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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaacacacttcttatgcattgatgctatgatatataacttaacataactggcatccttgggactttagattatccaactctttcctttctgttctttagATATGTGATGCGGTTGCTGTTGCTAAAATTCTGAATGCGTCTCTTGTGATCCCACATCTTGAAGTAAATCCTGTTTGGAAAGACACAAG

Basic information

species Oryza sativa
transcript LOC_Os09g24570.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os09g24570.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G057037_T01 (Zea mays), 3'ss of exon 4
gtaacacacttcttatgcattgatgctatgatat-ataacttaacataactggcatccttgggactttagattatccaactctttcctttctgttctttagATATGTGATGCGGTTGCTGTTGCTAAAATTCTGAATGCGTCTCTTGTGATCCCACATCTTGAAGTAAATCCTGTTTGGAAAGACACAAG
|||   | ||||| ||  | |  |  |||||| | |  || | | ||| ||  | |  |   | |||||||||  ||||||||||  || |  |||| ||||||||||||||  |||| ||||| || ||||| |||||  |||||||||||||||||||||||||||| ||||||||||| ||  ||||
gta-tgctcttctaat-tactattagtatgattttaggacatgagatagctttctttatccaggctttagattggccaactcttta-ttccaattctgtagATATGTGATGCCATTGCAGTTGCAAAGATTCTTAATGCTACTCTTGTGATCCCACATCTTGAAGTAAACCCTGTTTGGAAGGATTCAAG

upper sequence: LOC_Os09g24570.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA09G33160.1 (Glycine max), 3'ss of exon 4
gtaacacacttcttatgcattgatgctatgatatataacttaacataactggcatccttgggactttagattatccaactct----ttcctttctgttctttagATATGTGATGCGGTTGCTGTTGCTAAAATTCTGAATGCGTCTCTTGTGATCCCACATCTTGAAGTAAATCCTGTTTGGAAAGACACAAG
     |    | | | || ||   | || |||  | |  ||             |       |   |  || ||       |    ||   || | || | |||||||||||||| |||||||| || || || ||||||||  |||| ||||| ||| | |||||| |||||||||| |||  |||  ||||
---gtaggtatatgaagccttttagtta-gatcaaaagtttcctcgtgtgtatgtgtgaaaaatgatgtataatttggacttagtgtttaattattttgtgtagATATGTGATGCAGTTGCTGTGGCAAAGATACTGAATGCTACTCTGGTGATTCCATACCTTGAATTAAATCCTGTATGGCGAGATTCAAG

upper sequence: LOC_Os09g24570.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA01G02850.1 (Glycine max), 3'ss of exon 4
gtaacacacttcttatgcattgatgctatgatatataacttaacataactg-gcatccttgggactttagatt--atccaactctttcctttctgttctttagATATGTGATGCGGTTGCTGTTGCTAAAATTCTGAATGCGTCTCTTGTGATCCCACATCTTGAAGTAAATCCTGTTTGGAAAGACACAAG
||||   | |         || |    || | |  |    | |  |   || |  |      ||  |   |||  |||  | | ||   ||    || | |||||||||||||| ||||||||||| || || ||||||||  |||| ||||||||| | |||||| | |||||||| |||  |||  ||||
gtaa-gtattaaaagccttttaagtagatcaaaagtttgctcatgtgtgtgtgtgtgtgaaagatgtacaatttgatcttagtgttaaattatc-ttgtgtagATATGTGATGCAGTTGCTGTTGCAAAGATACTGAATGCTACTCTGGTGATCCCATACCTTGAACTGAATCCTGTATGGCGAGATTCAAG

upper sequence: LOC_Os09g24570.1 (Oryza sativa), 3'ss of exon 4
lower sequence: Vv00s0313g00030.t01 (Vitis vinifera), 3'ss of exon 4
----------------------------------------------gtaacacacttcttatgcat---tgatgctatgatatataacttaacataactggcatccttggga----ctt--tagattatccaactctttcctt-tctgttctttagATATGTGATGCGGTTGCTGTTGCTAAAATTCTGAATGCGTCTCTTGTGATCCCACATCTTGAAGTAAATCCTGTTTGGAAAGACACAAG
                                              || |   |   |  |  ||    ||||  | |    || |  || |  | ||  |  | |||  ||    |||  | | || | ||  ||||   || | |  | | ||||| |||||||| |||||||||||||| ||  | |||||  | ||||||||||||||||||||||| ||||||||||||   ||  | ||
gtaggtaattctaggtttgccactacattctatggatattaaaagggtcaaggatggcccaaacaggaatgattatctcggttaaatttttatgtcacatgtttgctttagaaaatcttggttggttgttcatatcttaatttgtattgtttgtagATTTGTGATGCTGTTGCTGTTGCTAAGATATTAAATGCTACACTTGTGATCCCACATCTTGAAGTGAATCCTGTTTGGCGGGATTCGAG

upper sequence: LOC_Os09g24570.1 (Oryza sativa), 3'ss of exon 4
lower sequence: PP1S215_43V6.1 (Physcomitrella patens), 3'ss of exon 4
---------------------------------gtaacacacttcttatgcattgatg-ctatgatatataacttaacataactggcatccttgggactttagattatccaactctttcctttctgttctttagATATGTGATGCGGTTGCTGTTGCTAAAATTCTGAATGCGTCTCTTGTGATCCCACATCTTGAAGTAAATCCTGTTTGGAAAGACACAAG
                                  ||| ||      | ||  | | || | ||| |||  |   | |  ||  || |||  |   |  | |   ||   |||||| ||| | |    |    |||| |||||||||||||||||||| ||||||||||||||  |||||||  | || ||| | || || ||||| |||||||||||| | ||
gtcagacttccttctaacagattttcttggattttaaaacttgctgtttgtctcgttggcaatgctattgatgattat-tagatgccattttattg--tatgtgttggtcaactcattcgtataatcttggcagATTTGTGATGCGGTTGCTGTTGCAAAAATTCTGAATGCAACTCTTGTTCTTCCTCATTTCGATGTTAATCCAGTTTGGAAAGACTCCAG

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|86885641|gb|CI309768.1|CI309768
EST:     GATATATCCAAGTATTTCTTGATGGTGGACTGAATCAGCAAAGAATGGGG                         ATATGTGATGCGGTTGCTGTTGCTAAAATTCTGAATGCGTCTCTTGTGATC
genomic: GATATATCCAAGTATTTCTTGATGGTGGACTGAATCAGCAAAGAATGGGGgtaacacact ... tgttctttagATATGTGATGCGGTTGCTGTTGCTAAAATTCTGAATGCGTCTCTTGTGATC
EST: gi|88422549|gb|CI571531.1|CI571531
EST:     GATATATCCAAGTATTTCTTGATGGTGGACTGAATCAGCAAAGAATGGGG                         ATATGTGATGC
genomic: GATATATCCAAGTATTTCTTGATGGTGGACTGAATCAGCAAAGAATGGGGgtaacacact ... tgttctttagATATGTGATGC
EST: gi|58606246|gb|CK034279.1|CK034279
EST:     GATATATCCAAGTATTTCTTGATGGTGGACTGAATCAGCAAAGAATGGGG                         ATATGTGATGCGGTTGCTGTTGCTAAAATTCTGAATGCGACTCTTGTGATC
genomic: GATATATCCAAGTATTTCTTGATGGTGGACTGAATCAGCAAAGAATGGGGgtaacacact ... tgttctttagATATGTGATGCGGTTGCTGTTGCTAAAATTCTGAATGCGTCTCTTGTGATC
EST: gi|88430811|gb|CI596925.1|CI596925
EST:     GATATATCCAAGTATTTCTTGATGGTGGACTGAATCAGCAAAGAATGGGG                         ATATGTGATG-GGTTGCTGTTGCTAAAATTCTGAATGCCTCTCTTGTGATC
genomic: GATATATCCAAGTATTTCTTGATGGTGGACTGAATCAGCAAAGAATGGGGgtaacacact ... tgttctttagATATGTGATGCGGTTGCTGTTGCTAAAATTCTGAATGCGTCTCTTGTGATC
EST: gi|88433774|gb|CI582096.1|CI582096
EST:     GATATATCCAAGTATTTCTTGATGGTGGACTGAATCAGCAAAGAATGGGG                         ATATGTGATGCGGT
genomic: GATATATCCAAGTATTTCTTGATGGTGGACTGAATCAGCAAAGAATGGGGgtaacacact ... tgttctttagATATGTGATGCGGT
EST: gi|88315799|gb|CI617272.1|CI617272
EST:     GATATATCCAAGTATTTCTTGATGGTGGACTGAATCAGCAAAGAATGGGG                         ATATGTGATGCGGTTGCT
genomic: GATATATCCAAGTATTTCTTGATGGTGGACTGAATCAGCAAAGAATGGGGgtaacacact ... tgttctttagATATGTGATGCGGTTGCT

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: 60 (upstream exon), 56 (downstream exon)
Score: 8

GGGTACCTTTGGAACCCACTGGATATATCCAAGTATTTCTTGATGGTGGACTGAATCAGCAAAGAATGGGGgtaacacact ... tgttctttagATATGTGATGCGGTTGCTGTTGCTAAAATTCTGAATGCGTCTCTTGTGATCCCACATCTTGAAGTAAATCCTGTTTGGAAAGACACAAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

taactggcatccttgggactttagattatccaactctttcctttctgttctttagATATGTGATGCGGTTGCTGTTGCTAAAATTCTGAATGCGTCTCTTGTGATCCCACATCTTGAAGTAAATCCTGTTTGGAAAGACACAAG
 acataac  putative branch site (score: 8)
                         ttatccaactctttcc  putative PPT
                   tttagattat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaacacacttcttatgcattgatgctatgatatataacttaacataactggcatccttgggactttagattatccaactctttcctttctgttctttagATATGTGATGCGGTTGCTGTTGCTAAAATTCTGAATGCGTCTCTTGTGATCCCACATCTTGAAGTAAATCCTGTTTGGAAAGACACAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG