Skip to another splice site:
1  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cagcctccgcttaatactctaatcaattcttgttcgcgagcgcgagaataataccactaatgatccagctaataataacactagcaactgtctcgtgcagTCGCTGTTCCCGGGGCTGTGGCTGACCGAGATCACCGCCGACGCCTACAAGGTCCCCGACGACTAGCACCACCACCCCAGCACCAGCTCCGGCTGGCCAG

Basic information

species Oryza sativa
transcript LOC_Os01g49440.1
intron # 1
splice site 3'
intron type U2

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|58600181|gb|CK010709.1|CK010709
EST:     CGCGGCGGCGGCCTCGGAAACGGCCTCGCGTCGTCCAGCGGCAGCTCGAT                         TCGCTGTTCCCGGGGCTGTGGCTGACCGAGATCGGCGCCGACGCCTACAAG
genomic: CGCGGCGGCGGCCTCGGAAACGGCCTCGCGTCGTCCAGCGGCAGCTCGATgtaagcccaa ... tctcgtgcagTCGCTGTTCCCGGGGCTGTGGCTGACCGAGATCACCGCCGACGCCTACAAG
EST: gi|88233588|gb|CI233437.1|CI233437
EST:     CGCGGCGGCGGCCTCGGAAACGGCCTCGCGTCGTCCAGCGGCAGCTCGAT                         TCGCTGTTCCCGGGGCTGTGGCTGACCGAGATCACCGCCGACGCCTACAAG
genomic: CGCGGCGGCGGCCTCGGAAACGGCCTCGCGTCGTCCAGCGGCAGCTCGATgtaagcccaa ... tctcgtgcagTCGCTGTTCCCGGGGCTGTGGCTGACCGAGATCACCGCCGACGCCTACAAG
EST: gi|38474055|gb|CF958187.1|CF958187
EST:     CGCGGCGGCGGCCTCGGAAACGGCCTCGCGTCGTCCAGCGGCAGCTCGAT                         TCGCTGTTCCCGGGGCTGTGGCTGACCGAGATCACCGCCGACGCCTACAAG
genomic: CGCGGCGGCGGCCTCGGAAACGGCCTCGCGTCGTCCAGCGGCAGCTCGATgtaagcccaa ... tctcgtgcagTCGCTGTTCCCGGGGCTGTGGCTGACCGAGATCACCGCCGACGCCTACAAG
EST: gi|88233657|gb|CI233506.1|CI233506
EST:     CGCGGCGGCGGCCTCGGAAACGGCCTCGCGTCGTCCAGCGGCAGCTCGAT                         TCGCTGTTCCCGGGGCTGTGGCTGACCGAGATCACCGCCGACGCCTACAAG
genomic: CGCGGCGGCGGCCTCGGAAACGGCCTCGCGTCGTCCAGCGGCAGCTCGATgtaagcccaa ... tctcgtgcagTCGCTGTTCCCGGGGCTGTGGCTGACCGAGATCACCGCCGACGCCTACAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gaataataccactaatgatccagctaataataacactagcaactgtctcgtgcagTCGCTGTTCCCGGGGCTGTGGCTGACCGAGATCACCGCCGACGCCTACAAGGTCCCCGACGACTAGCACCACCACCCCAGCACCAGCTCCGGCTGGCCAG
                           taataac  putative branch site (score: 1)
                                          ctgtctc  putative PPT
                        taataataacacta  TA-rich tract
















Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cagcctccgcttaatactctaatcaattcttgttcgcgagcgcgagaataataccactaatgatccagctaataataacactagcaactgtctcgtgcagTCGCTGTTCCCGGGGCTGTGGCTGACCGAGATCACCGCCGACGCCTACAAGGTCCCCGACGACTAGCACCACCACCCCAGCACCAGCTCCGGCTGGCCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTC
- - - - - - - - - - - - -attcttg
- - - - - - - - - - - - - - - - - - - - - -gagaataa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tccagct
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cactagc