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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAGAAGATGACACAGATCATGTTTGAGACCTTCAATTGCCCAGCAATGTATGTCGCAATCCAGGCTGTTCTATCCTTGTATGCTAGCGGTCGAACAACTGgtatgattattacctttgcaatagatcgtgttaaaattcaatgtgttggggggcagtgacacttcttttatctgcag

Basic information

species Oryza sativa
transcript LOC_Os05g36290.2
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os05g36290.2 (Oryza sativa), 5'ss of exon 3
lower sequence: GRMZM2G126010_T01 (Zea mays), 5'ss of exon 3
GAGAAGATGACACAGATCATGTTTGAGACCTTCAATTGCCCAGCAATGTATGTCGCAATCCAGGCTGTTCTATCCTTGTATGCTAGCGGTCGAACAACTGgtatgat---tattacctttgcaatagatcgtgtta---------aaattca---atgtgttggggggcagtgacacttcttttatctgcag---------------
||||| ||||| ||||| |||||||| |||||| | ||||||||||||||||| || |||||||||||||| || ||||| ||||| || ||||||||||||| |||   | |  |||  |  ||| || ||| ||         ||  |||   ||   |  ||      ||||||    | | | |  |                
GAGAAAATGACGCAGATTATGTTTGAAACCTTCGAATGCCCAGCAATGTATGTTGCTATCCAGGCTGTTCTTTCGTTGTACGCTAGTGGGCGAACAACTGgtaagatggctgtcgcctcagatatatatagtgatatgcactacaaagatcatacatacatacggcaatcctgacacggtctctttgtcaaatatctctgtgtgcag

upper sequence: LOC_Os05g36290.2 (Oryza sativa), 5'ss of exon 3
lower sequence: GLYMA06G15520.2 (Glycine max), 5'ss of exon 3
GAGAAGATGACACAGATCATGTTTGAGACCTTCAATTGCCCAGCAATGTATGTCGCAATCCAGGCTGTTCTATCCTTGTATGCTAGCGGTCGAACAACTGgtatga--ttattacc-tttgcaatagatcgtg--ttaaaattcaatgtgttggggggcagtgacacttcttttatctgcag
|| || ||||| || |||||||||||||||||||||   || || |||||||| || ||||||||||| || ||| | ||||| || ||||| ||||||||| ||   ||||| || | ||   ||  ||     ||    ||||   ||||        |   ||  ||||||     |||
GAAAAAATGACCCAAATCATGTTTGAGACCTTCAATGTGCCTGCCATGTATGTGGCCATCCAGGCTGTCCTCTCCCTATATGCAAGTGGTCGCACAACTGgtttgtacttatttccatctgtcttaattcactcctttgtcttcacattgttctatccttgaatcaaatctttttgaatcag

upper sequence: LOC_Os05g36290.2 (Oryza sativa), 5'ss of exon 3
lower sequence: GLYMA05G32220.1 (Glycine max), 5'ss of exon 2
GAGAAGATGACACAGATCATGTTTGAGACCTTCAATTGCCCAGCAATGTATGTCGCAATCCAGGCTGTTCTATCCTTGTATGCTAGCGGTCGAACAACTGgtatgattattacc-tttgcaatagatcgtg--ttaaaattcaatgtgttggggggcagtgacacttcttttatctgcag
|| |||||||| || |||||||||||||||||||||   || || |||||||| || |||||||||||||| ||||||||||| || ||||| ||||||||| ||  ||||||| | ||   |   || |   || | | |||     ||      | |   || ||| |||     |||
GAAAAGATGACCCAAATCATGTTTGAGACCTTCAATGTGCCTGCCATGTATGTGGCCATCCAGGCTGTTCTCTCCTTGTATGCCAGTGGTCGCACAACTGgtttgtatattaccatctgtcttgattcattcttttataatcacatcattctttccctgaatcaattcctttcaaaacag

upper sequence: LOC_Os05g36290.2 (Oryza sativa), 5'ss of exon 3
lower sequence: GLYMA08G15480.1 (Glycine max), 5'ss of exon 3
GAGAAGATGACACAGATCATGTTTGAGACCTTCAATTGCCCAGCAATGTATGTCGCAATCCAGGCTGTTCTATCCTTGTATGCTAGCGGTCGAACAACTGgtatgattattacc-tttgcaatagatcgtg--ttaaaattcaatgtgttggggggcagtgacacttcttttatctgcag
|| |||||||| || |||||||||||||||||||||   || || |||||||| || |||||||||||||| ||||||||||| || ||||| ||||||||| ||  ||| ||| | ||   |   || |   || | | |||   ||||      | |   || ||| |||     |||
GAAAAGATGACCCAAATCATGTTTGAGACCTTCAATGTGCCTGCCATGTATGTGGCCATCCAGGCTGTTCTCTCCTTGTATGCAAGTGGTCGCACAACTGgtttgtatatcaccatctgtcttgattcattcttttataatcacattgttctttccctgaatcaattccttttaaaacag

upper sequence: LOC_Os05g36290.2 (Oryza sativa), 5'ss of exon 3
lower sequence: GLYMA04G39380.2 (Glycine max), 5'ss of exon 3
GAGAAGATGACACAGATCATGTTTGAGACCTTCAATTGCCCAGCAATGTATGTCGCAATCCAGGCTGTTCTATCCTTGTATGCTAGCGGTCGAACAACTGgtatg-attattacct-----ttgcaatagatcgtgttaaaatt-caatgtgttggggggcagtgacacttcttttatctgcag
|| || ||||| || |||||||||||||||||||||   || || |||||||| || ||||| ||||| || ||| | ||||| || ||||| ||||||||| || |||  || |      || ||||  || || ||   ||  || |||  |       | | | | | ||||      |||
GAAAAAATGACCCAAATCATGTTTGAGACCTTCAATGTGCCTGCCATGTATGTGGCCATCCAAGCTGTCCTCTCCCTATATGCAAGTGGTCGCACAACTGgtttgtatttgtatccatctgtttcaattcatagttttgtcatcacattgttctttccctgaatca-aatactttctgaaacag

upper sequence: LOC_Os05g36290.2 (Oryza sativa), 5'ss of exon 3
lower sequence: AT1G49240.1 (Arabidopsis thaliana), 5'ss of exon 3
GAGAAGATGACACAGATCATGTTTGAGACCTTCAATTGCCCAGCAATGTATGTCGCAATCCAGGCTGTTCTATCCTTGTATGCTAGCGGTCGAACAACTGgtatgattattacctttg-caatagatcgtgttaaaattcaat----gtgttggggggcagtgacacttcttttatc-tgcag-------------
||||||||||| |||||||||||||||||||| ||||  ||||| |||||||| || || || |||||||||||  | || || || ||||| ||||| |||  | | ||||    || | | | |  |    ||  ||   |    || ||    |    || ||  |   | |   || |              
GAGAAGATGACTCAGATCATGTTTGAGACCTTTAATTCTCCAGCTATGTATGTTGCCATTCAAGCTGTTCTATCACTTTACGCCAGTGGTCGTACAACCGgttagttcattattaatgtcgagaaaatgaacaaagttttgttttctgtttttaatgattatgtcatattgatcacagtgaaatgattttctttag

upper sequence: LOC_Os05g36290.2 (Oryza sativa), 5'ss of exon 3
lower sequence: AT5G09810.1 (Arabidopsis thaliana), 5'ss of exon 3
GAGAAGATGACACAGATCATGTTTGAGACCTTCAATTGCCCAGCAATGTATGTCGCAATCCAGGCTGTTCTATCCTTGTATGCTAGCGGTCGAACAACTGgtatgattattacctttg------caa---tagatcgtgttaaaattcaa--tgtgttggggggcagtgacacttcttttatctgcag
||||||||||| ||||||||||||||||| ||||||  ||| || |||||||| || || ||||| ||||| ||  | ||||| || ||||| ||||| ||| |  || ||| || |       |||   |   |  | |||   |   |  ||| ||       |||    ||  |||| |   |||
GAGAAGATGACTCAGATCATGTTTGAGACATTCAATGTCCCTGCCATGTATGTTGCCATTCAGGCCGTTCTTTCTCTCTATGCCAGTGGTCGTACAACCGgt-tagttcttaactctaaacatccaagtctgagttatattatcttcttacttgtatttacttaaagtcgttctctttttgta-acag

upper sequence: LOC_Os05g36290.2 (Oryza sativa), 5'ss of exon 3
lower sequence: AT3G18780.1 (Arabidopsis thaliana), 5'ss of exon 2
GAGAAGATGACACAGATCATGTTTGAGACCTTCAATTGCCCAGCAATGTATGTCGCAATCCAGGCTGTTCTATCCTTGTATGCTAGCGGTCGAACAACTGgtatg---attattacctttgcaatagatcgtgttaaa-attcaatgtgttggggggcagtgacacttcttttatctgcag
||||||||||| || ||||||||||||||||| || |  || || ||||||||||| ||||| |||||||| |||||||| || || ||||| ||||| |||  |   ||| |   ||||    |    |   || |  |||   ||   || |      | |   | | || | | |   
GAGAAGATGACTCAAATCATGTTTGAGACCTTTAACTCTCCCGCTATGTATGTCGCCATCCAAGCTGTTCTCTCCTTGTACGCCAGTGGTCGTACAACCGgttagtacattttaggctttttgtttatactcattgatcattatttgaactgagctctgattatcttccattgaacag---

upper sequence: LOC_Os05g36290.2 (Oryza sativa), 5'ss of exon 3
lower sequence: EFJ17401 (Selaginella moellendorffii), 5'ss of exon 2
GAGAAGATGACACAGATCATGTTTGAGACCTTCAATTGCCCAGCAATGTATGTCGCAATCCAGGCTGTTCTATCCTTGTATGCTAGCGGTCGAACAACTGgtatgattattacctttgcaatagatcgtgttaaaattcaatgtgttggggggcagtgacacttctt--ttatctgcag---------------------------------------------------------------------------
||||||||||| ||||||||||| ||||||||||||  ||| || ||||| || || ||||| || || || ||  | || || || || || || || ||||||    ||   ||  |  | | | ||  || |   |||  || | |  |   ||  |  |||||  ||   |||                                                                             
GAGAAGATGACCCAGATCATGTTCGAGACCTTCAATGTCCCGGCCATGTACGTGGCGATCCAAGCAGTCCTTTCACTCTACGCGAGTGGACGCACTACCGgtatgga-gtttttttatcccttgcttgttctaga---caagatggttgatgcgtgtttcttttcttcgttgcttgcgatagacatgatgcttcaagttggttctacttttgtttttccctctaacacgttgtatgatcgtggtttgtgatcag

upper sequence: LOC_Os05g36290.2 (Oryza sativa), 5'ss of exon 3
lower sequence: EFJ35077 (Selaginella moellendorffii), 5'ss of exon 2
GAGAAGATGACACAGATCATGTTTGAGACCTTCAATTGCCCAGCAATGTATGTCGCAATCCAGGCTGTTCTATCCTTGTATGCTAGCGGTCGAACAACTGgtatgattattacctttgcaatagatcgtgttaaaattcaatgtgttggggggcagtgacacttctt--ttatctgcag----------------------------------------------------------------------------
||||||||||| ||||||||||| ||||||||||||  ||| || ||||| || |||||||| || || || ||  | || || || || || || || ||||||    ||   ||| |  | | | ||  || |   |||  || | |  |   ||  |  |||||  ||   |||                                                                              
GAGAAGATGACCCAGATCATGTTCGAGACCTTCAATGTCCCGGCCATGTACGTGGCAATCCAAGCAGTCCTTTCACTCTACGCGAGTGGACGCACTACCGgtatggagttttttttttcctttgcttgttctaga---caagatggttgatgcgtgtttcttttcttcgttgcttgcgatagacatgatgcttcaagttggttctacttttttttcttctctctaacacgttgtatgatcgtggtttgtgatcag

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|33793745|gb|CF322755.1|CF322755
EST:     TGTCGCAATCCAGGCTGTTCTATCCTTGTATGCTAGCGGTCGAACAACTG                         GTATCGTGCTTGACTCTGGTGATCGGTGTGAGCCACACTGTTCCAATATAT
genomic: TGTCGCAATCCAGGCTGTTCTATCCTTGTATGCTAGCGGTCGAACAACTGgtatgattat ... ttatctgcagGTATCGTGCTTGACTCTGGTGAT-GGTGTGAGCCACACTGTTCCAATATAT
EST: gi|33692460|gb|CF320699.1|CF320699
EST:     TGTCGCAATCCAGGCTGTTCTATCCTTGTATGCTAGCGGTCGAACAACTG                         GTATCGTGCTTGACTCTG
genomic: TGTCGCAATCCAGGCTGTTCTATCCTTGTATGCTAGCGGTCGAACAACTGgtatgattat ... ttatctgcagGTATCGTGCTTGACTCTG
EST: gi|33691169|gb|CF319408.1|CF319408
EST:     TGTCGCAATCCAGGCTGTTCTATCCTTGTATGCTAGCGGTCGAACAACTG                         GTATCGTGCTTGACTCTG
genomic: TGTCGCAATCCAGGCTGTTCTATCCTTGTATGCTAGCGGTCGAACAACTGgtatgattat ... ttatctgcagGTATCGTGCTTGACTCTG
EST: gi|33795246|gb|CF323495.1|CF323495
EST:     TGTCGCAATCCAGGCTGTTCTATCCTTGTATGCTAGCGGTCGAACAACTG                         GTATCGTGCTTGACTCTGGTGATG
genomic: TGTCGCAATCCAGGCTGTTCTATCCTTGTATGCTAGCGGTCGAACAACTGgtatgattat ... ttatctgcagGTATCGTGCTTGACTCTGGTGATG
EST: gi|33680314|gb|CF308553.1|CF308553
EST:     TGTCGCAATCCAGGCTGTTCTATCCTTGTATGCTAGCGGTCGAACAACTG                         GTATCGTGCTTGACTCTGGTGATGGTGTGAGCCACACTGTTCCAATATATG
genomic: TGTCGCAATCCAGGCTGTTCTATCCTTGTATGCTAGCGGTCGAACAACTGgtatgattat ... ttatctgcagGTATCGTGCTTGACTCTGGTGATGGTGTGAGCCACACTGTTCCAATATATG
EST: gi|33794076|gb|CF322928.1|CF322928
EST:     TGTCGCAATCCAGGCTGTTCTATCCTTGTATGCTAGCGGTCGAACAACTG                         GTATCGTGCTTGACTCTG
genomic: TGTCGCAATCCAGGCTGTTCTATCCTTGTATGCTAGCGGTCGAACAACTGgtatgattat ... ttatctgcagGTATCGTGCTTGACTCTG
EST: gi|58692537|gb|CK081224.1|CK081224
EST:     TGTCGCAATCCAGGCTGTTCTATCCTTGTATGCTAGCGGTCGAACAACTG                         GTATCGTGCTTGACTCTGGTGATGGTGTGAGCCACACTGTTCCAATATATG
genomic: TGTCGCAATCCAGGCTGTTCTATCCTTGTATGCTAGCGGTCGAACAACTGgtatgattat ... ttatctgcagGTATCGTGCTTGACTCTGGTGATGGTGTGAGCCACACTGTTCCAATATATG
EST: gi|27547333|gb|CA765360.2|CA765360
EST:     TGTCGCAATCCAGGCTGTTCTATCCTTGTATGCTAGCGGTCGAACAACTG                         GTATCGTGCTTGACTCTGGTGATGGTGTGAGCCACACTGTTCCAATATATG
genomic: TGTCGCAATCCAGGCTGTTCTATCCTTGTATGCTAGCGGTCGAACAACTGgtatgattat ... ttatctgcagGTATCGTGCTTGACTCTGGTGATGGTGTGAGCCACACTGTTCCAATATATG
EST: gi|33681940|gb|CF310179.1|CF310179
EST:     TGTCGCAATCCAGGCTGTTCTATCCTTGTATGCTAGCGGTCGAACAACTG                         GTATCGTGCTTGACTCT
genomic: TGTCGCAATCCAGGCTGTTCTATCCTTGTATGCTAGCGGTCGAACAACTGgtatgattat ... ttatctgcagGTATCGTGCTTGACTCT
EST: gi|33680684|gb|CF308923.1|CF308923
EST:     TGTCGCAATCCAGGCTGTTCTATCCTTGTATGCTAGCGGTCGAACAACTG                         GTATCGTGCTTGACTCTGGTGATGGTGTGAGCCACACTGTTCCAATATATG
genomic: TGTCGCAATCCAGGCTGTTCTATCCTTGTATGCTAGCGGTCGAACAACTGgtatgattat ... ttatctgcagGTATCGTGCTTGACTCTGGTGATGGTGTGAGCCACACTGTTCCAATATATG
EST: gi|56157719|gb|C25963.2|C25963
EST:     TGTCGCAATCCAGGCTGTTCTATCCTTGTATGCTAGCGGTCGAACAACTG                         GTATCGTGCTTGACTCTGGTGATGGTGTGAGCCACACTGTTCCAATATATG
genomic: TGTCGCAATCCAGGCTGTTCTATCCTTGTATGCTAGCGGTCGAACAACTGgtatgattat ... ttatctgcagGTATCGTGCTTGACTCTGGTGATGGTGTGAGCCACACTGTTCCAATATATG
EST: gi|218488055|gb|FG961019.1|FG961019
EST:     TGTCGCAATCCAGGCTGTTCTATCCTTGTATGCTAGCGGTCGAACAACTG                         GTATCGTGCTTGACTCTGGTGATGGTGTGAGCCACACTGTTCCAATATATG
genomic: TGTCGCAATCCAGGCTGTTCTATCCTTGTATGCTAGCGGTCGAACAACTGgtatgattat ... ttatctgcagGTATCGTGCTTGACTCTGGTGATGGTGTGAGCCACACTGTTCCAATATATG
EST: gi|55437174|gb|CV731786.1|CV731786
EST:     TGTCGCAATCCAGGCTGTTCTATCCTTGTATGCTAGCGGTCGAACAACTG                         GTATCGTGCTTGACTCTGGTGATGGTGTGAGCCACACTGTTCCAATATATG
genomic: TGTCGCAATCCAGGCTGTTCTATCCTTGTATGCTAGCGGTCGAACAACTGgtatgattat ... ttatctgcagGTATCGTGCTTGACTCTGGTGATGGTGTGAGCCACACTGTTCCAATATATG

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: 69 (upstream exon), 74 (downstream exon)
Score: 108

GAGAAGATGACACAGATCATGTTTGAGACCTTCAATTGCCCAGCAATGTATGTCGCAATCCAGGCTGTTCTATCCTTGTATGCTAGCGGTCGAACAACTGgtatgattat ... ttatctgcagGTATCGTGCTTGACTCTGGTGATGGTGTGAGCCACACTGTTCCAATATATGAAGGATATACGCTTCCTCATGCTATCCTCCGGTTGGATCTTGCTGGCCG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GAGAAGATGACACAGATCATGTTTGAGACCTTCAATTGCCCAGCAATGTATGTCGCAATCCAGGCTGTTCTATCCTTGTATGCTAGCGGTCGAACAACTGgtatgattattacctttgcaatagatcgtgttaaaattcaatgtgttggggggcagtgacacttcttttatctgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGTT