AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0239800


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0239800 MtrunA17_Chr2g0290831 94.805 77 4 0 17 93 1 77 1.41e-46 143
Msa0239800 MtrunA17_Chr3g0120541 49.315 73 37 0 18 90 3 75 1.03e-18 74.3
Msa0239800 MtrunA17_Chr6g0483521 57.143 70 30 0 17 86 1 70 4.22e-18 75.5
Msa0239800 MtrunA17_Chr6g0483581 52.703 74 35 0 17 90 1 74 1.10e-17 74.3
Msa0239800 MtrunA17_Chr6g0483561 52.113 71 34 0 17 87 1 71 6.64e-17 72.4
Msa0239800 MtrunA17_Chr6g0483511 54.286 70 32 0 17 86 1 70 6.88e-17 71.2
Msa0239800 MtrunA17_Chr3g0120551 47.945 73 38 0 18 90 3 75 9.24e-17 69.3
Msa0239800 MtrunA17_Chr3g0120531 48.611 72 36 1 18 88 3 74 3.09e-15 65.5
Msa0239800 MtrunA17_Chr5g0445581 40.000 65 39 0 17 81 1 65 6.35e-12 55.8
Msa0239800 MtrunA17_Chr5g0438551 43.421 76 42 1 19 93 2 77 1.56e-11 56.2
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0239800 AT4G05030.2 60.811 74 29 0 17 90 1 74 2.04e-24 88.2
Msa0239800 AT4G05030.1 61.111 72 28 0 19 90 36 107 2.17e-23 86.3
Msa0239800 AT3G20180.3 45.333 75 41 0 17 91 1 75 1.67e-16 69.3
Msa0239800 AT3G20180.2 43.421 76 43 0 16 91 19 94 2.87e-16 68.9
Msa0239800 AT3G20180.4 43.056 72 41 0 20 91 2 73 3.74e-14 63.2
Msa0239800 AT3G20180.1 43.478 69 39 0 23 91 3 71 6.76e-14 62.4
Msa0239800 AT3G07600.1 42.857 77 44 0 17 93 1 77 3.60e-13 61.6
Msa0239800 AT5G48290.1 41.558 77 45 0 17 93 1 77 7.15e-11 55.8

Find 21 sgRNAs with CRISPR-Local

Find 88 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TCAAAATATCATTACTTAAT+TGG 0.106114 2_2:+14373516 None:intergenic
CAAATTTAATGTTTAGCTTT+AGG 0.204714 2_2:-14373291 Msa0239800:three_prime_UTR
TTAGGAATATAATATATATT+TGG 0.223892 2_2:-14373273 Msa0239800:three_prime_UTR
AAAGACAAGATAGTAGTTAT+TGG 0.241019 2_2:-14373684 Msa0239800:CDS
AAAGCAATGGAGAGAGAAAA+AGG 0.349934 2_2:-14373436 Msa0239800:three_prime_UTR
ATATTTGGATTGGTATGTAA+TGG 0.411614 2_2:-14373258 Msa0239800:three_prime_UTR
TCAACAAAGTTGTCATCAAA+TGG 0.417779 2_2:+14373490 None:intergenic
AGCTACAACCTTGAGTGCCT+TGG 0.451895 2_2:+14373990 None:intergenic
TGGTATGTAATGGAATGAAA+TGG 0.466169 2_2:-14373248 Msa0239800:three_prime_UTR
CAAACTGAAATTGTCAGCTT+AGG 0.480321 2_2:-14373609 Msa0239800:CDS
ACTTAATTGGAAAATACAAA+AGG 0.486207 2_2:+14373529 None:intergenic
AAGGCACTCAAGGTTGTAGC+TGG 0.487303 2_2:-14373988 Msa0239800:CDS
AATATAATATATATTTGGAT+TGG 0.491812 2_2:-14373268 Msa0239800:three_prime_UTR
TTCTTATTGGTCAAAAGCAA+TGG 0.519411 2_2:-14373449 Msa0239800:three_prime_UTR
AAGATAGTAGTTATTGGAGA+TGG 0.521542 2_2:-14373678 Msa0239800:CDS
GCAGCAAAAGATTGTGATGA+GGG 0.535212 2_2:-14374040 Msa0239800:intron
GTGTCGCACCAAGGCACTCA+AGG 0.539664 2_2:-14373998 Msa0239800:CDS
AAGGTTGTAGCTGGAGCAAA+CGG 0.547469 2_2:-14373979 Msa0239800:intron
TTTCATCTCTGAAAACATGA+AGG 0.581141 2_2:-14374208 Msa0239800:intron
TGCAGCAAAAGATTGTGATG+AGG 0.660386 2_2:-14374041 Msa0239800:intron
ATGTCAAAAGTGTCGCACCA+AGG 0.695558 2_2:-14374007 Msa0239800:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! TTAGGAATATAATATATATT+TGG - chr2_2:14374327-14374346 Msa0239800:intron 10.0%
!! AATATAATATATATTTGGAT+TGG - chr2_2:14374332-14374351 Msa0239800:intron 10.0%
!! TTAGGAATATAATATATATT+TGG - chr2_2:14374327-14374346 Msa0239800:intron 10.0%
!! AATATAATATATATTTGGAT+TGG - chr2_2:14374332-14374351 Msa0239800:intron 10.0%
!! TCAAAATATCATTACTTAAT+TGG + chr2_2:14374087-14374106 None:intergenic 15.0%
!! TCAAAATATCATTACTTAAT+TGG + chr2_2:14374087-14374106 None:intergenic 15.0%
!! ACTTTATGCTAGAAATTTAT+CGG - chr2_2:14373233-14373252 Msa0239800:three_prime_UTR 20.0%
!! ATTTATATGTGATCAAACTT+GGG + chr2_2:14373343-14373362 None:intergenic 20.0%
!! AATTTATATGTGATCAAACT+TGG + chr2_2:14373344-14373363 None:intergenic 20.0%
!! AAGTTTGATCACATATAAAT+TGG - chr2_2:14373343-14373362 Msa0239800:three_prime_UTR 20.0%
!!! GTTACTAAAATTTTGTGATT+TGG - chr2_2:14373852-14373871 Msa0239800:intron 20.0%
!! AATTGTTTGAGAAAAAAAGT+TGG - chr2_2:14373967-14373986 Msa0239800:intron 20.0%
!!! TTTTATTTCAGTTTTTCAAC+TGG + chr2_2:14374028-14374047 None:intergenic 20.0%
!! ACTTAATTGGAAAATACAAA+AGG + chr2_2:14374074-14374093 None:intergenic 20.0%
!! TCAAAAAGAAGAAGAAAAAT+TGG + chr2_2:14374280-14374299 None:intergenic 20.0%
!!! CAAATTTAATGTTTAGCTTT+AGG - chr2_2:14374309-14374328 Msa0239800:intron 20.0%
!! ACTTTATGCTAGAAATTTAT+CGG - chr2_2:14373233-14373252 Msa0239800:three_prime_UTR 20.0%
!! ATTTATATGTGATCAAACTT+GGG + chr2_2:14373343-14373362 None:intergenic 20.0%
!! AATTTATATGTGATCAAACT+TGG + chr2_2:14373344-14373363 None:intergenic 20.0%
!! AAGTTTGATCACATATAAAT+TGG - chr2_2:14373343-14373362 Msa0239800:three_prime_UTR 20.0%
!!! GTTACTAAAATTTTGTGATT+TGG - chr2_2:14373852-14373871 Msa0239800:intron 20.0%
!! AATTGTTTGAGAAAAAAAGT+TGG - chr2_2:14373967-14373986 Msa0239800:intron 20.0%
!!! TTTTATTTCAGTTTTTCAAC+TGG + chr2_2:14374028-14374047 None:intergenic 20.0%
!! ACTTAATTGGAAAATACAAA+AGG + chr2_2:14374074-14374093 None:intergenic 20.0%
!! TCAAAAAGAAGAAGAAAAAT+TGG + chr2_2:14374280-14374299 None:intergenic 20.0%
!!! CAAATTTAATGTTTAGCTTT+AGG - chr2_2:14374309-14374328 Msa0239800:intron 20.0%
! ACATATAAATTGGATAACAC+AGG - chr2_2:14373353-14373372 Msa0239800:three_prime_UTR 25.0%
! TTAACGATTGAAATTAGTGA+CGG - chr2_2:14373717-14373736 Msa0239800:CDS 25.0%
! AAAGACAAGATAGTAGTTAT+TGG - chr2_2:14373916-14373935 Msa0239800:intron 25.0%
! AATAAGAAGTGAGAAAAACA+AGG + chr2_2:14374139-14374158 None:intergenic 25.0%
!!! TTGTTTTTCTCACTTCTTAT+TGG - chr2_2:14374138-14374157 Msa0239800:intron 25.0%
!!! ATATTTGGATTGGTATGTAA+TGG - chr2_2:14374342-14374361 Msa0239800:intron 25.0%
! ACATATAAATTGGATAACAC+AGG - chr2_2:14373353-14373372 Msa0239800:three_prime_UTR 25.0%
! TTAACGATTGAAATTAGTGA+CGG - chr2_2:14373717-14373736 Msa0239800:CDS 25.0%
! AAAGACAAGATAGTAGTTAT+TGG - chr2_2:14373916-14373935 Msa0239800:intron 25.0%
! AATAAGAAGTGAGAAAAACA+AGG + chr2_2:14374139-14374158 None:intergenic 25.0%
!!! TTGTTTTTCTCACTTCTTAT+TGG - chr2_2:14374138-14374157 Msa0239800:intron 25.0%
!!! ATATTTGGATTGGTATGTAA+TGG - chr2_2:14374342-14374361 Msa0239800:intron 25.0%
GCTAAGTCATTAATATCACA+AGG + chr2_2:14373278-14373297 None:intergenic 30.0%
! TTTCATCTCTGAAAACATGA+AGG - chr2_2:14373392-14373411 Msa0239800:three_prime_UTR 30.0%
AAGATAGTAGTTATTGGAGA+TGG - chr2_2:14373922-14373941 Msa0239800:intron 30.0%
TCAACAAAGTTGTCATCAAA+TGG + chr2_2:14374113-14374132 None:intergenic 30.0%
TTCTTATTGGTCAAAAGCAA+TGG - chr2_2:14374151-14374170 Msa0239800:intron 30.0%
!!! AACCACTTTTTGACAACTTT+TGG + chr2_2:14374236-14374255 None:intergenic 30.0%
! TGGTATGTAATGGAATGAAA+TGG - chr2_2:14374352-14374371 Msa0239800:intron 30.0%
GCTAAGTCATTAATATCACA+AGG + chr2_2:14373278-14373297 None:intergenic 30.0%
! TTTCATCTCTGAAAACATGA+AGG - chr2_2:14373392-14373411 Msa0239800:three_prime_UTR 30.0%
AAGATAGTAGTTATTGGAGA+TGG - chr2_2:14373922-14373941 Msa0239800:intron 30.0%
TCAACAAAGTTGTCATCAAA+TGG + chr2_2:14374113-14374132 None:intergenic 30.0%
TTCTTATTGGTCAAAAGCAA+TGG - chr2_2:14374151-14374170 Msa0239800:intron 30.0%
!!! AACCACTTTTTGACAACTTT+TGG + chr2_2:14374236-14374255 None:intergenic 30.0%
! TGGTATGTAATGGAATGAAA+TGG - chr2_2:14374352-14374371 Msa0239800:intron 30.0%
!! TTTTGTGATTTGGCAAATGC+AGG - chr2_2:14373862-14373881 Msa0239800:intron 35.0%
! AAATGCAGGTGTGAATTTTG+TGG - chr2_2:14373876-14373895 Msa0239800:intron 35.0%
! AATGCAGGTGTGAATTTTGT+GGG - chr2_2:14373877-14373896 Msa0239800:intron 35.0%
! TGTGAATTTTGTGGGATTAG+AGG - chr2_2:14373885-14373904 Msa0239800:intron 35.0%
! GTGAATTTTGTGGGATTAGA+GGG - chr2_2:14373886-14373905 Msa0239800:intron 35.0%
CAAACTGAAATTGTCAGCTT+AGG - chr2_2:14373991-14374010 Msa0239800:CDS 35.0%
AAAGCAATGGAGAGAGAAAA+AGG - chr2_2:14374164-14374183 Msa0239800:intron 35.0%
GTCCAAAAGTTGTCAAAAAG+TGG - chr2_2:14374231-14374250 Msa0239800:intron 35.0%
!! TTTTGTGATTTGGCAAATGC+AGG - chr2_2:14373862-14373881 Msa0239800:intron 35.0%
! AAATGCAGGTGTGAATTTTG+TGG - chr2_2:14373876-14373895 Msa0239800:intron 35.0%
! AATGCAGGTGTGAATTTTGT+GGG - chr2_2:14373877-14373896 Msa0239800:intron 35.0%
! TGTGAATTTTGTGGGATTAG+AGG - chr2_2:14373885-14373904 Msa0239800:intron 35.0%
! GTGAATTTTGTGGGATTAGA+GGG - chr2_2:14373886-14373905 Msa0239800:intron 35.0%
CAAACTGAAATTGTCAGCTT+AGG - chr2_2:14373991-14374010 Msa0239800:CDS 35.0%
AAAGCAATGGAGAGAGAAAA+AGG - chr2_2:14374164-14374183 Msa0239800:intron 35.0%
GTCCAAAAGTTGTCAAAAAG+TGG - chr2_2:14374231-14374250 Msa0239800:intron 35.0%
AACGTAAGTCAAAGTCTTGC+AGG + chr2_2:14373311-14373330 None:intergenic 40.0%
GTGATCAAACTTGGGAACAA+AGG + chr2_2:14373335-14373354 None:intergenic 40.0%
TGCAGCAAAAGATTGTGATG+AGG - chr2_2:14373559-14373578 Msa0239800:three_prime_UTR 40.0%
GCAGCAAAAGATTGTGATGA+GGG - chr2_2:14373560-14373579 Msa0239800:three_prime_UTR 40.0%
AGAGAGAAAAAGGAAGAGAG+AGG - chr2_2:14374174-14374193 Msa0239800:intron 40.0%
AACGTAAGTCAAAGTCTTGC+AGG + chr2_2:14373311-14373330 None:intergenic 40.0%
GTGATCAAACTTGGGAACAA+AGG + chr2_2:14373335-14373354 None:intergenic 40.0%
TGCAGCAAAAGATTGTGATG+AGG - chr2_2:14373559-14373578 Msa0239800:three_prime_UTR 40.0%
GCAGCAAAAGATTGTGATGA+GGG - chr2_2:14373560-14373579 Msa0239800:three_prime_UTR 40.0%
AGAGAGAAAAAGGAAGAGAG+AGG - chr2_2:14374174-14374193 Msa0239800:intron 40.0%
!! ATGTCAAAAGTGTCGCACCA+AGG - chr2_2:14373593-14373612 Msa0239800:CDS 45.0%
AAGGTTGTAGCTGGAGCAAA+CGG - chr2_2:14373621-14373640 Msa0239800:CDS 45.0%
!! ATGTCAAAAGTGTCGCACCA+AGG - chr2_2:14373593-14373612 Msa0239800:CDS 45.0%
AAGGTTGTAGCTGGAGCAAA+CGG - chr2_2:14373621-14373640 Msa0239800:CDS 45.0%
AGCTACAACCTTGAGTGCCT+TGG + chr2_2:14373613-14373632 None:intergenic 50.0%
! AAGGCACTCAAGGTTGTAGC+TGG - chr2_2:14373612-14373631 Msa0239800:CDS 50.0%
AGCTACAACCTTGAGTGCCT+TGG + chr2_2:14373613-14373632 None:intergenic 50.0%
! AAGGCACTCAAGGTTGTAGC+TGG - chr2_2:14373612-14373631 Msa0239800:CDS 50.0%
! GTGTCGCACCAAGGCACTCA+AGG - chr2_2:14373602-14373621 Msa0239800:CDS 60.0%
! GTGTCGCACCAAGGCACTCA+AGG - chr2_2:14373602-14373621 Msa0239800:CDS 60.0%
Chromosome Type Strat End Strand Name
chr2_2 gene 14373215 14374407 14373215 ID=Msa0239800;Name=Msa0239800
chr2_2 mRNA 14373215 14374407 14373215 ID=Msa0239800-mRNA-1;Parent=Msa0239800;Name=Msa0239800-mRNA-1;_AED=0.03;_eAED=0.03;_QI=0|0.66|0.5|0.75|0.66|0.75|4|375|93
chr2_2 exon 14373215 14373738 14373215 ID=Msa0239800-mRNA-1:exon:5974;Parent=Msa0239800-mRNA-1
chr2_2 exon 14373980 14374058 14373980 ID=Msa0239800-mRNA-1:exon:5973;Parent=Msa0239800-mRNA-1
chr2_2 exon 14374209 14374247 14374209 ID=Msa0239800-mRNA-1:exon:5972;Parent=Msa0239800-mRNA-1
chr2_2 exon 14374393 14374407 14374393 ID=Msa0239800-mRNA-1:exon:5971;Parent=Msa0239800-mRNA-1
chr2_2 CDS 14374393 14374407 14374393 ID=Msa0239800-mRNA-1:cds;Parent=Msa0239800-mRNA-1
chr2_2 CDS 14374209 14374247 14374209 ID=Msa0239800-mRNA-1:cds;Parent=Msa0239800-mRNA-1
chr2_2 CDS 14373980 14374058 14373980 ID=Msa0239800-mRNA-1:cds;Parent=Msa0239800-mRNA-1
chr2_2 CDS 14373590 14373738 14373590 ID=Msa0239800-mRNA-1:cds;Parent=Msa0239800-mRNA-1
chr2_2 three_prime_UTR 14373215 14373589 14373215 ID=Msa0239800-mRNA-1:three_prime_utr;Parent=Msa0239800-mRNA-1
Gene Sequence

>Msa0239800

ATGAATTTTCTAGAAGTTAAGTTTCTTAAGAATTTCATCTCTGAAAACATGAAGCAAAAGATTGTGATGAGGGTTAGCATGAGATGTCAAAAGTGTCGCACCAAGGCACTCAAGGTTGTAGCTGGAGCAAACGGTGTGAATTTTGTGGGATTAGAGGGAGATGAGAAAGACAAGATAGTAGTTATTGGAGATGGTGTAGATGCTGTCAAGTTGACAAATTGTTTGAGAAAAAAAGTTGGACAAACTGAAATTGTCAGCTTAGGAGAAGTTAAAGCCAGTTGA

Protein sequence

>Msa0239800

MNFLEVKFLKNFISENMKQKIVMRVSMRCQKCRTKALKVVAGANGVNFVGLEGDEKDKIVVIGDGVDAVKLTNCLRKKVGQTEIVSLGEVKAS*