AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene99879

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene99879.t1 MTR_4g123470 83.766 154 25 0 10 163 71 224 7.61e-95 274
MS.gene99879.t1 MTR_7g113060 81.579 38 7 0 126 163 3 40 2.04e-16 73.2
MS.gene99879.t1 MTR_7g025150 25.850 147 109 0 3 149 61 207 8.28e-11 58.5
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 31 sgRNAs with CRISPR-Local

Find 38 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TAGGGACTACCTCATACTTT+TGG 0.338565 3.2:+65189801 MS.gene99879:intron
CGATTGTTCTACGAGTTTAG+TGG 0.409935 3.2:+65189513 MS.gene99879:CDS
GTCATGTGTTTATCAACTCT+TGG 0.410006 3.2:-65190039 None:intergenic
ACCTTTGAGGTTCCTATCGT+TGG 0.413727 3.2:+65189663 MS.gene99879:CDS
TCCGAACATCACATTTGGTA+TGG 0.417548 3.2:-65189916 None:intergenic
ATCTACTTCCACCATGGTAC+TGG 0.424919 3.2:-65189554 None:intergenic
CTCATAACGTCGTTGACATA+TGG 0.440715 3.2:+65189477 MS.gene99879:CDS
CCGAACATCACATTTGGTAT+GGG 0.451435 3.2:-65189915 None:intergenic
AAGAATTTGCCAAAAGTATG+AGG 0.469320 3.2:-65189810 None:intergenic
TGCCGCACTCATTGAATGAT+AGG 0.473193 3.2:-65189625 None:intergenic
CCAAATGTGATGTTCGGAAA+AGG 0.475440 3.2:+65189921 MS.gene99879:CDS
CCCATACCAAATGTGATGTT+CGG 0.477035 3.2:+65189915 MS.gene99879:CDS
TTGTGTTGCCAATGGTATTG+AGG 0.514824 3.2:+65189956 MS.gene99879:CDS
CGAACATCACATTTGGTATG+GGG 0.552019 3.2:-65189914 None:intergenic
TCTGTATATTTGAGTCTCAC+AGG 0.555272 3.2:-65189888 None:intergenic
GTCTCCGGCCTCAATACCAT+TGG 0.575295 3.2:-65189964 None:intergenic
TTTCAAGTGCAAGTGCGTCA+TGG 0.580469 3.2:+65189995 MS.gene99879:CDS
TAACGTCGTTGACATATGGT+TGG 0.586271 3.2:+65189481 MS.gene99879:CDS
TGACACTTGCTAGATGGTGA+TGG 0.594754 3.2:+65189449 None:intergenic
GTTGCCAATGGTATTGAGGC+CGG 0.597504 3.2:+65189960 MS.gene99879:CDS
ATGTGATGTTCGGAAAAGGT+TGG 0.606400 3.2:+65189925 MS.gene99879:CDS
GACACTTGCTAGATGGTGAT+GGG 0.615365 3.2:+65189450 None:intergenic
GCCGCACTCATTGAATGATA+GGG 0.616026 3.2:-65189624 None:intergenic
TCGATCGACGAAATCACCTA+AGG 0.628108 3.2:+65189689 MS.gene99879:CDS
ACCCTATCATTCAATGAGTG+CGG 0.636716 3.2:+65189623 MS.gene99879:CDS
GTCGATCGATATCCAACGAT+AGG 0.637968 3.2:-65189675 None:intergenic
GTCGCTTTCCAGTACCATGG+TGG 0.664216 3.2:+65189546 MS.gene99879:CDS
GCACTCATTGAATGATAGGG+TGG 0.666571 3.2:-65189621 None:intergenic
TCCAACGATAGGAACCTCAA+AGG 0.670850 3.2:-65189664 None:intergenic
ATTGTCGCTTTCCAGTACCA+TGG 0.681766 3.2:+65189543 MS.gene99879:CDS
TTCGAAATCTACTTCCACCA+TGG 0.688810 3.2:-65189560 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! AGTTTTTTTCTTTTTTTTTA+GGG + chr3.2:65189783-65189802 MS.gene99879:intron 10.0%
!! TTAGATATATGCTATAATAA+AGG + chr3.2:65189741-65189760 MS.gene99879:intron 15.0%
!!! CAGTTTTTTTCTTTTTTTTT+AGG + chr3.2:65189782-65189801 MS.gene99879:intron 15.0%
!! AAAAAACAATAAACAACCTT+AGG - chr3.2:65189708-65189727 None:intergenic 20.0%
! AAGAATTTGCCAAAAGTATG+AGG - chr3.2:65189813-65189832 None:intergenic 30.0%
! ACTTTTGGCAAATTCTTTAG+AGG + chr3.2:65189816-65189835 MS.gene99879:CDS 30.0%
! CTTTTGGCAAATTCTTTAGA+GGG + chr3.2:65189817-65189836 MS.gene99879:CDS 30.0%
!! ATCGTTTTATTGTACCTTTG+AGG + chr3.2:65189650-65189669 MS.gene99879:CDS 30.0%
TCTGTATATTTGAGTCTCAC+AGG - chr3.2:65189891-65189910 None:intergenic 35.0%
ACCCTATCATTCAATGAGTG+CGG + chr3.2:65189623-65189642 MS.gene99879:CDS 40.0%
ATGTGATGTTCGGAAAAGGT+TGG + chr3.2:65189925-65189944 MS.gene99879:CDS 40.0%
CCAAATGTGATGTTCGGAAA+AGG + chr3.2:65189921-65189940 MS.gene99879:CDS 40.0%
CCCATACCAAATGTGATGTT+CGG + chr3.2:65189915-65189934 MS.gene99879:CDS 40.0%
CCGAACATCACATTTGGTAT+GGG - chr3.2:65189918-65189937 None:intergenic 40.0%
CGAACATCACATTTGGTATG+GGG - chr3.2:65189917-65189936 None:intergenic 40.0%
CGATTGTTCTACGAGTTTAG+TGG + chr3.2:65189513-65189532 MS.gene99879:CDS 40.0%
CTCATAACGTCGTTGACATA+TGG + chr3.2:65189477-65189496 MS.gene99879:CDS 40.0%
CTTGAAAAACAACACGTCTC+CGG - chr3.2:65189982-65190001 None:intergenic 40.0%
TAACGTCGTTGACATATGGT+TGG + chr3.2:65189481-65189500 MS.gene99879:CDS 40.0%
TCCGAACATCACATTTGGTA+TGG - chr3.2:65189919-65189938 None:intergenic 40.0%
TTCGAAATCTACTTCCACCA+TGG - chr3.2:65189563-65189582 None:intergenic 40.0%
TTGTGTTGCCAATGGTATTG+AGG + chr3.2:65189956-65189975 MS.gene99879:CDS 40.0%
! ACGAGTTTTTGTGTTGCCAA+TGG + chr3.2:65189948-65189967 MS.gene99879:CDS 40.0%
! CCTTTTCCGAACATCACATT+TGG - chr3.2:65189924-65189943 None:intergenic 40.0%
! TAGGGACTACCTCATACTTT+TGG + chr3.2:65189801-65189820 MS.gene99879:intron 40.0%
ATCTACTTCCACCATGGTAC+TGG - chr3.2:65189557-65189576 None:intergenic 45.0%
GCACTCATTGAATGATAGGG+TGG - chr3.2:65189624-65189643 None:intergenic 45.0%
GCCGCACTCATTGAATGATA+GGG - chr3.2:65189627-65189646 None:intergenic 45.0%
GTCGATCGATATCCAACGAT+AGG - chr3.2:65189678-65189697 None:intergenic 45.0%
TCCAACGATAGGAACCTCAA+AGG - chr3.2:65189667-65189686 None:intergenic 45.0%
TCGATCGACGAAATCACCTA+AGG + chr3.2:65189689-65189708 MS.gene99879:CDS 45.0%
TGCCGCACTCATTGAATGAT+AGG - chr3.2:65189628-65189647 None:intergenic 45.0%
! TTTCAAGTGCAAGTGCGTCA+TGG + chr3.2:65189995-65190014 MS.gene99879:CDS 45.0%
!! ACCTTTGAGGTTCCTATCGT+TGG + chr3.2:65189663-65189682 MS.gene99879:CDS 45.0%
!! ATTGTCGCTTTCCAGTACCA+TGG + chr3.2:65189543-65189562 MS.gene99879:CDS 45.0%
! GTTGCCAATGGTATTGAGGC+CGG + chr3.2:65189960-65189979 MS.gene99879:CDS 50.0%
GTCTCCGGCCTCAATACCAT+TGG - chr3.2:65189967-65189986 None:intergenic 55.0%
! GTCGCTTTCCAGTACCATGG+TGG + chr3.2:65189546-65189565 MS.gene99879:CDS 55.0%


Chromosome Type Strat End Strand Name
chr3.2 gene 65189462 65190049 65189462 ID=MS.gene99879
chr3.2 mRNA 65189462 65190049 65189462 ID=MS.gene99879.t1;Parent=MS.gene99879
chr3.2 exon 65189462 65189710 65189462 ID=MS.gene99879.t1.exon1;Parent=MS.gene99879.t1
chr3.2 CDS 65189462 65189710 65189462 ID=cds.MS.gene99879.t1;Parent=MS.gene99879.t1
chr3.2 exon 65189804 65190049 65189804 ID=MS.gene99879.t1.exon2;Parent=MS.gene99879.t1
chr3.2 CDS 65189804 65190049 65189804 ID=cds.MS.gene99879.t1;Parent=MS.gene99879.t1
Gene Sequence

>MS.gene99879

ATGGTGATGGGAATACTCATAACGTCGTTGACATATGGTTGGAGTGCATTGCGATTGTTCTACGAGTTTAGTGGAAGTAAGATTGTCGCTTTCCAGTACCATGGTGGAAGTAGATTTCGAATCTTTGTTTTTGCTCATAACATTACTCTAGCTGATTATCCACCCTATCATTCAATGAGTGCGGCAACATCGTTTTATTGTACCTTTGAGGTTCCTATCGTTGGATATCGATCGACGAAATCACCTAAGGTTGTTTATTGTTTTTTTGTTGCTATTCAATTAGATATATGCTATAATAAAGGATTTTTGTCTGTCATTAACAGTTTTTTTCTTTTTTTTTAGGGACTACCTCATACTTTTGGCAAATTCTTTAGAGGGAAACATCACGATTACGTAATGTTGTGCAGAACTTATGACAGTATCATTCCTGTGAGACTCAAATATACAGACGACCCCATACCAAATGTGATGTTCGGAAAAGGTTGGACGAGTTTTTGTGTTGCCAATGGTATTGAGGCCGGAGACGTGTTGTTTTTCAAGTGCAAGTGCGTCATGGACAAAAAATATGTTATCGTATCCAAGAGTTGA
Protein sequence

>MS.gene99879.t1

MVMGILITSLTYGWSALRLFYEFSGSKIVAFQYHGGSRFRIFVFAHNITLADYPPYHSMSAATSFYCTFEVPIVGYRSTKSPKGLPHTFGKFFRGKHHDYVMLCRTYDSIIPVRLKYTDDPIPNVMFGKGWTSFCVANGIEAGDVLFFKCKCVMDKKYVIVSKS