AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0396230

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0396230 MtrunA17_Chr3g0082821 86.885 61 7 1 1 60 1 61 3.06e-31 103
Msa0396230 MtrunA17_Chr3g0082851 64.151 53 18 1 6 57 5 57 1.78e-18 71.6
Msa0396230 MtrunA17_Chr3g0082801 52.174 69 29 2 1 65 4 72 1.14e-16 67.0
Msa0396230 MtrunA17_Chr3g0082831 50.877 57 26 2 1 57 1 55 3.08e-13 58.2
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 38 sgRNAs with CRISPR-Local

Find 118 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
ATTCATAATTCATCTATTTA+AGG 0.177671 3_2:+14122890 None:intergenic
TGTTGTAAATTCTCTTAAAT+TGG 0.217012 3_2:-14122755 Msa0396230:five_prime_UTR
ATTATAACCTTCTTCAAATA+AGG 0.229225 3_2:+14122718 None:intergenic
TTTCACCATCGTGATAATTC+TGG 0.271166 3_2:+14121993 None:intergenic
AAGAGTAATACTTACTTGTT+TGG 0.327595 3_2:+14122608 None:intergenic
GGAGGAGACGGACGAGGAGG+AGG 0.354746 3_2:+14122051 None:intergenic
AAGTTGACAACGAATAATAA+AGG 0.395846 3_2:-14121965 Msa0396230:three_prime_UTR
TACTTACTTGTTTGGTGATG+GGG 0.415555 3_2:+14122616 None:intergenic
TCAGTAGTACTCATAATATT+CGG 0.423798 3_2:+14121862 None:intergenic
AGAAGTGAATGAGGATTAGA+TGG 0.430273 3_2:+14122794 None:intergenic
AATATTCGGATACAACTCAT+AGG 0.432225 3_2:+14121876 None:intergenic
GGAGACGGACGAGGAGGAGG+AGG 0.438833 3_2:+14122054 None:intergenic
GTAAATTCTCTTAAATTGGC+AGG 0.446870 3_2:-14122751 Msa0396230:five_prime_UTR
AATACTTACTTGTTTGGTGA+TGG 0.447759 3_2:+14122614 None:intergenic
TCGTGATAATTCTGGTGCTC+TGG 0.463310 3_2:+14122001 None:intergenic
ATACATGCCTTATTTGAAGA+AGG 0.465132 3_2:-14122725 Msa0396230:exon
ATACTTACTTGTTTGGTGAT+GGG 0.468098 3_2:+14122615 None:intergenic
TAATCACGAACAGCAAAGTC+AGG 0.475555 3_2:+14122692 None:intergenic
GTTCGTGATTATCTTGTCAA+TGG 0.480879 3_2:-14122680 Msa0396230:CDS
GGAGGAGGAGGAGACGGACG+AGG 0.486616 3_2:+14122045 None:intergenic
CATCATGGACGAGGAGGAGG+AGG 0.496519 3_2:+14122033 None:intergenic
GATTATCTTGTCAATGGAAG+TGG 0.498618 3_2:-14122674 Msa0396230:CDS
AGTTGACAACGAATAATAAA+GGG 0.503141 3_2:-14121964 Msa0396230:three_prime_UTR
CTCTGGATTCATCAGCATCA+TGG 0.516113 3_2:+14122018 None:intergenic
CATCATCAACAATATAAAGT+AGG 0.517741 3_2:+14122103 None:intergenic
CAGCATCATGGACGAGGAGG+AGG 0.520582 3_2:+14122030 None:intergenic
ACGAGTGTGAGAAGTGAATG+AGG 0.527105 3_2:+14122785 None:intergenic
GAGGAGGAGGAGACTTATAG+TGG 0.528286 3_2:+14122067 None:intergenic
GGAGGAGGAGACGGACGAGG+AGG 0.539009 3_2:+14122048 None:intergenic
ATTCATCAGCATCATGGACG+AGG 0.579537 3_2:+14122024 None:intergenic
TGGAAGTGGCAACAACAGCA+AGG 0.598443 3_2:-14122660 Msa0396230:CDS
GACTTATAGTGGTGGCCGTG+TGG 0.602172 3_2:+14122078 None:intergenic
GGAAGTGGCAACAACAGCAA+GGG 0.653375 3_2:-14122659 Msa0396230:CDS
CATCAGCATCATGGACGAGG+AGG 0.669707 3_2:+14122027 None:intergenic
ATTGTTGATGATGTTCCACA+CGG 0.674884 3_2:-14122093 Msa0396230:CDS
GAGGAGGAGACTTATAGTGG+TGG 0.687321 3_2:+14122070 None:intergenic
CAACAGCAAGGGTACCACCG+TGG 0.716923 3_2:-14122648 Msa0396230:CDS
GAGCACCAGAATTATCACGA+TGG 0.765204 3_2:-14121998 Msa0396230:three_prime_UTR

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! TTTTTTTTAAATTAGATTAG+TGG + chr3_2:14121894-14121913 None:intergenic 10.0%
!!! TTTTTTTTAAATTAGATTAG+TGG + chr3_2:14121894-14121913 None:intergenic 10.0%
!! ATTCATAATTCATCTATTTA+AGG + chr3_2:14121865-14121884 None:intergenic 15.0%
!!! TGATTAATATTTGATTTAGT+CGG - chr3_2:14122250-14122269 Msa0396230:intron 15.0%
!! ATTCATAATTCATCTATTTA+AGG + chr3_2:14121865-14121884 None:intergenic 15.0%
!!! TGATTAATATTTGATTTAGT+CGG - chr3_2:14122250-14122269 Msa0396230:intron 15.0%
!! TGTTGTAAATTCTCTTAAAT+TGG - chr3_2:14121997-14122016 Msa0396230:three_prime_UTR 20.0%
!! ATTATAACCTTCTTCAAATA+AGG + chr3_2:14122037-14122056 None:intergenic 20.0%
!!! AATCAGATTTTACTTATTTC+TGG + chr3_2:14122235-14122254 None:intergenic 20.0%
!!! GTGGTTTTTTTTAGTAAAAA+TGG - chr3_2:14122521-14122540 Msa0396230:intron 20.0%
!! AAGCATACATAAATTTCAAA+TGG + chr3_2:14122573-14122592 None:intergenic 20.0%
!! TGTTGTAAATTCTCTTAAAT+TGG - chr3_2:14121997-14122016 Msa0396230:three_prime_UTR 20.0%
!! ATTATAACCTTCTTCAAATA+AGG + chr3_2:14122037-14122056 None:intergenic 20.0%
!!! AATCAGATTTTACTTATTTC+TGG + chr3_2:14122235-14122254 None:intergenic 20.0%
!!! GTGGTTTTTTTTAGTAAAAA+TGG - chr3_2:14122521-14122540 Msa0396230:intron 20.0%
!! AAGCATACATAAATTTCAAA+TGG + chr3_2:14122573-14122592 None:intergenic 20.0%
! AAGAGTAATACTTACTTGTT+TGG + chr3_2:14122147-14122166 None:intergenic 25.0%
!! CTTTTTGATCTAATAACTCT+CGG - chr3_2:14122164-14122183 Msa0396230:intron 25.0%
!! TTTTTGATCTAATAACTCTC+GGG - chr3_2:14122165-14122184 Msa0396230:intron 25.0%
!!! TGTCATTTTTCTACATATCT+AGG - chr3_2:14122397-14122416 Msa0396230:intron 25.0%
! CATCATCAACAATATAAAGT+AGG + chr3_2:14122652-14122671 None:intergenic 25.0%
! AAGTTGACAACGAATAATAA+AGG - chr3_2:14122787-14122806 Msa0396230:five_prime_UTR 25.0%
! AGTTGACAACGAATAATAAA+GGG - chr3_2:14122788-14122807 Msa0396230:five_prime_UTR 25.0%
! TCAGTAGTACTCATAATATT+CGG + chr3_2:14122893-14122912 None:intergenic 25.0%
! AAGAGTAATACTTACTTGTT+TGG + chr3_2:14122147-14122166 None:intergenic 25.0%
!! CTTTTTGATCTAATAACTCT+CGG - chr3_2:14122164-14122183 Msa0396230:intron 25.0%
!! TTTTTGATCTAATAACTCTC+GGG - chr3_2:14122165-14122184 Msa0396230:intron 25.0%
!!! TGTCATTTTTCTACATATCT+AGG - chr3_2:14122397-14122416 Msa0396230:intron 25.0%
! CATCATCAACAATATAAAGT+AGG + chr3_2:14122652-14122671 None:intergenic 25.0%
! AAGTTGACAACGAATAATAA+AGG - chr3_2:14122787-14122806 Msa0396230:five_prime_UTR 25.0%
! AGTTGACAACGAATAATAAA+GGG - chr3_2:14122788-14122807 Msa0396230:five_prime_UTR 25.0%
! TCAGTAGTACTCATAATATT+CGG + chr3_2:14122893-14122912 None:intergenic 25.0%
GTAAATTCTCTTAAATTGGC+AGG - chr3_2:14122001-14122020 Msa0396230:three_prime_UTR 30.0%
!! ATACATGCCTTATTTGAAGA+AGG - chr3_2:14122027-14122046 Msa0396230:exon 30.0%
! ATACTTACTTGTTTGGTGAT+GGG + chr3_2:14122140-14122159 None:intergenic 30.0%
! AATACTTACTTGTTTGGTGA+TGG + chr3_2:14122141-14122160 None:intergenic 30.0%
! GTTATTCAAGTTTCGATTTG+TGG - chr3_2:14122502-14122521 Msa0396230:intron 30.0%
AATATTCGGATACAACTCAT+AGG + chr3_2:14122879-14122898 None:intergenic 30.0%
GTAAATTCTCTTAAATTGGC+AGG - chr3_2:14122001-14122020 Msa0396230:three_prime_UTR 30.0%
!! ATACATGCCTTATTTGAAGA+AGG - chr3_2:14122027-14122046 Msa0396230:exon 30.0%
! ATACTTACTTGTTTGGTGAT+GGG + chr3_2:14122140-14122159 None:intergenic 30.0%
! AATACTTACTTGTTTGGTGA+TGG + chr3_2:14122141-14122160 None:intergenic 30.0%
! GTTATTCAAGTTTCGATTTG+TGG - chr3_2:14122502-14122521 Msa0396230:intron 30.0%
AATATTCGGATACAACTCAT+AGG + chr3_2:14122879-14122898 None:intergenic 30.0%
AGAAGTGAATGAGGATTAGA+TGG + chr3_2:14121961-14121980 None:intergenic 35.0%
GTTCGTGATTATCTTGTCAA+TGG - chr3_2:14122072-14122091 Msa0396230:CDS 35.0%
GATTATCTTGTCAATGGAAG+TGG - chr3_2:14122078-14122097 Msa0396230:CDS 35.0%
!! TACTTACTTGTTTGGTGATG+GGG + chr3_2:14122139-14122158 None:intergenic 35.0%
! TCTAATAACTCTCGGGTTTT+TGG - chr3_2:14122172-14122191 Msa0396230:intron 35.0%
! CTAATAACTCTCGGGTTTTT+GGG - chr3_2:14122173-14122192 Msa0396230:intron 35.0%
!! ATTGTTGATGATGTTCCACA+CGG - chr3_2:14122659-14122678 Msa0396230:CDS 35.0%
TTTCACCATCGTGATAATTC+TGG + chr3_2:14122762-14122781 None:intergenic 35.0%
AGAAGTGAATGAGGATTAGA+TGG + chr3_2:14121961-14121980 None:intergenic 35.0%
GTTCGTGATTATCTTGTCAA+TGG - chr3_2:14122072-14122091 Msa0396230:CDS 35.0%
GATTATCTTGTCAATGGAAG+TGG - chr3_2:14122078-14122097 Msa0396230:CDS 35.0%
!! TACTTACTTGTTTGGTGATG+GGG + chr3_2:14122139-14122158 None:intergenic 35.0%
! TCTAATAACTCTCGGGTTTT+TGG - chr3_2:14122172-14122191 Msa0396230:intron 35.0%
! CTAATAACTCTCGGGTTTTT+GGG - chr3_2:14122173-14122192 Msa0396230:intron 35.0%
!! ATTGTTGATGATGTTCCACA+CGG - chr3_2:14122659-14122678 Msa0396230:CDS 35.0%
TTTCACCATCGTGATAATTC+TGG + chr3_2:14122762-14122781 None:intergenic 35.0%
TAATCACGAACAGCAAAGTC+AGG + chr3_2:14122063-14122082 None:intergenic 40.0%
AGCTAGCAAGAATCAAGAAC+TGG - chr3_2:14122480-14122499 Msa0396230:intron 40.0%
TTGAGATTCCCAAACAGACA+TGG + chr3_2:14122620-14122639 None:intergenic 40.0%
CTGTTTGGGAATCTCAAAGA+CGG - chr3_2:14122623-14122642 Msa0396230:CDS 40.0%
TAATCACGAACAGCAAAGTC+AGG + chr3_2:14122063-14122082 None:intergenic 40.0%
AGCTAGCAAGAATCAAGAAC+TGG - chr3_2:14122480-14122499 Msa0396230:intron 40.0%
TTGAGATTCCCAAACAGACA+TGG + chr3_2:14122620-14122639 None:intergenic 40.0%
CTGTTTGGGAATCTCAAAGA+CGG - chr3_2:14122623-14122642 Msa0396230:CDS 40.0%
ACGAGTGTGAGAAGTGAATG+AGG + chr3_2:14121970-14121989 None:intergenic 45.0%
! TGATGGGGCTCAATTTTCCA+CGG + chr3_2:14122124-14122143 None:intergenic 45.0%
AAACAGACATGGCAGCAACA+TGG + chr3_2:14122609-14122628 None:intergenic 45.0%
ATGTTGCTGCCATGTCTGTT+TGG - chr3_2:14122608-14122627 Msa0396230:intron 45.0%
TGTTGCTGCCATGTCTGTTT+GGG - chr3_2:14122609-14122628 Msa0396230:intron 45.0%
ATTCATCAGCATCATGGACG+AGG + chr3_2:14122731-14122750 None:intergenic 45.0%
CTCTGGATTCATCAGCATCA+TGG + chr3_2:14122737-14122756 None:intergenic 45.0%
TCGTGATAATTCTGGTGCTC+TGG + chr3_2:14122754-14122773 None:intergenic 45.0%
GAGCACCAGAATTATCACGA+TGG - chr3_2:14122754-14122773 Msa0396230:five_prime_UTR 45.0%
ACGAGTGTGAGAAGTGAATG+AGG + chr3_2:14121970-14121989 None:intergenic 45.0%
! TGATGGGGCTCAATTTTCCA+CGG + chr3_2:14122124-14122143 None:intergenic 45.0%
AAACAGACATGGCAGCAACA+TGG + chr3_2:14122609-14122628 None:intergenic 45.0%
ATGTTGCTGCCATGTCTGTT+TGG - chr3_2:14122608-14122627 Msa0396230:intron 45.0%
TGTTGCTGCCATGTCTGTTT+GGG - chr3_2:14122609-14122628 Msa0396230:intron 45.0%
ATTCATCAGCATCATGGACG+AGG + chr3_2:14122731-14122750 None:intergenic 45.0%
CTCTGGATTCATCAGCATCA+TGG + chr3_2:14122737-14122756 None:intergenic 45.0%
TCGTGATAATTCTGGTGCTC+TGG + chr3_2:14122754-14122773 None:intergenic 45.0%
GAGCACCAGAATTATCACGA+TGG - chr3_2:14122754-14122773 Msa0396230:five_prime_UTR 45.0%
TGGAAGTGGCAACAACAGCA+AGG - chr3_2:14122092-14122111 Msa0396230:CDS 50.0%
GGAAGTGGCAACAACAGCAA+GGG - chr3_2:14122093-14122112 Msa0396230:CDS 50.0%
!! ACTCTCGGGTTTTTGGGAGA+AGG - chr3_2:14122179-14122198 Msa0396230:intron 50.0%
GAGGAGGAGACTTATAGTGG+TGG + chr3_2:14122685-14122704 None:intergenic 50.0%
GAGGAGGAGGAGACTTATAG+TGG + chr3_2:14122688-14122707 None:intergenic 50.0%
TGGAAGTGGCAACAACAGCA+AGG - chr3_2:14122092-14122111 Msa0396230:CDS 50.0%
GGAAGTGGCAACAACAGCAA+GGG - chr3_2:14122093-14122112 Msa0396230:CDS 50.0%
!! ACTCTCGGGTTTTTGGGAGA+AGG - chr3_2:14122179-14122198 Msa0396230:intron 50.0%
GAGGAGGAGACTTATAGTGG+TGG + chr3_2:14122685-14122704 None:intergenic 50.0%
GAGGAGGAGGAGACTTATAG+TGG + chr3_2:14122688-14122707 None:intergenic 50.0%
! TGGGGCTCAATTTTCCACGG+TGG + chr3_2:14122121-14122140 None:intergenic 55.0%
GACTTATAGTGGTGGCCGTG+TGG + chr3_2:14122677-14122696 None:intergenic 55.0%
CATCAGCATCATGGACGAGG+AGG + chr3_2:14122728-14122747 None:intergenic 55.0%
! TGGGGCTCAATTTTCCACGG+TGG + chr3_2:14122121-14122140 None:intergenic 55.0%
GACTTATAGTGGTGGCCGTG+TGG + chr3_2:14122677-14122696 None:intergenic 55.0%
CATCAGCATCATGGACGAGG+AGG + chr3_2:14122728-14122747 None:intergenic 55.0%
!! CAACAGCAAGGGTACCACCG+TGG - chr3_2:14122104-14122123 Msa0396230:CDS 60.0%
CATCATGGACGAGGAGGAGG+AGG + chr3_2:14122722-14122741 None:intergenic 60.0%
CAGCATCATGGACGAGGAGG+AGG + chr3_2:14122725-14122744 None:intergenic 60.0%
!! CAACAGCAAGGGTACCACCG+TGG - chr3_2:14122104-14122123 Msa0396230:CDS 60.0%
CATCATGGACGAGGAGGAGG+AGG + chr3_2:14122722-14122741 None:intergenic 60.0%
CAGCATCATGGACGAGGAGG+AGG + chr3_2:14122725-14122744 None:intergenic 60.0%
GGACGAGGAGGAGGAGGAGA+CGG + chr3_2:14122695-14122714 None:intergenic 65.0%
GGACGAGGAGGAGGAGGAGA+CGG + chr3_2:14122695-14122714 None:intergenic 65.0%
GGAGACGGACGAGGAGGAGG+AGG + chr3_2:14122701-14122720 None:intergenic 70.0%
GGAGGAGACGGACGAGGAGG+AGG + chr3_2:14122704-14122723 None:intergenic 70.0%
GGAGGAGGAGACGGACGAGG+AGG + chr3_2:14122707-14122726 None:intergenic 70.0%
GGAGGAGGAGGAGACGGACG+AGG + chr3_2:14122710-14122729 None:intergenic 70.0%
GGAGACGGACGAGGAGGAGG+AGG + chr3_2:14122701-14122720 None:intergenic 70.0%
GGAGGAGACGGACGAGGAGG+AGG + chr3_2:14122704-14122723 None:intergenic 70.0%
GGAGGAGGAGACGGACGAGG+AGG + chr3_2:14122707-14122726 None:intergenic 70.0%
GGAGGAGGAGGAGACGGACG+AGG + chr3_2:14122710-14122729 None:intergenic 70.0%
Chromosome Type Strat End Strand Name
chr3_2 gene 14121850 14122924 14121850 ID=Msa0396230;Name=Msa0396230
chr3_2 mRNA 14121850 14122924 14121850 ID=Msa0396230-mRNA-1;Parent=Msa0396230;Name=Msa0396230-mRNA-1;_AED=0.38;_eAED=0.38;_QI=181|1|1|1|1|1|2|185|72
chr3_2 exon 14121850 14122132 14121850 ID=Msa0396230-mRNA-1:exon:3274;Parent=Msa0396230-mRNA-1
chr3_2 exon 14122623 14122924 14122623 ID=Msa0396230-mRNA-1:exon:3273;Parent=Msa0396230-mRNA-1
chr3_2 five_prime_UTR 14122744 14122924 14122744 ID=Msa0396230-mRNA-1:five_prime_utr;Parent=Msa0396230-mRNA-1
chr3_2 CDS 14122623 14122743 14122623 ID=Msa0396230-mRNA-1:cds;Parent=Msa0396230-mRNA-1
chr3_2 CDS 14122035 14122132 14122035 ID=Msa0396230-mRNA-1:cds;Parent=Msa0396230-mRNA-1
chr3_2 three_prime_UTR 14121850 14122034 14121850 ID=Msa0396230-mRNA-1:three_prime_utr;Parent=Msa0396230-mRNA-1
Gene Sequence

>Msa0396230

ATGCCTTATTTGAAGAAGGTTATAATTAACCTGACTTTGCTGTTCGTGATTATCTTGTCAATGGAAGTGGCAACAACAGCAAGGGTACCACCGTGGAAAATTGAGCCCCATCACCAAACAAACGGACGCCTACTTTATATTGTTGATGATGTTCCACACGGCCACCACTATAAGTCTCCTCCTCCTCCTCGTCCGTCTCCTCCTCCTCCTCGTCCATGA
Protein sequence

>Msa0396230

MPYLKKVIINLTLLFVIILSMEVATTARVPPWKIEPHHQTNGRLLYIVDDVPHGHHYKSPPPPRPSPPPPRP*