AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1405630

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1405630 MtrunA17_Chr8g0339591 66.406 128 16 2 1 101 81 208 2.43e-49 155
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1405630 AT3G25120.1 36.538 104 51 1 1 89 78 181 4.97e-13 62.0

Find 32 sgRNAs with CRISPR-Local

Find 110 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
ATTTGGATCTGGTGCTCTTC+TGG 0.111419 tig0023154:-91414 Msa1405630:CDS
ATACAAAATGTTTAAGAATA+TGG 0.228966 tig0023154:+90870 None:intergenic
GCTCTTCTGGGGAGTTTATA+TGG 0.237787 tig0023154:-91401 Msa1405630:intron
AGTAAATAATTATTCAATAA+AGG 0.262738 tig0023154:+90590 None:intergenic
TTTGGATCTGGTGCTCTTCT+GGG 0.313608 tig0023154:-91413 Msa1405630:CDS
AAGAAGATTCTTGAGAAGAT+TGG 0.333995 tig0023154:-90907 Msa1405630:exon
AGAAGATTCTTGAGAAGATT+GGG 0.355774 tig0023154:-90906 Msa1405630:exon
ATTATTCAATAAAGGGATAC+AGG 0.379962 tig0023154:+90598 None:intergenic
AACTCTGTGATAGCAGGATT+TGG 0.382711 tig0023154:-91431 Msa1405630:CDS
GTAAATAATTATTCAATAAA+GGG 0.392919 tig0023154:+90591 None:intergenic
AAGAATCTTCTTTATCCCTT+AGG 0.400749 tig0023154:+90918 None:intergenic
AATGTCTTCAGCAGAGATTA+TGG 0.429496 tig0023154:-90816 Msa1405630:three_prime_UTR
GTGACTGCAACTAGGAAAAC+AGG 0.441697 tig0023154:-91470 Msa1405630:CDS
ACCATTCTGAAATTAAAAGA+TGG 0.462329 tig0023154:-91031 Msa1405630:CDS
GTGATAGCAGGATTTGGATC+TGG 0.475639 tig0023154:-91425 Msa1405630:CDS
AGTTAAAGATTTAATTCACT+TGG 0.484528 tig0023154:-90791 Msa1405630:three_prime_UTR
TTCTGAAATTAAAAGATGGT+TGG 0.491300 tig0023154:-91027 Msa1405630:CDS
CACTGGACAATGTCTACATA+AGG 0.496036 tig0023154:+90754 None:intergenic
GGGCAAGGATTCGAAGCCTA+AGG 0.496681 tig0023154:-90934 Msa1405630:CDS
TTGGATCTGGTGCTCTTCTG+GGG 0.516613 tig0023154:-91412 Msa1405630:CDS
AGAGCAGTTCCTTGCGCAGA+GGG 0.517334 tig0023154:-90954 Msa1405630:CDS
CTGTGGAACTCTGTGATAGC+AGG 0.518520 tig0023154:-91437 Msa1405630:CDS
AGTTCCTTGCGCAGAGGGCA+AGG 0.524214 tig0023154:-90949 Msa1405630:CDS
ATGAAATTGTGACTGCAACT+AGG 0.534018 tig0023154:-91478 Msa1405630:CDS
GAATCCTTGCCCTCTGCGCA+AGG 0.547182 tig0023154:+90945 None:intergenic
GAAGATTCTTGAGAAGATTG+GGG 0.575432 tig0023154:-90905 Msa1405630:exon
AAGAGCAGTTCCTTGCGCAG+AGG 0.584780 tig0023154:-90955 Msa1405630:CDS
TTCTTGAGAAGATTGGGGTG+AGG 0.593188 tig0023154:-90900 Msa1405630:exon
GGCAAGGATTCGAAGCCTAA+GGG 0.595170 tig0023154:-90933 Msa1405630:CDS
TATTGCTGAGAAACAAGCAC+AGG 0.620559 tig0023154:-90978 Msa1405630:CDS
AAACAGGACCTGAAAATCTG+TGG 0.633046 tig0023154:-91454 Msa1405630:CDS
GGACAATGTCTACATAAGGA+AGG 0.639614 tig0023154:+90758 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AACTAAAAAAATAAGAAATT+GGG + tig0023154:91229-91248 None:intergenic 10.0%
!! AAACTAAAAAAATAAGAAAT+TGG + tig0023154:91230-91249 None:intergenic 10.0%
!! TGTAAAATATAAAAAAGAAA+AGG + tig0023154:91379-91398 None:intergenic 10.0%
!! GTAAATAATTATTCAATAAA+GGG + tig0023154:91484-91503 None:intergenic 10.0%
!! AGTAAATAATTATTCAATAA+AGG + tig0023154:91485-91504 None:intergenic 10.0%
!! AACTAAAAAAATAAGAAATT+GGG + tig0023154:91229-91248 None:intergenic 10.0%
!! AAACTAAAAAAATAAGAAAT+TGG + tig0023154:91230-91249 None:intergenic 10.0%
!! TGTAAAATATAAAAAAGAAA+AGG + tig0023154:91379-91398 None:intergenic 10.0%
!! GTAAATAATTATTCAATAAA+GGG + tig0023154:91484-91503 None:intergenic 10.0%
!! AGTAAATAATTATTCAATAA+AGG + tig0023154:91485-91504 None:intergenic 10.0%
!! TAAGAAGTTGTATTAATTTA+TGG - tig0023154:90945-90964 Msa1405630:CDS 15.0%
!!! GTATTAATTTATGGAATTTT+AGG - tig0023154:90954-90973 Msa1405630:CDS 15.0%
!! ATACAAAATGTTTAAGAATA+TGG + tig0023154:91205-91224 None:intergenic 15.0%
!! TAAGAAGTTGTATTAATTTA+TGG - tig0023154:90945-90964 Msa1405630:CDS 15.0%
!!! GTATTAATTTATGGAATTTT+AGG - tig0023154:90954-90973 Msa1405630:CDS 15.0%
!! ATACAAAATGTTTAAGAATA+TGG + tig0023154:91205-91224 None:intergenic 15.0%
!!! TTAATTTATGGAATTTTAGG+CGG - tig0023154:90957-90976 Msa1405630:CDS 20.0%
!! AGTTAAAGATTTAATTCACT+TGG - tig0023154:91281-91300 Msa1405630:intron 20.0%
!!! TTAATTTATGGAATTTTAGG+CGG - tig0023154:90957-90976 Msa1405630:CDS 20.0%
!! AGTTAAAGATTTAATTCACT+TGG - tig0023154:91281-91300 Msa1405630:intron 20.0%
!!! ACCATTCTGAAATTAAAAGA+TGG - tig0023154:91041-91060 Msa1405630:CDS 25.0%
!!! ACCATCTTTTAATTTCAGAA+TGG + tig0023154:91045-91064 None:intergenic 25.0%
!!! TTCTGAAATTAAAAGATGGT+TGG - tig0023154:91045-91064 Msa1405630:CDS 25.0%
!! AATTTTTCTTGTGTTATCAC+TGG + tig0023154:91338-91357 None:intergenic 25.0%
! ATTATTCAATAAAGGGATAC+AGG + tig0023154:91477-91496 None:intergenic 25.0%
!!! ACCATTCTGAAATTAAAAGA+TGG - tig0023154:91041-91060 Msa1405630:CDS 25.0%
!!! ACCATCTTTTAATTTCAGAA+TGG + tig0023154:91045-91064 None:intergenic 25.0%
!!! TTCTGAAATTAAAAGATGGT+TGG - tig0023154:91045-91064 Msa1405630:CDS 25.0%
!! AATTTTTCTTGTGTTATCAC+TGG + tig0023154:91338-91357 None:intergenic 25.0%
! ATTATTCAATAAAGGGATAC+AGG + tig0023154:91477-91496 None:intergenic 25.0%
ATGATAGCATATAAAAGCGA+CGG + tig0023154:90792-90811 None:intergenic 30.0%
ACAATTATGTAGTAAGCTTG+TGG + tig0023154:90842-90861 None:intergenic 30.0%
TACTACATAATTGTGTCACA+TGG - tig0023154:90848-90867 Msa1405630:three_prime_UTR 30.0%
ATGCAGCTATTTATTATGCA+TGG + tig0023154:90893-90912 None:intergenic 30.0%
!!! TCTATCATTTTTGCTGTTGT+CGG - tig0023154:91002-91021 Msa1405630:CDS 30.0%
AAGAATCTTCTTTATCCCTT+AGG + tig0023154:91157-91176 None:intergenic 30.0%
AAGAAGATTCTTGAGAAGAT+TGG - tig0023154:91165-91184 Msa1405630:intron 30.0%
AGAAGATTCTTGAGAAGATT+GGG - tig0023154:91166-91185 Msa1405630:intron 30.0%
TGAAAAAGAATGCTACATGA+AGG + tig0023154:91451-91470 None:intergenic 30.0%
ATGATAGCATATAAAAGCGA+CGG + tig0023154:90792-90811 None:intergenic 30.0%
ACAATTATGTAGTAAGCTTG+TGG + tig0023154:90842-90861 None:intergenic 30.0%
TACTACATAATTGTGTCACA+TGG - tig0023154:90848-90867 Msa1405630:three_prime_UTR 30.0%
ATGCAGCTATTTATTATGCA+TGG + tig0023154:90893-90912 None:intergenic 30.0%
!!! TCTATCATTTTTGCTGTTGT+CGG - tig0023154:91002-91021 Msa1405630:CDS 30.0%
AAGAATCTTCTTTATCCCTT+AGG + tig0023154:91157-91176 None:intergenic 30.0%
AAGAAGATTCTTGAGAAGAT+TGG - tig0023154:91165-91184 Msa1405630:intron 30.0%
AGAAGATTCTTGAGAAGATT+GGG - tig0023154:91166-91185 Msa1405630:intron 30.0%
TGAAAAAGAATGCTACATGA+AGG + tig0023154:91451-91470 None:intergenic 30.0%
ATGAAATTGTGACTGCAACT+AGG - tig0023154:90594-90613 Msa1405630:three_prime_UTR 35.0%
TTTCTCCTCTTATTCTCTTG+AGG - tig0023154:90707-90726 Msa1405630:three_prime_UTR 35.0%
TGAGGCATACTTGTAATTCT+TGG - tig0023154:90725-90744 Msa1405630:three_prime_UTR 35.0%
! TTCTTGGTAGTCATAAACCA+TGG - tig0023154:90741-90760 Msa1405630:three_prime_UTR 35.0%
!!! CTATCATTTTTGCTGTTGTC+GGG - tig0023154:91003-91022 Msa1405630:CDS 35.0%
GAAGATTCTTGAGAAGATTG+GGG - tig0023154:91167-91186 Msa1405630:intron 35.0%
AATGTCTTCAGCAGAGATTA+TGG - tig0023154:91256-91275 Msa1405630:intron 35.0%
ATGAAATTGTGACTGCAACT+AGG - tig0023154:90594-90613 Msa1405630:three_prime_UTR 35.0%
TTTCTCCTCTTATTCTCTTG+AGG - tig0023154:90707-90726 Msa1405630:three_prime_UTR 35.0%
TGAGGCATACTTGTAATTCT+TGG - tig0023154:90725-90744 Msa1405630:three_prime_UTR 35.0%
! TTCTTGGTAGTCATAAACCA+TGG - tig0023154:90741-90760 Msa1405630:three_prime_UTR 35.0%
!!! CTATCATTTTTGCTGTTGTC+GGG - tig0023154:91003-91022 Msa1405630:CDS 35.0%
GAAGATTCTTGAGAAGATTG+GGG - tig0023154:91167-91186 Msa1405630:intron 35.0%
AATGTCTTCAGCAGAGATTA+TGG - tig0023154:91256-91275 Msa1405630:intron 35.0%
AAACAGGACCTGAAAATCTG+TGG - tig0023154:90618-90637 Msa1405630:three_prime_UTR 40.0%
! ACAGAGTTCCACAGATTTTC+AGG + tig0023154:90629-90648 None:intergenic 40.0%
AACTCTGTGATAGCAGGATT+TGG - tig0023154:90641-90660 Msa1405630:three_prime_UTR 40.0%
GTATGCCTCAAGAGAATAAG+AGG + tig0023154:90715-90734 None:intergenic 40.0%
AGACAGGTAAATCATCACCA+TGG + tig0023154:90761-90780 None:intergenic 40.0%
! GGAATTTTAGGCGGTCAATT+TGG - tig0023154:90966-90985 Msa1405630:CDS 40.0%
TATTGCTGAGAAACAAGCAC+AGG - tig0023154:91094-91113 Msa1405630:CDS 40.0%
GGACAATGTCTACATAAGGA+AGG + tig0023154:91317-91336 None:intergenic 40.0%
CACTGGACAATGTCTACATA+AGG + tig0023154:91321-91340 None:intergenic 40.0%
AAACAGGACCTGAAAATCTG+TGG - tig0023154:90618-90637 Msa1405630:three_prime_UTR 40.0%
! ACAGAGTTCCACAGATTTTC+AGG + tig0023154:90629-90648 None:intergenic 40.0%
AACTCTGTGATAGCAGGATT+TGG - tig0023154:90641-90660 Msa1405630:three_prime_UTR 40.0%
GTATGCCTCAAGAGAATAAG+AGG + tig0023154:90715-90734 None:intergenic 40.0%
AGACAGGTAAATCATCACCA+TGG + tig0023154:90761-90780 None:intergenic 40.0%
! GGAATTTTAGGCGGTCAATT+TGG - tig0023154:90966-90985 Msa1405630:CDS 40.0%
TATTGCTGAGAAACAAGCAC+AGG - tig0023154:91094-91113 Msa1405630:CDS 40.0%
GGACAATGTCTACATAAGGA+AGG + tig0023154:91317-91336 None:intergenic 40.0%
CACTGGACAATGTCTACATA+AGG + tig0023154:91321-91340 None:intergenic 40.0%
GTGACTGCAACTAGGAAAAC+AGG - tig0023154:90602-90621 Msa1405630:three_prime_UTR 45.0%
GTGATAGCAGGATTTGGATC+TGG - tig0023154:90647-90666 Msa1405630:three_prime_UTR 45.0%
ATTTGGATCTGGTGCTCTTC+TGG - tig0023154:90658-90677 Msa1405630:three_prime_UTR 45.0%
TTTGGATCTGGTGCTCTTCT+GGG - tig0023154:90659-90678 Msa1405630:three_prime_UTR 45.0%
! GCTCTTCTGGGGAGTTTATA+TGG - tig0023154:90671-90690 Msa1405630:three_prime_UTR 45.0%
TTCTTGAGAAGATTGGGGTG+AGG - tig0023154:91172-91191 Msa1405630:intron 45.0%
GTGACTGCAACTAGGAAAAC+AGG - tig0023154:90602-90621 Msa1405630:three_prime_UTR 45.0%
GTGATAGCAGGATTTGGATC+TGG - tig0023154:90647-90666 Msa1405630:three_prime_UTR 45.0%
ATTTGGATCTGGTGCTCTTC+TGG - tig0023154:90658-90677 Msa1405630:three_prime_UTR 45.0%
TTTGGATCTGGTGCTCTTCT+GGG - tig0023154:90659-90678 Msa1405630:three_prime_UTR 45.0%
! GCTCTTCTGGGGAGTTTATA+TGG - tig0023154:90671-90690 Msa1405630:three_prime_UTR 45.0%
TTCTTGAGAAGATTGGGGTG+AGG - tig0023154:91172-91191 Msa1405630:intron 45.0%
CTGTGGAACTCTGTGATAGC+AGG - tig0023154:90635-90654 Msa1405630:three_prime_UTR 50.0%
TTGGATCTGGTGCTCTTCTG+GGG - tig0023154:90660-90679 Msa1405630:three_prime_UTR 50.0%
GGCAAGGATTCGAAGCCTAA+GGG - tig0023154:91139-91158 Msa1405630:intron 50.0%
CTGTGGAACTCTGTGATAGC+AGG - tig0023154:90635-90654 Msa1405630:three_prime_UTR 50.0%
TTGGATCTGGTGCTCTTCTG+GGG - tig0023154:90660-90679 Msa1405630:three_prime_UTR 50.0%
GGCAAGGATTCGAAGCCTAA+GGG - tig0023154:91139-91158 Msa1405630:intron 50.0%
AGCGACGGTCAAGAACAGAC+AGG + tig0023154:90777-90796 None:intergenic 55.0%
AAGAGCAGTTCCTTGCGCAG+AGG - tig0023154:91117-91136 Msa1405630:intron 55.0%
AGAGCAGTTCCTTGCGCAGA+GGG - tig0023154:91118-91137 Msa1405630:intron 55.0%
GGGCAAGGATTCGAAGCCTA+AGG - tig0023154:91138-91157 Msa1405630:intron 55.0%
AGCGACGGTCAAGAACAGAC+AGG + tig0023154:90777-90796 None:intergenic 55.0%
AAGAGCAGTTCCTTGCGCAG+AGG - tig0023154:91117-91136 Msa1405630:intron 55.0%
AGAGCAGTTCCTTGCGCAGA+GGG - tig0023154:91118-91137 Msa1405630:intron 55.0%
GGGCAAGGATTCGAAGCCTA+AGG - tig0023154:91138-91157 Msa1405630:intron 55.0%
AGTTCCTTGCGCAGAGGGCA+AGG - tig0023154:91123-91142 Msa1405630:intron 60.0%
GAATCCTTGCCCTCTGCGCA+AGG + tig0023154:91130-91149 None:intergenic 60.0%
AGTTCCTTGCGCAGAGGGCA+AGG - tig0023154:91123-91142 Msa1405630:intron 60.0%
GAATCCTTGCCCTCTGCGCA+AGG + tig0023154:91130-91149 None:intergenic 60.0%
Chromosome Type Strat End Strand Name
tig0023154 gene 90590 91504 90590 ID=Msa1405630;Name=Msa1405630
tig0023154 mRNA 90590 91504 90590 ID=Msa1405630-mRNA-1;Parent=Msa1405630;Name=Msa1405630-mRNA-1;_AED=0.02;_eAED=0.02;_QI=0|1|0.5|1|1|0.5|2|326|101
tig0023154 exon 90590 91118 90590 ID=Msa1405630-mRNA-1:exon:24169;Parent=Msa1405630-mRNA-1
tig0023154 exon 91402 91504 91402 ID=Msa1405630-mRNA-1:exon:24168;Parent=Msa1405630-mRNA-1
tig0023154 CDS 91402 91504 91402 ID=Msa1405630-mRNA-1:cds;Parent=Msa1405630-mRNA-1
tig0023154 CDS 90916 91118 90916 ID=Msa1405630-mRNA-1:cds;Parent=Msa1405630-mRNA-1
tig0023154 three_prime_UTR 90590 90915 90590 ID=Msa1405630-mRNA-1:three_prime_utr;Parent=Msa1405630-mRNA-1
Gene Sequence

>Msa1405630

GCACATGAAATTGTGACTGCAACTAGGAAAACAGGACCTGAAAATCTGTGGAACTCTGTGATAGCAGGATTTGGATCTGGTGCTCTTCTGGGGAGTTTATATGGCGGTCAATTTGGTGCAACTTGTTGTTCTATCATTTTTGCTGTTGTCGGGACAACAGCAGATTTCACCATTCTGAAATTAAAAGATGGTTGGAGAATATATCAAGATATAAAGAAGATTATTGCTGAGAAACAAGCACAGGAAGAGCAGTTCCTTGCGCAGAGGGCAAGGATTCGAAGCCTAAGGGATAAAGAAGATTCTTGA
Protein sequence

>Msa1405630

AHEIVTATRKTGPENLWNSVIAGFGSGALLGSLYGGQFGATCCSIIFAVVGTTADFTILKLKDGWRIYQDIKKIIAEKQAQEEQFLAQRARIRSLRDKEDS*