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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtagtttacctgtcctctttaactttctacagtgttagccacttggatttcccttgcagtaactcgactattttttttagGGGAAGTTATTACAACCCAAGGATGATACATGGTCTGACTGTGCTAAAAATGGATATGCAG

Basic information

species Oryza sativa
transcript LOC_Os10g27340.2
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os10g27340.2 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G168506_T02 (Zea mays), 3'ss of exon 6
gtagtttacctgtcctctttaactttctacagtgttagccacttggatttcccttgcagtaactcgactattttttttagGGGAAGTTATTACAACCCAAGGATGATACATGGTCTGACTGTGCTAAAAATGGATATGCAG
||||| ||| ||||||   |   | | |||    |||       | ||  |  ||| | | ||| ||  |||   |  |||||||| |||| ||||||||||| || || |||||||| ||||| | ||| ||||||||||
gtagtgtacttgtccttcctg--tgtttacccccttaa------gaatgccagttgtaatgacttgaacattccat--agGGGAAGCTATTGCAACCCAAGGACGACACTTGGTCTGATTGTGCAAGAAACGGATATGCAG

upper sequence: LOC_Os10g27340.2 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G520535_T01 (Zea mays), 3'ss of exon 5
gtagtttacctgtcctctttaactttctacagtgttagccacttggatttcccttgcagtaactcgactattttttttagGGGAAGTTATTACAACCCAAGGATGATACATGGTCTGACTGTGCTAAAAATGGATATGCAG
||||||| | ||||||   |   | | ||| || |||       | ||  |  ||| |  ||||  |  |||   |  |||||||| |||||||||| |||||  | || |||||||| ||||| | ||||||||||||||
gtagtttgcttgtccttcctg--tgtttactgtcttaa------gaatgccagttgtaacaacttcaacattcaat--agGGGAAGCTATTACAACCGAAGGACAACACTTGGTCTGATTGTGCAAGAAATGGATATGCAG

upper sequence: LOC_Os10g27340.2 (Oryza sativa), 3'ss of exon 5
lower sequence: Vv14s0066g02170.t01 (Vitis vinifera), 3'ss of exon 6
gtagtttacctgtcct--ctttaactttctacagtgttagccacttggatttcccttgcagtaactcgact-attttttttagGGGAAGTTATTACAACCCAAGGATGATACATGGTCTGACTGTGCTAAAAATGGATATGCAG
|||  | |  | |  |    |||    ||  | |   |  || ||   || ||   |    ||||   |||  | || |  |||| |  || |  ||||| ||||||||||  |||||||| ||||||||||| || |||||||
gtaaatgatttctaatgatattaggactcgtctgcagtctcctctcctatctcatgtcatttaacataacttgtcttctacagGGAAGATTTTCTCAACCAAAGGATGATAGCTGGTCTGATTGTGCTAAAAAGGGTTATGCAG

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|27547637|gb|CA767386.2|CA767386
EST:     GGGAGAGACC-TCTTT-CNGAAGCAGAG                         GGGAAGTTATT-NAACCCAAGGATGATACATGGTCTGACTGTGCTAAAAAT
genomic: GGGAGAGACCATCTTTCCAGAAGCAGAGgtagtttacc ... ttttttttagGGGAAGTTATTACAACCCAAGGATGATACATGGTCTGACTGTGCTAAAAAT
EST: gi|38477887|gb|CF962020.1|CF962020
EST:     GGGAGAGACCATCTTTCCAGAAGCAGAG                         GGGAAGTTATTACAACCCAAGGATGATACATGGTCTGACTGTGCTAAAAAT
genomic: GGGAGAGACCATCTTTCCAGAAGCAGAGgtagtttacc ... ttttttttagGGGAAGTTATTACAACCCAAGGATGATACATGGTCTGACTGTGCTAAAAAT
EST: gi|300215545|gb|HO088171.1|HO088171
EST:     ACCTTTCAGACGTTGGGAAGGGGGGAGAGACCATCTTTCCAGAAGCAGAG                         GGGAAGTTATTACAACCCAAGGATGATACATGGTCTGACTGTGCTAAAAAT
genomic: ACCTTTCAGACGTTGGGAAGGGGGGAGAGACCATCTTTCCAGAAGCAGAGgtagtttacc ... ttttttttagGGGAAGTTATTACAACCCAAGGATGATACATGGTCTGACTGTGCTAAAAAT
EST: gi|86495858|gb|CI138491.1|CI138491
EST:     TGGGAAGGGGGGAGAGACCATCTTTCCAGAAGCAGAG                         GGGAAGTTATTACAACCCAAGGATGATACATGGTCTGACTGTGCTAAAAAT
genomic: TGGGAAGGGGGGAGAGACCATCTTTCCAGAAGCAGAGgtagtttacc ... ttttttttagGGGAAGTTATTACAACCCAAGGATGATACATGGTCTGACTGTGCTAAAAAT
EST: gi|3762086|gb|C99334.1|C99334
EST:     ACCTTTCAGACGTTGGGAAGGGGGGAGAGACCATCTTTCCAGAAGCAGAG                         GGGAAGTTATTACAACCCAAGGATGATACATGGTCTGACTGTGCTAAAAAT
genomic: ACCTTTCAGACGTTGGGAAGGGGGGAGAGACCATCTTTCCAGAAGCAGAGgtagtttacc ... ttttttttagGGGAAGTTATTACAACCCAAGGATGATACATGGTCTGACTGTGCTAAAAAT
EST: gi|38480066|gb|CF964155.1|CF964155
EST:     ACCTTTCAGACGTTGGGAAGGGGGGAGAGACCATCTTTCCAGAAGCAGAG                         GGGAAGTTATTACAACCCAAGGATGATACATGGTCTGACTGTGCTAAAAAT
genomic: ACCTTTCAGACGTTGGGAAGGGGGGAGAGACCATCTTTCCAGAAGCAGAGgtagtttacc ... ttttttttagGGGAAGTTATTACAACCCAAGGATGATACATGGTCTGACTGTGCTAAAAAT
EST: gi|11025657|gb|AU162258.1|AU162258
EST:     ACCTTTCAGACGTTGGGAAGGGGGGAGAGACCATCTTTCCAGAAGCAGAG                         GGGAAGTTATTACAACCCAAGGATGATACATGGTCTGACT
genomic: ACCTTTCAGACGTTGGGAAGGGGGGAGAGACCATCTTTCCAGAAGCAGAGgtagtttacc ... ttttttttagGGGAAGTTATTACAACCCAAGGATGATACATGGTCTGACT
EST: gi|86495712|gb|CI138345.1|CI138345
EST:     ACCTTTCAGACGTTGGGAAGGGGGGAGAGACCATCTTTCCAGAAGCAGAG                         GGGAAGTTATTACAACCCAAGGATGATACATGGTCTGACTGTGCTAAAAAT
genomic: ACCTTTCAGACGTTGGGAAGGGGGGAGAGACCATCTTTCCAGAAGCAGAGgtagtttacc ... ttttttttagGGGAAGTTATTACAACCCAAGGATGATACATGGTCTGACTGTGCTAAAAAT
EST: gi|86509561|gb|CI152194.1|CI152194
EST:     CATCTTTCCAGAAGCAGAG                         GGGAAGTTATTACAACCCAAGGATGATACATGGTCTGACTGTGCTAAAAAT
genomic: CATCTTTCCAGAAGCAGAGgtagtttacc ... ttttttttagGGGAAGTTATTACAACCCAAGGATGATACATGGTCTGACTGTGCTAAAAAT
EST: gi|87018479|gb|CI252233.1|CI252233
EST:     ACCTTTCAGACGTTGGGAAGGGGGGAGAGACCATCTTTCCAGAAGCAGAG                         GGGAAGTTATTACAACCCAAGGATGATACATGGTCTGACTGTGCTAAAAAT
genomic: ACCTTTCAGACGTTGGGAAGGGGGGAGAGACCATCTTTCCAGAAGCAGAGgtagtttacc ... ttttttttagGGGAAGTTATTACAACCCAAGGATGATACATGGTCTGACTGTGCTAAAAAT

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), 55 (downstream exon)
Score: 12

CAAAAATAATCAAGCTCTTGGAGGACATCGGATCGCCACTGTGCTCATGTACCTTTCAGACGTTGGGAAGGGGGGAGAGACCATCTTTCCAGAAGCAGAGgtagtttacc ... ttttttttagGGGAAGTTATTACAACCCAAGGATGATACATGGTCTGACTGTGCTAAAAATGGATATGCAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tctacagtgttagccacttggatttcccttgcagtaactcgactattttttttagGGGAAGTTATTACAACCCAAGGATGATACATGGTCTGACTGTGCTAAAAATGGATATGCAG
                               cagtaac  putative branch site (score: 12)
                                          ctatttttttt  putative PPT
                                         actatttttttta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtagtttacctgtcctctttaactttctacagtgttagccacttggatttcccttgcagtaactcgactattttttttagGGGAAGTTATTACAACCCAAGGATGATACATGGTCTGACTGTGCTAAAAATGGATATGCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGATG