AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene048906

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene048906.t1 MTR_8g099245 98.413 63 1 0 1 63 13 75 5.20e-37 118
MS.gene048906.t1 MTR_3g090830 70.270 37 11 0 19 55 27 63 5.29e-14 60.1
MS.gene048906.t1 MTR_6g086390 50.943 53 26 0 3 55 12 64 1.50e-12 56.2
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene048906.t1 AT3G61640 64.062 64 20 2 1 62 7 69 4.37e-19 73.2
MS.gene048906.t1 AT2G46330 73.333 45 12 0 19 63 26 70 1.41e-18 71.6
MS.gene048906.t1 AT5G53250 65.789 38 13 0 18 55 26 63 1.13e-13 59.3

Find 17 sgRNAs with CRISPR-Local

Find 48 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
AGCTTATTTGTTGATGTTGT+TGG 0.350496 4.2:+4709994 MS.gene048906:CDS
GTTTGAGCTTGAACAGCGGC+AGG 0.459763 4.2:-4709112 None:intergenic
TTTGTTGATGTTGTTGGCGC+TGG 0.487327 4.2:+4710000 MS.gene048906:CDS
AGAGAGAAAGTTACCGTCGC+TGG 0.490610 4.2:-4709158 None:intergenic
TGTAATGTGTTCAGGGTCAT+CGG 0.501208 4.2:+4709958 MS.gene048906:intron
TCGCTGGTAGGAGAAGGTGC+AGG 0.512007 4.2:-4709142 None:intergenic
CGCTGGTAGGAGAAGGTGCA+GGG 0.523424 4.2:-4709141 None:intergenic
AACAGCGGCAGGGAACGAAA+TGG 0.538815 4.2:-4709101 None:intergenic
TCAGGGTCATCGGTTGATCA+AGG 0.556824 4.2:+4709968 MS.gene048906:intron
ACTCACGTACATCATTCATT+CGG 0.558338 4.2:+4710024 MS.gene048906:CDS
TTACCGTCGCTGGTAGGAGA+AGG 0.584470 4.2:-4709148 None:intergenic
AGAAAGTTACCGTCGCTGGT+AGG 0.586425 4.2:-4709154 None:intergenic
TTTGAGCTTGAACAGCGGCA+GGG 0.641146 4.2:-4709111 None:intergenic
AAGAGTTTGAGCTTGAACAG+CGG 0.647341 4.2:-4709116 None:intergenic
CGAAATGGCGAAAATGAGAG+TGG 0.649027 4.2:-4709086 None:intergenic
GCACCTTCTCCTACCAGCGA+CGG 0.671933 4.2:+4709145 MS.gene048906:CDS
GCTGGTAGGAGAAGGTGCAG+GGG 0.704099 4.2:-4709140 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AAGAAATTCAAATTAGAAAA+TGG - chr4.2:4709752-4709771 None:intergenic 15.0%
!! TTAAATGTTCATAACTTTAA+AGG - chr4.2:4709516-4709535 None:intergenic 15.0%
!!! TTCAAATTCAAGTTAATTTT+AGG - chr4.2:4709723-4709742 None:intergenic 15.0%
!! AATTAAACAAAGAATACTCA+AGG - chr4.2:4709488-4709507 None:intergenic 20.0%
!! ATTAAACAAAGAATACTCAA+GGG - chr4.2:4709487-4709506 None:intergenic 20.0%
!! GAAAATTTATCAAAATACAG+TGG - chr4.2:4709917-4709936 None:intergenic 20.0%
!!! AAAACCTAATATTAACTTGA+GGG - chr4.2:4709403-4709422 None:intergenic 20.0%
!!! ACACTTTAATCTTTTTTTGA+AGG - chr4.2:4709549-4709568 None:intergenic 20.0%
!!! TTGAACTTTTGTAACTTAAA+AGG + chr4.2:4709568-4709587 MS.gene048906:intron 20.0%
! AAAAAACCTTTATAGACCAA+AGG + chr4.2:4709694-4709713 MS.gene048906:intron 25.0%
! ATGAAAAAATGCATGATTGT+AGG + chr4.2:4709849-4709868 MS.gene048906:intron 25.0%
! TGAAAAAATGCATGATTGTA+GGG + chr4.2:4709850-4709869 MS.gene048906:intron 25.0%
! TGCATGACATTTGTAATTTA+AGG - chr4.2:4709457-4709476 None:intergenic 25.0%
! TTAAACAAAGAATACTCAAG+GGG - chr4.2:4709486-4709505 None:intergenic 25.0%
!! AAACCTAATATTAACTTGAG+GGG - chr4.2:4709402-4709421 None:intergenic 25.0%
!! CAAAACCTAATATTAACTTG+AGG - chr4.2:4709404-4709423 None:intergenic 25.0%
!! GTTAATATTAGGTTTTGCTT+TGG + chr4.2:4709407-4709426 MS.gene048906:intron 25.0%
!!! AACTATTTTTGAATTTGCTG+AGG + chr4.2:4709782-4709801 MS.gene048906:intron 25.0%
!!! ACTATTTTTGAATTTGCTGA+GGG + chr4.2:4709783-4709802 MS.gene048906:intron 25.0%
!!! AGTTAATTTTAGGTTTCCTT+TGG - chr4.2:4709713-4709732 None:intergenic 25.0%
!!! ATTGTTTTTGTAATGTGTTC+AGG + chr4.2:4709950-4709969 MS.gene048906:intron 25.0%
!!! CTGATTTTTTCAGGAATAAA+AGG - chr4.2:4709289-4709308 None:intergenic 25.0%
!!! TTGTTTTTGTAATGTGTTCA+GGG + chr4.2:4709951-4709970 MS.gene048906:intron 25.0%
CAGATCTAGAAAAATAGATC+TGG - chr4.2:4709220-4709239 None:intergenic 30.0%
! AGCTTATTTGTTGATGTTGT+TGG + chr4.2:4709994-4710013 MS.gene048906:CDS 30.0%
!! CAGATCTATTTTTCTAGATC+TGG + chr4.2:4709218-4709237 MS.gene048906:intron 30.0%
ACTCACGTACATCATTCATT+CGG + chr4.2:4710024-4710043 MS.gene048906:CDS 35.0%
AGGTTTCCTTTGGTCTATAA+AGG - chr4.2:4709703-4709722 None:intergenic 35.0%
!!! AGATTGCAGCTGATTTTTTC+AGG - chr4.2:4709298-4709317 None:intergenic 35.0%
AAGAGTTTGAGCTTGAACAG+CGG - chr4.2:4709119-4709138 None:intergenic 40.0%
CCACCCCTCAAGTTAATATT+AGG + chr4.2:4709396-4709415 MS.gene048906:intron 40.0%
TGTAATGTGTTCAGGGTCAT+CGG + chr4.2:4709958-4709977 MS.gene048906:intron 40.0%
! CCTAATATTAACTTGAGGGG+TGG - chr4.2:4709399-4709418 None:intergenic 40.0%
CGAAATGGCGAAAATGAGAG+TGG - chr4.2:4709089-4709108 None:intergenic 45.0%
TTTGTTGATGTTGTTGGCGC+TGG + chr4.2:4710000-4710019 MS.gene048906:CDS 45.0%
!!! AAAAAATGAAATATTTTTTA+AGG + chr4.2:4709624-4709643 MS.gene048906:intron 5.0%
!!! AAAAATGAAATATTTTTTAA+GGG + chr4.2:4709625-4709644 MS.gene048906:intron 5.0%
AGAAAGTTACCGTCGCTGGT+AGG - chr4.2:4709157-4709176 None:intergenic 50.0%
AGAGAGAAAGTTACCGTCGC+TGG - chr4.2:4709161-4709180 None:intergenic 50.0%
TTTGAGCTTGAACAGCGGCA+GGG - chr4.2:4709114-4709133 None:intergenic 50.0%
! TCAGGGTCATCGGTTGATCA+AGG + chr4.2:4709968-4709987 MS.gene048906:intron 50.0%
AACAGCGGCAGGGAACGAAA+TGG - chr4.2:4709104-4709123 None:intergenic 55.0%
GTTTGAGCTTGAACAGCGGC+AGG - chr4.2:4709115-4709134 None:intergenic 55.0%
TTACCGTCGCTGGTAGGAGA+AGG - chr4.2:4709151-4709170 None:intergenic 55.0%
GCACCTTCTCCTACCAGCGA+CGG + chr4.2:4709145-4709164 MS.gene048906:CDS 60.0%
! CGCTGGTAGGAGAAGGTGCA+GGG - chr4.2:4709144-4709163 None:intergenic 60.0%
! GCTGGTAGGAGAAGGTGCAG+GGG - chr4.2:4709143-4709162 None:intergenic 60.0%
! TCGCTGGTAGGAGAAGGTGC+AGG - chr4.2:4709145-4709164 None:intergenic 60.0%


Chromosome Type Strat End Strand Name
chr4.2 gene 4709073 4710069 4709073 ID=MS.gene048906
chr4.2 mRNA 4709073 4710069 4709073 ID=MS.gene048906.t1;Parent=MS.gene048906
chr4.2 exon 4709073 4709166 4709073 ID=MS.gene048906.t1.exon1;Parent=MS.gene048906.t1
chr4.2 CDS 4709073 4709166 4709073 ID=cds.MS.gene048906.t1;Parent=MS.gene048906.t1
chr4.2 exon 4709972 4710069 4709972 ID=MS.gene048906.t1.exon2;Parent=MS.gene048906.t1
chr4.2 CDS 4709972 4710069 4709972 ID=cds.MS.gene048906.t1;Parent=MS.gene048906.t1
Gene Sequence

>MS.gene048906

ATGGCTATCATCGCCACTCTCATTTTCGCCATTTCGTTCCCTGCCGCTGTTCAAGCTCAAACTCTTGCCCCTGCACCTTCTCCTACCAGCGACGGTAACTTTCTCTCTCTTTTTCTTCTTAGATCTGATCTATCTATTATAATACCAGATCTATTTTTCTAGATCTGGATTTTGTGTATCTACATTTTACGTTGTTTCGATTTCACGTTCTTTCCTTTTATTCCTGAAAAAATCAGCTGCAATCTTATTTATTTAGTACTTGCATTGTTTTTATTTCTGATGAATTATTATCATTTTTTTAATGTTTAAATCTGATCAAATTGCCACCCCTCAAGTTAATATTAGGTTTTGCTTTGGTCTCTTAAATTTGTTTATTTTAGTCCTTAAATTACAAATGTCATGCAATTTAGCCCCTTGAGTATTCTTTGTTTAATTTTGATCCTTTAAAGTTATGAACATTTAACACTTTTGTTCCTTCAAAAAAAGATTAAAGTGTTGAACTTTTGTAACTTAAAAGGAACACAACATCTAATATTTGCAAGTTAAATGATAAAAAATGAAATATTTTTTAAGGGACAAAATTATTGTAACACGTGTAATTTAAGTCATCAAAATGAAATGAAAAAACCTTTATAGACCAAAGGAAACCTAAAATTAACTTGAATTTGAATTTGAACCATTTTCTAATTTGAATTTCTTTCTCTAAAAAAACTATTTTTGAATTTGCTGAGGGACTAAATCTAAACAAACAAACAAAAAAAAACTTACTTATAAAAATGAAAAAATGCATGATTGTAGGGACTAAAATCGTATTTATACTTTTTTAAAATATAACTATATACCACTGTATTTTGATAAATTTTCATCAGTTTTTAATATTGTTTTTGTAATGTGTTCAGGGTCATCGGTTGATCAAGGAATAGCTTATTTGTTGATGTTGTTGGCGCTGGTACTCACGTACATCATTCATTCGGCTGATATTTCATCTACTTTCTGA
Protein sequence

>MS.gene048906.t1

MAIIATLIFAISFPAAVQAQTLAPAPSPTSDGSSVDQGIAYLLMLLALVLTYIIHSADISSTF