AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1377820


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1377820 MtrunA17_Chr7g0270131 97.297 148 4 0 1 148 628 775 2.45e-95 291
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1377820 AT2G47330.1 51.908 131 50 5 19 147 640 759 1.25e-23 96.3

Find 48 sgRNAs with CRISPR-Local

Find 111 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TATTACTGAATCCTTCATTT+TGG 0.152380 tig0019985:+8847 Msa1377820:intergenic
CAACGAAGCTACTCCTAAAT+TGG 0.189044 tig0019985:+8886 Msa1377820:intergenic
CAGGAATGATGTCCCAATTT+AGG 0.287222 tig0019985:-8899 Msa1377820:CDS
GGCGAAGTCTTGATTTGATT+TGG 0.325501 tig0019985:-8452 Msa1377820:three_prime_UTR
AATTCCACTAGTCAAAATTC+TGG 0.335286 tig0019985:-8702 Msa1377820:CDS
ACACTAGCTGGCTTTGTATC+TGG 0.337129 tig0019985:-8795 Msa1377820:CDS
GCGTCATCTAACGCAGTTCC+AGG 0.353849 tig0019985:-8951 Msa1377820:CDS
GGTGTGCGCGGAGTTGATTT+TGG 0.387275 tig0019985:-9008 Msa1377820:CDS
ATTGTATTGAGTACTGAAAA+AGG 0.392866 tig0019985:-8375 Msa1377820:three_prime_UTR
CTAGTGGAATTTACAGTTGA+AGG 0.393513 tig0019985:+8714 Msa1377820:intergenic
GATGGCCTTCGCCTTTCTCT+AGG 0.422928 tig0019985:+8550 Msa1377820:intergenic
AGAAAAGGCAAAGGCAGAGG+TGG 0.426446 tig0019985:-9047 Msa1377820:CDS
TTTGTATCTGGTGGATCAAT+TGG 0.445406 tig0019985:-8783 Msa1377820:CDS
GTATGAATGCTCATATTTGT+AGG 0.446604 tig0019985:-8473 Msa1377820:three_prime_UTR
AAATGTTTGAGCCTTGGCTC+TGG 0.447230 tig0019985:+8330 Msa1377820:intergenic
GCTGTAAATTCTCTGCGAAC+AGG 0.449877 tig0019985:-8918 Msa1377820:CDS
GAGAGAAAATGTTTGAGCCT+TGG 0.462374 tig0019985:+8324 Msa1377820:intergenic
AGAGAAAGGCGAAGGCCATC+AGG 0.465859 tig0019985:-8547 Msa1377820:CDS
CTGGTCAGAACAACACGAAC+AGG 0.473022 tig0019985:-8671 Msa1377820:intron
AACGAAGCTACTCCTAAATT+GGG 0.473246 tig0019985:+8887 Msa1377820:intergenic
CTGTTCGTGTTGTTCTGACC+AGG 0.479959 tig0019985:+8672 Msa1377820:intergenic
AAGGCGAAGGCCATCAGGTT+GGG 0.481451 tig0019985:-8542 Msa1377820:CDS
GGGAGAAAAGGCAAAGGCAG+AGG 0.492204 tig0019985:-9050 Msa1377820:CDS
CAAAATTCTGGAGTAAATCC+TGG 0.496585 tig0019985:-8690 Msa1377820:CDS
AATAAGAGACCAACACTAGC+TGG 0.504667 tig0019985:-8807 Msa1377820:CDS
GTATCTGGTGGATCAATTGG+CGG 0.505944 tig0019985:-8780 Msa1377820:CDS
GAATTTACAGTTGAAGGAGC+AGG 0.508575 tig0019985:+8720 Msa1377820:intergenic
AAAGGCAAAGGCAGAGGTGG+GGG 0.509419 tig0019985:-9044 Msa1377820:CDS
GAAAAGGCAAAGGCAGAGGT+GGG 0.521254 tig0019985:-9046 Msa1377820:CDS
TCATCAACCTCCCAAAATGA+AGG 0.545123 tig0019985:-8858 Msa1377820:CDS
AAAGGCGAAGGCCATCAGGT+TGG 0.560748 tig0019985:-8543 Msa1377820:CDS
AAAAGGCAAAGGCAGAGGTG+GGG 0.567265 tig0019985:-9045 Msa1377820:CDS
TATTATCAATTGATAGAGCA+TGG 0.572994 tig0019985:-8425 Msa1377820:three_prime_UTR
TGGGGTCGTACTCATGAAAG+AGG 0.588959 tig0019985:+8295 None:intergenic
TGTTGTGTAGGTGGGAGAAA+AGG 0.593082 tig0019985:-9062 None:intergenic
GCAGGTGGCAAAGGTGTGCG+CGG 0.596293 tig0019985:-9020 Msa1377820:CDS
TTTACAGCAGCAGACCGACC+TGG 0.602830 tig0019985:+8933 Msa1377820:intergenic
GCAGTTCTAAACCTAGAGAA+AGG 0.605177 tig0019985:-8561 Msa1377820:intron
ATTCAGTAATAATACAAGCA+TGG 0.605916 tig0019985:-8835 Msa1377820:CDS
GTCGTACTCATGAAAGAGGT+AGG 0.607774 tig0019985:+8299 Msa1377820:intergenic
CTAGCTGGCTTTGTATCTGG+TGG 0.609199 tig0019985:-8792 Msa1377820:CDS
CATCTAACGCAGTTCCAGGT+CGG 0.613656 tig0019985:-8947 Msa1377820:CDS
AACTATCTATCCCAACCTGA+TGG 0.619017 tig0019985:+8532 Msa1377820:intergenic
GTATAGATATTCCAGAGCCA+AGG 0.641050 tig0019985:-8341 Msa1377820:three_prime_UTR
GATACAAAGCCAGCTAGTGT+TGG 0.641121 tig0019985:+8798 Msa1377820:intergenic
CTAAACCTAGAGAAAGGCGA+AGG 0.655176 tig0019985:-8555 Msa1377820:CDS
CATACACTTGAGTTTGACAG+CGG 0.680583 tig0019985:+8491 None:intergenic
GTAGGTGGGAGAAAAGGCAA+AGG 0.721472 tig0019985:-9056 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! ATTACTGAATCCTTCATTTT+GGG + tig0019985:8503-8522 Msa1377820:intergenic 25.0%
!! TATTACTGAATCCTTCATTT+TGG + tig0019985:8504-8523 Msa1377820:intergenic 25.0%
! ATTCAGTAATAATACAAGCA+TGG - tig0019985:8513-8532 Msa1377820:three_prime_UTR 25.0%
! TATTATCAATTGATAGAGCA+TGG - tig0019985:8923-8942 Msa1377820:CDS 25.0%
!!! ATTGTATTGAGTACTGAAAA+AGG - tig0019985:8973-8992 Msa1377820:CDS 25.0%
!! ATTACTGAATCCTTCATTTT+GGG + tig0019985:8503-8522 Msa1377820:intergenic 25.0%
!! TATTACTGAATCCTTCATTT+TGG + tig0019985:8504-8523 Msa1377820:intergenic 25.0%
! ATTCAGTAATAATACAAGCA+TGG - tig0019985:8513-8532 Msa1377820:three_prime_UTR 25.0%
! TATTATCAATTGATAGAGCA+TGG - tig0019985:8923-8942 Msa1377820:CDS 25.0%
!!! ATTGTATTGAGTACTGAAAA+AGG - tig0019985:8973-8992 Msa1377820:CDS 25.0%
AATTCCACTAGTCAAAATTC+TGG - tig0019985:8646-8665 Msa1377820:intron 30.0%
GTATGAATGCTCATATTTGT+AGG - tig0019985:8875-8894 Msa1377820:CDS 30.0%
AATTCCACTAGTCAAAATTC+TGG - tig0019985:8646-8665 Msa1377820:intron 30.0%
GTATGAATGCTCATATTTGT+AGG - tig0019985:8875-8894 Msa1377820:CDS 30.0%
AACGAAGCTACTCCTAAATT+GGG + tig0019985:8464-8483 Msa1377820:intergenic 35.0%
! TTTGTATCTGGTGGATCAAT+TGG - tig0019985:8565-8584 Msa1377820:intron 35.0%
CTAGTGGAATTTACAGTTGA+AGG + tig0019985:8637-8656 Msa1377820:intergenic 35.0%
!!! TACTCCAGAATTTTGACTAG+TGG + tig0019985:8653-8672 Msa1377820:intergenic 35.0%
!! CAAAATTCTGGAGTAAATCC+TGG - tig0019985:8658-8677 Msa1377820:intron 35.0%
AACGAAGCTACTCCTAAATT+GGG + tig0019985:8464-8483 Msa1377820:intergenic 35.0%
! TTTGTATCTGGTGGATCAAT+TGG - tig0019985:8565-8584 Msa1377820:intron 35.0%
CTAGTGGAATTTACAGTTGA+AGG + tig0019985:8637-8656 Msa1377820:intergenic 35.0%
!!! TACTCCAGAATTTTGACTAG+TGG + tig0019985:8653-8672 Msa1377820:intergenic 35.0%
!! CAAAATTCTGGAGTAAATCC+TGG - tig0019985:8658-8677 Msa1377820:intron 35.0%
CAGGAATGATGTCCCAATTT+AGG - tig0019985:8449-8468 Msa1377820:three_prime_UTR 40.0%
CAACGAAGCTACTCCTAAAT+TGG + tig0019985:8465-8484 Msa1377820:intergenic 40.0%
TCATCAACCTCCCAAAATGA+AGG - tig0019985:8490-8509 Msa1377820:three_prime_UTR 40.0%
! ACTGAATCCTTCATTTTGGG+AGG + tig0019985:8500-8519 Msa1377820:intergenic 40.0%
AATAAGAGACCAACACTAGC+TGG - tig0019985:8541-8560 Msa1377820:CDS 40.0%
GAATTTACAGTTGAAGGAGC+AGG + tig0019985:8631-8650 Msa1377820:intergenic 40.0%
!! GCAGTTCTAAACCTAGAGAA+AGG - tig0019985:8787-8806 Msa1377820:CDS 40.0%
AACTATCTATCCCAACCTGA+TGG + tig0019985:8819-8838 Msa1377820:intergenic 40.0%
CATACACTTGAGTTTGACAG+CGG + tig0019985:8860-8879 Msa1377820:intergenic 40.0%
! GGCGAAGTCTTGATTTGATT+TGG - tig0019985:8896-8915 Msa1377820:CDS 40.0%
GTATAGATATTCCAGAGCCA+AGG - tig0019985:9007-9026 Msa1377820:CDS 40.0%
GAGAGAAAATGTTTGAGCCT+TGG + tig0019985:9027-9046 Msa1377820:intergenic 40.0%
CAGGAATGATGTCCCAATTT+AGG - tig0019985:8449-8468 Msa1377820:three_prime_UTR 40.0%
CAACGAAGCTACTCCTAAAT+TGG + tig0019985:8465-8484 Msa1377820:intergenic 40.0%
TCATCAACCTCCCAAAATGA+AGG - tig0019985:8490-8509 Msa1377820:three_prime_UTR 40.0%
! ACTGAATCCTTCATTTTGGG+AGG + tig0019985:8500-8519 Msa1377820:intergenic 40.0%
AATAAGAGACCAACACTAGC+TGG - tig0019985:8541-8560 Msa1377820:CDS 40.0%
GAATTTACAGTTGAAGGAGC+AGG + tig0019985:8631-8650 Msa1377820:intergenic 40.0%
!! GCAGTTCTAAACCTAGAGAA+AGG - tig0019985:8787-8806 Msa1377820:CDS 40.0%
AACTATCTATCCCAACCTGA+TGG + tig0019985:8819-8838 Msa1377820:intergenic 40.0%
CATACACTTGAGTTTGACAG+CGG + tig0019985:8860-8879 Msa1377820:intergenic 40.0%
! GGCGAAGTCTTGATTTGATT+TGG - tig0019985:8896-8915 Msa1377820:CDS 40.0%
GTATAGATATTCCAGAGCCA+AGG - tig0019985:9007-9026 Msa1377820:CDS 40.0%
GAGAGAAAATGTTTGAGCCT+TGG + tig0019985:9027-9046 Msa1377820:intergenic 40.0%
!!! GTTGATTTTGGCTTGGGCAT+TGG - tig0019985:8352-8371 Msa1377820:three_prime_UTR 45.0%
GCTGTAAATTCTCTGCGAAC+AGG - tig0019985:8430-8449 Msa1377820:three_prime_UTR 45.0%
GATACAAAGCCAGCTAGTGT+TGG + tig0019985:8553-8572 Msa1377820:intergenic 45.0%
!! ACACTAGCTGGCTTTGTATC+TGG - tig0019985:8553-8572 Msa1377820:CDS 45.0%
! GTATCTGGTGGATCAATTGG+CGG - tig0019985:8568-8587 Msa1377820:intron 45.0%
CTAAACCTAGAGAAAGGCGA+AGG - tig0019985:8793-8812 Msa1377820:CDS 45.0%
AAATGTTTGAGCCTTGGCTC+TGG + tig0019985:9021-9040 Msa1377820:intergenic 45.0%
GTCGTACTCATGAAAGAGGT+AGG + tig0019985:9052-9071 Msa1377820:intergenic 45.0%
ACCTCTTTCATGAGTACGAC+CGG - tig0019985:9052-9071 Msa1377820:CDS 45.0%
!!! GTTGATTTTGGCTTGGGCAT+TGG - tig0019985:8352-8371 Msa1377820:three_prime_UTR 45.0%
GCTGTAAATTCTCTGCGAAC+AGG - tig0019985:8430-8449 Msa1377820:three_prime_UTR 45.0%
GATACAAAGCCAGCTAGTGT+TGG + tig0019985:8553-8572 Msa1377820:intergenic 45.0%
!! ACACTAGCTGGCTTTGTATC+TGG - tig0019985:8553-8572 Msa1377820:CDS 45.0%
! GTATCTGGTGGATCAATTGG+CGG - tig0019985:8568-8587 Msa1377820:intron 45.0%
CTAAACCTAGAGAAAGGCGA+AGG - tig0019985:8793-8812 Msa1377820:CDS 45.0%
AAATGTTTGAGCCTTGGCTC+TGG + tig0019985:9021-9040 Msa1377820:intergenic 45.0%
GTCGTACTCATGAAAGAGGT+AGG + tig0019985:9052-9071 Msa1377820:intergenic 45.0%
AGAAAAGGCAAAGGCAGAGG+TGG - tig0019985:8301-8320 Msa1377820:three_prime_UTR 50.0%
GAAAAGGCAAAGGCAGAGGT+GGG - tig0019985:8302-8321 Msa1377820:three_prime_UTR 50.0%
AAAAGGCAAAGGCAGAGGTG+GGG - tig0019985:8303-8322 Msa1377820:three_prime_UTR 50.0%
!!! CGCGGAGTTGATTTTGGCTT+GGG - tig0019985:8346-8365 Msa1377820:three_prime_UTR 50.0%
CATCTAACGCAGTTCCAGGT+CGG - tig0019985:8401-8420 Msa1377820:three_prime_UTR 50.0%
!! CTAGCTGGCTTTGTATCTGG+TGG - tig0019985:8556-8575 Msa1377820:CDS 50.0%
! CTGTTCGTGTTGTTCTGACC+AGG + tig0019985:8679-8698 Msa1377820:intergenic 50.0%
CTGGTCAGAACAACACGAAC+AGG - tig0019985:8677-8696 Msa1377820:CDS 50.0%
CCTCTTTCATGAGTACGACC+GGG - tig0019985:9053-9072 Msa1377820:CDS 50.0%
! TCTGCCTTTGCCTTTTCTCC+CGG + tig0019985:8299-8318 Msa1377820:intergenic 50.0%
AGAAAAGGCAAAGGCAGAGG+TGG - tig0019985:8301-8320 Msa1377820:three_prime_UTR 50.0%
GAAAAGGCAAAGGCAGAGGT+GGG - tig0019985:8302-8321 Msa1377820:three_prime_UTR 50.0%
AAAAGGCAAAGGCAGAGGTG+GGG - tig0019985:8303-8322 Msa1377820:three_prime_UTR 50.0%
!!! CGCGGAGTTGATTTTGGCTT+GGG - tig0019985:8346-8365 Msa1377820:three_prime_UTR 50.0%
CATCTAACGCAGTTCCAGGT+CGG - tig0019985:8401-8420 Msa1377820:three_prime_UTR 50.0%
!! CTAGCTGGCTTTGTATCTGG+TGG - tig0019985:8556-8575 Msa1377820:CDS 50.0%
! CTGTTCGTGTTGTTCTGACC+AGG + tig0019985:8679-8698 Msa1377820:intergenic 50.0%
CTGGTCAGAACAACACGAAC+AGG - tig0019985:8677-8696 Msa1377820:CDS 50.0%
GGGAGAAAAGGCAAAGGCAG+AGG - tig0019985:8298-8317 Msa1377820:three_prime_UTR 55.0%
AAAGGCAAAGGCAGAGGTGG+GGG - tig0019985:8304-8323 Msa1377820:three_prime_UTR 55.0%
!! GGTGTGCGCGGAGTTGATTT+TGG - tig0019985:8340-8359 Msa1377820:three_prime_UTR 55.0%
!!! GCGCGGAGTTGATTTTGGCT+TGG - tig0019985:8345-8364 Msa1377820:three_prime_UTR 55.0%
GCGTCATCTAACGCAGTTCC+AGG - tig0019985:8397-8416 Msa1377820:three_prime_UTR 55.0%
TTTACAGCAGCAGACCGACC+TGG + tig0019985:8418-8437 Msa1377820:intergenic 55.0%
GATGGCCTTCGCCTTTCTCT+AGG + tig0019985:8801-8820 Msa1377820:intergenic 55.0%
AGAGAAAGGCGAAGGCCATC+AGG - tig0019985:8801-8820 Msa1377820:CDS 55.0%
AAAGGCGAAGGCCATCAGGT+TGG - tig0019985:8805-8824 Msa1377820:CDS 55.0%
AAGGCGAAGGCCATCAGGTT+GGG - tig0019985:8806-8825 Msa1377820:CDS 55.0%
GGGAGAAAAGGCAAAGGCAG+AGG - tig0019985:8298-8317 Msa1377820:three_prime_UTR 55.0%
AAAGGCAAAGGCAGAGGTGG+GGG - tig0019985:8304-8323 Msa1377820:three_prime_UTR 55.0%
!! GGTGTGCGCGGAGTTGATTT+TGG - tig0019985:8340-8359 Msa1377820:three_prime_UTR 55.0%
!!! GCGCGGAGTTGATTTTGGCT+TGG - tig0019985:8345-8364 Msa1377820:three_prime_UTR 55.0%
GCGTCATCTAACGCAGTTCC+AGG - tig0019985:8397-8416 Msa1377820:three_prime_UTR 55.0%
TTTACAGCAGCAGACCGACC+TGG + tig0019985:8418-8437 Msa1377820:intergenic 55.0%
GATGGCCTTCGCCTTTCTCT+AGG + tig0019985:8801-8820 Msa1377820:intergenic 55.0%
AGAGAAAGGCGAAGGCCATC+AGG - tig0019985:8801-8820 Msa1377820:CDS 55.0%
AAAGGCGAAGGCCATCAGGT+TGG - tig0019985:8805-8824 Msa1377820:CDS 55.0%
AAGGCGAAGGCCATCAGGTT+GGG - tig0019985:8806-8825 Msa1377820:CDS 55.0%
! AAAGGCAGAGGTGGGGGTGC+AGG - tig0019985:8310-8329 Msa1377820:three_prime_UTR 65.0%
! GCAGGTGGCAAAGGTGTGCG+CGG - tig0019985:8328-8347 Msa1377820:three_prime_UTR 65.0%
! AAAGGCAGAGGTGGGGGTGC+AGG - tig0019985:8310-8329 Msa1377820:three_prime_UTR 65.0%
! GCAGGTGGCAAAGGTGTGCG+CGG - tig0019985:8328-8347 Msa1377820:three_prime_UTR 65.0%
! GGTGGGGGTGCAGGTGGCAA+AGG - tig0019985:8319-8338 Msa1377820:three_prime_UTR 70.0%
! GGTGGGGGTGCAGGTGGCAA+AGG - tig0019985:8319-8338 Msa1377820:three_prime_UTR 70.0%
! GGCAGAGGTGGGGGTGCAGG+TGG - tig0019985:8313-8332 Msa1377820:three_prime_UTR 75.0%
! GGCAGAGGTGGGGGTGCAGG+TGG - tig0019985:8313-8332 Msa1377820:three_prime_UTR 75.0%
Chromosome Type Strat End Strand Name
tig0019985 gene 8298 9072 8298 ID=Msa1377820;Name=Msa1377820
tig0019985 mRNA 8298 9072 8298 ID=Msa1377820-mRNA-1;Parent=Msa1377820;Name=Msa1377820-mRNA-1;_AED=0.00;_eAED=0.00;_QI=0|1|0.5|1|1|0.5|2|236|148
tig0019985 exon 8298 8579 8298 ID=Msa1377820-mRNA-1:exon:5823;Parent=Msa1377820-mRNA-1
tig0019985 exon 8672 9072 8672 ID=Msa1377820-mRNA-1:exon:5822;Parent=Msa1377820-mRNA-1
tig0019985 CDS 8672 9072 8672 ID=Msa1377820-mRNA-1:cds;Parent=Msa1377820-mRNA-1
tig0019985 CDS 8534 8579 8534 ID=Msa1377820-mRNA-1:cds;Parent=Msa1377820-mRNA-1
tig0019985 three_prime_UTR 8298 8533 8298 ID=Msa1377820-mRNA-1:three_prime_utr;Parent=Msa1377820-mRNA-1
Gene Sequence

>Msa1377820

GGGAGAAAAGGCAAAGGCAGAGGTGGGGGTGCAGGTGGCAAAGGTGTGCGCGGAGTTGATTTTGGCTTGGGCATTGGATATAGTACAGAGTCAAACAATGCGTCATCTAACGCAGTTCCAGGTCGGTCTGCTGCTGTAAATTCTCTGCGAACAGGAATGATGTCCCAATTTAGGAGTAGCTTCGTTGCTGCATCATCAACCTCCCAAAATGAAGGATTCAGTAATAATACAAGCATGGCTGTTAATAAGAGACCAACACTAGCTGGCTTTGTATCTGGTGGATCAATTGGCGGCGATATAAATACTCATCAGCAAACTGCTTCATACAATCCTGCTCCTTCAACTGTAAATTCCACTAGTCAAAATTCTGGAGTAAATCCTGGTCAGAACAACACGAACAGTTCTAAACCTAGAGAAAGGCGAAGGCCATCAGGTTGGGATAGATAG

Protein sequence

>Msa1377820

GRKGKGRGGGAGGKGVRGVDFGLGIGYSTESNNASSNAVPGRSAAVNSLRTGMMSQFRSSFVAASSTSQNEGFSNNTSMAVNKRPTLAGFVSGGSIGGDINTHQQTASYNPAPSTVNSTSQNSGVNPGQNNTNSSKPRERRRPSGWDR*