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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aaaataattgcattgcaaaatcttgcatctctatgttcttctaaacgtaaaactgctttctgcgtaactgtatgtaacaacaattgactcatggatgcagATAATCAATGTTGACAATGTCCAAGAAGCTGCAAGAGAGACTGATGGATACTTTATCAAAAGTGGCATTGTTACCGTGATCAAGGATGCTTTGCTCCCTA

Basic information

species Oryza sativa
transcript LOC_Os08g25734.1
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os08g25734.1 (Oryza sativa), 3'ss of exon 8
lower sequence: GRMZM2G163437_T01 (Zea mays), 3'ss of exon 8
--aaaataattgcattgcaaaat-cttgcatctctatgttcttctaaacgtaaaactgctttctgcgtaactgtatgtaacaacaattgactcatggatgcagATAATCAATGTTGACAATGTCCAAGAAGCTGCAAGAGAGACTGATGGATACTTTATCAAAAGTGGCATTGTTACCGTGATCAAGGATGCTTTGCTCCCTA
   |  |  |   ||    |||  |   ||  ||  | ||   ||   |  | |  |  | |   ||| | | | | | || | | | |  ||     |||||||| |||| | ||||||||| |||||||||||||| ||||| || || ||||| |||||| |||| ||||| || ||||||||||||||||| |||||||
cttagcttgtaatatgattaaacacgaacagttcattattagacttgccacacattttatatggccgtga-tatttctcacgagactcg--tcgatcttgcagATACTCAACGCTGACAATGTTCAAGAAGCTGCAAGGGAGACAGACGGGTACTTCATCAAAGGTGGAATTGTCACAGTGATCAAGGATGCTTTACTCCCTA

upper sequence: LOC_Os08g25734.1 (Oryza sativa), 3'ss of exon 8
lower sequence: GRMZM2G068506_T02 (Zea mays), 3'ss of exon 8
---------aaaataattgcattgcaaaatcttgcatctctatgttcttctaaacgtaaaactgctttctgcgtaactgtatgtaacaacaattgactcatggatgcagATAATCAATGTTGACAATGTCCAAGAAGCTGCAAGAGAGACTGATGGATACTTTATCAAAAGTGGCATTGTTACCGTGATCAAGGATGCTTTGCTCCCTA
          | |  |||  |  | |||  ||| |||   ||   | | ||      | || |  | | || | | | | || |  ||  |   |||||     || ||||| |||||| ||||||||| |||||||||||||  ||||| || || ||||| |||||| |||| ||||| || ||||||||||||||||| |||||||
ttcgcttgtcataggattaaacaggaaa--ctttcattattagactttcctg---ccacaaattttctatg-gcagcggcatttctcatga---gactcgatcttgtagATACTCAATGCTGACAATGTTCAAGAAGCTGCAATGGAGACAGACGGGTACTTCATCAAAGGTGGAATTGTCACAGTGATCAAGGATGCTTTACTCCCTA

upper sequence: LOC_Os08g25734.1 (Oryza sativa), 3'ss of exon 8
lower sequence: GLYMA14G01290.1 (Glycine max), 3'ss of exon 8
aaaataattgcattgcaaa--atcttgcatctctatgttcttctaaacgtaaaactgctttctgcgtaactgtatgtaac--aacaattgactcatggatgcagATAATCAATGTTGACAATGTCCAAGAAGCTGCAAGAGAGACTGATGGATACTTTATCAAAAGTGGCATTGTTACCGTGATCAAGGATGCTTTGCTCCCTA
   ||  || | || || |   | ||||    |  |||| |  |  | || | | || |    |      |  || |||   |    |||  ||    |  ||||| || ||   |||||||||||||||||||||||| || || ||||| || || || |||||||| ||||| || || ||||||||||||||  | ||||
---atgttttcttttcatactgtgttgccatacattgttttcattcatgtgaca-tgttacgagatattttaaatctaatctatggtttgtttccaatactcagATTATTAACAGTGACAATGTCCAAGAAGCTGCAAGGGAAACAGATGGGTATTTCATAAAAAGTGGGATTGTCACAGTAATCAAGGATGCTTTAATTCCTA

upper sequence: LOC_Os08g25734.1 (Oryza sativa), 3'ss of exon 8
lower sequence: GLYMA02G47460.1 (Glycine max), 3'ss of exon 8
-aaaataattgcattgcaaaatcttgcatctctatgttcttctaaacgtaaaactgctttctgcgtaactgtatgtaacaacaattgactcatggatgcagATAATCAATGTTGACAATGTCCAAGAAGCTGCAAGAGAGACTGATGGATACTTTATCAAAAGTGGCATTGTTACCGTGATCAAGGATGCTTTGCTCCCTA
 | || ||| || ||   |     |  |||  ||| ||| |  |   |  |   | |    |   | |   | |     | |  |||  ||       ||||| || ||   |||||||||||||||||||||||| || || ||||| || || || |||||||| ||||| || || ||||||||||||||  | ||||
gataaaaatggctttctcactaaatatatccatattttcattcatgtgacatgttacgagatattttaa-atctaatctatcgtttgtttccaattctcagATTATTAACAGTGACAATGTCCAAGAAGCTGCAAGGGAAACAGATGGGTATTTCATAAAAAGTGGGATTGTCACAGTAATCAAGGATGCTTTAATTCCTA

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|86844862|gb|CI340894.1|CI340894
EST:     TTAGAAGGGCAATCATCGACAAGAATGCTCGTATTGGAGATAATGTGAAG                         ATAATCAATGTTGACAATGTCCAAGAAGCTGCAAGAGAGACTGATGGATAC
genomic: TTAGAAGGGCAATCATCGACAAGAATGCTCGTATTGGAGATAATGTGAAGgtattccaaa ... atggatgcagATAATCAATGTTGACAATGTCCAAGAAGCTGCAAGAGAGACTGATGGATAC
EST: gi|89177014|gb|CI111214.1|CI111214
EST:     TTAGAAGGGCAATCATCGACAAGAATGCTCGTATTGGAGATAATGTGAAG                         ATAATCAATGTTGACAATGTCCAAGAAGCTGCAAGAGAGACTGATGGATAC
genomic: TTAGAAGGGCAATCATCGACAAGAATGCTCGTATTGGAGATAATGTGAAGgtattccaaa ... atggatgcagATAATCAATGTTGACAATGTCCAAGAAGCTGCAAGAGAGACTGATGGATAC
EST: gi|29681077|gb|CB677352.1|CB677352
EST:     TTAGAAGGGCAATCATCGACAAGAATGCTCGTATTGGAGATAATGTGAAG                         ATAATCAATGTTGACAATGTCCAAGAAGCTGCAAGAGAGACTGATGGATAC
genomic: TTAGAAGGGCAATCATCGACAAGAATGCTCGTATTGGAGATAATGTGAAGgtattccaaa ... atggatgcagATAATCAATGTTGACAATGTCCAAGAAGCTGCAAGAGAGACTGATGGATAC
EST: gi|86417728|gb|CI031937.1|CI031937
EST:     TTAGAAGGGCAATCATCGACAAGAATGCTCGTATTGGAGATAATGTGAAG                         ATAATCAATGTTGACAATGTCCAAGAAGCTGCAAGAGAGACTGATGGATAC
genomic: TTAGAAGGGCAATCATCGACAAGAATGCTCGTATTGGAGATAATGTGAAGgtattccaaa ... atggatgcagATAATCAATGTTGACAATGTCCAAGAAGCTGCAAGAGAGACTGATGGATAC
EST: gi|29612859|gb|CB617872.1|CB617872
EST:     TTAGAAGGGCAATCATCGACAAGAATGCTCGTATTGGAGATAATGTGAAG                         ATAATCAATGTTGACAATGTCCAAGAAGCTGCAAGAGAGACTGATGGATAC
genomic: TTAGAAGGGCAATCATCGACAAGAATGCTCGTATTGGAGATAATGTGAAGgtattccaaa ... atggatgcagATAATCAATGTTGACAATGTCCAAGAAGCTGCAAGAGAGACTGATGGATAC
EST: gi|38472262|gb|CF956393.1|CF956393
EST:     TTAGAAGGGCAATCATCGACAAGAATGCTCGTATTGGAGATAATGTGAAG                         ATAATCAATGTTGACAATGTCCAAGAAGCTGCAAGAGAGACTGATGGATAC
genomic: TTAGAAGGGCAATCATCGACAAGAATGCTCGTATTGGAGATAATGTGAAGgtattccaaa ... atggatgcagATAATCAATGTTGACAATGTCCAAGAAGCTGCAAGAGAGACTGATGGATAC
EST: gi|29671442|gb|CB667717.1|CB667717
EST:     TTAGAAGGGCAATCATCGACAAGAATGCTCGTATTGGAGATAATGTGAAG                         ATAATCAATGTTGACAATGTCCAAGAAGCTGCAAGAGAGACTGATGGATAC
genomic: TTAGAAGGGCAATCATCGACAAGAATGCTCGTATTGGAGATAATGTGAAGgtattccaaa ... atggatgcagATAATCAATGTTGACAATGTCCAAGAAGCTGCAAGAGAGACTGATGGATAC
EST: gi|86599888|gb|CI256050.1|CI256050
EST:     TTAGAAGGGCAATCATCGACAAGAATGCTCGTATTGGAAATAATGTGAAG                         ATAATCAATGTTGACAATGTCCAAGAAGCTGCAAGAGAGACTGATGGATAC
genomic: TTAGAAGGGCAATCATCGACAAGAATGCTCGTATTGGAGATAATGTGAAGgtattccaaa ... atggatgcagATAATCAATGTTGACAATGTCCAAGAAGCTGCAAGAGAGACTGATGGATAC
EST: gi|29660395|gb|CB656670.1|CB656670
EST:     TTAGAAGGGCAATCATCGACAAGAATGCTCGTATTGGAGATAATGTGAAG                         ATAATCAATGTTGACAATGTCCAAGAAGCTGCAAGAGAGACTGATGGATAC
genomic: TTAGAAGGGCAATCATCGACAAGAATGCTCGTATTGGAGATAATGTGAAGgtattccaaa ... atggatgcagATAATCAATGTTGACAATGTCCAAGAAGCTGCAAGAGAGACTGATGGATAC
EST: gi|88835869|gb|CI370974.1|CI370974
EST:     TTAGAA-GGCAATCATCGACAAGAATGCTCGTATTTGAGATAATGTGAAG                         ATAATCAATGTTGACAATGTCCAAGAAGCTGCAAGAGAGACTGATGGATAC
genomic: TTAGAAGGGCAATCATCGACAAGAATGCTCGTATTGGAGATAATGTGAAGgtattccaaa ... atggatgcagATAATCAATGTTGACAATGTCCAAGAAGCTGCAAGAGAGACTGATGGATAC
EST: gi|29620180|gb|CB625192.1|CB625192
EST:     TTAGAAGGGCAATCATCGACAAGAATGCTCGTATTGGAGATAATGTGAAG                         ATAATCAATGTTGACAATGTCCAAGAAGCTGCAAGAGAGACTGATGGATAC
genomic: TTAGAAGGGCAATCATCGACAAGAATGCTCGTATTGGAGATAATGTGAAGgtattccaaa ... atggatgcagATAATCAATGTTGACAATGTCCAAGAAGCTGCAAGAGAGACTGATGGATAC
EST: gi|29633748|gb|CB638757.1|CB638757
EST:     TTAGAAGGGCAATCATCGACAAGAATGCTCGTATTGGAGATAATGTGAAG                         ATAATCAATGTTGACAATGTCCAAGAAGCTGCAAGAGAGACTGATGGATAC
genomic: TTAGAAGGGCAATCATCGACAAGAATGCTCGTATTGGAGATAATGTGAAGgtattccaaa ... atggatgcagATAATCAATGTTGACAATGTCCAAGAAGCTGCAAGAGAGACTGATGGATAC

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: 480

CCTTGGTGAAAAAGGTGGCATTCCCATTGGTATTGGGAAGAATTGCCACATTAGAAGGGCAATCATCGACAAGAATGCTCGTATTGGAGATAATGTGAAGgtattccaaa ... atggatgcagATAATCAATGTTGACAATGTCCAAGAAGCTGCAAGAGAGACTGATGGATACTTTATCAAAAGTGGCATTGTTACCGTGATCAAGGATGCTTTGCTCCCTA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cgtaaaactgctttctgcgtaactgtatgtaacaacaattgactcatggatgcagATAATCAATGTTGACAATGTCCAAGAAGCTGCAAGAGAGACTGATGGATACTTTATCAAAAGTGGCATTGTTACCGTGATCAAGGATGCTTTGCTCCCTA
                                    aattgac  putative branch site (score: 480)
                         tatgtaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aaaataattgcattgcaaaatcttgcatctctatgttcttctaaacgtaaaactgctttctgcgtaactgtatgtaacaacaattgactcatggatgcagATAATCAATGTTGACAATGTCCAAGAAGCTGCAAGAGAGACTGATGGATACTTTATCAAAAGTGGCATTGTTACCGTGATCAAGGATGCTTTGCTCCCTA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG
aaaataa
- - - - - cattgca
- - - - - - - - - - tcttgca
- - - - - - - - - - - - - - - - -tgttctt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctgtatg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -caacaat