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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtaaagcaatggaggactatgaacttacatttcttatctgtgatggcatcttatttagaaggtgaacttgttcatcttgtagATATGAAAAGAGGCACTCCAACATTCCAGCTCACATTTCTCCATGCTTCCGTGTTAAGGAAGGTGACCATGTCATCATTGGCCAGTGCAG

Basic information

species Oryza sativa
transcript LOC_Os08g10608.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os08g10608.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA09G12430.1 (Glycine max), 3'ss of exon 4
-------gtaagtaaagcaatggaggactatgaacttacatttcttatctgtgatggcatcttatttagaaggtgaacttgttcatcttgtagATATGAAAAGAGGCACTCCAACATTCCAGCTCACATTTCTCCATGCTTCCGTGTTAAGGAAGGTGACCATGTCATCATTGGCCAGTGCAG
             | | |  ||| |  |  | |  ||    ||   ||        | | || || |      |   ||  |||   ||  |||||||||||| |||| || || |||||  | ||||| || || || ||||||||||||||||| || ||||| || |||||||| |||||
gtattccccttccatacctttggtgagcagtta--ttgttgtttacatggacagaagtaactaatgtttcttctttgctcattctattt--agATATGAAAAGCGGCATTCAAATATTCCTTCACACATATCACCTTGTTTCCGTGTTAAGGAAGGAGATCATGTTATTATTGGCCAATGCAG

upper sequence: LOC_Os08g10608.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA01G25840.1 (Glycine max), 3'ss of exon 1
gtaagtaaagcaatggaggactatgaacttacatttcttatctgtgatggcatcttatttagaaggtgaacttgttcatcttgtagATATGAAAAGAGGCACTCCAACATTCCAGCTCACATTTCTCCATGCTTCCGTGTTAAGGAAGGTGACCATGTCATCATTGGCCAGTGCAG
                     | | |   ||| || |||   |       |||   || |      |   |||||||   ||  |||||||||||| | || || || |||||||| ||||| || || || ||||||||||||||||| || |||                    
-------------------gtttttattgtac-ttgcttgcatacacaaacataacatgttttttctctgcttgttctattt--agATATGAAAAGCGTCATTCAAATATTCCAGCACACATATCACCTTGTTTCCGTGTTAAGGAAGGAGATCAT--------------------

upper sequence: LOC_Os08g10608.1 (Oryza sativa), 3'ss of exon 4
lower sequence: AT3G48930.1 (Arabidopsis thaliana), 3'ss of exon 4
gtaagtaaagcaatggaggactatgaacttacatttcttatctgtgatggcatcttattta-gaaggtgaacttgttcatcttgt-agATATGAAAAGAGGCACTCCAACATTCCAGCTCACATTTCTCCATGCTTCCGTGTTAAGGAAGGTGACCATGTCATCATTGGCCAGTGCAG
    |||||   ||  |     ||  ||||   |   |    | | |     |  | |||| ||| || |  |  ||  | || | || ||||| |||||||| || |||||||| |||||  | || ||||||||||||||||||||||| |||||| ||||||||||||| |||||
----gtaaattcatacattctcat--acttctttccatagagtcttacacattgatgtttaagaaagtaatatcctttttgttcttagGTATGAGAAGAGGCATTCAAACATTCCGGCTCATGTCTCACCATGCTTCCGTGTTAAGGAAGGAGACCATATCATCATTGGCCAATGCAG

upper sequence: LOC_Os08g10608.1 (Oryza sativa), 3'ss of exon 4
lower sequence: AT5G23740.1 (Arabidopsis thaliana), 3'ss of exon 4
gtaagtaaagcaatggaggactatgaactt-acatttcttatctgtgatggcatcttatt-----tagaaggtgaacttgttcatcttgt-agATATGAAAAGAGGCACTCCAACATTCCAGCTCACATTTCTCCATGCTTCCGTGTTAAGGAAGGTGACCATGTCATCATTGGCCAGTGCAG
||||||| |           |||||  ||| | |   ||   |   |||   |  | | |     || | | | | |||     | |  | |||||||| ||||| || |||||||| || || ||  | || || || |||||||| ||||||||||||||||||||||||||||| |||||
gtaagtacattgtgatgaacctatgttcttgatagagctgcgcaaagatataacatcaatgctgataaacgattatcttaaatttttcattagATATGAGAAGAGACATTCCAACATCCCTGCCCATGTCTCACCGTGTTTCCGTGTCAAGGAAGGTGACCATGTCATCATTGGCCAATGCAG

upper sequence: LOC_Os08g10608.1 (Oryza sativa), 3'ss of exon 4
lower sequence: Vv04s0008g06220.t01 (Vitis vinifera), 3'ss of exon 4
gtaagtaaagcaatggaggactatgaacttacatttctta---tctgtgatggcatcttatttagaaggtgaacttgt-tcatc-ttgtagATATGAAAAGAGGCACTCCAACATTCCAGCTCACATTTCTCCATGCTTCCGTGTTAAGGAAGGTGACCATGTCATCATTGGCCAGTGCAG
||| |  || | ||  |     |||||  |   ||| |     ||  |  |    | |    || ||  | || |||| |  ||  | ||||||||| ||||||||||| || || ||||| || || || |||||||||||||| || || ||||| ||||| || ||||||||||||||
gtagg--aaccgatttaattgaatgaatctttgtttttcgggctcctttctcttgtatggaatataatattaaattgtattgtcactctagATATGAGAAGAGGCACTCAAATATACCAGCACATATATCCCCATGCTTCCGTGTCAAAGAGGGTGATCATGTTATTATTGGCCAGTGCAG

upper sequence: LOC_Os08g10608.1 (Oryza sativa), 3'ss of exon 4
lower sequence: Vv11s0118g00680.t01 (Vitis vinifera), 3'ss of exon 4
gtaagtaaagcaatggaggactatgaacttacatttct--tatctgtgatggcatcttatttagaaggtga--acttgttcatcttg--------tagATATGAAAAGAGGCACTCCAACATTCCAGCTCACATTTCTCCATGCTTCCGTGTTAAGGAAGGTGACCATGTCATCATTGGCCAGTGCAG
| | ||    | |   |    | ||||     |||| |  | ||           ||| |  || || |||  | || ||| ||||          |||||||| ||||||||||| |||||||| |||||||  || |||||||||||||| |||||||| || ||||| || ||||||||||||||
gcatgttcctccagttatagttgtgaatgggtatttttactttccccagaatttgcttttcaagtagttgaccattttttcttctttgctgcattcagATATGAGAAGAGGCACTCAAACATTCCTGCTCACACATCGCCATGCTTCCGTGTGAAGGAAGGAGATCATGTTATTATTGGCCAGTGCAG

upper sequence: LOC_Os08g10608.1 (Oryza sativa), 3'ss of exon 4
lower sequence: PP1S51_307V6.1 (Physcomitrella patens), 3'ss of exon 4
-------------------------------------------------------------gtaagtaaagcaatggaggactatgaacttacatttcttatctgtgatggcatcttatttagaaggtgaacttg-ttcatcttgtagATATGAAAAGAGGCACTCCAACATTCCAGCTCACATTTCTCCATGCTTCCGTGTTAAGGAAGGTGACCATGTCATCATTGGCCAGTGCAG
                                                                | ||  |   || | ||   |||  | |  | |   |   |||     |   | ||   |   |||  |   ||| ||||| || || || ||||||||||| ||| |  | || ||| | || ||    |||||||||||||| |||||| | |||||||||||||| |||||
gtgggttttccttgcccctttcaattcgcattgtttaattgcttgactccataatatctgcaggattactgttttgaatgaacttgagatcaattgtgcgacacgtgcattgactattttcccatcatgacttgaattcctcttgcagGTACGAGAAGAGGCACTCAAACTTGGCCGCCCACGTCTCCCCTGCTTTCCGTGTTAAGGAGGGTGACAAGGTCATCATTGGCCAATGCAG

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|88569513|gb|CI660688.1|CI660688
EST:     ACAATCATCGTACGCAGAAACTACCTCCATTTTGTGAAGAAATATCAGCG                         ATATGAAAAGAGGCACTCCAACATTCCAGCTCACATTT
genomic: ACAATCATCGTACGCAGAAACTACCTCCATTTTGTGAAGAAATATCAGCGgtaagtaaag ... catcttgtagATATGAAAAGAGGCACTCCAACATTCCAGCTCACATTT
EST: gi|33659206|gb|CF281819.1|CF281819
EST:     ACAATCATCGGACGCAGAAACTACCTCCATTTTGTGAAGAAATATCAGCG                         ATATGAAAAGAGGCACTCCAGCATTCCAGCTGACATTTCTCCATGCTTCCG
genomic: ACAATCATCGTACGCAGAAACTACCTCCATTTTGTGAAGAAATATCAGCGgtaagtaaag ... catcttgtagATATGAAAAGAGGCACTCCAACATTCCAGCTCACATTTCTCCATGCTTCCG
EST: gi|33661075|gb|CF292042.1|CF292042
EST:     ACAATCATCGTACGCAGAAACTACCTCCATTTTGTGAAGAAATATCAGCG                         ATATGAAAAGAGGCACTCCAACATTCCAGCTCACATTTCTCCATGCTTCCG
genomic: ACAATCATCGTACGCAGAAACTACCTCCATTTTGTGAAGAAATATCAGCGgtaagtaaag ... catcttgtagATATGAAAAGAGGCACTCCAACATTCCAGCTCACATTTCTCCATGCTTCCG
EST: gi|55439213|gb|CV732908.1|CV732908
EST:     CTCCATTTTGTGAAGAAATATCAGCG                         ATATGAAAAGAGGCACTCCAACATTCCAGCTCACATTTTTCCATGCTTCCG
genomic: CTCCATTTTGTGAAGAAATATCAGCGgtaagtaaag ... catcttgtagATATGAAAAGAGGCACTCCAACATTCCAGCTCACATTTCTCCATGCTTCCG
EST: gi|88587591|gb|CI705349.1|CI705349
EST:     ACAATCATCGTACGCAGAAACTACCTCCATTTTGTGAAGAAATATCAGCG                         ATATGAAAAGAGGCA
genomic: ACAATCATCGTACGCAGAAACTACCTCCATTTTGTGAAGAAATATCAGCGgtaagtaaag ... catcttgtagATATGAAAAGAGGCA
EST: gi|9865837|gb|AU101587.1|AU101587
EST:     ACAATCATCGTACGCAGAAACTACCTCCATTTTGTGAAGAAATATCAGCG                         ATATGAAAAGAGGCACTCCAACATTCCAGCTCACATTTCTCCATGCTTCCG
genomic: ACAATCATCGTACGCAGAAACTACCTCCATTTTGTGAAGAAATATCAGCGgtaagtaaag ... catcttgtagATATGAAAAGAGGCACTCCAACATTCCAGCTCACATTTCTCCATGCTTCCG
EST: gi|58601143|gb|CK011671.1|CK011671
EST:     ACAATCATCGTACGCAGAAACTACCTCCATTTTGTGAAGAAATATCAGCG                         ATATGAAAAGAGGCACTCCAACATTCCAGCTCACATTTCTCCATGCTTCCG
genomic: ACAATCATCGTACGCAGAAACTACCTCCATTTTGTGAAGAAATATCAGCGgtaagtaaag ... catcttgtagATATGAAAAGAGGCACTCCAACATTCCAGCTCACATTTCTCCATGCTTCCG
EST: gi|86254941|gb|CI017061.1|CI017061
EST:     ACAATCATCGTACGCAGAAACTACCTCCATTTTGTGAAGAAATATCAGCG                         ATATGAAAAGAGGCACTCCAACATTCCAGCTCACATTTCTCCATGCTTCCG
genomic: ACAATCATCGTACGCAGAAACTACCTCCATTTTGTGAAGAAATATCAGCGgtaagtaaag ... catcttgtagATATGAAAAGAGGCACTCCAACATTCCAGCTCACATTTCTCCATGCTTCCG
EST: gi|163918131|gb|EG713997.1|EG713997
EST:     ACAATCATCGTACGCAGAAACTACCTCCATTTTGTGAAGAAATATCAGCG                         ATATGAAAAGAGGCACTCCAACATTCCAGCTCACATTTCTCCATGCTTCCG
genomic: ACAATCATCGTACGCAGAAACTACCTCCATTTTGTGAAGAAATATCAGCGgtaagtaaag ... catcttgtagATATGAAAAGAGGCACTCCAACATTCCAGCTCACATTTCTCCATGCTTCCG
EST: gi|58596143|gb|CK006671.1|CK006671
EST:     ACAATCATCGTACGCAGAAACTACCTCCATTTTGTGAAGAAATATCAGCG                         ATATGAAAAGAGGCACTCCAACATTCCAGCTCACATTTCTCCCTGCTTCCG
genomic: ACAATCATCGTACGCAGAAACTACCTCCATTTTGTGAAGAAATATCAGCGgtaagtaaag ... catcttgtagATATGAAAAGAGGCACTCCAACATTCCAGCTCACATTTCTCCATGCTTCCG
EST: gi|163917913|gb|EG713965.1|EG713965
EST:     ACAATCATCGTACGCAGAAACTACCTCCATTTTGTGAAGAAATATCAGCG                         ATATGAAAAGAGGCACTCCAACATTCCAGCTCACATTTCTCCATGCTTCCG
genomic: ACAATCATCGTACGCAGAAACTACCTCCATTTTGTGAAGAAATATCAGCGgtaagtaaag ... catcttgtagATATGAAAAGAGGCACTCCAACATTCCAGCTCACATTTCTCCATGCTTCCG

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), 41 (downstream exon)
Score: 22

TCAGAGGTAGAATTATTGCTGGAACATGCCACAGTGCCAAGATGAATAGGACAATCATCGTACGCAGAAACTACCTCCATTTTGTGAAGAAATATCAGCGgtaagtaaag ... catcttgtagATATGAAAAGAGGCACTCCAACATTCCAGCTCACATTTCTCCATGCTTCCGTGTTAAGGAAGGTGACCATGTCATCATTGGCCAGTGCAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

catttcttatctgtgatggcatcttatttagaaggtgaacttgttcatcttgtagATATGAAAAGAGGCACTCCAACATTCCAGCTCACATTTCTCCATGCTTCCGTGTTAAGGAAGGTGACCATGTCATCATTGGCCAGTGCAG
                                           ttcatctt  CT-rich tract
                    atcttattta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagtaaagcaatggaggactatgaacttacatttcttatctgtgatggcatcttatttagaaggtgaacttgttcatcttgtagATATGAAAAGAGGCACTCCAACATTCCAGCTCACATTTCTCCATGCTTCCGTGTTAAGGAAGGTGACCATGTCATCATTGGCCAGTGCAG

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