AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1143170


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1143170 MtrunA17_Chr4g0016701 98.785 247 1 1 1 247 1 245 1.77e-175 482
Msa1143170 MtrunA17_CPg0492981 98.785 247 1 1 1 247 1 245 1.77e-175 482
Msa1143170 MtrunA17_Chr4g0015611 98.785 247 1 1 1 247 1 245 1.77e-175 482
Msa1143170 MtrunA17_Chr3g0088491 92.661 218 11 1 30 247 2 214 1.10e-129 365
Msa1143170 MtrunA17_Chr7g0275151 73.494 166 11 1 82 247 2 134 1.65e-76 228
Msa1143170 MtrunA17_Chr4g0060751 67.273 165 8 1 83 247 11 129 1.10e-64 197
Msa1143170 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
Msa1143170 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 7_4:-18360737 Msa1143170:CDS
CAACATTTCTATTGGCAAAT+AGG 0.196864 7_4:-18361303 Msa1143170:CDS
AACATTTCTATTGGCAAATA+GGG 0.237546 7_4:-18361302 Msa1143170:CDS
CTAAGATGTTAATCGGTAAA+AGG 0.238850 7_4:+18360863 None:intergenic
GGTCCGTGGGTTCCGTTTAT+TGG 0.248543 7_4:-18361099 Msa1143170:CDS
TGAAATACCCGCATAGAAAT+AGG 0.255569 7_4:+18360933 None:intergenic
CCTATACCTGTTATGTTTCT+GGG 0.293135 7_4:-18360736 Msa1143170:CDS
CTCAAGTACTTATTACCTCT+TGG 0.341108 7_4:-18361263 Msa1143170:CDS
CGGATTTCTAACAACTAGAA+TGG 0.400438 7_4:+18361212 None:intergenic
AAATCTTCTAAGATGTTAAT+CGG 0.412258 7_4:+18360856 None:intergenic
ACCTTAGCTGCGGCTTATAT+AGG 0.418344 7_4:-18360676 Msa1143170:CDS
AGTAGTATTTATATCATTTG+TGG 0.424401 7_4:+18360984 None:intergenic
TCAAGTACTTATTACCTCTT+GGG 0.428139 7_4:-18361262 Msa1143170:CDS
GTAGTATTTATATCATTTGT+GGG 0.434707 7_4:+18360985 None:intergenic
AAGTCGAAAACTAAGTGATA+AGG 0.438506 7_4:+18360825 None:intergenic
AGAAACAAAGTTCCAATAAA+CGG 0.439134 7_4:+18361087 None:intergenic
ACTCAGATTGGAGAAGAATA+TGG 0.441550 7_4:-18361120 Msa1143170:CDS
AATAATCCCAGAAACATAAC+AGG 0.443207 7_4:+18360730 None:intergenic
CCCAGAAACATAACAGGTAT+AGG 0.450475 7_4:+18360736 None:intergenic
CCGGACGTTGGAATAGTTTG+CGG 0.455395 7_4:+18361192 None:intergenic
AAGTAGGTCAACATTTCTAT+TGG 0.460455 7_4:-18361311 Msa1143170:CDS
GGCTTATATAGGTGAATCTA+TGG 0.463562 7_4:-18360665 Msa1143170:CDS
TCACGTCTCGGATGAATTCA+AGG 0.477047 7_4:+18361148 None:intergenic
ATCGGTAAAAGGATTGGAGT+TGG 0.490463 7_4:+18360874 None:intergenic
GATATATCTGCTGTCGAAGT+AGG 0.493921 7_4:-18361327 Msa1143170:CDS
AGTCGAAAACTAAGTGATAA+GGG 0.500280 7_4:+18360826 None:intergenic
GACGTGAGCAAAACTCAGAT+TGG 0.510359 7_4:-18361132 Msa1143170:CDS
GTAAAAGGATTGGAGTTGGT+TGG 0.515104 7_4:+18360878 None:intergenic
AAAATTATAAAGTTACCTCA+TGG 0.526541 7_4:-18361021 Msa1143170:CDS
ACCTATATAAGCCGCAGCTA+AGG 0.529655 7_4:+18360675 None:intergenic
ATGTTAATCGGTAAAAGGAT+TGG 0.530907 7_4:+18360868 None:intergenic
CCGCAAACTATTCCAACGTC+CGG 0.541897 7_4:-18361192 Msa1143170:CDS
AAGAAATTCTGACCGGACGT+TGG 0.546490 7_4:+18361180 None:intergenic
TCAGTAGCCTATTTCTATGC+GGG 0.553188 7_4:-18360940 Msa1143170:CDS
ACATTTCTATTGGCAAATAG+GGG 0.561596 7_4:-18361301 Msa1143170:CDS
ACAGGTATAGGAACTACTAA+AGG 0.585481 7_4:+18360748 None:intergenic
TATATAGGTGAATCTATGGA+AGG 0.605539 7_4:-18360661 Msa1143170:CDS
TGGAGAAGAATATGGTCCGT+GGG 0.620080 7_4:-18361112 Msa1143170:CDS
TTGGAGAAGAATATGGTCCG+TGG 0.620994 7_4:-18361113 Msa1143170:CDS
TTTCTGGGATTATTTACAAG+CGG 0.630473 7_4:-18360721 Msa1143170:CDS
ATATTCAAAGAAATTCTGAC+CGG 0.632509 7_4:+18361173 None:intergenic
GTTCCAATAAACGGAACCCA+CGG 0.647484 7_4:+18361096 None:intergenic
GTCAGTAGCCTATTTCTATG+CGG 0.655321 7_4:-18360941 Msa1143170:CDS
GATAGCAATTACAACCCAAG+AGG 0.659110 7_4:+18361248 None:intergenic
GGTGCAGCTAATTCTCCATG+AGG 0.714976 7_4:+18361006 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! TATTTATTTTTGTTTCGAAT+TGG - chr7_4:18360958-18360977 Msa1143170:CDS 15.0%
!! AAAATTATAAAGTTACCTCA+TGG - chr7_4:18361002-18361021 Msa1143170:CDS 20.0%
!! GTAGTATTTATATCATTTGT+GGG + chr7_4:18361041-18361060 None:intergenic 20.0%
!! AGTAGTATTTATATCATTTG+TGG + chr7_4:18361042-18361061 None:intergenic 20.0%
!!! AAATCTTCTAAGATGTTAAT+CGG + chr7_4:18361170-18361189 None:intergenic 20.0%
! AACATTTCTATTGGCAAATA+GGG - chr7_4:18360721-18360740 Msa1143170:CDS 25.0%
! ATATTCAAAGAAATTCTGAC+CGG + chr7_4:18360853-18360872 None:intergenic 25.0%
! AGAAACAAAGTTCCAATAAA+CGG + chr7_4:18360939-18360958 None:intergenic 25.0%
!! GGTAACTTTATAATTTTCCA+AGG + chr7_4:18360999-18361018 None:intergenic 25.0%
!!! AAAAAAGGATTGGCTTATTT+TGG - chr7_4:18361113-18361132 Msa1143170:CDS 25.0%
AAGTAGGTCAACATTTCTAT+TGG - chr7_4:18360712-18360731 Msa1143170:CDS 30.0%
CAACATTTCTATTGGCAAAT+AGG - chr7_4:18360720-18360739 Msa1143170:CDS 30.0%
ACATTTCTATTGGCAAATAG+GGG - chr7_4:18360722-18360741 Msa1143170:CDS 30.0%
TCAAGTACTTATTACCTCTT+GGG - chr7_4:18360761-18360780 Msa1143170:CDS 30.0%
!! ATTTTTGTTTCGAATTGGTC+AGG - chr7_4:18360963-18360982 Msa1143170:CDS 30.0%
!! TTTTTGTTTCGAATTGGTCA+GGG - chr7_4:18360964-18360983 Msa1143170:CDS 30.0%
TATGCGGGTATTTCAAAAAA+AGG - chr7_4:18361098-18361117 Msa1143170:CDS 30.0%
GGGTATTTCAAAAAAAGGAT+TGG - chr7_4:18361103-18361122 Msa1143170:CDS 30.0%
ATGTTAATCGGTAAAAGGAT+TGG + chr7_4:18361158-18361177 None:intergenic 30.0%
CTAAGATGTTAATCGGTAAA+AGG + chr7_4:18361163-18361182 None:intergenic 30.0%
AGTCGAAAACTAAGTGATAA+GGG + chr7_4:18361200-18361219 None:intergenic 30.0%
AAGTCGAAAACTAAGTGATA+AGG + chr7_4:18361201-18361220 None:intergenic 30.0%
!! TCACTTAGTTTTCGACTTTT+CGG - chr7_4:18361203-18361222 Msa1143170:CDS 30.0%
AATAATCCCAGAAACATAAC+AGG + chr7_4:18361296-18361315 None:intergenic 30.0%
!! TTTCTGGGATTATTTACAAG+CGG - chr7_4:18361302-18361321 Msa1143170:CDS 30.0%
TATATAGGTGAATCTATGGA+AGG - chr7_4:18361362-18361381 Msa1143170:CDS 30.0%
CTCAAGTACTTATTACCTCT+TGG - chr7_4:18360760-18360779 Msa1143170:CDS 35.0%
CGGATTTCTAACAACTAGAA+TGG + chr7_4:18360814-18360833 None:intergenic 35.0%
ACTCAGATTGGAGAAGAATA+TGG - chr7_4:18360903-18360922 Msa1143170:CDS 35.0%
!! TTTTGTTTCGAATTGGTCAG+GGG - chr7_4:18360965-18360984 Msa1143170:CDS 35.0%
TGAAATACCCGCATAGAAAT+AGG + chr7_4:18361093-18361112 None:intergenic 35.0%
ACAGGTATAGGAACTACTAA+AGG + chr7_4:18361278-18361297 None:intergenic 35.0%
TCCTATACCTGTTATGTTTC+TGG - chr7_4:18361286-18361305 Msa1143170:CDS 35.0%
CCTATACCTGTTATGTTTCT+GGG - chr7_4:18361287-18361306 Msa1143170:CDS 35.0%
!! TATTTTTGCTACCTTAGCTG+CGG - chr7_4:18361337-18361356 Msa1143170:CDS 35.0%
GGCTTATATAGGTGAATCTA+TGG - chr7_4:18361358-18361377 Msa1143170:CDS 35.0%
GATATATCTGCTGTCGAAGT+AGG - chr7_4:18360696-18360715 Msa1143170:CDS 40.0%
GATAGCAATTACAACCCAAG+AGG + chr7_4:18360778-18360797 None:intergenic 40.0%
!! GTCAGTAGCCTATTTCTATG+CGG - chr7_4:18361082-18361101 Msa1143170:CDS 40.0%
!! TCAGTAGCCTATTTCTATGC+GGG - chr7_4:18361083-18361102 Msa1143170:CDS 40.0%
! GTAAAAGGATTGGAGTTGGT+TGG + chr7_4:18361148-18361167 None:intergenic 40.0%
ATCGGTAAAAGGATTGGAGT+TGG + chr7_4:18361152-18361171 None:intergenic 40.0%
CCCAGAAACATAACAGGTAT+AGG + chr7_4:18361290-18361309 None:intergenic 40.0%
AAGAAATTCTGACCGGACGT+TGG + chr7_4:18360846-18360865 None:intergenic 45.0%
TCACGTCTCGGATGAATTCA+AGG + chr7_4:18360878-18360897 None:intergenic 45.0%
! TCTGAGTTTTGCTCACGTCT+CGG + chr7_4:18360890-18360909 None:intergenic 45.0%
GACGTGAGCAAAACTCAGAT+TGG - chr7_4:18360891-18360910 Msa1143170:CDS 45.0%
TTGGAGAAGAATATGGTCCG+TGG - chr7_4:18360910-18360929 Msa1143170:CDS 45.0%
TGGAGAAGAATATGGTCCGT+GGG - chr7_4:18360911-18360930 Msa1143170:CDS 45.0%
GTTCCAATAAACGGAACCCA+CGG + chr7_4:18360930-18360949 None:intergenic 45.0%
ACCTTAGCTGCGGCTTATAT+AGG - chr7_4:18361347-18361366 Msa1143170:CDS 45.0%
ACCTATATAAGCCGCAGCTA+AGG + chr7_4:18361351-18361370 None:intergenic 45.0%
CCGGACGTTGGAATAGTTTG+CGG + chr7_4:18360834-18360853 None:intergenic 50.0%
CCGCAAACTATTCCAACGTC+CGG - chr7_4:18360831-18360850 Msa1143170:CDS 50.0%
GGTGCAGCTAATTCTCCATG+AGG + chr7_4:18361020-18361039 None:intergenic 50.0%
GGTCCGTGGGTTCCGTTTAT+TGG - chr7_4:18360924-18360943 Msa1143170:CDS 55.0%
! GGTCAGGGGCTCTTTTGCCT+TGG - chr7_4:18360979-18360998 Msa1143170:CDS 60.0%
Chromosome Type Strat End Strand Name
chr7_4 gene 18360651 18361394 18360651 ID=Msa1143170;Name=Msa1143170
chr7_4 mRNA 18360651 18361394 18360651 ID=Msa1143170-mRNA-1;Parent=Msa1143170;Name=Msa1143170-mRNA-1;_AED=0.48;_eAED=0.48;_QI=0|-1|0|1|-1|1|1|0|247
chr7_4 exon 18360651 18361394 18360651 ID=Msa1143170-mRNA-1:exon:4089;Parent=Msa1143170-mRNA-1
chr7_4 CDS 18360651 18361394 18360651 ID=Msa1143170-mRNA-1:cds;Parent=Msa1143170-mRNA-1
Gene Sequence

>Msa1143170

ATGAATGTTCTATTATGTTACATCAACACATTAAACAGATTCTATGATATATCTGCTGTCGAAGTAGGTCAACATTTCTATTGGCAAATAGGGGATTTTCAAGTGCATGCTCAAGTACTTATTACCTCTTGGGTTGTAATTGCTATCTTATTAATTTCAACCATTCTAGTTGTTAGAAATCCGCAAACTATTCCAACGTCCGGTCAGAATTTCTTTGAATATGTCCTTGAATTCATCCGAGACGTGAGCAAAACTCAGATTGGAGAAGAATATGGTCCGTGGGTTCCGTTTATTGGAACTTTGTTTCTATTTATTTTTGTTTCGAATTGGTCAGGGGCTCTTTTGCCTTGGAAAATTATAAAGTTACCTCATGGAGAATTAGCTGCACCCACAAATGATATAAATACTACTGTTGCATTAGCTTTACTTACGTCAGTAGCCTATTTCTATGCGGGTATTTCAAAAAAAGGATTGGCTTATTTTGGTAAATACATCCAACCAACTCCAATCCTTTTACCGATTAACATCTTAGAAGATTTCACAAAACCCTTATCACTTAGTTTTCGACTTTTCGGAAATATATTAGCTGATGAATTAGTAGTTGTTGTTCTTGTTTCGTTAGTACCTTTAGTAGTTCCTATACCTGTTATGTTTCTGGGATTATTTACAAGCGGTATTCAAGCTCTTATTTTTGCTACCTTAGCTGCGGCTTATATAGGTGAATCTATGGAAGGCCATCATTGA

Protein sequence

>Msa1143170

MNVLLCYINTLNRFYDISAVEVGQHFYWQIGDFQVHAQVLITSWVVIAILLISTILVVRNPQTIPTSGQNFFEYVLEFIRDVSKTQIGEEYGPWVPFIGTLFLFIFVSNWSGALLPWKIIKLPHGELAAPTNDINTTVALALLTSVAYFYAGISKKGLAYFGKYIQPTPILLPINILEDFTKPLSLSFRLFGNILADELVVVVLVSLVPLVVPIPVMFLGLFTSGIQALIFATLAAAYIGESMEGHH*