AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1459590


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1459590 MtrunA17_Chr4g0076191 95.361 194 6 1 1 194 1 191 3.22e-131 366
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1459590 AT4G16410.1 62.609 115 41 2 80 193 71 184 2.14e-43 143

Find 39 sgRNAs with CRISPR-Local

Find 49 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CAAGAGGGGTTGGAGGAATT+TGG 0.164087 tig0040335:-14512 None:intergenic
ATTCTCATCATTGCTATTCT+TGG 0.233178 tig0040335:+14959 Msa1459590:CDS
CACTTCTGGAAGAAGAGTTT+TGG 0.247345 tig0040335:+14831 Msa1459590:CDS
GAGCAAAAGGCATTGGCTTT+TGG 0.251573 tig0040335:+14797 Msa1459590:CDS
ATGATGAGAATTGCAGTAAT+TGG 0.254419 tig0040335:-14947 None:intergenic
TGGACCTGAAGGACCACTTC+TGG 0.347564 tig0040335:+14817 Msa1459590:CDS
TCTTCCAGAAGTGGTCCTTC+AGG 0.352779 tig0040335:-14821 None:intergenic
TTTAATGCCTAATACTTTGA+TGG 0.358229 tig0040335:-14576 None:intergenic
AATTCAAAGATTGTGATAAT+AGG 0.375780 tig0040335:+14731 Msa1459590:CDS
AGAAATGGAAGTTTCATTGA+TGG 0.380684 tig0040335:-14698 None:intergenic
ATCAAACCCATCAAAGTATT+AGG 0.381123 tig0040335:+14569 Msa1459590:CDS
CCACAGTTGGTGTGTGTTTG+AGG 0.388523 tig0040335:-14658 None:intergenic
GGTGTGTGTTTGAGGAAAAT+TGG 0.393174 tig0040335:-14650 None:intergenic
TTCTCAAGTCCTTACTGCTA+TGG 0.416025 tig0040335:+15000 Msa1459590:CDS
CTCATCATTGCTATTCTTGG+AGG 0.417146 tig0040335:+14962 Msa1459590:CDS
ATCATTGCTATTCTTGGAGG+TGG 0.422996 tig0040335:+14965 Msa1459590:CDS
CTTTGTGCATCTTCCACAGT+TGG 0.439217 tig0040335:-14671 None:intergenic
GAAAAGAGAACAAGAGGGGT+TGG 0.443409 tig0040335:-14522 None:intergenic
GAATGGAATGGATGAGCAAA+AGG 0.459747 tig0040335:+14784 Msa1459590:CDS
AAGAGAACAAGAGGGGTTGG+AGG 0.462285 tig0040335:-14519 None:intergenic
TTAATGCCTAATACTTTGAT+GGG 0.463239 tig0040335:-14575 None:intergenic
TGGGTTTGATAAATACTTGA+TGG 0.474365 tig0040335:-14556 None:intergenic
ATAATAGGAGCAGTTTCTCT+TGG 0.477281 tig0040335:+14746 Msa1459590:CDS
TGGGACAACGTGAGAAGGTA+TGG 0.479294 tig0040335:+14851 Msa1459590:CDS
AACTGTGGAAGATGCACAAA+GGG 0.491879 tig0040335:+14673 Msa1459590:CDS
GGTTGGAGGAATTTGGAAGC+TGG 0.507532 tig0040335:-14505 None:intergenic
TTCTTGAGAAGCTCAAATAT+AGG 0.508858 tig0040335:-14923 None:intergenic
AGGTGCAATATACACAATCT+TGG 0.535873 tig0040335:+14898 Msa1459590:CDS
CAAGTCCTTACTGCTATGGT+TGG 0.540150 tig0040335:+15004 Msa1459590:CDS
CAAAACTCTTCTTCCAGAAG+TGG 0.542465 tig0040335:-14830 None:intergenic
TTTGTTGGTTCTGAATGGAA+TGG 0.544407 tig0040335:+14772 Msa1459590:CDS
TGGAGTGAAAAGAGAACAAG+AGG 0.556434 tig0040335:-14528 None:intergenic
TATGCACTAACTGTTAGTAC+AGG 0.569987 tig0040335:+14878 Msa1459590:CDS
AATGGATGAGCAAAAGGCAT+TGG 0.578741 tig0040335:+14790 Msa1459590:CDS
AAACGCCAACCATAGCAGTA+AGG 0.591938 tig0040335:-15009 None:intergenic
CCTCAAACACACACCAACTG+TGG 0.606028 tig0040335:+14658 Msa1459590:CDS
GAGTGAAAAGAGAACAAGAG+GGG 0.620816 tig0040335:-14526 None:intergenic
CAACTGTGGAAGATGCACAA+AGG 0.630847 tig0040335:+14672 Msa1459590:CDS
GGAGTGAAAAGAGAACAAGA+GGG 0.645371 tig0040335:-14527 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! ATAAATACTTGATGGTTTTT+TGG - tig0040335:14551-14570 None:intergenic 20.0%
!!! AGTTTTATTGCATATTTTGA+AGG - tig0040335:14617-14636 None:intergenic 20.0%
!! AATTCAAAGATTGTGATAAT+AGG + tig0040335:14731-14750 Msa1459590:CDS 20.0%
! TTAATGCCTAATACTTTGAT+GGG - tig0040335:14578-14597 None:intergenic 25.0%
! TTTAATGCCTAATACTTTGA+TGG - tig0040335:14579-14598 None:intergenic 25.0%
!!! TTATTGCATATTTTGAAGGT+GGG - tig0040335:14613-14632 None:intergenic 25.0%
!!! TTTATTGCATATTTTGAAGG+TGG - tig0040335:14614-14633 None:intergenic 25.0%
!!! GAATTCTCATTTTCAAGAAA+TGG - tig0040335:14716-14735 None:intergenic 25.0%
TGGGTTTGATAAATACTTGA+TGG - tig0040335:14559-14578 None:intergenic 30.0%
! ATCAAACCCATCAAAGTATT+AGG + tig0040335:14569-14588 Msa1459590:CDS 30.0%
AGAAATGGAAGTTTCATTGA+TGG - tig0040335:14701-14720 None:intergenic 30.0%
! AGTTTCTCTTGGAATTTTGT+TGG + tig0040335:14757-14776 Msa1459590:CDS 30.0%
TTCTTGAGAAGCTCAAATAT+AGG - tig0040335:14926-14945 None:intergenic 30.0%
ATGATGAGAATTGCAGTAAT+TGG - tig0040335:14950-14969 None:intergenic 30.0%
! ATTCTCATCATTGCTATTCT+TGG + tig0040335:14959-14978 Msa1459590:CDS 30.0%
ATAATAGGAGCAGTTTCTCT+TGG + tig0040335:14746-14765 Msa1459590:CDS 35.0%
!!! GGAATTTTGTTGGTTCTGAA+TGG + tig0040335:14767-14786 Msa1459590:CDS 35.0%
!! TTTGTTGGTTCTGAATGGAA+TGG + tig0040335:14772-14791 Msa1459590:CDS 35.0%
!! ACTTCTGGAAGAAGAGTTTT+GGG + tig0040335:14832-14851 Msa1459590:CDS 35.0%
TATGCACTAACTGTTAGTAC+AGG + tig0040335:14878-14897 Msa1459590:CDS 35.0%
AGGTGCAATATACACAATCT+TGG + tig0040335:14898-14917 Msa1459590:CDS 35.0%
GAGTGAAAAGAGAACAAGAG+GGG - tig0040335:14529-14548 None:intergenic 40.0%
GGAGTGAAAAGAGAACAAGA+GGG - tig0040335:14530-14549 None:intergenic 40.0%
TGGAGTGAAAAGAGAACAAG+AGG - tig0040335:14531-14550 None:intergenic 40.0%
GGTGTGTGTTTGAGGAAAAT+TGG - tig0040335:14653-14672 None:intergenic 40.0%
AACTGTGGAAGATGCACAAA+GGG + tig0040335:14673-14692 Msa1459590:CDS 40.0%
GAATGGAATGGATGAGCAAA+AGG + tig0040335:14784-14803 Msa1459590:CDS 40.0%
! AATGGATGAGCAAAAGGCAT+TGG + tig0040335:14790-14809 Msa1459590:CDS 40.0%
CAAAACTCTTCTTCCAGAAG+TGG - tig0040335:14833-14852 None:intergenic 40.0%
!! CACTTCTGGAAGAAGAGTTT+TGG + tig0040335:14831-14850 Msa1459590:CDS 40.0%
! CTCATCATTGCTATTCTTGG+AGG + tig0040335:14962-14981 Msa1459590:CDS 40.0%
! ATCATTGCTATTCTTGGAGG+TGG + tig0040335:14965-14984 Msa1459590:CDS 40.0%
TTCTCAAGTCCTTACTGCTA+TGG + tig0040335:15000-15019 Msa1459590:CDS 40.0%
GAAAAGAGAACAAGAGGGGT+TGG - tig0040335:14525-14544 None:intergenic 45.0%
CTTTGTGCATCTTCCACAGT+TGG - tig0040335:14674-14693 None:intergenic 45.0%
CAACTGTGGAAGATGCACAA+AGG + tig0040335:14672-14691 Msa1459590:CDS 45.0%
!!! GAGCAAAAGGCATTGGCTTT+TGG + tig0040335:14797-14816 Msa1459590:CDS 45.0%
!!! AGTTTTGGGACAACGTGAGA+AGG + tig0040335:14846-14865 Msa1459590:CDS 45.0%
CAAGTCCTTACTGCTATGGT+TGG + tig0040335:15004-15023 Msa1459590:CDS 45.0%
AAACGCCAACCATAGCAGTA+AGG - tig0040335:15012-15031 None:intergenic 45.0%
GGTTGGAGGAATTTGGAAGC+TGG - tig0040335:14508-14527 None:intergenic 50.0%
CAAGAGGGGTTGGAGGAATT+TGG - tig0040335:14515-14534 None:intergenic 50.0%
AAGAGAACAAGAGGGGTTGG+AGG - tig0040335:14522-14541 None:intergenic 50.0%
! CCACAGTTGGTGTGTGTTTG+AGG - tig0040335:14661-14680 None:intergenic 50.0%
CCTCAAACACACACCAACTG+TGG + tig0040335:14658-14677 Msa1459590:CDS 50.0%
!!! GCATTGGCTTTTGGACCTGA+AGG + tig0040335:14806-14825 Msa1459590:CDS 50.0%
TCTTCCAGAAGTGGTCCTTC+AGG - tig0040335:14824-14843 None:intergenic 50.0%
TGGGACAACGTGAGAAGGTA+TGG + tig0040335:14851-14870 Msa1459590:CDS 50.0%
TGGACCTGAAGGACCACTTC+TGG + tig0040335:14817-14836 Msa1459590:CDS 55.0%
Chromosome Type Strat End Strand Name
tig0040335 gene 14476 15060 14476 ID=Msa1459590;Name=Msa1459590
tig0040335 mRNA 14476 15060 14476 ID=Msa1459590-mRNA-1;Parent=Msa1459590;Name=Msa1459590-mRNA-1;_AED=0.00;_eAED=0.02;_QI=0|-1|0|1|-1|1|1|0|194
tig0040335 exon 14476 15060 14476 ID=Msa1459590-mRNA-1:exon:22300;Parent=Msa1459590-mRNA-1
tig0040335 CDS 14476 15060 14476 ID=Msa1459590-mRNA-1:cds;Parent=Msa1459590-mRNA-1
Gene Sequence

>Msa1459590

ATGAAAAATCTTAGCTTGAAATTAAAGCTCCAGCTTCCAAATTCCTCCAACCCCTCTTGTTCTCTTTTCACTCCAAAAAACCATCAAGTATTTATCAAACCCATCAAAGTATTAGGCATTAAAAACTTCAAAAACCCACCTTCAAAATATGCAATAAAACTTAGAGAAGCTTCTCCAATTTTCCTCAAACACACACCAACTGTGGAAGATGCACAAAGGGCACCATCAATGAAACTTCCATTTCTTGAAAATGAGAATTCAAAGATTGTGATAATAGGAGCAGTTTCTCTTGGAATTTTGTTGGTTCTGAATGGAATGGATGAGCAAAAGGCATTGGCTTTTGGACCTGAAGGACCACTTCTGGAAGAAGAGTTTTGGGACAACGTGAGAAGGTATGGTTTGTATGCACTAACTGTTAGTACAGGTGCAATATACACAATCTTGGTGCCTATATTTGAGCTTCTCAAGAATCCAATTACTGCAATTCTCATCATTGCTATTCTTGGAGGTGGTTTCTACATTGTTTCTCAAGTCCTTACTGCTATGGTTGGCGTTTCTGATTTTAGTTATGATTATGCAAACTAG

Protein sequence

>Msa1459590

MKNLSLKLKLQLPNSSNPSCSLFTPKNHQVFIKPIKVLGIKNFKNPPSKYAIKLREASPIFLKHTPTVEDAQRAPSMKLPFLENENSKIVIIGAVSLGILLVLNGMDEQKALAFGPEGPLLEEEFWDNVRRYGLYALTVSTGAIYTILVPIFELLKNPITAILIIAILGGGFYIVSQVLTAMVGVSDFSYDYAN*