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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gtgctgtacataacacctatctgtgtgcagttctgctcttgtttttgaagtaactatacatttataaacatgctatttactcaagtaataacatcaatagGTCGTGAGCAACCCTGAGAAGACTCCACTTCATACTTTCTTCTGCAGCTATGACTTGACAGACATGCCTTCAGGGACCAAG

Basic information

species Oryza sativa
transcript LOC_Os08g42420.3
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os08g42420.3 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G138425_T02 (Zea mays), 3'ss of exon 3
-gtgctgtacataac---acctatctgtgtgcagttctgctcttgtttttgaagtaactatacatttataaacatgctatttactcaagtaataacatcaatagGTCGTGAGCAACCCTGAGAAGACTCCACTTCATACTTTCTTCTGCAGCTATGACTTGACAGACATGCCTTCAGGGACCAAG
   | | ||||  |    |  ||    | |||    |||| |   |||| | |||     | |   | |    |   | |  | | ||  ||| || |  | |||| || |||||||| ||||||||||||||||||||||||||||||| |||||||||||  ||||||||| | || ||||||
aaagatttacaggatctgatttacacatctgcg--cctgcccac-ttttgggagttgtattccgagtctctgtacaat-tgaaataaaaaaatgactttgacagGTGGTAAGCAACCCAGAGAAGACTCCACTTCATACTTTCTTCTGCAACTATGACTTGAGTGACATGCCTCCTGGAACCAAG

upper sequence: LOC_Os08g42420.3 (Oryza sativa), 3'ss of exon 4
lower sequence: EFJ28764 (Selaginella moellendorffii), 3'ss of exon 2
gtgctgtacataacacctatctgtgtgcagttctgctcttgtttttgaagtaactatacatttataaacatgcta-tttactcaagtaat--aacatcaatagGTCGTGAGCAACCCTGAGAAGACTCCACTTCATACTTTCTTCTGCAGCTATGACTTGACAGACATGCCTTCAGGGACCAAG
                                             | ||||   ||| | || |      | ||| ||| ||||||   |  |       ||||| |||||||| || || ||||| ||  | ||||| ||| |||||||||||||||||||||| |||||  |||| ||||||
--------------------------------------------gtaaagtgtttattcgttga--ggtgtcctagttttctcaagggctctattggttgtagGTGGTGAGCAATCCAGAAAAGACCCCTGTACATACATTCATCTGCAGCTATGACTTGACAGATATGCCACCAGGAACCAAG
















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|33683475|gb|CF311714.1|CF311714
EST:     GATCAGCCAAAAGTCGCTTACGGATCCCTGTTAAGGGCAGGATACAGCTG                         GTCGTGAGCAACCCTGAGAAGACTCCACTTCATACTTTCTTCTGCAGCTAT
genomic: GATCAGCCAAAAGTCGCTTACGGATCCCTGTTAAGGGCAGGATACAGCTGgtactatatt ... acatcaatagGTCGTGAGCAACCCTGAGAAGACTCCACTTCATACTTTCTTCTGCAGCTAT
EST: gi|58695877|gb|CK084564.1|CK084564
EST:     GATCAGCCAAAAGTCGCTTACGGATCCCTGTTAAGGGCAGGATACAACTG                         GTCGTGAGCAACCCTGAGAAGACTCCACTTCATACTTTCTTCTGCAGCTAT
genomic: GATCAGCCAAAAGTCGCTTACGGATCCCTGTTAAGGGCAGGATACAGCTGgtactatatt ... acatcaatagGTCGTGAGCAACCCTGAGAAGACTCCACTTCATACTTTCTTCTGCAGCTAT
EST: gi|58587810|gb|CF986118.1|CF986118
EST:     GGGCAGGATACAACTG                         GTCGTGAGCAACCCTGAGAAGACTCCACTTCATACTTTCTTCTGCAGCTAT
genomic: GGGCAGGATACAGCTGgtactatatt ... acatcaatagGTCGTGAGCAACCCTGAGAAGACTCCACTTCATACTTTCTTCTGCAGCTAT
EST: gi|29674773|gb|CB671048.1|CB671048
EST:     GATCAGCCAAAAGTCGCTTACGGATCCCTGTTAAGGGCAGGATACAGCTG                         GTCGTGAGCAACCCTGAGAAGACTCCACTTCATACTTTCTTCTGCAGCTAT
genomic: GATCAGCCAAAAGTCGCTTACGGATCCCTGTTAAGGGCAGGATACAGCTGgtactatatt ... acatcaatagGTCGTGAGCAACCCTGAGAAGACTCCACTTCATACTTTCTTCTGCAGCTAT
EST: gi|25797222|gb|CA753183.1|CA753183
EST:     GATCAGCCAAAAGTCGCTTACGGATCCCTGTTAAGGGCAGGATACAACTG                         GTCGTGAGCAACCCTGAGAAGACTCCACTTCATACTTTCTTCTGCAGCTAT
genomic: GATCAGCCAAAAGTCGCTTACGGATCCCTGTTAAGGGCAGGATACAGCTGgtactatatt ... acatcaatagGTCGTGAGCAACCCTGAGAAGACTCCACTTCATACTTTCTTCTGCAGCTAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgaagtaactatacatttataaacatgctatttactcaagtaataacatcaatagGTCGTGAGCAACCCTGAGAAGACTCCACTTCATACTTTCTTCTGCAGCTATGACTTGACAGACATGCCTTCAGGGACCAAG
                                        taataac  putative branch site (score: 1)
     taactatacatttata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgctgtacataacacctatctgtgtgcagttctgctcttgtttttgaagtaactatacatttataaacatgctatttactcaagtaataacatcaatagGTCGTGAGCAACCCTGAGAAGACTCCACTTCATACTTTCTTCTGCAGCTATGACTTGACAGACATGCCTTCAGGGACCAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGCT