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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagtcaaatattatctattgatatttatagattgatacttttaacgaatttcatactgaaataactagttttgtcactgtatttttagAACCTTTATTGGGCTGATAGCGGTGACCTAGTTGCAATAGCAAGTGATACATCATTCTACATACTGAAGTACAAC

Basic information

species Oryza sativa
transcript LOC_Os06g05180.2
intron # 13
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os06g05180.2 (Oryza sativa), 3'ss of exon 13
lower sequence: GRMZM2G095348_T02 (Zea mays), 3'ss of exon 12
gtgagtcaaatattatctattgatatttatagattg-atacttttaacgaattt-catactgaaataactagttttgtcactgtatttttagAACCTTTATTGGGCTGATAGCGGTGACCTAGTTGCAATAGCAAGTGATACATCATTCTACATACTGAAGTACAAC
|||| |||| |||||| | ||  |   |  | |||   ||  |  || | ||     ||||   |    |   ||| ||| || |||| |||||| |||| ||||||||||| ||||||||||||||||||||||||||||||||||||||||| || |||||||| 
gtgaatcaagtattattttttcttgggtggaaattttgtatgtaaaatgtatgagtttactattaaccttttctttatca-tgcatttatagAACGTTTACTGGGCTGATAGTGGTGACCTAGTTGCAATAGCAAGTGATACATCATTCTACATCCTCAAGTACAAT

upper sequence: LOC_Os06g05180.2 (Oryza sativa), 3'ss of exon 13
lower sequence: GRMZM2G000645_T01 (Zea mays), 3'ss of exon 13
gtgagtcaaa--tattatctattgatatttatagattgatacttttaacgaatttcatactgaaataactagttttgtcactgtatttttagAACCTTTATTGGGCTGATAGCGGTGACCTAGTTGCAATAGCAAGTGATACATCATTCTACATACTGAAGTACAAC
||||||||||  |||||| | |   |   |  | |||  |  | |  | || ||| ||| | |  |   |   ||| ||| ||| ||| |||||  |||| ||||||||||| ||||||||||||||||||||||||||||||||||||||||| || |||||||| 
gtgagtcaaaagtattatttttccttgggtggaaatt--ttgtatgtatgagtttaatattaacct---tttgtttatca-tgtgtttatagAATGTTTACTGGGCTGATAGTGGTGACCTAGTTGCAATAGCAAGTGATACATCATTCTACATCCTCAAGTACAAT

upper sequence: LOC_Os06g05180.2 (Oryza sativa), 3'ss of exon 13
lower sequence: GLYMA13G43680.2 (Glycine max), 3'ss of exon 13
gtgagtcaaatattatctattgatatttatagattgatacttttaacgaat-ttcatactgaaataactagttttgtcactgtattt---ttagAACCTTTATTGGGCTGATAGCGGTGACCTAGTTGCAATAGCAAGTGATACATCATTCTACATACTGAAGTACAAC
|| |||  | | | ||    ||| |||||   ||     |||||      | |||||  |  ||||  || |||||| | |    ||   | ||||||| || |||||||| || ||||| |||||  |||| || || ||||||||||||||||| ||||||||||| 
gtaagt--actttgattaggtgacatttagttatctgctcttttccttcttattcattgtttaata--taattttgttattaatcttgtgtcagAACCTCTACTGGGCTGACAGTGGTGATCTAGTAACAATTGCTAGCGATACATCATTCTACATTCTGAAGTACAAT

upper sequence: LOC_Os06g05180.2 (Oryza sativa), 3'ss of exon 13
lower sequence: GLYMA07G03890.2 (Glycine max), 3'ss of exon 2
gtgagtcaaatattatctattgatatttatagattgatacttttaacgaatttcatactgaaa-taactagttttgtcactgtattttt-----agAACCTTTATTGGGCTGATAGCGGTGACCTAGTTGCAATAGCAAGTGATACATCATTCTACATACTGAAGTACAAC
|| |||    |   ||    ||| ||    || ||  | ||||||      ||| |||||    |   || |||||| |   | || ||     ||||||| || ||||||||||| ||||| |||||  | || || ||||||||||||||||| || ||||||||||| 
gtaagt--gcttgcatgaggtgacatc---agctttctgcttttattt--cttcttactgtttcttgttaattttgttaaaattttcttgtgtcagAACCTCTACTGGGCTGATAGTGGTGATCTAGTGACGATTGCTAGTGATACATCATTCTATATCCTGAAGTACAAT

upper sequence: LOC_Os06g05180.2 (Oryza sativa), 3'ss of exon 13
lower sequence: GLYMA08G22140.1 (Glycine max), 3'ss of exon 13
gtgagtcaaatattatctattgatatttatagattgatacttttaacgaatttcatactgaaataactagttttgtcactgtattttt-----agAACCTTTATTGGGCTGATAGCGGTGACCTAGTTGCAATAGCAAGTGATACATCATTCTACATACTGAAGTACAAC
       || |  |  |    | |      || ||  | ||||||      ||| |||||   |   || |||||| |   | || ||     ||||||| || |||||||||||||||||  ||||  | || || ||||||||||||||||| || || |||||||| 
-----gtaagtgcttgcatgaggtggcatcagctttctgcttttattt--cttcttactgt--ttcttatttttgttaaatttttcttgtgtcagAACCTGTACTGGGCTGATAGCGGTGATTTAGTGACGATTGCTAGTGATACATCATTCTATATCCTTAAGTACAAT

upper sequence: LOC_Os06g05180.2 (Oryza sativa), 3'ss of exon 13
lower sequence: GLYMA15G01680.1 (Glycine max), 3'ss of exon 13
gtgagtcaaatattatctattgatatttatagattgatacttttaa--cgaatttcatactgaaataactagttttgtcactgtatttttagAACCTTTATTGGGCTGATAGCGGTGACCTAGTTGCAATAGCAAGTGATACATCATTCTACATACTGAAGTACAAC
|| |||  | | | ||    ||| || ||   ||     |||||    |  |||   |  | || | | |  | || |   | |  | | ||||||| || |||||||| || ||||| |||||  |||| || |||||||||||||||||||| ||||||||||| 
gtaagt--actttgattaggtgacatctagttatctgctcttttccttcttattcgttgtttaatttaattttgttatttatcttgtgtcagAACCTCTACTGGGCTGACAGTGGTGATCTAGTAACAATTGCTAGTGATACATCATTCTACATTCTGAAGTACAAT

upper sequence: LOC_Os06g05180.2 (Oryza sativa), 3'ss of exon 13
lower sequence: AT1G79990.1 (Arabidopsis thaliana), 3'ss of exon 17
----------------------------------------------------------------------------------------------------gtgagtcaaatattatctattgatatttatagattgatacttttaacgaatttcatactgaaataactagttttgtcactgtatttttagAACCTTTATTGGGCTGATAGCGGTGACCTAGTTGCAATAGCAAGTGATACATCATTCTACATACTGAAGTACAAC
                                                                                                    ||   | |  |   || ||     |     |||||| ||||  |  |  ||| ||   | ||     | ||||  ||| |||   || |||| ||||||||||| || || ||||| ||||||||||| || |||||||||||||||||||| || |||| ||| 
gtaagtgcttatataccagaagtagatccattagtttctacaagaaaatagtttataggttacgttttcagtaatatttttattggagaaatacaaaagagttccttatctgaaatttaaacgcaaaagcagattggtactgctcgcttatt-cacttttaacgtttttgtttattcaatgt---ttcagAATCTTTATTGGGCGGACAGTGGTGATCTAGTTGCAATTGCCAGTGATACATCATTCTACATCCTTAAGTTCAAT

upper sequence: LOC_Os06g05180.2 (Oryza sativa), 3'ss of exon 13
lower sequence: AT3G15980.2 (Arabidopsis thaliana), 3'ss of exon 13
----------------------------------------------------gtgagtcaaatattatctattgatatttatagattgatacttttaacgaatttcatactgaaataactagttttgtcactgtatttttagAACCTTTATTGGGCTGATAGCGGTGACCTAGTTGCAATAGCAAGTGATACATCATTCTACATACTGAAGTACAAC
                                                       | ||     |||  | ||  | |   | ||  | |  |   ||  | | || |    || |   || |    | |    ||||  |||| |||||||||||||| || |||||  |||| || || || |||||||| |||||||||||  |||||||||| 
gtatccaattaccttgtctctgttgtgagaagttagcattcatcacttttttccaattctgtcgttacattttattttcagttgaaagttg-tcccaattagtgtctttactaactctttactcccatgaa-aaatttgcagAATCTTTATTGGGCTGAAAGTGGTGATTTAGTAGCCATTGCTAGTGATACGTCATTCTACATCTTGAAGTACAAT

upper sequence: LOC_Os06g05180.2 (Oryza sativa), 3'ss of exon 13
lower sequence: Vv09s0002g04810.t01 (Vitis vinifera), 3'ss of exon 13
gtgagt-caaatattat---ctattgatatttatagattgatacttttaacgaatttca-----tactgaaataactagttttgtcactgtattttt-----------agAACCTTTATTGGGCTGATAGCGGTGACCTAGTTGCAATAGCAAGTGATACATCATTCTACATACTGAAGTACAAC
|| ||  | || || ||   || |||       | |  |  |  |  |  |  | | ||     |  | ||||      ||||     | | |||||           ||||||| |||||||||||||| || ||  | || || || || |||||||||||||| ||||| ||||||||||| 
gtaagcactaacatgatggcctgttggctaccgtggtattgttttcatgccacactgcaggaattgattaaatgttccttttttcttttctttttttttcactatttcagAACCTCTATTGGGCTGATAGTGGGGATTTGGTGGCCATTGCCAGTGATACATCATTTTACATCCTGAAGTACAAT

upper sequence: LOC_Os06g05180.2 (Oryza sativa), 3'ss of exon 13
lower sequence: Vv11s0016g04180.t01 (Vitis vinifera), 3'ss of exon 13
--gtgagtcaaatattatctattgatatttatagattgatacttttaacgaatttcatactgaaataactagttttgtcactgtatttttagAACCTTTATTGGGCTGATAGCGGTGACCTAGTTGCAATAGCAAGTGATACATCATTCTACATACTGAAGTACAAC
   ||     || |   |   || | | |||     |  |      |  |||  | ||| |  | |   | |  | ||  |  |||||  |||| ||||||||||||||||| |||||  |||| ||||| ||||||||| ||||||| |||||  | |||||||| 
gcatgttctcaaaaagcttacttcacaattaccaggttttggccacagagaaactaatagttcatttctttgggtggtttcaatatttc-agAATCTTTATTGGGCTGATAGTGGTGATTTAGTGGCAATTGCAAGTGATTCATCATTTTACATCTTAAAGTACAAT

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|58660118|gb|CK048798.1|CK048798
EST:     ATGACTGGGCTGACTGTAGACTAATACGCCGCATTGATGTGAATGTCAAA                         AACCTTTATTGGGCTGATAGCGGTGACCTAGTTGCAATAGCAAGTGATACA
genomic: ATGACTGGGCTGACTGTAGACTAATACGCCGCATTGATGTGAATGTCAAAgtgagtcaaa ... gtatttttagAACCTTTATTGGGCTGATAGCGGTGACCTAGTTGCAATAGCAAGTGATACA
EST: gi|29630380|gb|CB635389.1|CB635389
EST:     ATGACTGGGCTGACTGTAGACTAATACGCCGCATTGATGTGAATGTCAAA                         AACCTTTATTGGGCTGATAGCGGTGACCTAGTTGCAATAGCAAGTGATACA
genomic: ATGACTGGGCTGACTGTAGACTAATACGCCGCATTGATGTGAATGTCAAAgtgagtcaaa ... gtatttttagAACCTTTATTGGGCTGATAGCGGTGACCTAGTTGCAATAGCAAGTGATACA

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: 60

TTTTGGTGGAATATTATTGGCGATGTGTTCCAGTGATTTCATTTGCTTTTATGACTGGGCTGACTGTAGACTAATACGCCGCATTGATGTGAATGTCAAAgtgagtcaaa ... gtatttttagAACCTTTATTGGGCTGATAGCGGTGACCTAGTTGCAATAGCAAGTGATACATCATTCTACATACTGAAGTACAAC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gatacttttaacgaatttcatactgaaataactagttttgtcactgtatttttagAACCTTTATTGGGCTGATAGCGGTGACCTAGTTGCAATAGCAAGTGATACATCATTCTACATACTGAAGTACAAC
                         aaataac  putative branch site (score: 60)
                                              tattttt  putative PPT
                         aaataactagtttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagtcaaatattatctattgatatttatagattgatacttttaacgaatttcatactgaaataactagttttgtcactgtatttttagAACCTTTATTGGGCTGATAGCGGTGACCTAGTTGCAATAGCAAGTGATACATCATTCTACATACTGAAGTACAAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGAAG