AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1016510

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1016510 MtrunA17_Chr7g0231881 97.600 125 2 1 1 124 1 125 3.70e-89 254
Msa1016510 MtrunA17_Chr8g0334651 57.273 110 33 3 1 110 1 96 8.00e-37 120
Msa1016510 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
Msa1016510 AT3G60520.1 54.478 134 46 6 1 124 1 129 8.15e-35 117
Msa1016510 AT1G02070.1 54.615 130 49 4 5 124 2 131 2.60e-34 115
Msa1016510 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:+33268584 None:intergenic
AACCAACCGATCGGAATATT+CGG 0.326610 7_1:-33267872 Msa1016510:CDS
TTGATGATCCACCATTCTTA+TGG 0.333830 7_1:+33268539 None:intergenic
AGGTATTGTAGCAACTACTA+TGG 0.356994 7_1:-33268006 Msa1016510:CDS
GGTCACCGGTTTCTTTGAAT+TGG 0.367398 7_1:+33267915 None:intergenic
TGTCGCGACGATCTCATTTC+CGG 0.389983 7_1:+33267894 None:intergenic
CGGAGATAGAACAGTGTGAT+TGG 0.433454 7_1:-33267975 Msa1016510:CDS
TTGCAACGGAAAAGTTTGTC+AGG 0.456065 7_1:+33268483 None:intergenic
ACCAACCGATCGGAATATTC+GGG 0.471379 7_1:-33267871 Msa1016510:CDS
TGGCACCAATTCAAAGAAAC+CGG 0.486182 7_1:-33267920 Msa1016510:CDS
AAAGTAATACATACGAGTGT+TGG 0.487858 7_1:+33268442 None:intergenic
TCAACTTCTCTTGTTATGAG+TGG 0.496632 7_1:-33267594 Msa1016510:three_prime_UTR
GCGGTCCGTGGCGACGGCGA+AGG 0.502361 7_1:+33267790 None:intergenic
CGTGTGGCGGTCCGTGGCGA+CGG 0.515666 7_1:+33267784 None:intergenic
ACGATCTCATTTCCGGTCAC+CGG 0.516236 7_1:+33267901 None:intergenic
ATCACCACACATGCAACAAA+CGG 0.517973 7_1:+33268515 None:intergenic
GAAGAGGGTGGCTCTGAGAA+GGG 0.527687 7_1:-33267820 Msa1016510:CDS
TGTTGCATGTGTGGTGATGT+TGG 0.529954 7_1:-33268510 Msa1016510:CDS
TGAAGAGGGTGGCTCTGAGA+AGG 0.532977 7_1:-33267821 Msa1016510:CDS
ATACATACGAGTGTTGGAAT+CGG 0.550310 7_1:+33268448 None:intergenic
AGAGTCCTTCGCCGTCGCCA+CGG 0.553436 7_1:-33267795 Msa1016510:CDS
TACCTACGTGTGGCGGTCCG+TGG 0.554233 7_1:+33267778 None:intergenic
ACCCGAATATTCCGATCGGT+TGG 0.554818 7_1:+33267870 None:intergenic
AATCTTGAATAAGAAGAAGA+AGG 0.555136 7_1:-33267717 Msa1016510:three_prime_UTR
TTGAAGGTGAGAGTGAGAGA+TGG 0.555165 7_1:+33268613 None:intergenic
AATTCAAAGAAACCGGTGAC+CGG 0.559840 7_1:-33267913 Msa1016510:CDS
AAACAACATGATCGTGAAGA+GGG 0.586473 7_1:-33267835 Msa1016510:CDS
ACGAGTGTTGGAATCGGTGG+CGG 0.586739 7_1:+33268454 None:intergenic
TGTGCAGCACACCATAAGAA+TGG 0.588391 7_1:-33268550 Msa1016510:exon
GGTGGCGGCATTTGTTGCAA+CGG 0.592229 7_1:+33268469 None:intergenic
CAAACCGTTTGTTGCATGTG+TGG 0.594835 7_1:-33268519 Msa1016510:CDS
AAGAGGGTGGCTCTGAGAAG+GGG 0.612751 7_1:-33267819 Msa1016510:CDS
TAAACAACATGATCGTGAAG+AGG 0.621485 7_1:-33267836 Msa1016510:CDS
GAGAAGCTTGTACCTACGTG+TGG 0.625438 7_1:+33267768 None:intergenic
CATACGAGTGTTGGAATCGG+TGG 0.628121 7_1:+33268451 None:intergenic
TCTCACCCGAATATTCCGAT+CGG 0.641982 7_1:+33267866 None:intergenic
CGTCGCGACAACCAACCGAT+CGG 0.647059 7_1:-33267881 Msa1016510:CDS
ACGTAGGTACAAGCTTCTCA+AGG 0.654964 7_1:-33267764 Msa1016510:CDS
AAGCTTGTACCTACGTGTGG+CGG 0.656745 7_1:+33267771 None:intergenic
CAACATGATCGTGAAGAGGG+TGG 0.664857 7_1:-33267832 Msa1016510:CDS
GCAGCACACCATAAGAATGG+TGG 0.664995 7_1:-33268547 Msa1016510:exon
CAACTACTATGGAGAACTAG+CGG 0.694469 7_1:-33267995 Msa1016510:CDS
CGCCACGGACCGCCACACGT+AGG 0.759309 7_1:-33267780 Msa1016510:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! TATGAAATCTTTTATTTAAT+TGG - chr7_1:33267826-33267845 Msa1016510:CDS 10.0%
!!! ATGAAATCTTTTATTTAATT+GGG - chr7_1:33267827-33267846 Msa1016510:CDS 10.0%
!!! CAACATTAAAATAAATTTTA+AGG + chr7_1:33268146-33268165 None:intergenic 10.0%
!!! ATTTTAATGTTGTTTTTTTA+AGG - chr7_1:33268154-33268173 Msa1016510:intron 10.0%
!!! TATGAAATCTTTTATTTAAT+TGG - chr7_1:33267826-33267845 Msa1016510:CDS 10.0%
!!! ATGAAATCTTTTATTTAATT+GGG - chr7_1:33267827-33267846 Msa1016510:CDS 10.0%
!!! CAACATTAAAATAAATTTTA+AGG + chr7_1:33268146-33268165 None:intergenic 10.0%
!!! ATTTTAATGTTGTTTTTTTA+AGG - chr7_1:33268154-33268173 Msa1016510:intron 10.0%
!!! TGAAATCTTTTATTTAATTG+GGG - chr7_1:33267828-33267847 Msa1016510:CDS 15.0%
!!! CAAGTATATTATTTTTTGTT+TGG - chr7_1:33267966-33267985 Msa1016510:CDS 15.0%
!!! GAGATTGTTATTATTTTATT+AGG - chr7_1:33268105-33268124 Msa1016510:intron 15.0%
!!! TGAAATCTTTTATTTAATTG+GGG - chr7_1:33267828-33267847 Msa1016510:CDS 15.0%
!!! CAAGTATATTATTTTTTGTT+TGG - chr7_1:33267966-33267985 Msa1016510:CDS 15.0%
!!! GAGATTGTTATTATTTTATT+AGG - chr7_1:33268105-33268124 Msa1016510:intron 15.0%
!!! GAAATCTTTTATTTAATTGG+GGG - chr7_1:33267829-33267848 Msa1016510:CDS 20.0%
!! TAACCATAGTATAAAACATT+AGG - chr7_1:33267991-33268010 Msa1016510:CDS 20.0%
!! AACCATAGTATAAAACATTA+GGG - chr7_1:33267992-33268011 Msa1016510:CDS 20.0%
!!! GAAATCTTTTATTTAATTGG+GGG - chr7_1:33267829-33267848 Msa1016510:CDS 20.0%
!! TAACCATAGTATAAAACATT+AGG - chr7_1:33267991-33268010 Msa1016510:CDS 20.0%
!! AACCATAGTATAAAACATTA+GGG - chr7_1:33267992-33268011 Msa1016510:CDS 20.0%
! AACACGACTTTATAACTTTA+TGG + chr7_1:33267933-33267952 None:intergenic 25.0%
!! TTGAATTTTTCTCTTCACTT+TGG + chr7_1:33268233-33268252 None:intergenic 25.0%
! GAGAAAAATTCAAGACATAT+TGG - chr7_1:33268240-33268259 Msa1016510:intron 25.0%
! AATCTTGAATAAGAAGAAGA+AGG - chr7_1:33268463-33268482 Msa1016510:CDS 25.0%
! AACACGACTTTATAACTTTA+TGG + chr7_1:33267933-33267952 None:intergenic 25.0%
!! TTGAATTTTTCTCTTCACTT+TGG + chr7_1:33268233-33268252 None:intergenic 25.0%
! GAGAAAAATTCAAGACATAT+TGG - chr7_1:33268240-33268259 Msa1016510:intron 25.0%
! AATCTTGAATAAGAAGAAGA+AGG - chr7_1:33268463-33268482 Msa1016510:CDS 25.0%
AAGAAAAAATGTGATCAGTG+AGG + chr7_1:33267542-33267561 None:intergenic 30.0%
! GATAAAAAGGGGAATTTTGA+AGG + chr7_1:33267586-33267605 None:intergenic 30.0%
AGAGTTGTGATGATAAAAAG+GGG + chr7_1:33267597-33267616 None:intergenic 30.0%
CAGAGTTGTGATGATAAAAA+GGG + chr7_1:33267598-33267617 None:intergenic 30.0%
ACAGAGTTGTGATGATAAAA+AGG + chr7_1:33267599-33267618 None:intergenic 30.0%
AAAGTAATACATACGAGTGT+TGG + chr7_1:33267741-33267760 None:intergenic 30.0%
!! ATCTTTTATTTAATTGGGGG+TGG - chr7_1:33267832-33267851 Msa1016510:CDS 30.0%
! GACCCTAATGTTTTATACTA+TGG + chr7_1:33267997-33268016 None:intergenic 30.0%
AAGAAAAAATGTGATCAGTG+AGG + chr7_1:33267542-33267561 None:intergenic 30.0%
! GATAAAAAGGGGAATTTTGA+AGG + chr7_1:33267586-33267605 None:intergenic 30.0%
AGAGTTGTGATGATAAAAAG+GGG + chr7_1:33267597-33267616 None:intergenic 30.0%
CAGAGTTGTGATGATAAAAA+GGG + chr7_1:33267598-33267617 None:intergenic 30.0%
ACAGAGTTGTGATGATAAAA+AGG + chr7_1:33267599-33267618 None:intergenic 30.0%
AAAGTAATACATACGAGTGT+TGG + chr7_1:33267741-33267760 None:intergenic 30.0%
!! ATCTTTTATTTAATTGGGGG+TGG - chr7_1:33267832-33267851 Msa1016510:CDS 30.0%
! GACCCTAATGTTTTATACTA+TGG + chr7_1:33267997-33268016 None:intergenic 30.0%
AACTAACCCAACACCAAAAA+AGG + chr7_1:33267507-33267526 None:intergenic 35.0%
! TTGATGATCCACCATTCTTA+TGG + chr7_1:33267644-33267663 None:intergenic 35.0%
!! ATACATACGAGTGTTGGAAT+CGG + chr7_1:33267735-33267754 None:intergenic 35.0%
! AGGTATTGTAGCAACTACTA+TGG - chr7_1:33268174-33268193 Msa1016510:intron 35.0%
TAAACAACATGATCGTGAAG+AGG - chr7_1:33268344-33268363 Msa1016510:intron 35.0%
AAACAACATGATCGTGAAGA+GGG - chr7_1:33268345-33268364 Msa1016510:intron 35.0%
! TCAACTTCTCTTGTTATGAG+TGG - chr7_1:33268586-33268605 Msa1016510:five_prime_UTR 35.0%
AACTAACCCAACACCAAAAA+AGG + chr7_1:33267507-33267526 None:intergenic 35.0%
! TTGATGATCCACCATTCTTA+TGG + chr7_1:33267644-33267663 None:intergenic 35.0%
!! ATACATACGAGTGTTGGAAT+CGG + chr7_1:33267735-33267754 None:intergenic 35.0%
! AGGTATTGTAGCAACTACTA+TGG - chr7_1:33268174-33268193 Msa1016510:intron 35.0%
TAAACAACATGATCGTGAAG+AGG - chr7_1:33268344-33268363 Msa1016510:intron 35.0%
AAACAACATGATCGTGAAGA+GGG - chr7_1:33268345-33268364 Msa1016510:intron 35.0%
! TCAACTTCTCTTGTTATGAG+TGG - chr7_1:33268586-33268605 Msa1016510:five_prime_UTR 35.0%
ATCACCACACATGCAACAAA+CGG + chr7_1:33267668-33267687 None:intergenic 40.0%
TTGCAACGGAAAAGTTTGTC+AGG + chr7_1:33267700-33267719 None:intergenic 40.0%
CAACTACTATGGAGAACTAG+CGG - chr7_1:33268185-33268204 Msa1016510:intron 40.0%
TGGCACCAATTCAAAGAAAC+CGG - chr7_1:33268260-33268279 Msa1016510:intron 40.0%
AATTCAAAGAAACCGGTGAC+CGG - chr7_1:33268267-33268286 Msa1016510:intron 40.0%
AACCAACCGATCGGAATATT+CGG - chr7_1:33268308-33268327 Msa1016510:intron 40.0%
ATCACCACACATGCAACAAA+CGG + chr7_1:33267668-33267687 None:intergenic 40.0%
TTGCAACGGAAAAGTTTGTC+AGG + chr7_1:33267700-33267719 None:intergenic 40.0%
CAACTACTATGGAGAACTAG+CGG - chr7_1:33268185-33268204 Msa1016510:intron 40.0%
TGGCACCAATTCAAAGAAAC+CGG - chr7_1:33268260-33268279 Msa1016510:intron 40.0%
AATTCAAAGAAACCGGTGAC+CGG - chr7_1:33268267-33268286 Msa1016510:intron 40.0%
AACCAACCGATCGGAATATT+CGG - chr7_1:33268308-33268327 Msa1016510:intron 40.0%
TTGAAGGTGAGAGTGAGAGA+TGG + chr7_1:33267570-33267589 None:intergenic 45.0%
TGTGCAGCACACCATAAGAA+TGG - chr7_1:33267630-33267649 Msa1016510:three_prime_UTR 45.0%
! CAAACCGTTTGTTGCATGTG+TGG - chr7_1:33267661-33267680 Msa1016510:three_prime_UTR 45.0%
! TGTTGCATGTGTGGTGATGT+TGG - chr7_1:33267670-33267689 Msa1016510:three_prime_UTR 45.0%
CGGAGATAGAACAGTGTGAT+TGG - chr7_1:33268205-33268224 Msa1016510:intron 45.0%
!! GGTCACCGGTTTCTTTGAAT+TGG + chr7_1:33268268-33268287 None:intergenic 45.0%
ACCAACCGATCGGAATATTC+GGG - chr7_1:33268309-33268328 Msa1016510:intron 45.0%
TCTCACCCGAATATTCCGAT+CGG + chr7_1:33268317-33268336 None:intergenic 45.0%
ACGTAGGTACAAGCTTCTCA+AGG - chr7_1:33268416-33268435 Msa1016510:intron 45.0%
TTGAAGGTGAGAGTGAGAGA+TGG + chr7_1:33267570-33267589 None:intergenic 45.0%
TGTGCAGCACACCATAAGAA+TGG - chr7_1:33267630-33267649 Msa1016510:three_prime_UTR 45.0%
! CAAACCGTTTGTTGCATGTG+TGG - chr7_1:33267661-33267680 Msa1016510:three_prime_UTR 45.0%
! TGTTGCATGTGTGGTGATGT+TGG - chr7_1:33267670-33267689 Msa1016510:three_prime_UTR 45.0%
CGGAGATAGAACAGTGTGAT+TGG - chr7_1:33268205-33268224 Msa1016510:intron 45.0%
!! GGTCACCGGTTTCTTTGAAT+TGG + chr7_1:33268268-33268287 None:intergenic 45.0%
ACCAACCGATCGGAATATTC+GGG - chr7_1:33268309-33268328 Msa1016510:intron 45.0%
TCTCACCCGAATATTCCGAT+CGG + chr7_1:33268317-33268336 None:intergenic 45.0%
ACGTAGGTACAAGCTTCTCA+AGG - chr7_1:33268416-33268435 Msa1016510:intron 45.0%
GCAGCACACCATAAGAATGG+TGG - chr7_1:33267633-33267652 Msa1016510:three_prime_UTR 50.0%
!! CATACGAGTGTTGGAATCGG+TGG + chr7_1:33267732-33267751 None:intergenic 50.0%
ACGATCTCATTTCCGGTCAC+CGG + chr7_1:33268282-33268301 None:intergenic 50.0%
TGTCGCGACGATCTCATTTC+CGG + chr7_1:33268289-33268308 None:intergenic 50.0%
ACCCGAATATTCCGATCGGT+TGG + chr7_1:33268313-33268332 None:intergenic 50.0%
CAACATGATCGTGAAGAGGG+TGG - chr7_1:33268348-33268367 Msa1016510:intron 50.0%
AAGCTTGTACCTACGTGTGG+CGG + chr7_1:33268412-33268431 None:intergenic 50.0%
GAGAAGCTTGTACCTACGTG+TGG + chr7_1:33268415-33268434 None:intergenic 50.0%
GCAGCACACCATAAGAATGG+TGG - chr7_1:33267633-33267652 Msa1016510:three_prime_UTR 50.0%
!! CATACGAGTGTTGGAATCGG+TGG + chr7_1:33267732-33267751 None:intergenic 50.0%
ACGATCTCATTTCCGGTCAC+CGG + chr7_1:33268282-33268301 None:intergenic 50.0%
TGTCGCGACGATCTCATTTC+CGG + chr7_1:33268289-33268308 None:intergenic 50.0%
ACCCGAATATTCCGATCGGT+TGG + chr7_1:33268313-33268332 None:intergenic 50.0%
CAACATGATCGTGAAGAGGG+TGG - chr7_1:33268348-33268367 Msa1016510:intron 50.0%
AAGCTTGTACCTACGTGTGG+CGG + chr7_1:33268412-33268431 None:intergenic 50.0%
GAGAAGCTTGTACCTACGTG+TGG + chr7_1:33268415-33268434 None:intergenic 50.0%
! GGTGGCGGCATTTGTTGCAA+CGG + chr7_1:33267714-33267733 None:intergenic 55.0%
!! ACGAGTGTTGGAATCGGTGG+CGG + chr7_1:33267729-33267748 None:intergenic 55.0%
!! TGAAGAGGGTGGCTCTGAGA+AGG - chr7_1:33268359-33268378 Msa1016510:intron 55.0%
!! GAAGAGGGTGGCTCTGAGAA+GGG - chr7_1:33268360-33268379 Msa1016510:intron 55.0%
!! AAGAGGGTGGCTCTGAGAAG+GGG - chr7_1:33268361-33268380 Msa1016510:intron 55.0%
! GGTGGCGGCATTTGTTGCAA+CGG + chr7_1:33267714-33267733 None:intergenic 55.0%
!! ACGAGTGTTGGAATCGGTGG+CGG + chr7_1:33267729-33267748 None:intergenic 55.0%
!! TGAAGAGGGTGGCTCTGAGA+AGG - chr7_1:33268359-33268378 Msa1016510:intron 55.0%
!! GAAGAGGGTGGCTCTGAGAA+GGG - chr7_1:33268360-33268379 Msa1016510:intron 55.0%
!! AAGAGGGTGGCTCTGAGAAG+GGG - chr7_1:33268361-33268380 Msa1016510:intron 55.0%
CGTCGCGACAACCAACCGAT+CGG - chr7_1:33268299-33268318 Msa1016510:intron 60.0%
CGTCGCGACAACCAACCGAT+CGG - chr7_1:33268299-33268318 Msa1016510:intron 60.0%
AGAGTCCTTCGCCGTCGCCA+CGG - chr7_1:33268385-33268404 Msa1016510:intron 65.0%
TACCTACGTGTGGCGGTCCG+TGG + chr7_1:33268405-33268424 None:intergenic 65.0%
AGAGTCCTTCGCCGTCGCCA+CGG - chr7_1:33268385-33268404 Msa1016510:intron 65.0%
TACCTACGTGTGGCGGTCCG+TGG + chr7_1:33268405-33268424 None:intergenic 65.0%
CGTGTGGCGGTCCGTGGCGA+CGG + chr7_1:33268399-33268418 None:intergenic 75.0%
CGCCACGGACCGCCACACGT+AGG - chr7_1:33268400-33268419 Msa1016510:intron 75.0%
CGTGTGGCGGTCCGTGGCGA+CGG + chr7_1:33268399-33268418 None:intergenic 75.0%
CGCCACGGACCGCCACACGT+AGG - chr7_1:33268400-33268419 Msa1016510:intron 75.0%
! GCGGTCCGTGGCGACGGCGA+AGG + chr7_1:33268393-33268412 None:intergenic 80.0%
! GCGGTCCGTGGCGACGGCGA+AGG + chr7_1:33268393-33268412 None:intergenic 80.0%
Chromosome Type Strat End Strand Name
chr7_1 gene 33267500 33268702 33267500 ID=Msa1016510;Name=Msa1016510
chr7_1 mRNA 33267500 33268702 33267500 ID=Msa1016510-mRNA-1;Parent=Msa1016510;Name=Msa1016510-mRNA-1;_AED=0.01;_eAED=0.01;_QI=149|1|1|1|1|1|2|250|124
chr7_1 exon 33267500 33268026 33267500 ID=Msa1016510-mRNA-1:exon:6500;Parent=Msa1016510-mRNA-1
chr7_1 exon 33268456 33268702 33268456 ID=Msa1016510-mRNA-1:exon:6499;Parent=Msa1016510-mRNA-1
chr7_1 five_prime_UTR 33268554 33268702 33268554 ID=Msa1016510-mRNA-1:five_prime_utr;Parent=Msa1016510-mRNA-1
chr7_1 CDS 33268456 33268553 33268456 ID=Msa1016510-mRNA-1:cds;Parent=Msa1016510-mRNA-1
chr7_1 CDS 33267750 33268026 33267750 ID=Msa1016510-mRNA-1:cds;Parent=Msa1016510-mRNA-1
chr7_1 three_prime_UTR 33267500 33267749 33267500 ID=Msa1016510-mRNA-1:three_prime_utr;Parent=Msa1016510-mRNA-1
Gene Sequence

>Msa1016510

ATGGTGGATCATCAAACCGTTTGTTGCATGTGTGGTGATGTTGGTTTTCCTGACAAACTTTTCCGTTGCAACAAATGCCGCCACCGATTCCAACACTCGTATTGTAGCAACTACTATGGAGAACTAGCGGAGATAGAACAGTGTGATTGGTGCCAAAGTGAAGAGAAAAATTCAAGACATATTGGCACCAATTCAAAGAAACCGGTGACCGGAAATGAGATCGTCGCGACAACCAACCGATCGGAATATTCGGGTGAGAAAATCATTAAACAACATGATCGTGAAGAGGGTGGCTCTGAGAAGGGGAAGAGTCCTTCGCCGTCGCCACGGACCGCCACACGTAGGTACAAGCTTCTCAAGGATGTAATGTGTTAG
Protein sequence

>Msa1016510

MVDHQTVCCMCGDVGFPDKLFRCNKCRHRFQHSYCSNYYGELAEIEQCDWCQSEEKNSRHIGTNSKKPVTGNEIVATTNRSEYSGEKIIKQHDREEGGSEKGKSPSPSPRTATRRYKLLKDVMC*