AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0273400


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0273400 MtrunA17_Chr2g0283451 98.750 80 1 0 1 80 1 80 6.26e-50 151
Msa0273400 MtrunA17_Chr2g0325441 73.684 76 20 0 5 80 2 77 4.07e-35 114
Msa0273400 MtrunA17_Chr4g0040991 75.000 76 19 0 5 80 2 77 5.92e-35 113
Msa0273400 MtrunA17_Chr2g0324911 59.459 74 30 0 7 80 5 78 9.40e-21 77.8
Msa0273400 MtrunA17_Chr4g0040491 56.944 72 31 0 9 80 8 79 1.61e-14 62.0
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0273400 AT2G31090.1 75.000 76 17 1 5 80 2 75 3.46e-27 94.4
Msa0273400 AT2G20562.1 60.870 69 27 0 12 80 5 73 5.39e-20 76.3

Find 28 sgRNAs with CRISPR-Local

Find 32 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CCTTTGTAGGTGCAGTTATT+TGG 0.227999 2_3:+4928380 Msa0273400:CDS
AACCACTCCATAACCTTAAT+TGG 0.239487 2_3:-4928604 None:intergenic
TCTCTCATAATCTCCTTTGT+AGG 0.287883 2_3:+4928367 Msa0273400:CDS
TCTCATCAAGGCTCCAATTA+AGG 0.314893 2_3:+4928591 Msa0273400:CDS
CACATGGTTAATTACCTAAT+GGG 0.332162 2_3:-4928274 None:intergenic
ACACATGGTTAATTACCTAA+TGG 0.347508 2_3:-4928275 None:intergenic
TTTAAGAACTTCAACCCATT+AGG 0.359993 2_3:+4928260 None:intergenic
CAAGGCTCCAATTAAGGTTA+TGG 0.360751 2_3:+4928597 Msa0273400:CDS
TCTATTCTAACATGGAATCT+TGG 0.376692 2_3:-4928632 None:intergenic
GGTGCAGTTATTTGGATTGT+TGG 0.388294 2_3:+4928388 Msa0273400:CDS
GTGCAGTTATTTGGATTGTT+GGG 0.397665 2_3:+4928389 Msa0273400:CDS
GTTTGCTCTGGCTCTCATCA+AGG 0.420977 2_3:+4928579 Msa0273400:CDS
CCTCATAGTTGAGTTTGCTC+TGG 0.438328 2_3:+4928567 Msa0273400:CDS
GATTGTAAATTCAGGCCTCT+TGG 0.461509 2_3:+4928313 Msa0273400:CDS
ATGAGAGACAAGAAAGCAAA+AGG 0.478563 2_3:-4928352 None:intergenic
AGAAAGCAAAAGGAAGGCCT+AGG 0.499755 2_3:-4928342 None:intergenic
TTAACCATGTGTTGCTGTTG+TGG 0.511293 2_3:+4928286 Msa0273400:exon
CCAGAGCAAACTCAACTATG+AGG 0.515083 2_3:-4928567 None:intergenic
GTGGTGAGGATTGTAAATTC+AGG 0.531054 2_3:+4928305 Msa0273400:CDS
CCAAATAACTGCACCTACAA+AGG 0.535186 2_3:-4928380 None:intergenic
ATATCTCTTCTATTCTAACA+TGG 0.596081 2_3:-4928640 None:intergenic
CATGTGTTGCTGTTGTGGTG+AGG 0.609312 2_3:+4928291 Msa0273400:exon
GAGACAAGAAAGCAAAAGGA+AGG 0.614663 2_3:-4928348 None:intergenic
AGGGTCACGCAAAGACAGCA+TGG 0.623057 2_3:-4928547 None:intergenic
CAGAGCAAACTCAACTATGA+GGG 0.623831 2_3:-4928566 None:intergenic
CTCACCACAACAGCAACACA+TGG 0.630485 2_3:-4928290 None:intergenic
CTCCAATTAAGGTTATGGAG+TGG 0.661349 2_3:+4928602 Msa0273400:CDS
AGGCCTAGGAGAAAACCAAG+AGG 0.747286 2_3:-4928328 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AAAAGAAAATACTAATAGAT+GGG - chr2_3:4928431-4928450 None:intergenic 15.0%
!! CAAAAGAAAATACTAATAGA+TGG - chr2_3:4928432-4928451 None:intergenic 20.0%
! AATGTGTATGATGCTATATA+TGG + chr2_3:4928499-4928518 Msa0273400:intron 25.0%
CACATGGTTAATTACCTAAT+GGG - chr2_3:4928277-4928296 None:intergenic 30.0%
ACACATGGTTAATTACCTAA+TGG - chr2_3:4928278-4928297 None:intergenic 30.0%
ATGAGAGACAAGAAAGCAAA+AGG - chr2_3:4928355-4928374 None:intergenic 35.0%
TCTCTCATAATCTCCTTTGT+AGG + chr2_3:4928367-4928386 Msa0273400:CDS 35.0%
GTGCAGTTATTTGGATTGTT+GGG + chr2_3:4928389-4928408 Msa0273400:CDS 35.0%
CTAATAGATGGGAAAAGAGA+GGG - chr2_3:4928420-4928439 None:intergenic 35.0%
ACTAATAGATGGGAAAAGAG+AGG - chr2_3:4928421-4928440 None:intergenic 35.0%
TGTATGATGCTATATATGGC+AGG + chr2_3:4928503-4928522 Msa0273400:intron 35.0%
AACCACTCCATAACCTTAAT+TGG - chr2_3:4928607-4928626 None:intergenic 35.0%
! TTAACCATGTGTTGCTGTTG+TGG + chr2_3:4928286-4928305 Msa0273400:exon 40.0%
GTGGTGAGGATTGTAAATTC+AGG + chr2_3:4928305-4928324 Msa0273400:CDS 40.0%
GATTGTAAATTCAGGCCTCT+TGG + chr2_3:4928313-4928332 Msa0273400:CDS 40.0%
GAGACAAGAAAGCAAAAGGA+AGG - chr2_3:4928351-4928370 None:intergenic 40.0%
CCAAATAACTGCACCTACAA+AGG - chr2_3:4928383-4928402 None:intergenic 40.0%
CCTTTGTAGGTGCAGTTATT+TGG + chr2_3:4928380-4928399 Msa0273400:CDS 40.0%
GGTGCAGTTATTTGGATTGT+TGG + chr2_3:4928388-4928407 Msa0273400:CDS 40.0%
CAGAGCAAACTCAACTATGA+GGG - chr2_3:4928569-4928588 None:intergenic 40.0%
TCTCATCAAGGCTCCAATTA+AGG + chr2_3:4928591-4928610 Msa0273400:CDS 40.0%
CAAGGCTCCAATTAAGGTTA+TGG + chr2_3:4928597-4928616 Msa0273400:CDS 40.0%
CTCCAATTAAGGTTATGGAG+TGG + chr2_3:4928602-4928621 Msa0273400:CDS 40.0%
AGAAAGCAAAAGGAAGGCCT+AGG - chr2_3:4928345-4928364 None:intergenic 45.0%
CCAGAGCAAACTCAACTATG+AGG - chr2_3:4928570-4928589 None:intergenic 45.0%
! CCTCATAGTTGAGTTTGCTC+TGG + chr2_3:4928567-4928586 Msa0273400:CDS 45.0%
CTCACCACAACAGCAACACA+TGG - chr2_3:4928293-4928312 None:intergenic 50.0%
! CATGTGTTGCTGTTGTGGTG+AGG + chr2_3:4928291-4928310 Msa0273400:exon 50.0%
!! AGGCCTCTTGGTTTTCTCCT+AGG + chr2_3:4928325-4928344 Msa0273400:CDS 50.0%
AGGCCTAGGAGAAAACCAAG+AGG - chr2_3:4928331-4928350 None:intergenic 50.0%
!! GTTTGCTCTGGCTCTCATCA+AGG + chr2_3:4928579-4928598 Msa0273400:CDS 50.0%
AGGGTCACGCAAAGACAGCA+TGG - chr2_3:4928550-4928569 None:intergenic 55.0%
Chromosome Type Strat End Strand Name
chr2_3 gene 4928263 4928648 4928263 ID=Msa0273400;Name=Msa0273400
chr2_3 mRNA 4928263 4928648 4928263 ID=Msa0273400-mRNA-1;Parent=Msa0273400;Name=Msa0273400-mRNA-1;_AED=0.15;_eAED=0.15;_QI=29|1|0.5|1|1|1|2|0|80
chr2_3 exon 4928263 4928410 4928263 ID=Msa0273400-mRNA-1:exon:2443;Parent=Msa0273400-mRNA-1
chr2_3 exon 4928525 4928648 4928525 ID=Msa0273400-mRNA-1:exon:2444;Parent=Msa0273400-mRNA-1
chr2_3 five_prime_UTR 4928263 4928291 4928263 ID=Msa0273400-mRNA-1:five_prime_utr;Parent=Msa0273400-mRNA-1
chr2_3 CDS 4928292 4928410 4928292 ID=Msa0273400-mRNA-1:cds;Parent=Msa0273400-mRNA-1
chr2_3 CDS 4928525 4928648 4928525 ID=Msa0273400-mRNA-1:cds;Parent=Msa0273400-mRNA-1
Gene Sequence

>Msa0273400

ATGTGTTGCTGTTGTGGTGAGGATTGTAAATTCAGGCCTCTTGGTTTTCTCCTAGGCCTTCCTTTTGCTTTCTTGTCTCTCATAATCTCCTTTGTAGGTGCAGTTATTTGGATTGTTGGGTTGACTTTGACATGTATATGTCCATGCTGTCTTTGCGTGACCCTCATAGTTGAGTTTGCTCTGGCTCTCATCAAGGCTCCAATTAAGGTTATGGAGTGGTTCACATCCAAGATTCCATGTTAG

Protein sequence

>Msa0273400

MCCCCGEDCKFRPLGFLLGLPFAFLSLIISFVGAVIWIVGLTLTCICPCCLCVTLIVEFALALIKAPIKVMEWFTSKIPC*