AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0496710


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0496710 MtrunA17_Chr5g0404321 59.259 243 29 5 1 175 1 241 4.35e-81 246
Msa0496710 MtrunA17_Chr8g0373001 44.398 241 66 4 1 175 1 239 7.14e-58 186
Msa0496710 MtrunA17_Chr8g0373361 40.598 234 78 7 1 175 11 242 9.83e-45 152
Msa0496710 MtrunA17_Chr1g0155301 37.165 261 76 6 1 175 1 259 2.35e-43 149
Msa0496710 MtrunA17_Chr8g0373331 42.029 207 78 5 1 175 1 197 8.58e-42 143
Msa0496710 MtrunA17_Chr2g0278511 36.145 249 79 8 1 175 1 243 1.08e-36 131
Msa0496710 MtrunA17_Chr1g0201891 35.772 246 81 8 1 175 1 240 1.92e-36 130
Msa0496710 MtrunA17_Chr2g0286441 38.679 212 87 6 4 175 17 225 3.36e-35 127
Msa0496710 MtrunA17_Chr2g0315641 35.577 208 91 4 3 170 19 223 1.21e-32 119
Msa0496710 MtrunA17_Chr1g0156151 36.449 214 66 7 1 146 1 212 1.62e-30 110
Msa0496710 MtrunA17_Chr1g0196071 36.413 184 74 4 27 170 50 230 5.47e-29 110
Msa0496710 MtrunA17_Chr2g0315651 34.021 194 81 4 15 167 25 212 3.68e-27 105
Msa0496710 MtrunA17_Chr8g0373351 38.462 143 55 7 25 163 17 130 2.45e-18 80.1
Msa0496710 MtrunA17_Chr8g0373341 33.645 214 42 8 1 135 1 193 2.03e-13 67.0
Msa0496710 MtrunA17_Chr3g0091401 50.000 70 34 1 64 133 9 77 6.59e-13 62.0
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0496710 AT2G18280.2 39.407 236 77 5 1 175 1 231 5.24e-44 150
Msa0496710 AT2G18280.1 39.407 236 77 5 1 175 1 231 5.24e-44 150
Msa0496710 AT1G25280.1 38.498 213 89 3 5 175 37 249 3.58e-39 138
Msa0496710 AT1G76900.2 35.968 253 78 9 1 175 1 247 1.23e-35 129
Msa0496710 AT1G76900.1 35.968 253 78 9 1 175 1 247 1.23e-35 129
Msa0496710 AT1G76900.3 35.968 253 78 9 1 175 1 247 1.23e-35 129
Msa0496710 AT1G47270.3 39.444 180 58 4 27 165 44 213 1.53e-32 120
Msa0496710 AT1G47270.1 39.444 180 58 4 27 165 69 238 1.89e-32 120
Msa0496710 AT1G47270.2 39.444 180 58 4 27 165 68 237 1.99e-32 120
Msa0496710 AT2G47900.2 37.368 190 76 3 27 175 52 239 1.84e-31 117
Msa0496710 AT2G47900.1 37.368 190 76 3 27 175 52 239 1.84e-31 117
Msa0496710 AT2G47900.3 37.173 191 76 3 27 175 52 240 2.45e-31 117
Msa0496710 AT1G43640.1 33.673 196 84 5 23 175 51 243 4.80e-31 116
Msa0496710 AT1G53320.1 35.979 189 79 3 27 175 44 230 3.47e-30 113
Msa0496710 AT1G43640.2 33.889 180 73 5 39 175 1 177 4.17e-26 102
Msa0496710 AT3G06380.1 33.333 222 95 7 1 175 1 216 8.02e-26 102
Msa0496710 AT5G18680.1 36.126 191 78 4 26 175 38 225 1.85e-25 101
Msa0496710 AT1G61940.2 40.964 83 43 1 33 109 4 86 2.00e-15 72.4
Msa0496710 AT1G25280.3 52.239 67 31 1 110 175 5 71 6.30e-12 62.8
Msa0496710 AT1G25280.2 52.239 67 31 1 110 175 5 71 6.30e-12 62.8
Msa0496710 AT1G61940.1 46.552 58 25 1 33 84 4 61 4.24e-11 60.1

Find 52 sgRNAs with CRISPR-Local

Find 67 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
AAAACTCAGGTCTAACATTT+TGG 0.098131 3_4:-28221922 Msa0496710:CDS
CTCCTACTGGACCGGCTATT+TGG 0.181607 3_4:+28221840 None:intergenic
CCAGTAGGAGATTTCTTTCT+AGG 0.241845 3_4:-28221827 Msa0496710:CDS
TCCTATTTCGTTAAATCAGC+TGG 0.277516 3_4:-28222154 Msa0496710:CDS
TAGCTATATGCTTGAACTCT+TGG 0.354614 3_4:+28221795 None:intergenic
CGTCAACCTTCCACACTCTT+CGG 0.358084 3_4:+28222179 None:intergenic
GTCAACCTTCCACACTCTTC+GGG 0.361120 3_4:+28222180 None:intergenic
CCCAGCTGATTTAACGAAAT+AGG 0.367273 3_4:+28222153 None:intergenic
TAGAAGAGACTGAGACTTCT+TGG 0.372030 3_4:-28222263 Msa0496710:CDS
GTGCTCCTGTGTGTGAATCA+TGG 0.450066 3_4:-28222233 Msa0496710:CDS
AGGCAACCTCCACATGGATC+TGG 0.456221 3_4:-28221870 Msa0496710:CDS
ATACAATGCTATGCTTCATC+AGG 0.460680 3_4:-28222114 Msa0496710:CDS
ATATGAGCAATTCAGCTCAT+AGG 0.461752 3_4:+28221756 None:intergenic
ACCAATTTAGCAGGGACAAT+GGG 0.465957 3_4:-28222328 Msa0496710:intron
TAGGAGATTTCTTTCTAGGC+AGG 0.469861 3_4:-28221823 Msa0496710:CDS
AACTCAAGGAGATGAGGGAT+GGG 0.484739 3_4:-28222446 Msa0496710:CDS
CGTTCCAGCAATGCGTATGT+TGG 0.488866 3_4:-28221945 Msa0496710:CDS
CCTATTTCGTTAAATCAGCT+GGG 0.495267 3_4:-28222153 Msa0496710:CDS
GAACTCAAGGAGATGAGGGA+TGG 0.505860 3_4:-28222447 Msa0496710:CDS
TGTTGTTGAGAAGCATAGTA+CGG 0.514474 3_4:-28222470 Msa0496710:CDS
CCTAGAAAGAAATCTCCTAC+TGG 0.516235 3_4:+28221827 None:intergenic
TCACTATATACGACATTGAC+AGG 0.521151 3_4:-28221890 Msa0496710:CDS
AAAGAAATCTCCTACTGGAC+CGG 0.552476 3_4:+28221832 None:intergenic
AAGCATAGTACGGGAACTCA+AGG 0.555180 3_4:-28222460 Msa0496710:CDS
AAGGAGATGAGGGATGGGAT+TGG 0.557067 3_4:-28222441 Msa0496710:CDS
TGCTACTTGATATAATTCGA+AGG 0.558581 3_4:-28222287 Msa0496710:CDS
AACCAATTTAGCAGGGACAA+TGG 0.568016 3_4:-28222329 Msa0496710:intron
AATGTCGTATATAGTGAACT+TGG 0.574240 3_4:+28221896 None:intergenic
GCTACTTGATATAATTCGAA+GGG 0.575810 3_4:-28222286 Msa0496710:CDS
GTTGTTGAGAAGCATAGTAC+GGG 0.578798 3_4:-28222469 Msa0496710:CDS
CTGGAATTCAACCAAATAGC+CGG 0.579251 3_4:-28221851 Msa0496710:CDS
CAATGCTATGCTTCATCAGG+AGG 0.579693 3_4:-28222111 Msa0496710:CDS
GATGAAGCATAGCATTGTAT+CGG 0.589668 3_4:+28222117 None:intergenic
TACGGGAACTCAAGGAGATG+AGG 0.591073 3_4:-28222452 Msa0496710:CDS
CTGAACAATCTCTTGTGTAA+CGG 0.594307 3_4:+28222206 None:intergenic
ACGGGAACTCAAGGAGATGA+GGG 0.594362 3_4:-28222451 Msa0496710:CDS
ATGCGTATGTTGGAAAACTC+AGG 0.599772 3_4:-28221935 Msa0496710:CDS
AGCAATTCAGCTCATAGGAA+TGG 0.600877 3_4:+28221761 None:intergenic
AGACTCCCGAAGAGTGTGGA+AGG 0.609764 3_4:-28222185 Msa0496710:CDS
TCACACACAGGAGCACAAGA+AGG 0.618611 3_4:+28222240 None:intergenic
TCCTGTGTGTGAATCATGGA+GGG 0.620710 3_4:-28222229 Msa0496710:CDS
AATGCTATGCTTCATCAGGA+GGG 0.642327 3_4:-28222110 Msa0496710:CDS
GTTCAGACTCCCGAAGAGTG+TGG 0.642949 3_4:-28222189 Msa0496710:CDS
CATTGTATCGGAGAATCACA+AGG 0.642959 3_4:+28222129 None:intergenic
GCCCTCCATGATTCACACAC+AGG 0.647670 3_4:+28222228 None:intergenic
ATTGGTAATACGTCGAGGAG+AGG 0.649495 3_4:-28222423 Msa0496710:CDS
CTCCTGTGTGTGAATCATGG+AGG 0.651561 3_4:-28222230 Msa0496710:CDS
ATTGACAGGCAACCTCCACA+TGG 0.655106 3_4:-28221876 Msa0496710:CDS
AACCAAATAGCCGGTCCAGT+AGG 0.657951 3_4:-28221842 Msa0496710:CDS
TGAATTCCAGATCCATGTGG+AGG 0.693280 3_4:+28221864 None:intergenic
ATGGGATTGGTAATACGTCG+AGG 0.700501 3_4:-28222428 Msa0496710:CDS
GGTTGAATTCCAGATCCATG+TGG 0.703182 3_4:+28221861 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
! TGCTACTTGATATAATTCGA+AGG - chr3_4:28221951-28221970 Msa0496710:CDS 30.0%
GCTACTTGATATAATTCGAA+GGG - chr3_4:28221952-28221971 Msa0496710:CDS 30.0%
TCTGCGTATCTATTGTATTA+TGG - chr3_4:28222162-28222181 Msa0496710:CDS 30.0%
GTATCTATTGTATTATGGAC+TGG - chr3_4:28222167-28222186 Msa0496710:CDS 30.0%
! CTTATAGTCTCATTTTCCAA+TGG + chr3_4:28222195-28222214 None:intergenic 30.0%
TATTAGCTGCCAAAAAGATA+AGG - chr3_4:28222219-28222238 Msa0496710:CDS 30.0%
CACAGACTTAATCATATCTA+TGG - chr3_4:28222253-28222272 Msa0496710:CDS 30.0%
! AAAACTCAGGTCTAACATTT+TGG - chr3_4:28222316-28222335 Msa0496710:CDS 30.0%
! AAACTCAGGTCTAACATTTT+GGG - chr3_4:28222317-28222336 Msa0496710:CDS 30.0%
AATGTCGTATATAGTGAACT+TGG + chr3_4:28222345-28222364 None:intergenic 30.0%
! TGTTGTTGAGAAGCATAGTA+CGG - chr3_4:28221768-28221787 Msa0496710:CDS 35.0%
ATCACTTGAACCAATTTAGC+AGG - chr3_4:28221901-28221920 Msa0496710:CDS 35.0%
TCACTTGAACCAATTTAGCA+GGG - chr3_4:28221902-28221921 Msa0496710:CDS 35.0%
CTGAACAATCTCTTGTGTAA+CGG + chr3_4:28222035-28222054 None:intergenic 35.0%
TCCTATTTCGTTAAATCAGC+TGG - chr3_4:28222084-28222103 Msa0496710:intron 35.0%
CCTATTTCGTTAAATCAGCT+GGG - chr3_4:28222085-28222104 Msa0496710:CDS 35.0%
GATGAAGCATAGCATTGTAT+CGG + chr3_4:28222124-28222143 None:intergenic 35.0%
ATACAATGCTATGCTTCATC+AGG - chr3_4:28222124-28222143 Msa0496710:CDS 35.0%
AAAAAGATAAGGAAGACAGC+CGG - chr3_4:28222230-28222249 Msa0496710:CDS 35.0%
AGATATGATTAAGTCTGTGC+CGG + chr3_4:28222252-28222271 None:intergenic 35.0%
TCACTATATACGACATTGAC+AGG - chr3_4:28222348-28222367 Msa0496710:intron 35.0%
TAGCTATATGCTTGAACTCT+TGG + chr3_4:28222446-28222465 None:intergenic 35.0%
! GTTGTTGAGAAGCATAGTAC+GGG - chr3_4:28221769-28221788 Msa0496710:CDS 40.0%
AACCAATTTAGCAGGGACAA+TGG - chr3_4:28221909-28221928 Msa0496710:CDS 40.0%
ACCAATTTAGCAGGGACAAT+GGG - chr3_4:28221910-28221929 Msa0496710:CDS 40.0%
TAGAAGAGACTGAGACTTCT+TGG - chr3_4:28221975-28221994 Msa0496710:intron 40.0%
! CCCAGCTGATTTAACGAAAT+AGG + chr3_4:28222088-28222107 None:intergenic 40.0%
CATTGTATCGGAGAATCACA+AGG + chr3_4:28222112-28222131 None:intergenic 40.0%
AATGCTATGCTTCATCAGGA+GGG - chr3_4:28222128-28222147 Msa0496710:CDS 40.0%
! GGCTGTCTTCCTTATCTTTT+TGG + chr3_4:28222231-28222250 None:intergenic 40.0%
! TTTTCCAACATACGCATTGC+TGG + chr3_4:28222300-28222319 None:intergenic 40.0%
ATGCGTATGTTGGAAAACTC+AGG - chr3_4:28222303-28222322 Msa0496710:CDS 40.0%
CTGGAATTCAACCAAATAGC+CGG - chr3_4:28222387-28222406 Msa0496710:intron 40.0%
AAAGAAATCTCCTACTGGAC+CGG + chr3_4:28222409-28222428 None:intergenic 40.0%
CCTAGAAAGAAATCTCCTAC+TGG + chr3_4:28222414-28222433 None:intergenic 40.0%
CCAGTAGGAGATTTCTTTCT+AGG - chr3_4:28222411-28222430 Msa0496710:intron 40.0%
TAGGAGATTTCTTTCTAGGC+AGG - chr3_4:28222415-28222434 Msa0496710:intron 40.0%
AAGCATAGTACGGGAACTCA+AGG - chr3_4:28221778-28221797 Msa0496710:CDS 45.0%
AACTCAAGGAGATGAGGGAT+GGG - chr3_4:28221792-28221811 Msa0496710:CDS 45.0%
! ATGGGATTGGTAATACGTCG+AGG - chr3_4:28221810-28221829 Msa0496710:CDS 45.0%
! ATTGGTAATACGTCGAGGAG+AGG - chr3_4:28221815-28221834 Msa0496710:CDS 45.0%
ACCCATTGTCCCTGCTAAAT+TGG + chr3_4:28221914-28221933 None:intergenic 45.0%
TCCTGTGTGTGAATCATGGA+GGG - chr3_4:28222009-28222028 Msa0496710:intron 45.0%
CAATGCTATGCTTCATCAGG+AGG - chr3_4:28222127-28222146 Msa0496710:CDS 45.0%
!! GTATTATGGACTGGTGCCAT+TGG - chr3_4:28222176-28222195 Msa0496710:CDS 45.0%
TGAATTCCAGATCCATGTGG+AGG + chr3_4:28222377-28222396 None:intergenic 45.0%
GGTTGAATTCCAGATCCATG+TGG + chr3_4:28222380-28222399 None:intergenic 45.0%
TACGGGAACTCAAGGAGATG+AGG - chr3_4:28221786-28221805 Msa0496710:CDS 50.0%
ACGGGAACTCAAGGAGATGA+GGG - chr3_4:28221787-28221806 Msa0496710:CDS 50.0%
GAACTCAAGGAGATGAGGGA+TGG - chr3_4:28221791-28221810 Msa0496710:CDS 50.0%
AAGGAGATGAGGGATGGGAT+TGG - chr3_4:28221797-28221816 Msa0496710:CDS 50.0%
TAATACGTCGAGGAGAGGTG+TGG - chr3_4:28221820-28221839 Msa0496710:CDS 50.0%
! AATACGTCGAGGAGAGGTGT+GGG - chr3_4:28221821-28221840 Msa0496710:CDS 50.0%
! TCACACACAGGAGCACAAGA+AGG + chr3_4:28222001-28222020 None:intergenic 50.0%
GTGCTCCTGTGTGTGAATCA+TGG - chr3_4:28222005-28222024 Msa0496710:intron 50.0%
CTCCTGTGTGTGAATCATGG+AGG - chr3_4:28222008-28222027 Msa0496710:intron 50.0%
GTCAACCTTCCACACTCTTC+GGG + chr3_4:28222061-28222080 None:intergenic 50.0%
CGTCAACCTTCCACACTCTT+CGG + chr3_4:28222062-28222081 None:intergenic 50.0%
CGTTCCAGCAATGCGTATGT+TGG - chr3_4:28222293-28222312 Msa0496710:CDS 50.0%
ATTGACAGGCAACCTCCACA+TGG - chr3_4:28222362-28222381 Msa0496710:intron 50.0%
AACCAAATAGCCGGTCCAGT+AGG - chr3_4:28222396-28222415 Msa0496710:intron 50.0%
GCCCTCCATGATTCACACAC+AGG + chr3_4:28222013-28222032 None:intergenic 55.0%
GTTCAGACTCCCGAAGAGTG+TGG - chr3_4:28222049-28222068 Msa0496710:intron 55.0%
! AGACTCCCGAAGAGTGTGGA+AGG - chr3_4:28222053-28222072 Msa0496710:intron 55.0%
AGGCAACCTCCACATGGATC+TGG - chr3_4:28222368-28222387 Msa0496710:intron 55.0%
CTCCTACTGGACCGGCTATT+TGG + chr3_4:28222401-28222420 None:intergenic 55.0%
! CGAGGAGAGGTGTGGGTAGT+AGG - chr3_4:28221828-28221847 Msa0496710:CDS 60.0%
Chromosome Type Strat End Strand Name
chr3_4 gene 28221767 28222493 28221767 ID=Msa0496710;Name=Msa0496710
chr3_4 mRNA 28221767 28222493 28221767 ID=Msa0496710-mRNA-1;Parent=Msa0496710;Name=Msa0496710-mRNA-1;_AED=0.30;_eAED=0.30;_QI=0|0|0|1|1|1|3|0|178
chr3_4 exon 28222422 28222493 28222422 ID=Msa0496710-mRNA-1:exon:6574;Parent=Msa0496710-mRNA-1
chr3_4 exon 28222085 28222337 28222085 ID=Msa0496710-mRNA-1:exon:6573;Parent=Msa0496710-mRNA-1
chr3_4 exon 28221767 28221978 28221767 ID=Msa0496710-mRNA-1:exon:6572;Parent=Msa0496710-mRNA-1
chr3_4 CDS 28222422 28222493 28222422 ID=Msa0496710-mRNA-1:cds;Parent=Msa0496710-mRNA-1
chr3_4 CDS 28222085 28222337 28222085 ID=Msa0496710-mRNA-1:cds;Parent=Msa0496710-mRNA-1
chr3_4 CDS 28221767 28221978 28221767 ID=Msa0496710-mRNA-1:cds;Parent=Msa0496710-mRNA-1
Gene Sequence

>Msa0496710

ATGTTGTTGAGAAGCATAGTACGGGAACTCAAGGAGATGAGGGATGGGATTGGTAATACGTCGAGGAGAGGTGGACAATGGGTGAATATACAATCTGAATTGCTACTTGATATAATTCGAAGGGTAGAAGAGACTGAGACTTCTTGGCCTTCTTGTGCTCCTGTGTGTGAATCATGGAGGGCCGTTACACAAGAGATTGTTCAGACTCCCGAAGAGTGTGGAAGGTTGACGTTTCCTATTTCGTTAAATCAGCTGGGTCCTTGTGATTCTCCGATACAATGCTATGCTTCATCAGGAGGGATAGAGAAACTTCTGCGTATCTATTTCGATTTTTCTCGTTCCAGCAATGCGTATGTTGGAAAACTCAGGTCTAACATTTTGGGAACCAAGTTCACTATATACGACATTGACAGGCAACCTCCACATGGATCTGGAATTCAACCAAATAGCCGGTCCAGTAGGAGATTTCTTTCTAGGCAGGTGTCTCCAAGAGTTCAAGCATATAGCTATATTGTTAGCACCATTCCTATGAGCTGA

Protein sequence

>Msa0496710

MLLRSIVRELKEMRDGIGNTSRRGGQWVNIQSELLLDIIRRVEETETSWPSCAPVCESWRAVTQEIVQTPEECGRLTFPISLNQLGPCDSPIQCYASSGGIEKLLRIYFDFSRSSNAYVGKLRSNILGTKFTIYDIDRQPPHGSGIQPNSRSSRRFLSRQVSPRVQAYSYIVSTIPMS*