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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ctgtatctttgctccttttaacttcccttccagtcaatggttgattttactttgaaagggttaatgacttctgaattctgacgagtgattcttcttgcagGATTGATGCCCTTCTCGGATGTGATTTTACAATTTGAGAGGACATGTCGAAATGCTTCAGAGTCGATAAG

Basic information

species Oryza sativa
transcript LOC_Os11g42420.2
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os11g42420.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G348675_T02 (Zea mays), 3'ss of exon 2
-ctgtatctttgc-tccttttaacttcccttccagtcaatggttgattttactttgaaagggttaatgacttctgaattctgacgagtgattcttcttgcagGATTGATGCCCTTCTCGGATGTGATTTTACAATTTGAGAGGACATGTCGAAATGCTTCAGAGTCGATAAG
 || | |  |||  |    | |  |       ||  |     ||  |||   |||   ||  || ||  ||| ||   | | | |  |   |  | || |||| ||||||| |||| | ||||| |||  |||||||||||||||||||||||||||||| ||||| || ||
gctatgttcttgggttgcatgagataaagcaacacccttcacttcctttccattttccag--ttcattgcttgtgctatttaatgtctctgttctgtttcagGTTTGATGCACTTCCCTGATGTAATTCAACAATTTGAGAGGACATGTCGAAATGCTTCGGAGTCAATCAG

upper sequence: LOC_Os11g42420.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G348675_T02 (Zea mays), 3'ss of exon 25
---------------ctgtatctttgc-tccttttaacttcccttccagtcaatggttgattttactttgaaagggttaatgacttctgaattctgacgagtgattcttcttgcagGATTGATGCCCTTCTCGGATGTGATTTTACAATTTGAGAGGACATGTCGAAATGCTTCAGAGTCGATAAG
               || | |  |||  |    | |  |       ||  |     ||  |||   |||   ||  || ||  ||| ||   | | | |  |   |  | || |||| ||||||| |||| | ||||| |||  |||||||||||||||||||||||||||||| ||||| || ||
gtgtgtaggtcttagctatgttcttgggttgcatgagataaagcaacacccttcacttcctttccattttccag--ttcattgcttgtgctatttaatgtctctgttctgtttcagGTTTGATGCACTTCCCTGATGTAATTCAACAATTTGAGAGGACATGTCGAAATGCTTCGGAGTCAATCAG
















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|29622702|gb|CB627713.1|CB627713
EST:     AGAAACAACTTCTACAATTTTTGCATCCCTCCTTGATTCTGCAATCCAAG                         GATTGATGCCCTTCTCGGATGTGATTTTACAATTTGAGAGGACATGTCGAA
genomic: AGAAACAACTTCTACAATTTTTGCATCCCTCCTTGATTCTGCAATCCAAGgttggtacaa ... cttcttgcagGATTGATGCCCTTCTCGGATGTGATTTTACAATTTGAGAGGACATGTCGAA




















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: 48 (upstream exon), 70 (downstream exon)
Score: 9

CGGTCGGCATTGAAATCAGTCAAACTGGAGGAGGATATGCCACATGAAGGAGAAACAACTTCTACAATTTTTGCATCCCTCCTTGATTCTGCAATCCAAGgttggtacaa ... cttcttgcagGATTGATGCCCTTCTCGGATGTGATTTTACAATTTGAGAGGACATGTCGAAATGCTTCAGAGTCGATAAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttactttgaaagggttaatgacttctgaattctgacgagtgattcttcttgcagGATTGATGCCCTTCTCGGATGTGATTTTACAATTTGAGAGGACATGTCGAAATGCTTCAGAGTCGATAAG
                              ttctgac  putative branch site (score: 9)
                                           ttcttcttgc  putative PPT
     tttgaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ctgtatctttgctccttttaacttcccttccagtcaatggttgattttactttgaaagggttaatgacttctgaattctgacgagtgattcttcttgcagGATTGATGCCCTTCTCGGATGTGATTTTACAATTTGAGAGGACATGTCGAAATGCTTCAGAGTCGATAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
ctgtatc
- - - - ttgctcc
- - - - - - - - - - - - -ccttcca
- - - - - - - - - - - - - - - - - - atggttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - acttctg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - attctga