AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1403330

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1403330 MtrunA17_Chr4g0003101 88.462 52 6 0 1 52 184 235 8.32e-29 105
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1403330 AT1G15290.2 55.769 52 23 0 1 52 153 204 1.38e-14 65.9
Msa1403330 AT1G15290.1 55.769 52 23 0 1 52 153 204 1.39e-14 65.9

Find 31 sgRNAs with CRISPR-Local

Find 118 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TTACTTTCAGATTCAGATTC+AGG 0.227644 tig0022951:-76409 Msa1403330:intron
TAACAGTTTATCTAGCGATT+AGG 0.277835 tig0022951:+76857 None:intergenic
CACAAATTGTGATTCAATAT+CGG 0.293147 tig0022951:-76702 Msa1403330:five_prime_UTR
AACAGTTTATCTAGCGATTA+GGG 0.310080 tig0022951:+76858 None:intergenic
ACAAAACACTAGTTATATTA+AGG 0.313616 tig0022951:+75871 None:intergenic
CAAGACTAAGAGTAGAAGAT+AGG 0.335113 tig0022951:-75932 Msa1403330:three_prime_UTR
TTTGAAGAAATGTGAATTGA+AGG 0.370761 tig0022951:-76457 Msa1403330:CDS
TTCATCCGACGCCGAAGTTG+TGG 0.424970 tig0022951:-76658 Msa1403330:CDS
TTGTGAGGAATTTGTTTACT+TGG 0.445810 tig0022951:-76903 Msa1403330:five_prime_UTR
TCATCCGACGCCGAAGTTGT+GGG 0.454363 tig0022951:-76657 Msa1403330:CDS
AATTTATTATAAAATATAAG+AGG 0.455639 tig0022951:+75732 None:intergenic
TTGAAGGAAGAAGATGATAG+AGG 0.499044 tig0022951:-76441 Msa1403330:CDS
CAAAAGACGGGGCAATTACA+AGG 0.508315 tig0022951:-75958 Msa1403330:three_prime_UTR
GACAAGGCTTGAGAAACAAT+TGG 0.508496 tig0022951:-75989 Msa1403330:three_prime_UTR
AAGACTAAGAGTAGAAGATA+GGG 0.508621 tig0022951:-75931 Msa1403330:three_prime_UTR
GAAGAAGATGATAGAGGCAA+AGG 0.512391 tig0022951:-76435 Msa1403330:CDS
TTGGCAAAAGAGCAAAAGAC+GGG 0.528765 tig0022951:-75970 Msa1403330:three_prime_UTR
TGATTCAATATCGGAGAATG+TGG 0.542320 tig0022951:-76693 Msa1403330:five_prime_UTR
GATTGGGTAAAAGTTGAAGA+AGG 0.561791 tig0022951:-76016 Msa1403330:exon
AGAGACTCACGCAAAATCAG+AGG 0.576920 tig0022951:+76599 None:intergenic
ACAAGTCACCATCAATATGA+AGG 0.583661 tig0022951:+75804 None:intergenic
ATCGGAGAATGTGGGAATGG+TGG 0.584217 tig0022951:-76684 Msa1403330:exon
AAATCCCACAACTTCGGCGT+CGG 0.597204 tig0022951:+76653 None:intergenic
AATATCGGAGAATGTGGGAA+TGG 0.601867 tig0022951:-76687 Msa1403330:exon
GAGACTCACGCAAAATCAGA+GGG 0.603386 tig0022951:+76600 None:intergenic
ATTGGCAAAAGAGCAAAAGA+CGG 0.635114 tig0022951:-75971 Msa1403330:three_prime_UTR
GATTCAATATCGGAGAATGT+GGG 0.665724 tig0022951:-76692 Msa1403330:five_prime_UTR
AGTTGAAGAAGGCAACGACA+AGG 0.678134 tig0022951:-76005 Msa1403330:three_prime_UTR
TGTTTGATGAAATGATTGTG+AGG 0.699167 tig0022951:-76918 Msa1403330:five_prime_UTR
TGGCAAAAGAGCAAAAGACG+GGG 0.714282 tig0022951:-75969 Msa1403330:three_prime_UTR
AGACTCACGCAAAATCAGAG+GGG 0.781912 tig0022951:+76601 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! AATTTTTATGCGTTTTTGTT+AGG - tig0022951:76105-76124 Msa1403330:intron 20.0%
!!! ATTTTTATGCGTTTTTGTTA+GGG - tig0022951:76106-76125 Msa1403330:intron 20.0%
!! ATAAAGTTTATGCAAGTTAA+AGG + tig0022951:76409-76428 None:intergenic 20.0%
!! TAAAAAGAAAAACAGAATTC+TGG + tig0022951:76469-76488 None:intergenic 20.0%
!!! GAATTCTGTTTTTCTTTTTA+AGG - tig0022951:76469-76488 Msa1403330:intron 20.0%
!! ACAAAACACTAGTTATATTA+AGG + tig0022951:76767-76786 None:intergenic 20.0%
!!! AATTTTTATGCGTTTTTGTT+AGG - tig0022951:76105-76124 Msa1403330:intron 20.0%
!!! ATTTTTATGCGTTTTTGTTA+GGG - tig0022951:76106-76125 Msa1403330:intron 20.0%
!! ATAAAGTTTATGCAAGTTAA+AGG + tig0022951:76409-76428 None:intergenic 20.0%
!! TAAAAAGAAAAACAGAATTC+TGG + tig0022951:76469-76488 None:intergenic 20.0%
!!! GAATTCTGTTTTTCTTTTTA+AGG - tig0022951:76469-76488 Msa1403330:intron 20.0%
!! ACAAAACACTAGTTATATTA+AGG + tig0022951:76767-76786 None:intergenic 20.0%
! CACAAATTGTGATTCAATAT+CGG - tig0022951:75933-75952 Msa1403330:three_prime_UTR 25.0%
! TTTGAAGAAATGTGAATTGA+AGG - tig0022951:76178-76197 Msa1403330:intron 25.0%
! TTATTGCATTTCATTGAGTT+AGG - tig0022951:76256-76275 Msa1403330:intron 25.0%
! TATTTGTAGCTATTCAAAGT+GGG + tig0022951:76360-76379 None:intergenic 25.0%
! ATATTTGTAGCTATTCAAAG+TGG + tig0022951:76361-76380 None:intergenic 25.0%
! TTTGTGTTTGATCAATCATA+TGG - tig0022951:76589-76608 Msa1403330:intron 25.0%
!!! AATCATATGGTTTTGTAGAT+TGG - tig0022951:76602-76621 Msa1403330:intron 25.0%
!!! ATCATATGGTTTTGTAGATT+GGG - tig0022951:76603-76622 Msa1403330:intron 25.0%
!! ATTTTACACCTTCATATTGA+TGG - tig0022951:76823-76842 Msa1403330:five_prime_UTR 25.0%
!! GTGTATTTTATGACTAATGT+CGG - tig0022951:76872-76891 Msa1403330:five_prime_UTR 25.0%
!! TGTATTTTATGACTAATGTC+GGG - tig0022951:76873-76892 Msa1403330:five_prime_UTR 25.0%
! CACAAATTGTGATTCAATAT+CGG - tig0022951:75933-75952 Msa1403330:three_prime_UTR 25.0%
! TTTGAAGAAATGTGAATTGA+AGG - tig0022951:76178-76197 Msa1403330:intron 25.0%
! TTATTGCATTTCATTGAGTT+AGG - tig0022951:76256-76275 Msa1403330:intron 25.0%
! TATTTGTAGCTATTCAAAGT+GGG + tig0022951:76360-76379 None:intergenic 25.0%
! ATATTTGTAGCTATTCAAAG+TGG + tig0022951:76361-76380 None:intergenic 25.0%
! TTTGTGTTTGATCAATCATA+TGG - tig0022951:76589-76608 Msa1403330:intron 25.0%
!!! AATCATATGGTTTTGTAGAT+TGG - tig0022951:76602-76621 Msa1403330:intron 25.0%
!!! ATCATATGGTTTTGTAGATT+GGG - tig0022951:76603-76622 Msa1403330:intron 25.0%
!! ATTTTACACCTTCATATTGA+TGG - tig0022951:76823-76842 Msa1403330:five_prime_UTR 25.0%
!! GTGTATTTTATGACTAATGT+CGG - tig0022951:76872-76891 Msa1403330:five_prime_UTR 25.0%
!! TGTATTTTATGACTAATGTC+GGG - tig0022951:76873-76892 Msa1403330:five_prime_UTR 25.0%
! TTGTGAGGAATTTGTTTACT+TGG - tig0022951:75732-75751 Msa1403330:three_prime_UTR 30.0%
AACAGTTTATCTAGCGATTA+GGG + tig0022951:75780-75799 None:intergenic 30.0%
TAACAGTTTATCTAGCGATT+AGG + tig0022951:75781-75800 None:intergenic 30.0%
! GCAATGAATCAACTTTTCAA+AGG + tig0022951:75826-75845 None:intergenic 30.0%
TCATAAAAATCCCACAACTT+CGG + tig0022951:75991-76010 None:intergenic 30.0%
AACATTTGACATGGTGATAA+GGG - tig0022951:76132-76151 Msa1403330:intron 30.0%
TTACTTTCAGATTCAGATTC+AGG - tig0022951:76226-76245 Msa1403330:intron 30.0%
GAGTAAAAGAAAGACTCTAA+AGG + tig0022951:76548-76567 None:intergenic 30.0%
AAGACTAAGAGTAGAAGATA+GGG - tig0022951:76704-76723 Msa1403330:five_prime_UTR 30.0%
! TTGTGAGGAATTTGTTTACT+TGG - tig0022951:75732-75751 Msa1403330:three_prime_UTR 30.0%
AACAGTTTATCTAGCGATTA+GGG + tig0022951:75780-75799 None:intergenic 30.0%
TAACAGTTTATCTAGCGATT+AGG + tig0022951:75781-75800 None:intergenic 30.0%
! GCAATGAATCAACTTTTCAA+AGG + tig0022951:75826-75845 None:intergenic 30.0%
TCATAAAAATCCCACAACTT+CGG + tig0022951:75991-76010 None:intergenic 30.0%
AACATTTGACATGGTGATAA+GGG - tig0022951:76132-76151 Msa1403330:intron 30.0%
TTACTTTCAGATTCAGATTC+AGG - tig0022951:76226-76245 Msa1403330:intron 30.0%
GAGTAAAAGAAAGACTCTAA+AGG + tig0022951:76548-76567 None:intergenic 30.0%
AAGACTAAGAGTAGAAGATA+GGG - tig0022951:76704-76723 Msa1403330:five_prime_UTR 30.0%
TGATTCAATATCGGAGAATG+TGG - tig0022951:75942-75961 Msa1403330:three_prime_UTR 35.0%
GATTCAATATCGGAGAATGT+GGG - tig0022951:75943-75962 Msa1403330:three_prime_UTR 35.0%
TTAGGGTTGAACATTTGACA+TGG - tig0022951:76123-76142 Msa1403330:intron 35.0%
GAACATTTGACATGGTGATA+AGG - tig0022951:76131-76150 Msa1403330:intron 35.0%
TTGAAGGAAGAAGATGATAG+AGG - tig0022951:76194-76213 Msa1403330:intron 35.0%
ATGCAAGTTAAAGGAACTCA+CGG + tig0022951:76400-76419 None:intergenic 35.0%
!! CTAAAGGCACTTCATTGTTT+AGG + tig0022951:76532-76551 None:intergenic 35.0%
! CTTTCTTTTACTCTTCTCAG+AGG - tig0022951:76555-76574 Msa1403330:intron 35.0%
GATTGGGTAAAAGTTGAAGA+AGG - tig0022951:76619-76638 Msa1403330:CDS 35.0%
ATTGGCAAAAGAGCAAAAGA+CGG - tig0022951:76664-76683 Msa1403330:CDS 35.0%
CAAGACTAAGAGTAGAAGAT+AGG - tig0022951:76703-76722 Msa1403330:five_prime_UTR 35.0%
ACAAGTCACCATCAATATGA+AGG + tig0022951:76834-76853 None:intergenic 35.0%
TGATTCAATATCGGAGAATG+TGG - tig0022951:75942-75961 Msa1403330:three_prime_UTR 35.0%
GATTCAATATCGGAGAATGT+GGG - tig0022951:75943-75962 Msa1403330:three_prime_UTR 35.0%
TTAGGGTTGAACATTTGACA+TGG - tig0022951:76123-76142 Msa1403330:intron 35.0%
GAACATTTGACATGGTGATA+AGG - tig0022951:76131-76150 Msa1403330:intron 35.0%
TTGAAGGAAGAAGATGATAG+AGG - tig0022951:76194-76213 Msa1403330:intron 35.0%
ATGCAAGTTAAAGGAACTCA+CGG + tig0022951:76400-76419 None:intergenic 35.0%
!! CTAAAGGCACTTCATTGTTT+AGG + tig0022951:76532-76551 None:intergenic 35.0%
! CTTTCTTTTACTCTTCTCAG+AGG - tig0022951:76555-76574 Msa1403330:intron 35.0%
GATTGGGTAAAAGTTGAAGA+AGG - tig0022951:76619-76638 Msa1403330:CDS 35.0%
ATTGGCAAAAGAGCAAAAGA+CGG - tig0022951:76664-76683 Msa1403330:CDS 35.0%
CAAGACTAAGAGTAGAAGAT+AGG - tig0022951:76703-76722 Msa1403330:five_prime_UTR 35.0%
ACAAGTCACCATCAATATGA+AGG + tig0022951:76834-76853 None:intergenic 35.0%
AATATCGGAGAATGTGGGAA+TGG - tig0022951:75948-75967 Msa1403330:three_prime_UTR 40.0%
GAAGAAGATGATAGAGGCAA+AGG - tig0022951:76200-76219 Msa1403330:intron 40.0%
AAGTTAAAGGAACTCACGGT+GGG + tig0022951:76396-76415 None:intergenic 40.0%
AATTCTGGTACTAGAGAGTC+AGG + tig0022951:76454-76473 None:intergenic 40.0%
GACAAGGCTTGAGAAACAAT+TGG - tig0022951:76646-76665 Msa1403330:CDS 40.0%
TTGGCAAAAGAGCAAAAGAC+GGG - tig0022951:76665-76684 Msa1403330:CDS 40.0%
AATATCGGAGAATGTGGGAA+TGG - tig0022951:75948-75967 Msa1403330:three_prime_UTR 40.0%
GAAGAAGATGATAGAGGCAA+AGG - tig0022951:76200-76219 Msa1403330:intron 40.0%
AAGTTAAAGGAACTCACGGT+GGG + tig0022951:76396-76415 None:intergenic 40.0%
AATTCTGGTACTAGAGAGTC+AGG + tig0022951:76454-76473 None:intergenic 40.0%
GACAAGGCTTGAGAAACAAT+TGG - tig0022951:76646-76665 Msa1403330:CDS 40.0%
TTGGCAAAAGAGCAAAAGAC+GGG - tig0022951:76665-76684 Msa1403330:CDS 40.0%
AGACTCACGCAAAATCAGAG+GGG + tig0022951:76037-76056 None:intergenic 45.0%
GAGACTCACGCAAAATCAGA+GGG + tig0022951:76038-76057 None:intergenic 45.0%
AGAGACTCACGCAAAATCAG+AGG + tig0022951:76039-76058 None:intergenic 45.0%
AATGTGTGATGCTGCTGTCT+TGG - tig0022951:76328-76347 Msa1403330:intron 45.0%
AGTTAAAGGAACTCACGGTG+GGG + tig0022951:76395-76414 None:intergenic 45.0%
CAAGTTAAAGGAACTCACGG+TGG + tig0022951:76397-76416 None:intergenic 45.0%
AGTTGAAGAAGGCAACGACA+AGG - tig0022951:76630-76649 Msa1403330:CDS 45.0%
TGGCAAAAGAGCAAAAGACG+GGG - tig0022951:76666-76685 Msa1403330:CDS 45.0%
CAAAAGACGGGGCAATTACA+AGG - tig0022951:76677-76696 Msa1403330:exon 45.0%
AGACTCACGCAAAATCAGAG+GGG + tig0022951:76037-76056 None:intergenic 45.0%
GAGACTCACGCAAAATCAGA+GGG + tig0022951:76038-76057 None:intergenic 45.0%
AGAGACTCACGCAAAATCAG+AGG + tig0022951:76039-76058 None:intergenic 45.0%
AATGTGTGATGCTGCTGTCT+TGG - tig0022951:76328-76347 Msa1403330:intron 45.0%
AGTTAAAGGAACTCACGGTG+GGG + tig0022951:76395-76414 None:intergenic 45.0%
CAAGTTAAAGGAACTCACGG+TGG + tig0022951:76397-76416 None:intergenic 45.0%
AGTTGAAGAAGGCAACGACA+AGG - tig0022951:76630-76649 Msa1403330:CDS 45.0%
TGGCAAAAGAGCAAAAGACG+GGG - tig0022951:76666-76685 Msa1403330:CDS 45.0%
CAAAAGACGGGGCAATTACA+AGG - tig0022951:76677-76696 Msa1403330:exon 45.0%
!! AATTTATTATAAAATATAAG+AGG + tig0022951:76906-76925 None:intergenic 5.0%
!! AATTTATTATAAAATATAAG+AGG + tig0022951:76906-76925 None:intergenic 5.0%
ATCGGAGAATGTGGGAATGG+TGG - tig0022951:75951-75970 Msa1403330:three_prime_UTR 50.0%
AAATCCCACAACTTCGGCGT+CGG + tig0022951:75985-76004 None:intergenic 50.0%
TGGTACTAGAGAGTCAGGCA+CGG + tig0022951:76449-76468 None:intergenic 50.0%
ATCGGAGAATGTGGGAATGG+TGG - tig0022951:75951-75970 Msa1403330:three_prime_UTR 50.0%
AAATCCCACAACTTCGGCGT+CGG + tig0022951:75985-76004 None:intergenic 50.0%
TGGTACTAGAGAGTCAGGCA+CGG + tig0022951:76449-76468 None:intergenic 50.0%
TTCATCCGACGCCGAAGTTG+TGG - tig0022951:75977-75996 Msa1403330:three_prime_UTR 55.0%
TCATCCGACGCCGAAGTTGT+GGG - tig0022951:75978-75997 Msa1403330:three_prime_UTR 55.0%
TTCATCCGACGCCGAAGTTG+TGG - tig0022951:75977-75996 Msa1403330:three_prime_UTR 55.0%
TCATCCGACGCCGAAGTTGT+GGG - tig0022951:75978-75997 Msa1403330:three_prime_UTR 55.0%
Chromosome Type Strat End Strand Name
tig0022951 gene 75718 76939 75718 ID=Msa1403330;Name=Msa1403330
tig0022951 mRNA 75718 76939 75718 ID=Msa1403330-mRNA-1;Parent=Msa1403330;Name=Msa1403330-mRNA-1;_AED=0.27;_eAED=0.27;_QI=249|1|1|1|0.5|0.66|3|311|53
tig0022951 exon 75718 76037 75718 ID=Msa1403330-mRNA-1:exon:19217;Parent=Msa1403330-mRNA-1
tig0022951 exon 76410 76480 76410 ID=Msa1403330-mRNA-1:exon:19216;Parent=Msa1403330-mRNA-1
tig0022951 exon 76609 76939 76609 ID=Msa1403330-mRNA-1:exon:19215;Parent=Msa1403330-mRNA-1
tig0022951 five_prime_UTR 76691 76939 76691 ID=Msa1403330-mRNA-1:five_prime_utr;Parent=Msa1403330-mRNA-1
tig0022951 CDS 76609 76690 76609 ID=Msa1403330-mRNA-1:cds;Parent=Msa1403330-mRNA-1
tig0022951 CDS 76410 76480 76410 ID=Msa1403330-mRNA-1:cds;Parent=Msa1403330-mRNA-1
tig0022951 CDS 76029 76037 76029 ID=Msa1403330-mRNA-1:cds;Parent=Msa1403330-mRNA-1
tig0022951 three_prime_UTR 75718 76028 75718 ID=Msa1403330-mRNA-1:three_prime_utr;Parent=Msa1403330-mRNA-1
Gene Sequence

>Msa1403330

ATGGTGGCTATTCATCCGACGCCGAAGTTGTGGGATTTTTATGAGTTCTTTTCGTTTTCGAATCTCACCCCTCTGATTTTGCATTTGAAGAAATGTGAATTGAAGGAAGAAGATGATAGAGGCAAAGGAGATTACTTTCAGATTCAGATTCAGATTGGGTAA
Protein sequence

>Msa1403330

MVAIHPTPKLWDFYEFFSFSNLTPLILHLKKCELKEEDDRGKGDYFQIQIQIG*