AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1300700

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1300700 MtrunA17_Chr4g0063791 91.011 178 3 5 1 167 1 176 3.16e-110 311
Msa1300700 MtrunA17_Chr2g0333051 38.889 144 64 4 28 162 5 133 5.58e-19 78.2
Msa1300700 MtrunA17_Chr4g0003391 35.915 142 69 4 28 167 5 126 5.15e-14 65.1
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1300700 AT3G15760.1 39.568 139 67 5 31 166 9 133 4.19e-16 71.2
Msa1300700 AT1G52565.1 39.552 134 59 4 28 159 8 121 1.02e-14 67.4

Find 36 sgRNAs with CRISPR-Local

Find 103 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CAAGATCTACTATATTATTT+TGG 0.176418 8_3:-62355101 None:intergenic
GATTGGCTTATTGTTGAATT+TGG 0.199091 8_3:+62354709 Msa1300700:exon
CTATTCTGTTAAGGTGAATT+AGG 0.229252 8_3:+62354901 Msa1300700:three_prime_UTR
TACAAAGCTGCTCTGTTTGC+AGG 0.285163 8_3:-62354654 None:intergenic
AACAGAGCAGCTTTGTATAA+TGG 0.334899 8_3:+62354660 Msa1300700:CDS
TCTCTTCATAACTCTAATAA+AGG 0.367080 8_3:+62355010 Msa1300700:three_prime_UTR
TTATTACCTCTATTCTGTTA+AGG 0.389886 8_3:+62354892 Msa1300700:three_prime_UTR
AAACATGGTGAAGAGAGAAT+TGG 0.390105 8_3:-62354287 None:intergenic
AACATGGTGAAGAGAGAATT+GGG 0.400815 8_3:-62354286 None:intergenic
CTACGTTCTTGTTTATCCTC+TGG 0.413516 8_3:+62354339 Msa1300700:CDS
GATAAACAAGAACGTAGAAT+AGG 0.433110 8_3:-62354333 None:intergenic
CCGAACTAAAATTTGAACAT+TGG 0.462032 8_3:-62355049 None:intergenic
TGAAGAAAAGAAGAAAGGAT+TGG 0.472608 8_3:-62354165 None:intergenic
TTTGATGAAAAGTGAGAAAG+TGG 0.480831 8_3:-62354140 None:intergenic
GAAATTGAATTCAAGATCAA+AGG 0.482344 8_3:+62354590 Msa1300700:CDS
TCTAGAAGTACAGTAAAAGT+AGG 0.512331 8_3:+62354825 Msa1300700:three_prime_UTR
AAGGTTCAAAAGAATTGTAA+TGG 0.522701 8_3:+62354609 Msa1300700:CDS
GTTGTGGATTCATGTAAAGA+TGG 0.540155 8_3:+62354504 Msa1300700:CDS
AATTCACCTTAACAGAATAG+AGG 0.541511 8_3:-62354898 None:intergenic
GCAACCGCCATGGCTGTCTC+CGG 0.543566 8_3:+62354228 Msa1300700:CDS
AGATCGTGTGAATCAACGAT+TGG 0.545757 8_3:+62354692 Msa1300700:CDS
CATATTAGAAGCAGCCAACA+AGG 0.553674 8_3:-62354109 None:intergenic
GTTCAAAAGAATTGTAATGG+TGG 0.561934 8_3:+62354612 Msa1300700:CDS
TGCTGTCTTTGCAACCGCCA+TGG 0.563392 8_3:+62354218 Msa1300700:CDS
AGCAAGGATGATGACTGTGC+CGG 0.571426 8_3:-62354247 None:intergenic
TAGGAAATAGAAGTTGATGA+AGG 0.571660 8_3:+62354844 Msa1300700:three_prime_UTR
ATTTCTGAAGACGGAGAGCA+AGG 0.583155 8_3:-62354263 None:intergenic
AGAATTGGGATTTCTGAAGA+CGG 0.611480 8_3:-62354272 None:intergenic
GACTGTGCCGGAGACAGCCA+TGG 0.611754 8_3:-62354235 None:intergenic
TGCAAAGACAGCACCTTGTG+AGG 0.629596 8_3:-62354208 None:intergenic
CTCTAATAAAGGAAATTATG+CGG 0.638575 8_3:+62355021 Msa1300700:three_prime_UTR
TCTTCAATGATTACCTCACA+AGG 0.650992 8_3:+62354195 Msa1300700:CDS
ATATTAGAAGCAGCCAACAA+GGG 0.667558 8_3:-62354108 None:intergenic
AATGGTGGAAACGAGAACAG+AGG 0.717333 8_3:+62354627 Msa1300700:CDS
AAGTACAGAAAACAACAACA+TGG 0.727013 8_3:+62354531 Msa1300700:CDS
TGTGCCGGAGACAGCCATGG+CGG 0.736789 8_3:-62354232 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! TTTTTTGTTAACATAATTCT+TGG + chr8_3:62354420-62354439 Msa1300700:intron 15.0%
!!! ATAATTTTGTTCATAGTTTT+AGG + chr8_3:62354936-62354955 Msa1300700:three_prime_UTR 15.0%
!!! TAATCTTGTTCATATTTTTT+AGG + chr8_3:62354960-62354979 Msa1300700:three_prime_UTR 15.0%
!!! AATCTTGTTCATATTTTTTA+GGG + chr8_3:62354961-62354980 Msa1300700:three_prime_UTR 15.0%
!!! TTTTTTGTTAACATAATTCT+TGG + chr8_3:62354420-62354439 Msa1300700:intron 15.0%
!!! ATAATTTTGTTCATAGTTTT+AGG + chr8_3:62354936-62354955 Msa1300700:three_prime_UTR 15.0%
!!! TAATCTTGTTCATATTTTTT+AGG + chr8_3:62354960-62354979 Msa1300700:three_prime_UTR 15.0%
!!! AATCTTGTTCATATTTTTTA+GGG + chr8_3:62354961-62354980 Msa1300700:three_prime_UTR 15.0%
!!! TGTTTTGAAGAAAAGAAGAA+AGG - chr8_3:62354173-62354192 None:intergenic 25.0%
!! AACAAGGTTTTTCTCTTTTT+AGG + chr8_3:62354392-62354411 Msa1300700:intron 25.0%
!! ACAAGGTTTTTCTCTTTTTA+GGG + chr8_3:62354393-62354412 Msa1300700:intron 25.0%
!!! TTCTTTGTTTTCTTTTCATC+TGG - chr8_3:62354453-62354472 None:intergenic 25.0%
! GAAATTGAATTCAAGATCAA+AGG + chr8_3:62354590-62354609 Msa1300700:CDS 25.0%
! AAGGTTCAAAAGAATTGTAA+TGG + chr8_3:62354609-62354628 Msa1300700:CDS 25.0%
! TTATTACCTCTATTCTGTTA+AGG + chr8_3:62354892-62354911 Msa1300700:three_prime_UTR 25.0%
!!! TTAGGGTAATTTTGTTATGT+TGG + chr8_3:62354978-62354997 Msa1300700:three_prime_UTR 25.0%
! TCTCTTCATAACTCTAATAA+AGG + chr8_3:62355010-62355029 Msa1300700:three_prime_UTR 25.0%
! CTCTAATAAAGGAAATTATG+CGG + chr8_3:62355021-62355040 Msa1300700:three_prime_UTR 25.0%
!!! CCAATGTTCAAATTTTAGTT+CGG + chr8_3:62355049-62355068 Msa1300700:three_prime_UTR 25.0%
!!! TGTTTTGAAGAAAAGAAGAA+AGG - chr8_3:62354173-62354192 None:intergenic 25.0%
!! AACAAGGTTTTTCTCTTTTT+AGG + chr8_3:62354392-62354411 Msa1300700:intron 25.0%
!! ACAAGGTTTTTCTCTTTTTA+GGG + chr8_3:62354393-62354412 Msa1300700:intron 25.0%
!!! TTCTTTGTTTTCTTTTCATC+TGG - chr8_3:62354453-62354472 None:intergenic 25.0%
! GAAATTGAATTCAAGATCAA+AGG + chr8_3:62354590-62354609 Msa1300700:CDS 25.0%
! AAGGTTCAAAAGAATTGTAA+TGG + chr8_3:62354609-62354628 Msa1300700:CDS 25.0%
! TTATTACCTCTATTCTGTTA+AGG + chr8_3:62354892-62354911 Msa1300700:three_prime_UTR 25.0%
!!! TTAGGGTAATTTTGTTATGT+TGG + chr8_3:62354978-62354997 Msa1300700:three_prime_UTR 25.0%
! TCTCTTCATAACTCTAATAA+AGG + chr8_3:62355010-62355029 Msa1300700:three_prime_UTR 25.0%
! CTCTAATAAAGGAAATTATG+CGG + chr8_3:62355021-62355040 Msa1300700:three_prime_UTR 25.0%
!!! CCAATGTTCAAATTTTAGTT+CGG + chr8_3:62355049-62355068 Msa1300700:three_prime_UTR 25.0%
TTTGATGAAAAGTGAGAAAG+TGG - chr8_3:62354143-62354162 None:intergenic 30.0%
TGAAGAAAAGAAGAAAGGAT+TGG - chr8_3:62354168-62354187 None:intergenic 30.0%
AAGAAGAAGAAGAAGAAACA+TGG - chr8_3:62354305-62354324 None:intergenic 30.0%
GATAAACAAGAACGTAGAAT+AGG - chr8_3:62354336-62354355 None:intergenic 30.0%
AGTAAAAAGTAACTTACCAG+AGG - chr8_3:62354358-62354377 None:intergenic 30.0%
!!! GAAAAGAGTTAGTTTTGCTA+AGG + chr8_3:62354479-62354498 Msa1300700:CDS 30.0%
AAGTACAGAAAACAACAACA+TGG + chr8_3:62354531-62354550 Msa1300700:CDS 30.0%
GTTCAAAAGAATTGTAATGG+TGG + chr8_3:62354612-62354631 Msa1300700:CDS 30.0%
!! GATTGGCTTATTGTTGAATT+TGG + chr8_3:62354709-62354728 Msa1300700:exon 30.0%
! TCTAGAAGTACAGTAAAAGT+AGG + chr8_3:62354825-62354844 Msa1300700:three_prime_UTR 30.0%
!! TAGGAAATAGAAGTTGATGA+AGG + chr8_3:62354844-62354863 Msa1300700:three_prime_UTR 30.0%
!! TAACTGCAACTATGTTTTTG+TGG - chr8_3:62354875-62354894 None:intergenic 30.0%
AATTCACCTTAACAGAATAG+AGG - chr8_3:62354901-62354920 None:intergenic 30.0%
CTATTCTGTTAAGGTGAATT+AGG + chr8_3:62354901-62354920 Msa1300700:three_prime_UTR 30.0%
CCGAACTAAAATTTGAACAT+TGG - chr8_3:62355052-62355071 None:intergenic 30.0%
TTTGATGAAAAGTGAGAAAG+TGG - chr8_3:62354143-62354162 None:intergenic 30.0%
TGAAGAAAAGAAGAAAGGAT+TGG - chr8_3:62354168-62354187 None:intergenic 30.0%
AAGAAGAAGAAGAAGAAACA+TGG - chr8_3:62354305-62354324 None:intergenic 30.0%
GATAAACAAGAACGTAGAAT+AGG - chr8_3:62354336-62354355 None:intergenic 30.0%
AGTAAAAAGTAACTTACCAG+AGG - chr8_3:62354358-62354377 None:intergenic 30.0%
!!! GAAAAGAGTTAGTTTTGCTA+AGG + chr8_3:62354479-62354498 Msa1300700:CDS 30.0%
AAGTACAGAAAACAACAACA+TGG + chr8_3:62354531-62354550 Msa1300700:CDS 30.0%
GTTCAAAAGAATTGTAATGG+TGG + chr8_3:62354612-62354631 Msa1300700:CDS 30.0%
!! GATTGGCTTATTGTTGAATT+TGG + chr8_3:62354709-62354728 Msa1300700:exon 30.0%
! TCTAGAAGTACAGTAAAAGT+AGG + chr8_3:62354825-62354844 Msa1300700:three_prime_UTR 30.0%
!! TAGGAAATAGAAGTTGATGA+AGG + chr8_3:62354844-62354863 Msa1300700:three_prime_UTR 30.0%
!! TAACTGCAACTATGTTTTTG+TGG - chr8_3:62354875-62354894 None:intergenic 30.0%
AATTCACCTTAACAGAATAG+AGG - chr8_3:62354901-62354920 None:intergenic 30.0%
CTATTCTGTTAAGGTGAATT+AGG + chr8_3:62354901-62354920 Msa1300700:three_prime_UTR 30.0%
CCGAACTAAAATTTGAACAT+TGG - chr8_3:62355052-62355071 None:intergenic 30.0%
TCTTCAATGATTACCTCACA+AGG + chr8_3:62354195-62354214 Msa1300700:CDS 35.0%
! AGAATTGGGATTTCTGAAGA+CGG - chr8_3:62354275-62354294 None:intergenic 35.0%
AACATGGTGAAGAGAGAATT+GGG - chr8_3:62354289-62354308 None:intergenic 35.0%
AAACATGGTGAAGAGAGAAT+TGG - chr8_3:62354290-62354309 None:intergenic 35.0%
CTACACACATTGAACAAACA+AGG + chr8_3:62354376-62354395 Msa1300700:intron 35.0%
!! TAGTTTTGCTAAGGATGTTG+TGG + chr8_3:62354488-62354507 Msa1300700:CDS 35.0%
GTTGTGGATTCATGTAAAGA+TGG + chr8_3:62354504-62354523 Msa1300700:CDS 35.0%
! AACAGAGCAGCTTTGTATAA+TGG + chr8_3:62354660-62354679 Msa1300700:CDS 35.0%
!! TGCAACTATGTTTTTGTGGT+GGG - chr8_3:62354871-62354890 None:intergenic 35.0%
TCTTCAATGATTACCTCACA+AGG + chr8_3:62354195-62354214 Msa1300700:CDS 35.0%
! AGAATTGGGATTTCTGAAGA+CGG - chr8_3:62354275-62354294 None:intergenic 35.0%
AACATGGTGAAGAGAGAATT+GGG - chr8_3:62354289-62354308 None:intergenic 35.0%
AAACATGGTGAAGAGAGAAT+TGG - chr8_3:62354290-62354309 None:intergenic 35.0%
CTACACACATTGAACAAACA+AGG + chr8_3:62354376-62354395 Msa1300700:intron 35.0%
!! TAGTTTTGCTAAGGATGTTG+TGG + chr8_3:62354488-62354507 Msa1300700:CDS 35.0%
GTTGTGGATTCATGTAAAGA+TGG + chr8_3:62354504-62354523 Msa1300700:CDS 35.0%
! AACAGAGCAGCTTTGTATAA+TGG + chr8_3:62354660-62354679 Msa1300700:CDS 35.0%
!! TGCAACTATGTTTTTGTGGT+GGG - chr8_3:62354871-62354890 None:intergenic 35.0%
! CTACGTTCTTGTTTATCCTC+TGG + chr8_3:62354339-62354358 Msa1300700:CDS 40.0%
AGATCGTGTGAATCAACGAT+TGG + chr8_3:62354692-62354711 Msa1300700:CDS 40.0%
!! CTGCAACTATGTTTTTGTGG+TGG - chr8_3:62354872-62354891 None:intergenic 40.0%
CATATTAGAAGCAGCCAACA+AGG - chr8_3:62354112-62354131 None:intergenic 40.0%
! CTACGTTCTTGTTTATCCTC+TGG + chr8_3:62354339-62354358 Msa1300700:CDS 40.0%
AGATCGTGTGAATCAACGAT+TGG + chr8_3:62354692-62354711 Msa1300700:CDS 40.0%
!! CTGCAACTATGTTTTTGTGG+TGG - chr8_3:62354872-62354891 None:intergenic 40.0%
! ATTTCTGAAGACGGAGAGCA+AGG - chr8_3:62354266-62354285 None:intergenic 45.0%
! AATGGTGGAAACGAGAACAG+AGG + chr8_3:62354627-62354646 Msa1300700:CDS 45.0%
TACAAAGCTGCTCTGTTTGC+AGG - chr8_3:62354657-62354676 None:intergenic 45.0%
! ATTTCTGAAGACGGAGAGCA+AGG - chr8_3:62354266-62354285 None:intergenic 45.0%
! AATGGTGGAAACGAGAACAG+AGG + chr8_3:62354627-62354646 Msa1300700:CDS 45.0%
TACAAAGCTGCTCTGTTTGC+AGG - chr8_3:62354657-62354676 None:intergenic 45.0%
TGCAAAGACAGCACCTTGTG+AGG - chr8_3:62354211-62354230 None:intergenic 50.0%
AGCAAGGATGATGACTGTGC+CGG - chr8_3:62354250-62354269 None:intergenic 50.0%
TGCAAAGACAGCACCTTGTG+AGG - chr8_3:62354211-62354230 None:intergenic 50.0%
AGCAAGGATGATGACTGTGC+CGG - chr8_3:62354250-62354269 None:intergenic 50.0%
TGCTGTCTTTGCAACCGCCA+TGG + chr8_3:62354218-62354237 Msa1300700:CDS 55.0%
TGCTGTCTTTGCAACCGCCA+TGG + chr8_3:62354218-62354237 Msa1300700:CDS 55.0%
GCAACCGCCATGGCTGTCTC+CGG + chr8_3:62354228-62354247 Msa1300700:CDS 65.0%
TGTGCCGGAGACAGCCATGG+CGG - chr8_3:62354235-62354254 None:intergenic 65.0%
GACTGTGCCGGAGACAGCCA+TGG - chr8_3:62354238-62354257 None:intergenic 65.0%
GCAACCGCCATGGCTGTCTC+CGG + chr8_3:62354228-62354247 Msa1300700:CDS 65.0%
TGTGCCGGAGACAGCCATGG+CGG - chr8_3:62354235-62354254 None:intergenic 65.0%
GACTGTGCCGGAGACAGCCA+TGG - chr8_3:62354238-62354257 None:intergenic 65.0%
Chromosome Type Strat End Strand Name
chr8_3 gene 62354110 62355120 62354110 ID=Msa1300700;Name=Msa1300700
chr8_3 mRNA 62354110 62355120 62354110 ID=Msa1300700-mRNA-1;Parent=Msa1300700;Name=Msa1300700-mRNA-1;_AED=0.05;_eAED=0.05;_QI=19|1|1|1|1|1|2|395|167
chr8_3 exon 62354110 62354360 62354110 ID=Msa1300700-mRNA-1:exon:18507;Parent=Msa1300700-mRNA-1
chr8_3 exon 62354454 62355120 62354454 ID=Msa1300700-mRNA-1:exon:18508;Parent=Msa1300700-mRNA-1
chr8_3 five_prime_UTR 62354110 62354128 62354110 ID=Msa1300700-mRNA-1:five_prime_utr;Parent=Msa1300700-mRNA-1
chr8_3 CDS 62354129 62354360 62354129 ID=Msa1300700-mRNA-1:cds;Parent=Msa1300700-mRNA-1
chr8_3 CDS 62354454 62354725 62354454 ID=Msa1300700-mRNA-1:cds;Parent=Msa1300700-mRNA-1
chr8_3 three_prime_UTR 62354726 62355120 62354726 ID=Msa1300700-mRNA-1:three_prime_utr;Parent=Msa1300700-mRNA-1
Gene Sequence

>Msa1300700

ATGAGACTATACCACTTTCTCACTTTTCATCAAAGACCAATCCTTTCTTCTTTTCTTCAAAACATGTCTTCAATGATTACCTCACAAGGTGCTGTCTTTGCAACCGCCATGGCTGTCTCCGGCACAGTCATCATCCTTGCTCTCCGTCTTCAGAAATCCCAATTCTCTCTTCACCATGTTTCTTCTTCTTCTTCTTCTTCAACTCCTATTCTACGTTCTTGTTTATCCTCTGATGAAAAGAAAACAAAGAAACTGAAGAAAAGAGTTAGTTTTGCTAAGGATGTTGTGGATTCATGTAAAGATGGAGAAAAGTACAGAAAACAACAACATGGTACTAGTACTATGAATAATACTACTAAACATTCTTTGAAATTGAATTCAAGATCAAAGGTTCAAAAGAATTGTAATGGTGGAAACGAGAACAGAGGAATGCCTGCAAACAGAGCAGCTTTGTATAATGGAATTCTTAGAGATCGTGTGAATCAACGATTGGCTTATTGTTGA
Protein sequence

>Msa1300700

MRLYHFLTFHQRPILSSFLQNMSSMITSQGAVFATAMAVSGTVIILALRLQKSQFSLHHVSSSSSSSTPILRSCLSSDEKKTKKLKKRVSFAKDVVDSCKDGEKYRKQQHGTSTMNNTTKHSLKLNSRSKVQKNCNGGNENRGMPANRAALYNGILRDRVNQRLAYC*