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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgtgagtcttcaaatattgtgcaattatccgttctgttttactactccaagtacttggcaaattagtgaaaacaattaatgaatatttccagGGTAAATTGAGGGAAAGAAATCCTGGAAATGCTCTTTTGGAG

Basic information

species Oryza sativa
transcript LOC_Os01g48990.1
intron # 4
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|703010|gb|D49301.1|D49301
EST:     GACGGCAGCAGAACAG                         GGTAAATTGAGGGAAAGAAATCCTGGAAATNCTCTTTTGGAG
genomic: GACGGCAGCAGAACAGgtgtgagtct ... atatttccagGGTAAATTGAGGGAAAGAAATCCTGGAAATGCTCTTTTGGAG
EST: gi|88336261|gb|CI648848.1|CI648848
EST:     ATGCCGCTACATTATCTATCGATGACTTCTACTTGACGGCAGCAGAACAG                         GGTAAATTGAGGGAAAGAAATCCTGGAAATGCTCTTTTGGAG
genomic: ATGCCGCTACATTATCTATCGATGACTTCTACTTGACGGCAGCAGAACAGgtgtgagtct ... atatttccagGGTAAATTGAGGGAAAGAAATCCTGGAAATGCTCTTTTGGAG
EST: gi|88330501|gb|CI633714.1|CI633714
EST:     ATGCCGCTACATTATCTATCGATGACTTCTACTTGACGGCAGCAGAACAG                         GGTAAATTGAGGGAAAGAAATCCTGGAAATGCTCTTTTGGAG
genomic: ATGCCGCTACATTATCTATCGATGACTTCTACTTGACGGCAGCAGAACAGgtgtgagtct ... atatttccagGGTAAATTGAGGGAAAGAAATCCTGGAAATGCTCTTTTGGAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttactactccaagtacttggcaaattagtgaaaacaattaatgaatatttccagGGTAAATTGAGGGAAAGAAATCCTGGAAATGCTCTTTTGGAG
                                    aattaat  putative branch site (score: 3)
                                              tatttcc  putative PPT
                      aaattagtgaaaacaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgtgagtcttcaaatattgtgcaattatccgttctgttttactactccaagtacttggcaaattagtgaaaacaattaatgaatatttccagGGTAAATTGAGGGAAAGAAATCCTGGAAATGCTCTTTTGGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGGAG