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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTTTTTGTGGCTTATGGCTGTTGGTACCATTCTTTGTGCATCATACTGGTCAGCATGGAGTGCTCGAGAAGCAGTTATTGAACAAGAGAAGCTTCTAAAGgttctgaacagaagcttatttgactattgttctggattttgtttgcttgaaaagagaactaacagtcatttggtttatgtag

Basic information

species Oryza sativa
transcript LOC_Os02g57710.1
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g57710.1 (Oryza sativa), 5'ss of exon 5
lower sequence: GRMZM2G096343_T01 (Zea mays), 5'ss of exon 5
GTTTTTGTGGCTTATGGCTGTTGGTACCATTCTTTGTGCATCATACTGGTCAGCATGGAGTGCTCGAGAAGCAGTTATTGAACAAGAGAAGCTTCTAAAGgttctgaaca--gaagcttatttgactattgttctggattttgtttgcttgaaaaga--gaactaacagtcatttggtttatgtag-
|||| ||||||||||||| |||||||||||||||||||||||||||||||||||||||||||| |||||||||| ||||||||||||||||||||| |||||||| |||    || ||| ||||| |  | ||     |||||  | |||||||| |  | ||| ||||   ||   |   |||   
GTTTCTGTGGCTTATGGCAGTTGGTACCATTCTTTGTGCATCATACTGGTCAGCATGGAGTGCCCGAGAAGCAGATATTGAACAAGAGAAGCTTCTGAAGgttctaaaccccaaatcttgtttgatttctattgctagttttgcgtacttgaaaaaaagggactgacag--gttcaatacttgttag

upper sequence: LOC_Os02g57710.1 (Oryza sativa), 5'ss of exon 5
lower sequence: GLYMA03G01100.2 (Glycine max), 5'ss of exon 5
GTTTTTGTGGCTTATGGCTGTTGGTACCATTCTTTGTGCATCATACTGGTCAGCATGGAGTGCTCGAGAAGCAGTTATTGAACAAGAGAAGCTTCTAAAGgttctgaacagaagcttatttgactattgttctggattttgtttgcttgaaaagagaactaacagtcatttggtt------tatgtag------------
||||||||||||||||||||||||||||||| |   ||| || || ||||| || ||||||||| |||||||||  ||||| |||||||||||| ||||||||    |       || | || | | | | ||   | |   | |  |||||| |  |  || ||  |  ||  |      ||   ||            
GTTTTTGTGGCTTATGGCTGTTGGTACCATTTTAATTGCTTCTTATTGGTCTGCCTGGAGTGCTAGAGAAGCAGCAATTGAGCAAGAGAAGCTTTTAAAGgttacctagttccttttttgtgccaactttactatctctaaatagagtgaaaataataagaatagaaaaatgagtaggagctaaacagaaccaaaccaaa

upper sequence: LOC_Os02g57710.1 (Oryza sativa), 5'ss of exon 5
lower sequence: GLYMA11G02540.1 (Glycine max), 5'ss of exon 5
GTTTTTGTGGCTTATGGCTGTTGGTACCATTCTTTGTGCATCATACTGGTCAGCATGGAGTGCTCGAGAAGCAGTTATTGAACAAGAGAAGCTTCTAAAGgttctgaacagaagcttatttgactattgttc----tggatt-----ttgtttgcttgaaaag-----------agaactaacagtca----tttggtttatgtag
 ||| | ||| | ||||| |||  ||| ||  | ||||||||||| |||||||| ||||   | |||||||||| ||||||||| || ||||| ||||||||             |  |||     ||  ||    ||||||     || ||| ||| | | |           |  ||| || || |    |||  ||| | |||
ATTTCTTTGGATGATGGCAGTTCTTACAATATTGTGTGCATCATATTGGTCAGCTTGGACAACCCGAGAAGCAGCTATTGAACAGGATAAGCTACTAAAGgtatgtttttcctattcttttagtattttctcaagttggattctcatttcttttcttaatatgttgttgatgctactacttactgttaattttttcttttttatag

upper sequence: LOC_Os02g57710.1 (Oryza sativa), 5'ss of exon 5
lower sequence: GLYMA09G39500.1 (Glycine max), 5'ss of exon 5
GTTTTTGTGGCTTATGGCTGTTGGTACCATTCTTTGTGCATCATACTGGTCAGCATGGAGTGCTCGAGAAGCAGTTATTGAACAAGAGAAGCTTCTAAAGgttctgaacagaagcttatttgactattgttctggattttgtttgcttgaaaagagaactaacagtcatt--tggtttatgtag------------------
|||||| |||||||||||||||||||||||||| ||||| || |||||||| || |||   ||  ||||  | |  ||||| || ||||||||  ||||||||            | ||    | ||| | |    ||||  ||     | |  |  | ||   || ||   |||  ||  ||                   
GTTTTTATGGCTTATGGCTGTTGGTACCATTCTCTGTGCTTCTTACTGGTCTGCCTGGTCAGCAAGAGAGTCTGCCATTGAGCAGGAGAAGCTATTAAAGgttactggtttcttttcatcc--caattttacgaatttttccttatacaagacaaatattattggtgatcgatggaatacataagttaacaaagacccatgg

upper sequence: LOC_Os02g57710.1 (Oryza sativa), 5'ss of exon 5
lower sequence: GLYMA18G46760.1 (Glycine max), 5'ss of exon 5
GTTTTTGTGGCTTATGGCTGTTGGTACCATTCTTTGTGCATCATACTGGTCAGCATGGAGTGCTCGAGAAGCAGTTATTGAACAAGAGAAGCTTCTAAAGgttctgaacagaagcttatttgactattgttctggattttgtttgcttgaaaagagaactaacagtcatttggtttatgtag--------------------
|||||| |||||||||||||| ||||||||||| ||||| || |||||||| || |||| |||  ||||  | |  ||||| || ||||||||  ||||||||            | ||   | | || |||    ||||   |     | |     | ||   || | | |    ||  |                     
GTTTTTATGGCTTATGGCTGTCGGTACCATTCTCTGTGCTTCTTACTGGTCTGCCTGGACTGCAAGAGAGTCTGCCATTGAGCAGGAGAAGCTATTAAAGgttactggtttcttttcatgccaattttattc--atttttccatatacaagacacttattattggtgaatggaggaatacaaaagttaacaaagacacatgg

upper sequence: LOC_Os02g57710.1 (Oryza sativa), 5'ss of exon 5
lower sequence: GLYMA07G07610.1 (Glycine max), 5'ss of exon 5
GTTTTTGTGGCTTATGGCTGTTGGTACCATTCTTTGTGCATCATACTGGTCAGCATGGAGTGCTCGAGAAGCAGTTATTGAACAAGAGAAGCTTCTAAAGgtt--ctgaacagaagcttatttgactattgt---tctggattttgtttgcttgaaaa---gagaactaacagtcatttggtttatgtag----------
|||| |||||||||||||||||||||||||| |   ||| || || ||||| || ||||||||| |||||||||  |||||||||||||||||| ||||||||  ||          ||     ||| |  |   |||  || | ||     | | ||    | ||  |  || ||        |||  |          
GTTTCTGTGGCTTATGGCTGTTGGTACCATTTTAATTGCTTCTTATTGGTCTGCCTGGAGTGCTAGAGAAGCAGCAATTGAACAAGAGAAGCTTTTAAAGgttacctagttcctttttttcccaactttactctctctcaatatagtgaaaataataatataaaaatgaggagccaaaccaaaaatgctgaaaagacaaa

upper sequence: LOC_Os02g57710.1 (Oryza sativa), 5'ss of exon 5
lower sequence: AT1G63690.1 (Arabidopsis thaliana), 5'ss of exon 5
GTTTTTGTGGCTTATGGCTGTTGGTACCATTCTTTGTGCATCATACTGGTCAGCATGGAGTGCTCGAGAAGCAGTTATTGAACAAGAGAAGCTTCTAAAGgttctgaacagaa-gcttatttg--------actattgttctgg----attttgtttgcttgaaaag---agaactaacagtcatttggtttatgtag--
 ||||||||| | |||||  ||||||||||| | |||||||| || ||||| ||||||||||| |||||||||| ||||||||| || ||||| || |||||     |       ||||||||        | ||||   || |    |||| ||| | | |  |||   |  |  ||| | || |  ||   |      
CTTTTTGTGGTTAATGGCAATTGGTACCATTTTATGTGCATCTTATTGGTCTGCATGGAGTGCCCGAGAAGCAGCTATTGAACATGATAAGCTACTGAAGgtcagacattttctacttatttgggaataataatattaggctaggaagatttagttcgatgggtaaggataacataaactgccaataagtaagtcctttg

upper sequence: LOC_Os02g57710.1 (Oryza sativa), 5'ss of exon 5
lower sequence: Vv02s0025g03400.t01 (Vitis vinifera), 5'ss of exon 5
GTTTTTGTGGCTTATGGCTGTTGGTACCATTCTTTGTGCATCATACTGGTCAGCATGGAGTGCTCGAGAAGCAGTTATTGAACAAGAGAAGCTTCTAAAGgt--tctgaacagaagcttatttgacta---ttgttctgg--attttgtttgcttgaaaagagaactaaca-gtcatttggtttatgtag-----------------------------------
 ||  | ||||| ||||| |||||||| ||  | |||||||| || ||||| |||||||||||  |||| |||| ||||||||| || ||||| ||||||||  ||||     || | ||  | | ||   ||  ||  |  ||||| ||  ||   |  |     |  || ||  |   | ||||| |                                    
TTTCCTATGGCTGATGGCAGTTGGTACTATCTTGTGTGCATCTTATTGGTCTGCATGGAGTGCCAGAGAGGCAGCTATTGAACAGGACAAGCTACTAAAGgtcatctgttgccaatcctagctaattaggttttctccagtaatttttttctctcttagggtagggtctcatgtgctgcagcttatgaatggtccctgatatatgaagtaaacttgttcttatag

upper sequence: LOC_Os02g57710.1 (Oryza sativa), 5'ss of exon 5
lower sequence: Vv15s0046g02460.t01 (Vitis vinifera), 5'ss of exon 5
GTTTTTGTGGCTTATGGCTGTTGGTACCATTCTTTGTGCATCATACTGGTCAGCATGGAGTGCTCGAGAAGCAGTTATTGAACAAGAGAAGCTTCTAAAGgt-----tctgaacagaagcttatttgactat-tgttctggattttgtttgcttgaaaagagaactaacagtcattt--ggtttatgtag--------------------------------------------
|||||||||||| ||||| |||||||||||| | | |||||| |||||||| |||||||||||  ||||||||| || ||| || || |||||  |||||||     |||    ||   ||  | |  | || | || ||      |    | | |     |   ||| | || |||  |  | ||  |                                             
GTTTTTGTGGCTCATGGCCGTTGGTACCATTTTATCTGCATCTTACTGGTCTGCATGGAGTGCCAGAGAAGCAGCTAATGAGCAGGACAAGCTATTAAAGgtaaacttctccttagttactgttatttccatctcttttgaggagggaactccttactcatgggttaagaatcctttctgaatgatccatttgttcttccattgaatgtatggactgttttttttatcttgtag

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|87006789|gb|CI285823.1|CI285823
EST:     CAGCATGGAGTGCTCGAGAAGCAGTTATTGAACAAGAGAAGCTTCTAAAG                         GATGGCCATGAAAGCTCACTAAACTTAGAGGCTGGTGGTTCTAGTGGCATG
genomic: CAGCATGGAGTGCTCGAGAAGCAGTTATTGAACAAGAGAAGCTTCTAAAGgttctgaaca ... gtttatgtagGATGGCCATGAAAGTTCACTAAACTTAGAGGCTGGTGGTTCTAGTGGCATG
EST: gi|300216268|gb|HO088053.1|HO088053
EST:     CTCGAG-AGCAGTTATTGAACACGAGAAGCTTCTAAAG                         GATGGCCATGAAAGTTCACTAAACTTAGAGGCTGGTGGTTCTAGTGGCATG
genomic: CTCGAGAAGCAGTTATTGAACAAGAGAAGCTTCTAAAGgttctgaaca ... gtttatgtagGATGGCCATGAAAGTTCACTAAACTTAGAGGCTGGTGGTTCTAGTGGCATG
EST: gi|29677466|gb|CB673741.1|CB673741
EST:     CAGCATGGAGTGCTCGAGAAGCAGTTATTGAACAAGAGAAGCTTCTACAG                         GATGGCCATGACAGTTCACT
genomic: CAGCATGGAGTGCTCGAGAAGCAGTTATTGAACAAGAGAAGCTTCTAAAGgttctgaaca ... gtttatgtagGATGGCCATGAAAGTTCACT
EST: gi|29623066|gb|CB628077.1|CB628077
EST:     CAGCATGGAGTGCTCGAGAAGCAGTTATTGAACAAGAGAAGCTTCTAAAG                         GATGGCCATGAAAGTTCACTAAACTTAGAGGCTGGTGGTTCTAGTGGCATG
genomic: CAGCATGGAGTGCTCGAGAAGCAGTTATTGAACAAGAGAAGCTTCTAAAGgttctgaaca ... gtttatgtagGATGGCCATGAAAGTTCACTAAACTTAGAGGCTGGTGGTTCTAGTGGCATG

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), 73 (downstream exon)
Score: 29

GTTTTTGTGGCTTATGGCTGTTGGTACCATTCTTTGTGCATCATACTGGTCAGCATGGAGTGCTCGAGAAGCAGTTATTGAACAAGAGAAGCTTCTAAAGgttctgaaca ... gtttatgtagGATGGCCATGAAAGTTCACTAAACTTAGAGGCTGGTGGTTCTAGTGGCATGGTAGATATCAACATGACATCGGCAATACTGTTTGTTGTTATTGCATCTT




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTTTTTGTGGCTTATGGCTGTTGGTACCATTCTTTGTGCATCATACTGGTCAGCATGGAGTGCTCGAGAAGCAGTTATTGAACAAGAGAAGCTTCTAAAGgttctgaacagaagcttatttgactattgttctggattttgtttgcttgaaaagagaactaacagtcatttggtttatgtag

- - - - - - - - - - - - - - - - - - - - - - - - - -  CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC