AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene06050

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene06050.t1 MTR_8g099245 98.413 63 1 0 1 63 13 75 5.20e-37 118
MS.gene06050.t1 MTR_3g090830 70.270 37 11 0 19 55 27 63 5.29e-14 60.1
MS.gene06050.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.gene06050.t1 AT3G61640 64.062 64 20 2 1 62 7 69 4.37e-19 73.2
MS.gene06050.t1 AT2G46330 73.333 45 12 0 19 63 26 70 1.41e-18 71.6
MS.gene06050.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 4.1:+4819113 MS.gene06050:CDS
GTTTGAGCTTGAACAGCGGC+AGG 0.459763 4.1:-4818231 None:intergenic
TTTGTTGATGTTGTTGGCGC+TGG 0.487327 4.1:+4819119 MS.gene06050:CDS
AGAGAGAAAGTTACCGTCGC+TGG 0.490610 4.1:-4818277 None:intergenic
TGTAATGTGTTCAGGGTCAT+CGG 0.501208 4.1:+4819077 MS.gene06050:intron
TCGCTGGTAGGAGAAGGTGC+AGG 0.512007 4.1:-4818261 None:intergenic
CGCTGGTAGGAGAAGGTGCA+GGG 0.523424 4.1:-4818260 None:intergenic
AACAGCGGCAGGGAACGAAA+TGG 0.538815 4.1:-4818220 None:intergenic
TCAGGGTCATCGGTTGATCA+AGG 0.556824 4.1:+4819087 MS.gene06050:intron
ACTCACGTACATCATTCATT+CGG 0.558338 4.1:+4819143 MS.gene06050:CDS
TTACCGTCGCTGGTAGGAGA+AGG 0.584470 4.1:-4818267 None:intergenic
AGAAAGTTACCGTCGCTGGT+AGG 0.586425 4.1:-4818273 None:intergenic
TTTGAGCTTGAACAGCGGCA+GGG 0.641146 4.1:-4818230 None:intergenic
AAGAGTTTGAGCTTGAACAG+CGG 0.647341 4.1:-4818235 None:intergenic
CGAAATGGCGAAAATGAGAG+TGG 0.649027 4.1:-4818205 None:intergenic
GCACCTTCTCCTACCAGCGA+CGG 0.671933 4.1:+4818264 MS.gene06050:CDS
GCTGGTAGGAGAAGGTGCAG+GGG 0.704099 4.1:-4818259 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AAGAAATTCAAATTAGAAAA+TGG - chr4.1:4818871-4818890 None:intergenic 15.0%
!! TTAAATGTTCATAACTTTAA+AGG - chr4.1:4818635-4818654 None:intergenic 15.0%
!!! TTCAAATTCAAGTTAATTTT+AGG - chr4.1:4818842-4818861 None:intergenic 15.0%
!! AATTAAACAAAGAATACTCA+AGG - chr4.1:4818607-4818626 None:intergenic 20.0%
!! ATTAAACAAAGAATACTCAA+GGG - chr4.1:4818606-4818625 None:intergenic 20.0%
!! GAAAATTTATCAAAATACAG+TGG - chr4.1:4819036-4819055 None:intergenic 20.0%
!!! AAAACCTAATATTAACTTGA+GGG - chr4.1:4818522-4818541 None:intergenic 20.0%
!!! ACACTTTAATCTTTTTTTGA+AGG - chr4.1:4818668-4818687 None:intergenic 20.0%
!!! TTGAACTTTTGTAACTTAAA+AGG + chr4.1:4818687-4818706 MS.gene06050:intron 20.0%
! AAAAAACCTTTATAGACCAA+AGG + chr4.1:4818813-4818832 MS.gene06050:intron 25.0%
! ATGAAAAAATGCATGATTGT+AGG + chr4.1:4818968-4818987 MS.gene06050:intron 25.0%
! TGAAAAAATGCATGATTGTA+GGG + chr4.1:4818969-4818988 MS.gene06050:intron 25.0%
! TGCATGACATTTGTAATTTA+AGG - chr4.1:4818576-4818595 None:intergenic 25.0%
! TTAAACAAAGAATACTCAAG+GGG - chr4.1:4818605-4818624 None:intergenic 25.0%
!! AAACCTAATATTAACTTGAG+GGG - chr4.1:4818521-4818540 None:intergenic 25.0%
!! CAAAACCTAATATTAACTTG+AGG - chr4.1:4818523-4818542 None:intergenic 25.0%
!! GTTAATATTAGGTTTTGCTT+TGG + chr4.1:4818526-4818545 MS.gene06050:intron 25.0%
!!! AACTATTTTTGAATTTGCTG+AGG + chr4.1:4818901-4818920 MS.gene06050:intron 25.0%
!!! ACTATTTTTGAATTTGCTGA+GGG + chr4.1:4818902-4818921 MS.gene06050:intron 25.0%
!!! AGTTAATTTTAGGTTTCCTT+TGG - chr4.1:4818832-4818851 None:intergenic 25.0%
!!! ATTGTTTTTGTAATGTGTTC+AGG + chr4.1:4819069-4819088 MS.gene06050:intron 25.0%
!!! CTGATTTTTTCAGGAATAAA+AGG - chr4.1:4818408-4818427 None:intergenic 25.0%
!!! TTGTTTTTGTAATGTGTTCA+GGG + chr4.1:4819070-4819089 MS.gene06050:intron 25.0%
CAGATCTAGAAAAATAGATC+TGG - chr4.1:4818339-4818358 None:intergenic 30.0%
! AGCTTATTTGTTGATGTTGT+TGG + chr4.1:4819113-4819132 MS.gene06050:CDS 30.0%
!! CAGATCTATTTTTCTAGATC+TGG + chr4.1:4818337-4818356 MS.gene06050:intron 30.0%
ACTCACGTACATCATTCATT+CGG + chr4.1:4819143-4819162 MS.gene06050:CDS 35.0%
AGGTTTCCTTTGGTCTATAA+AGG - chr4.1:4818822-4818841 None:intergenic 35.0%
!!! AGATTGCAGCTGATTTTTTC+AGG - chr4.1:4818417-4818436 None:intergenic 35.0%
AAGAGTTTGAGCTTGAACAG+CGG - chr4.1:4818238-4818257 None:intergenic 40.0%
CCACCCCTCAAGTTAATATT+AGG + chr4.1:4818515-4818534 MS.gene06050:intron 40.0%
TGTAATGTGTTCAGGGTCAT+CGG + chr4.1:4819077-4819096 MS.gene06050:intron 40.0%
! CCTAATATTAACTTGAGGGG+TGG - chr4.1:4818518-4818537 None:intergenic 40.0%
CGAAATGGCGAAAATGAGAG+TGG - chr4.1:4818208-4818227 None:intergenic 45.0%
TTTGTTGATGTTGTTGGCGC+TGG + chr4.1:4819119-4819138 MS.gene06050:CDS 45.0%
!!! AAAAAATGAAATATTTTTTA+AGG + chr4.1:4818743-4818762 MS.gene06050:intron 5.0%
!!! AAAAATGAAATATTTTTTAA+GGG + chr4.1:4818744-4818763 MS.gene06050:intron 5.0%
AGAAAGTTACCGTCGCTGGT+AGG - chr4.1:4818276-4818295 None:intergenic 50.0%
AGAGAGAAAGTTACCGTCGC+TGG - chr4.1:4818280-4818299 None:intergenic 50.0%
TTTGAGCTTGAACAGCGGCA+GGG - chr4.1:4818233-4818252 None:intergenic 50.0%
! TCAGGGTCATCGGTTGATCA+AGG + chr4.1:4819087-4819106 MS.gene06050:intron 50.0%
AACAGCGGCAGGGAACGAAA+TGG - chr4.1:4818223-4818242 None:intergenic 55.0%
GTTTGAGCTTGAACAGCGGC+AGG - chr4.1:4818234-4818253 None:intergenic 55.0%
TTACCGTCGCTGGTAGGAGA+AGG - chr4.1:4818270-4818289 None:intergenic 55.0%
GCACCTTCTCCTACCAGCGA+CGG + chr4.1:4818264-4818283 MS.gene06050:CDS 60.0%
! CGCTGGTAGGAGAAGGTGCA+GGG - chr4.1:4818263-4818282 None:intergenic 60.0%
! GCTGGTAGGAGAAGGTGCAG+GGG - chr4.1:4818262-4818281 None:intergenic 60.0%
! TCGCTGGTAGGAGAAGGTGC+AGG - chr4.1:4818264-4818283 None:intergenic 60.0%


Chromosome Type Strat End Strand Name
chr4.1 gene 4818192 4819188 4818192 ID=MS.gene06050
chr4.1 mRNA 4818192 4819188 4818192 ID=MS.gene06050.t1;Parent=MS.gene06050
chr4.1 exon 4818192 4818285 4818192 ID=MS.gene06050.t1.exon1;Parent=MS.gene06050.t1
chr4.1 CDS 4818192 4818285 4818192 ID=cds.MS.gene06050.t1;Parent=MS.gene06050.t1
chr4.1 exon 4819091 4819188 4819091 ID=MS.gene06050.t1.exon2;Parent=MS.gene06050.t1
chr4.1 CDS 4819091 4819188 4819091 ID=cds.MS.gene06050.t1;Parent=MS.gene06050.t1
Gene Sequence

>MS.gene06050

ATGGCTATCATCGCCACTCTCATTTTCGCCATTTCGTTCCCTGCCGCTGTTCAAGCTCAAACTCTTGCCCCTGCACCTTCTCCTACCAGCGACGGTAACTTTCTCTCTCTTTTTCTTCTTAGATCTGATCTATCTATTATAATACCAGATCTATTTTTCTAGATCTGGATTTTGTGTATCTACATTTTACGTTGTTTCGATTTCACGTTCTTTCCTTTTATTCCTGAAAAAATCAGCTGCAATCTTATTTATTTAGTACTTGCATTGTTTTTATTTCTGATGAATTATTATCATTTTTTTAATGTTTAAATCTGATCAAATTGCCACCCCTCAAGTTAATATTAGGTTTTGCTTTGGTCTCTTAAATTTGTTTATTTTAGTCCTTAAATTACAAATGTCATGCAATTTAGCCCCTTGAGTATTCTTTGTTTAATTTTGATCCTTTAAAGTTATGAACATTTAACTCTTTTGTTCCTTCAAAAAAAGATTAAAGTGTTGAACTTTTGTAACTTAAAAGGAACACAACATCTAATATTTGCAAGTTAAATGATAAAAAATGAAATATTTTTTAAGGGACAAAATTATTGTAACACGTGTAATTTAAGTCATCAAAATGAAATGAAAAAACCTTTATAGACCAAAGGAAACCTAAAATTAACTTGAATTTGAATTTGAACCATTTTCTAATTTGAATTTCTTTCTCTAAAAAAACTATTTTTGAATTTGCTGAGGGACTAAATCTAAACAAACAAACAAAAAAAAACTTACTTATAAAAATGAAAAAATGCATGATTGTAGGGACTAAAATCGTATTTATACTTTTTTAAAATATAACTATATACCACTGTATTTTGATAAATTTTCATCAGTTTTTAATATTGTTTTTGTAATGTGTTCAGGGTCATCGGTTGATCAAGGAATAGCTTATTTGTTGATGTTGTTGGCGCTGGTACTCACGTACATCATTCATTCGGCTGATATTTCATCTACTTTCTGA
Protein sequence

>MS.gene06050.t1

MAIIATLIFAISFPAAVQAQTLAPAPSPTSDGSSVDQGIAYLLMLLALVLTYIIHSADISSTF