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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgaggcctttcgcaatctcaatcacttctcatcagatgaattactagatttgcttgcccattgcttttaataagttattctatccccatttacggaatttctattggtattctcctgttagGTATGTCTTCGGTTGCTCATACACACACAATGTTGCTCCAAAAGGGAAGTTCATTGCATTTGTGTCTACAGAAGCAGAGACTGACCATCCAGAGTCTGAG

Basic information

species Oryza sativa
transcript LOC_Os05g34540.1
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os05g34540.1 (Oryza sativa), 3'ss of exon 10
lower sequence: GRMZM2G117507_T01 (Zea mays), 3'ss of exon 10
gtgaggcctttcgcaatctcaatcacttctcatcagatgaattactagatttgcttgcccattgcttttaataag----ttattctatccccatttacggaatttctattggtattctcctgttagGTATGTCTTCGGTTGCTCATACACACACAATGTTGCTCCAAAAGGGAAGTTCATTGCATTTGTGTCTACAGAAGCAGAGACTGACCATCCAGAGTCTGAG
|||||||||| | ||  || ||  | || ||||   || ||| ||||||||| |||   || |  | | ||  ||     ||| ||   | || ||| |  |||||||| ||||||||| |  ||||||||| ||| ||||||||||||| ||||||||||| |||| ||||||||||||||||||||||||| ||||||||||||||||  ||||  ||||||||
gtgaggcctt-ctcatgctgaaatagttttcatttcattaatgactagatttacttaaacagttttatcaaacagatcactatgcttgacacagttatgatatttctatcggtattctctttctagGTATGTTTTCTGTTGCTCATACACGCACAATGTTGCACCAAGAGGGAAGTTCATTGCATTTGTGTCTGCAGAAGCAGAGACTGATAATCCCCAGTCTGAG

upper sequence: LOC_Os05g34540.1 (Oryza sativa), 3'ss of exon 10
lower sequence: GRMZM2G435373_T02 (Zea mays), 3'ss of exon 10
gtgaggcctttcgcaatctcaatcacttctcatcagatgaattactagatttgcttgcccattgcttttaataagttattctatccccatttacggaatttctattggtattctcctgttagGTATGTCTTCGGTTGCTCATACACACACAATGTTGCTCCAAAAGGGAAGTTCATTGCATTTGTGTCTACAGAAGCAGAGACTGACCATCCAGAGTCTGAG
|| |||||||     || |  | |   | |||||  |||      |  |     ||  | |     |         ||| ||   | || ||| |  |||||| | ||||||||| | |||||||||| ||| |||| |||||||| ||||||||||| |||| ||||||||||||||||||||||||| ||||||||||||||||  | ||  | ||||||
gtaaggccttctctcatgttgaactagtttcatctcatg-----ttgaacacttttatcgaacagatc------actatgcttgacacaattatgatatttctgtcggtattctctttttagGTATGTTTTCTGTTGTTCATACACGCACAATGTTGCGCCAAGAGGGAAGTTCATTGCATTTGTGTCTGCAGAAGCAGAGACTGATAACCCGCAATCTGAG

upper sequence: LOC_Os05g34540.1 (Oryza sativa), 3'ss of exon 10
lower sequence: GRMZM2G318942_T01 (Zea mays), 3'ss of exon 7
gtgaggcctt-tcgcaatctcaatcacttctcatcagatgaattactagatttgcttgcccattgcttttaataagttattctatccccatttacggaatttctattggtattctcctgttagGTATGTCTTCGGTTGCTCATACACACACAATGTTGCTCCAAAAGGGAAGTTCATTGCATTTGTGTCTACAGAAGCAGAGACTGACCATCCAGAGTCTGAG
|||||||||| || ||  || ||  | || ||||   || ||| |||||||||     |   |  |    |      ||| ||   | || ||| |  |||||||       |||| |  ||||||||| ||| ||||||||||||| ||||||||||| |||| ||||||||| | |  |||||||||| ||||||||||||||||  ||||  ||||||||
gtgaggccttctctcatgctgaaatagttttcatttcattaatgactagatttaaacacttttatcaaacagatcactatgcttgacacagttatgatatttcta-------tctctttctagGTATGTTTTCTGTTGCTCATACACGCACAATGTTGCACCAAGAGGGAAGTTGAATATATTTGTGTCTGCAGAAGCAGAGACTGATAATCCCCAGTCTGAG

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|29644095|gb|CB649102.1|CB649102
EST:     CAGTCCAGATTATTTTGCCACAGAAACAACTTGGACGCAAGTCAGACAT                         GTATGTCTTCGGTTGCTCATACACACACAATGTTGCTCCAAAAGGGAAGTT
genomic: CAGTCCAGATTATTTTGCCACAGAAACAACTTGGACGCAAGTCAGACATgtgaggcctt ... ctcctgttagGTATGTCTTCGGTTGCTCATACACACACAATGTTGCTCCAAAAGGGAAGTT
EST: gi|29674550|gb|CB670825.1|CB670825
EST:     TCAGTCCAGATTATTTTGCCACAGAAACAACTTGGACGCAAGTCAGACAT                         GTATGTCTTCGGTTGCTCATACACACACAATGTTGCTCCAAAAGGGAAGTT
genomic: TCAGTCCAGATTATTTTGCCACAGAAACAACTTGGACGCAAGTCAGACATgtgaggcctt ... ctcctgttagGTATGTCTTCGGTTGCTCATACACACACAATGTTGCTCCAAAAGGGAAGTT
EST: gi|29689602|gb|CB685877.1|CB685877
EST:     TCAGTCCAGATTATTTTGCCACAGAAACAACTTGGACGCAAGTCAGACAT                         GTATGTCTTCGGTTGCTCATACACACACAATGTTGCTCCAAAAGGGAAGTT
genomic: TCAGTCCAGATTATTTTGCCACAGAAACAACTTGGACGCAAGTCAGACATgtgaggcctt ... ctcctgttagGTATGTCTTCGGTTGCTCATACACACACAATGTTGCTCCAAAAGGGAAGTT
EST: gi|396941200|gb|HO188409.1|HO188409
EST:     TCAGTCCAGATTATTTTGCCACAGAAACAACTTGGACGCAAGTCAGACAT                         GTATGTCTTCGGTTGCTCATACACACACAATGTTGCTCCAAAAGGGAAGTT
genomic: TCAGTCCAGATTATTTTGCCACAGAAACAACTTGGACGCAAGTCAGACATgtgaggcctt ... ctcctgttagGTATGTCTTCGGTTGCTCATACACACACAATGTTGCTCCAAAAGGGAAGTT
EST: gi|38471265|gb|CF955396.1|CF955396
EST:     TCAGTCCAGATTATTTTGCCACAGAAACAACTTGGACGCAAGTCAGACAT                         GTATGTCTTCGGTTGCTCATACACACACAATGTTGCTCCAAAAGGGAAGTT
genomic: TCAGTCCAGATTATTTTGCCACAGAAACAACTTGGACGCAAGTCAGACATgtgaggcctt ... ctcctgttagGTATGTCTTCGGTTGCTCATACACACACAATGTTGCTCCAAAAGGGAAGTT
EST: gi|702923|gb|D49214.1|D49214
EST:     TCAGTCCAGATTATTTTGCCACAGAAACAACTTGGACGCAAGTCAGACAT                         GTATGTCTTCGGTTGCTCATACACACACAATGTTGCTCCAAAAGGGAAGTT
genomic: TCAGTCCAGATTATTTTGCCACAGAAACAACTTGGACGCAAGTCAGACATgtgaggcctt ... ctcctgttagGTATGTCTTCGGTTGCTCATACACACACAATGTTGCTCCAAAAGGGAAGTT
EST: gi|29667501|gb|CB663776.1|CB663776
EST:     CTTGGACGCAAGTCAGACAT                         GTATGTCTTCGGTTGCTCATACACACACAATGTTGCTCCAAAAGGGAAGTT
genomic: CTTGGACGCAAGTCAGACATgtgaggcctt ... ctcctgttagGTATGTCTTCGGTTGCTCATACACACACAATGTTGCTCCAAAAGGGAAGTT
EST: gi|58592473|gb|CF990781.1|CF990781
EST:     TCAGTCCAGATTATTTTGCCACAGAAACAACTTGGACGCAAGTCAGACAT                         GTATGTCTTCGGTTGCTCATACACACACAATGTTGCTCCAAAAGGGAAGTT
genomic: TCAGTCCAGATTATTTTGCCACAGAAACAACTTGGACGCAAGTCAGACATgtgaggcctt ... ctcctgttagGTATGTCTTCGGTTGCTCATACACACACAATGTTGCTCCAAAAGGGAAGTT
EST: gi|4880961|gb|AU065260.1|AU065260
EST:     TCAGTCCAGATTATTTTGCCACAGAAACAACTTGGACGCAAGTCAGACAT                         GTATGTCTTCGGTTGCTCATACACACACAATGTTGGCTCCAAAAGGGAAGT
genomic: TCAGTCCAGATTATTTTGCCACAGAAACAACTTGGACGCAAGTCAGACATgtgaggcctt ... ctcctgttagGTATGTCTTCGGTTGCTCATACACACACAATGTTG-CTCCAAAAGGGAAGT
EST: gi|218500069|gb|FG955684.1|FG955684
EST:     TCAGTCCAGATTATTTTGCCACAGAAACAACTTGGACGCAAGTCAGACAT                         GTATGTCTTCGGTTGCTCATACACACACAATGTTGCTCCAAAAGGGAAGTT
genomic: TCAGTCCAGATTATTTTGCCACAGAAACAACTTGGACGCAAGTCAGACATgtgaggcctt ... ctcctgttagGTATGTCTTCGGTTGCTCATACACACACAATGTTGCTCCAAAAGGGAAGTT
EST: gi|87028068|gb|CI257228.1|CI257228
EST:     GCCACAGAAACAACTTGGACGCAAGTCAGACAT                         GTATGTCTTCGGTTGCTCATACACACACAATGTTGCTCCAAAAGGGAAGTT
genomic: GCCACAGAAACAACTTGGACGCAAGTCAGACATgtgaggcctt ... ctcctgttagGTATGTCTTCGGTTGCTCATACACACACAATGTTGCTCCAAAAGGGAAGTT

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), 69 (downstream exon)
Score: 121

GCGCTATTGCTATTATGAGCCACCCGATTGCAAACACAAATGACTCGCACTCAGTCCAGATTATTTTGCCACAGAAACAACTTGGACGCAAGTCAGACATgtgaggcctt ... ctcctgttagGTATGTCTTCGGTTGCTCATACACACACAATGTTGCTCCAAAAGGGAAGTTCATTGCATTTGTGTCTACAGAAGCAGAGACTGACCATCCAGAGTCTGAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttaataagttattctatccccatttacggaatttctattggtattctcctgttagGTATGTCTTCGGTTGCTCATACACACACAATGTTGCTCCAAAAGGGAAGTTCATTGCATTTGTGTCTACAGAAGCAGAGACTGACCATCCAGAGTCTGAG
 ttttaat  putative branch site (score: 121)
                                           ttctcctgtt  putative PPT
                             aatttctatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgaggcctttcgcaatctcaatcacttctcatcagatgaattactagatttgcttgcccattgcttttaataagttattctatccccatttacggaatttctattggtattctcctgttagGTATGTCTTCGGTTGCTCATACACACACAATGTTGCTCCAAAAGGGAAGTTCATTGCATTTGTGTCTACAGAAGCAGAGACTGACCATCCAGAGTCTGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGC