AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene85229

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 21 sgRNAs with CRISPR-Local

Find 69 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
ACTGTTGGTGCTGGTGTTGC+TGG 0.278594 2.4:-4543304 MS.gene85229:CDS
CGATGTAGGCGAAGTTAATT+CGG 0.329255 2.4:-4543356 MS.gene85229:intron
TATTGCTCTGGTTGTACTCT+TGG 0.344765 2.4:-4543281 MS.gene85229:CDS
GGGTTCAATTTCATTGATGA+TGG 0.393070 2.4:+4543857 None:intergenic
CTCATCAACATATCGGCATC+AGG 0.407565 2.4:-4542839 MS.gene85229:CDS
ATTGCTCTGGTTGTACTCTT+GGG 0.449876 2.4:-4543280 MS.gene85229:CDS
TGGTGTTGCTGGTATTGCTC+TGG 0.454038 2.4:-4543293 MS.gene85229:CDS
AATGTTATCACTGTTGGTGC+TGG 0.466483 2.4:-4543313 MS.gene85229:CDS
CATTTCCCTCATCAACATAT+CGG 0.470848 2.4:-4542846 MS.gene85229:CDS
TCAAGAGCAAGAACTGGAAC+AGG 0.482132 2.4:+4543715 None:intergenic
CCAGTTCTTGCTCTTGACAT+CGG 0.484096 2.4:-4543709 MS.gene85229:CDS
GCAGTTATCAACATCTTCGT+TGG 0.491361 2.4:-4542883 MS.gene85229:intron
CTCTGGTTGTACTCTTGGGA+AGG 0.498339 2.4:-4543276 MS.gene85229:intron
CCGATGTCAAGAGCAAGAAC+TGG 0.503027 2.4:+4543709 None:intergenic
GGTTCAATTTCATTGATGAT+GGG 0.521972 2.4:+4543858 None:intergenic
ATATCGGCATCAGGGCAACT+TGG 0.528755 2.4:-4542830 MS.gene85229:intron
GATGCTAATGTTATCACTGT+TGG 0.589755 2.4:-4543319 MS.gene85229:CDS
TCATCAACATATCGGCATCA+GGG 0.604907 2.4:-4542838 MS.gene85229:CDS
AACTGGAACAGGAACAACAA+AGG 0.628523 2.4:+4543726 None:intergenic
CTGATGCCGATATGTTGATG+AGG 0.666580 2.4:+4542840 None:intergenic
TGATGCCGATATGTTGATGA+GGG 0.679239 2.4:+4542841 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! TATAGATTGATTTTATATTT+GGG - chr2.4:4543696-4543715 MS.gene85229:intron 10.0%
!! TACTGGATTTATTATATTTA+GGG - chr2.4:4543045-4543064 MS.gene85229:intron 15.0%
!! TTACTGGATTTATTATATTT+AGG - chr2.4:4543044-4543063 MS.gene85229:intron 15.0%
!!! AAGTTTTGATTTGATTTATT+TGG - chr2.4:4543420-4543439 MS.gene85229:intron 15.0%
!!! CTATAGATTGATTTTATATT+TGG - chr2.4:4543695-4543714 MS.gene85229:intron 15.0%
!! ACTGGATTTATTATATTTAG+GGG - chr2.4:4543046-4543065 MS.gene85229:intron 20.0%
!! TTACATATAAACAAAACACA+CGG + chr2.4:4543605-4543624 None:intergenic 20.0%
! AAAATAATTCTGATGAGATG+AGG + chr2.4:4543026-4543045 None:intergenic 25.0%
! AAGTGAGAATAATAAAGACA+AGG + chr2.4:4543845-4543864 None:intergenic 25.0%
! AATGAAACAAACAGGAAAAT+AGG + chr2.4:4543581-4543600 None:intergenic 25.0%
! GTTAATTCGGAAAAATTCAA+CGG - chr2.4:4543273-4543292 MS.gene85229:intron 25.0%
! TTGTAATTTAGTCAAACCAT+TGG - chr2.4:4543365-4543384 MS.gene85229:intron 25.0%
!! AAAATCTGGAACTTAACTAA+CGG + chr2.4:4542784-4542803 None:intergenic 25.0%
!! CTTAAGAAGTGTAATTATGA+AGG - chr2.4:4543211-4543230 MS.gene85229:intron 25.0%
!! GTCTTTATTATTCTCACTTT+TGG - chr2.4:4543846-4543865 MS.gene85229:intron 25.0%
!!! TCTCATCAGAATTATTTTAC+TGG - chr2.4:4543028-4543047 MS.gene85229:intron 25.0%
AAGTTCGTTCAATCACAAAT+GGG - chr2.4:4542989-4543008 MS.gene85229:intron 30.0%
ATATTTAGGGGATAGAATGA+AGG - chr2.4:4543058-4543077 MS.gene85229:intron 30.0%
TGAACAAACATGATGAAAAG+AGG + chr2.4:4542970-4542989 None:intergenic 30.0%
! AAATCAACAAAATCTGGAAC+AGG + chr2.4:4542841-4542860 None:intergenic 30.0%
! AAATCTGGAACTTAACTAAC+GGG + chr2.4:4542783-4542802 None:intergenic 30.0%
! ACTTCTTAAGCATCTTTTCA+AGG + chr2.4:4543201-4543220 None:intergenic 30.0%
! GGTTCAATTTCATTGATGAT+GGG + chr2.4:4542761-4542780 None:intergenic 30.0%
! GTTAAGTTCCAGATTTTCAA+TGG - chr2.4:4542787-4542806 MS.gene85229:intron 30.0%
ACAAGCAGCAAATTCAATCA+AGG + chr2.4:4543534-4543553 None:intergenic 35.0%
ACGCGAAAATCAACAAAATC+TGG + chr2.4:4542847-4542866 None:intergenic 35.0%
AGGAATGTGAAAGACAAAAG+TGG + chr2.4:4543825-4543844 None:intergenic 35.0%
ATTGTGACGATTATCGATGT+AGG - chr2.4:4543246-4543265 MS.gene85229:intron 35.0%
CAAGTTCGTTCAATCACAAA+TGG - chr2.4:4542988-4543007 MS.gene85229:intron 35.0%
CATTTCCCTCATCAACATAT+CGG - chr2.4:4543770-4543789 MS.gene85229:intron 35.0%
GATGCTAATGTTATCACTGT+TGG - chr2.4:4543297-4543316 MS.gene85229:CDS 35.0%
GGGTTCAATTTCATTGATGA+TGG + chr2.4:4542762-4542781 None:intergenic 35.0%
! AATCTGGAACTTAACTAACG+GGG + chr2.4:4542782-4542801 None:intergenic 35.0%
! GAAGGTGATTCTTGTGTTTT+GGG - chr2.4:4543076-4543095 MS.gene85229:intron 35.0%
! TGAAGGTGATTCTTGTGTTT+TGG - chr2.4:4543075-4543094 MS.gene85229:intron 35.0%
!! TCTCACTTTTGGTTAAATGC+AGG - chr2.4:4543857-4543876 MS.gene85229:CDS 35.0%
AACTGGAACAGGAACAACAA+AGG + chr2.4:4542893-4542912 None:intergenic 40.0%
AATGTTATCACTGTTGGTGC+TGG - chr2.4:4543303-4543322 MS.gene85229:CDS 40.0%
AGAGATGAACTTGGATCCAA+TGG + chr2.4:4543384-4543403 None:intergenic 40.0%
ATTGCTCTGGTTGTACTCTT+GGG - chr2.4:4543336-4543355 MS.gene85229:CDS 40.0%
CAAGAATTTGCCATCCAACA+TGG - chr2.4:4543167-4543186 MS.gene85229:intron 40.0%
CACACGGAAATGAAACAAAC+AGG + chr2.4:4543589-4543608 None:intergenic 40.0%
CATGCAACAAGAGATGAACT+TGG + chr2.4:4543393-4543412 None:intergenic 40.0%
CGATGTAGGCGAAGTTAATT+CGG - chr2.4:4543260-4543279 MS.gene85229:intron 40.0%
GAACAGGACCATTGAAAATC+TGG + chr2.4:4542798-4542817 None:intergenic 40.0%
GCAGTTATCAACATCTTCGT+TGG - chr2.4:4543733-4543752 MS.gene85229:CDS 40.0%
GTTGGATGGCAAATTCTTGT+TGG + chr2.4:4543166-4543185 None:intergenic 40.0%
TATTGCTCTGGTTGTACTCT+TGG - chr2.4:4543335-4543354 MS.gene85229:CDS 40.0%
TCAAGGATCTTAAGCCATGT+TGG + chr2.4:4543184-4543203 None:intergenic 40.0%
TCATCAACATATCGGCATCA+GGG - chr2.4:4543778-4543797 MS.gene85229:intron 40.0%
TTGGGAGGTAGGAGTAAAAA+TGG - chr2.4:4543094-4543113 MS.gene85229:intron 40.0%
! AATCTGGAACAGGAACAACA+CGG + chr2.4:4542831-4542850 None:intergenic 40.0%
! TGATGCCGATATGTTGATGA+GGG + chr2.4:4543778-4543797 None:intergenic 40.0%
!!! ATTCTTGTGTTTTGGGAGGT+AGG - chr2.4:4543083-4543102 MS.gene85229:intron 40.0%
ACAAAGGCGATGAGAAAAGC+TGG + chr2.4:4542877-4542896 None:intergenic 45.0%
CCAGTTCTTGCTCTTGACAT+CGG - chr2.4:4542907-4542926 MS.gene85229:intron 45.0%
CTCATCAACATATCGGCATC+AGG - chr2.4:4543777-4543796 MS.gene85229:intron 45.0%
CTGATGCCGATATGTTGATG+AGG + chr2.4:4543779-4543798 None:intergenic 45.0%
GGATCTTAAGCCATGTTGGA+TGG + chr2.4:4543180-4543199 None:intergenic 45.0%
TCAAGAGCAAGAACTGGAAC+AGG + chr2.4:4542904-4542923 None:intergenic 45.0%
!! GGTGATTCTTGTGTTTTGGG+AGG - chr2.4:4543079-4543098 MS.gene85229:intron 45.0%
ACACGGTGGAAAACTGGAAC+AGG + chr2.4:4542814-4542833 None:intergenic 50.0%
ATATCGGCATCAGGGCAACT+TGG - chr2.4:4543786-4543805 MS.gene85229:intron 50.0%
CCGATGTCAAGAGCAAGAAC+TGG + chr2.4:4542910-4542929 None:intergenic 50.0%
CTCTGGTTGTACTCTTGGGA+AGG - chr2.4:4543340-4543359 MS.gene85229:CDS 50.0%
GGAACAACACGGTGGAAAAC+TGG + chr2.4:4542820-4542839 None:intergenic 50.0%
!! TGGTGTTGCTGGTATTGCTC+TGG - chr2.4:4543323-4543342 MS.gene85229:CDS 50.0%
CTGGAACAGGAACAACACGG+TGG + chr2.4:4542828-4542847 None:intergenic 55.0%
!! ACTGTTGGTGCTGGTGTTGC+TGG - chr2.4:4543312-4543331 MS.gene85229:CDS 55.0%


Chromosome Type Strat End Strand Name
chr2.4 gene 4542746 4543892 4542746 ID=MS.gene85229
chr2.4 mRNA 4542746 4543892 4542746 ID=MS.gene85229.t1;Parent=MS.gene85229
chr2.4 exon 4543856 4543892 4543856 ID=MS.gene85229.t1.exon1;Parent=MS.gene85229.t1
chr2.4 CDS 4543856 4543892 4543856 ID=cds.MS.gene85229.t1;Parent=MS.gene85229.t1
chr2.4 exon 4543701 4543760 4543701 ID=MS.gene85229.t1.exon2;Parent=MS.gene85229.t1
chr2.4 CDS 4543701 4543760 4543701 ID=cds.MS.gene85229.t1;Parent=MS.gene85229.t1
chr2.4 exon 4543277 4543370 4543277 ID=MS.gene85229.t1.exon3;Parent=MS.gene85229.t1
chr2.4 CDS 4543277 4543370 4543277 ID=cds.MS.gene85229.t1;Parent=MS.gene85229.t1
chr2.4 exon 4542831 4542901 4542831 ID=MS.gene85229.t1.exon4;Parent=MS.gene85229.t1
chr2.4 CDS 4542831 4542901 4542831 ID=cds.MS.gene85229.t1;Parent=MS.gene85229.t1
chr2.4 exon 4542746 4542759 4542746 ID=MS.gene85229.t1.exon5;Parent=MS.gene85229.t1
chr2.4 CDS 4542746 4542759 4542746 ID=cds.MS.gene85229.t1;Parent=MS.gene85229.t1
Gene Sequence

>MS.gene85229

ATGAAATTAAAACCCATCATCAATGAAATTGAACCCCGTTAGTTAAGTTCCAGATTTTCAATGGTCCTGTTCCAGTTTTCCACCGTGTTGTTCCTGTTCCAGATTTTGTTGATTTTCGCGTTTGTGTACCAGCTTTTCTCATCGCCTTTGTTGTTCCTGTTCCAGTTCTTGCTCTTGACATCGGATTCAACTGTTACTTCTCTCATCTTATAAGATTTGTTCCTCTTTTCATCATGTTTGTTCAAGTTCGTTCAATCACAAATGGGTCACTTTTGTTCCTCATCTCATCAGAATTATTTTACTGGATTTATTATATTTAGGGGATAGAATGAAGGTGATTCTTGTGTTTTGGGAGGTAGGAGTAAAAATGGTTATTAAGTTAGAAGTCAGTAGTTAACTGTAAGTATATGAGATTAACCAACAAGAATTTGCCATCCAACATGGCTTAAGATCCTTGAAAAGATGCTTAAGAAGTGTAATTATGAAGGTTTGTTTCTTAAATTGTGACGATTATCGATGTAGGCGAAGTTAATTCGGAAAAATTCAACGGTGATGCTAATGTTATCACTGTTGGTGCTGGTGTTGCTGGTATTGCTCTGGTTGTACTCTTGGGAAGGTATTGTAATTTAGTCAAACCATTGGATCCAAGTTCATCTCTTGTTGCATGTGTTTAGAAGTTTTGATTTGATTTATTTGGTGATTGAACTAGATAAATTTTGAATTAATAAGTGTTAGTTAGTTGCTGCTTGTGAATTCAGTTTCAGTTGATTTGTGTTTTTAACAATCCTTGATTGAATTTGCTGCTTGTAATTTGATTTGATTAGCTTGCTGACCTATTTTCCTGTTTGTTTCATTTCCGTGTGTTTTGTTTATATGTAAAATTTGAGTTTTTTTTTTAGATCTCTGCTAGTTAATTTTCTGTTAACACTCAAAATTATTTGATTGTTTTCTATAGATTGATTTTATATTTGGGTAATTGTAATTTATGCAGTTATCAACATCTTCGTTGGCATTTGTTTATCTGCATTTCCCTCATCAACATATCGGCATCAGGGCAACTTGGTAACACATTTTCGCCACTTTTGTCTTTCACATTCCTTGTCTTTATTATTCTCACTTTTGGTTAAATGCAGGTGAACAAGCTTAA
Protein sequence

>MS.gene85229.t1

MKLKPIINEIEPPFLIAFVVPVPVLALDIGFNCEVNSEKFNGDANVITVGAGVAGIALVVLLGSYQHLRWHLFICISLINISASGQLGEQA