA+TGG - chr8_1:73526246-73526265 Msa1213390:intron 45.0%
CTAACAGAGAATCTGCTCGT+CGG + chr8_1:73526400-73526419 Msa1213400:CDS 45.0%
GGTGATTCACTTGATACCAC+AGG - chr8_1:73526458-73526477 Msa1213390:intron 45.0%
GTATCAAGTGAATCACCTGC+AGG + chr8_1:73526461-73526480 Msa1213400:CDS 45.0%
AGATAGTACCGCTTGAAGAG+AGG - chr8_1:73526580-73526599 Msa1213390:intron 45.0%
TTGGTTACGACCGGAAATGT+TGG + chr8_1:73526606-73526625 Msa1213400:CDS 45.0%
! CGGAAGCATAGGGTACTTCA+TGG - chr8_1:73526095-73526114 Msa1213390:intron 50.0%
GGGTTGGAGAAGGATAGGAA+AGG - chr8_1:73526128-73526147 Msa1213390:intron 50.0%
! ATGGGTTTCTGGGTTGGAGA+AGG - chr8_1:73526138-73526157 Msa1213390:intron 50.0%
GAACTCAAGCCTGCAAAACC+TGG + chr8_1:73526161-73526180 Msa1213400:CDS 50.0%
GTCGTTAGAGAGGTGAAGCT+GGG - chr8_1:73526259-73526278 Msa1213390:intron 50.0%
TGTCGTTAGAGAGGTGAAGC+TGG - chr8_1:73526260-73526279 Msa1213390:intron 50.0%
AGCAGCGAATTGAAGTCCTG+TGG + chr8_1:73526439-73526458 Msa1213400:CDS 50.0%
ATACCTCACCACATCCCTAG+TGG + chr8_1:73526630-73526649 Msa1213400:CDS 50.0%
! GACGAGTTGAAAGGTTGGCT+GGG - chr8_1:73526659-73526678 Msa1213390:intron 50.0%
! AGACGAGTTGAAAGGTTGGC+TGG - chr8_1:73526660-73526679 Msa1213390:intron 50.0%
GACTGTCGCTGTCGTTAGAG+AGG - chr8_1:73526269-73526288 Msa1213390:intron 55.0%
! ATTGATGGTTCAGCGCCTGC+AGG - chr8_1:73526479-73526498 Msa1213390:intron 55.0%
AAGCCACTAGGGATGTGGTG+AGG - chr8_1:73526636-73526655 Msa1213390:intron 55.0%
CTGGGAAGCCACTAGGGATG+TGG - chr8_1:73526641-73526660 Msa1213390:intron 60.0%
! GGTTGGCTGGGAAGCCACTA+GGG - chr8_1:73526647-73526666 Msa1213390:intron 60.0%
! AGGTTGGCTGGGAAGCCACT+AGG - chr8_1:73526648-73526667 Msa1213390:intron 60.0%
Chromosome Type Strat End Strand Name
chr8_1 gene 73526069 73526722 73526069 ID=Msa1213400;Name=Msa1213400
chr8_1 mRNA 73526069 73526722 73526069 ID=Msa1213400-mRNA-1;Parent=Msa1213400;Name=Msa1213400-mRNA-1;_AED=0.10;_eAED=0.35;_QI=0|-1|0|1|-1|1|1|0|217
chr8_1 exon 73526069 73526722 73526069 ID=Msa1213400-mRNA-1:exon:24995;Parent=Msa1213400-mRNA-1
chr8_1 CDS 73526069 73526722 73526069 ID=Msa1213400-mRNA-1:cds;Parent=Msa1213400-mRNA-1
Gene Sequence

>Msa1213400

ATGGTACGCAATGACGAGGAACTCCATGAAGTACCCTATGCTTCCGTAATACAGTACCTTTCCTATCCTTCTCCAACCCAGAAACCCATCATGAACTCAAGCCTGCAAAACCTGGAAAATGGAGAAGGCCATTCTTTGACCCATCTGTATCCATCTCAAGGTTTACATGATATTCCATTTCACTACTCCCAGCTTCACCTCTCTAACGACAGCGACAGTCCCATTCAAATTCCAGACCATAAATCTTCTCCCAACTCATCATCAAACAGTAACAACAACTCTGGTAAAGCAAAGGATCTCCTTGATGATCGAAAGAAGAAAAGGATGTTCTCTAACAGAGAATCTGCTCGTCGGTCGCGAATGAGAAAGAAGCAGCGAATTGAAGTCCTGTGGTATCAAGTGAATCACCTGCAGGCGCTGAACCATCAATTGTCCCAAAAGATCATTTACTTGTTGGAATGTAACCAACTAATCAACCAACAAAATGCTCAACTTAAAGGCAAAGTTTCCTCTCTTCAAGCGGTACTATCTACTTTGTTGGTTACGACCGGAAATGTTGGTATACCTCACCACATCCCTAGTGGCTTCCCAGCCAACCTTTCAACTCGTCTAGTTTCAAACTTACAATTTCCCGAGCATAGCGATTTTGAGTAG
Protein sequence

>Msa1213400

MVRNDEELHEVPYASVIQYLSYPSPTQKPIMNSSLQNLENGEGHSLTHLYPSQGLHDIPFHYSQLHLSNDSDSPIQIPDHKSSPNSSSNSNNNSGKAKDLLDDRKKKRMFSNRESARRSRMRKKQRIEVLWYQVNHLQALNHQLSQKIIYLLECNQLINQQNAQLKGKVSSLQAVLSTLLVTTGNVGIPHHIPSGFPANLSTRLVSNLQFPEHSDFE*