AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar ZhongmuNo.1 / MsG0480023406.01


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MsG0480023406.01.T02 MTR_8g092340 86.441 59 7 1 1 58 19 77 7.26e-31 102
MsG0480023406.01.T02 MTR_3g095180 50.000 64 25 2 2 58 22 85 5.89e-12 55.1
MsG0480023406.01.T01 MTR_8g092340 92.308 78 4 2 1 77 1 77 1.55e-46 143
MsG0480023406.01.T01 MTR_3g095180 49.412 85 35 3 1 77 1 85 6.24e-19 73.6
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 18 sgRNAs with CRISPR-Local

Find 21 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TCTAACATGATTTATATATA+TGG 0.255031 4:+84782008 MsG0480023406.01.T01:intron
ATCGGTGGCTTCCTTCTTGC+TGG 0.286574 4:-84782158 None:intergenic
TAAGGTAGATCATATGTTTA+AGG 0.311443 4:+84782085 MsG0480023406.01.T01:CDS
AATGAGTAATACTCATAATA+AGG 0.356818 4:+84782067 MsG0480023406.01.T01:CDS
AAAAGTCGAATTATTTAAGA+TGG 0.436642 4:+84781793 MsG0480023406.01.T01:exon
ACAATATTTCAATTGTGAAT+CGG 0.450645 4:-84782176 None:intergenic
ATAACTTAATACCTCTAGCT+TGG 0.497100 4:-84781877 None:intergenic
TAACTTAATACCTCTAGCTT+GGG 0.523329 4:-84781876 None:intergenic
GAAGGAATAGAACCACTACT+AGG 0.529646 4:-84781838 None:intergenic
GGCAAAAGAAGAACATAATG+TGG 0.544421 4:+84782106 MsG0480023406.01.T01:CDS
AAACAAACGTTTCCTAGTAG+TGG 0.554374 4:+84781826 MsG0480023406.01.T01:CDS
TGGTGCAGCACGAACTCTGA+AGG 0.582207 4:+84782028 MsG0480023406.01.T01:intron
ATATTTCAATTGTGAATCGG+TGG 0.587562 4:-84782173 None:intergenic
TGGATTACACTCCAGCAAGA+AGG 0.596499 4:+84782147 MsG0480023406.01.T01:CDS
GCAAAAGAAGAACATAATGT+GGG 0.604097 4:+84782107 MsG0480023406.01.T01:CDS
GGGTAGATATGAAACAGAGA+AGG 0.633587 4:-84781856 None:intergenic
TTCATATCTACCCAAGCTAG+AGG 0.668712 4:+84781866 MsG0480023406.01.T01:CDS
ATACATATTGATATGATACA+CGG 0.690316 4:+84782319 MsG0480023406.01.T01:three_prime_UTR

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! GATTATGATTTTATTAAAAA+AGG - Chr4:84781957-84781976 None:intergenic 10.0%
!! GATTATGTTCTTAATTATAT+TGG + Chr4:84781905-84781924 MsG0480023406.01.T01:intron 15.0%
!! TCTAACATGATTTATATATA+TGG + Chr4:84782008-84782027 MsG0480023406.01.T01:intron 15.0%
!! AAAAGTCGAATTATTTAAGA+TGG + Chr4:84781793-84781812 MsG0480023406.01.T01:exon 20.0%
!! AATGAGTAATACTCATAATA+AGG + Chr4:84782067-84782086 MsG0480023406.01.T01:CDS 20.0%
!! ACAATATTTCAATTGTGAAT+CGG - Chr4:84782179-84782198 None:intergenic 20.0%
!! ATACATATTGATATGATACA+CGG + Chr4:84782319-84782338 MsG0480023406.01.T01:three_prime_UTR 20.0%
! TAAGGTAGATCATATGTTTA+AGG + Chr4:84782085-84782104 MsG0480023406.01.T01:CDS 25.0%
ATAACTTAATACCTCTAGCT+TGG - Chr4:84781880-84781899 None:intergenic 30.0%
ATATTTCAATTGTGAATCGG+TGG - Chr4:84782176-84782195 None:intergenic 30.0%
GCAAAAGAAGAACATAATGT+GGG + Chr4:84782107-84782126 MsG0480023406.01.T01:CDS 30.0%
! TAACTTAATACCTCTAGCTT+GGG - Chr4:84781879-84781898 None:intergenic 30.0%
AAACAAACGTTTCCTAGTAG+TGG + Chr4:84781826-84781845 MsG0480023406.01.T01:CDS 35.0%
GGCAAAAGAAGAACATAATG+TGG + Chr4:84782106-84782125 MsG0480023406.01.T01:CDS 35.0%
!! GGGAGATGAAGTATTTTCAA+TGG + Chr4:84782127-84782146 MsG0480023406.01.T01:CDS 35.0%
GAAGGAATAGAACCACTACT+AGG - Chr4:84781841-84781860 None:intergenic 40.0%
GGGTAGATATGAAACAGAGA+AGG - Chr4:84781859-84781878 None:intergenic 40.0%
TTCATATCTACCCAAGCTAG+AGG + Chr4:84781866-84781885 MsG0480023406.01.T01:CDS 40.0%
TGGATTACACTCCAGCAAGA+AGG + Chr4:84782147-84782166 MsG0480023406.01.T01:CDS 45.0%
ATCGGTGGCTTCCTTCTTGC+TGG - Chr4:84782161-84782180 None:intergenic 55.0%
TGGTGCAGCACGAACTCTGA+AGG + Chr4:84782028-84782047 MsG0480023406.01.T01:intron 55.0%
Chromosome Type Strat End Strand Name
Chr4 gene 84781725 84782362 84781725 ID=MsG0480023406.01;Name=MsG0480023406.01
Chr4 mRNA 84781725 84782362 84781725 ID=MsG0480023406.01.T01;Parent=MsG0480023406.01;Name=MsG0480023406.01.T01;_AED=0.18;_eAED=0.18;_QI=87|0|0.5|1|0|0|2|172|77
Chr4 exon 84781725 84781887 84781725 ID=MsG0480023406.01.T01:exon:5704;Parent=MsG0480023406.01.T01
Chr4 exon 84782033 84782362 84782033 ID=MsG0480023406.01.T01:exon:5705;Parent=MsG0480023406.01.T01
Chr4 five_prime_UTR 84781725 84781811 84781725 ID=MsG0480023406.01.T01:five_prime_utr;Parent=MsG0480023406.01.T01
Chr4 CDS 84781812 84781887 84781812 ID=MsG0480023406.01.T01:cds;Parent=MsG0480023406.01.T01
Chr4 CDS 84782033 84782190 84782033 ID=MsG0480023406.01.T01:cds;Parent=MsG0480023406.01.T01
Chr4 three_prime_UTR 84782191 84782362 84782191 ID=MsG0480023406.01.T01:three_prime_utr;Parent=MsG0480023406.01.T01
Chr4 mRNA 84782014 84782190 84782014 ID=MsG0480023406.01.T02;Parent=MsG0480023406.01;Name=MsG0480023406.01.T02;_AED=0.38;_eAED=0.38;_QI=0|-1|0|1|-1|0|1|0|58
Chr4 exon 84782014 84782190 84782014 ID=MsG0480023406.01.T02:exon:5706;Parent=MsG0480023406.01.T02
Chr4 CDS 84782014 84782190 84782014 ID=MsG0480023406.01.T02:cds;Parent=MsG0480023406.01.T02
Gene Sequence

>MsG0480023406.01.T02

ATGATTTATATATATGGTGCAGCACGAACTCTGAAGGAAAAAAGCAATGATGTAATGAGTAATACTCATAATAAGGTAGATCATATGTTTAAGGCAAAAGAAGAACATAATGTGGGAGATGAAGTATTTTCAATGGATTACACTCCAGCAAGAAGGAAGCCACCGATTCACAATTGA

>MsG0480023406.01.T01

ATGGCTATTGCACAAAACAAACGTTTCCTAGTAGTGGTTCTATTCCTTCTCTGTTTCATATCTACCCAAGCTAGAGCAGCACGAACTCTGAAGGAAAAAAGCAATGATGTAATGAGTAATACTCATAATAAGGTAGATCATATGTTTAAGGCAAAAGAAGAACATAATGTGGGAGATGAAGTATTTTCAATGGATTACACTCCAGCAAGAAGGAAGCCACCGATTCACAATTGA

Protein sequence

>MsG0480023406.01.T02

MIYIYGAARTLKEKSNDVMSNTHNKVDHMFKAKEEHNVGDEVFSMDYTPARRKPPIHN*

>MsG0480023406.01.T01

MAIAQNKRFLVVVLFLLCFISTQARAARTLKEKSNDVMSNTHNKVDHMFKAKEEHNVGDEVFSMDYTPARRKPPIHN*