AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene049396


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene049396.t1 MTR_3g094080 98.830 171 2 0 1 171 1 171 8.58e-126 350
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene049396.t1 AT3G56290 60.694 173 62 2 1 169 1 171 2.94e-69 207

Find 29 sgRNAs with CRISPR-Local

Find 40 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TTCTTCCTTCTTCTCTTGTT+TGG 0.250102 3.1:+75218369 None:intergenic
GCTAGAGAAGCCACAAAATC+TGG 0.342436 3.1:-75218253 MS.gene049396:CDS
CACTTGTCTTGCTTCACCCT+TGG 0.361736 3.1:+75217858 None:intergenic
AACATGCAAGGTATGCAAAA+AGG 0.370388 3.1:-75217884 MS.gene049396:CDS
TGTGCAGAGAAGGCAAAATC+TGG 0.391867 3.1:-75217805 MS.gene049396:CDS
GGAGCTCTTAGAAGGAAAAT+TGG 0.394746 3.1:-75218112 MS.gene049396:CDS
GAGAATATGTTGAAGAGGGT+TGG 0.421247 3.1:-75217915 MS.gene049396:CDS
AGAATATGTTGAAGAGGGTT+GGG 0.437524 3.1:-75217914 MS.gene049396:CDS
TGCAGTATGGAGCTCTTAGA+AGG 0.445617 3.1:-75218120 MS.gene049396:intron
TGAGCATCTTGTGCGGATCT+TGG 0.446163 3.1:+75218289 None:intergenic
AACATACATAAATGGGTCTT+GGG 0.452482 3.1:-75218501 None:intergenic
GAACATACATAAATGGGTCT+TGG 0.457157 3.1:-75218502 None:intergenic
TTCAGCCAAACAAGAGAAGA+AGG 0.459242 3.1:-75218374 MS.gene049396:CDS
GTATAATAAGGAGGGGTCAA+TGG 0.496878 3.1:+75218472 None:intergenic
GAAAATTGGTGGGACTTACA+AGG 0.499480 3.1:-75218098 MS.gene049396:CDS
GCAAGACAAGTGGACAAGCT+TGG 0.505588 3.1:-75217847 MS.gene049396:CDS
AATCTGGAGAACAAATGAGC+AGG 0.519508 3.1:-75218237 MS.gene049396:CDS
CTCTTAGAAGGAAAATTGGT+GGG 0.533115 3.1:-75218108 MS.gene049396:CDS
AGAACAAATGAGCAGGGAGC+AGG 0.543107 3.1:-75218230 MS.gene049396:intron
GGATGGAGAATATGTTGAAG+AGG 0.544093 3.1:-75217920 MS.gene049396:CDS
TCATGTAGCATGTGCAGAGA+AGG 0.566077 3.1:-75217815 MS.gene049396:CDS
ATCTGGAGAACAAATGAGCA+GGG 0.576834 3.1:-75218236 MS.gene049396:CDS
AGATGCTCAGCTTATACAAG+AGG 0.596458 3.1:-75218275 MS.gene049396:CDS
GATGGAGAATATGTTGAAGA+GGG 0.605246 3.1:-75217919 MS.gene049396:CDS
GCTCTTAGAAGGAAAATTGG+TGG 0.606049 3.1:-75218109 MS.gene049396:CDS
AAAACTTGTATAATAAGGAG+GGG 0.613562 3.1:+75218465 None:intergenic
CAAGGGTGAAGCAAGACAAG+TGG 0.622923 3.1:-75217857 MS.gene049396:CDS
TTGGGTAGACAAAACATGCA+AGG 0.654898 3.1:-75217896 MS.gene049396:CDS
TATAAGCTGAGCATCTTGTG+CGG 0.655921 3.1:+75218282 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AAAAACTTGTATAATAAGGA+GGG + chr3.1:75217803-75217822 None:intergenic 20.0%
!! GAAGAAAAACTTGTATAATA+AGG + chr3.1:75217807-75217826 None:intergenic 20.0%
!!! AATTATAGGAGTATATTGTT+TGG - chr3.1:75218277-75218296 MS.gene049396:CDS 20.0%
!!! TTTTTCAAATCTTATGTTGA+AGG - chr3.1:75218191-75218210 MS.gene049396:intron 20.0%
!!! TTTTTGTAAATAATGCAGTA+TGG - chr3.1:75218131-75218150 MS.gene049396:intron 20.0%
! AAAACTTGTATAATAAGGAG+GGG + chr3.1:75217802-75217821 None:intergenic 25.0%
! GAAAAACTTGTATAATAAGG+AGG + chr3.1:75217804-75217823 None:intergenic 25.0%
!! CATGTGATTAGTTGAATTAT+AGG - chr3.1:75218263-75218282 MS.gene049396:CDS 25.0%
! AGTTTTTCTTCAAAGTCATC+AGG - chr3.1:75217816-75217835 MS.gene049396:CDS 30.0%
AACATGCAAGGTATGCAAAA+AGG - chr3.1:75218380-75218399 MS.gene049396:CDS 35.0%
AGAATATGTTGAAGAGGGTT+GGG - chr3.1:75218350-75218369 MS.gene049396:CDS 35.0%
CTCTTAGAAGGAAAATTGGT+GGG - chr3.1:75218156-75218175 MS.gene049396:intron 35.0%
GATGGAGAATATGTTGAAGA+GGG - chr3.1:75218345-75218364 MS.gene049396:CDS 35.0%
TTCTTCCTTCTTCTCTTGTT+TGG + chr3.1:75217898-75217917 None:intergenic 35.0%
! AATCTTGTTGTATTGAGCAG+TGG - chr3.1:75218323-75218342 MS.gene049396:CDS 35.0%
! CATTTGTTCTCCAGATTTTG+TGG + chr3.1:75218024-75218043 None:intergenic 35.0%
AATCTGGAGAACAAATGAGC+AGG - chr3.1:75218027-75218046 MS.gene049396:intron 40.0%
AGATGCTCAGCTTATACAAG+AGG - chr3.1:75217989-75218008 MS.gene049396:intron 40.0%
ATCTGGAGAACAAATGAGCA+GGG - chr3.1:75218028-75218047 MS.gene049396:intron 40.0%
GAAAATTGGTGGGACTTACA+AGG - chr3.1:75218166-75218185 MS.gene049396:intron 40.0%
GAGAATATGTTGAAGAGGGT+TGG - chr3.1:75218349-75218368 MS.gene049396:CDS 40.0%
GCTCTTAGAAGGAAAATTGG+TGG - chr3.1:75218155-75218174 MS.gene049396:intron 40.0%
GGAGCTCTTAGAAGGAAAAT+TGG - chr3.1:75218152-75218171 MS.gene049396:intron 40.0%
GGATGGAGAATATGTTGAAG+AGG - chr3.1:75218344-75218363 MS.gene049396:CDS 40.0%
GTATAATAAGGAGGGGTCAA+TGG + chr3.1:75217795-75217814 None:intergenic 40.0%
GTATGCAAAAAGGACACCAA+GGG - chr3.1:75218390-75218409 MS.gene049396:CDS 40.0%
TATAAGCTGAGCATCTTGTG+CGG + chr3.1:75217985-75218004 None:intergenic 40.0%
TTCAGCCAAACAAGAGAAGA+AGG - chr3.1:75217890-75217909 MS.gene049396:CDS 40.0%
TTGGGTAGACAAAACATGCA+AGG - chr3.1:75218368-75218387 MS.gene049396:CDS 40.0%
TTGTTGTATTGAGCAGTGGA+TGG - chr3.1:75218327-75218346 MS.gene049396:CDS 40.0%
GCTAGAGAAGCCACAAAATC+TGG - chr3.1:75218011-75218030 MS.gene049396:intron 45.0%
GGTATGCAAAAAGGACACCA+AGG - chr3.1:75218389-75218408 MS.gene049396:CDS 45.0%
TCATGTAGCATGTGCAGAGA+AGG - chr3.1:75218449-75218468 MS.gene049396:CDS 45.0%
TGCAGTATGGAGCTCTTAGA+AGG - chr3.1:75218144-75218163 MS.gene049396:intron 45.0%
TGTGCAGAGAAGGCAAAATC+TGG - chr3.1:75218459-75218478 MS.gene049396:CDS 45.0%
AGAACAAATGAGCAGGGAGC+AGG - chr3.1:75218034-75218053 MS.gene049396:intron 50.0%
CAAGGGTGAAGCAAGACAAG+TGG - chr3.1:75218407-75218426 MS.gene049396:CDS 50.0%
CACTTGTCTTGCTTCACCCT+TGG + chr3.1:75218409-75218428 None:intergenic 50.0%
GCAAGACAAGTGGACAAGCT+TGG - chr3.1:75218417-75218436 MS.gene049396:CDS 50.0%
TGAGCATCTTGTGCGGATCT+TGG + chr3.1:75217978-75217997 None:intergenic 50.0%


Chromosome Type Strat End Strand Name
chr3.1 gene 75217774 75218512 75217774 ID=MS.gene049396
chr3.1 mRNA 75217774 75218512 75217774 ID=MS.gene049396.t1;Parent=MS.gene049396
chr3.1 exon 75218231 75218512 75218231 ID=MS.gene049396.t1.exon1;Parent=MS.gene049396.t1
chr3.1 CDS 75218231 75218512 75218231 ID=cds.MS.gene049396.t1;Parent=MS.gene049396.t1
chr3.1 exon 75218074 75218137 75218074 ID=MS.gene049396.t1.exon2;Parent=MS.gene049396.t1
chr3.1 CDS 75218074 75218137 75218074 ID=cds.MS.gene049396.t1;Parent=MS.gene049396.t1
chr3.1 exon 75217774 75217943 75217774 ID=MS.gene049396.t1.exon3;Parent=MS.gene049396.t1
chr3.1 CDS 75217774 75217943 75217774 ID=cds.MS.gene049396.t1;Parent=MS.gene049396.t1
Gene Sequence

>MS.gene049396

ATGGGTCTTGGGACTTTGCCATTGACCCCTCCTTATTATACAAGTTTTTCTTCAAAGTCATCAGGACTTGTACATAAAAATACTAATAATTGCAATAGAAGCAAAAAATTCATAGTTTCAGCCAAACAAGAGAAGAAGGAAGAAGATAAGAATAAGCAATCTTTTTTTACTAGTGTAACTGATGCTCTTGATTTTGCTCAACCAAGATCCGCACAAGATGCTCAGCTTATACAAGAGGCTAGAGAAGCCACAAAATCTGGAGAACAAATGAGCAGGGAGCAGGTATATTATAATTAATCTTCTAAATTGTTCATCTTTCATAATCAATAATCTTTATGATTCTCTTTAATTTTTATATTTTTGTAAATAATGCAGTATGGAGCTCTTAGAAGGAAAATTGGTGGGACTTACAAGGATTTTTTCAAATCTTATGTTGAAGGTATAGTTACTAATGAAATAAAAAATTGATACAATATGCTCTTAAAGAAGCATGTGATTAGTTGAATTATAGGAGTATATTGTTTGGTTTAGAAACATAATTGAAACATTAATCTTGTTGTATTGAGCAGTGGATGGAGAATATGTTGAAGAGGGTTGGGTAGACAAAACATGCAAGGTATGCAAAAAGGACACCAAGGGTGAAGCAAGACAAGTGGACAAGCTTGGAAGATATGTTCATGTAGCATGTGCAGAGAAGGCAAAATCTGGAAACTTCTTTACCAGACTCTTCTTTTTATGA

Protein sequence

>MS.gene049396.t1

MGLGTLPLTPPYYTSFSSKSSGLVHKNTNNCNRSKKFIVSAKQEKKEEDKNKQSFFTSVTDALDFAQPRSAQDAQLIQEAREATKSGEQMSREQYGALRRKIGGTYKDFFKSYVEVDGEYVEEGWVDKTCKVCKKDTKGEARQVDKLGRYVHVACAEKAKSGNFFTRLFFL