AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0934550

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0934550 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
Msa0934550 AT1G15290.2 55.769 52 23 0 1 52 153 204 1.38e-14 65.9
Msa0934550 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 6_3:-4390088 Msa0934550:intron
TAACAGTTTATCTAGCGATT+AGG 0.277835 6_3:+4390536 None:intergenic
CACAAATTGTGATTCAATAT+CGG 0.293147 6_3:-4390381 Msa0934550:five_prime_UTR
AACAGTTTATCTAGCGATTA+GGG 0.310080 6_3:+4390537 None:intergenic
ACAAAACACTAGTTATATTA+AGG 0.313616 6_3:+4389550 None:intergenic
CAAGACTAAGAGTAGAAGAT+AGG 0.335113 6_3:-4389611 Msa0934550:three_prime_UTR
TTTGAAGAAATGTGAATTGA+AGG 0.370761 6_3:-4390136 Msa0934550:CDS
TTCATCCGACGCCGAAGTTG+TGG 0.424970 6_3:-4390337 Msa0934550:CDS
TTGTGAGGAATTTGTTTACT+TGG 0.445810 6_3:-4390582 Msa0934550:five_prime_UTR
TCATCCGACGCCGAAGTTGT+GGG 0.454363 6_3:-4390336 Msa0934550:CDS
AATTTATTATAAAATATAAG+AGG 0.455639 6_3:+4389411 None:intergenic
TTGAAGGAAGAAGATGATAG+AGG 0.499044 6_3:-4390120 Msa0934550:CDS
CAAAAGACGGGGCAATTACA+AGG 0.508315 6_3:-4389637 Msa0934550:three_prime_UTR
GACAAGGCTTGAGAAACAAT+TGG 0.508496 6_3:-4389668 Msa0934550:three_prime_UTR
AAGACTAAGAGTAGAAGATA+GGG 0.508621 6_3:-4389610 Msa0934550:three_prime_UTR
GAAGAAGATGATAGAGGCAA+AGG 0.512391 6_3:-4390114 Msa0934550:CDS
TTGGCAAAAGAGCAAAAGAC+GGG 0.528765 6_3:-4389649 Msa0934550:three_prime_UTR
TGATTCAATATCGGAGAATG+TGG 0.542320 6_3:-4390372 Msa0934550:five_prime_UTR
GATTGGGTAAAAGTTGAAGA+AGG 0.561791 6_3:-4389695 Msa0934550:exon
AGAGACTCACGCAAAATCAG+AGG 0.576920 6_3:+4390278 None:intergenic
ACAAGTCACCATCAATATGA+AGG 0.583661 6_3:+4389483 None:intergenic
ATCGGAGAATGTGGGAATGG+TGG 0.584217 6_3:-4390363 Msa0934550:exon
AAATCCCACAACTTCGGCGT+CGG 0.597204 6_3:+4390332 None:intergenic
AATATCGGAGAATGTGGGAA+TGG 0.601867 6_3:-4390366 Msa0934550:exon
GAGACTCACGCAAAATCAGA+GGG 0.603386 6_3:+4390279 None:intergenic
ATTGGCAAAAGAGCAAAAGA+CGG 0.635114 6_3:-4389650 Msa0934550:three_prime_UTR
GATTCAATATCGGAGAATGT+GGG 0.665724 6_3:-4390371 Msa0934550:five_prime_UTR
AGTTGAAGAAGGCAACGACA+AGG 0.678134 6_3:-4389684 Msa0934550:three_prime_UTR
TGTTTGATGAAATGATTGTG+AGG 0.699167 6_3:-4390597 Msa0934550:five_prime_UTR
TGGCAAAAGAGCAAAAGACG+GGG 0.714282 6_3:-4389648 Msa0934550:three_prime_UTR
AGACTCACGCAAAATCAGAG+GGG 0.781912 6_3:+4390280 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! AATTTTTATGCGTTTTTGTT+AGG - chr6_3:4389784-4389803 Msa0934550:intron 20.0%
!!! ATTTTTATGCGTTTTTGTTA+GGG - chr6_3:4389785-4389804 Msa0934550:intron 20.0%
!! ATAAAGTTTATGCAAGTTAA+AGG + chr6_3:4390088-4390107 None:intergenic 20.0%
!! TAAAAAGAAAAACAGAATTC+TGG + chr6_3:4390148-4390167 None:intergenic 20.0%
!!! GAATTCTGTTTTTCTTTTTA+AGG - chr6_3:4390148-4390167 Msa0934550:intron 20.0%
!! ACAAAACACTAGTTATATTA+AGG + chr6_3:4390446-4390465 None:intergenic 20.0%
!!! AATTTTTATGCGTTTTTGTT+AGG - chr6_3:4389784-4389803 Msa0934550:intron 20.0%
!!! ATTTTTATGCGTTTTTGTTA+GGG - chr6_3:4389785-4389804 Msa0934550:intron 20.0%
!! ATAAAGTTTATGCAAGTTAA+AGG + chr6_3:4390088-4390107 None:intergenic 20.0%
!! TAAAAAGAAAAACAGAATTC+TGG + chr6_3:4390148-4390167 None:intergenic 20.0%
!!! GAATTCTGTTTTTCTTTTTA+AGG - chr6_3:4390148-4390167 Msa0934550:intron 20.0%
!! ACAAAACACTAGTTATATTA+AGG + chr6_3:4390446-4390465 None:intergenic 20.0%
! CACAAATTGTGATTCAATAT+CGG - chr6_3:4389612-4389631 Msa0934550:three_prime_UTR 25.0%
! TTTGAAGAAATGTGAATTGA+AGG - chr6_3:4389857-4389876 Msa0934550:intron 25.0%
! TTATTGCATTTCATTGAGTT+AGG - chr6_3:4389935-4389954 Msa0934550:intron 25.0%
! TATTTGTAGCTATTCAAAGT+GGG + chr6_3:4390039-4390058 None:intergenic 25.0%
! ATATTTGTAGCTATTCAAAG+TGG + chr6_3:4390040-4390059 None:intergenic 25.0%
! TTTGTGTTTGATCAATCATA+TGG - chr6_3:4390268-4390287 Msa0934550:intron 25.0%
!!! AATCATATGGTTTTGTAGAT+TGG - chr6_3:4390281-4390300 Msa0934550:intron 25.0%
!!! ATCATATGGTTTTGTAGATT+GGG - chr6_3:4390282-4390301 Msa0934550:intron 25.0%
!! ATTTTACACCTTCATATTGA+TGG - chr6_3:4390502-4390521 Msa0934550:five_prime_UTR 25.0%
!! GTGTATTTTATGACTAATGT+CGG - chr6_3:4390551-4390570 Msa0934550:five_prime_UTR 25.0%
!! TGTATTTTATGACTAATGTC+GGG - chr6_3:4390552-4390571 Msa0934550:five_prime_UTR 25.0%
! CACAAATTGTGATTCAATAT+CGG - chr6_3:4389612-4389631 Msa0934550:three_prime_UTR 25.0%
! TTTGAAGAAATGTGAATTGA+AGG - chr6_3:4389857-4389876 Msa0934550:intron 25.0%
! TTATTGCATTTCATTGAGTT+AGG - chr6_3:4389935-4389954 Msa0934550:intron 25.0%
! TATTTGTAGCTATTCAAAGT+GGG + chr6_3:4390039-4390058 None:intergenic 25.0%
! ATATTTGTAGCTATTCAAAG+TGG + chr6_3:4390040-4390059 None:intergenic 25.0%
! TTTGTGTTTGATCAATCATA+TGG - chr6_3:4390268-4390287 Msa0934550:intron 25.0%
!!! AATCATATGGTTTTGTAGAT+TGG - chr6_3:4390281-4390300 Msa0934550:intron 25.0%
!!! ATCATATGGTTTTGTAGATT+GGG - chr6_3:4390282-4390301 Msa0934550:intron 25.0%
!! ATTTTACACCTTCATATTGA+TGG - chr6_3:4390502-4390521 Msa0934550:five_prime_UTR 25.0%
!! GTGTATTTTATGACTAATGT+CGG - chr6_3:4390551-4390570 Msa0934550:five_prime_UTR 25.0%
!! TGTATTTTATGACTAATGTC+GGG - chr6_3:4390552-4390571 Msa0934550:five_prime_UTR 25.0%
! TTGTGAGGAATTTGTTTACT+TGG - chr6_3:4389411-4389430 Msa0934550:three_prime_UTR 30.0%
AACAGTTTATCTAGCGATTA+GGG + chr6_3:4389459-4389478 None:intergenic 30.0%
TAACAGTTTATCTAGCGATT+AGG + chr6_3:4389460-4389479 None:intergenic 30.0%
! GCAATGAATCAACTTTTCAA+AGG + chr6_3:4389505-4389524 None:intergenic 30.0%
TCATAAAAATCCCACAACTT+CGG + chr6_3:4389670-4389689 None:intergenic 30.0%
AACATTTGACATGGTGATAA+GGG - chr6_3:4389811-4389830 Msa0934550:intron 30.0%
TTACTTTCAGATTCAGATTC+AGG - chr6_3:4389905-4389924 Msa0934550:intron 30.0%
GAGTAAAAGAAAGACTCTAA+AGG + chr6_3:4390227-4390246 None:intergenic 30.0%
AAGACTAAGAGTAGAAGATA+GGG - chr6_3:4390383-4390402 Msa0934550:five_prime_UTR 30.0%
! TTGTGAGGAATTTGTTTACT+TGG - chr6_3:4389411-4389430 Msa0934550:three_prime_UTR 30.0%
AACAGTTTATCTAGCGATTA+GGG + chr6_3:4389459-4389478 None:intergenic 30.0%
TAACAGTTTATCTAGCGATT+AGG + chr6_3:4389460-4389479 None:intergenic 30.0%
! GCAATGAATCAACTTTTCAA+AGG + chr6_3:4389505-4389524 None:intergenic 30.0%
TCATAAAAATCCCACAACTT+CGG + chr6_3:4389670-4389689 None:intergenic 30.0%
AACATTTGACATGGTGATAA+GGG - chr6_3:4389811-4389830 Msa0934550:intron 30.0%
TTACTTTCAGATTCAGATTC+AGG - chr6_3:4389905-4389924 Msa0934550:intron 30.0%
GAGTAAAAGAAAGACTCTAA+AGG + chr6_3:4390227-4390246 None:intergenic 30.0%
AAGACTAAGAGTAGAAGATA+GGG - chr6_3:4390383-4390402 Msa0934550:five_prime_UTR 30.0%
TGATTCAATATCGGAGAATG+TGG - chr6_3:4389621-4389640 Msa0934550:three_prime_UTR 35.0%
GATTCAATATCGGAGAATGT+GGG - chr6_3:4389622-4389641 Msa0934550:three_prime_UTR 35.0%
TTAGGGTTGAACATTTGACA+TGG - chr6_3:4389802-4389821 Msa0934550:intron 35.0%
GAACATTTGACATGGTGATA+AGG - chr6_3:4389810-4389829 Msa0934550:intron 35.0%
TTGAAGGAAGAAGATGATAG+AGG - chr6_3:4389873-4389892 Msa0934550:intron 35.0%
ATGCAAGTTAAAGGAACTCA+CGG + chr6_3:4390079-4390098 None:intergenic 35.0%
!! CTAAAGGCACTTCATTGTTT+AGG + chr6_3:4390211-4390230 None:intergenic 35.0%
! CTTTCTTTTACTCTTCTCAG+AGG - chr6_3:4390234-4390253 Msa0934550:intron 35.0%
GATTGGGTAAAAGTTGAAGA+AGG - chr6_3:4390298-4390317 Msa0934550:CDS 35.0%
ATTGGCAAAAGAGCAAAAGA+CGG - chr6_3:4390343-4390362 Msa0934550:CDS 35.0%
CAAGACTAAGAGTAGAAGAT+AGG - chr6_3:4390382-4390401 Msa0934550:five_prime_UTR 35.0%
ACAAGTCACCATCAATATGA+AGG + chr6_3:4390513-4390532 None:intergenic 35.0%
TGATTCAATATCGGAGAATG+TGG - chr6_3:4389621-4389640 Msa0934550:three_prime_UTR 35.0%
GATTCAATATCGGAGAATGT+GGG - chr6_3:4389622-4389641 Msa0934550:three_prime_UTR 35.0%
TTAGGGTTGAACATTTGACA+TGG - chr6_3:4389802-4389821 Msa0934550:intron 35.0%
GAACATTTGACATGGTGATA+AGG - chr6_3:4389810-4389829 Msa0934550:intron 35.0%
TTGAAGGAAGAAGATGATAG+AGG - chr6_3:4389873-4389892 Msa0934550:intron 35.0%
ATGCAAGTTAAAGGAACTCA+CGG + chr6_3:4390079-4390098 None:intergenic 35.0%
!! CTAAAGGCACTTCATTGTTT+AGG + chr6_3:4390211-4390230 None:intergenic 35.0%
! CTTTCTTTTACTCTTCTCAG+AGG - chr6_3:4390234-4390253 Msa0934550:intron 35.0%
GATTGGGTAAAAGTTGAAGA+AGG - chr6_3:4390298-4390317 Msa0934550:CDS 35.0%
ATTGGCAAAAGAGCAAAAGA+CGG - chr6_3:4390343-4390362 Msa0934550:CDS 35.0%
CAAGACTAAGAGTAGAAGAT+AGG - chr6_3:4390382-4390401 Msa0934550:five_prime_UTR 35.0%
ACAAGTCACCATCAATATGA+AGG + chr6_3:4390513-4390532 None:intergenic 35.0%
AATATCGGAGAATGTGGGAA+TGG - chr6_3:4389627-4389646 Msa0934550:three_prime_UTR 40.0%
GAAGAAGATGATAGAGGCAA+AGG - chr6_3:4389879-4389898 Msa0934550:intron 40.0%
AAGTTAAAGGAACTCACGGT+GGG + chr6_3:4390075-4390094 None:intergenic 40.0%
AATTCTGGTACTAGAGAGTC+AGG + chr6_3:4390133-4390152 None:intergenic 40.0%
GACAAGGCTTGAGAAACAAT+TGG - chr6_3:4390325-4390344 Msa0934550:CDS 40.0%
TTGGCAAAAGAGCAAAAGAC+GGG - chr6_3:4390344-4390363 Msa0934550:CDS 40.0%
AATATCGGAGAATGTGGGAA+TGG - chr6_3:4389627-4389646 Msa0934550:three_prime_UTR 40.0%
GAAGAAGATGATAGAGGCAA+AGG - chr6_3:4389879-4389898 Msa0934550:intron 40.0%
AAGTTAAAGGAACTCACGGT+GGG + chr6_3:4390075-4390094 None:intergenic 40.0%
AATTCTGGTACTAGAGAGTC+AGG + chr6_3:4390133-4390152 None:intergenic 40.0%
GACAAGGCTTGAGAAACAAT+TGG - chr6_3:4390325-4390344 Msa0934550:CDS 40.0%
TTGGCAAAAGAGCAAAAGAC+GGG - chr6_3:4390344-4390363 Msa0934550:CDS 40.0%
AGACTCACGCAAAATCAGAG+GGG + chr6_3:4389716-4389735 None:intergenic 45.0%
GAGACTCACGCAAAATCAGA+GGG + chr6_3:4389717-4389736 None:intergenic 45.0%
AGAGACTCACGCAAAATCAG+AGG + chr6_3:4389718-4389737 None:intergenic 45.0%
AATGTGTGATGCTGCTGTCT+TGG - chr6_3:4390007-4390026 Msa0934550:intron 45.0%
AGTTAAAGGAACTCACGGTG+GGG + chr6_3:4390074-4390093 None:intergenic 45.0%
CAAGTTAAAGGAACTCACGG+TGG + chr6_3:4390076-4390095 None:intergenic 45.0%
AGTTGAAGAAGGCAACGACA+AGG - chr6_3:4390309-4390328 Msa0934550:CDS 45.0%
TGGCAAAAGAGCAAAAGACG+GGG - chr6_3:4390345-4390364 Msa0934550:CDS 45.0%
CAAAAGACGGGGCAATTACA+AGG - chr6_3:4390356-4390375 Msa0934550:exon 45.0%
AGACTCACGCAAAATCAGAG+GGG + chr6_3:4389716-4389735 None:intergenic 45.0%
GAGACTCACGCAAAATCAGA+GGG + chr6_3:4389717-4389736 None:intergenic 45.0%
AGAGACTCACGCAAAATCAG+AGG + chr6_3:4389718-4389737 None:intergenic 45.0%
AATGTGTGATGCTGCTGTCT+TGG - chr6_3:4390007-4390026 Msa0934550:intron 45.0%
AGTTAAAGGAACTCACGGTG+GGG + chr6_3:4390074-4390093 None:intergenic 45.0%
CAAGTTAAAGGAACTCACGG+TGG + chr6_3:4390076-4390095 None:intergenic 45.0%
AGTTGAAGAAGGCAACGACA+AGG - chr6_3:4390309-4390328 Msa0934550:CDS 45.0%
TGGCAAAAGAGCAAAAGACG+GGG - chr6_3:4390345-4390364 Msa0934550:CDS 45.0%
CAAAAGACGGGGCAATTACA+AGG - chr6_3:4390356-4390375 Msa0934550:exon 45.0%
!! AATTTATTATAAAATATAAG+AGG + chr6_3:4390585-4390604 None:intergenic 5.0%
!! AATTTATTATAAAATATAAG+AGG + chr6_3:4390585-4390604 None:intergenic 5.0%
ATCGGAGAATGTGGGAATGG+TGG - chr6_3:4389630-4389649 Msa0934550:three_prime_UTR 50.0%
AAATCCCACAACTTCGGCGT+CGG + chr6_3:4389664-4389683 None:intergenic 50.0%
TGGTACTAGAGAGTCAGGCA+CGG + chr6_3:4390128-4390147 None:intergenic 50.0%
ATCGGAGAATGTGGGAATGG+TGG - chr6_3:4389630-4389649 Msa0934550:three_prime_UTR 50.0%
AAATCCCACAACTTCGGCGT+CGG + chr6_3:4389664-4389683 None:intergenic 50.0%
TGGTACTAGAGAGTCAGGCA+CGG + chr6_3:4390128-4390147 None:intergenic 50.0%
TTCATCCGACGCCGAAGTTG+TGG - chr6_3:4389656-4389675 Msa0934550:three_prime_UTR 55.0%
TCATCCGACGCCGAAGTTGT+GGG - chr6_3:4389657-4389676 Msa0934550:three_prime_UTR 55.0%
TTCATCCGACGCCGAAGTTG+TGG - chr6_3:4389656-4389675 Msa0934550:three_prime_UTR 55.0%
TCATCCGACGCCGAAGTTGT+GGG - chr6_3:4389657-4389676 Msa0934550:three_prime_UTR 55.0%
Chromosome Type Strat End Strand Name
chr6_3 gene 4389397 4390618 4389397 ID=Msa0934550;Name=Msa0934550
chr6_3 mRNA 4389397 4390618 4389397 ID=Msa0934550-mRNA-1;Parent=Msa0934550;Name=Msa0934550-mRNA-1;_AED=0.27;_eAED=0.27;_QI=249|1|1|1|0.5|0.66|3|311|53
chr6_3 exon 4389397 4389716 4389397 ID=Msa0934550-mRNA-1:exon:1396;Parent=Msa0934550-mRNA-1
chr6_3 exon 4390089 4390159 4390089 ID=Msa0934550-mRNA-1:exon:1395;Parent=Msa0934550-mRNA-1
chr6_3 exon 4390288 4390618 4390288 ID=Msa0934550-mRNA-1:exon:1394;Parent=Msa0934550-mRNA-1
chr6_3 five_prime_UTR 4390370 4390618 4390370 ID=Msa0934550-mRNA-1:five_prime_utr;Parent=Msa0934550-mRNA-1
chr6_3 CDS 4390288 4390369 4390288 ID=Msa0934550-mRNA-1:cds;Parent=Msa0934550-mRNA-1
chr6_3 CDS 4390089 4390159 4390089 ID=Msa0934550-mRNA-1:cds;Parent=Msa0934550-mRNA-1
chr6_3 CDS 4389708 4389716 4389708 ID=Msa0934550-mRNA-1:cds;Parent=Msa0934550-mRNA-1
chr6_3 three_prime_UTR 4389397 4389707 4389397 ID=Msa0934550-mRNA-1:three_prime_utr;Parent=Msa0934550-mRNA-1
Gene Sequence

>Msa0934550

ATGGTGGCTATTCATCCGACGCCGAAGTTGTGGGATTTTTATGAGTTCTTTTCGTTTTCGAATCTCACCCCTCTGATTTTGCATTTGAAGAAATGTGAATTGAAGGAAGAAGATGATAGAGGCAAAGGAGATTACTTTCAGATTCAGATTCAGATTGGGTAA
Protein sequence

>Msa0934550

MVAIHPTPKLWDFYEFFSFSNLTPLILHLKKCELKEEDDRGKGDYFQIQIQIG*