AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar ZhongmuNo.1 / MsG0480023723.01


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MsG0480023723.01.T01 MTR_8g099885 83.505 97 2 1 1 97 649 731 1.29e-48 164
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MsG0480023723.01.T01 AT1G55090 50.000 100 24 3 1 97 649 725 1.79e-22 90.5

Find 41 sgRNAs with CRISPR-Local

Find 55 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GTTGAATGTGGTTGTTTAAA+AGG 0.218262 4:+89014909 None:intergenic
ATCTTGCATTATAAAGAAAT+TGG 0.239593 4:+89015709 None:intergenic
GTTATTCACCAGAGGATAAT+AGG 0.260783 4:-89015743 MsG0480023723.01.T01:CDS
CACCGACTCATTTAGTTTAG+AGG 0.270557 4:-89015079 MsG0480023723.01.T01:three_prime_UTR
TTCAATTAGATTCCGACATT+TGG 0.271951 4:+89015543 None:intergenic
GGAATCTATATATATTTGTT+TGG 0.277682 4:+89015451 None:intergenic
CAAGATGGCCGTATCAATTT+CGG 0.328849 4:-89015692 MsG0480023723.01.T01:CDS
GGAGTTGCTGCCGCAGGTTC+AGG 0.335423 4:-89015570 MsG0480023723.01.T01:CDS
GAATCTATATATATTTGTTT+GGG 0.357101 4:+89015452 None:intergenic
CATGTGCAAGACTGCAAATC+TGG 0.364062 4:-89015475 MsG0480023723.01.T01:three_prime_UTR
AGTTCTTATGATTTAAAGTC+AGG 0.396488 4:-89015889 MsG0480023723.01.T01:CDS
CTATAACAAACTGAACTTGT+TGG 0.398444 4:-89015272 MsG0480023723.01.T01:three_prime_UTR
ACTACATACCTCAGCATGAT+AGG 0.404154 4:+89015909 None:intergenic
TTAGATGGTGTTGGTGGAAT+GGG 0.436891 4:-89015591 MsG0480023723.01.T01:CDS
TCAGTGGCATCTTCATTAGA+TGG 0.470114 4:-89015606 MsG0480023723.01.T01:CDS
CGATGAACTCGTACATGAGC+TGG 0.481111 4:-89015664 MsG0480023723.01.T01:CDS
TAGTAATCATACACAACGTC+TGG 0.485318 4:+89015147 None:intergenic
TACACTACACATGGGATGAA+AGG 0.491139 4:+89015392 None:intergenic
ACACTACACATGGGATGAAA+GGG 0.496650 4:+89015393 None:intergenic
ATTAGATGGTGTTGGTGGAA+TGG 0.513323 4:-89015592 MsG0480023723.01.T01:CDS
AATTTCTTTATAATGCAAGA+TGG 0.525324 4:-89015707 MsG0480023723.01.T01:CDS
GACTAAGTTTAAGTTGAATG+TGG 0.544570 4:+89014897 None:intergenic
AGATCAAACCTATTATCCTC+TGG 0.548297 4:+89015735 None:intergenic
GCATCTTCATTAGATGGTGT+TGG 0.549571 4:-89015600 MsG0480023723.01.T01:CDS
TCTTCATTAGATGGTGTTGG+TGG 0.558046 4:-89015597 MsG0480023723.01.T01:CDS
CTCTAAACTAAATGAGTCGG+TGG 0.562499 4:+89015080 None:intergenic
AGATGACGATGCAATATGAA+AGG 0.565960 4:-89015317 MsG0480023723.01.T01:three_prime_UTR
GTTCTTATGATTTAAAGTCA+GGG 0.568915 4:-89015888 MsG0480023723.01.T01:CDS
ATGAAGATGCCACTGACTCA+TGG 0.574225 4:+89015613 None:intergenic
ATTTGGATTGCCTGAACCTG+CGG 0.574902 4:+89015560 None:intergenic
GGAATGGGAGTTGCTGCCGC+AGG 0.585359 4:-89015576 MsG0480023723.01.T01:CDS
CATACCTCAGCATGATAGGA+AGG 0.586185 4:+89015913 None:intergenic
AGAGAAATAGAACAATGAGT+AGG 0.593110 4:+89014972 None:intergenic
ATCCTCTAAACTAAATGAGT+CGG 0.595099 4:+89015077 None:intergenic
ATCAGCAAACCATGAGTCAG+TGG 0.626159 4:-89015622 MsG0480023723.01.T01:CDS
GGTTCAGGCAATCCAAATGT+CGG 0.627370 4:-89015555 MsG0480023723.01.T01:CDS
CTTGCAGAGTTATTCACCAG+AGG 0.641776 4:-89015751 MsG0480023723.01.T01:intron
GACACCTTCCTATCATGCTG+AGG 0.642869 4:-89015917 MsG0480023723.01.T01:CDS
AGCATGATAGGAAGGTGTCA+AGG 0.654248 4:+89015921 None:intergenic
AAAGTCAGGGTTGAATTGCG+AGG 0.669268 4:-89015875 MsG0480023723.01.T01:intron
ATGATAGGAAGGTGTCAAGG+TGG 0.706059 4:+89015924 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! TACTTTATTTTGTTTTATTA+GGG + Chr4:89015271-89015290 None:intergenic 10.0%
!!! TTACTTTATTTTGTTTTATT+AGG + Chr4:89015272-89015291 None:intergenic 10.0%
!! GAATCTATATATATTTGTTT+GGG + Chr4:89015330-89015349 None:intergenic 15.0%
!!! ACTTTATTTTGTTTTATTAG+GGG + Chr4:89015270-89015289 None:intergenic 15.0%
!! AATTTCTTTATAATGCAAGA+TGG - Chr4:89015072-89015091 MsG0480023723.01.T01:three_prime_UTR 20.0%
!! ATCTTGCATTATAAAGAAAT+TGG + Chr4:89015073-89015092 None:intergenic 20.0%
!! GGAATCTATATATATTTGTT+TGG + Chr4:89015331-89015350 None:intergenic 20.0%
!!! GTCTTATGCTAAAAATTTTA+TGG - Chr4:89015543-89015562 MsG0480023723.01.T01:exon 20.0%
! CATAGTGTGCTATAAAAATA+TGG + Chr4:89015352-89015371 None:intergenic 25.0%
!! AAAATGTTTTACACTACACA+TGG + Chr4:89015399-89015418 None:intergenic 25.0%
!! AAATGTTTTACACTACACAT+GGG + Chr4:89015398-89015417 None:intergenic 25.0%
!! AGTTCTTATGATTTAAAGTC+AGG - Chr4:89014890-89014909 MsG0480023723.01.T01:three_prime_UTR 25.0%
!! GTTCTTATGATTTAAAGTCA+GGG - Chr4:89014891-89014910 MsG0480023723.01.T01:three_prime_UTR 25.0%
!! TGCTAAAAATTTTATGGTGA+AGG - Chr4:89015549-89015568 MsG0480023723.01.T01:CDS 25.0%
!!! TTATTTTGTTTTATTAGGGG+AGG + Chr4:89015267-89015286 None:intergenic 25.0%
AGAGAAATAGAACAATGAGT+AGG + Chr4:89015810-89015829 None:intergenic 30.0%
ATCCTCTAAACTAAATGAGT+CGG + Chr4:89015705-89015724 None:intergenic 30.0%
CTATAACAAACTGAACTTGT+TGG - Chr4:89015507-89015526 MsG0480023723.01.T01:three_prime_UTR 30.0%
GTTGAATGTGGTTGTTTAAA+AGG + Chr4:89015873-89015892 None:intergenic 30.0%
TTCAATTAGATTCCGACATT+TGG + Chr4:89015239-89015258 None:intergenic 30.0%
! TCGATTTTCCGAAATTGATA+CGG + Chr4:89015098-89015117 None:intergenic 30.0%
!! GACTAAGTTTAAGTTGAATG+TGG + Chr4:89015885-89015904 None:intergenic 30.0%
AGATCAAACCTATTATCCTC+TGG + Chr4:89015047-89015066 None:intergenic 35.0%
AGATGACGATGCAATATGAA+AGG - Chr4:89015462-89015481 MsG0480023723.01.T01:three_prime_UTR 35.0%
GTTATTCACCAGAGGATAAT+AGG - Chr4:89015036-89015055 MsG0480023723.01.T01:three_prime_UTR 35.0%
TAGTAATCATACACAACGTC+TGG + Chr4:89015635-89015654 None:intergenic 35.0%
! ATTCACGCTCCTAAAGATTT+TGG - Chr4:89014932-89014951 MsG0480023723.01.T01:three_prime_UTR 35.0%
ACACTACACATGGGATGAAA+GGG + Chr4:89015389-89015408 None:intergenic 40.0%
ACTACATACCTCAGCATGAT+AGG + Chr4:89014873-89014892 None:intergenic 40.0%
CAAGATGGCCGTATCAATTT+CGG - Chr4:89015087-89015106 MsG0480023723.01.T01:three_prime_UTR 40.0%
CTCTAAACTAAATGAGTCGG+TGG + Chr4:89015702-89015721 None:intergenic 40.0%
GCATCTTCATTAGATGGTGT+TGG - Chr4:89015179-89015198 MsG0480023723.01.T01:three_prime_UTR 40.0%
TACACTACACATGGGATGAA+AGG + Chr4:89015390-89015409 None:intergenic 40.0%
TCAGTGGCATCTTCATTAGA+TGG - Chr4:89015173-89015192 MsG0480023723.01.T01:three_prime_UTR 40.0%
! TCTTCATTAGATGGTGTTGG+TGG - Chr4:89015182-89015201 MsG0480023723.01.T01:three_prime_UTR 40.0%
!! ATTAGATGGTGTTGGTGGAA+TGG - Chr4:89015187-89015206 MsG0480023723.01.T01:three_prime_UTR 40.0%
!! CACCGACTCATTTAGTTTAG+AGG - Chr4:89015700-89015719 MsG0480023723.01.T01:CDS 40.0%
!! TTAGATGGTGTTGGTGGAAT+GGG - Chr4:89015188-89015207 MsG0480023723.01.T01:three_prime_UTR 40.0%
AAAGTCAGGGTTGAATTGCG+AGG - Chr4:89014904-89014923 MsG0480023723.01.T01:three_prime_UTR 45.0%
ATCAGCAAACCATGAGTCAG+TGG - Chr4:89015157-89015176 MsG0480023723.01.T01:three_prime_UTR 45.0%
ATTTGGATTGCCTGAACCTG+CGG + Chr4:89015222-89015241 None:intergenic 45.0%
CATACCTCAGCATGATAGGA+AGG + Chr4:89014869-89014888 None:intergenic 45.0%
CATGTGCAAGACTGCAAATC+TGG - Chr4:89015304-89015323 MsG0480023723.01.T01:three_prime_UTR 45.0%
CTTGCAGAGTTATTCACCAG+AGG - Chr4:89015028-89015047 MsG0480023723.01.T01:three_prime_UTR 45.0%
GAGAACCGGCCAAAATCTTT+AGG + Chr4:89014944-89014963 None:intergenic 45.0%
GGTTCAGGCAATCCAAATGT+CGG - Chr4:89015224-89015243 MsG0480023723.01.T01:three_prime_UTR 45.0%
!! ACGCTCCTAAAGATTTTGGC+CGG - Chr4:89014936-89014955 MsG0480023723.01.T01:three_prime_UTR 45.0%
!! AGCATGATAGGAAGGTGTCA+AGG + Chr4:89014861-89014880 None:intergenic 45.0%
!! ATGAAGATGCCACTGACTCA+TGG + Chr4:89015169-89015188 None:intergenic 45.0%
!! ATGATAGGAAGGTGTCAAGG+TGG + Chr4:89014858-89014877 None:intergenic 45.0%
CGATGAACTCGTACATGAGC+TGG - Chr4:89015115-89015134 MsG0480023723.01.T01:three_prime_UTR 50.0%
GACACCTTCCTATCATGCTG+AGG - Chr4:89014862-89014881 MsG0480023723.01.T01:three_prime_UTR 50.0%
GAGAGAGAGAGAGAGAGAAC+CGG + Chr4:89014958-89014977 None:intergenic 50.0%
GGAATGGGAGTTGCTGCCGC+AGG - Chr4:89015203-89015222 MsG0480023723.01.T01:three_prime_UTR 65.0%
GGAGTTGCTGCCGCAGGTTC+AGG - Chr4:89015209-89015228 MsG0480023723.01.T01:three_prime_UTR 65.0%
Chromosome Type Strat End Strand Name
Chr4 gene 89014851 89015950 89014851 ID=MsG0480023723.01;Name=MsG0480023723.01
Chr4 mRNA 89014851 89015950 89014851 ID=MsG0480023723.01.T01;Parent=MsG0480023723.01;Name=MsG0480023723.01.T01;_AED=0.49;_eAED=0.50;_QI=0|0|0.5|1|1|1|2|697|97
Chr4 exon 89014851 89015766 89014851 ID=MsG0480023723.01.T01:exon:25216;Parent=MsG0480023723.01.T01
Chr4 exon 89015876 89015950 89015876 ID=MsG0480023723.01.T01:exon:25215;Parent=MsG0480023723.01.T01
Chr4 CDS 89015876 89015950 89015876 ID=MsG0480023723.01.T01:cds;Parent=MsG0480023723.01.T01
Chr4 CDS 89015548 89015766 89015548 ID=MsG0480023723.01.T01:cds;Parent=MsG0480023723.01.T01
Chr4 three_prime_UTR 89014851 89015547 89014851 ID=MsG0480023723.01.T01:three_prime_utr;Parent=MsG0480023723.01.T01
Gene Sequence

>MsG0480023723.01.T01

ATGACCACCTTGACACCTTCCTATCATGCTGAGGTATGTAGTTCTTATGATTTAAAGTCAGGGTTGAATTGCGAGAGTTATTCACCAGAGGATAATAGGTTTGATCTTCGCCAATTTCTTTATAATGCAAGATGGCCGTATCAATTTCGGAAAATCGATGAACTCGTACATGAGCTGGATGTCAAAGATGTTCAAGAATCAGCAAACCATGAGTCAGTGGCATCTTCATTAGATGGTGTTGGTGGAATGGGAGTTGCTGCCGCAGGTTCAGGCAATCCAAATGTCGGAATCTAA

Protein sequence

>MsG0480023723.01.T01

MTTLTPSYHAEVCSSYDLKSGLNCESYSPEDNRFDLRQFLYNARWPYQFRKIDELVHELDVKDVQESANHESVASSLDGVGGMGVAAAGSGNPNVGI*