AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0590650


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0590650 MtrunA17_Chr4g0008411 97.462 197 5 0 1 197 1 197 6.99e-138 385
Msa0590650 MtrunA17_Chr4g0008421 73.301 206 46 3 1 201 88 289 1.33e-103 300
Msa0590650 MtrunA17_Chr7g0266341 37.000 200 108 10 11 201 102 292 7.50e-24 95.9
Msa0590650 MtrunA17_Chr2g0306771 37.500 192 94 6 11 201 211 377 3.70e-22 92.4
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0590650 AT2G37970.1 60.648 216 69 3 1 201 32 246 4.41e-89 262
Msa0590650 AT5G20140.1 34.031 191 103 5 11 201 206 373 3.20e-21 90.1
Msa0590650 AT3G10130.1 36.683 199 110 9 11 201 115 305 1.31e-19 85.1
Msa0590650 AT5G20140.2 33.898 177 94 5 11 187 206 359 9.89e-19 83.6

Find 38 sgRNAs with CRISPR-Local

Find 52 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TGACAAAGATGGTGGGTTTA+AGG 0.186605 4_2:+14217179 Msa0590650:CDS
GAGGAAGGTGGGAAGAAATA+TGG 0.218011 4_2:+14217441 Msa0590650:CDS
TTTGATATGGGATTAGTATT+TGG 0.244674 4_2:+14217036 None:intergenic
AAATATGGGGTGGTGACTTT+TGG 0.302611 4_2:+14217456 Msa0590650:CDS
TTCTTCTCATTTGTTACAAC+TGG 0.303094 4_2:-14217327 None:intergenic
CGATTACAATTCCAATGTTT+AGG 0.308020 4_2:+14217595 Msa0590650:CDS
TTGTCACCTTTGAATGTTGA+TGG 0.319242 4_2:-14217162 None:intergenic
AGGAAGGTGGGAAGAAATAT+GGG 0.347201 4_2:+14217442 Msa0590650:CDS
ATCATCATGGTTCATTCAAC+AGG 0.393338 4_2:-14217636 None:intergenic
GGAGAAGTTGAGGTTGTGTT+TGG 0.422907 4_2:+14217515 Msa0590650:CDS
TTTGAATGTTGATGGATCAT+AGG 0.426497 4_2:-14217154 None:intergenic
ATCACAACCCTCTCATCAAT+AGG 0.466452 4_2:-14217414 None:intergenic
TTGTGATAAGAGAGGAAGGT+GGG 0.471919 4_2:+14217430 Msa0590650:CDS
AGGGTTGTGATAAGAGAGGA+AGG 0.486753 4_2:+14217426 Msa0590650:CDS
AGGAGAAGGTGGAGAAGTTG+AGG 0.492065 4_2:+14217505 Msa0590650:CDS
TCCAATGTTTAGGACTAATG+AGG 0.513944 4_2:+14217605 Msa0590650:CDS
AGGTTGTGTTTGGAGAAAGA+TGG 0.524733 4_2:+14217525 Msa0590650:CDS
TGAGAGGGTTGTGATAAGAG+AGG 0.529346 4_2:+14217422 Msa0590650:CDS
GGCAAGTGATGAAGTGGTGA+AGG 0.533494 4_2:+14217485 Msa0590650:CDS
TATGATCCATCAACATTCAA+AGG 0.542632 4_2:+14217156 Msa0590650:CDS
AACATTGGAATTGTAATCGC+AGG 0.545246 4_2:-14217591 None:intergenic
ACCTAAGCCTATTGATGAGA+GGG 0.548573 4_2:+14217407 Msa0590650:CDS
TGAAGTGGTGAAGGAGAAGG+TGG 0.549018 4_2:+14217494 Msa0590650:CDS
ACCCTCTCATCAATAGGCTT+AGG 0.549333 4_2:-14217408 None:intergenic
ACCTCATTAGTCCTAAACAT+TGG 0.561532 4_2:-14217606 None:intergenic
ATTGGAATTGTAATCGCAGG+TGG 0.568955 4_2:-14217588 None:intergenic
TGATGAAGTGGTGAAGGAGA+AGG 0.572950 4_2:+14217491 Msa0590650:CDS
ACATTCAAAGGTGACAAAGA+TGG 0.580055 4_2:+14217168 Msa0590650:CDS
TTCAAAGGTGACAAAGATGG+TGG 0.592548 4_2:+14217171 Msa0590650:CDS
GTGATTTCAGCTACTAGAGA+AGG 0.604224 4_2:-14217132 None:intergenic
TACCTAAGCCTATTGATGAG+AGG 0.615966 4_2:+14217406 Msa0590650:CDS
AGGAGTGGCAAGTGATGAAG+TGG 0.624838 4_2:+14217479 Msa0590650:CDS
AACAAATGAGAAGAACAAGA+TGG 0.636525 4_2:+14217335 Msa0590650:CDS
TCAAAGGTGACAAAGATGGT+GGG 0.643345 4_2:+14217172 Msa0590650:CDS
AGGTGGGAAGAAATATGGGG+TGG 0.665542 4_2:+14217446 Msa0590650:CDS
GTTGTGATAAGAGAGGAAGG+TGG 0.671478 4_2:+14217429 Msa0590650:CDS
GGAAGGTGGGAAGAAATATG+GGG 0.684324 4_2:+14217443 Msa0590650:CDS
GACTTCACCAGTTATCACAA+AGG 0.689440 4_2:+14217266 Msa0590650:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! GTTTTGAGTATTTCATATTT+TGG - chr4_2:14217081-14217100 None:intergenic 20.0%
!!! AAGGTTTTAGTTGATTACAT+AGG + chr4_2:14217198-14217217 Msa0590650:CDS 25.0%
!! GTTGATTACATAGGAATTTT+TGG + chr4_2:14217207-14217226 Msa0590650:CDS 25.0%
!!! TTTTGTGTTTTTGTGTTTTG+AGG - chr4_2:14217237-14217256 None:intergenic 25.0%
!!! TCTACTTTTTCATACATAGA+AGG - chr4_2:14217381-14217400 None:intergenic 25.0%
! TTCTATGTATGAAAAAGTAG+AGG + chr4_2:14217380-14217399 Msa0590650:CDS 25.0%
!!! AAAGATGGTTTTAAGGTTAT+TGG + chr4_2:14217540-14217559 Msa0590650:CDS 25.0%
!!! GTTATTGGAGATTTTTTGTT+GGG + chr4_2:14217555-14217574 Msa0590650:CDS 25.0%
! TTTGAATGTTGATGGATCAT+AGG - chr4_2:14217157-14217176 None:intergenic 30.0%
TATGATCCATCAACATTCAA+AGG + chr4_2:14217156-14217175 Msa0590650:CDS 30.0%
! TTGTTTTCCTTTGTGATAAC+TGG - chr4_2:14217276-14217295 None:intergenic 30.0%
! TTCTTCTCATTTGTTACAAC+TGG - chr4_2:14217330-14217349 None:intergenic 30.0%
AACAAATGAGAAGAACAAGA+TGG + chr4_2:14217335-14217354 Msa0590650:CDS 30.0%
!! TTTGGAGAAAGATGGTTTTA+AGG + chr4_2:14217533-14217552 Msa0590650:CDS 30.0%
!!! GGTTATTGGAGATTTTTTGT+TGG + chr4_2:14217554-14217573 Msa0590650:CDS 30.0%
CGATTACAATTCCAATGTTT+AGG + chr4_2:14217595-14217614 Msa0590650:CDS 30.0%
!!! TCGGATTACATAGTTTTGTG+TGG - chr4_2:14217103-14217122 None:intergenic 35.0%
!! CTAGAGAAGGTGCATATTTT+CGG - chr4_2:14217122-14217141 None:intergenic 35.0%
TTGTCACCTTTGAATGTTGA+TGG - chr4_2:14217165-14217184 None:intergenic 35.0%
ACATTCAAAGGTGACAAAGA+TGG + chr4_2:14217168-14217187 Msa0590650:CDS 35.0%
!!! TTGGAGATTTTTTGTTGGGT+AGG + chr4_2:14217559-14217578 Msa0590650:CDS 35.0%
AACATTGGAATTGTAATCGC+AGG - chr4_2:14217594-14217613 None:intergenic 35.0%
! TCCAATGTTTAGGACTAATG+AGG + chr4_2:14217605-14217624 Msa0590650:CDS 35.0%
ACCTCATTAGTCCTAAACAT+TGG - chr4_2:14217609-14217628 None:intergenic 35.0%
GTGATTTCAGCTACTAGAGA+AGG - chr4_2:14217135-14217154 None:intergenic 40.0%
TTCAAAGGTGACAAAGATGG+TGG + chr4_2:14217171-14217190 Msa0590650:CDS 40.0%
TCAAAGGTGACAAAGATGGT+GGG + chr4_2:14217172-14217191 Msa0590650:CDS 40.0%
!! TGACAAAGATGGTGGGTTTA+AGG + chr4_2:14217179-14217198 Msa0590650:CDS 40.0%
GACTTCACCAGTTATCACAA+AGG + chr4_2:14217266-14217285 Msa0590650:CDS 40.0%
TACCTAAGCCTATTGATGAG+AGG + chr4_2:14217406-14217425 Msa0590650:CDS 40.0%
ACCTAAGCCTATTGATGAGA+GGG + chr4_2:14217407-14217426 Msa0590650:CDS 40.0%
ATCACAACCCTCTCATCAAT+AGG - chr4_2:14217417-14217436 None:intergenic 40.0%
TTGTGATAAGAGAGGAAGGT+GGG + chr4_2:14217430-14217449 Msa0590650:CDS 40.0%
AGGAAGGTGGGAAGAAATAT+GGG + chr4_2:14217442-14217461 Msa0590650:CDS 40.0%
! AAATATGGGGTGGTGACTTT+TGG + chr4_2:14217456-14217475 Msa0590650:CDS 40.0%
AGGTTGTGTTTGGAGAAAGA+TGG + chr4_2:14217525-14217544 Msa0590650:CDS 40.0%
ATTGGAATTGTAATCGCAGG+TGG - chr4_2:14217591-14217610 None:intergenic 40.0%
ACCCTCTCATCAATAGGCTT+AGG - chr4_2:14217411-14217430 None:intergenic 45.0%
TGAGAGGGTTGTGATAAGAG+AGG + chr4_2:14217422-14217441 Msa0590650:CDS 45.0%
AGGGTTGTGATAAGAGAGGA+AGG + chr4_2:14217426-14217445 Msa0590650:CDS 45.0%
GTTGTGATAAGAGAGGAAGG+TGG + chr4_2:14217429-14217448 Msa0590650:CDS 45.0%
GAGGAAGGTGGGAAGAAATA+TGG + chr4_2:14217441-14217460 Msa0590650:CDS 45.0%
GGAAGGTGGGAAGAAATATG+GGG + chr4_2:14217443-14217462 Msa0590650:CDS 45.0%
TGATGAAGTGGTGAAGGAGA+AGG + chr4_2:14217491-14217510 Msa0590650:CDS 45.0%
GGAGAAGTTGAGGTTGTGTT+TGG + chr4_2:14217515-14217534 Msa0590650:CDS 45.0%
AGGTGGGAAGAAATATGGGG+TGG + chr4_2:14217446-14217465 Msa0590650:CDS 50.0%
! TATGGGGTGGTGACTTTTGG+AGG + chr4_2:14217459-14217478 Msa0590650:CDS 50.0%
AGGAGTGGCAAGTGATGAAG+TGG + chr4_2:14217479-14217498 Msa0590650:CDS 50.0%
GGCAAGTGATGAAGTGGTGA+AGG + chr4_2:14217485-14217504 Msa0590650:CDS 50.0%
TGAAGTGGTGAAGGAGAAGG+TGG + chr4_2:14217494-14217513 Msa0590650:CDS 50.0%
AGGAGAAGGTGGAGAAGTTG+AGG + chr4_2:14217505-14217524 Msa0590650:CDS 50.0%
!! GGTGGTGACTTTTGGAGGAG+TGG + chr4_2:14217464-14217483 Msa0590650:CDS 55.0%
Chromosome Type Strat End Strand Name
chr4_2 gene 14217042 14217647 14217042 ID=Msa0590650;Name=Msa0590650
chr4_2 mRNA 14217042 14217647 14217042 ID=Msa0590650-mRNA-1;Parent=Msa0590650;Name=Msa0590650-mRNA-1;_AED=0.25;_eAED=0.26;_QI=0|-1|0|1|-1|1|1|0|201
chr4_2 exon 14217042 14217647 14217042 ID=Msa0590650-mRNA-1:exon:4129;Parent=Msa0590650-mRNA-1
chr4_2 CDS 14217042 14217647 14217042 ID=Msa0590650-mRNA-1:cds;Parent=Msa0590650-mRNA-1
Gene Sequence

>Msa0590650

ATGGGATTAGTATTTGGAAGATTTAGTGCTGAGACACCAAAATATGAAATACTCAAAACCACACAAAACTATGTAATCCGAAAATATGCACCTTCTCTAGTAGCTGAAATCACCTATGATCCATCAACATTCAAAGGTGACAAAGATGGTGGGTTTAAGGTTTTAGTTGATTACATAGGAATTTTTGGTAAACCTCAAAACACAAAAACACAAAAAATCTCAATGACTTCACCAGTTATCACAAAGGAAAACAAAAATTTTTCAGAAAAGATTGCTATGACAGTACCAGTTGTAACAAATGAGAAGAACAAGATGGTGACTATGCAGTTTACTTTGCCTTCTATGTATGAAAAAGTAGAGGAAGTACCTAAGCCTATTGATGAGAGGGTTGTGATAAGAGAGGAAGGTGGGAAGAAATATGGGGTGGTGACTTTTGGAGGAGTGGCAAGTGATGAAGTGGTGAAGGAGAAGGTGGAGAAGTTGAGGTTGTGTTTGGAGAAAGATGGTTTTAAGGTTATTGGAGATTTTTTGTTGGGTAGGTATAATCCACCTGCGATTACAATTCCAATGTTTAGGACTAATGAGGTTTTGATTCCTGTTGAATGA

Protein sequence

>Msa0590650

MGLVFGRFSAETPKYEILKTTQNYVIRKYAPSLVAEITYDPSTFKGDKDGGFKVLVDYIGIFGKPQNTKTQKISMTSPVITKENKNFSEKIAMTVPVVTNEKNKMVTMQFTLPSMYEKVEEVPKPIDERVVIREEGGKKYGVVTFGGVASDEVVKEKVEKLRLCLEKDGFKVIGDFLLGRYNPPAITIPMFRTNEVLIPVE*