AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1394160


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1394160 MtrunA17_Chr4g0016701 98.785 247 1 1 1 247 1 245 1.77e-175 482
Msa1394160 MtrunA17_CPg0492981 98.785 247 1 1 1 247 1 245 1.77e-175 482
Msa1394160 MtrunA17_Chr4g0015611 98.785 247 1 1 1 247 1 245 1.77e-175 482
Msa1394160 MtrunA17_Chr3g0088491 92.661 218 11 1 30 247 2 214 1.10e-129 365
Msa1394160 MtrunA17_Chr7g0275151 73.494 166 11 1 82 247 2 134 1.65e-76 228
Msa1394160 MtrunA17_Chr4g0060751 67.273 165 8 1 83 247 11 129 1.10e-64 197
Msa1394160 MtrunA17_Chr6g0460191 74.468 94 24 0 154 247 8 101 1.73e-28 103
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1394160 ATCG00150.1 91.165 249 20 1 1 247 1 249 1.75e-151 422

Find 45 sgRNAs with CRISPR-Local

Find 57 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TCCTATACCTGTTATGTTTC+TGG 0.052609 tig0021785:-73023 Msa1394160:CDS
CAACATTTCTATTGGCAAAT+AGG 0.196864 tig0021785:-73589 Msa1394160:CDS
AACATTTCTATTGGCAAATA+GGG 0.237546 tig0021785:-73588 Msa1394160:CDS
CTAAGATGTTAATCGGTAAA+AGG 0.238850 tig0021785:+73149 None:intergenic
GGTCCGTGGGTTCCGTTTAT+TGG 0.248543 tig0021785:-73385 Msa1394160:CDS
TGAAATACCCGCATAGAAAT+AGG 0.255569 tig0021785:+73219 None:intergenic
CCTATACCTGTTATGTTTCT+GGG 0.293135 tig0021785:-73022 Msa1394160:CDS
CTCAAGTACTTATTACCTCT+TGG 0.341108 tig0021785:-73549 Msa1394160:CDS
CGGATTTCTAACAACTAGAA+TGG 0.400438 tig0021785:+73498 None:intergenic
AAATCTTCTAAGATGTTAAT+CGG 0.412258 tig0021785:+73142 None:intergenic
ACCTTAGCTGCGGCTTATAT+AGG 0.418344 tig0021785:-72962 Msa1394160:CDS
AGTAGTATTTATATCATTTG+TGG 0.424401 tig0021785:+73270 None:intergenic
TCAAGTACTTATTACCTCTT+GGG 0.428139 tig0021785:-73548 Msa1394160:CDS
GTAGTATTTATATCATTTGT+GGG 0.434707 tig0021785:+73271 None:intergenic
AAGTCGAAAACTAAGTGATA+AGG 0.438506 tig0021785:+73111 None:intergenic
AGAAACAAAGTTCCAATAAA+CGG 0.439134 tig0021785:+73373 None:intergenic
ACTCAGATTGGAGAAGAATA+TGG 0.441550 tig0021785:-73406 Msa1394160:CDS
AATAATCCCAGAAACATAAC+AGG 0.443207 tig0021785:+73016 None:intergenic
CCCAGAAACATAACAGGTAT+AGG 0.450475 tig0021785:+73022 None:intergenic
CCGGACGTTGGAATAGTTTG+CGG 0.455395 tig0021785:+73478 None:intergenic
AAGTAGGTCAACATTTCTAT+TGG 0.460455 tig0021785:-73597 Msa1394160:CDS
GGCTTATATAGGTGAATCTA+TGG 0.463562 tig0021785:-72951 Msa1394160:CDS
TCACGTCTCGGATGAATTCA+AGG 0.477047 tig0021785:+73434 None:intergenic
ATCGGTAAAAGGATTGGAGT+TGG 0.490463 tig0021785:+73160 None:intergenic
GATATATCTGCTGTCGAAGT+AGG 0.493921 tig0021785:-73613 Msa1394160:CDS
AGTCGAAAACTAAGTGATAA+GGG 0.500280 tig0021785:+73112 None:intergenic
GACGTGAGCAAAACTCAGAT+TGG 0.510359 tig0021785:-73418 Msa1394160:CDS
GTAAAAGGATTGGAGTTGGT+TGG 0.515104 tig0021785:+73164 None:intergenic
AAAATTATAAAGTTACCTCA+TGG 0.526541 tig0021785:-73307 Msa1394160:CDS
ACCTATATAAGCCGCAGCTA+AGG 0.529655 tig0021785:+72961 None:intergenic
ATGTTAATCGGTAAAAGGAT+TGG 0.530907 tig0021785:+73154 None:intergenic
CCGCAAACTATTCCAACGTC+CGG 0.541897 tig0021785:-73478 Msa1394160:CDS
AAGAAATTCTGACCGGACGT+TGG 0.546490 tig0021785:+73466 None:intergenic
TCAGTAGCCTATTTCTATGC+GGG 0.553188 tig0021785:-73226 Msa1394160:CDS
ACATTTCTATTGGCAAATAG+GGG 0.561596 tig0021785:-73587 Msa1394160:CDS
ACAGGTATAGGAACTACTAA+AGG 0.585481 tig0021785:+73034 None:intergenic
TATATAGGTGAATCTATGGA+AGG 0.605539 tig0021785:-72947 Msa1394160:CDS
TGGAGAAGAATATGGTCCGT+GGG 0.620080 tig0021785:-73398 Msa1394160:CDS
TTGGAGAAGAATATGGTCCG+TGG 0.620994 tig0021785:-73399 Msa1394160:CDS
TTTCTGGGATTATTTACAAG+CGG 0.630473 tig0021785:-73007 Msa1394160:CDS
ATATTCAAAGAAATTCTGAC+CGG 0.632509 tig0021785:+73459 None:intergenic
GTTCCAATAAACGGAACCCA+CGG 0.647484 tig0021785:+73382 None:intergenic
GTCAGTAGCCTATTTCTATG+CGG 0.655321 tig0021785:-73227 Msa1394160:CDS
GATAGCAATTACAACCCAAG+AGG 0.659110 tig0021785:+73534 None:intergenic
GGTGCAGCTAATTCTCCATG+AGG 0.714976 tig0021785:+73292 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! TATTTATTTTTGTTTCGAAT+TGG - tig0021785:73244-73263 Msa1394160:CDS 15.0%
!! AAAATTATAAAGTTACCTCA+TGG - tig0021785:73288-73307 Msa1394160:CDS 20.0%
!! GTAGTATTTATATCATTTGT+GGG + tig0021785:73327-73346 None:intergenic 20.0%
!! AGTAGTATTTATATCATTTG+TGG + tig0021785:73328-73347 None:intergenic 20.0%
!!! AAATCTTCTAAGATGTTAAT+CGG + tig0021785:73456-73475 None:intergenic 20.0%
! AACATTTCTATTGGCAAATA+GGG - tig0021785:73007-73026 Msa1394160:CDS 25.0%
! ATATTCAAAGAAATTCTGAC+CGG + tig0021785:73139-73158 None:intergenic 25.0%
! AGAAACAAAGTTCCAATAAA+CGG + tig0021785:73225-73244 None:intergenic 25.0%
!! GGTAACTTTATAATTTTCCA+AGG + tig0021785:73285-73304 None:intergenic 25.0%
!!! AAAAAAGGATTGGCTTATTT+TGG - tig0021785:73399-73418 Msa1394160:CDS 25.0%
AAGTAGGTCAACATTTCTAT+TGG - tig0021785:72998-73017 Msa1394160:CDS 30.0%
CAACATTTCTATTGGCAAAT+AGG - tig0021785:73006-73025 Msa1394160:CDS 30.0%
ACATTTCTATTGGCAAATAG+GGG - tig0021785:73008-73027 Msa1394160:CDS 30.0%
TCAAGTACTTATTACCTCTT+GGG - tig0021785:73047-73066 Msa1394160:CDS 30.0%
!! ATTTTTGTTTCGAATTGGTC+AGG - tig0021785:73249-73268 Msa1394160:CDS 30.0%
!! TTTTTGTTTCGAATTGGTCA+GGG - tig0021785:73250-73269 Msa1394160:CDS 30.0%
TATGCGGGTATTTCAAAAAA+AGG - tig0021785:73384-73403 Msa1394160:CDS 30.0%
GGGTATTTCAAAAAAAGGAT+TGG - tig0021785:73389-73408 Msa1394160:CDS 30.0%
ATGTTAATCGGTAAAAGGAT+TGG + tig0021785:73444-73463 None:intergenic 30.0%
CTAAGATGTTAATCGGTAAA+AGG + tig0021785:73449-73468 None:intergenic 30.0%
AGTCGAAAACTAAGTGATAA+GGG + tig0021785:73486-73505 None:intergenic 30.0%
AAGTCGAAAACTAAGTGATA+AGG + tig0021785:73487-73506 None:intergenic 30.0%
!! TCACTTAGTTTTCGACTTTT+CGG - tig0021785:73489-73508 Msa1394160:CDS 30.0%
AATAATCCCAGAAACATAAC+AGG + tig0021785:73582-73601 None:intergenic 30.0%
!! TTTCTGGGATTATTTACAAG+CGG - tig0021785:73588-73607 Msa1394160:CDS 30.0%
TATATAGGTGAATCTATGGA+AGG - tig0021785:73648-73667 Msa1394160:CDS 30.0%
CTCAAGTACTTATTACCTCT+TGG - tig0021785:73046-73065 Msa1394160:CDS 35.0%
CGGATTTCTAACAACTAGAA+TGG + tig0021785:73100-73119 None:intergenic 35.0%
ACTCAGATTGGAGAAGAATA+TGG - tig0021785:73189-73208 Msa1394160:CDS 35.0%
!! TTTTGTTTCGAATTGGTCAG+GGG - tig0021785:73251-73270 Msa1394160:CDS 35.0%
TGAAATACCCGCATAGAAAT+AGG + tig0021785:73379-73398 None:intergenic 35.0%
ACAGGTATAGGAACTACTAA+AGG + tig0021785:73564-73583 None:intergenic 35.0%
TCCTATACCTGTTATGTTTC+TGG - tig0021785:73572-73591 Msa1394160:CDS 35.0%
CCTATACCTGTTATGTTTCT+GGG - tig0021785:73573-73592 Msa1394160:CDS 35.0%
!! TATTTTTGCTACCTTAGCTG+CGG - tig0021785:73623-73642 Msa1394160:CDS 35.0%
GGCTTATATAGGTGAATCTA+TGG - tig0021785:73644-73663 Msa1394160:CDS 35.0%
GATATATCTGCTGTCGAAGT+AGG - tig0021785:72982-73001 Msa1394160:CDS 40.0%
GATAGCAATTACAACCCAAG+AGG + tig0021785:73064-73083 None:intergenic 40.0%
!! GTCAGTAGCCTATTTCTATG+CGG - tig0021785:73368-73387 Msa1394160:CDS 40.0%
!! TCAGTAGCCTATTTCTATGC+GGG - tig0021785:73369-73388 Msa1394160:CDS 40.0%
! GTAAAAGGATTGGAGTTGGT+TGG + tig0021785:73434-73453 None:intergenic 40.0%
ATCGGTAAAAGGATTGGAGT+TGG + tig0021785:73438-73457 None:intergenic 40.0%
CCCAGAAACATAACAGGTAT+AGG + tig0021785:73576-73595 None:intergenic 40.0%
AAGAAATTCTGACCGGACGT+TGG + tig0021785:73132-73151 None:intergenic 45.0%
TCACGTCTCGGATGAATTCA+AGG + tig0021785:73164-73183 None:intergenic 45.0%
! TCTGAGTTTTGCTCACGTCT+CGG + tig0021785:73176-73195 None:intergenic 45.0%
GACGTGAGCAAAACTCAGAT+TGG - tig0021785:73177-73196 Msa1394160:CDS 45.0%
TTGGAGAAGAATATGGTCCG+TGG - tig0021785:73196-73215 Msa1394160:CDS 45.0%
TGGAGAAGAATATGGTCCGT+GGG - tig0021785:73197-73216 Msa1394160:CDS 45.0%
GTTCCAATAAACGGAACCCA+CGG + tig0021785:73216-73235 None:intergenic 45.0%
ACCTTAGCTGCGGCTTATAT+AGG - tig0021785:73633-73652 Msa1394160:CDS 45.0%
ACCTATATAAGCCGCAGCTA+AGG + tig0021785:73637-73656 None:intergenic 45.0%
CCGGACGTTGGAATAGTTTG+CGG + tig0021785:73120-73139 None:intergenic 50.0%
CCGCAAACTATTCCAACGTC+CGG - tig0021785:73117-73136 Msa1394160:CDS 50.0%
GGTGCAGCTAATTCTCCATG+AGG + tig0021785:73306-73325 None:intergenic 50.0%
GGTCCGTGGGTTCCGTTTAT+TGG - tig0021785:73210-73229 Msa1394160:CDS 55.0%
! GGTCAGGGGCTCTTTTGCCT+TGG - tig0021785:73265-73284 Msa1394160:CDS 60.0%
Chromosome Type Strat End Strand Name
tig0021785 gene 72937 73680 72937 ID=Msa1394160;Name=Msa1394160
tig0021785 mRNA 72937 73680 72937 ID=Msa1394160-mRNA-1;Parent=Msa1394160;Name=Msa1394160-mRNA-1;_AED=0.44;_eAED=0.44;_QI=0|-1|0|1|-1|1|1|0|247
tig0021785 exon 72937 73680 72937 ID=Msa1394160-mRNA-1:exon:14202;Parent=Msa1394160-mRNA-1
tig0021785 CDS 72937 73680 72937 ID=Msa1394160-mRNA-1:cds;Parent=Msa1394160-mRNA-1
Gene Sequence

>Msa1394160

ATGAATGTTCTATTATGTTACATCAACACATTAAACAGATTCTATGATATATCTGCTGTCGAAGTAGGTCAACATTTCTATTGGCAAATAGGGGATTTTCAAGTGCATGCTCAAGTACTTATTACCTCTTGGGTTGTAATTGCTATCTTATTAATTTCAACCATTCTAGTTGTTAGAAATCCGCAAACTATTCCAACGTCCGGTCAGAATTTCTTTGAATATGTCCTTGAATTCATCCGAGACGTGAGCAAAACTCAGATTGGAGAAGAATATGGTCCGTGGGTTCCGTTTATTGGAACTTTGTTTCTATTTATTTTTGTTTCGAATTGGTCAGGGGCTCTTTTGCCTTGGAAAATTATAAAGTTACCTCATGGAGAATTAGCTGCACCCACAAATGATATAAATACTACTGTTGCATTAGCTTTACTTACGTCAGTAGCCTATTTCTATGCGGGTATTTCAAAAAAAGGATTGGCTTATTTTGGTAAATACATCCAACCAACTCCAATCCTTTTACCGATTAACATCTTAGAAGATTTCACAAAACCCTTATCACTTAGTTTTCGACTTTTCGGAAATATATTAGCTGATGAATTAGTAGTTGTTGTTCTTGTTTCGTTAGTACCTTTAGTAGTTCCTATACCTGTTATGTTTCTGGGATTATTTACAAGCGGTATTCAAGCTCTTATTTTTGCTACCTTAGCTGCGGCTTATATAGGTGAATCTATGGAAGGCCATCATTGA

Protein sequence

>Msa1394160

MNVLLCYINTLNRFYDISAVEVGQHFYWQIGDFQVHAQVLITSWVVIAILLISTILVVRNPQTIPTSGQNFFEYVLEFIRDVSKTQIGEEYGPWVPFIGTLFLFIFVSNWSGALLPWKIIKLPHGELAAPTNDINTTVALALLTSVAYFYAGISKKGLAYFGKYIQPTPILLPINILEDFTKPLSLSFRLFGNILADELVVVVLVSLVPLVVPIPVMFLGLFTSGIQALIFATLAAAYIGESMEGHH*