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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgctgaactggagtatttctcatgttaaatactcccatatatataagctgatacataaatagataatgtagtattggtttttgcagTGAAATCAAGTTCCATATATGTGGCGTGGGCAGCCTCGCGAGCACCGAGAAGAGGAGCTCTATCCTTTGCCGTACATGTAAATAAAGAAAAAAAAAGAAG

Basic information

species Oryza sativa
transcript LOC_Os02g01170.1
intron # 10
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|29678536|gb|CB674811.1|CB674811
EST:     CCAGCCGCTGTGGACAAAGCTTGAAGGACAGAGTCTCCCTTCAGACACAG                         TGAAATCAAGTTCCATATATGTGGCGTGGGCAGCCTCGCGAGCACCGAGAA
genomic: CCAGCCGCTGTGGACAAAGCTTGAAGGACAGAGTCTCCCTTCAGACACAGgtgctgaact ... gtttttgcagTGAAATCAAGTTCCATATATGTGGCGTGGGCAGCCTCGCGAGCACCGAGAA
EST: gi|88847007|gb|CI001279.1|CI001279
EST:     CCAGCCGCTGTGGACAAAGCTTGAAGGACAGAGTCTCCCTTCAGACACAG                         TGAAATCAAGTTCCATATATGTGGCGTGGGCAGCCTCGCGAGCACCGAGAA
genomic: CCAGCCGCTGTGGACAAAGCTTGAAGGACAGAGTCTCCCTTCAGACACAGgtgctgaact ... gtttttgcagTGAAATCAAGTTCCATATATGTGGCGTGGGCAGCCTCGCGAGCACCGAGAA
EST: gi|29664291|gb|CB660566.1|CB660566
EST:     CCAGCCGCTGTGGACAAAGCTTGAAGGACAGAGTCTCCCTTCAGACACAG                         TGAAATCAAGTTCCATATATGTGGCGTGGGCAGCCTCGCGAGCACCGAGAA
genomic: CCAGCCGCTGTGGACAAAGCTTGAAGGACAGAGTCTCCCTTCAGACACAGgtgctgaact ... gtttttgcagTGAAATCAAGTTCCATATATGTGGCGTGGGCAGCCTCGCGAGCACCGAGAA
EST: gi|88837611|gb|CI078971.1|CI078971
EST:     CCAGCCGCTGTGGACAAAGCTTGAAGGACAGAGTCTCCCTTCAGACACAG                         TGAAATCAAGTTCCATATATGTGGCGTGGGCAGCCTCGCGAGCACCGAGAA
genomic: CCAGCCGCTGTGGACAAAGCTTGAAGGACAGAGTCTCCCTTCAGACACAGgtgctgaact ... gtttttgcagTGAAATCAAGTTCCATATATGTGGCGTGGGCAGCCTCGCGAGCACCGAGAA
EST: gi|29678538|gb|CB674813.1|CB674813
EST:     CCAGCCGCTGTGGACAAAGCTTGAAGGACAGAGTCTCCCTTCAGACACAG                         TGAAATCAAGTTCCATATATGTGGCGTGGGCAGCCTCGCGAGCACCGAGAA
genomic: CCAGCCGCTGTGGACAAAGCTTGAAGGACAGAGTCTCCCTTCAGACACAGgtgctgaact ... gtttttgcagTGAAATCAAGTTCCATATATGTGGCGTGGGCAGCCTCGCGAGCACCGAGAA
EST: gi|29670955|gb|CB667230.1|CB667230
EST:     CCAGCCGCTGTGGACAAAGCTTGAAGGACAGAGTCTCCCTTCAGACACAG                         TGAAATCAAGTTCCATATATGTGGCGTGGGCAGCCTCGCGAGCACCGAGAA
genomic: CCAGCCGCTGTGGACAAAGCTTGAAGGACAGAGTCTCCCTTCAGACACAGgtgctgaact ... gtttttgcagTGAAATCAAGTTCCATATATGTGGCGTGGGCAGCCTCGCGAGCACCGAGAA
EST: gi|58594862|gb|CF993170.1|CF993170
EST:     CCAGCCGCTGTGGACAAAGCTTGAAGGACAGAGTCTCCCTTCAGACACAG                         TGAAATCAAGTTCCATATATGTGGCGTGGGCAGCCTCGCGAGCACCGAGAA
genomic: CCAGCCGCTGTGGACAAAGCTTGAAGGACAGAGTCTCCCTTCAGACACAGgtgctgaact ... gtttttgcagTGAAATCAAGTTCCATATATGTGGCGTGGGCAGCCTCGCGAGCACCGAGAA
EST: gi|66922255|gb|CX109103.1|CX109103
EST:     CCAGCCGCTGTGGACAAAGCTTGAAGGACAGAGTCTCCCTTCAGACACAG                         TGAAATCAAGTTCCATATATGTGGCGTGGGCAGCCTCAGACGAGCACCGAG
genomic: CCAGCCGCTGTGGACAAAGCTTGAAGGACAGAGTCTCCCTTCAGACACAGgtgctgaact ... gtttttgcagTGAAATCAAGTTCCATATATGTGGCGTGGGCAGCCTC-G-CGAGCACCGAG
EST: gi|29640685|gb|CB645694.1|CB645694
EST:     CCAGCCGCTGTGGACAAAGCTTGAAGGACAGAGTCTCCCTTCAGACACAG                         TGAAATCAAGTTCCATATATGTGGCGTGGGCAGCCTCGCGAGCACCGAGAA
genomic: CCAGCCGCTGTGGACAAAGCTTGAAGGACAGAGTCTCCCTTCAGACACAGgtgctgaact ... gtttttgcagTGAAATCAAGTTCCATATATGTGGCGTGGGCAGCCTCGCGAGCACCGAGAA
EST: gi|29628307|gb|CB633318.1|CB633318
EST:     CCAGCCGCTGTGGACAAAGCTTGAAGGACAGAGTCTCCCTTCAGACACAG                         TGAAATCAAGTTCCATAT--GTGGCGTGGGCAGCCTCGCGAGCACCGAGAA
genomic: CCAGCCGCTGTGGACAAAGCTTGAAGGACAGAGTCTCCCTTCAGACACAGgtgctgaact ... gtttttgcagTGAAATCAAGTTCCATATATGTGGCGTGGGCAGCCTCGCGAGCACCGAGAA
EST: gi|86424983|gb|CI070080.1|CI070080
EST:     CCAGCCGCTGTGGACAAAGCTTGAAGGACAGAGTCTTCCTTCAGACACAG                         TGAAATCAAGTTCCATATATGTGGCGTGGGCAGCCTCGCGAGCACCGAGAA
genomic: CCAGCCGCTGTGGACAAAGCTTGAAGGACAGAGTCTCCCTTCAGACACAGgtgctgaact ... gtttttgcagTGAAATCAAGTTCCATATATGTGGCGTGGGCAGCCTCGCGAGCACCGAGAA
EST: gi|25807633|gb|CA763594.1|CA763594
EST:     CCAGCCGCTGTGGACAAAGCTTGAAGGACAGAGTCTCCCTTCAGACACAG                         TGAAATCAAGTTCCATATATGTGGCGTGGGCAGCCTCGCGAGCACCGAGAA
genomic: CCAGCCGCTGTGGACAAAGCTTGAAGGACAGAGTCTCCCTTCAGACACAGgtgctgaact ... gtttttgcagTGAAATCAAGTTCCATATATGTGGCGTGGGCAGCCTCGCGAGCACCGAGAA

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: 72 (upstream exon), 75 (downstream exon)
Score: 37

ATCCAGAATTAGTTTCTTTGTTGCCCGTGTGACATAATAGGTTGAGGCTACCAGCCGCTGTGGACAAAGCTTGAAGGACAGAGTCTCCCTTCAGACACAGgtgctgaact ... gtttttgcagTGAAATCAAGTTCCATATATGTGGCGTGGGCAGCCTCGCGAGCACCGAGAAGAGGAGCTCTATCCTTTGCCGTACATGTAAATAAAGAAAAAAAAAGAAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctcccatatatataagctgatacataaatagataatgtagtattggtttttgcagTGAAATCAAGTTCCATATATGTGGCGTGGGCAGCCTCGCGAGCACCGAGAAGAGGAGCTCTATCCTTTGCCGTACATGTAAATAAAGAAAAAAAAAGAAG
              agctgat  putative branch site (score: 37)
                                              tttttgc  putative PPT
                       ataaatagataatgta  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
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---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgctgaactggagtatttctcatgttaaatactcccatatatataagctgatacataaatagataatgtagtattggtttttgcagTGAAATCAAGTTCCATATATGTGGCGTGGGCAGCCTCGCGAGCACCGAGAAGAGGAGCTCTATCCTTTGCCGTACATGTAAATAAAGAAAAAAAAAGAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG