AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0819020


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0819020 MtrunA17_Chr5g0437911 73.684 76 7 1 10 85 1 63 1.22e-32 115
Msa0819020 MtrunA17_Chr5g0437901 71.053 76 8 1 10 85 1 62 1.44e-30 109
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0819020 AT2G40410.1 63.158 76 20 2 10 85 1 68 1.10e-23 90.1
Msa0819020 AT2G40410.2 62.821 78 17 3 10 85 1 68 1.68e-23 91.3

Find 26 sgRNAs with CRISPR-Local

Find 116 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TAGGGATTGTTGACTTTCTA+TGG 0.278264 5_3:+55122358 Msa0819020:intron
ACATGTTGTGTCTTCTAAAA+AGG 0.296671 5_3:+55121842 Msa0819020:CDS
TCAATTATTCGTTCAACAAT+TGG 0.299674 5_3:+55121498 Msa0819020:CDS
ACATGTCTGCTTAGTCCTTC+AGG 0.390784 5_3:-55121825 None:intergenic
GGTTCAACAGCTACTTCAAC+TGG 0.393087 5_3:-55122400 None:intergenic
TGTTGTTGGTTGGAAGCAAT+TGG 0.485423 5_3:-55121544 None:intergenic
GGATGATCATCAGATGTTGT+TGG 0.524132 5_3:-55121558 None:intergenic
GATCATCAGATGTTGTTGGT+TGG 0.536125 5_3:-55121554 None:intergenic
TAACTTTCAAAACACCTCCC+AGG 0.556186 5_3:+55121665 Msa0819020:CDS
GTTGGAAGCAATTGGCATAG+AGG 0.559396 5_3:-55121536 None:intergenic
ATTTCATATTGTACTCCTTG+AGG 0.564927 5_3:-55122439 None:intergenic
ACTCCTTGAGGTAAAGATGT+AGG 0.571865 5_3:-55122427 None:intergenic
ACGAATAATTGAAGAAACCA+TGG 0.578705 5_3:-55121487 None:intergenic
GAAACACCAACGGTGGATTG+TGG 0.598681 5_3:-55121579 None:intergenic
GAAACACCAACGGTGGATTG+TGG 0.598681 5_3:-55121621 None:intergenic
TGAGGTAAAGATGTAGGAGG+AGG 0.606495 5_3:-55122421 None:intergenic
CCTCCTACATCTTTACCTCA+AGG 0.623673 5_3:+55122424 Msa0819020:three_prime_UTR
CCTTGAGGTAAAGATGTAGG+AGG 0.635074 5_3:-55122424 None:intergenic
GATCATCCACAATCCACCGT+TGG 0.640077 5_3:+55121573 Msa0819020:CDS
GATCATCCACAATCCACCGT+TGG 0.640077 5_3:+55121615 Msa0819020:CDS
AGCAAGAGCTGAAACACCAA+CGG 0.667239 5_3:-55121631 None:intergenic
AGCAAGAGCTGAAACACCAA+CGG 0.669678 5_3:-55121589 None:intergenic
TCAACTGGAGTATGTGACAG+TGG 0.679694 5_3:-55122385 None:intergenic
AACAAAATAGGTTACCTGGG+AGG 0.716149 5_3:-55121679 None:intergenic
AAGAGCTGAAACACCAACGG+TGG 0.734495 5_3:-55121586 None:intergenic
AAGAGCTGAAACACCAACGG+TGG 0.734495 5_3:-55121628 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! TTATATTGTTTTGAATTTGA+AGG + chr5_3:55122097-55122116 Msa0819020:intron 15.0%
!!! TTATATTGTTTTGAATTTGA+AGG + chr5_3:55122097-55122116 Msa0819020:intron 15.0%
!!! ATGTTTTTGAGTAACAAAAT+AGG - chr5_3:55121694-55121713 None:intergenic 20.0%
!! AATTAAGTAGAATTGAAGTT+TGG - chr5_3:55122251-55122270 None:intergenic 20.0%
!! AACTTCAATTCTACTTAATT+TGG + chr5_3:55122251-55122270 Msa0819020:intron 20.0%
!!! TGTTTTGTTGTTTGATTTAT+AGG + chr5_3:55122339-55122358 Msa0819020:intron 20.0%
!!! GTTTTGTTGTTTGATTTATA+GGG + chr5_3:55122340-55122359 Msa0819020:intron 20.0%
!!! ATGTTTTTGAGTAACAAAAT+AGG - chr5_3:55121694-55121713 None:intergenic 20.0%
!! AATTAAGTAGAATTGAAGTT+TGG - chr5_3:55122251-55122270 None:intergenic 20.0%
!! AACTTCAATTCTACTTAATT+TGG + chr5_3:55122251-55122270 Msa0819020:intron 20.0%
!!! TGTTTTGTTGTTTGATTTAT+AGG + chr5_3:55122339-55122358 Msa0819020:intron 20.0%
!!! GTTTTGTTGTTTGATTTATA+GGG + chr5_3:55122340-55122359 Msa0819020:intron 20.0%
! TCAATTATTCGTTCAACAAT+TGG + chr5_3:55121498-55121517 Msa0819020:CDS 25.0%
!! TGGTAAAAAGAGTAGAATTT+TGG - chr5_3:55121746-55121765 None:intergenic 25.0%
! TATATGCACATGTTACAAAA+TGG - chr5_3:55121775-55121794 None:intergenic 25.0%
! GTAAAAGAAAATTACACTGA+CGG + chr5_3:55122031-55122050 Msa0819020:intron 25.0%
!! GCATTAAAGGGTATAATAAT+TGG - chr5_3:55122073-55122092 None:intergenic 25.0%
! CAATATAAGCAAGCATTAAA+GGG - chr5_3:55122085-55122104 None:intergenic 25.0%
! ACAATATAAGCAAGCATTAA+AGG - chr5_3:55122086-55122105 None:intergenic 25.0%
! AGGTATAGAAAGTTAATAGA+TGG + chr5_3:55122117-55122136 Msa0819020:intron 25.0%
! ATAGAAAGTTAATAGATGGT+TGG + chr5_3:55122121-55122140 Msa0819020:intron 25.0%
! TCAATTATTCGTTCAACAAT+TGG + chr5_3:55121498-55121517 Msa0819020:CDS 25.0%
!! TGGTAAAAAGAGTAGAATTT+TGG - chr5_3:55121746-55121765 None:intergenic 25.0%
! TATATGCACATGTTACAAAA+TGG - chr5_3:55121775-55121794 None:intergenic 25.0%
! GTAAAAGAAAATTACACTGA+CGG + chr5_3:55122031-55122050 Msa0819020:intron 25.0%
!! GCATTAAAGGGTATAATAAT+TGG - chr5_3:55122073-55122092 None:intergenic 25.0%
! CAATATAAGCAAGCATTAAA+GGG - chr5_3:55122085-55122104 None:intergenic 25.0%
! ACAATATAAGCAAGCATTAA+AGG - chr5_3:55122086-55122105 None:intergenic 25.0%
! AGGTATAGAAAGTTAATAGA+TGG + chr5_3:55122117-55122136 Msa0819020:intron 25.0%
! ATAGAAAGTTAATAGATGGT+TGG + chr5_3:55122121-55122140 Msa0819020:intron 25.0%
AGTAACAAAATAGGTTACCT+GGG - chr5_3:55121685-55121704 None:intergenic 30.0%
!! GTAGAATTTTGGTAAGTTTG+AGG - chr5_3:55121735-55121754 None:intergenic 30.0%
!!! AATCTTTTTTAGGTTCCTGA+AGG + chr5_3:55121810-55121829 Msa0819020:intron 30.0%
! ACATGTTGTGTCTTCTAAAA+AGG + chr5_3:55121842-55121861 Msa0819020:CDS 30.0%
ACAGTGCATAGAAATTAATC+TGG - chr5_3:55121949-55121968 None:intergenic 30.0%
!! CTTGTTATTCTGACATTGAA+AGG + chr5_3:55122189-55122208 Msa0819020:intron 30.0%
!!! CCTCAACATCTTCTTTTTTA+TGG - chr5_3:55122215-55122234 None:intergenic 30.0%
CCATAAAAAAGAAGATGTTG+AGG + chr5_3:55122212-55122231 Msa0819020:intron 30.0%
AGTAACAAAATAGGTTACCT+GGG - chr5_3:55121685-55121704 None:intergenic 30.0%
!! GTAGAATTTTGGTAAGTTTG+AGG - chr5_3:55121735-55121754 None:intergenic 30.0%
!!! AATCTTTTTTAGGTTCCTGA+AGG + chr5_3:55121810-55121829 Msa0819020:intron 30.0%
! ACATGTTGTGTCTTCTAAAA+AGG + chr5_3:55121842-55121861 Msa0819020:CDS 30.0%
ACAGTGCATAGAAATTAATC+TGG - chr5_3:55121949-55121968 None:intergenic 30.0%
!! CTTGTTATTCTGACATTGAA+AGG + chr5_3:55122189-55122208 Msa0819020:intron 30.0%
!!! CCTCAACATCTTCTTTTTTA+TGG - chr5_3:55122215-55122234 None:intergenic 30.0%
CCATAAAAAAGAAGATGTTG+AGG + chr5_3:55122212-55122231 Msa0819020:intron 30.0%
GAGTAACAAAATAGGTTACC+TGG - chr5_3:55121686-55121705 None:intergenic 35.0%
TGCACATGTTACAAAATGGT+GGG - chr5_3:55121771-55121790 None:intergenic 35.0%
ATGCACATGTTACAAAATGG+TGG - chr5_3:55121772-55121791 None:intergenic 35.0%
GTTAATAGATGGTTGGAAAG+AGG + chr5_3:55122128-55122147 Msa0819020:intron 35.0%
!! TAGGGATTGTTGACTTTCTA+TGG + chr5_3:55122358-55122377 Msa0819020:intron 35.0%
GAGTAACAAAATAGGTTACC+TGG - chr5_3:55121686-55121705 None:intergenic 35.0%
TGCACATGTTACAAAATGGT+GGG - chr5_3:55121771-55121790 None:intergenic 35.0%
ATGCACATGTTACAAAATGG+TGG - chr5_3:55121772-55121791 None:intergenic 35.0%
GTTAATAGATGGTTGGAAAG+AGG + chr5_3:55122128-55122147 Msa0819020:intron 35.0%
!! TAGGGATTGTTGACTTTCTA+TGG + chr5_3:55122358-55122377 Msa0819020:intron 35.0%
! TGTTGTTGGTTGGAAGCAAT+TGG - chr5_3:55121547-55121566 None:intergenic 40.0%
GATCATCAGATGTTGTTGGT+TGG - chr5_3:55121557-55121576 None:intergenic 40.0%
GGATGATCATCAGATGTTGT+TGG - chr5_3:55121561-55121580 None:intergenic 40.0%
TAACTTTCAAAACACCTCCC+AGG + chr5_3:55121665-55121684 Msa0819020:CDS 40.0%
AACAAAATAGGTTACCTGGG+AGG - chr5_3:55121682-55121701 None:intergenic 40.0%
! ATGTTACAAAATGGTGGGGT+TGG - chr5_3:55121766-55121785 None:intergenic 40.0%
GCACATGTTACAAAATGGTG+GGG - chr5_3:55121770-55121789 None:intergenic 40.0%
CTAAAAAGGCTCAAGCTATG+TGG + chr5_3:55121856-55121875 Msa0819020:CDS 40.0%
ACTCCTTGAGGTAAAGATGT+AGG - chr5_3:55122430-55122449 None:intergenic 40.0%
! TGTTGTTGGTTGGAAGCAAT+TGG - chr5_3:55121547-55121566 None:intergenic 40.0%
GATCATCAGATGTTGTTGGT+TGG - chr5_3:55121557-55121576 None:intergenic 40.0%
GGATGATCATCAGATGTTGT+TGG - chr5_3:55121561-55121580 None:intergenic 40.0%
TAACTTTCAAAACACCTCCC+AGG + chr5_3:55121665-55121684 Msa0819020:CDS 40.0%
AACAAAATAGGTTACCTGGG+AGG - chr5_3:55121682-55121701 None:intergenic 40.0%
! ATGTTACAAAATGGTGGGGT+TGG - chr5_3:55121766-55121785 None:intergenic 40.0%
GCACATGTTACAAAATGGTG+GGG - chr5_3:55121770-55121789 None:intergenic 40.0%
CTAAAAAGGCTCAAGCTATG+TGG + chr5_3:55121856-55121875 Msa0819020:CDS 40.0%
ACTCCTTGAGGTAAAGATGT+AGG - chr5_3:55122430-55122449 None:intergenic 40.0%
GTTGGAAGCAATTGGCATAG+AGG - chr5_3:55121539-55121558 None:intergenic 45.0%
AGCAAGAGCTGAAACACCAA+CGG - chr5_3:55121592-55121611 None:intergenic 45.0%
AGCAAGAGCTGAAACACCAA+CGG - chr5_3:55121592-55121611 None:intergenic 45.0%
ACATGTCTGCTTAGTCCTTC+AGG - chr5_3:55121828-55121847 None:intergenic 45.0%
! ACAAGACTAGCTGCTTCTTC+AGG - chr5_3:55122174-55122193 None:intergenic 45.0%
TCAACTGGAGTATGTGACAG+TGG - chr5_3:55122388-55122407 None:intergenic 45.0%
GGTTCAACAGCTACTTCAAC+TGG - chr5_3:55122403-55122422 None:intergenic 45.0%
TGAGGTAAAGATGTAGGAGG+AGG - chr5_3:55122424-55122443 None:intergenic 45.0%
CCTTGAGGTAAAGATGTAGG+AGG - chr5_3:55122427-55122446 None:intergenic 45.0%
CCTCCTACATCTTTACCTCA+AGG + chr5_3:55122424-55122443 Msa0819020:three_prime_UTR 45.0%
GTTGGAAGCAATTGGCATAG+AGG - chr5_3:55121539-55121558 None:intergenic 45.0%
AGCAAGAGCTGAAACACCAA+CGG - chr5_3:55121592-55121611 None:intergenic 45.0%
AGCAAGAGCTGAAACACCAA+CGG - chr5_3:55121592-55121611 None:intergenic 45.0%
ACATGTCTGCTTAGTCCTTC+AGG - chr5_3:55121828-55121847 None:intergenic 45.0%
! ACAAGACTAGCTGCTTCTTC+AGG - chr5_3:55122174-55122193 None:intergenic 45.0%
TCAACTGGAGTATGTGACAG+TGG - chr5_3:55122388-55122407 None:intergenic 45.0%
GGTTCAACAGCTACTTCAAC+TGG - chr5_3:55122403-55122422 None:intergenic 45.0%
TGAGGTAAAGATGTAGGAGG+AGG - chr5_3:55122424-55122443 None:intergenic 45.0%
CCTTGAGGTAAAGATGTAGG+AGG - chr5_3:55122427-55122446 None:intergenic 45.0%
CCTCCTACATCTTTACCTCA+AGG + chr5_3:55122424-55122443 Msa0819020:three_prime_UTR 45.0%
!!! TTTATTTTTTAATCTTTTTT+AGG + chr5_3:55121800-55121819 Msa0819020:intron 5.0%
!!! TTTATTTTTTAATCTTTTTT+AGG + chr5_3:55121800-55121819 Msa0819020:intron 5.0%
GATCATCCACAATCCACCGT+TGG + chr5_3:55121573-55121592 Msa0819020:CDS 50.0%
!! GAAACACCAACGGTGGATTG+TGG - chr5_3:55121582-55121601 None:intergenic 50.0%
AAGAGCTGAAACACCAACGG+TGG - chr5_3:55121589-55121608 None:intergenic 50.0%
GATCATCCACAATCCACCGT+TGG + chr5_3:55121573-55121592 Msa0819020:CDS 50.0%
!! GAAACACCAACGGTGGATTG+TGG - chr5_3:55121582-55121601 None:intergenic 50.0%
AAGAGCTGAAACACCAACGG+TGG - chr5_3:55121589-55121608 None:intergenic 50.0%
GATCATCCACAATCCACCGT+TGG + chr5_3:55121573-55121592 Msa0819020:CDS 50.0%
!! GAAACACCAACGGTGGATTG+TGG - chr5_3:55121582-55121601 None:intergenic 50.0%
AAGAGCTGAAACACCAACGG+TGG - chr5_3:55121589-55121608 None:intergenic 50.0%
GATCATCCACAATCCACCGT+TGG + chr5_3:55121573-55121592 Msa0819020:CDS 50.0%
!! GAAACACCAACGGTGGATTG+TGG - chr5_3:55121582-55121601 None:intergenic 50.0%
AAGAGCTGAAACACCAACGG+TGG - chr5_3:55121589-55121608 None:intergenic 50.0%
AAGAGGCAAGACCACCACCT+AGG + chr5_3:55122145-55122164 Msa0819020:intron 55.0%
TCTTCAGGTGTCCTAGGTGG+TGG - chr5_3:55122159-55122178 None:intergenic 55.0%
GCTTCTTCAGGTGTCCTAGG+TGG - chr5_3:55122162-55122181 None:intergenic 55.0%
GCTGCTTCTTCAGGTGTCCT+AGG - chr5_3:55122165-55122184 None:intergenic 55.0%
AAGAGGCAAGACCACCACCT+AGG + chr5_3:55122145-55122164 Msa0819020:intron 55.0%
TCTTCAGGTGTCCTAGGTGG+TGG - chr5_3:55122159-55122178 None:intergenic 55.0%
GCTTCTTCAGGTGTCCTAGG+TGG - chr5_3:55122162-55122181 None:intergenic 55.0%
GCTGCTTCTTCAGGTGTCCT+AGG - chr5_3:55122165-55122184 None:intergenic 55.0%
Chromosome Type Strat End Strand Name
chr5_3 gene 55121489 55122458 55121489 ID=Msa0819020;Name=Msa0819020
chr5_3 mRNA 55121489 55122458 55121489 ID=Msa0819020-mRNA-1;Parent=Msa0819020;Name=Msa0819020-mRNA-1;_AED=0.46;_eAED=0.51;_QI=0|0|0.33|1|1|1|3|88|87
chr5_3 exon 55121489 55121686 55121489 ID=Msa0819020-mRNA-1:exon:16720;Parent=Msa0819020-mRNA-1
chr5_3 exon 55121822 55121877 55121822 ID=Msa0819020-mRNA-1:exon:16721;Parent=Msa0819020-mRNA-1
chr5_3 exon 55122361 55122458 55122361 ID=Msa0819020-mRNA-1:exon:16722;Parent=Msa0819020-mRNA-1
chr5_3 CDS 55121489 55121686 55121489 ID=Msa0819020-mRNA-1:cds;Parent=Msa0819020-mRNA-1
chr5_3 CDS 55121822 55121877 55121822 ID=Msa0819020-mRNA-1:cds;Parent=Msa0819020-mRNA-1
chr5_3 CDS 55122361 55122370 55122361 ID=Msa0819020-mRNA-1:cds;Parent=Msa0819020-mRNA-1
chr5_3 three_prime_UTR 55122371 55122458 55122371 ID=Msa0819020-mRNA-1:three_prime_utr;Parent=Msa0819020-mRNA-1
Gene Sequence

>Msa0819020

ATGGTTTCTTCAATTATTCGTTCAACAATTGGAAATGCTCTGAGATTCCTCTATGCCAATTGCTTCCAACCAACAACATCTGATGATCATCCACAATCCACCGTTGGTGTTTCAGCTCTTGCTGATGATCATCCACAATCCACCGTTGGTGTTTCAGCTCTTGCTCATGATCTCTTTAACTTTCAAAACACCTCCCAGGTTCCTGAAGGACTAAGCAGACATGTTGTGTCTTCTAAAAAGGCTCAAGCTATGTGGGATTGTTGA

Protein sequence

>Msa0819020

MVSSIIRSTIGNALRFLYANCFQPTTSDDHPQSTVGVSALADDHPQSTVGVSALAHDLFNFQNTSQVPEGLSRHVVSSKKAQAMWDC*