AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1460650


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1460650 MtrunA17_Chr4g0074391 82.479 234 1 1 1 234 1 194 1.27e-131 369
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1460650 AT5G13510.1 73.626 182 48 0 49 230 39 220 6.73e-102 295
Msa1460650 AT3G12370.1 59.589 146 57 1 66 209 15 160 9.53e-62 191

Find 51 sgRNAs with CRISPR-Local

Find 61 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
ACAACGAGTTTCGTTGTTTC+AGG 0.234422 tig0041017:-4293 None:intergenic
GGGTGGGTTGAATGGGTTAA+TGG 0.255392 tig0041017:-4084 None:intergenic
TATGATGTGGGTGGGTTGAA+TGG 0.273148 tig0041017:-4092 None:intergenic
TCTTTCTGAAAATCTCTATA+AGG 0.284478 tig0041017:-4440 None:intergenic
GATGGATAAACGGTGGGTTT+TGG 0.306620 tig0041017:-4132 None:intergenic
GAAAAGTCCTTCTTCTGCTT+TGG 0.317270 tig0041017:+4592 Msa1460650:CDS
CGAGATTTATGCTAATTTGT+TGG 0.337443 tig0041017:+4562 Msa1460650:CDS
AGAACTTATCATGGTTCTTA+AGG 0.338473 tig0041017:+4640 Msa1460650:CDS
GAAGCCTTTGTAGTTGATTC+CGG 0.344742 tig0041017:-4234 None:intergenic
GAAGCTTGAAGAACAGGAAC+AGG 0.372574 tig0041017:+4673 Msa1460650:CDS
GGGTTAGTATTTGAAAAGAT+TGG 0.377643 tig0041017:-4058 None:intergenic
GAGATTTATGCTAATTTGTT+GGG 0.387159 tig0041017:+4563 Msa1460650:CDS
GCGTGAAATTGCGGCGTTGA+TGG 0.388449 tig0041017:-4150 None:intergenic
TATTTGAAAAGATTGGGTTT+TGG 0.407544 tig0041017:-4051 None:intergenic
TCAAGTTTCTTAAACTCGTC+AGG 0.408323 tig0041017:-4521 None:intergenic
AAGTTCTTGAAATTGTTTAA+CGG 0.413631 tig0041017:-4258 None:intergenic
TTGGTTTGTATGATGTGGGT+GGG 0.413650 tig0041017:-4100 None:intergenic
GGTGGGTTGAATGGGTTAAT+GGG 0.421794 tig0041017:-4083 None:intergenic
TATTAAGAAGCTTGAAGAAC+AGG 0.423944 tig0041017:+4667 Msa1460650:CDS
ATGATGTGGGTGGGTTGAAT+GGG 0.424540 tig0041017:-4091 None:intergenic
GGTTAGTATTTGAAAAGATT+GGG 0.435588 tig0041017:-4057 None:intergenic
GGTTGAATGGGTTAATGGGT+CGG 0.447317 tig0041017:-4079 None:intergenic
GGTCTTGGTTTGTATGATGT+GGG 0.456359 tig0041017:-4104 None:intergenic
TTGGTTTATAAAGCACTTGA+AGG 0.462572 tig0041017:+4329 Msa1460650:CDS
GTTGAATGGGTTAATGGGTC+GGG 0.472813 tig0041017:-4078 None:intergenic
TTTCTTTGTGCGTGAAATTG+CGG 0.473934 tig0041017:-4159 None:intergenic
TTCTCTAGCAGGAGCTTGAA+TGG 0.482406 tig0041017:-4621 None:intergenic
CTTGGTTTGTATGATGTGGG+TGG 0.491348 tig0041017:-4101 None:intergenic
TTGCGGCGTTGATGGATAAA+CGG 0.507344 tig0041017:-4142 None:intergenic
GGGTCTTGGTTTGTATGATG+TGG 0.515588 tig0041017:-4105 None:intergenic
AGCACTTGAAGGAACACAAT+GGG 0.519774 tig0041017:+4340 Msa1460650:CDS
ACATTCATACCTGTCATACA+TGG 0.531583 tig0041017:-4374 None:intergenic
TCCTGCTAGAGAACTTATCA+TGG 0.541437 tig0041017:+4631 Msa1460650:CDS
AATAGCAGAAGGAATCTCTT+CGG 0.548948 tig0041017:-4414 None:intergenic
ACCATGATAAGTTCTCTAGC+AGG 0.549644 tig0041017:-4632 None:intergenic
TAGAGTTGCAGTAGCTTCCA+TGG 0.562853 tig0041017:-4006 None:intergenic
GGCGTTGATGGATAAACGGT+GGG 0.563964 tig0041017:-4138 None:intergenic
CTATAAGGCTTAATAGCAGA+AGG 0.564004 tig0041017:-4425 None:intergenic
GTAGTAACCAAAGCAGAAGA+AGG 0.565336 tig0041017:-4599 None:intergenic
ACGCTGAAACCATGTATGAC+AGG 0.579109 tig0041017:+4365 Msa1460650:CDS
GCATAAATCTCGCCGCGTGT+CGG 0.580599 tig0041017:-4551 None:intergenic
CGTTGTTGCAAAGAACACAT+TGG 0.598449 tig0041017:+4310 Msa1460650:CDS
GAAAACTGTTACCTCCTCGC+CGG 0.614670 tig0041017:+4215 Msa1460650:CDS
CGGCGTTGATGGATAAACGG+TGG 0.618873 tig0041017:-4139 None:intergenic
CTTGAAACATTGCCGACACG+CGG 0.624834 tig0041017:+4539 Msa1460650:CDS
AAGCTTGAAGAACAGGAACA+GGG 0.635295 tig0041017:+4674 Msa1460650:CDS
TGTAGTTGATTCCGGCGAGG+AGG 0.639688 tig0041017:-4226 None:intergenic
AAGCACTTGAAGGAACACAA+TGG 0.664659 tig0041017:+4339 Msa1460650:CDS
GTATGACAGGTATGAATGTG+TGG 0.676357 tig0041017:+4378 Msa1460650:CDS
CTCGCCGGAATCAACTACAA+AGG 0.676602 tig0041017:+4230 Msa1460650:CDS
CTTTGTAGTTGATTCCGGCG+AGG 0.687827 tig0041017:-4229 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AAGTTCTTGAAATTGTTTAA+CGG - tig0041017:4261-4280 None:intergenic 20.0%
!! TATTTGAAAAGATTGGGTTT+TGG - tig0041017:4054-4073 None:intergenic 25.0%
! GGTTAGTATTTGAAAAGATT+GGG - tig0041017:4060-4079 None:intergenic 25.0%
!! TCTTTCTGAAAATCTCTATA+AGG - tig0041017:4443-4462 None:intergenic 25.0%
!!! GTTTTTGAAGGGAAATTTTA+TGG + tig0041017:4497-4516 Msa1460650:CDS 25.0%
!!! GAGATTTATGCTAATTTGTT+GGG + tig0041017:4563-4582 Msa1460650:CDS 25.0%
! GGGTTAGTATTTGAAAAGAT+TGG - tig0041017:4061-4080 None:intergenic 30.0%
!! GTTTTCAAGCTGTTCTTTTA+CGG - tig0041017:4201-4220 None:intergenic 30.0%
! TTGGTTTATAAAGCACTTGA+AGG + tig0041017:4329-4348 Msa1460650:CDS 30.0%
! CTTGAAGAGAATGATTTTAC+TGG + tig0041017:4470-4489 Msa1460650:CDS 30.0%
! CGAGATTTATGCTAATTTGT+TGG + tig0041017:4562-4581 Msa1460650:CDS 30.0%
AGAACTTATCATGGTTCTTA+AGG + tig0041017:4640-4659 Msa1460650:CDS 30.0%
TATTAAGAAGCTTGAAGAAC+AGG + tig0041017:4667-4686 Msa1460650:CDS 30.0%
!! TTGAAAAGATTGGGTTTTGG+TGG - tig0041017:4051-4070 None:intergenic 35.0%
TTTCTTTGTGCGTGAAATTG+CGG - tig0041017:4162-4181 None:intergenic 35.0%
! CTGTTCTTTTACGGTTTCAA+CGG - tig0041017:4192-4211 None:intergenic 35.0%
ACATTCATACCTGTCATACA+TGG - tig0041017:4377-4396 None:intergenic 35.0%
AATAGCAGAAGGAATCTCTT+CGG - tig0041017:4417-4436 None:intergenic 35.0%
CTATAAGGCTTAATAGCAGA+AGG - tig0041017:4428-4447 None:intergenic 35.0%
!!! TTTACTGGTGCTGTTTTTGA+AGG + tig0041017:4485-4504 Msa1460650:CDS 35.0%
!!! TTACTGGTGCTGTTTTTGAA+GGG + tig0041017:4486-4505 Msa1460650:CDS 35.0%
TCAAGTTTCTTAAACTCGTC+AGG - tig0041017:4524-4543 None:intergenic 35.0%
!! AAAGATTGGGTTTTGGTGGA+TGG - tig0041017:4047-4066 None:intergenic 40.0%
!! TTGGTTTGTATGATGTGGGT+GGG - tig0041017:4103-4122 None:intergenic 40.0%
!! GGTCTTGGTTTGTATGATGT+GGG - tig0041017:4107-4126 None:intergenic 40.0%
!!! AAACGGTGGGTTTTGGAAAT+GGG - tig0041017:4128-4147 None:intergenic 40.0%
!!! TAAACGGTGGGTTTTGGAAA+TGG - tig0041017:4129-4148 None:intergenic 40.0%
! GAAGCCTTTGTAGTTGATTC+CGG - tig0041017:4237-4256 None:intergenic 40.0%
! ACAACGAGTTTCGTTGTTTC+AGG - tig0041017:4296-4315 None:intergenic 40.0%
CGTTGTTGCAAAGAACACAT+TGG + tig0041017:4310-4329 Msa1460650:CDS 40.0%
AAGCACTTGAAGGAACACAA+TGG + tig0041017:4339-4358 Msa1460650:CDS 40.0%
AGCACTTGAAGGAACACAAT+GGG + tig0041017:4340-4359 Msa1460650:CDS 40.0%
GTATGACAGGTATGAATGTG+TGG + tig0041017:4378-4397 Msa1460650:CDS 40.0%
GAAAAGTCCTTCTTCTGCTT+TGG + tig0041017:4592-4611 Msa1460650:CDS 40.0%
GTAGTAACCAAAGCAGAAGA+AGG - tig0041017:4602-4621 None:intergenic 40.0%
TCCTGCTAGAGAACTTATCA+TGG + tig0041017:4631-4650 Msa1460650:CDS 40.0%
ACCATGATAAGTTCTCTAGC+AGG - tig0041017:4635-4654 None:intergenic 40.0%
AAGCTTGAAGAACAGGAACA+GGG + tig0041017:4674-4693 Msa1460650:CDS 40.0%
!! GTTGAATGGGTTAATGGGTC+GGG - tig0041017:4081-4100 None:intergenic 45.0%
!! GGTTGAATGGGTTAATGGGT+CGG - tig0041017:4082-4101 None:intergenic 45.0%
!! GGTGGGTTGAATGGGTTAAT+GGG - tig0041017:4086-4105 None:intergenic 45.0%
!! ATGATGTGGGTGGGTTGAAT+GGG - tig0041017:4094-4113 None:intergenic 45.0%
!! TATGATGTGGGTGGGTTGAA+TGG - tig0041017:4095-4114 None:intergenic 45.0%
!! CTTGGTTTGTATGATGTGGG+TGG - tig0041017:4104-4123 None:intergenic 45.0%
!! GGGTCTTGGTTTGTATGATG+TGG - tig0041017:4108-4127 None:intergenic 45.0%
!!! TGGGTTTTGGAAATGGGTCT+TGG - tig0041017:4122-4141 None:intergenic 45.0%
!! GATGGATAAACGGTGGGTTT+TGG - tig0041017:4135-4154 None:intergenic 45.0%
!! TTGCGGCGTTGATGGATAAA+CGG - tig0041017:4145-4164 None:intergenic 45.0%
ACGCTGAAACCATGTATGAC+AGG + tig0041017:4365-4384 Msa1460650:CDS 45.0%
TTCTCTAGCAGGAGCTTGAA+TGG - tig0041017:4624-4643 None:intergenic 45.0%
GAAGCTTGAAGAACAGGAAC+AGG + tig0041017:4673-4692 Msa1460650:CDS 45.0%
!! GGGTGGGTTGAATGGGTTAA+TGG - tig0041017:4087-4106 None:intergenic 50.0%
!! GGCGTTGATGGATAAACGGT+GGG - tig0041017:4141-4160 None:intergenic 50.0%
GAAAACTGTTACCTCCTCGC+CGG + tig0041017:4215-4234 Msa1460650:CDS 50.0%
! CTTTGTAGTTGATTCCGGCG+AGG - tig0041017:4232-4251 None:intergenic 50.0%
CTCGCCGGAATCAACTACAA+AGG + tig0041017:4230-4249 Msa1460650:CDS 50.0%
CTTGAAACATTGCCGACACG+CGG + tig0041017:4539-4558 Msa1460650:CDS 50.0%
!! CGGCGTTGATGGATAAACGG+TGG - tig0041017:4142-4161 None:intergenic 55.0%
! GCGTGAAATTGCGGCGTTGA+TGG - tig0041017:4153-4172 None:intergenic 55.0%
! TGTAGTTGATTCCGGCGAGG+AGG - tig0041017:4229-4248 None:intergenic 55.0%
GCATAAATCTCGCCGCGTGT+CGG - tig0041017:4554-4573 None:intergenic 55.0%
Chromosome Type Strat End Strand Name
tig0041017 gene 4008 4712 4008 ID=Msa1460650;Name=Msa1460650
tig0041017 mRNA 4008 4712 4008 ID=Msa1460650-mRNA-1;Parent=Msa1460650;Name=Msa1460650-mRNA-1;_AED=0.11;_eAED=0.11;_QI=0|-1|0|1|-1|1|1|0|234
tig0041017 exon 4008 4712 4008 ID=Msa1460650-mRNA-1:exon:22837;Parent=Msa1460650-mRNA-1
tig0041017 CDS 4008 4712 4008 ID=Msa1460650-mRNA-1:cds;Parent=Msa1460650-mRNA-1
Gene Sequence

>Msa1460650

ATGGAAGCTACTGCAACTCTACTCAGCTTCTCTCTTCCATCCACCAAAACCCAATCTTTTCAAATACTAACCCGACCCATTAACCCATTCAACCCACCCACATCATACAAACCAAGACCCATTTCCAAAACCCACCGTTTATCCATCAACGCCGCAATTTCACGCACAAAGAAAGAAGAAACCGTTGAAACCGTAAAAGAACAGCTTGAAAACTGTTACCTCCTCGCCGGAATCAACTACAAAGGCTTCACCGTTAAACAATTTCAAGAACTTAGAAAAACTCTTCCTGAAACAACGAAACTCGTTGTTGCAAAGAACACATTGGTTTATAAAGCACTTGAAGGAACACAATGGGAGACGCTGAAACCATGTATGACAGGTATGAATGTGTGGTTGTTTGTTCATACCGAAGAGATTCCTTCTGCTATTAAGCCTTATAGAGATTTTCAGAAAGAGAAGAAGCTTGAAGAGAATGATTTTACTGGTGCTGTTTTTGAAGGGAAATTTTATGGTCCTGACGAGTTTAAGAAACTTGAAACATTGCCGACACGCGGCGAGATTTATGCTAATTTGTTGGGTTCTTTGAAAAGTCCTTCTTCTGCTTTGGTTACTACCATTCAAGCTCCTGCTAGAGAACTTATCATGGTTCTTAAGGCACATATTAAGAAGCTTGAAGAACAGGAACAGGGTAGTGCTGTTCTATAG

Protein sequence

>Msa1460650

MEATATLLSFSLPSTKTQSFQILTRPINPFNPPTSYKPRPISKTHRLSINAAISRTKKEETVETVKEQLENCYLLAGINYKGFTVKQFQELRKTLPETTKLVVAKNTLVYKALEGTQWETLKPCMTGMNVWLFVHTEEIPSAIKPYRDFQKEKKLEENDFTGAVFEGKFYGPDEFKKLETLPTRGEIYANLLGSLKSPSSALVTTIQAPARELIMVLKAHIKKLEEQEQGSAVL*