AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0311440


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0311440 MtrunA17_Chr2g0280471 96.988 166 5 0 1 166 1 166 1.74e-118 331
Msa0311440 MtrunA17_Chr2g0280451 86.747 166 22 0 1 166 1 166 6.79e-105 297
Msa0311440 MtrunA17_Chr7g0249341 56.627 166 53 1 1 166 1 147 4.82e-64 193
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0311440 AT5G56260.1 75.301 166 41 0 1 166 1 166 1.61e-90 261
Msa0311440 AT5G56260.2 75.301 166 41 0 1 166 1 166 1.61e-90 261
Msa0311440 AT5G56260.5 75.301 166 41 0 1 166 1 166 1.61e-90 261
Msa0311440 AT5G56260.4 75.301 166 41 0 1 166 33 198 1.07e-89 260
Msa0311440 AT5G56260.3 75.301 166 41 0 1 166 33 198 1.07e-89 260
Msa0311440 AT3G02770.1 65.060 166 58 0 1 166 1 166 9.65e-78 229
Msa0311440 AT5G16450.2 65.060 166 58 0 1 166 1 166 1.48e-77 228
Msa0311440 AT5G16450.1 65.060 166 58 0 1 166 1 166 1.48e-77 228

Find 37 sgRNAs with CRISPR-Local

Find 47 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TGCTCTTGTTGGAGGGAATT+TGG 0.199853 2_4:+6312460 Msa0311440:CDS
TGGCCAGTCTCGGGCATTCT+CGG 0.281731 2_4:+6312325 Msa0311440:CDS
GCACAAAACATGGGGTGGTC+TGG 0.304278 2_4:+6312491 Msa0311440:CDS
GGCCAGTCTCGGGCATTCTC+GGG 0.351904 2_4:+6312326 Msa0311440:CDS
TGGTCTGGGATTGTTGTGAA+TGG 0.381293 2_4:+6312506 Msa0311440:CDS
AAAAGGAGAAGGAAGAGTTT+TGG 0.387441 2_4:+6312409 Msa0311440:CDS
CACAAAACATGGGGTGGTCT+GGG 0.391877 2_4:+6312492 Msa0311440:CDS
CCCGAGACTGGCCATACATC+TGG 0.415145 2_4:-6312316 None:intergenic
GCCCCGAGAATGCCCGAGAC+TGG 0.420007 2_4:-6312328 None:intergenic
TCAAGTTGGTGTTAGAGCTT+TGG 0.422544 2_4:+6312562 Msa0311440:CDS
AACGCAACACATTTAACAAA+TGG 0.449158 2_4:+6312266 Msa0311440:CDS
TCCAGATGTATGGCCAGTCT+CGG 0.458278 2_4:+6312315 Msa0311440:CDS
GGTGCAGTTGGCACAAAACA+TGG 0.464361 2_4:+6312481 Msa0311440:CDS
CATCCAGTGTTCCAGATGTA+TGG 0.472302 2_4:+6312305 Msa0311440:CDS
CAGTCTAGTACTATTTCAAA+TGG 0.479945 2_4:-6312723 None:intergenic
TCAAATGGACAACTCAAACT+TGG 0.482072 2_4:-6312708 None:intergenic
TGGAGGGAATTTGGTGCAGT+TGG 0.484334 2_4:+6312469 Msa0311440:CDS
AGAGAACTTCTTGAAACAAA+AGG 0.491488 2_4:+6312392 Msa0311440:CDS
GAGATTAATTTGTGTCAAGT+TGG 0.491931 2_4:+6312548 Msa0311440:CDS
CATGTTGCTGTTTATGTTGG+AGG 0.502059 2_4:+6312629 Msa0311440:CDS
AAACATGTTGCTGTTTATGT+TGG 0.508506 2_4:+6312626 Msa0311440:CDS
TGGCCATACATCTGGAACAC+TGG 0.512769 2_4:-6312308 None:intergenic
CCAGATGTATGGCCAGTCTC+GGG 0.532810 2_4:+6312316 Msa0311440:CDS
GTGTCACATATCTCTGCTGT+TGG 0.545822 2_4:-6312242 None:intergenic
GCCAGTCTCGGGCATTCTCG+GGG 0.553955 2_4:+6312327 Msa0311440:CDS
AGCATGAGGTGTGCTCTTGT+TGG 0.557997 2_4:+6312449 Msa0311440:CDS
ATGAGGTGTGCTCTTGTTGG+AGG 0.569564 2_4:+6312452 Msa0311440:CDS
CTTCTTGAAACAAAAGGAGA+AGG 0.585218 2_4:+6312398 Msa0311440:CDS
TGGCTCTATGCAGATAATGA+TGG 0.590987 2_4:+6312674 Msa0311440:CDS
ATTTAACAAATGGTGACTTG+AGG 0.616446 2_4:+6312276 Msa0311440:CDS
AGTGTTTGAAGACAATGTGT+TGG 0.617013 2_4:+6312367 Msa0311440:CDS
GTGCAGTTGGCACAAAACAT+GGG 0.623381 2_4:+6312482 Msa0311440:CDS
GAATGGTTGTATTAGAGATG+TGG 0.623790 2_4:+6312523 Msa0311440:CDS
TGAGGTGTGCTCTTGTTGGA+GGG 0.651891 2_4:+6312453 Msa0311440:CDS
AGTTGGCACAAAACATGGGG+TGG 0.672135 2_4:+6312486 Msa0311440:CDS
TGCAGTTGGCACAAAACATG+GGG 0.672279 2_4:+6312483 Msa0311440:CDS
TTGATGGAGGAGGAAGCATG+AGG 0.673507 2_4:+6312435 Msa0311440:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! ATTGTCTTCAAACACTTTTA+CGG - chr2_4:6312363-6312382 None:intergenic 25.0%
! CCACTTAAATCCAATAAAAA+CGG + chr2_4:6312593-6312612 Msa0311440:CDS 25.0%
AACGCAACACATTTAACAAA+TGG + chr2_4:6312266-6312285 Msa0311440:CDS 30.0%
ATTTAACAAATGGTGACTTG+AGG + chr2_4:6312276-6312295 Msa0311440:CDS 30.0%
AGAGAACTTCTTGAAACAAA+AGG + chr2_4:6312392-6312411 Msa0311440:CDS 30.0%
!! GAGATTAATTTGTGTCAAGT+TGG + chr2_4:6312548-6312567 Msa0311440:CDS 30.0%
!! CCGTTTTTATTGGATTTAAG+TGG - chr2_4:6312596-6312615 None:intergenic 30.0%
AAATCCAATAAAAACGGTAC+TGG + chr2_4:6312599-6312618 Msa0311440:CDS 30.0%
!! AAACATGTTGCTGTTTATGT+TGG + chr2_4:6312626-6312645 Msa0311440:CDS 30.0%
! AACACTTTTACGGTAACAAC+AGG - chr2_4:6312353-6312372 None:intergenic 35.0%
AGTGTTTGAAGACAATGTGT+TGG + chr2_4:6312367-6312386 Msa0311440:CDS 35.0%
CTTCTTGAAACAAAAGGAGA+AGG + chr2_4:6312398-6312417 Msa0311440:CDS 35.0%
! AAAAGGAGAAGGAAGAGTTT+TGG + chr2_4:6312409-6312428 Msa0311440:CDS 35.0%
!!! GGAAGAGTTTTGGTTATTGA+TGG + chr2_4:6312419-6312438 Msa0311440:CDS 35.0%
!!! AGAGTTTTGGTTATTGATGG+AGG + chr2_4:6312422-6312441 Msa0311440:CDS 35.0%
GAATGGTTGTATTAGAGATG+TGG + chr2_4:6312523-6312542 Msa0311440:CDS 35.0%
!! TTCACCAGTACCGTTTTTAT+TGG - chr2_4:6312606-6312625 None:intergenic 35.0%
!! CTTTTATTCGTGATGGAGAA+TGG + chr2_4:6312654-6312673 Msa0311440:CDS 35.0%
TCAAATGGACAACTCAAACT+TGG - chr2_4:6312711-6312730 None:intergenic 35.0%
!!! GTTTTGGTTATTGATGGAGG+AGG + chr2_4:6312425-6312444 Msa0311440:CDS 40.0%
!! TCAAGTTGGTGTTAGAGCTT+TGG + chr2_4:6312562-6312581 Msa0311440:CDS 40.0%
!! CATGTTGCTGTTTATGTTGG+AGG + chr2_4:6312629-6312648 Msa0311440:CDS 40.0%
! GGAGGAACTTTTATTCGTGA+TGG + chr2_4:6312647-6312666 Msa0311440:CDS 40.0%
! TGGCTCTATGCAGATAATGA+TGG + chr2_4:6312674-6312693 Msa0311440:CDS 40.0%
GTGTCACATATCTCTGCTGT+TGG - chr2_4:6312245-6312264 None:intergenic 45.0%
CATCCAGTGTTCCAGATGTA+TGG + chr2_4:6312305-6312324 Msa0311440:CDS 45.0%
TGCTCTTGTTGGAGGGAATT+TGG + chr2_4:6312460-6312479 Msa0311440:CDS 45.0%
GTGCAGTTGGCACAAAACAT+GGG + chr2_4:6312482-6312501 Msa0311440:CDS 45.0%
TGCAGTTGGCACAAAACATG+GGG + chr2_4:6312483-6312502 Msa0311440:CDS 45.0%
! TGGTCTGGGATTGTTGTGAA+TGG + chr2_4:6312506-6312525 Msa0311440:CDS 45.0%
! TGGCCATACATCTGGAACAC+TGG - chr2_4:6312311-6312330 None:intergenic 50.0%
TCCAGATGTATGGCCAGTCT+CGG + chr2_4:6312315-6312334 Msa0311440:CDS 50.0%
! TTGATGGAGGAGGAAGCATG+AGG + chr2_4:6312435-6312454 Msa0311440:CDS 50.0%
AGCATGAGGTGTGCTCTTGT+TGG + chr2_4:6312449-6312468 Msa0311440:CDS 50.0%
ATGAGGTGTGCTCTTGTTGG+AGG + chr2_4:6312452-6312471 Msa0311440:CDS 50.0%
TGAGGTGTGCTCTTGTTGGA+GGG + chr2_4:6312453-6312472 Msa0311440:CDS 50.0%
!! TGGAGGGAATTTGGTGCAGT+TGG + chr2_4:6312469-6312488 Msa0311440:CDS 50.0%
GGTGCAGTTGGCACAAAACA+TGG + chr2_4:6312481-6312500 Msa0311440:CDS 50.0%
AGTTGGCACAAAACATGGGG+TGG + chr2_4:6312486-6312505 Msa0311440:CDS 50.0%
CACAAAACATGGGGTGGTCT+GGG + chr2_4:6312492-6312511 Msa0311440:CDS 50.0%
CCAGATGTATGGCCAGTCTC+GGG + chr2_4:6312316-6312335 Msa0311440:CDS 55.0%
GCACAAAACATGGGGTGGTC+TGG + chr2_4:6312491-6312510 Msa0311440:CDS 55.0%
! CCCGAGACTGGCCATACATC+TGG - chr2_4:6312319-6312338 None:intergenic 60.0%
TGGCCAGTCTCGGGCATTCT+CGG + chr2_4:6312325-6312344 Msa0311440:CDS 60.0%
GGCCAGTCTCGGGCATTCTC+GGG + chr2_4:6312326-6312345 Msa0311440:CDS 65.0%
GCCAGTCTCGGGCATTCTCG+GGG + chr2_4:6312327-6312346 Msa0311440:CDS 65.0%
GCCCCGAGAATGCCCGAGAC+TGG - chr2_4:6312331-6312350 None:intergenic 70.0%
Chromosome Type Strat End Strand Name
chr2_4 gene 6312230 6312730 6312230 ID=Msa0311440;Name=Msa0311440
chr2_4 mRNA 6312230 6312730 6312230 ID=Msa0311440-mRNA-1;Parent=Msa0311440;Name=Msa0311440-mRNA-1;_AED=0.22;_eAED=0.23;_QI=0|-1|0|1|-1|1|1|0|166
chr2_4 exon 6312230 6312730 6312230 ID=Msa0311440-mRNA-1:exon:2415;Parent=Msa0311440-mRNA-1
chr2_4 CDS 6312230 6312730 6312230 ID=Msa0311440-mRNA-1:cds;Parent=Msa0311440-mRNA-1
Gene Sequence

>Msa0311440

ATGGATTCTCTACCAACAGCAGAGATATGTGACACAAACGCAACACATTTAACAAATGGTGACTTGAGGATACTTCATCCAGTGTTCCAGATGTATGGCCAGTCTCGGGCATTCTCGGGGCCTGTTGTTACCGTAAAAGTGTTTGAAGACAATGTGTTGGTAAGAGAACTTCTTGAAACAAAAGGAGAAGGAAGAGTTTTGGTTATTGATGGAGGAGGAAGCATGAGGTGTGCTCTTGTTGGAGGGAATTTGGTGCAGTTGGCACAAAACATGGGGTGGTCTGGGATTGTTGTGAATGGTTGTATTAGAGATGTGGATGAGATTAATTTGTGTCAAGTTGGTGTTAGAGCTTTGGCTTCTCATCCACTTAAATCCAATAAAAACGGTACTGGTGAAAAACATGTTGCTGTTTATGTTGGAGGAACTTTTATTCGTGATGGAGAATGGCTCTATGCAGATAATGATGGTATCATTGTATCCAAGTTTGAGTTGTCCATTTGA

Protein sequence

>Msa0311440

MDSLPTAEICDTNATHLTNGDLRILHPVFQMYGQSRAFSGPVVTVKVFEDNVLVRELLETKGEGRVLVIDGGGSMRCALVGGNLVQLAQNMGWSGIVVNGCIRDVDEINLCQVGVRALASHPLKSNKNGTGEKHVAVYVGGTFIRDGEWLYADNDGIIVSKFELSI*