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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCGGTTCCCCGTCGACCACGAGATCAACTCGAAGATCTGTCTCTGGCGCGGCCACCCGTGGAACCTTGAGGTCGATGCCGTTGTCAATTCGACAAATGAGgtcggaattcgcttagctgctagcctcgtggtgttggcgtgctgctaatgttacagttgatatgataagttttgtggttggtgtag

Basic information

species Oryza sativa
transcript LOC_Os03g05660.1
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g05660.1 (Oryza sativa), 5'ss of exon 1
lower sequence: GRMZM2G100707_T01 (Zea mays), 5'ss of exon 1
GCGGTTCCCCGTCGACCACGAGATCAACTCGAAGATCTGTCTCTGGCGCGGCCACCCGTGGAACCTTGAGGTCGATGCCGTTGTCAATTCGACAAATGAGgtcggaattcgcttagctgctagcc--tcgtggtgttggcgtgctgctaatgttacagttgatatgataagttttgtggttggtgtag
|||||||||||||||  |||||||||||||||||||||  |||||||| ||||| ||||||||||| |||||||| ||||| ||||| || || || |||||||| |||| ||   | | |   |  ||  | | | |   |||| | |  |  | | |       || | || || ||||| |||||
GCGGTTCCCCGTCGATTACGAGATCAACTCGAAGATCTACCTCTGGCGAGGCCATCCGTGGAACCTCGAGGTCGACGCCGTCGTCAACTCCACCAACGAGgtcgggattctctcctcggttgttcaatcaagctat-gaaatgcttcaatcgagatactgatggccattacttctgaggttg-tgtag

upper sequence: LOC_Os03g05660.1 (Oryza sativa), 5'ss of exon 1
lower sequence: GLYMA02G12670.1 (Glycine max), 5'ss of exon 2
GCGGTTCCCCGTCGACCACGAGATCAACTCGAAGATCTGTCTCTGGCGCGGCCACCCGTGGAACCTTGAGGTCGATGCCGTTGTCAATTCGACAAATGAGgtcggaattcgcttagctgc-----tagcctcgtggtgttggcgtgctgctaatgtt---acagttgatatgataagttttg---tggttggtgtag---
  |||| || || ||||| ||  | || || ||||| |   | ||| | ||  |||| |||||||||||||| ||||| || || |||||||| ||||||||  |     || |   ||      | || | ||| |||||  ||   | |  | ||   | | |||    | |  |||||    |  ||||| | |   
AAGGTTTCCTGTTGACCATGAAGTTAATTCTAAGATATACTTGTGGAGGGGGAACCCCTGGAACCTTGAGGTTGATGCTGTGGTAAATTCGACGAATGAGgtgagtgagtgcgtgtgtgtatgtgttgcttagtgctgttgtagtttagtttttctttatatatttgtgtagtttggttttacttttcttggtttggtaa

upper sequence: LOC_Os03g05660.1 (Oryza sativa), 5'ss of exon 1
lower sequence: GLYMA01G06730.1 (Glycine max), 5'ss of exon 2
GCGGTTCCCCGTCGACCACGAGATCAACTCGAAGATCTGTCTCTGGCGCGGCCACCCGTGGAACCTTGAGGTCGATGCCGTTGTCAATTCGACAAATGAGgtcggaattcgcttagctgc---tagcctcgtggtgttggcgtgctgctaatgttacagttgatatgataagttttg----tggttggtgtag--------
  |||| || || ||||| ||  | || |||||||| |   | ||| | ||  |||| |||||||||||||| ||||| || || ||||| |||||||||||  |     || |   ||    | || |     ||| |    | |  |  |  || |  || | |  |  |||||     |  ||||| | |        
AAGGTTTCCTGTTGACCATGAAGTGAATTCGAAGATATACTTGTGGAGGGGGAACCCCTGGAACCTTGAGGTGGATGCTGTGGTAAATTCAACAAATGAGgtgagtgagtgcatgtgtgtgtgtggcttaaaattgtagtttagttcttctttatataactg-tgtagtttgtttttacttttcttggttttgtaattgca

upper sequence: LOC_Os03g05660.1 (Oryza sativa), 5'ss of exon 1
lower sequence: AT1G69340.1 (Arabidopsis thaliana), 5'ss of exon 2
GCGGTTCCCCGTCGACCACGAGATCAACTCGAAGATCTGTCTCTGGCGCGGCCACCCGTGGAACCTTGAGGTCGATGCCGTTGTCAATTCGACAAATGAGgtcggaa---ttcgcttagctgc--tagcct-cgtggtgttggcgtgctgctaatgtta--cagttgatatgat-aagttttgtggttggtgtag-----
   ||| || || || |||||||| ||||| |  || |  || ||| | ||  | || |||||||||||||| ||||| ||||| |||||||||||||||||  ||    |||    |  |    | || | || |    |    | ||  ||||||    | | ||||||| | ||  ||| | | |  || ||     
TAAGTTTCCTGTTGATCACGAGATAAACTCTAGAATATACCTTTGGAGAGGGGAACCTTGGAACCTTGAGGTTGATGCTGTTGTAAATTCGACAAATGAGgtaagatgatttcaaggaattatatttgcttgcgagtaagtaagtttctcttaatgtgcgtctgatgatatggttaaaatttcttggtattggaggacag

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|33793226|gb|CF322493.1|CF322493
EST:     GCCACCCGTGGAACCTTGAGGTCGATGCCGTTGTCAATTCGACAAATGAG                         AACTTGGACGAGGCGCATAGTAGTCCAGGGCTGCATGCAGCGGCTGGGCCA
genomic: GCCACCCGTGGAACCTTGAGGTCGATGCCGTTGTCAATTCGACAAATGAGgtcggaattc ... gttggtgtagAACTTGGACGAGGCGCATAGTAGTCCAGGGCTGCATGCAGCGGCTGGGCCA
EST: gi|58677193|gb|CK065880.1|CK065880
EST:     GCCACCCGTGGAACCTTGAGGTCGATG-CGTTGTCAATTCGAGAAATGAG                         AACTTGGACGAGGCGCATAGTAGTCCAGGGTCTGCATGCAGCGGCTGGGCC
genomic: GCCACCCGTGGAACCTTGAGGTCGATGCCGTTGTCAATTCGACAAATGAGgtcggaattc ... gttggtgtagAACTTGGACGAGGCGCATAGTAGTCCAGGG-CTGCATGCAGCGGCTGGGCC

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), 71 (downstream exon)
Score: 5

GCGGTTCCCCGTCGACCACGAGATCAACTCGAAGATCTGTCTCTGGCGCGGCCACCCGTGGAACCTTGAGGTCGATGCCGTTGTCAATTCGACAAATGAGgtcggaattc ... gttggtgtagAACTTGGACGAGGCGCATAGTAGTCCAGGGCTGCATGCAGCGGCTGGGCCAGGGCTCGCCGAGGAGTGCACCACCCTG




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