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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAAATCGTTTGCATCTGCATCAGCAGACAATATAAAGAAGTTTAGCCTGCCCAAAGGCGAATTTCTACACAATATGCTgtgagcattcttttcacattgttttttgttaacagtgtttgtgatatttttttttatgtaaatagcactggcatattatattgtgcattgtaaaatgctt...

Basic information

species Oryza sativa
transcript LOC_Os03g21990.1
intron # 15
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g21990.1 (Oryza sativa), 5'ss of exon 15
lower sequence: GRMZM2G017089_T02 (Zea mays), 5'ss of exon 12
----------------------GAAATCGTTTGCATCTGCATCAGCAGACAATATAAAGAAGTTTAGCCTGCCCAAAGGCGAATTTCTACACAATATGCTgtgagcattcttttcacattgttttt-tgttaacagtgtttgtga---tatttttttttatgtaaatagcactggcatatta-tattgtgcattgtaaaatgctt
                      |||| | |||||||| ||||||||||||||  |||||||||||| ||| ||||||||||||||||| ||||| ||||||||||  |||  |  |  |  ||||  | || ||| |||   |||    ||| |  || |||   |  |  ||     |||| |||         ||  |     
TATATAGCAACCCTTTTTTCAGGAAAGCATTTGCATCAGCATCAGCAGACAACGTAAAGAAGTTTAACCTTCCCAAAGGCGAATTTCTGCACAACATGCTgtgagtcttccatatatttaattttcattttcacattgtaactgaacacattgtggttcatgcttactgtgctacatgattaatatcaaaagccatatca-----

upper sequence: LOC_Os03g21990.1 (Oryza sativa), 5'ss of exon 15
lower sequence: GRMZM2G017089_T01 (Zea mays), 5'ss of exon 13
GAAATCGTTTGCATCTGCATCAGCAGACAATATAAAGAAGTTTAGCCTGCCCAAAGGCGAATTTCTACACAATATGCTgtgagcattcttttcacattgttttt-tgttaacagtgtttgtga---tatttttttttatgtaaatagcactggcatatta-tattgtgcattgtaaaatgctt
|||| | |||||||| ||||||||||||||  |||||||||||| ||| ||||||||||||||||| ||||| ||||||||||  |||  |  |  |  ||||  | || ||| |||   |||    ||| |  || |||   |  |  ||     |||| |||         ||  |     
GAAAGCATTTGCATCAGCATCAGCAGACAACGTAAAGAAGTTTAACCTTCCCAAAGGCGAATTTCTGCACAACATGCTgtgagtcttccatatatttaattttcattttcacattgtaactgaacacattgtggttcatgcttactgtgctacatgattaatatcaaaagccatatca-----

upper sequence: LOC_Os03g21990.1 (Oryza sativa), 5'ss of exon 15
lower sequence: GLYMA15G15960.1 (Glycine max), 5'ss of exon 14
GAAATCGTTTGCATCTGCATCAGCAGACAATATAAAGAAGTTTAGCCTGCCCAAAGGCGAATTTCTACACAATATGCTgtgagcattcttttcacattgttttttgttaacagtgtttgtgatatttttttttat--gtaa-atagcactggcatattatattgtgcattgtaaaatgctt
| || | ||||||||||| ||||| |||||||| || ||||| | ||| || ||||| |||||| | ||||| ||||||||||  |  |   |  ||| ||      |    ||| ||  |  ||  ||  | |   |||  ||    |  |      | | ||   | | | || ||   
GCAAGCTTTTGCATCTGCTTCAGCTGACAATATTAAAAAGTTCAACCTTCCAAAAGGAGAATTTTTGCACAACATGCTgtgagt-tcttaaacttatttttaccaaatttgtgtgattagggaatcattaatgaatggtaggatctttcctggggggcaaaatgccaaatatgaattgt--

upper sequence: LOC_Os03g21990.1 (Oryza sativa), 5'ss of exon 15
lower sequence: GLYMA09G04910.1 (Glycine max), 5'ss of exon 14
GAAATCGTTTGCATCTGCATCAGCAGACAATATAAAGAAGTTTAGCCTGCCCAAAGGCGAATTTCTACACAATATGCTgtgagcattcttttcacattgttttttgttaacagtgtttgtgatatttttttttatg--taaatagcactggcatattatattgtgcattgtaaaatgctt
| || | ||||||||||| ||||| |||||||| || ||||| | ||| || ||||| ||||||   ||||||||||||||||  |  |   |  ||| ||      | |     || | ||    ||  |  |||  |  ||    |  |      | | ||   | | | |  ||   
GCAAGCTTTTGCATCTGCTTCAGCTGACAATATTAAAAAGTTCACCCTTCCAAAAGGAGAATTTTGCCACAATATGCTgtgagt-tcataaacttatttttaccaaattatgtgattagggaatcattaatgaatggctggatttttcctgggggacaaaatgccaaatatgatttgtc-

upper sequence: LOC_Os03g21990.1 (Oryza sativa), 5'ss of exon 15
lower sequence: Vv05s0077g02310.t01 (Vitis vinifera), 5'ss of exon 14
GAAATCGTTTGCATCTGCATCAGCAGACAATATAAAGAAGTTTAGCCTGCCCAAAGGCGAATTTCTACACAATATGCTgtgagcattcttttcacattgttttttgttaacagtgtttgtgatatttttttttatgtaaatagcactggcatattatattgtgcat---tgtaaaatgctt----
| |  | ||||||||||||||||| ||||| |||||||| ||||  || || ||||| |||||| | ||||| ||||||||||     ||| ||      | | ||||   | | |||   ||         ||  || | |  | ||   | || |  | || ||   || | |||| ||    
GCATACTTTTGCATCTGCATCAGCTGACAACATAAAGAAATTTAATCTTCCGAAAGGGGAATTTTTGCACAACATGCTgtgagt----tttccaacaaactctatgtttgta-tatttccaattaccaaaactagatataca--attgctcttttgtgatttgaatatatgcataatgatttaga

upper sequence: LOC_Os03g21990.1 (Oryza sativa), 5'ss of exon 15
lower sequence: PP1S169_73V6.1 (Physcomitrella patens), 5'ss of exon 12
GAAATCGTTTGCATCTGCATCAGCAGACAATATAAAGAAGTTTAGCCTGCCCAAAGGCGAATTTCTACACAATATGCTgtgagcattcttttcacattgttttttgttaacagtgtttgtgatatttttttttatgt----aaatagcactggcatattatattgtgcattgtaaaatgctt
  |  | ||  | || || ||||||||||| |||||||||||| | |||||||| || || ||| |||| || ||||||| ||  |||||| |  |   |  |  | |  |  ||||  |  | | |   || || |     | || ||         |   || | ||||  | | |    
ACACACCTTCACCTCAGCTTCAGCAGACAACATAAAGAAGTTTCGGCTGCCCAAGGGAGAGTTTTTACATAACATGCTgtaagtgttctttgcgaaacttaatcaggtg-ctatgttcatattgtctgcattcatcttttggagtatcatccttgatgtgccttatccattcaatagtt---

upper sequence: LOC_Os03g21990.1 (Oryza sativa), 5'ss of exon 15
lower sequence: EFJ17196 (Selaginella moellendorffii), 5'ss of exon 9
GAAATCGTTTGCATCTGCATCAGCAGACAATATAAAGAAGTTTAGCCTGCCCAAAGGCGAATTTCTACACAATATGCTgtgagcattcttttcacattgttttttgttaacagtgtttgtgatatttttttttatgtaaatagcactggcatattatattgtgcattgtaaaatgctt
|    ||||||||||||| ||||| |||||||| |||||||| ||| |||| |  ||||| ||| | ||||| ||||||| ||       || |     ||| |  || | || ||    || |  |      |  |  | |    | |  | || | |                   
GCCCGCGTTTGCATCTGCCTCAGCGGACAATATTAAGAAGTTCAGCTTGCCGAGGGGCGAGTTTGTGCACAACATGCTgtaag-------ttaattccttttctgtttgatagcgtc---gaaacgtc---aaaattggacatggtttgtgtgttttctcacag--------------

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|88451871|gb|CI694646.1|CI694646
EST:     AATATAAAGAAGTTTAGCCTGCCCAAAGGCGAATTTCTACACAATATGCT                         GTCCCAGCAGAAAACCATCATAAACTCAATGGCTGTAAATGAAGATGGTGT
genomic: AATATAAAGAAGTTTAGCCTGCCCAAAGGCGAATTTCTACACAATATGCTgtgagcattc ... cacctttcagGTCCCAGCAGAAAACCATCATAAACTCAATGGCTGTAAATGAAGATGGTGT
EST: gi|33691858|gb|CF320097.1|CF320097
EST:     AATATAAAGAAGTTTAGCCTGCCCAAAGGCGAATTTCTACACAATATGCT                         GTCCCAGCAGAAAACCATCATAAACTCAATGGCTGTAAATGAAGATGGTGT
genomic: AATATAAAGAAGTTTAGCCTGCCCAAAGGCGAATTTCTACACAATATGCTgtgagcattc ... cacctttcagGTCCCAGCAGAAAACCATCATAAACTCAATGGCTGTAAATGAAGATGGTGT
EST: gi|29643709|gb|CB648716.1|CB648716
EST:     AATATAAAGAAGTTTAGCCTGCCCAAAGGCGAATTTCTACACAATATGCT                         GTCCCAGCAGAAAACCATCATAAACTCAATGGCTGTAAATGAAGATGGTGT
genomic: AATATAAAGAAGTTTAGCCTGCCCAAAGGCGAATTTCTACACAATATGCTgtgagcattc ... cacctttcagGTCCCAGCAGAAAACCATCATAAACTCAATGGCTGTAAATGAAGATGGTGT
EST: gi|29679953|gb|CB676228.1|CB676228
EST:     AATATAAAGAAGTTTAGCCTGCCCAAAGGCGAATTTCTACACAATATGCT                         GTCCCAGCAGAAAACCATCATAAACTCAATGGCTGTAAATGAAGATGGTGT
genomic: AATATAAAGAAGTTTAGCCTGCCCAAAGGCGAATTTCTACACAATATGCTgtgagcattc ... cacctttcagGTCCCAGCAGAAAACCATCATAAACTCAATGGCTGTAAATGAAGATGGTGT
EST: gi|29633915|gb|CB638924.1|CB638924
EST:     TTTAGCCTGCCCAAAGGCGAATTTTTACACAATATGCT                         GTCCCAGCAGAAAACCATCATAAACTCAATGGCTGTAAATGAAGATGGTGT
genomic: TTTAGCCTGCCCAAAGGCGAATTTCTACACAATATGCTgtgagcattc ... cacctttcagGTCCCAGCAGAAAACCATCATAAACTCAATGGCTGTAAATGAAGATGGTGT
EST: gi|29643713|gb|CB648720.1|CB648720
EST:     AATATAAAGAAGTTTAGCCTGCCCAAAGGCGAATTTCTACACAATATGCT                         GTCCCAGCAGAAAACCATCATAAACTCAATGGCTGTAAATGAAGATGGTGT
genomic: AATATAAAGAAGTTTAGCCTGCCCAAAGGCGAATTTCTACACAATATGCTgtgagcattc ... cacctttcagGTCCCAGCAGAAAACCATCATAAACTCAATGGCTGTAAATGAAGATGGTGT
EST: gi|88969983|gb|CI383485.1|CI383485
EST:     TCTACACAATATGCT                         GTCCCAGCAGAAAACCATCATAAACTCAATGGCTGTAAATGAAGATGGTGT
genomic: TCTACACAATATGCTgtgagcattc ... cacctttcagGTCCCAGCAGAAAACCATCATAAACTCAATGGCTGTAAATGAAGATGGTGT
EST: gi|86421611|gb|CI057600.1|CI057600
EST:     AAGTTTAGCCTGCCCAAAGGCGAATTTCTACACAATATGCT                         GTCCCAGCAGAAAACCATCATAAACTCAATGGCTGTAAATGAAGATGGTGT
genomic: AAGTTTAGCCTGCCCAAAGGCGAATTTCTACACAATATGCTgtgagcattc ... cacctttcagGTCCCAGCAGAAAACCATCATAAACTCAATGGCTGTAAATGAAGATGGTGT

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: 72 (upstream exon), 65 (downstream exon)
Score: 27

GAAATCGTTTGCATCTGCATCAGCAGACAATATAAAGAAGTTTAGCCTGCCCAAAGGCGAATTTCTACACAATATGCTgtgagcattc ... cacctttcagGTCCCAGCAGAAAACCATCATAAACTCAATGGCTGTAAATGAAGATGGTGTCTTGGCAACTGGAG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GAAATCGTTTGCATCTGCATCAGCAGACAATATAAAGAAGTTTAGCCTGCCCAAAGGCGAATTTCTACACAATATGCTgtgagcattcttttcacattgttttttgttaacagtgtttgtgatatttttttttatgtaaatagcactggcatattatattgtgcattgtaaaatgctt

- - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - -  AGAAGT