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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtagaggtgggctgcgcttcgttcaacatcgcacgtgcaatctttgacacacctgaataattccctgttatttcatatcccagGGTACCCAACATTTAGAGGACAGGTCCTCAACGGCAGTCAGCTGTGGGATCTTATTGAAGGGCTGGCGGAAAACGATTTATTGCATTATACCCATTTATT

Basic information

species Oryza sativa
transcript LOC_Os12g40830.3
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os12g40830.3 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G069758_T02 (Zea mays), 3'ss of exon 4
gtagaggtgggctgcgcttcgttcaacatcgcacgtgcaatctttgacacacctgaataattccctgttatttcatatcccagGGTACCCAACATTTAGAGGACAGGTCCTCAACGGCAGTCAGCTGTGGGATCTTATTGAAGGGCTGGCGGAAAACGATTTATTGCATTATACCCATTTATT
||| | ||     | |  | || ||  ||| |           |||  |||| | || ||||||  ||| | |  |||| |||| ||||||||||||||||| ||||| || || ||||  ||||| ||||| ||||||||||| |||| ||||||  | ||  | |||||||||||||||||
gtaaatgtatatcgtggat-gtacacaatctcgtacaattcacttgggacacataaacaattcca-gttgtgtgttatctcagGATACCCAACATTTAGAGGTCAGGTTCTTAATGGCAAACAGCTCTGGGACCTTATTGAAGGACTGGAGGAAAATCAGTTGCTTCATTATACCCATTTATT
















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|88580749|gb|CI697698.1|CI697698
EST:     GGGCTTTGATGTGGATCCGATAAACTCGGTACAGTTTTCTAATCATACAG                         GGTACCCAACATTTAGAGGACAGGTCCTCAACGGCAGTCAGCTGTGGGATC
genomic: GGGCTTTGATGTGGATCCGATAAACTCGGTACAGTTTTCTAATCATACAGgtagaggtgg ... catatcccagGGTACCCAACATTTAGAGGACAGGTCCTCAACGGCAGTCAGCTGTGGGATC
EST: gi|88443713|gb|CI591938.1|CI591938
EST:     GGGCTTTGATGTGGATCCGATAAACTCGGTACAGTTTTCTAATCATACAG                         GGTACCCAACATTTAGAGGACAGGTCCTCAACGGCAGTCAGCTGTGGGATC
genomic: GGGCTTTGATGTGGATCCGATAAACTCGGTACAGTTTTCTAATCATACAGgtagaggtgg ... catatcccagGGTACCCAACATTTAGAGGACAGGTCCTCAACGGCAGTCAGCTGTGGGATC
EST: gi|88339276|gb|CI633847.1|CI633847
EST:     GGGCTTTGATGTGGATCCGATAAANTCGGTACAGTTTTCTAATCATACAG                         GGTACCCAACATTTAGAGGACAGGTCCTCAACGGCAGTCAGCTGTGGGATC
genomic: GGGCTTTGATGTGGATCCGATAAACTCGGTACAGTTTTCTAATCATACAGgtagaggtgg ... catatcccagGGTACCCAACATTTAGAGGACAGGTCCTCAACGGCAGTCAGCTGTGGGATC
EST: gi|88448481|gb|CI693864.1|CI693864
EST:     GGGCTTTGATGTGGATCCGATAAACTCGGTACAGTTTTCTAATCATACAG                         GGTACCCAACATTTAGAGGACAGGTCCTCAACGGCAGTCAGCTGTGGGATC
genomic: GGGCTTTGATGTGGATCCGATAAACTCGGTACAGTTTTCTAATCATACAGgtagaggtgg ... catatcccagGGTACCCAACATTTAGAGGACAGGTCCTCAACGGCAGTCAGCTGTGGGATC
EST: gi|88355870|gb|CI625499.1|CI625499
EST:     GGGCTTTGATGTGGATCCGATAAACTCGGTACAGTTTTCTAATCATACAG                         GGTACCCAACATTTAGAGGACAGGTCCTCAACGGCAGTCAGCTGTGGGATC
genomic: GGGCTTTGATGTGGATCCGATAAACTCGGTACAGTTTTCTAATCATACAGgtagaggtgg ... catatcccagGGTACCCAACATTTAGAGGACAGGTCCTCAACGGCAGTCAGCTGTGGGATC
EST: gi|88341926|gb|CI644263.1|CI644263
EST:     GGGCTTTGATGTGGATCCGATAAACTCGGTANAGTTTTCTAATCATACAG                         GGTACCCAACATTTAGAGGACAGGTCCTCAACGGCAGTCAGCTGTGGGATC
genomic: GGGCTTTGATGTGGATCCGATAAACTCGGTACAGTTTTCTAATCATACAGgtagaggtgg ... catatcccagGGTACCCAACATTTAGAGGACAGGTCCTCAACGGCAGTCAGCTGTGGGATC
EST: gi|88301040|gb|CI592220.1|CI592220
EST:     GGGCTTTGATGTGGATCCGATAAACTCGGTACAGTTTTCTAATCATACAG                         GGTACCCAACATTTAGAGGACAGGTCCTCAACGGCAGTCAGCTGTGGGATC
genomic: GGGCTTTGATGTGGATCCGATAAACTCGGTACAGTTTTCTAATCATACAGgtagaggtgg ... catatcccagGGTACCCAACATTTAGAGGACAGGTCCTCAACGGCAGTCAGCTGTGGGATC
EST: gi|88337186|gb|CI628272.1|CI628272
EST:     GGGCTTTGATGTGGATCCGATAAACTCGGTACAGTTTTCTAATCATACAG                         GGTACCCAAAATTTAGAGGACAGGTCCTCAACGGCAGTCAGCTGTGGGATC
genomic: GGGCTTTGATGTGGATCCGATAAACTCGGTACAGTTTTCTAATCATACAGgtagaggtgg ... catatcccagGGTACCCAACATTTAGAGGACAGGTCCTCAACGGCAGTCAGCTGTGGGATC
EST: gi|58661072|gb|CK049752.1|CK049752
EST:     GGGCTTTGATGTGGATCCGATAAACTCGGTACAGTTTTCTAATCATACAG                         GGTACCCAACATTTAGAGGACAGGTCCTCAACGGCAGTCAGCTGTGGGATC
genomic: GGGCTTTGATGTGGATCCGATAAACTCGGTACAGTTTTCTAATCATACAGgtagaggtgg ... catatcccagGGTACCCAACATTTAGAGGACAGGTCCTCAACGGCAGTCAGCTGTGGGATC
EST: gi|88335844|gb|CI645445.1|CI645445
EST:     GGGCTTTGATGTGGATCCGATAAACTCGGTACAGTTTTCTAATCATACAG                         GGTACCCAACATTTAGAGGACAGGTCCTCAACGGCAGTCAGCTGTGGGATC
genomic: GGGCTTTGATGTGGATCCGATAAACTCGGTACAGTTTTCTAATCATACAGgtagaggtgg ... catatcccagGGTACCCAACATTTAGAGGACAGGTCCTCAACGGCAGTCAGCTGTGGGATC
EST: gi|88385774|gb|CI566636.1|CI566636
EST:     GGCTTTGATGTGGATCCGATAAACCTCGGTACAGTTTTCTAATCATACAG                         GGTACCCAACATTTACAGGACAGGTCCTCAACGGCAGTCAGCTGTGGGATC
genomic: GGCTTTGATGTGGATCCGATAAAC-TCGGTACAGTTTTCTAATCATACAGgtagaggtgg ... catatcccagGGTACCCAACATTTAGAGGACAGGTCCTCAACGGCAGTCAGCTGTGGGATC
EST: gi|88424098|gb|CI689800.1|CI689800
EST:     GGGCTTTGATGTGGATCCGATAAACTCGGTACAGTTTTCTAATCATACAG                         GGTACCCAACATTTAGAGGACAGGTCCTCAACGGCAGTCAGCTGTGGGATC
genomic: GGGCTTTGATGTGGATCCGATAAACTCGGTACAGTTTTCTAATCATACAGgtagaggtgg ... catatcccagGGTACCCAACATTTAGAGGACAGGTCCTCAACGGCAGTCAGCTGTGGGATC
EST: gi|66924011|gb|CX110859.1|CX110859
EST:     GGGCTTTGATGTGGATCCGATAAACTCGGTACAGTTTTCTAATCATACAG                         GGTACCCAACATTTAGAGGACAGGTCCTCAACGGCAGTCAGCTGTGGGATC
genomic: GGGCTTTGATGTGGATCCGATAAACTCGGTACAGTTTTCTAATCATACAGgtagaggtgg ... catatcccagGGTACCCAACATTTAGAGGACAGGTCCTCAACGGCAGTCAGCTGTGGGATC

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: 74 (upstream exon), 75 (downstream exon)
Score: 19

GGATACGTTGGCAACAAATCAGCAGTCTTTCCCCTGCAACTCCTGGGCTTTGATGTGGATCCGATAAACTCGGTACAGTTTTCTAATCATACAGgtagaggtgg ... catatcccagGGTACCCAACATTTAGAGGACAGGTCCTCAACGGCAGTCAGCTGTGGGATCTTATTGAAGGGCTGGCGGAAAACGATTTATTGCATTATACCCATTTATT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcgcacgtgcaatctttgacacacctgaataattccctgttatttcatatcccagGGTACCCAACATTTAGAGGACAGGTCCTCAACGGCAGTCAGCTGTGGGATCTTATTGAAGGGCTGGCGGAAAACGATTTATTGCATTATACCCATTTATT
             ctttgac  putative branch site (score: 19)
                                ttccctgttatttc  putative PPT
                                       ttatttcatat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtagaggtgggctgcgcttcgttcaacatcgcacgtgcaatctttgacacacctgaataattccctgttatttcatatcccagGGTACCCAACATTTAGAGGACAGGTCCTCAACGGCAGTCAGCTGTGGGATCTTATTGAAGGGCTGGCGGAAAACGATTTATTGCATTATACCCATTTATT

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