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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaattcctctttcagctgcagctgcactattctcatcatatgcttttagtatgtgccttggtccattgaacttactatattctgttttcgatttgcagTCTGCAACTGAAACATCTAATGTAGATGGACCTGAGGACAACAATGACTCTGACGAGGAAGATGAAGAGGAAGAGGAAGAGAAAACATCTTCAGCGAAGA

Basic information

species Oryza sativa
transcript LOC_Os01g56140.1
intron # 7
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|32947889|gb|BP184461.1|BP184461
EST:     TGGATAATTCAGATTCTGTCCAAGAGGAACCTTCGGTGGAGGCTACAGTG                         TCTGCAACTGAAACATCTAATGTAGATGGACCTGAGGACAACAATGACTCT
genomic: TGGATAATTCAGATTCTGTCCAAGAGGAACCTTCGGTGGAGGCTACAGTGgtaattcctc ... cgatttgcagTCTGCAACTGAAACATCTAATGTAGATGGACCTGAGGACAACAATGACTCT
EST: gi|89173827|gb|CI041720.1|CI041720
EST:     TGGATAATTCAGATTCTGTCCAAGAGGAACCTTCGGTGGAGGCTACAGTG                         TCTGCAACTGAAACATCTAATGTAGATGGACCTGAGGACAACAATGACTCT
genomic: TGGATAATTCAGATTCTGTCCAAGAGGAACCTTCGGTGGAGGCTACAGTGgtaattcctc ... cgatttgcagTCTGCAACTGAAACATCTAATGTAGATGGACCTGAGGACAACAATGACTCT
EST: gi|33799065|gb|CF325392.1|CF325392
EST:     TGGATAATTCAGATTCTGTCCAAGAGGAACCTTCGGTGGAGGCTACAGTG                         TCTGCAACTGAAACATCTAATGTAGATGGACCTGAGGACAACAATGACTCT
genomic: TGGATAATTCAGATTCTGTCCAAGAGGAACCTTCGGTGGAGGCTACAGTGgtaattcctc ... cgatttgcagTCTGCAACTGAAACATCTAATGTAGATGGACCTGAGGACAACAATGACTCT
EST: gi|24468778|gb|CA305727.1|CA305727
EST:     TGGATAATTCAGATTCTGTCCAAGAGGAACCTTCGGTGGAGGCTACAGTG                         TCTGCAACTGAAACATCTAATGTAGATGGACCTGAGGACAACAATGACTCT
genomic: TGGATAATTCAGATTCTGTCCAAGAGGAACCTTCGGTGGAGGCTACAGTGgtaattcctc ... cgatttgcagTCTGCAACTGAAACATCTAATGTAGATGGACCTGAGGACAACAATGACTCT
EST: gi|88688999|gb|CI732575.1|CI732575
EST:     TGGATAATTCAGATTCTGTCCAAGAGGAACCTTCGGTGGAGGCTACAGTG                         TCTGCAACTGAAACATCTAATGTAGATGGACCTGAGGA
genomic: TGGATAATTCAGATTCTGTCCAAGAGGAACCTTCGGTGGAGGCTACAGTGgtaattcctc ... cgatttgcagTCTGCAACTGAAACATCTAATGTAGATGGACCTGAGGA
EST: gi|88834303|gb|CI000667.1|CI000667
EST:     TGGATAATTCAGATTCTGTCCAAGAGGAACCTTCGGTGGAGGCTACAGTG                         TCTGCAACTGAAACATCTAATGTAGATGGACCTGAGGACAACAATGACTCT
genomic: TGGATAATTCAGATTCTGTCCAAGAGGAACCTTCGGTGGAGGCTACAGTGgtaattcctc ... cgatttgcagTCTGCAACTGAAACATCTAATGTAGATGGACCTGAGGACAACAATGACTCT
EST: gi|88984271|gb|CI020186.1|CI020186
EST:     TGGATAATTCAGATTCTGTCCAAGAGGAACCTTCGGTGGAGGCTACAGTG                         TCTGCAACTGAAACATCTAATGTAGATGGACCTGAGGACAACAATGACTCT
genomic: TGGATAATTCAGATTCTGTCCAAGAGGAACCTTCGGTGGAGGCTACAGTGgtaattcctc ... cgatttgcagTCTGCAACTGAAACATCTAATGTAGATGGACCTGAGGACAACAATGACTCT
EST: gi|58030303|gb|CX727846.1|CX727846
EST:     TGGATAATTCAGATTCTGTCCAAGAGGAACCTTCGGTGGAGGCTACAGTG                         TCTGCAACTGAAACATCTAATGTAGATGGACCTGAGGACAACAATGACTCT
genomic: TGGATAATTCAGATTCTGTCCAAGAGGAACCTTCGGTGGAGGCTACAGTGgtaattcctc ... cgatttgcagTCTGCAACTGAAACATCTAATGTAGATGGACCTGAGGACAACAATGACTCT
EST: gi|88689004|gb|CI732580.1|CI732580
EST:     TGGATAATTCAGATTCTGTCCAAGAGGAACCTTCGGTGGAGGCTACAGTG                         TCTGCAACTGAAACATCTAATGTAGATGGACCTGAGGAC
genomic: TGGATAATTCAGATTCTGTCCAAGAGGAACCTTCGGTGGAGGCTACAGTGgtaattcctc ... cgatttgcagTCTGCAACTGAAACATCTAATGTAGATGGACCTGAGGAC
EST: gi|29634265|gb|CB639274.1|CB639274
EST:     TGGATAATTCAGATTCTGTCCAAGAGGAACCTTCGGTGGAGGCTACAGTG                         TCTGCAACTGAAACATCTAATGTAGATGGACCTGAGGACAACAATGACTCT
genomic: TGGATAATTCAGATTCTGTCCAAGAGGAACCTTCGGTGGAGGCTACAGTGgtaattcctc ... cgatttgcagTCTGCAACTGAAACATCTAATGTAGATGGACCTGAGGACAACAATGACTCT
EST: gi|88841064|gb|CI001026.1|CI001026
EST:     TGGATAATTCAGATTCTGTCCAAGAGGAACCTTCGGTGGAGGCTACAGTG                         TCTGCAACTGAAACATCTAATGTAGATGGACCTGAGGACAACAATGACTCT
genomic: TGGATAATTCAGATTCTGTCCAAGAGGAACCTTCGGTGGAGGCTACAGTGgtaattcctc ... cgatttgcagTCTGCAACTGAAACATCTAATGTAGATGGACCTGAGGACAACAATGACTCT

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: 75 (upstream exon), 75 (downstream exon)
Score: 16

ACCAGGAGAACCAGCTTCATCTGTTGATGTGCCTTACGTGAACGGAATAGTGGATAATTCAGATTCTGTCCAAGAGGAACCTTCGGTGGAGGCTACAGTGgtaattcctc ... cgatttgcagTCTGCAACTGAAACATCTAATGTAGATGGACCTGAGGACAACAATGACTCTGACGAGGAAGATGAAGAGGAAGAGGAAGAGAAAACATCTTCAGCGAAGA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttttagtatgtgccttggtccattgaacttactatattctgttttcgatttgcagTCTGCAACTGAAACATCTAATGTAGATGGACCTGAGGACAACAATGACTCTGACGAGGAAGATGAAGAGGAAGAGGAAGAGAAAACATCTTCAGCGAAGA
                         aacttac  putative branch site (score: 16)
                                    ttctgttttc  putative PPT
                            ttactatatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaattcctctttcagctgcagctgcactattctcatcatatgcttttagtatgtgccttggtccattgaacttactatattctgttttcgatttgcagTCTGCAACTGAAACATCTAATGTAGATGGACCTGAGGACAACAATGACTCTGACGAGGAAGATGAAGAGGAAGAGGAAGAGAAAACATCTTCAGCGAAGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA
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- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CGAAGA