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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTATGGCAATGGAGTCCCAAGCAGAGGCACTCGGTCAGTTGGCAACTGATGATCTTGAAGGAAAGgtaaatttgacattgtggactaaattttcgtggatatcactgaggtaattagatgatctgatcgttgttatttatttgtgcacag

Basic information

species Oryza sativa
transcript LOC_Os01g67000.1
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g67000.1 (Oryza sativa), 5'ss of exon 9
lower sequence: GRMZM2G024607_T02 (Zea mays), 5'ss of exon 8
TTATGGCAATGGAGTCCCAAGCAGAGGCACTCGGTCAGTTGGCAACTGATGATCTTGAAGGAAAGgtaaatttgacattgtggactaaattttcgtggatatcactgaggtaattagatgatc--tgatcgttgttatttatttgtgcacag
||||||| ||||| |||||||| ||||||||||| || || |||||||| ||||| ||||||||||||||  |||     |  || |     || |   ||    ||   | ||   ||||    |||       |||||||  ||| ||||
TTATGGCGATGGAATCCCAAGCGGAGGCACTCGGCCAATTAGCAACTGACGATCTAGAAGGAAAGgtaaaaatga--acatttacaaggcagtcataagtac--ttgccttgatctaatgacacatgactacctgtatttatcggtg-acag

upper sequence: LOC_Os01g67000.1 (Oryza sativa), 5'ss of exon 9
lower sequence: GRMZM2G017077_T01 (Zea mays), 5'ss of exon 9
TTATGGCAATGGAGTCCCAAGCAGAGGCACTCGGTCAGTTGGCAACTGATGATCTTGAAGGAAAGgtaaatttgacattgtggactaaattttcgtggatatcactgaggtaattagatgatctgatcgttgttatttatttgtgcacag
||||||| ||||| |||||||||||||||||||| ||||| |||||||||||| | ||||||||||||||  | |   | |     |||      |  |||        ||  | | || |  |||  ||   |||||||| ||| ||||
TTATGGCGATGGAATCCCAAGCAGAGGCACTCGGCCAGTTAGCAACTGATGATTTAGAAGGAAAGgtaaaaataaacattta---caaaccaatataaatacttgccttgtgctaatatcacatgactgtctctatttattggtgaacag

upper sequence: LOC_Os01g67000.1 (Oryza sativa), 5'ss of exon 9
lower sequence: GLYMA11G13300.1 (Glycine max), 5'ss of exon 9
TTATGGCAATGGAGTCCCAAGCAGAGGCACTCGGTCAGTTGGCAACTGATGATCTTGAAGGAAAGgtaaatttgacattgtg-gactaaattttcgtggatatcactgaggtaattagat--gatctgatcgt-tgttatttatttgtgcacag-----------
|  || |||||||||||||||| || || || || |||||| ||| ||||||||||||||||||||||    | | ||  ||  |||  |  ||  |   |||   | |  |  | || |  ||  ||| ||  |   | |||   |   | ||           
TGTTGACAATGGAGTCCCAAGCTGAAGCTCTTGGCCAGTTGACAAGTGATGATCTTGAAGGAAAGgtagtaattatatcatgtaacttcaaatttatttgtatgcattatatgttgagcttggaaatgaacgaatacaagttaaaaggaaaaagaaaactagatt

upper sequence: LOC_Os01g67000.1 (Oryza sativa), 5'ss of exon 9
lower sequence: GLYMA12G05330.1 (Glycine max), 5'ss of exon 9
TTATGGCAATGGAGTCCCAAGCAGAGGCACTCGGTCAGTTGGCAACTGATGATCTTGAAGGAAAGgta--aatttgacattgtggactaaatttt---cgtggatatcac-tgaggtaattagatgatctgatcgttgttatttatttgtgcacag-----------
|  ||||||||||||||||||| || || || || |||||| ||| ||||||||||||||||||||||  ||||  ||  |||    | || |||    ||    || |  ||  | | || ||       ||   |     |||   |   | ||           
TGTTGGCAATGGAGTCCCAAGCTGAAGCTCTTGGCCAGTTGACAAGTGATGATCTTGAAGGAAAGgtagtaattataccatgtaacttcaagtttatatgtatgcattatatgttgaacttggaaag--gaatgaatacaggttaaaaggaaaaagaaaactagatt

upper sequence: LOC_Os01g67000.1 (Oryza sativa), 5'ss of exon 9
lower sequence: Vv04s0023g00780.t01 (Vitis vinifera), 5'ss of exon 9
TTATGGCAATGGAGTCCCAAGCAGAGGCACTCGGTCAGTTGGCAACTGATGATCTTGAAGGAAAGgtaa--atttgacattgtggactaaattttcgtggatatcact----gaggtaattagatgatctgatcgt-tgttattt--atttgtgcacag------
|  | || |||||||| ||||| |||||||||  ||||||  | ||||||||||| |||||||||||||   ||    ||| |    ||   ||   |   |  | ||    |   ||      |  | | | | | || || ||  |  | || | |       
TGTTAGCCATGGAGTCTCAAGCTGAGGCACTCAATCAGTTAACCACTGATGATCTGGAAGGAAAGgtaactgttcttaattttcttttatggttcactacctgcctcttcatgttctagccctttttttttagcatatgctactttgaaatatgtatatttgatt

upper sequence: LOC_Os01g67000.1 (Oryza sativa), 5'ss of exon 9
lower sequence: Vv05s0094g00150.t01 (Vitis vinifera), 5'ss of exon 8
TTATGGCAATGGAGTCCCAAGCAGAGGCACTCGGTCAGTTGGCAACTGATGATCTTGAAGGAAAGgtaaat-ttgacattgtggactaaattttcgtggatatcactgaggtaattagatgatctgatcgttgttatttatttgtgcacag-----------------
|  || ||||||||||||||||||||||||| || |||||  |  ||||||| ||||| |||||||||  | ||  |  | |  |||   | ||| |   | ||| |    | |  | |||||||      | |||   |  |      |                  
TGTTGACAATGGAGTCCCAAGCAGAGGCACTGGGCCAGTTAACTTCTGATGAGCTTGACGGAAAGgtagctgttatctctctttactccttattcttttgtctcaata---ttaagaaatgatctcccaagtattaaaaaaataaaatgaaataaaacaaaaaaggca

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|11564773|gb|AU165409.1|AU165409
EST:     CCCAAGCAGAGGCACTCGGTCAGTTGGCAACTGATGATCTTGAAGGAAAG                         TTTGCATTGCTTGAGACTTCATCGGTTGATGATGACCTTGCACAAATGAAA
genomic: CCCAAGCAGAGGCACTCGGTCAGTTGGCAACTGATGATCTTGAAGGAAAGgtaaatttga ... ttgtgcacagTTTGCATTGCTTGAGACTTCATCGGTTGATGATGACCTTGCACAAATGAAA
EST: gi|88987357|gb|CI034321.1|CI034321
EST:     ATGATCTTGAAGGAAAG                         TTTGCATTGCTTGAGACTTCATCGGTTGATGATGACCTTGCACAAATGAAA
genomic: ATGATCTTGAAGGAAAGgtaaatttga ... ttgtgcacagTTTGCATTGCTTGAGACTTCATCGGTTGATGATGACCTTGCACAAATGAAA
EST: gi|87007164|gb|CI277239.1|CI277239
EST:     CCCAAGCAGAGGCACTCGGTCAGTTGGCAACTGATGATCTTGAAGGAAAG                         TTTGCATTGCTTGAGACTTCATCGGTTGATGATGACCTTGCACAAATGAAA
genomic: CCCAAGCAGAGGCACTCGGTCAGTTGGCAACTGATGATCTTGAAGGAAAGgtaaatttga ... ttgtgcacagTTTGCATTGCTTGAGACTTCATCGGTTGATGATGACCTTGCACAAATGAAA
EST: gi|33797534|gb|CF324627.1|CF324627
EST:     CCCAAGCAGAGGCACTCGGTCAGTTGGCAACTGATGATCTTGAAGGAAAG                         TTTGCATTGCTTGAGACTTCATCGGTTGATGATGACCTTGCACAAATGAAA
genomic: CCCAAGCAGAGGCACTCGGTCAGTTGGCAACTGATGATCTTGAAGGAAAGgtaaatttga ... ttgtgcacagTTTGCATTGCTTGAGACTTCATCGGTTGATGATGACCTTGCACAAATGAAA
EST: gi|88995507|gb|CI022830.1|CI022830
EST:     CCCAAGCAGAGGCACTCGGTCAGTTGGCAACTGATGATCTTGAAGGAAAG                         TTTGCATTGCTTGAGACTTCATCGGTTGATGATGACCTTGCACAAATGAAA
genomic: CCCAAGCAGAGGCACTCGGTCAGTTGGCAACTGATGATCTTGAAGGAAAGgtaaatttga ... ttgtgcacagTTTGCATTGCTTGAGACTTCATCGGTTGATGATGACCTTGCACAAATGAAA
EST: gi|88988016|gb|CI018059.1|CI018059
EST:     CCCAAGCAGAGGCACTCGGTCAGTTGGCAACTGATGATCTTGAAGGAAAG                         TTTGCATTGCTTGAGACTTCATCGGTTGATGATGACCTTGCACAAATGAAA
genomic: CCCAAGCAGAGGCACTCGGTCAGTTGGCAACTGATGATCTTGAAGGAAAGgtaaatttga ... ttgtgcacagTTTGCATTGCTTGAGACTTCATCGGTTGATGATGACCTTGCACAAATGAAA
EST: gi|86594857|gb|CI258111.1|CI258111
EST:     CCCAAGCAGAGGCACTCGGTCAGTTGGCAACTGATGATCTTGAAGGAAAG                         TTTGCATTGCTTGAGACTTCATCGGTTGATGATGACCTTGCACAAATGAAA
genomic: CCCAAGCAGAGGCACTCGGTCAGTTGGCAACTGATGATCTTGAAGGAAAGgtaaatttga ... ttgtgcacagTTTGCATTGCTTGAGACTTCATCGGTTGATGATGACCTTGCACAAATGAAA
EST: gi|88200513|gb|CI200363.1|CI200363
EST:     CCCAAGCAGAGGCACTCGGTCAGTTGGCAACTGATGATCTTGAAGGAAAG                         TTTGCATTGCTTGAGACTTCATCGGTTGATGATGACCTTGCACAAATGAAA
genomic: CCCAAGCAGAGGCACTCGGTCAGTTGGCAACTGATGATCTTGAAGGAAAGgtaaatttga ... ttgtgcacagTTTGCATTGCTTGAGACTTCATCGGTTGATGATGACCTTGCACAAATGAAA
EST: gi|86497463|gb|CI140096.1|CI140096
EST:     CCCAAGCAGAGGCACTCGGTCAGTTGGCAACTGATGATCTTGAAGGAAAG                         TTTGCATTGCTTGAGACTTCATCGGTTAATGATGACCTTGCACAAATGAAA
genomic: CCCAAGCAGAGGCACTCGGTCAGTTGGCAACTGATGATCTTGAAGGAAAGgtaaatttga ... ttgtgcacagTTTGCATTGCTTGAGACTTCATCGGTTGATGATGACCTTGCACAAATGAAA
EST: gi|86593881|gb|CI260110.1|CI260110
EST:     CCCAAGCAGAGGCACTCGGTCAGTTGGCAACTGATGATCTTGAAGGAAAG                         TTTGCATTGCTTGAGACTTCATCGGTTGATGATGACCTTGCACAAATGAAA
genomic: CCCAAGCAGAGGCACTCGGTCAGTTGGCAACTGATGATCTTGAAGGAAAGgtaaatttga ... ttgtgcacagTTTGCATTGCTTGAGACTTCATCGGTTGATGATGACCTTGCACAAATGAAA
EST: gi|88228435|gb|CI227915.1|CI227915
EST:     ATCTTGAAGGAAAG                         TTTGCATTGCTTGAGACTTCATCGGTTGATGATGACCTTGCACAAATGAAA
genomic: ATCTTGAAGGAAAGgtaaatttga ... ttgtgcacagTTTGCATTGCTTGAGACTTCATCGGTTGATGATGACCTTGCACAAATGAAA
EST: gi|86493106|gb|CI135739.1|CI135739
EST:     CCCAAGCAGAGGCACTCGGTCAGTTGGCAACTGATGATCTTGAAGGAAAG                         TTTGCATTGCTTGAGACTTCATCGGTTGATGATGACCTTGCACAAATGAAA
genomic: CCCAAGCAGAGGCACTCGGTCAGTTGGCAACTGATGATCTTGAAGGAAAGgtaaatttga ... ttgtgcacagTTTGCATTGCTTGAGACTTCATCGGTTGATGATGACCTTGCACAAATGAAA
EST: gi|86432017|gb|CI085628.1|CI085628
EST:     CCCAAGCAGAGGCACTCGGTCAGTTGGCAACTGATGATCTTGAAGGAAAG                         TTTGCATTGCTTGAGACTTCATCGGTTGATGATGACCTTGCACAAATGAAA
genomic: CCCAAGCAGAGGCACTCGGTCAGTTGGCAACTGATGATCTTGAAGGAAAGgtaaatttga ... ttgtgcacagTTTGCATTGCTTGAGACTTCATCGGTTGATGATGACCTTGCACAAATGAAA

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), 63 (downstream exon)
Score: 59

TTATGGCAATGGAGTCCCAAGCAGAGGCACTCGGTCAGTTGGCAACTGATGATCTTGAAGGAAAGgtaaatttga ... ttgtgcacagTTTGCATTGCTTGAGACTTCATCGGTTGATGATGACCTTGCACAAATGAAAAAGGAAATTTCTGGAAGCTCTTCG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TTATGGCAATGGAGTCCCAAGCAGAGGCACTCGGTCAGTTGGCAACTGATGATCTTGAAGGAAAGgtaaatttgacattgtggactaaattttcgtggatatcactgaggtaattagatgatctgatcgttgttatttatttgtgcacag

- - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAA