AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0534410


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0534410 MtrunA17_Chr4g0008411 97.970 197 4 0 1 197 1 197 2.05e-139 389
Msa0534410 MtrunA17_Chr4g0008421 73.786 206 45 3 1 201 88 289 1.07e-104 303
Msa0534410 MtrunA17_Chr7g0266341 37.500 200 107 10 11 201 102 292 4.25e-25 99.0
Msa0534410 MtrunA17_Chr2g0306771 37.500 192 94 6 11 201 211 377 3.35e-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
Msa0534410 AT2G37970.1 60.185 216 70 3 1 201 32 246 1.13e-88 261
Msa0534410 AT5G20140.1 34.031 191 103 5 11 201 206 373 2.37e-21 90.5
Msa0534410 AT3G10130.1 37.500 200 107 10 11 201 115 305 3.59e-20 86.7
Msa0534410 AT5G20140.2 33.898 177 94 5 11 187 206 359 8.36e-19 83.6

Find 36 sgRNAs with CRISPR-Local

Find 50 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
AGACAAAGATGGTGGGTTTA+AGG 0.180691 4_1:+9877874 Msa0534410:CDS
TTTGATATGGGTTTAGTATT+TGG 0.199696 4_1:+9877731 None:intergenic
GAAGAAGGTGGGAAGAAATA+TGG 0.237445 4_1:+9878136 Msa0534410:CDS
TTGTCTCCTTTGAATGTTGA+TGG 0.274828 4_1:-9877857 None:intergenic
AAATATGGGGTGGTGACTTT+TGG 0.302611 4_1:+9878151 Msa0534410:CDS
CGATTACAATTCCAATGTTT+AGG 0.308020 4_1:+9878290 Msa0534410:CDS
TTCTTCTCATTTGTCACAAC+TGG 0.315475 4_1:-9878022 None:intergenic
ATCCATCACGTTCATTCAAC+AGG 0.374063 4_1:-9878331 None:intergenic
AAGAAGGTGGGAAGAAATAT+GGG 0.405616 4_1:+9878137 Msa0534410:CDS
GGAGAAGTTGAGGTTGTGTT+TGG 0.422907 4_1:+9878210 Msa0534410:CDS
TTTGAATGTTGATGGATCAT+AGG 0.424014 4_1:-9877849 None:intergenic
ATCACAACCCTCTCATCAAT+AGG 0.466452 4_1:-9878109 None:intergenic
AGGAGAAGGTGGAGAAGTTG+AGG 0.492065 4_1:+9878200 Msa0534410:CDS
AGGGTTGTGATAAGAGAAGA+AGG 0.496954 4_1:+9878121 Msa0534410:CDS
TCCAATGTTTAGGACTAATG+AGG 0.513944 4_1:+9878300 Msa0534410:CDS
AGGTTGTGTTTGGAGAAAGA+TGG 0.524733 4_1:+9878220 Msa0534410:CDS
GGCAAGTGATGAAGTGGTGA+AGG 0.533494 4_1:+9878180 Msa0534410:CDS
TATGATCCATCAACATTCAA+AGG 0.540575 4_1:+9877851 Msa0534410:CDS
TTGTGATAAGAGAAGAAGGT+GGG 0.544794 4_1:+9878125 Msa0534410:CDS
AACATTGGAATTGTAATCGC+AGG 0.545246 4_1:-9878286 None:intergenic
ACCTAAGCCTATTGATGAGA+GGG 0.548573 4_1:+9878102 Msa0534410:CDS
TGAAGTGGTGAAGGAGAAGG+TGG 0.549018 4_1:+9878189 Msa0534410:CDS
ACCCTCTCATCAATAGGCTT+AGG 0.549333 4_1:-9878103 None:intergenic
ATTGGAATTGTAATCGCAGG+TGG 0.568955 4_1:-9878283 None:intergenic
ACCTCATTAGTCCTAAACAT+TGG 0.572004 4_1:-9878301 None:intergenic
TGATGAAGTGGTGAAGGAGA+AGG 0.572950 4_1:+9878186 Msa0534410:CDS
TTCAAAGGAGACAAAGATGG+TGG 0.597630 4_1:+9877866 Msa0534410:CDS
GTGATTTCAGCTACTAGAGA+AGG 0.604224 4_1:-9877827 None:intergenic
ACATTCAAAGGAGACAAAGA+TGG 0.611112 4_1:+9877863 Msa0534410:CDS
TACCTAAGCCTATTGATGAG+AGG 0.615966 4_1:+9878101 Msa0534410:CDS
AGGAGTGGCAAGTGATGAAG+TGG 0.624838 4_1:+9878174 Msa0534410:CDS
TCAAAGGAGACAAAGATGGT+GGG 0.635974 4_1:+9877867 Msa0534410:CDS
GTTGTGATAAGAGAAGAAGG+TGG 0.672643 4_1:+9878124 Msa0534410:CDS
AGGTGGGAAGAAATATGGGG+TGG 0.678173 4_1:+9878141 Msa0534410:CDS
GACAAATGAGAAGAACAAGA+TGG 0.687039 4_1:+9878030 Msa0534410:CDS
AGAAGGTGGGAAGAAATATG+GGG 0.696955 4_1:+9878138 Msa0534410:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! GTTTTGAGTATTTCATATTT+TGG - chr4_1:9877776-9877795 None:intergenic 20.0%
!!! AAGGTTTTAGTTGATTACAT+AGG + chr4_1:9877893-9877912 Msa0534410:CDS 25.0%
!! GTTGATTACATAGGAATTTT+TGG + chr4_1:9877902-9877921 Msa0534410:CDS 25.0%
!!! TTTTGTGTTTTTGTGTTTTG+TGG - chr4_1:9877932-9877951 None:intergenic 25.0%
!!! TCTACTTTTTCATACATAGA+AGG - chr4_1:9878076-9878095 None:intergenic 25.0%
! TTCTATGTATGAAAAAGTAG+AGG + chr4_1:9878075-9878094 Msa0534410:CDS 25.0%
!!! AAAGATGGTTTTAAGGTTAT+TGG + chr4_1:9878235-9878254 Msa0534410:CDS 25.0%
!!! GTTATTGGAGATTTTTTGTT+GGG + chr4_1:9878250-9878269 Msa0534410:CDS 25.0%
! TTTGAATGTTGATGGATCAT+AGG - chr4_1:9877852-9877871 None:intergenic 30.0%
TATGATCCATCAACATTCAA+AGG + chr4_1:9877851-9877870 Msa0534410:CDS 30.0%
!! TTGTTTTGCTTTGTGATAAC+TGG - chr4_1:9877971-9877990 None:intergenic 30.0%
!! TTTGGAGAAAGATGGTTTTA+AGG + chr4_1:9878228-9878247 Msa0534410:CDS 30.0%
!!! GGTTATTGGAGATTTTTTGT+TGG + chr4_1:9878249-9878268 Msa0534410:CDS 30.0%
CGATTACAATTCCAATGTTT+AGG + chr4_1:9878290-9878309 Msa0534410:CDS 30.0%
!!! TCGGATTACATAGTTTTGTG+TGG - chr4_1:9877798-9877817 None:intergenic 35.0%
!! CTAGAGAAGGTGCATATTTT+CGG - chr4_1:9877817-9877836 None:intergenic 35.0%
TTGTCTCCTTTGAATGTTGA+TGG - chr4_1:9877860-9877879 None:intergenic 35.0%
ACATTCAAAGGAGACAAAGA+TGG + chr4_1:9877863-9877882 Msa0534410:CDS 35.0%
TTCTTCTCATTTGTCACAAC+TGG - chr4_1:9878025-9878044 None:intergenic 35.0%
GACAAATGAGAAGAACAAGA+TGG + chr4_1:9878030-9878049 Msa0534410:CDS 35.0%
TTGTGATAAGAGAAGAAGGT+GGG + chr4_1:9878125-9878144 Msa0534410:CDS 35.0%
AAGAAGGTGGGAAGAAATAT+GGG + chr4_1:9878137-9878156 Msa0534410:CDS 35.0%
!!! TTGGAGATTTTTTGTTGGGT+AGG + chr4_1:9878254-9878273 Msa0534410:CDS 35.0%
AACATTGGAATTGTAATCGC+AGG - chr4_1:9878289-9878308 None:intergenic 35.0%
! TCCAATGTTTAGGACTAATG+AGG + chr4_1:9878300-9878319 Msa0534410:CDS 35.0%
ACCTCATTAGTCCTAAACAT+TGG - chr4_1:9878304-9878323 None:intergenic 35.0%
GTGATTTCAGCTACTAGAGA+AGG - chr4_1:9877830-9877849 None:intergenic 40.0%
TTCAAAGGAGACAAAGATGG+TGG + chr4_1:9877866-9877885 Msa0534410:CDS 40.0%
TCAAAGGAGACAAAGATGGT+GGG + chr4_1:9877867-9877886 Msa0534410:CDS 40.0%
!! AGACAAAGATGGTGGGTTTA+AGG + chr4_1:9877874-9877893 Msa0534410:CDS 40.0%
TACCTAAGCCTATTGATGAG+AGG + chr4_1:9878101-9878120 Msa0534410:CDS 40.0%
ACCTAAGCCTATTGATGAGA+GGG + chr4_1:9878102-9878121 Msa0534410:CDS 40.0%
ATCACAACCCTCTCATCAAT+AGG - chr4_1:9878112-9878131 None:intergenic 40.0%
AGGGTTGTGATAAGAGAAGA+AGG + chr4_1:9878121-9878140 Msa0534410:CDS 40.0%
GTTGTGATAAGAGAAGAAGG+TGG + chr4_1:9878124-9878143 Msa0534410:CDS 40.0%
GAAGAAGGTGGGAAGAAATA+TGG + chr4_1:9878136-9878155 Msa0534410:CDS 40.0%
AGAAGGTGGGAAGAAATATG+GGG + chr4_1:9878138-9878157 Msa0534410:CDS 40.0%
! AAATATGGGGTGGTGACTTT+TGG + chr4_1:9878151-9878170 Msa0534410:CDS 40.0%
AGGTTGTGTTTGGAGAAAGA+TGG + chr4_1:9878220-9878239 Msa0534410:CDS 40.0%
ATTGGAATTGTAATCGCAGG+TGG - chr4_1:9878286-9878305 None:intergenic 40.0%
ACCCTCTCATCAATAGGCTT+AGG - chr4_1:9878106-9878125 None:intergenic 45.0%
TGATGAAGTGGTGAAGGAGA+AGG + chr4_1:9878186-9878205 Msa0534410:CDS 45.0%
GGAGAAGTTGAGGTTGTGTT+TGG + chr4_1:9878210-9878229 Msa0534410:CDS 45.0%
AGGTGGGAAGAAATATGGGG+TGG + chr4_1:9878141-9878160 Msa0534410:CDS 50.0%
! TATGGGGTGGTGACTTTTGG+AGG + chr4_1:9878154-9878173 Msa0534410:CDS 50.0%
AGGAGTGGCAAGTGATGAAG+TGG + chr4_1:9878174-9878193 Msa0534410:CDS 50.0%
GGCAAGTGATGAAGTGGTGA+AGG + chr4_1:9878180-9878199 Msa0534410:CDS 50.0%
TGAAGTGGTGAAGGAGAAGG+TGG + chr4_1:9878189-9878208 Msa0534410:CDS 50.0%
AGGAGAAGGTGGAGAAGTTG+AGG + chr4_1:9878200-9878219 Msa0534410:CDS 50.0%
!! GGTGGTGACTTTTGGAGGAG+TGG + chr4_1:9878159-9878178 Msa0534410:CDS 55.0%
Chromosome Type Strat End Strand Name
chr4_1 gene 9877737 9878342 9877737 ID=Msa0534410;Name=Msa0534410
chr4_1 mRNA 9877737 9878342 9877737 ID=Msa0534410-mRNA-1;Parent=Msa0534410;Name=Msa0534410-mRNA-1;_AED=0.25;_eAED=0.26;_QI=0|-1|0|1|-1|1|1|0|201
chr4_1 exon 9877737 9878342 9877737 ID=Msa0534410-mRNA-1:exon:3182;Parent=Msa0534410-mRNA-1
chr4_1 CDS 9877737 9878342 9877737 ID=Msa0534410-mRNA-1:cds;Parent=Msa0534410-mRNA-1
Gene Sequence

>Msa0534410

ATGGGTTTAGTATTTGGAAGATTTAGTGCTGAGACACCAAAATATGAAATACTCAAAACCACACAAAACTATGTAATCCGAAAATATGCACCTTCTCTAGTAGCTGAAATCACCTATGATCCATCAACATTCAAAGGAGACAAAGATGGTGGGTTTAAGGTTTTAGTTGATTACATAGGAATTTTTGGTAAACCACAAAACACAAAAACACAAAAAATTTCAATGACTTCTCCAGTTATCACAAAGCAAAACAAGAGTTCTTCAGAAAAGATTGCTATGACAGTACCAGTTGTGACAAATGAGAAGAACAAGATGGTGACTATGCAGTTTACTTTGCCTTCTATGTATGAAAAAGTAGAGGAAGTACCTAAGCCTATTGATGAGAGGGTTGTGATAAGAGAAGAAGGTGGGAAGAAATATGGGGTGGTGACTTTTGGAGGAGTGGCAAGTGATGAAGTGGTGAAGGAGAAGGTGGAGAAGTTGAGGTTGTGTTTGGAGAAAGATGGTTTTAAGGTTATTGGAGATTTTTTGTTGGGTAGGTATAATCCACCTGCGATTACAATTCCAATGTTTAGGACTAATGAGGTTCTGATTCCTGTTGAATGA

Protein sequence

>Msa0534410

MGLVFGRFSAETPKYEILKTTQNYVIRKYAPSLVAEITYDPSTFKGDKDGGFKVLVDYIGIFGKPQNTKTQKISMTSPVITKQNKSSSEKIAMTVPVVTNEKNKMVTMQFTLPSMYEKVEEVPKPIDERVVIREEGGKKYGVVTFGGVASDEVVKEKVEKLRLCLEKDGFKVIGDFLLGRYNPPAITIPMFRTNEVLIPVE*