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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGGTGTGCGTGCCTGGCGTGCCCAACCACCTGACCTACGCCGACTTCGGCCGCTTCTGCGCATCCTGGGCCTCCCACATCCTCGAGACGCGCATCATCAGgtatcgtcgggtctcgattctcagttgggtgaaagcttcgctgatgataattctccgtagtagtagtagtagtagtagtagtagtagtagtagtagtaga...

Basic information

species Oryza sativa
transcript LOC_Os02g09060.1
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g09060.1 (Oryza sativa), 5'ss of exon 2
lower sequence: GRMZM2G041561_T01 (Zea mays), 5'ss of exon 2
GGGTGTGCGTGCCTGGCGTGCCCAACCACCTGACCTACGCCGACTTCGGCCGCTTCTGCGCATCCTGGGCCTCCCACATCCTCGAGACGCGCATCATCAGgta--tcgtcgggtctcgattctca-gttgggtgaaagcttcgctgatgataattctccgtagtagtagt-agtagtagtagtagtagtagtagtagtagtaga
||||||||||||  | ||||||||||||| ||||||||||||||||| |||| |||||||   |||  | | | ||||  ||||||| ||||||| ||||||   ||     | ||     |||  | |  |     | | ||||    ||  ||  | |      |||  ||||||   | |||| |     |   || |   
GGGTGTGCGTGCTCGCCGTGCCCAACCACATGACCTACGCCGACTTCTGCCGTTTCTGCGGCGCCTTCGTCCCTCACACACTCGAGATGCGCATCGTCAGgttgctcacattgccttatcactcctgctatgccttggttacgcttcatatggttg-ctgcttccctagcgagtagtctcaatagttgggtctgagttaat---
















Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|29677959|gb|CB674234.1|CB674234
EST:     CGCTTCTGCGCATCCTGGGCCTCCCACATCCTCGAGACGCGCATCATCAG                         GATTGATGGGGTGGAGGATCAGTACGGCGTTCTTATAAAATTCGACACTCA
genomic: CGCTTCTGCGCATCCTGGGCCTCCCACATCCTCGAGACGCGCATCATCAGgtatcgtcgg ... atgtttgtagGATTGATGGGGTGGAGGATCAGTACGGCGTTCTTATAAAATTCGACACTCA
EST: gi|88580349|gb|CI697269.1|CI697269
EST:     CGCTTCTGCGCATCCTGGGCCTCCCACATCCTCGAGACGCGCATCATCAG                         GATTGATGGGGTGGAGGATCAGTACGGCGTTCTTATAAAATTCGACACTCA
genomic: CGCTTCTGCGCATCCTGGGCCTCCCACATCCTCGAGACGCGCATCATCAGgtatcgtcgg ... atgtttgtagGATTGATGGGGTGGAGGATCAGTACGGCGTTCTTATAAAATTCGACACTCA
EST: gi|88587192|gb|CI704925.1|CI704925
EST:     CGCTTCTGCGCATCCTGGGCCTCCCACATCCTCGAGACGCGCATCATCAG                         GATTGATGGGGTGGAGGATCAGTACGGCGTCCTTATAAAATTCGACACTCA
genomic: CGCTTCTGCGCATCCTGGGCCTCCCACATCCTCGAGACGCGCATCATCAGgtatcgtcgg ... atgtttgtagGATTGATGGGGTGGAGGATCAGTACGGCGTTCTTATAAAATTCGACACTCA
EST: gi|88436585|gb|CI691313.1|CI691313
EST:     CGCTTCTGCGCATCCTGGGCCTCCCACATCCTCGAGACGCGCATCATCAG                         GATTGATGGGGTGGAGGATCAGTACGGCGTTCTTATAAAATTCGACACTCA
genomic: CGCTTCTGCGCATCCTGGGCCTCCCACATCCTCGAGACGCGCATCATCAGgtatcgtcgg ... atgtttgtagGATTGATGGGGTGGAGGATCAGTACGGCGTTCTTATAAAATTCGACACTCA
EST: gi|88405001|gb|CI685440.1|CI685440
EST:     CGCTTCTGCGCATCCTGGGCCTCCCACATCCTCGAGACGCGCATCATCAG                         GATTGATGGGGTGGAGGATCAGTACGGCGTTCTTATAAAATTCGACACTCA
genomic: CGCTTCTGCGCATCCTGGGCCTCCCACATCCTCGAGACGCGCATCATCAGgtatcgtcgg ... atgtttgtagGATTGATGGGGTGGAGGATCAGTACGGCGTTCTTATAAAATTCGACACTCA
EST: gi|88440811|gb|CI693379.1|CI693379
EST:     CGCTTCTGCGCATCCTGGGCCTCCCACATCCTCGAGACGCGCATCATCAG                         GATTGATGGGGTGGAGGATCAGTACGGCGTTCTTATAAAATTCGACACTCA
genomic: CGCTTCTGCGCATCCTGGGCCTCCCACATCCTCGAGACGCGCATCATCAGgtatcgtcgg ... atgtttgtagGATTGATGGGGTGGAGGATCAGTACGGCGTTCTTATAAAATTCGACACTCA
EST: gi|88378864|gb|CI681683.1|CI681683
EST:     CGCTTCTGCGCATCCTGGGCCTCCCACATCCTCGAGACGCGCATCATCAG                         GATTGATGGGGTGGAGGATCAGTACGGCGTTCTTATAAAATTCGACACTCA
genomic: CGCTTCTGCGCATCCTGGGCCTCCCACATCCTCGAGACGCGCATCATCAGgtatcgtcgg ... atgtttgtagGATTGATGGGGTGGAGGATCAGTACGGCGTTCTTATAAAATTCGACACTCA

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 1 RNA-Seqlibrary.


Block sizes: 60 (upstream exon), 65 (downstream exon)
Score: 24

GGGTGTGCGTGCCTGGCGTGCCCAACCACCTGACCTACGCCGACTTCGGCCGCTTCTGCGCATCCTGGGCCTCCCACATCCTCGAGACGCGCATCATCAGgtatcgtcgg ... atgtttgtagGATTGATGGGGTGGAGGATCAGTACGGCGTTCTTATAAAATTCGACACTCAGAGCTTCACGGATAGCTTCTACATGAGCTTTAACGGGAATCGGTTCTCA




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