AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1016500

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1016500 MtrunA17_Chr7g0231881 97.600 125 2 1 1 124 1 125 3.70e-89 254
Msa1016500 MtrunA17_Chr8g0334651 57.273 110 33 3 1 110 1 96 8.00e-37 120
Msa1016500 MtrunA17_Chr5g0427021 49.057 53 27 0 5 57 14 66 3.11e-13 63.2
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1016500 AT3G60520.1 54.478 134 46 6 1 124 1 129 8.15e-35 117
Msa1016500 AT1G02070.1 54.615 130 49 4 5 124 2 131 2.60e-34 115
Msa1016500 AT3G60520.2 48.000 100 38 5 34 124 24 118 2.32e-15 67.4

Find 43 sgRNAs with CRISPR-Local

Find 126 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
ACAGAGTTGTGATGATAAAA+AGG 0.210311 7_1:+33234090 None:intergenic
AACCAACCGATCGGAATATT+CGG 0.326610 7_1:-33233378 Msa1016500:CDS
TTGATGATCCACCATTCTTA+TGG 0.333830 7_1:+33234045 None:intergenic
AGGTATTGTAGCAACTACTA+TGG 0.356994 7_1:-33233512 Msa1016500:CDS
GGTCACCGGTTTCTTTGAAT+TGG 0.367398 7_1:+33233421 None:intergenic
TGTCGCGACGATCTCATTTC+CGG 0.389983 7_1:+33233400 None:intergenic
CGGAGATAGAACAGTGTGAT+TGG 0.433454 7_1:-33233481 Msa1016500:CDS
TTGCAACGGAAAAGTTTGTC+AGG 0.456065 7_1:+33233989 None:intergenic
ACCAACCGATCGGAATATTC+GGG 0.471379 7_1:-33233377 Msa1016500:CDS
TGGCACCAATTCAAAGAAAC+CGG 0.486182 7_1:-33233426 Msa1016500:CDS
AAAGTAATACATACGAGTGT+TGG 0.487858 7_1:+33233948 None:intergenic
TCAACTTCTCTTGTTATGAG+TGG 0.496632 7_1:-33233100 Msa1016500:three_prime_UTR
GCGGTCCGTGGCGACGGCGA+AGG 0.502361 7_1:+33233296 None:intergenic
CGTGTGGCGGTCCGTGGCGA+CGG 0.515666 7_1:+33233290 None:intergenic
ACGATCTCATTTCCGGTCAC+CGG 0.516236 7_1:+33233407 None:intergenic
ATCACCACACATGCAACAAA+CGG 0.517973 7_1:+33234021 None:intergenic
GAAGAGGGTGGCTCTGAGAA+GGG 0.527687 7_1:-33233326 Msa1016500:CDS
TGTTGCATGTGTGGTGATGT+TGG 0.529954 7_1:-33234016 Msa1016500:CDS
TGAAGAGGGTGGCTCTGAGA+AGG 0.532977 7_1:-33233327 Msa1016500:CDS
ATACATACGAGTGTTGGAAT+CGG 0.550310 7_1:+33233954 None:intergenic
AGAGTCCTTCGCCGTCGCCA+CGG 0.553436 7_1:-33233301 Msa1016500:CDS
TACCTACGTGTGGCGGTCCG+TGG 0.554233 7_1:+33233284 None:intergenic
ACCCGAATATTCCGATCGGT+TGG 0.554818 7_1:+33233376 None:intergenic
AATCTTGAATAAGAAGAAGA+AGG 0.555136 7_1:-33233223 Msa1016500:three_prime_UTR
TTGAAGGTGAGAGTGAGAGA+TGG 0.555165 7_1:+33234119 None:intergenic
AATTCAAAGAAACCGGTGAC+CGG 0.559840 7_1:-33233419 Msa1016500:CDS
AAACAACATGATCGTGAAGA+GGG 0.586473 7_1:-33233341 Msa1016500:CDS
ACGAGTGTTGGAATCGGTGG+CGG 0.586739 7_1:+33233960 None:intergenic
TGTGCAGCACACCATAAGAA+TGG 0.588391 7_1:-33234056 Msa1016500:exon
GGTGGCGGCATTTGTTGCAA+CGG 0.592229 7_1:+33233975 None:intergenic
CAAACCGTTTGTTGCATGTG+TGG 0.594835 7_1:-33234025 Msa1016500:CDS
AAGAGGGTGGCTCTGAGAAG+GGG 0.612751 7_1:-33233325 Msa1016500:CDS
TAAACAACATGATCGTGAAG+AGG 0.621485 7_1:-33233342 Msa1016500:CDS
GAGAAGCTTGTACCTACGTG+TGG 0.625438 7_1:+33233274 None:intergenic
CATACGAGTGTTGGAATCGG+TGG 0.628121 7_1:+33233957 None:intergenic
TCTCACCCGAATATTCCGAT+CGG 0.641982 7_1:+33233372 None:intergenic
CGTCGCGACAACCAACCGAT+CGG 0.647059 7_1:-33233387 Msa1016500:CDS
ACGTAGGTACAAGCTTCTCA+AGG 0.654964 7_1:-33233270 Msa1016500:CDS
AAGCTTGTACCTACGTGTGG+CGG 0.656745 7_1:+33233277 None:intergenic
CAACATGATCGTGAAGAGGG+TGG 0.664857 7_1:-33233338 Msa1016500:CDS
GCAGCACACCATAAGAATGG+TGG 0.664995 7_1:-33234053 Msa1016500:exon
CAACTACTATGGAGAACTAG+CGG 0.694469 7_1:-33233501 Msa1016500:CDS
CGCCACGGACCGCCACACGT+AGG 0.759309 7_1:-33233286 Msa1016500:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! TATGAAATCTTTTATTTAAT+TGG - chr7_1:33233332-33233351 Msa1016500:CDS 10.0%
!!! ATGAAATCTTTTATTTAATT+GGG - chr7_1:33233333-33233352 Msa1016500:CDS 10.0%
!!! CAACATTAAAATAAATTTTA+AGG + chr7_1:33233652-33233671 None:intergenic 10.0%
!!! ATTTTAATGTTGTTTTTTTA+AGG - chr7_1:33233660-33233679 Msa1016500:intron 10.0%
!!! TATGAAATCTTTTATTTAAT+TGG - chr7_1:33233332-33233351 Msa1016500:CDS 10.0%
!!! ATGAAATCTTTTATTTAATT+GGG - chr7_1:33233333-33233352 Msa1016500:CDS 10.0%
!!! CAACATTAAAATAAATTTTA+AGG + chr7_1:33233652-33233671 None:intergenic 10.0%
!!! ATTTTAATGTTGTTTTTTTA+AGG - chr7_1:33233660-33233679 Msa1016500:intron 10.0%
!!! TGAAATCTTTTATTTAATTG+GGG - chr7_1:33233334-33233353 Msa1016500:CDS 15.0%
!!! CAAGTATATTATTTTTTGTT+TGG - chr7_1:33233472-33233491 Msa1016500:CDS 15.0%
!!! GAGATTGTTATTATTTTATT+AGG - chr7_1:33233611-33233630 Msa1016500:intron 15.0%
!!! TGAAATCTTTTATTTAATTG+GGG - chr7_1:33233334-33233353 Msa1016500:CDS 15.0%
!!! CAAGTATATTATTTTTTGTT+TGG - chr7_1:33233472-33233491 Msa1016500:CDS 15.0%
!!! GAGATTGTTATTATTTTATT+AGG - chr7_1:33233611-33233630 Msa1016500:intron 15.0%
!!! GAAATCTTTTATTTAATTGG+GGG - chr7_1:33233335-33233354 Msa1016500:CDS 20.0%
!! TAACCATAGTATAAAACATT+AGG - chr7_1:33233497-33233516 Msa1016500:CDS 20.0%
!! AACCATAGTATAAAACATTA+GGG - chr7_1:33233498-33233517 Msa1016500:CDS 20.0%
!!! GAAATCTTTTATTTAATTGG+GGG - chr7_1:33233335-33233354 Msa1016500:CDS 20.0%
!! TAACCATAGTATAAAACATT+AGG - chr7_1:33233497-33233516 Msa1016500:CDS 20.0%
!! AACCATAGTATAAAACATTA+GGG - chr7_1:33233498-33233517 Msa1016500:CDS 20.0%
! AACACGACTTTATAACTTTA+TGG + chr7_1:33233439-33233458 None:intergenic 25.0%
!! TTGAATTTTTCTCTTCACTT+TGG + chr7_1:33233739-33233758 None:intergenic 25.0%
! GAGAAAAATTCAAGACATAT+TGG - chr7_1:33233746-33233765 Msa1016500:intron 25.0%
! AATCTTGAATAAGAAGAAGA+AGG - chr7_1:33233969-33233988 Msa1016500:CDS 25.0%
! AACACGACTTTATAACTTTA+TGG + chr7_1:33233439-33233458 None:intergenic 25.0%
!! TTGAATTTTTCTCTTCACTT+TGG + chr7_1:33233739-33233758 None:intergenic 25.0%
! GAGAAAAATTCAAGACATAT+TGG - chr7_1:33233746-33233765 Msa1016500:intron 25.0%
! AATCTTGAATAAGAAGAAGA+AGG - chr7_1:33233969-33233988 Msa1016500:CDS 25.0%
AAGAAAAAATGTGATCAGTG+AGG + chr7_1:33233048-33233067 None:intergenic 30.0%
! GATAAAAAGGGGAATTTTGA+AGG + chr7_1:33233092-33233111 None:intergenic 30.0%
AGAGTTGTGATGATAAAAAG+GGG + chr7_1:33233103-33233122 None:intergenic 30.0%
CAGAGTTGTGATGATAAAAA+GGG + chr7_1:33233104-33233123 None:intergenic 30.0%
ACAGAGTTGTGATGATAAAA+AGG + chr7_1:33233105-33233124 None:intergenic 30.0%
AAAGTAATACATACGAGTGT+TGG + chr7_1:33233247-33233266 None:intergenic 30.0%
!! ATCTTTTATTTAATTGGGGG+TGG - chr7_1:33233338-33233357 Msa1016500:CDS 30.0%
! GACCCTAATGTTTTATACTA+TGG + chr7_1:33233503-33233522 None:intergenic 30.0%
AAGAAAAAATGTGATCAGTG+AGG + chr7_1:33233048-33233067 None:intergenic 30.0%
! GATAAAAAGGGGAATTTTGA+AGG + chr7_1:33233092-33233111 None:intergenic 30.0%
AGAGTTGTGATGATAAAAAG+GGG + chr7_1:33233103-33233122 None:intergenic 30.0%
CAGAGTTGTGATGATAAAAA+GGG + chr7_1:33233104-33233123 None:intergenic 30.0%
ACAGAGTTGTGATGATAAAA+AGG + chr7_1:33233105-33233124 None:intergenic 30.0%
AAAGTAATACATACGAGTGT+TGG + chr7_1:33233247-33233266 None:intergenic 30.0%
!! ATCTTTTATTTAATTGGGGG+TGG - chr7_1:33233338-33233357 Msa1016500:CDS 30.0%
! GACCCTAATGTTTTATACTA+TGG + chr7_1:33233503-33233522 None:intergenic 30.0%
AACTAACCCAACACCAAAAA+AGG + chr7_1:33233013-33233032 None:intergenic 35.0%
! TTGATGATCCACCATTCTTA+TGG + chr7_1:33233150-33233169 None:intergenic 35.0%
!! ATACATACGAGTGTTGGAAT+CGG + chr7_1:33233241-33233260 None:intergenic 35.0%
! AGGTATTGTAGCAACTACTA+TGG - chr7_1:33233680-33233699 Msa1016500:intron 35.0%
TAAACAACATGATCGTGAAG+AGG - chr7_1:33233850-33233869 Msa1016500:intron 35.0%
AAACAACATGATCGTGAAGA+GGG - chr7_1:33233851-33233870 Msa1016500:intron 35.0%
! TCAACTTCTCTTGTTATGAG+TGG - chr7_1:33234092-33234111 Msa1016500:five_prime_UTR 35.0%
AACTAACCCAACACCAAAAA+AGG + chr7_1:33233013-33233032 None:intergenic 35.0%
! TTGATGATCCACCATTCTTA+TGG + chr7_1:33233150-33233169 None:intergenic 35.0%
!! ATACATACGAGTGTTGGAAT+CGG + chr7_1:33233241-33233260 None:intergenic 35.0%
! AGGTATTGTAGCAACTACTA+TGG - chr7_1:33233680-33233699 Msa1016500:intron 35.0%
TAAACAACATGATCGTGAAG+AGG - chr7_1:33233850-33233869 Msa1016500:intron 35.0%
AAACAACATGATCGTGAAGA+GGG - chr7_1:33233851-33233870 Msa1016500:intron 35.0%
! TCAACTTCTCTTGTTATGAG+TGG - chr7_1:33234092-33234111 Msa1016500:five_prime_UTR 35.0%
ATCACCACACATGCAACAAA+CGG + chr7_1:33233174-33233193 None:intergenic 40.0%
TTGCAACGGAAAAGTTTGTC+AGG + chr7_1:33233206-33233225 None:intergenic 40.0%
CAACTACTATGGAGAACTAG+CGG - chr7_1:33233691-33233710 Msa1016500:intron 40.0%
TGGCACCAATTCAAAGAAAC+CGG - chr7_1:33233766-33233785 Msa1016500:intron 40.0%
AATTCAAAGAAACCGGTGAC+CGG - chr7_1:33233773-33233792 Msa1016500:intron 40.0%
AACCAACCGATCGGAATATT+CGG - chr7_1:33233814-33233833 Msa1016500:intron 40.0%
ATCACCACACATGCAACAAA+CGG + chr7_1:33233174-33233193 None:intergenic 40.0%
TTGCAACGGAAAAGTTTGTC+AGG + chr7_1:33233206-33233225 None:intergenic 40.0%
CAACTACTATGGAGAACTAG+CGG - chr7_1:33233691-33233710 Msa1016500:intron 40.0%
TGGCACCAATTCAAAGAAAC+CGG - chr7_1:33233766-33233785 Msa1016500:intron 40.0%
AATTCAAAGAAACCGGTGAC+CGG - chr7_1:33233773-33233792 Msa1016500:intron 40.0%
AACCAACCGATCGGAATATT+CGG - chr7_1:33233814-33233833 Msa1016500:intron 40.0%
TTGAAGGTGAGAGTGAGAGA+TGG + chr7_1:33233076-33233095 None:intergenic 45.0%
TGTGCAGCACACCATAAGAA+TGG - chr7_1:33233136-33233155 Msa1016500:three_prime_UTR 45.0%
! CAAACCGTTTGTTGCATGTG+TGG - chr7_1:33233167-33233186 Msa1016500:three_prime_UTR 45.0%
! TGTTGCATGTGTGGTGATGT+TGG - chr7_1:33233176-33233195 Msa1016500:three_prime_UTR 45.0%
CGGAGATAGAACAGTGTGAT+TGG - chr7_1:33233711-33233730 Msa1016500:intron 45.0%
!! GGTCACCGGTTTCTTTGAAT+TGG + chr7_1:33233774-33233793 None:intergenic 45.0%
ACCAACCGATCGGAATATTC+GGG - chr7_1:33233815-33233834 Msa1016500:intron 45.0%
TCTCACCCGAATATTCCGAT+CGG + chr7_1:33233823-33233842 None:intergenic 45.0%
ACGTAGGTACAAGCTTCTCA+AGG - chr7_1:33233922-33233941 Msa1016500:intron 45.0%
TTGAAGGTGAGAGTGAGAGA+TGG + chr7_1:33233076-33233095 None:intergenic 45.0%
TGTGCAGCACACCATAAGAA+TGG - chr7_1:33233136-33233155 Msa1016500:three_prime_UTR 45.0%
! CAAACCGTTTGTTGCATGTG+TGG - chr7_1:33233167-33233186 Msa1016500:three_prime_UTR 45.0%
! TGTTGCATGTGTGGTGATGT+TGG - chr7_1:33233176-33233195 Msa1016500:three_prime_UTR 45.0%
CGGAGATAGAACAGTGTGAT+TGG - chr7_1:33233711-33233730 Msa1016500:intron 45.0%
!! GGTCACCGGTTTCTTTGAAT+TGG + chr7_1:33233774-33233793 None:intergenic 45.0%
ACCAACCGATCGGAATATTC+GGG - chr7_1:33233815-33233834 Msa1016500:intron 45.0%
TCTCACCCGAATATTCCGAT+CGG + chr7_1:33233823-33233842 None:intergenic 45.0%
ACGTAGGTACAAGCTTCTCA+AGG - chr7_1:33233922-33233941 Msa1016500:intron 45.0%
GCAGCACACCATAAGAATGG+TGG - chr7_1:33233139-33233158 Msa1016500:three_prime_UTR 50.0%
!! CATACGAGTGTTGGAATCGG+TGG + chr7_1:33233238-33233257 None:intergenic 50.0%
ACGATCTCATTTCCGGTCAC+CGG + chr7_1:33233788-33233807 None:intergenic 50.0%
TGTCGCGACGATCTCATTTC+CGG + chr7_1:33233795-33233814 None:intergenic 50.0%
ACCCGAATATTCCGATCGGT+TGG + chr7_1:33233819-33233838 None:intergenic 50.0%
CAACATGATCGTGAAGAGGG+TGG - chr7_1:33233854-33233873 Msa1016500:intron 50.0%
AAGCTTGTACCTACGTGTGG+CGG + chr7_1:33233918-33233937 None:intergenic 50.0%
GAGAAGCTTGTACCTACGTG+TGG + chr7_1:33233921-33233940 None:intergenic 50.0%
GCAGCACACCATAAGAATGG+TGG - chr7_1:33233139-33233158 Msa1016500:three_prime_UTR 50.0%
!! CATACGAGTGTTGGAATCGG+TGG + chr7_1:33233238-33233257 None:intergenic 50.0%
ACGATCTCATTTCCGGTCAC+CGG + chr7_1:33233788-33233807 None:intergenic 50.0%
TGTCGCGACGATCTCATTTC+CGG + chr7_1:33233795-33233814 None:intergenic 50.0%
ACCCGAATATTCCGATCGGT+TGG + chr7_1:33233819-33233838 None:intergenic 50.0%
CAACATGATCGTGAAGAGGG+TGG - chr7_1:33233854-33233873 Msa1016500:intron 50.0%
AAGCTTGTACCTACGTGTGG+CGG + chr7_1:33233918-33233937 None:intergenic 50.0%
GAGAAGCTTGTACCTACGTG+TGG + chr7_1:33233921-33233940 None:intergenic 50.0%
! GGTGGCGGCATTTGTTGCAA+CGG + chr7_1:33233220-33233239 None:intergenic 55.0%
!! ACGAGTGTTGGAATCGGTGG+CGG + chr7_1:33233235-33233254 None:intergenic 55.0%
!! TGAAGAGGGTGGCTCTGAGA+AGG - chr7_1:33233865-33233884 Msa1016500:intron 55.0%
!! GAAGAGGGTGGCTCTGAGAA+GGG - chr7_1:33233866-33233885 Msa1016500:intron 55.0%
!! AAGAGGGTGGCTCTGAGAAG+GGG - chr7_1:33233867-33233886 Msa1016500:intron 55.0%
! GGTGGCGGCATTTGTTGCAA+CGG + chr7_1:33233220-33233239 None:intergenic 55.0%
!! ACGAGTGTTGGAATCGGTGG+CGG + chr7_1:33233235-33233254 None:intergenic 55.0%
!! TGAAGAGGGTGGCTCTGAGA+AGG - chr7_1:33233865-33233884 Msa1016500:intron 55.0%
!! GAAGAGGGTGGCTCTGAGAA+GGG - chr7_1:33233866-33233885 Msa1016500:intron 55.0%
!! AAGAGGGTGGCTCTGAGAAG+GGG - chr7_1:33233867-33233886 Msa1016500:intron 55.0%
CGTCGCGACAACCAACCGAT+CGG - chr7_1:33233805-33233824 Msa1016500:intron 60.0%
CGTCGCGACAACCAACCGAT+CGG - chr7_1:33233805-33233824 Msa1016500:intron 60.0%
AGAGTCCTTCGCCGTCGCCA+CGG - chr7_1:33233891-33233910 Msa1016500:intron 65.0%
TACCTACGTGTGGCGGTCCG+TGG + chr7_1:33233911-33233930 None:intergenic 65.0%
AGAGTCCTTCGCCGTCGCCA+CGG - chr7_1:33233891-33233910 Msa1016500:intron 65.0%
TACCTACGTGTGGCGGTCCG+TGG + chr7_1:33233911-33233930 None:intergenic 65.0%
CGTGTGGCGGTCCGTGGCGA+CGG + chr7_1:33233905-33233924 None:intergenic 75.0%
CGCCACGGACCGCCACACGT+AGG - chr7_1:33233906-33233925 Msa1016500:intron 75.0%
CGTGTGGCGGTCCGTGGCGA+CGG + chr7_1:33233905-33233924 None:intergenic 75.0%
CGCCACGGACCGCCACACGT+AGG - chr7_1:33233906-33233925 Msa1016500:intron 75.0%
! GCGGTCCGTGGCGACGGCGA+AGG + chr7_1:33233899-33233918 None:intergenic 80.0%
! GCGGTCCGTGGCGACGGCGA+AGG + chr7_1:33233899-33233918 None:intergenic 80.0%
Chromosome Type Strat End Strand Name
chr7_1 gene 33233006 33234208 33233006 ID=Msa1016500;Name=Msa1016500
chr7_1 mRNA 33233006 33234208 33233006 ID=Msa1016500-mRNA-1;Parent=Msa1016500;Name=Msa1016500-mRNA-1;_AED=0.01;_eAED=0.01;_QI=149|1|1|1|1|1|2|250|124
chr7_1 exon 33233006 33233532 33233006 ID=Msa1016500-mRNA-1:exon:6498;Parent=Msa1016500-mRNA-1
chr7_1 exon 33233962 33234208 33233962 ID=Msa1016500-mRNA-1:exon:6497;Parent=Msa1016500-mRNA-1
chr7_1 five_prime_UTR 33234060 33234208 33234060 ID=Msa1016500-mRNA-1:five_prime_utr;Parent=Msa1016500-mRNA-1
chr7_1 CDS 33233962 33234059 33233962 ID=Msa1016500-mRNA-1:cds;Parent=Msa1016500-mRNA-1
chr7_1 CDS 33233256 33233532 33233256 ID=Msa1016500-mRNA-1:cds;Parent=Msa1016500-mRNA-1
chr7_1 three_prime_UTR 33233006 33233255 33233006 ID=Msa1016500-mRNA-1:three_prime_utr;Parent=Msa1016500-mRNA-1
Gene Sequence

>Msa1016500

ATGGTGGATCATCAAACCGTTTGTTGCATGTGTGGTGATGTTGGTTTTCCTGACAAACTTTTCCGTTGCAACAAATGCCGCCACCGATTCCAACACTCGTATTGTAGCAACTACTATGGAGAACTAGCGGAGATAGAACAGTGTGATTGGTGCCAAAGTGAAGAGAAAAATTCAAGACATATTGGCACCAATTCAAAGAAACCGGTGACCGGAAATGAGATCGTCGCGACAACCAACCGATCGGAATATTCGGGTGAGAAAATCATTAAACAACATGATCGTGAAGAGGGTGGCTCTGAGAAGGGGAAGAGTCCTTCGCCGTCGCCACGGACCGCCACACGTAGGTACAAGCTTCTCAAGGATGTAATGTGTTAG
Protein sequence

>Msa1016500

MVDHQTVCCMCGDVGFPDKLFRCNKCRHRFQHSYCSNYYGELAEIEQCDWCQSEEKNSRHIGTNSKKPVTGNEIVATTNRSEYSGEKIIKQHDREEGGSEKGKSPSPSPRTATRRYKLLKDVMC*