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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgtgaactgatccattattttatattgcaaaagcgagagatgcagatgcacaacttctcaaatctgaccatacttttctgtactctgactgctgttccagGTGAAGAGCTATTGGCTAAACTCAGACGGCGCGGACGTTATCAATCACATGATGGATAATTTTATCGTCTAGTCCCTGAACTCTACGTGCTGCACTGTAC

Basic information

species Oryza sativa
transcript LOC_Os08g34750.1
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os08g34750.1 (Oryza sativa), 3'ss of exon 9
lower sequence: GRMZM5G820727_T01 (Zea mays), 3'ss of exon 10
-------------------------------tgtgaactgatccattattttatattgcaaaagcgagagatgcagatgcacaacttctcaaatctgaccatacttttctgtactctgactgctgttccagGTGAAGAGCTATTGGCTAAACTCAGACGGCGCGGACGTTATCAATCACATGATGGATAATTTTATCGTCTAGTCCCTGAACTCTACGTGCTGCACTGTAC
                               |  ||||  ||| |||  ||   | |    |  |     |    | |  |   ||     | ||| | || | |  ||     |  | |   |||  |||||||| ||||||||||||||||| || || || ||||| ||||| ||||||||||| ||||| ||||||||||                           
aagtaatattcttttattgtgcatggcctcgtccgaacccatc-atttcttagcactttttatcctcccaacattg-tttatgcctggcacattctcatcagAATAATCGACTATTCGGCCAATGT--CAGGTGAAAAGCTATTGGCTAAACTCGGATGGAGCAGACGTGATCAACCACATGATGGACAATTTCATCGTCTAGT---------------------------

upper sequence: LOC_Os08g34750.1 (Oryza sativa), 3'ss of exon 9
lower sequence: GRMZM5G820727_T02 (Zea mays), 3'ss of exon 9
----tgtgaactgatccattattttatattgcaaaagcgagagatgcagatgcacaacttctcaaatctgaccatacttttctgtactctgactgctgttccagGTGAAGAGCTATTGGCTAAACTCAGACGGCGCGGACGTTATCAATCACATGATGGATAATTTTATCGTCTAGTCCCTGAACTC-TACGTGCTGCACTGTAC
    |  ||||  ||| |||  ||   | |    |  |     |    | |  |   ||     | ||| | || | |  ||     |  | |   |||  |||||||| ||||||||||||||||| || || || ||||| ||||| ||||||||||| ||||| |||||||||||| || |  | |     || |  |||  
ctcgtccgaacccatc-atttcttagcactttttatcctcccaacattg-tttatgcctggcacattctcatcagaataatcgactattcggccaatgt--cagGTGAAAAGCTATTGGCTAAACTCGGATGGAGCAGACGTGATCAACCACATGATGGACAATTTCATCGTCTAGTCCATGGAGGCATGAAGCCTACGTTGTG-
















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|29687209|gb|CB683484.1|CB683484
EST:     TGAGCTTCCAGAAAAGTAGTCAAAGATTGGTTGCGCATAACACCATCCAG                         GTGAAGAGCTATTGGCTAAACTCAGACGGCGCGGACGTTATCAATCACATG
genomic: TGAGCTTCCAGAAAAGTAGTCAAAGATTGGTTGCGCATAACACCATCCAGgtgtgaactt ... gctgttccagGTGAAGAGCTATTGGCTAAACTCAGACGGCGCGGACGTTATCAATCACATG
EST: gi|29624696|gb|CB629707.1|CB629707
EST:     TGAGCTTCCAGAAAAGTAGTCAAAGATTGGTTGCGCATAACACCATCCAG                         GTGAAGAGCTATTGGCTAAACTCAGACGGCGCGGACGTTATCAATCACATG
genomic: TGAGCTTCCAGAAAAGTAGTCAAAGATTGGTTGCGCATAACACCATCCAGgtgtgaactt ... gctgttccagGTGAAGAGCTATTGGCTAAACTCAGACGGCGCGGACGTTATCAATCACATG
EST: gi|27577773|gb|CB000468.1|CB000468
EST:     TGAGCTTCCAGAAAAGTAGTCAAAGATTGGTTGCGCATAACACCATCCAG                         GTGAAGAGCTATTGGCTAAACTCAGACGGCGCGGACGTTATCAATCACATG
genomic: TGAGCTTCCAGAAAAGTAGTCAAAGATTGGTTGCGCATAACACCATCCAGgtgtgaactt ... gctgttccagGTGAAGAGCTATTGGCTAAACTCAGACGGCGCGGACGTTATCAATCACATG
EST: gi|29677871|gb|CB674146.1|CB674146
EST:     TGAGCTTCCAGAAAAGTAGTCAAAGATTGGTTGCGCATAACACCATCCAG                         GTGAAGAGCTATTGGCTAAACTCAGACGGCGCGGACGTTATCAATCACATG
genomic: TGAGCTTCCAGAAAAGTAGTCAAAGATTGGTTGCGCATAACACCATCCAGgtgtgaactt ... gctgttccagGTGAAGAGCTATTGGCTAAACTCAGACGGCGCGGACGTTATCAATCACATG
EST: gi|29678642|gb|CB674917.1|CB674917
EST:     TGAGCTTCCAGAAAAGTAGTCAAAGATTGGTTGCGCATAACACCATCCAG                         GTGAAGAGCTATTGGCTAAACTCAGACGGCGCGGACGTTATCAATCACATG
genomic: TGAGCTTCCAGAAAAGTAGTCAAAGATTGGTTGCGCATAACACCATCCAGgtgtgaactt ... gctgttccagGTGAAGAGCTATTGGCTAAACTCAGACGGCGCGGACGTTATCAATCACATG
EST: gi|33683118|gb|CF311357.1|CF311357
EST:     TGAGCTTCCAGAAAAGTAGTCAAAGATTGGTTGCGCATAACACCATCCAG                         GT-AAGAGCTATTGGCTAAACTCAGACGGCGCGGACGTTATCAATCACATG
genomic: TGAGCTTCCAGAAAAGTAGTCAAAGATTGGTTGCGCATAACACCATCCAGgtgtgaactt ... gctgttccagGTGAAGAGCTATTGGCTAAACTCAGACGGCGCGGACGTTATCAATCACATG
EST: gi|29674047|gb|CB670322.1|CB670322
EST:     TGAGCTTCCAGAAAAGTAGTCAAAGATTGGTTGCGCATAACACCATCCAG                         GTGAAGAGCTATTGGCTAAACTCAGACGGCGCGGACGTTATCAATCACATG
genomic: TGAGCTTCCAGAAAAGTAGTCAAAGATTGGTTGCGCATAACACCATCCAGgtgtgaactt ... gctgttccagGTGAAGAGCTATTGGCTAAACTCAGACGGCGCGGACGTTATCAATCACATG
EST: gi|88228444|gb|CI227924.1|CI227924
EST:     TGAGCTTCCAGAAAAGTAGTCAAAGATTGGTTGCGCATAACACCATCCAG                         GTGAAGAGCTATTGGCTAAACTCAGACGGCGCGGACGTTATCAATCACATG
genomic: TGAGCTTCCAGAAAAGTAGTCAAAGATTGGTTGCGCATAACACCATCCAGgtgtgaactt ... gctgttccagGTGAAGAGCTATTGGCTAAACTCAGACGGCGCGGACGTTATCAATCACATG
EST: gi|55410008|gb|CV722384.1|CV722384
EST:     TGAGCTTCCAGAAAAGTAGTCAAAGATTGGTTGCGCATAACACCATCCAG                         GTGAAGAGCTATTGGCTAAACTCAGACGGCGCGGACGTTATCAATCACATG
genomic: TGAGCTTCCAGAAAAGTAGTCAAAGATTGGTTGCGCATAACACCATCCAGgtgtgaactt ... gctgttccagGTGAAGAGCTATTGGCTAAACTCAGACGGCGCGGACGTTATCAATCACATG

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: 50 (upstream exon), 58 (downstream exon)
Score: 4

AGGAGATGATTAGAGGCCTTACACAAGTACCGTGGGAACGTGTTGATGTGAGCTTCCAGAAAAGTAGTCAAAGATTGGTTGCGCATAACACCATCCAGgtgtgaactt ... gctgttccagGTGAAGAGCTATTGGCTAAACTCAGACGGCGCGGACGTTATCAATCACATGATGGATAATTTTATCGTCTAGTCCCTGAACTCTACGTGCTGCACTGTAC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atgcacaacttctcaaatctgaccatacttttctgtactctgactgctgttccagGTGAAGAGCTATTGGCTAAACTCAGACGGCGCGGACGTTATCAATCACATGATGGATAATTTTATCGTCTAGTCCCTGAACTCTACGTGCTGCACTGTAC
                                     ctctgac  putative branch site (score: 4)
                                              ctgttcc  putative PPT
                        atactttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgtgaactgatccattattttatattgcaaaagcgagagatgcagatgcacaacttctcaaatctgaccatacttttctgtactctgactgctgttccagGTGAAGAGCTATTGGCTAAACTCAGACGGCGCGGACGTTATCAATCACATGATGGATAATTTTATCGTCTAGTCCCTGAACTCTACGTGCTGCACTGTAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC
- tgaactg
- - - - - - - - - - - - ttgcaaa
- - - - - - - - - - - - - - - - - - -agatgca
- - - - - - - - - - - - - - - - - - - - - - gatgcac