AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene007971

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene007971.t1 MTR_4g123470 84.416 154 24 0 10 163 71 224 9.52e-97 279
MS.gene007971.t1 MTR_7g113060 78.947 38 8 0 126 163 3 40 8.52e-16 71.6
MS.gene007971.t1 MTR_7g025150 26.531 147 108 0 3 149 61 207 2.68e-12 62.8
MS.gene007971.t1 MTR_4g085790 27.815 151 101 3 3 149 61 207 2.76e-12 62.8
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 32 sgRNAs with CRISPR-Local

Find 39 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TAGGGACTACCTCATACTTT+TGG 0.338565 3.3:+62713944 MS.gene007971:intron
CGATTGTTCTACGAGTTTAG+TGG 0.409935 3.3:+62713657 MS.gene007971:CDS
GTCATGTGTTTATCAACTCT+TGG 0.410006 3.3:-62714182 None:intergenic
ACCTTTGAGGTTCCTATCGT+TGG 0.413727 3.3:+62713807 MS.gene007971:CDS
TCCGAACATCACATTTGGTA+TGG 0.417548 3.3:-62714059 None:intergenic
ATCTACTTCCACCATGGTAC+TGG 0.424919 3.3:-62713698 None:intergenic
CCGAACATCACATTTGGTAT+GGG 0.451435 3.3:-62714058 None:intergenic
AAGAATTTGCCAAAAGTATG+AGG 0.469320 3.3:-62713953 None:intergenic
TGCCGCACTCATTGAATGAT+AGG 0.473193 3.3:-62713769 None:intergenic
CCAAATGTGATGTTCGGAAA+AGG 0.475440 3.3:+62714064 MS.gene007971:CDS
CCCATACCAAATGTGATGTT+CGG 0.477035 3.3:+62714058 MS.gene007971:CDS
CGAACATCACATTTGGTATG+GGG 0.552019 3.3:-62714057 None:intergenic
TCTGTATATTTGAGTCTCAC+AGG 0.555272 3.3:-62714031 None:intergenic
TTGTGTTGCCAATGGTATTG+AGG 0.563081 3.3:+62714099 MS.gene007971:CDS
GTCTCCGGCCTCAATACCAT+TGG 0.575295 3.3:-62714107 None:intergenic
CTCATAACGTCGTTGACAGA+TGG 0.587552 3.3:+62713621 MS.gene007971:CDS
TTTCAAGTGCAAGTGTGTCA+TGG 0.589305 3.3:+62714138 MS.gene007971:CDS
TAACGTCGTTGACAGATGGT+TGG 0.592218 3.3:+62713625 MS.gene007971:CDS
TGACACTTGCTAGATGGTGA+TGG 0.594754 3.3:+62713593 None:intergenic
GTTGCCAATGGTATTGAGGC+CGG 0.597504 3.3:+62714103 MS.gene007971:CDS
ATGTGATGTTCGGAAAAGGT+TGG 0.606400 3.3:+62714068 MS.gene007971:CDS
GACACTTGCTAGATGGTGAT+GGG 0.615365 3.3:+62713594 None:intergenic
GCCGCACTCATTGAATGATA+GGG 0.616026 3.3:-62713768 None:intergenic
TCGATCGACGAAATCACCTA+AGG 0.628108 3.3:+62713833 MS.gene007971:CDS
ACCCTATCATTCAATGAGTG+CGG 0.636716 3.3:+62713767 MS.gene007971:CDS
GTCGATCGATATCCAACGAT+AGG 0.637968 3.3:-62713819 None:intergenic
CACGATTACGTAATGTTGTG+CGG 0.649204 3.3:+62713989 MS.gene007971:CDS
GTCGCTTTCCAGTACCATGG+TGG 0.664216 3.3:+62713690 MS.gene007971:CDS
GCACTCATTGAATGATAGGG+TGG 0.666571 3.3:-62713765 None:intergenic
TCCAACGATAGGAACCTCAA+AGG 0.670850 3.3:-62713808 None:intergenic
ATTGTCGCTTTCCAGTACCA+TGG 0.681766 3.3:+62713687 MS.gene007971:CDS
TTCGAAATCTACTTCCACCA+TGG 0.688810 3.3:-62713704 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! TTAGATATATGCTATAATAA+AGG + chr3.3:62713885-62713904 MS.gene007971:intron 15.0%
!!! ACAGTTTTTTTCTTTTTTTT+AGG + chr3.3:62713925-62713944 MS.gene007971:intron 15.0%
!!! CAGTTTTTTTCTTTTTTTTA+GGG + chr3.3:62713926-62713945 MS.gene007971:intron 15.0%
!! AAAAAACAATAAACAACCTT+AGG - chr3.3:62713852-62713871 None:intergenic 20.0%
! AAGAATTTGCCAAAAGTATG+AGG - chr3.3:62713956-62713975 None:intergenic 30.0%
! ACTTTTGGCAAATTCTTTAG+AGG + chr3.3:62713959-62713978 MS.gene007971:CDS 30.0%
! CTTTTGGCAAATTCTTTAGA+GGG + chr3.3:62713960-62713979 MS.gene007971:CDS 30.0%
!! ATCGTTTTATTGTACCTTTG+AGG + chr3.3:62713794-62713813 MS.gene007971:CDS 30.0%
TCTGTATATTTGAGTCTCAC+AGG - chr3.3:62714034-62714053 None:intergenic 35.0%
! ACGAATTTTTGTGTTGCCAA+TGG + chr3.3:62714091-62714110 MS.gene007971:CDS 35.0%
ACCCTATCATTCAATGAGTG+CGG + chr3.3:62713767-62713786 MS.gene007971:CDS 40.0%
ATGTGATGTTCGGAAAAGGT+TGG + chr3.3:62714068-62714087 MS.gene007971:CDS 40.0%
CACGATTACGTAATGTTGTG+CGG + chr3.3:62713989-62714008 MS.gene007971:CDS 40.0%
CCAAATGTGATGTTCGGAAA+AGG + chr3.3:62714064-62714083 MS.gene007971:CDS 40.0%
CCCATACCAAATGTGATGTT+CGG + chr3.3:62714058-62714077 MS.gene007971:CDS 40.0%
CCGAACATCACATTTGGTAT+GGG - chr3.3:62714061-62714080 None:intergenic 40.0%
CGAACATCACATTTGGTATG+GGG - chr3.3:62714060-62714079 None:intergenic 40.0%
CGATTGTTCTACGAGTTTAG+TGG + chr3.3:62713657-62713676 MS.gene007971:CDS 40.0%
CTTGAAAAACAACACGTCTC+CGG - chr3.3:62714125-62714144 None:intergenic 40.0%
TCCGAACATCACATTTGGTA+TGG - chr3.3:62714062-62714081 None:intergenic 40.0%
TTCGAAATCTACTTCCACCA+TGG - chr3.3:62713707-62713726 None:intergenic 40.0%
TTGTGTTGCCAATGGTATTG+AGG + chr3.3:62714099-62714118 MS.gene007971:CDS 40.0%
! CCTTTTCCGAACATCACATT+TGG - chr3.3:62714067-62714086 None:intergenic 40.0%
! TAGGGACTACCTCATACTTT+TGG + chr3.3:62713944-62713963 MS.gene007971:intron 40.0%
! TTTCAAGTGCAAGTGTGTCA+TGG + chr3.3:62714138-62714157 MS.gene007971:CDS 40.0%
ATCTACTTCCACCATGGTAC+TGG - chr3.3:62713701-62713720 None:intergenic 45.0%
CTCATAACGTCGTTGACAGA+TGG + chr3.3:62713621-62713640 MS.gene007971:CDS 45.0%
GCACTCATTGAATGATAGGG+TGG - chr3.3:62713768-62713787 None:intergenic 45.0%
GCCGCACTCATTGAATGATA+GGG - chr3.3:62713771-62713790 None:intergenic 45.0%
GTCGATCGATATCCAACGAT+AGG - chr3.3:62713822-62713841 None:intergenic 45.0%
TAACGTCGTTGACAGATGGT+TGG + chr3.3:62713625-62713644 MS.gene007971:CDS 45.0%
TCCAACGATAGGAACCTCAA+AGG - chr3.3:62713811-62713830 None:intergenic 45.0%
TCGATCGACGAAATCACCTA+AGG + chr3.3:62713833-62713852 MS.gene007971:CDS 45.0%
TGCCGCACTCATTGAATGAT+AGG - chr3.3:62713772-62713791 None:intergenic 45.0%
!! ACCTTTGAGGTTCCTATCGT+TGG + chr3.3:62713807-62713826 MS.gene007971:CDS 45.0%
!! ATTGTCGCTTTCCAGTACCA+TGG + chr3.3:62713687-62713706 MS.gene007971:CDS 45.0%
! GTTGCCAATGGTATTGAGGC+CGG + chr3.3:62714103-62714122 MS.gene007971:CDS 50.0%
GTCTCCGGCCTCAATACCAT+TGG - chr3.3:62714110-62714129 None:intergenic 55.0%
! GTCGCTTTCCAGTACCATGG+TGG + chr3.3:62713690-62713709 MS.gene007971:CDS 55.0%


Chromosome Type Strat End Strand Name
chr3.3 gene 62713606 62714192 62713606 ID=MS.gene007971
chr3.3 mRNA 62713606 62714192 62713606 ID=MS.gene007971.t1;Parent=MS.gene007971
chr3.3 exon 62713606 62713854 62713606 ID=MS.gene007971.t1.exon1;Parent=MS.gene007971.t1
chr3.3 CDS 62713606 62713854 62713606 ID=cds.MS.gene007971.t1;Parent=MS.gene007971.t1
chr3.3 exon 62713947 62714192 62713947 ID=MS.gene007971.t1.exon2;Parent=MS.gene007971.t1
chr3.3 CDS 62713947 62714192 62713947 ID=cds.MS.gene007971.t1;Parent=MS.gene007971.t1
Gene Sequence

>MS.gene007971

ATGGTGATGGGAATACTCATAACGTCGTTGACAGATGGTTGGAGTGCATTGCGATTGTTCTACGAGTTTAGTGGAAGTAAGATTGTCGCTTTCCAGTACCATGGTGGAAGTAGATTTCGAATCTTTGTTTTTGCTCATAACATTACTCTAGCTGATTATCCACCCTATCATTCAATGAGTGCGGCAACATCGTTTTATTGTACCTTTGAGGTTCCTATCGTTGGATATCGATCGACGAAATCACCTAAGGTTGTTTATTGTTTTTTTGTTGCTATTCAATTAGATATATGCTATAATAAAGGATTTTTGTCTGTCATTAACAGTTTTTTTCTTTTTTTTAGGGACTACCTCATACTTTTGGCAAATTCTTTAGAGGGAAACATCACGATTACGTAATGTTGTGCGGAACTTATGACAGTATCATTCCTGTGAGACTCAAATATACAGACGACCCCATACCAAATGTGATGTTCGGAAAAGGTTGGACGAATTTTTGTGTTGCCAATGGTATTGAGGCCGGAGACGTGTTGTTTTTCAAGTGCAAGTGTGTCATGGACAAAAAATATGTTATCGTATCCAAGAGTTGA
Protein sequence

>MS.gene007971.t1

MVMGILITSLTDGWSALRLFYEFSGSKIVAFQYHGGSRFRIFVFAHNITLADYPPYHSMSAATSFYCTFEVPIVGYRSTKSPKGLPHTFGKFFRGKHHDYVMLCGTYDSIIPVRLKYTDDPIPNVMFGKGWTNFCVANGIEAGDVLFFKCKCVMDKKYVIVSKS