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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGACTTCTTTTCTCACTTGGAGATGCATCTCCGCCAGGAGCATCCACCATTATGTGGAAGAGATCACATGGCCTACAGATCTGCTTATTTTCCAGTGAAGgtgatatattattttttttgtttagattagctagtatgtcaaccaacacagatattatcacaaatgcatatatttataacttttttaccactttgtcggatagaatatccaggtgtaaaggcagttggcagtatctgttttatgtttgatgatggagtttcgttttggtttgtttcag

Basic information

species Oryza sativa
transcript LOC_Os02g04480.1
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g04480.1 (Oryza sativa), 5'ss of exon 2
lower sequence: GRMZM2G096972_T01 (Zea mays), 5'ss of exon 2
TGACTTCTTTTCTCACTTGGAGATGCATCTCCGCCAGGAGCATCCACCATTATGTGGAAGAGATCACATGGCCTACAGATCTGCTTATTTTCCAGTGAAGgtgatatattattttttttgtttagattagctagtatgtcaaccaacacagatattatcacaaatgcatatatttataacttttttaccactttgtcggatagaatatccaggtgtaaaggcagttggcagtatctgttttatgtttgatgatggagtttcgttttggtttgtttcag
||| ||||| |||||||||||||||||||| || ||||||||||||||||| |||||||||||||||||||| ||||||||||| ||||||||||||||||| | ||     ||  ||   || |||| | ||    | | |   | |    | | ||   ||     || | |  | ||    |   || | |||  |   ||                                                                          
TGATTTCTTCTCTCACTTGGAGATGCATCTGCGTCAGGAGCATCCACCATTGTGTGGAAGAGATCACATGGCTTACAGATCTGCCTATTTTCCAGTGAAGgtaaaatg----ttccttgaattggatttgttaaccaggcgatatataatactctgattctaatattctacaat-gtcaccaagtgcacattatgttagcatgag-------------------------------------------------------------------------

upper sequence: LOC_Os02g04480.1 (Oryza sativa), 5'ss of exon 2
lower sequence: GLYMA20G38460.1 (Glycine max), 5'ss of exon 2
TGACTTCTTTTCTCACTTGGAGATGCATCTCCGCCAGGAGCATCCACCATTATGTGGAAGAGATCACATGGCCTACAGATCTGCTTATTTTCCAGTGAAGgtgatatattattttttttgtttagattagctagtatgt-caaccaacacaga-tattatcacaaatgcatatatttataacttttttaccactttgtcggatagaatatccaggtgtaaaggcagttggcagtatctgttttatgtttgatgatggagtttcgttttggtttgtttcag
||| ||||||||||| |||||||||||| |  | ||||| || ||||| || ||||||||||| |||||||| || |||||||| |||||||| || ||||| |||  |  |   | || | | | ||      | | | ||   |    | |  |||||     ||  ||||  | | | | | ||  |   | | |                                                                                  
TGATTTCTTTTCTCATTTGGAGATGCATATGAGGCAGGATCACCCACCTTTGTGTGGAAGAGACCACATGGCATATAGATCTGCCTATTTTCCTGTTAAGgt-atacctagtcaatattatgttgtttgttctttctattcagttattggaaagcattatttgctatctatatgataagagcatcttccctgttatatttt-------------------------------------------------------------------------------

upper sequence: LOC_Os02g04480.1 (Oryza sativa), 5'ss of exon 2
lower sequence: GLYMA10G43750.1 (Glycine max), 5'ss of exon 2
TGACTTCTTTTCTCACTTGGAGATGCATCTCCGCCAGGAGCATCCACCATTATGTGGAAGAGATCACATGGCCTACAGATCTGCTTATTTTCCAGTGAAGgtg-atatattattttttttgtttagattagctagtatgtcaaccaacacagatattatcacaaatgcatatatttataacttttttaccactttgtcgg-atagaatatccaggtgtaaaggcagttggcagtatctgttttatgtttgatgatggagtttcgttttggtttgtttcag
||| ||||||||||| |||||||||||| |  | ||||| || ||||| || ||||||||||| |||||||| || |||||||| |||||||| || |||||  |  || |   | || |||||    |  ||| | ||| |    |   |   |||||     ||   |||  | | | | |  |  |   | | |    ||                                                                             
TGATTTCTTTTCTCATTTGGAGATGCATATGAGGCAGGATCACCCACCTTTGTGTGGAAGAGACCACATGGCATATAGATCTGCCTATTTTCCTGTTAAGgtatacctaatcaatgttatgtttgttctttctattctgttattgga---aagcattatttgctatctgtatgataagagcatcctccctgttatattttcat-----------------------------------------------------------------------------

upper sequence: LOC_Os02g04480.1 (Oryza sativa), 5'ss of exon 2
lower sequence: Vv00s0317g00100.t01 (Vitis vinifera), 5'ss of exon 2
TGACTTCTTTTCTCACTTGGAGATGCATCTCCGCCAGGAGCATCCACCATTATGTGGAAGAGATCACATGGCCTACAGATCTGCTTATTTTCCAGTGAAGgtgatatattattttttttgtttagattagctagtatgtcaacca-acacagatattatcacaaatgca-tatatttataacttttttaccactttgtcggatagaatatccaggtgtaaaggcagttggcagtatctgttttatgtttgatgatggagtttcgttttggtttgtttcag
|||||||||||||||||||||||||||| |  | ||||| || |||||  | |||||||||||||||||||| |||||||||||||||||||| || |||||||  | ||   ||  ||||       |      |  |    || |     |  | | || | |   | ||||  | | | | |||| |   ||| ||                                                                                 
TGACTTCTTTTCTCACTTGGAGATGCATATGAGACAGGAACACCCACCTCTGTGTGGAAGAGATCACATGGCTTACAGATCTGCTTATTTTCCTGTTAAGgtgaactctttgcttcattgtcccctcaaatgcacacatttttcacattgccaagtcaccatagacctactataaatttcattatttttctcttttctct--------------------------------------------------------------------------------

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|66919004|gb|CX105852.1|CX105852
EST:     TATGTGGAAGAGATCACATGGCCTACAGATCTGCTTATTTTCCAGTGAAG                         GATGTGATTGATGGTGACCTCTGTGAGCAGTTTCCATCCCTCCCAGCTGAT
genomic: TATGTGGAAGAGATCACATGGCCTACAGATCTGCTTATTTTCCAGTGAAGgtgatatatt ... tttgtttcagGATGTGATTGATGGTGACCTCTGTGAGCAGTTTCCATCCCTCCCAGCTGAT
EST: gi|86480173|gb|CI122806.1|CI122806
EST:     TATGTGGAAGAGATCACATGGCCTACAGATCTGCTTATTTTCCAGTGAAG                         GATGTGATTGATGGTGACCTCTGTGAGCAGTTTCCATCCCTCCCAGCTGAT
genomic: TATGTGGAAGAGATCACATGGCCTACAGATCTGCTTATTTTCCAGTGAAGgtgatatatt ... tttgtttcagGATGTGATTGATGGTGACCTCTGTGAGCAGTTTCCATCCCTCCCAGCTGAT
EST: gi|58596700|gb|CK007228.1|CK007228
EST:     TATGTGGAAGAGATCACATGGCCTACAGATCTGCTTATTTTCCAGTGAAG                         GATGTGATTGATGGTGACCTCTGTGAGCAGTTTCCATCCCTCCCAGCTGAT
genomic: TATGTGGAAGAGATCACATGGCCTACAGATCTGCTTATTTTCCAGTGAAGgtgatatatt ... tttgtttcagGATGTGATTGATGGTGACCTCTGTGAGCAGTTTCCATCCCTCCCAGCTGAT
EST: gi|88265817|gb|CI376719.1|CI376719
EST:     TGCTTATTTTCCAGTGAAG                         GATGTGATTGATGGTGACCTCTGTGACCAGTTTCCATCCCTCCCACCTGAT
genomic: TGCTTATTTTCCAGTGAAGgtgatatatt ... tttgtttcagGATGTGATTGATGGTGACCTCTGTGAGCAGTTTCCATCCCTCCCAGCTGAT
EST: gi|58600332|gb|CK010860.1|CK010860
EST:     TATGTGGAAGAGATCACATGGCCTACAGATCTGCTTATTTTCCAGTGAAG                         GATGTGATTGATGGTGACCTCTGTGAGCAGTTTCCATCCCTCCCAGCTGAT
genomic: TATGTGGAAGAGATCACATGGCCTACAGATCTGCTTATTTTCCAGTGAAGgtgatatatt ... tttgtttcagGATGTGATTGATGGTGACCTCTGTGAGCAGTTTCCATCCCTCCCAGCTGAT
EST: gi|29627316|gb|CB632327.1|CB632327
EST:     TATGTGGAAGAGATCACATGGCCTACAGATCTGCTTATTTTCCAGTGAAG                         GATGTGATTGATGGTGACCTCTGTGAGCAGTTTCCATCCCTCCCAGCTGAT
genomic: TATGTGGAAGAGATCACATGGCCTACAGATCTGCTTATTTTCCAGTGAAGgtgatatatt ... tttgtttcagGATGTGATTGATGGTGACCTCTGTGAGCAGTTTCCATCCCTCCCAGCTGAT
EST: gi|86870600|gb|CI323476.1|CI323476
EST:     GGCCTACAGATCTGCTTATTTTCCAGTGAAG                         GATGTGATTGATGGTGACCTCTGTGAGCAGTTTCCATCCCTCCCAGCTGAT
genomic: GGCCTACAGATCTGCTTATTTTCCAGTGAAGgtgatatatt ... tttgtttcagGATGTGATTGATGGTGACCTCTGTGAGCAGTTTCCATCCCTCCCAGCTGAT
EST: gi|88966253|gb|CI119388.1|CI119388
EST:     TATGTGGAAGAGATCACATGGCCTACAGATCTGCTTATTTTCCAGTGAAG                         GATGTGATTGATGGTGACCTCTGTGAGCAGTTTCCATCCCTCCCAGCTGAT
genomic: TATGTGGAAGAGATCACATGGCCTACAGATCTGCTTATTTTCCAGTGAAGgtgatatatt ... tttgtttcagGATGTGATTGATGGTGACCTCTGTGAGCAGTTTCCATCCCTCCCAGCTGAT
EST: gi|88384316|gb|CI551242.1|CI551242
EST:     TATGTGGAAGAGATCACATGGCCTACAGATCTGCTTATTTTCCAGTGAAG                         GATGTGATTGATGGTGACCTCTGTGAGCAGTTTCCATCCCTCCCAGCTGAT
genomic: TATGTGGAAGAGATCACATGGCCTACAGATCTGCTTATTTTCCAGTGAAGgtgatatatt ... tttgtttcagGATGTGATTGATGGTGACCTCTGTGAGCAGTTTCCATCCCTCCCAGCTGAT
EST: gi|88254064|gb|CI352690.1|CI352690
EST:     TCTGCTTATTTTCCAGTGAAG                         GATGTGATTGATGGTGACCTCTGTGAGCAGTTTCCATCCCTCCCAGCTGAT
genomic: TCTGCTTATTTTCCAGTGAAGgtgatatatt ... tttgtttcagGATGTGATTGATGGTGACCTCTGTGAGCAGTTTCCATCCCTCCCAGCTGAT
EST: gi|88464402|gb|CI544863.1|CI544863
EST:     GATCACATGGCCTACAGATCTGCTTATTTTCCAGTGAAG                         GATGTGATTGATGGTGACCTCTGTGAGCAGTTTCCATCCCTCCCAGCTGAT
genomic: GATCACATGGCCTACAGATCTGCTTATTTTCCAGTGAAGgtgatatatt ... tttgtttcagGATGTGATTGATGGTGACCTCTGTGAGCAGTTTCCATCCCTCCCAGCTGAT
EST: gi|86480168|gb|CI122801.1|CI122801
EST:     TATGTGGAAGAGATCACATGGCCTACAGATCTGCTTATTTTCCAGTGAAG                         GATGTGATTGATGGTGACCTCTGTGAGCAGTTTCCATCCCTCCCAGCTGAT
genomic: TATGTGGAAGAGATCACATGGCCTACAGATCTGCTTATTTTCCAGTGAAGgtgatatatt ... tttgtttcagGATGTGATTGATGGTGACCTCTGTGAGCAGTTTCCATCCCTCCCAGCTGAT
EST: gi|87023293|gb|CI272121.1|CI272121
EST:     TATGTGGAAGAGATCACATGGCCTACAGATCTGCTTATTTTCCAGTGAA-                         GATGTTGATTGATGGTGACCTCTGTGAGCAGTTTCCATCCCTCCCAGCTGA
genomic: TATGTGGAAGAGATCACATGGCCTACAGATCTGCTTATTTTCCAGTGAAGgtgatatatt ... tttgtttcagGATG-TGATTGATGGTGACCTCTGTGAGCAGTTTCCATCCCTCCCAGCTGA
EST: gi|86481938|gb|CI124571.1|CI124571
EST:     TATGTGGAAGAGATCACATGGCCTACAGATCTGCTTATTTTCCAGTGAAG                         GATGTGATTGATGGTGACCTCTGTGAGCAGTTTCCATCCCTCCCAGCTGAT
genomic: TATGTGGAAGAGATCACATGGCCTACAGATCTGCTTATTTTCCAGTGAAGgtgatatatt ... tttgtttcagGATGTGATTGATGGTGACCTCTGTGAGCAGTTTCCATCCCTCCCAGCTGAT

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: 68 (upstream exon), 63 (downstream exon)
Score: 24

TGACTTCTTTTCTCACTTGGAGATGCATCTCCGCCAGGAGCATCCACCATTATGTGGAAGAGATCACATGGCCTACAGATCTGCTTATTTTCCAGTGAAGgtgatatatt ... tttgtttcagGATGTGATTGATGGTGACCTCTGTGAGCAGTTTCCATCCCTCCCAGCTGATATGCAAAGGAAGATTGCCGATGAACTCGACAGAACTCCTGGTGAAATCC




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGACTTCTTTTCTCACTTGGAGATGCATCTCCGCCAGGAGCATCCACCATTATGTGGAAGAGATCACATGGCCTACAGATCTGCTTATTTTCCAGTGAAGgtgatatattattttttttgtttagattagctagtatgtcaaccaacacagatattatcacaaatgcatatatttataacttttttaccactttgtcggatagaatatccaggtgtaaaggcagttggcagtatctgttttatgtttgatgatggagtttcgttttggtttgtttcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGATCA