AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene51649


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene51649.t1 MTR_3g010000 91.358 162 2 1 1 162 1 150 1.43e-104 296
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene51649.t1 AT1G55670 70.303 165 41 3 1 162 1 160 1.38e-77 228

Find 23 sgRNAs with CRISPR-Local

Find 37 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GGTTATGATCCAAGTTTCTT+TGG 0.281064 3.4:-4864042 MS.gene51649:CDS
TTGCTCAGGTAAGCCTTGTT+TGG 0.325198 3.4:+4864224 None:intergenic
TATTGTTGCTTACTATATCT+TGG 0.334380 3.4:-4864079 MS.gene51649:CDS
GTTAAAACCAACAGGATCAT+TGG 0.338510 3.4:+4864137 None:intergenic
CCTTGGAAGGATAAGCTTGA+TGG 0.391675 3.4:+4864423 None:intergenic
CAAGGCTTACCTGAGCAAAA+TGG 0.416510 3.4:-4864219 MS.gene51649:CDS
TCAACAAGGTTAAAACCAAC+AGG 0.475786 3.4:+4864129 None:intergenic
TTGTGAGAGGGTTGAAACCT+TGG 0.480579 3.4:+4864406 None:intergenic
CTTAAATCCAATGATCCTGT+TGG 0.489692 3.4:-4864144 MS.gene51649:CDS
AAATATCAACCAAAGAAACT+TGG 0.505006 3.4:+4864033 None:intergenic
CTTAAGCTTATCACAAGTGA+AGG 0.506695 3.4:+4864309 None:intergenic
CCATCAAGCTTATCCTTCCA+AGG 0.510872 3.4:-4864423 MS.gene51649:CDS
AGCTGGTGACAAACGTGCTA+AGG 0.525842 3.4:-4864181 MS.gene51649:CDS
TAATGCATGAGTTGATATCA+TGG 0.550417 3.4:+4864485 None:intergenic
ATCTTGGCTACTTCTAGCAA+TGG 0.561786 3.4:-4864063 MS.gene51649:CDS
AGAGAAAATGTAGCCAAACA+AGG 0.605177 3.4:-4864237 MS.gene51649:CDS
AAGGTTTCAACCCTCTCACA+AGG 0.615424 3.4:-4864404 MS.gene51649:CDS
CTTGTGATAAGCTTAAGCAC+TGG 0.620138 3.4:-4864303 MS.gene51649:CDS
GAGAGGGTTGAAACCTTGGA+AGG 0.621275 3.4:+4864410 None:intergenic
TTAAGCTTATCACAAGTGAA+GGG 0.638403 3.4:+4864310 None:intergenic
ATGAGTTGATATCATGGATG+AGG 0.640889 3.4:+4864491 None:intergenic
GGTGTGACACACTTTGAAGC+TGG 0.654419 3.4:-4864198 MS.gene51649:CDS
CCCAAGCCAAAACATCAACA+AGG 0.663918 3.4:+4864115 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! TATTGTTGCTTACTATATCT+TGG - chr3.4:4864463-4864482 MS.gene51649:CDS 25.0%
!! TTTTAACCTTGTTGATGTTT+TGG - chr3.4:4864421-4864440 MS.gene51649:CDS 25.0%
ACCTTCCTAAAAACAATGAA+AGG + chr3.4:4864265-4864284 None:intergenic 30.0%
TTAAGCTTATCACAAGTGAA+GGG + chr3.4:4864235-4864254 None:intergenic 30.0%
! CTTGAAAATCTCTTTTTGCT+TGG + chr3.4:4864188-4864207 None:intergenic 30.0%
!! AGTTTTGTGTTTTTGAATGG+TGG + chr3.4:4864087-4864106 None:intergenic 30.0%
!! GTGAGTTTTGTGTTTTTGAA+TGG + chr3.4:4864090-4864109 None:intergenic 30.0%
!! TAATGCATGAGTTGATATCA+TGG + chr3.4:4864060-4864079 None:intergenic 30.0%
AGAGAAAATGTAGCCAAACA+AGG - chr3.4:4864305-4864324 MS.gene51649:CDS 35.0%
CTTAAATCCAATGATCCTGT+TGG - chr3.4:4864398-4864417 MS.gene51649:CDS 35.0%
CTTAAGCTTATCACAAGTGA+AGG + chr3.4:4864236-4864255 None:intergenic 35.0%
GGTTATGATCCAAGTTTCTT+TGG - chr3.4:4864500-4864519 MS.gene51649:CDS 35.0%
GTTAAAACCAACAGGATCAT+TGG + chr3.4:4864408-4864427 None:intergenic 35.0%
TCAACAAGGTTAAAACCAAC+AGG + chr3.4:4864416-4864435 None:intergenic 35.0%
! GTTTGGCTACATTTTCTCTT+TGG + chr3.4:4864304-4864323 None:intergenic 35.0%
!! ATGAGTTGATATCATGGATG+AGG + chr3.4:4864054-4864073 None:intergenic 35.0%
!!! ACTGGCCTTTCATTGTTTTT+AGG - chr3.4:4864257-4864276 MS.gene51649:CDS 35.0%
!!! GCCTTTCATTGTTTTTAGGA+AGG - chr3.4:4864261-4864280 MS.gene51649:CDS 35.0%
ATCTTGGCTACTTCTAGCAA+TGG - chr3.4:4864479-4864498 MS.gene51649:CDS 40.0%
CTTGTGATAAGCTTAAGCAC+TGG - chr3.4:4864239-4864258 MS.gene51649:CDS 40.0%
! ACTTTTGTTGACCTTGTGAG+AGG + chr3.4:4864152-4864171 None:intergenic 40.0%
! CTTTTGTTGACCTTGTGAGA+GGG + chr3.4:4864151-4864170 None:intergenic 40.0%
!!! ACCTTGTTGATGTTTTGGCT+TGG - chr3.4:4864426-4864445 MS.gene51649:CDS 40.0%
!!! CCTTGTTGATGTTTTGGCTT+GGG - chr3.4:4864427-4864446 MS.gene51649:CDS 40.0%
!!! CTTGTTGATGTTTTGGCTTG+GGG - chr3.4:4864428-4864447 MS.gene51649:CDS 40.0%
AAGGTTTCAACCCTCTCACA+AGG - chr3.4:4864138-4864157 MS.gene51649:CDS 45.0%
CAAGGCTTACCTGAGCAAAA+TGG - chr3.4:4864323-4864342 MS.gene51649:CDS 45.0%
CCATCAAGCTTATCCTTCCA+AGG - chr3.4:4864119-4864138 MS.gene51649:CDS 45.0%
CCCAAGCCAAAACATCAACA+AGG + chr3.4:4864430-4864449 None:intergenic 45.0%
CCTTGGAAGGATAAGCTTGA+TGG + chr3.4:4864122-4864141 None:intergenic 45.0%
TTGTGAGAGGGTTGAAACCT+TGG + chr3.4:4864139-4864158 None:intergenic 45.0%
! TGTGTCACACCATTTTGCTC+AGG + chr3.4:4864335-4864354 None:intergenic 45.0%
!! TTGCTCAGGTAAGCCTTGTT+TGG + chr3.4:4864321-4864340 None:intergenic 45.0%
!!! GTTTTGGCTTGGGGTTCTTT+AGG - chr3.4:4864437-4864456 MS.gene51649:CDS 45.0%
AGCTGGTGACAAACGTGCTA+AGG - chr3.4:4864361-4864380 MS.gene51649:CDS 50.0%
GAGAGGGTTGAAACCTTGGA+AGG + chr3.4:4864135-4864154 None:intergenic 50.0%
!! GGTGTGACACACTTTGAAGC+TGG - chr3.4:4864344-4864363 MS.gene51649:CDS 50.0%


Chromosome Type Strat End Strand Name
chr3.4 gene 4864038 4864526 4864038 ID=MS.gene51649
chr3.4 mRNA 4864038 4864526 4864038 ID=MS.gene51649.t1;Parent=MS.gene51649
chr3.4 exon 4864038 4864526 4864038 ID=MS.gene51649.t1.exon1;Parent=MS.gene51649.t1
chr3.4 CDS 4864038 4864526 4864038 ID=cds.MS.gene51649.t1;Parent=MS.gene51649.t1
Gene Sequence

>MS.gene51649

ATGGCAGCTTCAGCCTCATCCATGATATCAACTCATGCATTAACAACCACCATTCAAAAACACAAAACTCACAATCTCAAGCCATCAAGCTTATCCTTCCAAGGTTTCAACCCTCTCACAAGGTCAACAAAAGTCAACACATTCACACCAAGCAAAAAGAGATTTTCAAGTGTTGTTGTCAAAGCTGAACTCAACCCTTCACTTGTGATAAGCTTAAGCACTGGCCTTTCATTGTTTTTAGGAAGGTTTGTGTTTTTCAACTTCCAAAGAGAAAATGTAGCCAAACAAGGCTTACCTGAGCAAAATGGTGTGACACACTTTGAAGCTGGTGACAAACGTGCTAAGGAATATGTTAGCTTGCTTAAATCCAATGATCCTGTTGGTTTTAACCTTGTTGATGTTTTGGCTTGGGGTTCTTTAGGTCATATTGTTGCTTACTATATCTTGGCTACTTCTAGCAATGGTTATGATCCAAGTTTCTTTGGTTGA

Protein sequence

>MS.gene51649.t1

MAASASSMISTHALTTTIQKHKTHNLKPSSLSFQGFNPLTRSTKVNTFTPSKKRFSSVVVKAELNPSLVISLSTGLSLFLGRFVFFNFQRENVAKQGLPEQNGVTHFEAGDKRAKEYVSLLKSNDPVGFNLVDVLAWGSLGHIVAYYILATSSNGYDPSFFG