AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0231180


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0231180 MtrunA17_Chr2g0277481 91.503 153 10 1 1 153 1 150 6.85e-101 286
Msa0231180 MtrunA17_Chr8g0380641 61.290 155 46 3 3 153 4 148 3.17e-62 188
Msa0231180 MtrunA17_Chr4g0026331 58.519 135 42 3 28 151 23 154 9.72e-51 159
Msa0231180 MtrunA17_Chr1g0210661 55.705 149 53 4 6 151 15 153 8.20e-50 157
Msa0231180 MtrunA17_Chr1g0210631 55.333 150 58 3 3 151 76 217 8.21e-50 159
Msa0231180 MtrunA17_Chr2g0321501 61.157 121 43 2 32 151 37 154 4.50e-48 152
Msa0231180 MtrunA17_Chr5g0394481 38.947 95 57 1 57 151 50 143 1.61e-17 74.3
Msa0231180 MtrunA17_Chr4g0054691 39.024 82 50 0 70 151 77 158 1.01e-16 73.2
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0231180 AT1G60950.1 64.626 147 47 3 6 151 5 147 4.03e-61 186
Msa0231180 AT1G10960.1 63.699 146 50 2 6 151 5 147 7.72e-55 169
Msa0231180 AT2G27510.1 50.318 157 69 4 1 151 1 154 2.26e-45 146
Msa0231180 AT5G10000.1 43.662 142 75 3 14 151 7 147 1.13e-34 118
Msa0231180 AT4G14890.1 34.043 141 82 3 21 151 5 144 1.28e-18 77.8
Msa0231180 AT1G32550.1 37.037 108 68 0 44 151 46 153 5.81e-18 76.6
Msa0231180 AT1G32550.2 34.677 124 62 3 44 151 46 166 2.78e-12 62.0

Find 34 sgRNAs with CRISPR-Local

Find 39 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TCAAATTCTTGAGTTCCTTC+TGG 0.323416 2_2:+3374392 None:intergenic
GAACCAGCTCTGCATGAGTA+TGG 0.373256 2_2:+3374314 None:intergenic
ATGATCAGATTGAAGAAGGT+TGG 0.396228 2_2:-3374223 Msa0231180:CDS
TTCTTCCTTGTGAGTCTCAA+TGG 0.400867 2_2:+3374163 None:intergenic
TCAAGAATGTAAACATCATC+TGG 0.411090 2_2:+3374365 None:intergenic
GGTTCTTGTTCTTCATGTGC+TGG 0.425033 2_2:-3374296 Msa0231180:CDS
ACCGCTGGGAAAAGCCTTTG+TGG 0.440903 2_2:+3374493 None:intergenic
GCAACCGCACCTGCTTTGTA+TGG 0.461704 2_2:-3374584 Msa0231180:CDS
GTGCTGACTGACACTGGCAT+TGG 0.464692 2_2:+3374527 None:intergenic
TGATCAGATTGAAGAAGGTT+GGG 0.468092 2_2:-3374222 Msa0231180:CDS
CTTCCATACTCATGCAGAGC+TGG 0.477015 2_2:-3374317 Msa0231180:CDS
CTTGACCATGCTGAGGAAGT+TGG 0.477077 2_2:-3374347 Msa0231180:CDS
CATTGGCTGCCTCCTGAGGA+AGG 0.479539 2_2:+3374544 None:intergenic
AGTTGCAATGGCTAGTTACA+AGG 0.482157 2_2:-3374429 Msa0231180:CDS
CAGTGAGCACCTCCTTCCTC+AGG 0.501999 2_2:-3374556 Msa0231180:CDS
AGCCTTTGTGGTTGTTGTGG+TGG 0.506920 2_2:+3374505 None:intergenic
CTTCAATCTGATCATCATCA+AGG 0.519281 2_2:+3374231 None:intergenic
TGTGCTGGCAAAGTTGCTGC+TGG 0.520711 2_2:-3374281 Msa0231180:CDS
AAAAGCCTTTGTGGTTGTTG+TGG 0.532495 2_2:+3374502 None:intergenic
GATGATGATCAGATTGAAGA+AGG 0.539674 2_2:-3374227 Msa0231180:CDS
GTGGTGGTGCTGACTGACAC+TGG 0.553388 2_2:+3374521 None:intergenic
CTGGCATTGGCTGCCTCCTG+AGG 0.569091 2_2:+3374540 None:intergenic
TGGCTGCCTCCTGAGGAAGG+AGG 0.573079 2_2:+3374547 None:intergenic
ACTGCAGTTCCATACAAAGC+AGG 0.605761 2_2:+3374575 None:intergenic
GTGAAGCTTGTTACACCAGA+AGG 0.613290 2_2:-3374407 Msa0231180:CDS
TGAGCACCTCCTTCCTCAGG+AGG 0.621811 2_2:-3374553 Msa0231180:CDS
TGGTGATCTTGCAGTTGCAA+TGG 0.626955 2_2:-3374441 Msa0231180:CDS
AAAAGTAACACAGGAAAGCG+TGG 0.634896 2_2:-3374461 Msa0231180:CDS
TTACATTCTTGACCATGCTG+AGG 0.655914 2_2:-3374354 Msa0231180:CDS
CAATACCAACTTCCTCAGCA+TGG 0.657416 2_2:+3374342 None:intergenic
GGTGAAGTTGATCAGTCAGA+TGG 0.657495 2_2:-3374260 Msa0231180:CDS
CACCACCACAACAACCACAA+AGG 0.670170 2_2:-3374507 Msa0231180:CDS
AGTTCCATACAAAGCAGGTG+CGG 0.688139 2_2:+3374580 None:intergenic
TGTTACCATTGAGACTCACA+AGG 0.695016 2_2:-3374168 Msa0231180:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! TTTGGTTTAAAAAGTAACAC+AGG - chr2_2:3374265-3374284 Msa0231180:CDS 25.0%
TCAAGAATGTAAACATCATC+TGG + chr2_2:3374373-3374392 None:intergenic 30.0%
! CTTTTTAAACCAAAACCGCT+GGG + chr2_2:3374259-3374278 None:intergenic 35.0%
! ACTTTTTAAACCAAAACCGC+TGG + chr2_2:3374260-3374279 None:intergenic 35.0%
TCAAATTCTTGAGTTCCTTC+TGG + chr2_2:3374346-3374365 None:intergenic 35.0%
CTTCAATCTGATCATCATCA+AGG + chr2_2:3374507-3374526 None:intergenic 35.0%
GATGATGATCAGATTGAAGA+AGG - chr2_2:3374508-3374527 Msa0231180:CDS 35.0%
ATGATCAGATTGAAGAAGGT+TGG - chr2_2:3374512-3374531 Msa0231180:CDS 35.0%
TGATCAGATTGAAGAAGGTT+GGG - chr2_2:3374513-3374532 Msa0231180:CDS 35.0%
AAAAGCCTTTGTGGTTGTTG+TGG + chr2_2:3374236-3374255 None:intergenic 40.0%
AAAAGTAACACAGGAAAGCG+TGG - chr2_2:3374274-3374293 Msa0231180:CDS 40.0%
! AGTTGCAATGGCTAGTTACA+AGG - chr2_2:3374306-3374325 Msa0231180:CDS 40.0%
TTACATTCTTGACCATGCTG+AGG - chr2_2:3374381-3374400 Msa0231180:CDS 40.0%
TGTTACCATTGAGACTCACA+AGG - chr2_2:3374567-3374586 Msa0231180:CDS 40.0%
TTCTTCCTTGTGAGTCTCAA+TGG + chr2_2:3374575-3374594 None:intergenic 40.0%
AGTTCCATACAAAGCAGGTG+CGG + chr2_2:3374158-3374177 None:intergenic 45.0%
ACTGCAGTTCCATACAAAGC+AGG + chr2_2:3374163-3374182 None:intergenic 45.0%
TGGTGATCTTGCAGTTGCAA+TGG - chr2_2:3374294-3374313 Msa0231180:CDS 45.0%
!! GTGAAGCTTGTTACACCAGA+AGG - chr2_2:3374328-3374347 Msa0231180:CDS 45.0%
CAATACCAACTTCCTCAGCA+TGG + chr2_2:3374396-3374415 None:intergenic 45.0%
GGTTCTTGTTCTTCATGTGC+TGG - chr2_2:3374439-3374458 Msa0231180:CDS 45.0%
! GGTGAAGTTGATCAGTCAGA+TGG - chr2_2:3374475-3374494 Msa0231180:CDS 45.0%
CACCACCACAACAACCACAA+AGG - chr2_2:3374228-3374247 Msa0231180:CDS 50.0%
AGCCTTTGTGGTTGTTGTGG+TGG + chr2_2:3374233-3374252 None:intergenic 50.0%
! ACCACAAAGGCTTTTCCCAG+CGG - chr2_2:3374241-3374260 Msa0231180:CDS 50.0%
! AAGGCTTTTCCCAGCGGTTT+TGG - chr2_2:3374247-3374266 Msa0231180:CDS 50.0%
CTTGACCATGCTGAGGAAGT+TGG - chr2_2:3374388-3374407 Msa0231180:CDS 50.0%
CTTCCATACTCATGCAGAGC+TGG - chr2_2:3374418-3374437 Msa0231180:CDS 50.0%
GAACCAGCTCTGCATGAGTA+TGG + chr2_2:3374424-3374443 None:intergenic 50.0%
GCAACCGCACCTGCTTTGTA+TGG - chr2_2:3374151-3374170 Msa0231180:CDS 55.0%
!! GTGCTGACTGACACTGGCAT+TGG + chr2_2:3374211-3374230 None:intergenic 55.0%
ACCGCTGGGAAAAGCCTTTG+TGG + chr2_2:3374245-3374264 None:intergenic 55.0%
! TGTGCTGGCAAAGTTGCTGC+TGG - chr2_2:3374454-3374473 Msa0231180:CDS 55.0%
CAGTGAGCACCTCCTTCCTC+AGG - chr2_2:3374179-3374198 Msa0231180:CDS 60.0%
TGAGCACCTCCTTCCTCAGG+AGG - chr2_2:3374182-3374201 Msa0231180:CDS 60.0%
! CATTGGCTGCCTCCTGAGGA+AGG + chr2_2:3374194-3374213 None:intergenic 60.0%
!! GTGGTGGTGCTGACTGACAC+TGG + chr2_2:3374217-3374236 None:intergenic 60.0%
TGGCTGCCTCCTGAGGAAGG+AGG + chr2_2:3374191-3374210 None:intergenic 65.0%
!! CTGGCATTGGCTGCCTCCTG+AGG + chr2_2:3374198-3374217 None:intergenic 65.0%
Chromosome Type Strat End Strand Name
chr2_2 gene 3374148 3374609 3374148 ID=Msa0231180;Name=Msa0231180
chr2_2 mRNA 3374148 3374609 3374148 ID=Msa0231180-mRNA-1;Parent=Msa0231180;Name=Msa0231180-mRNA-1;_AED=0.01;_eAED=0.01;_QI=0|-1|0|1|-1|1|1|0|153
chr2_2 exon 3374148 3374609 3374148 ID=Msa0231180-mRNA-1:exon:1284;Parent=Msa0231180-mRNA-1
chr2_2 CDS 3374148 3374609 3374148 ID=Msa0231180-mRNA-1:cds;Parent=Msa0231180-mRNA-1
Gene Sequence

>Msa0231180

ATGGCAACCGCACCTGCTTTGTATGGAACTGCAGTGAGCACCTCCTTCCTCAGGAGGCAGCCAATGCCAGTGTCAGTCAGCACCACCACAACAACCACAAAGGCTTTTCCCAGCGGTTTTGGTTTAAAAAGTAACACAGGAAAGCGTGGTGATCTTGCAGTTGCAATGGCTAGTTACAAGGTGAAGCTTGTTACACCAGAAGGAACTCAAGAATTTGAATGTCCAGATGATGTTTACATTCTTGACCATGCTGAGGAAGTTGGTATTGAACTTCCATACTCATGCAGAGCTGGTTCTTGTTCTTCATGTGCTGGCAAAGTTGCTGCTGGTGAAGTTGATCAGTCAGATGGTTCTTTCCTTGATGATGATCAGATTGAAGAAGGTTGGGTTCTTACATGTGTTGCTTATGCTAAGTCTGATGTTACCATTGAGACTCACAAGGAAGAAGAACTCACTGCTTAA

Protein sequence

>Msa0231180

MATAPALYGTAVSTSFLRRQPMPVSVSTTTTTTKAFPSGFGLKSNTGKRGDLAVAMASYKVKLVTPEGTQEFECPDDVYILDHAEEVGIELPYSCRAGSCSSCAGKVAAGEVDQSDGSFLDDDQIEEGWVLTCVAYAKSDVTIETHKEEELTA*