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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttgatatgctccatagttttgatctcaagctgttttgttttaatgtcctgaatatgatggcatatgttcttgtcctattacagTCTGATCAGAATGTCAAAGAGAAGGTATTAACTATGATAGATACATGGCAAGAAGCATTCGGGGGACCACGTGCAAGATATCCACAGTACTATGCAGCGT

Basic information

species Oryza sativa
transcript LOC_Os01g12880.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g12880.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G153138_T01 (Zea mays), 3'ss of exon 3
gtttgatatgctccatagttttgatctcaagctgttttgttttaatgtcctgaa----tatgatggcatatgttcttgtcctattacagTCTGATCAGAATGTCAAAGAGAAGGTATTAACTATGATAGATACATGGCAAGAAGCATTCGGGGGACCACGTGCAAGATATCCACAGTACTATGCAGCGT
|||  ||||| | |||  ||   |       || | || || |||||  |||      ||||||||  | | || || || | |||||||||||||    ||| |||||||| |||||     ||||||||||||||||||||||||| |||||||||||||||||||||||||| ||||||||||| |
gttcaatatgtttcatgcttgcaaaactctact-tcttattctaatgaactgctggcttatgatgg--tgttttgttttcatgttacagTCTGATCCTCGTGTTAAAGAGAAAGTATTGGTGCTGATAGATACATGGCAAGAAGCATTTGGGGGACCACGTGCAAGATATCCACAATACTATGCAGCAT

upper sequence: LOC_Os01g12880.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G062953_T02 (Zea mays), 3'ss of exon 3
gtttgatatgctccatagttttgatctcaagctgttttgttttaatgtcctgaa----tatgatggcatatgttcttgtcctattacagTCTGATCAGAATGTCAAAGAGAAGGTATTAACTATGATAGATACATGGCAAGAAGCATTCGGGGGACCACGTGCAAGATATCCACAGTACTATGCAGCGT
|||  ||||||| |||  ||   |        | | || || |||||  |||      | ||||||||| |  | || || | |||||||||||||    ||| ||||||||||||||     ||||||||||||||||||| |  || |||||| ||| ||||||||||||||| ||||||||||| |
gttcaatatgcttcatgcttgcaaaactgtagt-tcttattctaatgaactgctggtttctgatggcattt--tgttttcatgttacagTCTGATCCTCGTGTTAAAGAGAAGGTATTGGTGCTGATAGATACATGGCAAGACGTGTTTGGGGGATCACATGCAAGATATCCACAATACTATGCAGCAT

upper sequence: LOC_Os01g12880.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA06G08710.1 (Glycine max), 3'ss of exon 3
gtttgatatgctccatagttttgatctcaagctgttttgttttaatgtcctgaatatgatgg-catatgttcttgtcctattacagTCTGATCAGAATGTCAAAGAGAAGGTATTAACTATGATAGATACATGGCAAGAAGCATTCGGGGGACCACGTGCAAGATATCCACAGTACTATGCAGCGT
   |  ||   | ||| |  ||  | |     |   |  ||| |   |    | |||| |   ||||| |      |  |||  || ||||| |  |||||| ||||||| |||| | | | |||||||| ||||||||||| || || || ||| | ||||||||||||||||| |||||||| |
--gtattagttttcatggcattcctatttta-tacctgatttcatcatgaaaagtatgtttatcatatttatcacacaaattgtagCCTGATTACCATGTCAGAGAGAAGATATTGATTCTTATAGATACTTGGCAAGAAGCTTTTGGAGGGCCAAGGGCAAGATATCCACAGTATTATGCAGCAT

upper sequence: LOC_Os01g12880.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA04G08600.1 (Glycine max), 3'ss of exon 3
------------gtttgatatgctccatagttttgatctcaagctgttttgttttaatgtcctgaatatgatgg-catatgttcttgtcctattacagTCTGATCAGAATGTCAAAGAGAAGGTATTAACTATGATAGATACATGGCAAGAAGCATTCGGGGGACCACGTGCAAGATATCCACAGTACTATGCAGCGT
             || ||| |  | |||||  ||  | |     |   |  ||| |   |    |||||| |   ||||| |      |  |||  || ||||| |  |||||| ||||||| |||| | | | |||||||| ||||||||||| || || ||  || | ||||||||||||||||| |||||||| |
gtattgatatttcttggatgt-tttcatagccttcctatttta-tacctgatttcatcatgaaaaatatgtttatcatatttatcacgcaaattgtagCCTGATTATCATGTCAGAGAGAAGATATTGATTCTTATAGATACTTGGCAAGAAGCTTTTGGAGGGTCAAGGGCAAGATATCCACAGTATTATGCAGCAT

upper sequence: LOC_Os01g12880.1 (Oryza sativa), 3'ss of exon 3
lower sequence: Vv04s0008g03720.t01 (Vitis vinifera), 3'ss of exon 3
--------gtttgatatgctccatagttttgatctcaagctgttttgttttaatgtcctgaata------tgatggcatatgttcttgtcctattacagTCTGATCAGAATGTCAAAGAGAAGGTATTAACTATGATAGATACATGGCAAGAAGCATTCGGGGGACCACGTGCAAGATATCCACAGTACTATGCAGCGT
        ||     | |  ||||  ||||| || | || |   ||  |||| |   | ||  |      | || | || | |||| |    ||| ||| |||||  | |||||| ||||||| |||| | | |||||||||| ||||||||||| || || |||||| | |||||||||||||| |||||||| || |
gtcagactgtcattcaagtaccatttttttgttccctagtttcatttatttacttatccgagaaacctgttcatagtatttattct-gcaaaattgcagCCTGATTTGCATGTCAGAGAGAAGATATTGATTCTGATAGATACTTGGCAAGAAGCTTTTGGAGGACCAAGGGCAAGATATCCACAATACTATGCTGCAT

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|66924080|gb|CX110928.1|CX110928
EST:     TTGCAGAAAGAGATGTGTTGCATGAGATGGTGAAGATAGTGAAGAAAAAG                         TCTGATCAGAATGTCAAAGAGAAGGTATTAACTATGATAGATACATGGCAA
genomic: TTGCAGAAAGAGATGTGTTGCATGAGATGGTGAAGATAGTGAAGAAAAAGgtttgatatg ... cctattacagTCTGATCAGAATGTCAAAGAGAAGGTATTAACTATGATAGATACATGGCAA
EST: gi|58654984|gb|CK043664.1|CK043664
EST:     TTGCAGAAAGAGATGTGTTGCATGAGATGGTGAAGATAGTGAAGAAAAAG                         TCCGATCAGAATGTCAAAGAGAAGGTATTAACTATGATAGATACATGGCAA
genomic: TTGCAGAAAGAGATGTGTTGCATGAGATGGTGAAGATAGTGAAGAAAAAGgtttgatatg ... cctattacagTCTGATCAGAATGTCAAAGAGAAGGTATTAACTATGATAGATACATGGCAA
EST: gi|29674265|gb|CB670540.1|CB670540
EST:     TTGCAGAAAGAGATGTGTTGCATGAGATGGTGAAGATAGTGAAGAAAAAG                         TCTGATCAGAATGTCAAAGAGAAGGTATTAACTATGATAGATACATGGCAA
genomic: TTGCAGAAAGAGATGTGTTGCATGAGATGGTGAAGATAGTGAAGAAAAAGgtttgatatg ... cctattacagTCTGATCAGAATGTCAAAGAGAAGGTATTAACTATGATAGATACATGGCAA
EST: gi|58692666|gb|CK081353.1|CK081353
EST:     AGAGATGTGTTGCATGAGATGGTGAAGATAGTGAAGAAAAAG                         TCCGATCAGAATGTCAAAGAGAAGGTATTAACTATGATAGATACATGGCAA
genomic: AGAGATGTGTTGCATGAGATGGTGAAGATAGTGAAGAAAAAGgtttgatatg ... cctattacagTCTGATCAGAATGTCAAAGAGAAGGTATTAACTATGATAGATACATGGCAA

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: 71 (upstream exon), 74 (downstream exon)
Score: 52

CTCTTGGAAACTGCAATCAAGAACTGTGGGGATATATTCCACATGCATGTTGCAGAAAGAGATGTGTTGCATGAGATGGTGAAGATAGTGAAGAAAAAGgtttgatatg ... cctattacagTCTGATCAGAATGTCAAAGAGAAGGTATTAACTATGATAGATACATGGCAAGAAGCATTCGGGGGACCACGTGCAAGATATCCACAGTACTATGCAGCGT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gctgttttgttttaatgtcctgaatatgatggcatatgttcttgtcctattacagTCTGATCAGAATGTCAAAGAGAAGGTATTAACTATGATAGATACATGGCAAGAAGCATTCGGGGGACCACGTGCAAGATATCCACAGTACTATGCAGCGT
         ttttaat  putative branch site (score: 52)
                                      ttcttgtcct  putative PPT
     tttgttttaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtttgatatgctccatagttttgatctcaagctgttttgttttaatgtcctgaatatgatggcatatgttcttgtcctattacagTCTGATCAGAATGTCAAAGAGAAGGTATTAACTATGATAGATACATGGCAAGAAGCATTCGGGGGACCACGTGCAAGATATCCACAGTACTATGCAGCGT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAGA