AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1380610


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1380610 MtrunA17_Chr4g0016701 98.785 247 1 1 1 247 1 245 1.77e-175 482
Msa1380610 MtrunA17_CPg0492981 98.785 247 1 1 1 247 1 245 1.77e-175 482
Msa1380610 MtrunA17_Chr4g0015611 98.785 247 1 1 1 247 1 245 1.77e-175 482
Msa1380610 MtrunA17_Chr3g0088491 92.661 218 11 1 30 247 2 214 1.10e-129 365
Msa1380610 MtrunA17_Chr7g0275151 73.494 166 11 1 82 247 2 134 1.65e-76 228
Msa1380610 MtrunA17_Chr4g0060751 67.273 165 8 1 83 247 11 129 1.10e-64 197
Msa1380610 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
Msa1380610 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 tig0020386:-25328 Msa1380610:CDS
CAACATTTCTATTGGCAAAT+AGG 0.196864 tig0020386:-25894 Msa1380610:CDS
AACATTTCTATTGGCAAATA+GGG 0.237546 tig0020386:-25893 Msa1380610:CDS
CTAAGATGTTAATCGGTAAA+AGG 0.238850 tig0020386:+25454 None:intergenic
GGTCCGTGGGTTCCGTTTAT+TGG 0.248543 tig0020386:-25690 Msa1380610:CDS
TGAAATACCCGCATAGAAAT+AGG 0.255569 tig0020386:+25524 None:intergenic
CCTATACCTGTTATGTTTCT+GGG 0.293135 tig0020386:-25327 Msa1380610:CDS
CTCAAGTACTTATTACCTCT+TGG 0.341108 tig0020386:-25854 Msa1380610:CDS
CGGATTTCTAACAACTAGAA+TGG 0.400438 tig0020386:+25803 None:intergenic
AAATCTTCTAAGATGTTAAT+CGG 0.412258 tig0020386:+25447 None:intergenic
ACCTTAGCTGCGGCTTATAT+AGG 0.418344 tig0020386:-25267 Msa1380610:CDS
AGTAGTATTTATATCATTTG+TGG 0.424401 tig0020386:+25575 None:intergenic
TCAAGTACTTATTACCTCTT+GGG 0.428139 tig0020386:-25853 Msa1380610:CDS
GTAGTATTTATATCATTTGT+GGG 0.434707 tig0020386:+25576 None:intergenic
AAGTCGAAAACTAAGTGATA+AGG 0.438506 tig0020386:+25416 None:intergenic
AGAAACAAAGTTCCAATAAA+CGG 0.439134 tig0020386:+25678 None:intergenic
ACTCAGATTGGAGAAGAATA+TGG 0.441550 tig0020386:-25711 Msa1380610:CDS
AATAATCCCAGAAACATAAC+AGG 0.443207 tig0020386:+25321 None:intergenic
CCCAGAAACATAACAGGTAT+AGG 0.450475 tig0020386:+25327 None:intergenic
CCGGACGTTGGAATAGTTTG+CGG 0.455395 tig0020386:+25783 None:intergenic
AAGTAGGTCAACATTTCTAT+TGG 0.460455 tig0020386:-25902 Msa1380610:CDS
GGCTTATATAGGTGAATCTA+TGG 0.463562 tig0020386:-25256 Msa1380610:CDS
TCACGTCTCGGATGAATTCA+AGG 0.477047 tig0020386:+25739 None:intergenic
ATCGGTAAAAGGATTGGAGT+TGG 0.490463 tig0020386:+25465 None:intergenic
GATATATCTGCTGTCGAAGT+AGG 0.493921 tig0020386:-25918 Msa1380610:CDS
AGTCGAAAACTAAGTGATAA+GGG 0.500280 tig0020386:+25417 None:intergenic
GACGTGAGCAAAACTCAGAT+TGG 0.510359 tig0020386:-25723 Msa1380610:CDS
GTAAAAGGATTGGAGTTGGT+TGG 0.515104 tig0020386:+25469 None:intergenic
AAAATTATAAAGTTACCTCA+TGG 0.526541 tig0020386:-25612 Msa1380610:CDS
ACCTATATAAGCCGCAGCTA+AGG 0.529655 tig0020386:+25266 None:intergenic
ATGTTAATCGGTAAAAGGAT+TGG 0.530907 tig0020386:+25459 None:intergenic
CCGCAAACTATTCCAACGTC+CGG 0.541897 tig0020386:-25783 Msa1380610:CDS
AAGAAATTCTGACCGGACGT+TGG 0.546490 tig0020386:+25771 None:intergenic
TCAGTAGCCTATTTCTATGC+GGG 0.553188 tig0020386:-25531 Msa1380610:CDS
ACATTTCTATTGGCAAATAG+GGG 0.561596 tig0020386:-25892 Msa1380610:CDS
ACAGGTATAGGAACTACTAA+AGG 0.585481 tig0020386:+25339 None:intergenic
TATATAGGTGAATCTATGGA+AGG 0.605539 tig0020386:-25252 Msa1380610:CDS
TGGAGAAGAATATGGTCCGT+GGG 0.620080 tig0020386:-25703 Msa1380610:CDS
TTGGAGAAGAATATGGTCCG+TGG 0.620994 tig0020386:-25704 Msa1380610:CDS
TTTCTGGGATTATTTACAAG+CGG 0.630473 tig0020386:-25312 Msa1380610:CDS
ATATTCAAAGAAATTCTGAC+CGG 0.632509 tig0020386:+25764 None:intergenic
GTTCCAATAAACGGAACCCA+CGG 0.647484 tig0020386:+25687 None:intergenic
GTCAGTAGCCTATTTCTATG+CGG 0.655321 tig0020386:-25532 Msa1380610:CDS
GATAGCAATTACAACCCAAG+AGG 0.659110 tig0020386:+25839 None:intergenic
GGTGCAGCTAATTCTCCATG+AGG 0.714976 tig0020386:+25597 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! TATTTATTTTTGTTTCGAAT+TGG - tig0020386:25549-25568 Msa1380610:CDS 15.0%
!! AAAATTATAAAGTTACCTCA+TGG - tig0020386:25593-25612 Msa1380610:CDS 20.0%
!! GTAGTATTTATATCATTTGT+GGG + tig0020386:25632-25651 None:intergenic 20.0%
!! AGTAGTATTTATATCATTTG+TGG + tig0020386:25633-25652 None:intergenic 20.0%
!!! AAATCTTCTAAGATGTTAAT+CGG + tig0020386:25761-25780 None:intergenic 20.0%
! AACATTTCTATTGGCAAATA+GGG - tig0020386:25312-25331 Msa1380610:CDS 25.0%
! ATATTCAAAGAAATTCTGAC+CGG + tig0020386:25444-25463 None:intergenic 25.0%
! AGAAACAAAGTTCCAATAAA+CGG + tig0020386:25530-25549 None:intergenic 25.0%
!! GGTAACTTTATAATTTTCCA+AGG + tig0020386:25590-25609 None:intergenic 25.0%
!!! AAAAAAGGATTGGCTTATTT+TGG - tig0020386:25704-25723 Msa1380610:CDS 25.0%
AAGTAGGTCAACATTTCTAT+TGG - tig0020386:25303-25322 Msa1380610:CDS 30.0%
CAACATTTCTATTGGCAAAT+AGG - tig0020386:25311-25330 Msa1380610:CDS 30.0%
ACATTTCTATTGGCAAATAG+GGG - tig0020386:25313-25332 Msa1380610:CDS 30.0%
TCAAGTACTTATTACCTCTT+GGG - tig0020386:25352-25371 Msa1380610:CDS 30.0%
!! ATTTTTGTTTCGAATTGGTC+AGG - tig0020386:25554-25573 Msa1380610:CDS 30.0%
!! TTTTTGTTTCGAATTGGTCA+GGG - tig0020386:25555-25574 Msa1380610:CDS 30.0%
TATGCGGGTATTTCAAAAAA+AGG - tig0020386:25689-25708 Msa1380610:CDS 30.0%
GGGTATTTCAAAAAAAGGAT+TGG - tig0020386:25694-25713 Msa1380610:CDS 30.0%
ATGTTAATCGGTAAAAGGAT+TGG + tig0020386:25749-25768 None:intergenic 30.0%
CTAAGATGTTAATCGGTAAA+AGG + tig0020386:25754-25773 None:intergenic 30.0%
AGTCGAAAACTAAGTGATAA+GGG + tig0020386:25791-25810 None:intergenic 30.0%
AAGTCGAAAACTAAGTGATA+AGG + tig0020386:25792-25811 None:intergenic 30.0%
!! TCACTTAGTTTTCGACTTTT+CGG - tig0020386:25794-25813 Msa1380610:CDS 30.0%
AATAATCCCAGAAACATAAC+AGG + tig0020386:25887-25906 None:intergenic 30.0%
!! TTTCTGGGATTATTTACAAG+CGG - tig0020386:25893-25912 Msa1380610:CDS 30.0%
TATATAGGTGAATCTATGGA+AGG - tig0020386:25953-25972 Msa1380610:CDS 30.0%
CTCAAGTACTTATTACCTCT+TGG - tig0020386:25351-25370 Msa1380610:CDS 35.0%
CGGATTTCTAACAACTAGAA+TGG + tig0020386:25405-25424 None:intergenic 35.0%
ACTCAGATTGGAGAAGAATA+TGG - tig0020386:25494-25513 Msa1380610:CDS 35.0%
!! TTTTGTTTCGAATTGGTCAG+GGG - tig0020386:25556-25575 Msa1380610:CDS 35.0%
TGAAATACCCGCATAGAAAT+AGG + tig0020386:25684-25703 None:intergenic 35.0%
ACAGGTATAGGAACTACTAA+AGG + tig0020386:25869-25888 None:intergenic 35.0%
TCCTATACCTGTTATGTTTC+TGG - tig0020386:25877-25896 Msa1380610:CDS 35.0%
CCTATACCTGTTATGTTTCT+GGG - tig0020386:25878-25897 Msa1380610:CDS 35.0%
!! TATTTTTGCTACCTTAGCTG+CGG - tig0020386:25928-25947 Msa1380610:CDS 35.0%
GGCTTATATAGGTGAATCTA+TGG - tig0020386:25949-25968 Msa1380610:CDS 35.0%
GATATATCTGCTGTCGAAGT+AGG - tig0020386:25287-25306 Msa1380610:CDS 40.0%
GATAGCAATTACAACCCAAG+AGG + tig0020386:25369-25388 None:intergenic 40.0%
!! GTCAGTAGCCTATTTCTATG+CGG - tig0020386:25673-25692 Msa1380610:CDS 40.0%
!! TCAGTAGCCTATTTCTATGC+GGG - tig0020386:25674-25693 Msa1380610:CDS 40.0%
! GTAAAAGGATTGGAGTTGGT+TGG + tig0020386:25739-25758 None:intergenic 40.0%
ATCGGTAAAAGGATTGGAGT+TGG + tig0020386:25743-25762 None:intergenic 40.0%
CCCAGAAACATAACAGGTAT+AGG + tig0020386:25881-25900 None:intergenic 40.0%
AAGAAATTCTGACCGGACGT+TGG + tig0020386:25437-25456 None:intergenic 45.0%
TCACGTCTCGGATGAATTCA+AGG + tig0020386:25469-25488 None:intergenic 45.0%
! TCTGAGTTTTGCTCACGTCT+CGG + tig0020386:25481-25500 None:intergenic 45.0%
GACGTGAGCAAAACTCAGAT+TGG - tig0020386:25482-25501 Msa1380610:CDS 45.0%
TTGGAGAAGAATATGGTCCG+TGG - tig0020386:25501-25520 Msa1380610:CDS 45.0%
TGGAGAAGAATATGGTCCGT+GGG - tig0020386:25502-25521 Msa1380610:CDS 45.0%
GTTCCAATAAACGGAACCCA+CGG + tig0020386:25521-25540 None:intergenic 45.0%
ACCTTAGCTGCGGCTTATAT+AGG - tig0020386:25938-25957 Msa1380610:CDS 45.0%
ACCTATATAAGCCGCAGCTA+AGG + tig0020386:25942-25961 None:intergenic 45.0%
CCGGACGTTGGAATAGTTTG+CGG + tig0020386:25425-25444 None:intergenic 50.0%
CCGCAAACTATTCCAACGTC+CGG - tig0020386:25422-25441 Msa1380610:CDS 50.0%
GGTGCAGCTAATTCTCCATG+AGG + tig0020386:25611-25630 None:intergenic 50.0%
GGTCCGTGGGTTCCGTTTAT+TGG - tig0020386:25515-25534 Msa1380610:CDS 55.0%
! GGTCAGGGGCTCTTTTGCCT+TGG - tig0020386:25570-25589 Msa1380610:CDS 60.0%
Chromosome Type Strat End Strand Name
tig0020386 gene 25242 25985 25242 ID=Msa1380610;Name=Msa1380610
tig0020386 mRNA 25242 25985 25242 ID=Msa1380610-mRNA-1;Parent=Msa1380610;Name=Msa1380610-mRNA-1;_AED=0.47;_eAED=0.47;_QI=0|-1|0|1|-1|1|1|0|247
tig0020386 exon 25242 25985 25242 ID=Msa1380610-mRNA-1:exon:7193;Parent=Msa1380610-mRNA-1
tig0020386 CDS 25242 25985 25242 ID=Msa1380610-mRNA-1:cds;Parent=Msa1380610-mRNA-1
Gene Sequence

>Msa1380610

ATGAATGTTCTATTATGTTACATCAACACATTAAACAGATTCTATGATATATCTGCTGTCGAAGTAGGTCAACATTTCTATTGGCAAATAGGGGATTTTCAAGTGCATGCTCAAGTACTTATTACCTCTTGGGTTGTAATTGCTATCTTATTAATTTCAACCATTCTAGTTGTTAGAAATCCGCAAACTATTCCAACGTCCGGTCAGAATTTCTTTGAATATGTCCTTGAATTCATCCGAGACGTGAGCAAAACTCAGATTGGAGAAGAATATGGTCCGTGGGTTCCGTTTATTGGAACTTTGTTTCTATTTATTTTTGTTTCGAATTGGTCAGGGGCTCTTTTGCCTTGGAAAATTATAAAGTTACCTCATGGAGAATTAGCTGCACCCACAAATGATATAAATACTACTGTTGCATTAGCTTTACTTACGTCAGTAGCCTATTTCTATGCGGGTATTTCAAAAAAAGGATTGGCTTATTTTGGTAAATACATCCAACCAACTCCAATCCTTTTACCGATTAACATCTTAGAAGATTTCACAAAACCCTTATCACTTAGTTTTCGACTTTTCGGAAATATATTAGCTGATGAATTAGTAGTTGTTGTTCTTGTTTCGTTAGTACCTTTAGTAGTTCCTATACCTGTTATGTTTCTGGGATTATTTACAAGCGGTATTCAAGCTCTTATTTTTGCTACCTTAGCTGCGGCTTATATAGGTGAATCTATGGAAGGCCATCATTGA

Protein sequence

>Msa1380610

MNVLLCYINTLNRFYDISAVEVGQHFYWQIGDFQVHAQVLITSWVVIAILLISTILVVRNPQTIPTSGQNFFEYVLEFIRDVSKTQIGEEYGPWVPFIGTLFLFIFVSNWSGALLPWKIIKLPHGELAAPTNDINTTVALALLTSVAYFYAGISKKGLAYFGKYIQPTPILLPINILEDFTKPLSLSFRLFGNILADELVVVVLVSLVPLVVPIPVMFLGLFTSGIQALIFATLAAAYIGESMEGHH*