AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1338550

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1338550 MtrunA17_Chr7g0252921 97.248 109 2 1 1 108 1 109 2.73e-69 214
Msa1338550 MtrunA17_Chr7g0252891 78.899 109 22 1 1 108 23 131 2.12e-55 178
Msa1338550 MtrunA17_Chr4g0015031 77.982 109 23 1 1 108 12 120 1.42e-54 176
Msa1338550 MtrunA17_Chr7g0252911 81.053 95 18 0 14 108 16 110 2.52e-51 167
Msa1338550 MtrunA17_Chr7g0252881 80.000 95 19 0 14 108 16 110 5.75e-51 166
Msa1338550 MtrunA17_Chr7g0252861 58.095 105 43 1 5 108 29 133 1.26e-35 126
Msa1338550 MtrunA17_Chr6g0461671 54.167 96 44 0 13 108 51 146 5.68e-30 111
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1338550 AT5G18280.1 57.143 77 33 0 30 106 58 134 1.59e-24 96.7
Msa1338550 AT3G04080.1 46.237 93 50 0 14 106 41 133 4.60e-21 87.0
Msa1338550 AT1G14240.1 36.364 88 53 2 22 107 50 136 5.98e-11 58.2
Msa1338550 AT1G14240.4 36.364 88 53 2 22 107 50 136 5.98e-11 58.2
Msa1338550 AT1G14240.2 36.364 88 53 2 22 107 50 136 5.98e-11 58.2
Msa1338550 AT1G14240.3 36.364 88 53 2 22 107 50 136 6.52e-11 58.2

Find 33 sgRNAs with CRISPR-Local

Find 92 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CCCAAGCTTAACGGGTGTTT+TGG 0.201215 tig0002256:-41143 None:intergenic
TATATTGTTTCCATGATATT+GGG 0.324491 tig0002256:-40689 None:intergenic
GTATATTGTTTCCATGATAT+TGG 0.332361 tig0002256:-40690 None:intergenic
GAGGTTAGAGTTTCTTGTTT+TGG 0.355671 tig0002256:-40733 None:intergenic
AGAGACTCTGCTGCTTCCTT+CGG 0.385467 tig0002256:-41071 None:intergenic
TATGCTAGTTGTGTTATAAC+CGG 0.415958 tig0002256:+40563 Msa1338550:five_prime_UTR
ATCTGCGTATGCACTCAAAC+CGG 0.416171 tig0002256:-41045 None:intergenic
CCCAAAACACCCGTTAAGCT+TGG 0.417106 tig0002256:+41142 Msa1338550:three_prime_UTR
AAAACCAACCCAAGCTTAAC+GGG 0.428946 tig0002256:-41151 None:intergenic
CTTTCTGCTTGCTCTAAAAG+TGG 0.437669 tig0002256:-41098 None:intergenic
GAAAACCAACCCAAGCTTAA+CGG 0.444431 tig0002256:-41152 None:intergenic
CAGTTAGTTAGATGAATTGA+AGG 0.446721 tig0002256:-40536 None:intergenic
CCAAAACACCCGTTAAGCTT+GGG 0.455246 tig0002256:+41143 Msa1338550:three_prime_UTR
ATCTCTTCCTCCCAATATCA+TGG 0.459648 tig0002256:+40679 Msa1338550:CDS
TACGCTGTCGTCTTTGATGC+TGG 0.466964 tig0002256:+40757 Msa1338550:CDS
GTCTTTGATGCTGGTAGCAC+CGG 0.473853 tig0002256:+40766 Msa1338550:CDS
TATTGGGAGGAAGAGATTGT+AGG 0.515388 tig0002256:-40673 None:intergenic
TAGTATGTGGCCAGTGGGAA+GGG 0.525439 tig0002256:-40600 None:intergenic
AACTTAGATCTTCTTCACAT+TGG 0.536252 tig0002256:+40820 Msa1338550:CDS
AAATAAGCATATGATTGGTA+AGG 0.538345 tig0002256:+40472 Msa1338550:five_prime_UTR
TTCATGTTGTAGACAACGCC+CGG 0.539719 tig0002256:+41026 Msa1338550:intron
TCTGCGTATGCACTCAAACC+GGG 0.541965 tig0002256:-41044 None:intergenic
AAAATAGTTTCCCTTCCCAC+TGG 0.542743 tig0002256:+40590 Msa1338550:five_prime_UTR
AACACCCGTTAAGCTTGGGT+TGG 0.554576 tig0002256:+41147 Msa1338550:three_prime_UTR
GTAGACATGAACACGGCTAC+CGG 0.589772 tig0002256:-40785 None:intergenic
TCCATGCTTGTTGTAGTATG+TGG 0.591213 tig0002256:-40613 None:intergenic
ATCAAAGACGACAGCGTACG+AGG 0.591264 tig0002256:-40752 None:intergenic
GCCACATACTACAACAAGCA+TGG 0.594864 tig0002256:+40612 Msa1338550:exon
GTAGTATGTGGCCAGTGGGA+AGG 0.602099 tig0002256:-40601 None:intergenic
TGTTGTAGTATGTGGCCAGT+GGG 0.622928 tig0002256:-40605 None:intergenic
ATTGTTTCCATGATATTGGG+AGG 0.626102 tig0002256:-40686 None:intergenic
CAAAATGGTAGACATGAACA+CGG 0.665622 tig0002256:-40792 None:intergenic
TTGTTGTAGTATGTGGCCAG+TGG 0.699635 tig0002256:-40606 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! ATTAATTAAATATTACATCT+TGG + tig0002256:40871-40890 Msa1338550:intron 10.0%
!! ATTAATTAAATATTACATCT+TGG + tig0002256:40871-40890 Msa1338550:intron 10.0%
!!! GCATAATATTTTAATCAAAT+TGG + tig0002256:40506-40525 Msa1338550:five_prime_UTR 15.0%
!!! GCATAATATTTTAATCAAAT+TGG + tig0002256:40506-40525 Msa1338550:five_prime_UTR 15.0%
!! TATATTGTTTCCATGATATT+GGG - tig0002256:40692-40711 None:intergenic 20.0%
!!! TTTTGGAAATATTTTACGAT+TGG - tig0002256:40719-40738 None:intergenic 20.0%
!!! TGATGTTGAGTTTTATAATA+AGG + tig0002256:40846-40865 Msa1338550:CDS 20.0%
!! AATTAATTAACGCAGAATTA+TGG + tig0002256:40912-40931 Msa1338550:intron 20.0%
!!! TTACAATGTCTTAATTTTGA+TGG + tig0002256:41175-41194 Msa1338550:three_prime_UTR 20.0%
!! TATATTGTTTCCATGATATT+GGG - tig0002256:40692-40711 None:intergenic 20.0%
!!! TTTTGGAAATATTTTACGAT+TGG - tig0002256:40719-40738 None:intergenic 20.0%
!!! TGATGTTGAGTTTTATAATA+AGG + tig0002256:40846-40865 Msa1338550:CDS 20.0%
!! AATTAATTAACGCAGAATTA+TGG + tig0002256:40912-40931 Msa1338550:intron 20.0%
!!! TTACAATGTCTTAATTTTGA+TGG + tig0002256:41175-41194 Msa1338550:three_prime_UTR 20.0%
!!! CCAATCATATGCTTATTTTT+AGG - tig0002256:40470-40489 None:intergenic 25.0%
! CCTAAAAATAAGCATATGAT+TGG + tig0002256:40467-40486 Msa1338550:five_prime_UTR 25.0%
! AAATAAGCATATGATTGGTA+AGG + tig0002256:40472-40491 Msa1338550:five_prime_UTR 25.0%
! GTATATTGTTTCCATGATAT+TGG - tig0002256:40693-40712 None:intergenic 25.0%
!!! GATCTAAGTTTTGATCAAAA+TGG - tig0002256:40810-40829 None:intergenic 25.0%
!!! CCAATCATATGCTTATTTTT+AGG - tig0002256:40470-40489 None:intergenic 25.0%
! CCTAAAAATAAGCATATGAT+TGG + tig0002256:40467-40486 Msa1338550:five_prime_UTR 25.0%
! AAATAAGCATATGATTGGTA+AGG + tig0002256:40472-40491 Msa1338550:five_prime_UTR 25.0%
! GTATATTGTTTCCATGATAT+TGG - tig0002256:40693-40712 None:intergenic 25.0%
!!! GATCTAAGTTTTGATCAAAA+TGG - tig0002256:40810-40829 None:intergenic 25.0%
CAGTTAGTTAGATGAATTGA+AGG - tig0002256:40539-40558 None:intergenic 30.0%
TATGCTAGTTGTGTTATAAC+CGG + tig0002256:40563-40582 Msa1338550:five_prime_UTR 30.0%
!!! AAGGGAAACTATTTTGAAAC+CGG - tig0002256:40585-40604 None:intergenic 30.0%
AACTTAGATCTTCTTCACAT+TGG + tig0002256:40820-40839 Msa1338550:CDS 30.0%
CAGTTAGTTAGATGAATTGA+AGG - tig0002256:40539-40558 None:intergenic 30.0%
TATGCTAGTTGTGTTATAAC+CGG + tig0002256:40563-40582 Msa1338550:five_prime_UTR 30.0%
!!! AAGGGAAACTATTTTGAAAC+CGG - tig0002256:40585-40604 None:intergenic 30.0%
AACTTAGATCTTCTTCACAT+TGG + tig0002256:40820-40839 Msa1338550:CDS 30.0%
ATTGTTTCCATGATATTGGG+AGG - tig0002256:40689-40708 None:intergenic 35.0%
!! GAGGTTAGAGTTTCTTGTTT+TGG - tig0002256:40736-40755 None:intergenic 35.0%
CAAAATGGTAGACATGAACA+CGG - tig0002256:40795-40814 None:intergenic 35.0%
ATTGTTTCCATGATATTGGG+AGG - tig0002256:40689-40708 None:intergenic 35.0%
!! GAGGTTAGAGTTTCTTGTTT+TGG - tig0002256:40736-40755 None:intergenic 35.0%
CAAAATGGTAGACATGAACA+CGG - tig0002256:40795-40814 None:intergenic 35.0%
AAAATAGTTTCCCTTCCCAC+TGG + tig0002256:40590-40609 Msa1338550:five_prime_UTR 40.0%
!! TCCATGCTTGTTGTAGTATG+TGG - tig0002256:40616-40635 None:intergenic 40.0%
TATTGGGAGGAAGAGATTGT+AGG - tig0002256:40676-40695 None:intergenic 40.0%
ATCTCTTCCTCCCAATATCA+TGG + tig0002256:40679-40698 Msa1338550:CDS 40.0%
!! CTTTCTGCTTGCTCTAAAAG+TGG - tig0002256:41101-41120 None:intergenic 40.0%
AAAACCAACCCAAGCTTAAC+GGG - tig0002256:41154-41173 None:intergenic 40.0%
GAAAACCAACCCAAGCTTAA+CGG - tig0002256:41155-41174 None:intergenic 40.0%
AAAATAGTTTCCCTTCCCAC+TGG + tig0002256:40590-40609 Msa1338550:five_prime_UTR 40.0%
!! TCCATGCTTGTTGTAGTATG+TGG - tig0002256:40616-40635 None:intergenic 40.0%
TATTGGGAGGAAGAGATTGT+AGG - tig0002256:40676-40695 None:intergenic 40.0%
ATCTCTTCCTCCCAATATCA+TGG + tig0002256:40679-40698 Msa1338550:CDS 40.0%
!! CTTTCTGCTTGCTCTAAAAG+TGG - tig0002256:41101-41120 None:intergenic 40.0%
AAAACCAACCCAAGCTTAAC+GGG - tig0002256:41154-41173 None:intergenic 40.0%
GAAAACCAACCCAAGCTTAA+CGG - tig0002256:41155-41174 None:intergenic 40.0%
TGTTGTAGTATGTGGCCAGT+GGG - tig0002256:40608-40627 None:intergenic 45.0%
TTGTTGTAGTATGTGGCCAG+TGG - tig0002256:40609-40628 None:intergenic 45.0%
GCCACATACTACAACAAGCA+TGG + tig0002256:40612-40631 Msa1338550:exon 45.0%
TTCATGTTGTAGACAACGCC+CGG + tig0002256:41026-41045 Msa1338550:intron 45.0%
ATCTGCGTATGCACTCAAAC+CGG - tig0002256:41048-41067 None:intergenic 45.0%
TGCATACGCAGATAATCCGA+AGG + tig0002256:41055-41074 Msa1338550:CDS 45.0%
!! CCAAGCTTAACGGGTGTTTT+GGG - tig0002256:41145-41164 None:intergenic 45.0%
CCAAAACACCCGTTAAGCTT+GGG + tig0002256:41143-41162 Msa1338550:three_prime_UTR 45.0%
TGTTGTAGTATGTGGCCAGT+GGG - tig0002256:40608-40627 None:intergenic 45.0%
TTGTTGTAGTATGTGGCCAG+TGG - tig0002256:40609-40628 None:intergenic 45.0%
GCCACATACTACAACAAGCA+TGG + tig0002256:40612-40631 Msa1338550:exon 45.0%
TTCATGTTGTAGACAACGCC+CGG + tig0002256:41026-41045 Msa1338550:intron 45.0%
ATCTGCGTATGCACTCAAAC+CGG - tig0002256:41048-41067 None:intergenic 45.0%
TGCATACGCAGATAATCCGA+AGG + tig0002256:41055-41074 Msa1338550:CDS 45.0%
!! CCAAGCTTAACGGGTGTTTT+GGG - tig0002256:41145-41164 None:intergenic 45.0%
CCAAAACACCCGTTAAGCTT+GGG + tig0002256:41143-41162 Msa1338550:three_prime_UTR 45.0%
TAGTATGTGGCCAGTGGGAA+GGG - tig0002256:40603-40622 None:intergenic 50.0%
ATCAAAGACGACAGCGTACG+AGG - tig0002256:40755-40774 None:intergenic 50.0%
TACGCTGTCGTCTTTGATGC+TGG + tig0002256:40757-40776 Msa1338550:CDS 50.0%
GTCTTTGATGCTGGTAGCAC+CGG + tig0002256:40766-40785 Msa1338550:CDS 50.0%
GTAGACATGAACACGGCTAC+CGG - tig0002256:40788-40807 None:intergenic 50.0%
TCTGCGTATGCACTCAAACC+GGG - tig0002256:41047-41066 None:intergenic 50.0%
! AGAGACTCTGCTGCTTCCTT+CGG - tig0002256:41074-41093 None:intergenic 50.0%
!! GTTTTGGGCTGCAGATTCAC+AGG - tig0002256:41130-41149 None:intergenic 50.0%
CCCAAAACACCCGTTAAGCT+TGG + tig0002256:41142-41161 Msa1338550:three_prime_UTR 50.0%
!! CCCAAGCTTAACGGGTGTTT+TGG - tig0002256:41146-41165 None:intergenic 50.0%
AACACCCGTTAAGCTTGGGT+TGG + tig0002256:41147-41166 Msa1338550:three_prime_UTR 50.0%
TAGTATGTGGCCAGTGGGAA+GGG - tig0002256:40603-40622 None:intergenic 50.0%
ATCAAAGACGACAGCGTACG+AGG - tig0002256:40755-40774 None:intergenic 50.0%
TACGCTGTCGTCTTTGATGC+TGG + tig0002256:40757-40776 Msa1338550:CDS 50.0%
GTCTTTGATGCTGGTAGCAC+CGG + tig0002256:40766-40785 Msa1338550:CDS 50.0%
GTAGACATGAACACGGCTAC+CGG - tig0002256:40788-40807 None:intergenic 50.0%
TCTGCGTATGCACTCAAACC+GGG - tig0002256:41047-41066 None:intergenic 50.0%
! AGAGACTCTGCTGCTTCCTT+CGG - tig0002256:41074-41093 None:intergenic 50.0%
!! GTTTTGGGCTGCAGATTCAC+AGG - tig0002256:41130-41149 None:intergenic 50.0%
CCCAAAACACCCGTTAAGCT+TGG + tig0002256:41142-41161 Msa1338550:three_prime_UTR 50.0%
!! CCCAAGCTTAACGGGTGTTT+TGG - tig0002256:41146-41165 None:intergenic 50.0%
AACACCCGTTAAGCTTGGGT+TGG + tig0002256:41147-41166 Msa1338550:three_prime_UTR 50.0%
GTAGTATGTGGCCAGTGGGA+AGG - tig0002256:40604-40623 None:intergenic 55.0%
GTAGTATGTGGCCAGTGGGA+AGG - tig0002256:40604-40623 None:intergenic 55.0%
Chromosome Type Strat End Strand Name
tig0002256 gene 40423 41201 40423 ID=Msa1338550;Name=Msa1338550
tig0002256 mRNA 40423 41201 40423 ID=Msa1338550-mRNA-1;Parent=Msa1338550;Name=Msa1338550-mRNA-1;_AED=0.00;_eAED=0.00;_QI=208|1|1|1|1|1|2|68|110
tig0002256 exon 40423 40867 40423 ID=Msa1338550-mRNA-1:exon:1675;Parent=Msa1338550-mRNA-1
tig0002256 exon 41038 41201 41038 ID=Msa1338550-mRNA-1:exon:1676;Parent=Msa1338550-mRNA-1
tig0002256 five_prime_UTR 40423 40630 40423 ID=Msa1338550-mRNA-1:five_prime_utr;Parent=Msa1338550-mRNA-1
tig0002256 CDS 40631 40867 40631 ID=Msa1338550-mRNA-1:cds;Parent=Msa1338550-mRNA-1
tig0002256 CDS 41038 41133 41038 ID=Msa1338550-mRNA-1:cds;Parent=Msa1338550-mRNA-1
tig0002256 three_prime_UTR 41134 41201 41134 ID=Msa1338550-mRNA-1:three_prime_utr;Parent=Msa1338550-mRNA-1
Gene Sequence

>Msa1338550

ATGGAGTTTCTAATTAAACTCATCGCATTTCTACTCTTAATGCCTACAATCTCTTCCTCCCAATATCATGGAAACAATATACTCACCAATCGTAAAATATTTCCAAAACAAGAAACTCTAACCTCGTACGCTGTCGTCTTTGATGCTGGTAGCACCGGTAGCCGTGTTCATGTCTACCATTTTGATCAAAACTTAGATCTTCTTCACATTGGCAATGATGTTGAGTTTTATAATAAGACAACGCCCGGTTTGAGTGCATACGCAGATAATCCGAAGGAAGCAGCAGAGTCTCTAATTCCACTTTTAGAGCAAGCAGAAAGAGTGTTCCTGTGA
Protein sequence

>Msa1338550

MEFLIKLIAFLLLMPTISSSQYHGNNILTNRKIFPKQETLTSYAVVFDAGSTGSRVHVYHFDQNLDLLHIGNDVEFYNKTTPGLSAYADNPKEAAESLIPLLEQAERVFL*