Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCTTCCATCGAGATACAGGGATTCAGTGAGGGCGATCAGGCCAGGGCTGCCCCTCTTCCTCTACAACTACTCCACCCACCAGCTCCACGGCATCTTCGAGgtaataattttgggtgtagctatatctatgacgccatatttttcactaaaaaatagtcgacatgtatttacattctaatttcctaaagtacatatgtgat...

Basic information

species Oryza sativa
transcript LOC_Os01g36950.2
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g36950.3 (Oryza sativa), 5'ss of exon 2
lower sequence: AC207342.3_FGT008 (Zea mays), 5'ss of exon 2
GCTTCCATCGAGATACAGGGATTCAGTGAGGGCGATCAGGCCAGGGCTGCCCCTCTTCCTCTACAACTACTCCACCCACCAGCTCCACGGCATCTTCGAGgtaataattttgggtgtagctatatcta--tgacgccatatttttcactaaaaaatagtcgacatgtatttacattctaatttcctaaagtacatatgtgat
||| || ||||| |||||||| || ||| |||| ||| | || ||||||||||||||||||||||||||||||||||||||||| |||||||||||| |||||    |   |    |  |  || | |    |  ||  ||||  |  |  |   |  ||  ||| |||   |      ||    |   |  ||   |    
GCTGCCGTCGAGGTACAGGGACTCGGTGCGGGCCATCCGCCCGGGGCTGCCCCTCTTCCTCTACAACTACTCCACCCACCAGCTGCACGGCATCTTCAAGgta-cggtacagtacattacagtagccagccaattcctgatttgccttttcatcttcatctgcatctatgctctcatggatccggttccgatcaccag----

upper sequence: LOC_Os01g36950.3 (Oryza sativa), 5'ss of exon 2
lower sequence: GRMZM2G071154_T01 (Zea mays), 5'ss of exon 2
GCTTCCATCGAGATACAGGGATTCAGTGAGGGCGATCAGGCCAGGGCTGCCCCTCTTCCTCTACAACTACTCCACCCACCAGCTCCACGGCATCTTCGAGgta----ataattttgggt------gtagcta-tatctatgacgccatatttttcactaaaaaatagtcgacatg-tatttacattctaatttcctaaagtacatatgtgat----------------------------
||| || || || |||||||| || ||| | || ||| | || || ||||||||||||||||||||||||||||| |||||||||||||||||||||||||||    | |     |         ||||| | || | |   ||   |    ||  ||      |  |      | | |      |     ||| |    |  ||    ||                             
GCTGCCGTCCAGGTACAGGGACTCTGTGCGTGCTATCCGCCCGGGACTGCCCCTCTTCCTCTACAACTACTCCACGCACCAGCTCCACGGCATCTTCGAGgtacagtacagcacagcacagcacagtagccactagccagttcgtggttccctttccttgcttcttcttcgttcgctgtccttgcttcttcttcgttcgctgtattcacgaggacccggttccgatcctccgatcgccag

upper sequence: LOC_Os01g36950.3 (Oryza sativa), 5'ss of exon 2
lower sequence: GLYMA13G10640.1 (Glycine max), 5'ss of exon 2
GCTTCCATCGAGATACAGGGATTCAGTGAGGGCGATCAGGCCAGGGCTGCCCCTCTTCCTCTACAACTACTCCACCCACCAGCTCCACGGCATCTTCGAGgtaataattttgggtgtagctatatctatgacgccatattt--ttcactaaaaaatagtcgacatgtatttacattctaatttcctaaagtacatatgtgat----------------------------------------------------------------------------------------
 || ||  |  | ||||| |||||||| ||  | || |  |||||| ||||||| || || |||||||||||||| ||||| ||||| || ||||| ||||||    || || || |     | ||| |       | |||  ||   |  |  |   |       |    |   |    |||    |  |  |  | ||                                                                                          
TCTGCCTCCACGGTACAGAGATTCAGTTAGAACAATAACTCCAGGGTTGCCCCTTTTTCTGTACAACTACTCCACTCACCAACTCCATGGTATCTTTGAGgtat--gttgtgtgtattttcttttcttttcttttttttttagtttgttgcatcactttaatttgatgaaaatgcttccgtttttggagatcaagttatggattaggccatcacttttagatttagcagctatggtctaattaagagtaacaataattataataattaatgtttggtggggtttgttcag

upper sequence: LOC_Os01g36950.3 (Oryza sativa), 5'ss of exon 2
lower sequence: Vv02s0025g01720.t01 (Vitis vinifera), 5'ss of exon 2
GCTTCCATCGAGATACAGGGATTCAGTGAGGGCGATCAGGCCAGGGCTGCCCCTCTTCCTCTACAACTACTCCACCCACCAGCTCCACGGCATCTTCGAGgt--------------aataattttggg---tgtagctatatctatgacgccatatttttcactaaaaaatagtcgacatg-tatttacattctaatttcctaaagtacatat-gtgat------------------------
  | ||  | || ||| | ||||||||| |||| || |  |||||  | ||||| ||||||||||| ||||||||||||||||| || ||  | || |||||              || |||  |      || ||  ||   | |       |    ||  || ||||||| | ||     |||| |     | || |  |  | ||   |   | |                         
TTTGCCTCCCAGGTACCGTGATTCAGTGCGGGCTATAACCCCAGGATTACCCCTTTTCCTCTACAATTACTCCACCCACCAGCTTCATGGAGTTTTTGAGgtttgtatttctttctaagaatcataaactctgcagtaattcatgtattcttttggggttttctcaaaaatattagattcaatattcagcacttcatgttttggattatgcaccattacctaatgttatacttgtatgttcag

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|570114|gb|D40963.1|D40963
EST:     CCCTCTTCCTCTACAACTACTCCACCCACCAGCTCCACGGCATCTTCGAG                         GCTGCGAGTTTTGGCGGAACAAACATCGATCCGACGGCGTTGGAGGACAAG
genomic: CCCTCTTCCTCTACAACTACTCCACCCACCAGCTCCACGGCATCTTCGAGgtaataattt ... tttcattcagGCTGCGAGCTTTGGCGGAACAAACATCGATCCGACGGCGTGGGAGGACAAG
EST: gi|33684836|gb|CF313075.1|CF313075
EST:     CTTCTTTCCTCTACAANTACTCCACCCACCAGCTCCACGGCATCTTCGAG                         GCTGCGAGCTTTGGCGGAACAAACATCGATCCGACGGCGTGGGAGGACAAG
genomic: CCTC-TTCCTCTACAACTACTCCACCCACCAGCTCCACGGCATCTTCGAGgtaataattt ... tttcattcagGCTGCGAGCTTTGGCGGAACAAACATCGATCCGACGGCGTGGGAGGACAAG
EST: gi|29675526|gb|CB671801.1|CB671801
EST:     CCCTCTTCCTCTACAAGTACTCCACCCACCAGCTCCACGGCATCTTCGAG                         GCTGCGAGCTTTGGCGGAACAAACATCGATCCGACGGCGTGGGAGGACAAG
genomic: CCCTCTTCCTCTACAACTACTCCACCCACCAGCTCCACGGCATCTTCGAGgtaataattt ... tttcattcagGCTGCGAGCTTTGGCGGAACAAACATCGATCCGACGGCGTGGGAGGACAAG
EST: gi|313080398|gb|HO213406.1|HO213406
EST:     CCCTCTTCCTCTACAACTACTCCACCCACCAGCTCCACGGCATCTTCGAG                         GCTGCGAGCTTTGGCGGAACAAACATCGATCCGACGGCGTGGGAGGACAAG
genomic: CCCTCTTCCTCTACAACTACTCCACCCACCAGCTCCACGGCATCTTCGAGgtaataattt ... tttcattcagGCTGCGAGCTTTGGCGGAACAAACATCGATCCGACGGCGTGGGAGGACAAG
EST: gi|86599861|gb|CI256023.1|CI256023
EST:     AACTACTCCACCCACCAGCTCCACGGCATCTTCGAG                         GCTGCGAGCTTTGGCGGAACAAACATCGATCCGACGGCGTGGGAGGACAAG
genomic: AACTACTCCACCCACCAGCTCCACGGCATCTTCGAGgtaataattt ... tttcattcagGCTGCGAGCTTTGGCGGAACAAACATCGATCCGACGGCGTGGGAGGACAAG
EST: gi|88847460|gb|CI015953.1|CI015953
EST:     CCCTCTTCCTCTACAACTACTCCACCCACCAGCTCCACGGCATCTTCGAG                         GCTGCGAGCTTTGGCGGAACAAACATCGATCCGACGGCGTGGGAGGACAAG
genomic: CCCTCTTCCTCTACAACTACTCCACCCACCAGCTCCACGGCATCTTCGAGgtaataattt ... tttcattcagGCTGCGAGCTTTGGCGGAACAAACATCGATCCGACGGCGTGGGAGGACAAG
EST: gi|88829644|gb|CI074514.1|CI074514
EST:     CCCTCTTCCTCTACAACTACTCCACCCACCAGCTCCACGGCATCTTCGAG                         GCTGCGAGCTTTGGCGGAACAAACATCGATCCGACGGCGTGGGAGGACAAG
genomic: CCCTCTTCCTCTACAACTACTCCACCCACCAGCTCCACGGCATCTTCGAGgtaataattt ... tttcattcagGCTGCGAGCTTTGGCGGAACAAACATCGATCCGACGGCGTGGGAGGACAAG
EST: gi|313080399|gb|HO213407.1|HO213407
EST:     CCCTCTTCCTCTACAACTACTCCACCCACCAGCTCCACGGCATCTTCGAG                         GCTGCGAGCTTTGGCGGAACAAACATCGATCCGACGGCGTGGGAGGACAAG
genomic: CCCTCTTCCTCTACAACTACTCCACCCACCAGCTCCACGGCATCTTCGAGgtaataattt ... tttcattcagGCTGCGAGCTTTGGCGGAACAAACATCGATCCGACGGCGTGGGAGGACAAG
EST: gi|86498989|gb|CI141622.1|CI141622
EST:     GGCATCTTCGAG                         GCTGCGAGCTTTGGCGGAACAAACATCGATCCGACGGCGTGGGAGGACAAG
genomic: GGCATCTTCGAGgtaataattt ... tttcattcagGCTGCGAGCTTTGGCGGAACAAACATCGATCCGACGGCGTGGGAGGACAAG
EST: gi|29680788|gb|CB677063.1|CB677063
EST:     ACAANTACTCCACCCACCAGCTCCACGGCATCTTCGAG                         GCTGCGAGCTTTGGCGGAACAAACATCGATCCGACGGCGTGGGAGGACAAG
genomic: ACAACTACTCCACCCACCAGCTCCACGGCATCTTCGAGgtaataattt ... tttcattcagGCTGCGAGCTTTGGCGGAACAAACATCGATCCGACGGCGTGGGAGGACAAG
EST: gi|29681137|gb|CB677412.1|CB677412
EST:     CCCTCTTCCTCTACAACTACTCCACCCACCAGCTCCACGGCATCTTCGAG                         GCTGCGAGCTTTGGCGGAACAAACATCGATCCGACGGCGTGGGAGGACAAG
genomic: CCCTCTTCCTCTACAACTACTCCACCCACCAGCTCCACGGCATCTTCGAGgtaataattt ... tttcattcagGCTGCGAGCTTTGGCGGAACAAACATCGATCCGACGGCGTGGGAGGACAAG
EST: gi|29658386|gb|CB654661.1|CB654661
EST:     CCCTCTTCCTCTACAACTACTCCACCCACCAGCTCCACGGCATCTTCGAG                         GCTGCGAGCTTTGGCGGAACAAACATCGATCCGACGGCGTGGGAGGACAAG
genomic: CCCTCTTCCTCTACAACTACTCCACCCACCAGCTCCACGGCATCTTCGAGgtaataattt ... tttcattcagGCTGCGAGCTTTGGCGGAACAAACATCGATCCGACGGCGTGGGAGGACAAG
EST: gi|29657456|gb|CB653731.1|CB653731
EST:     CCCTCTTCCTTTACAACTACTCCACCCACCAGCTCCACGGCATCTTTGAG                         GCTGCGAGCTTTGGCGGAACAAACATCGATCCGACGGCGTGGGAGGACAAG
genomic: CCCTCTTCCTCTACAACTACTCCACCCACCAGCTCCACGGCATCTTCGAGgtaataattt ... tttcattcagGCTGCGAGCTTTGGCGGAACAAACATCGATCCGACGGCGTGGGAGGACAAG
EST: gi|29658418|gb|CB654693.1|CB654693
EST:     AACTACTCCACCCACCAGCTCCACGGCATCTTTGAG                         GCTGCGAGCTTTGGCGGAACAAACATCGATCCGACGGCGTGGGAGGACAAG
genomic: AACTACTCCACCCACCAGCTCCACGGCATCTTCGAGgtaataattt ... tttcattcagGCTGCGAGCTTTGGCGGAACAAACATCGATCCGACGGCGTGGGAGGACAAG
EST: gi|9884513|gb|BE607346.1|BE607346
EST:     CCCTCTTCCTCTACAACTACTCCACCCACCAGCTCCACGGCATCTTCGAG                         GCTGCGAGCTTTGGCGGAACAAACATCGATCCGACGGCGTGGGAGGACAAG
genomic: CCCTCTTCCTCTACAACTACTCCACCCACCAGCTCCACGGCATCTTCGAGgtaataattt ... tttcattcagGCTGCGAGCTTTGGCGGAACAAACATCGATCCGACGGCGTGGGAGGACAAG
EST: gi|29657554|gb|CB653829.1|CB653829
EST:     CCCTCTTCCTCTACAAATACTCCACCCACCAGCTCCACGGCATCTTCGAG                         GCTGCGAGCTTTGGCGGAACAAACATCGATCCGACGGCGTGGGAGGACAAG
genomic: CCCTCTTCCTCTACAACTACTCCACCCACCAGCTCCACGGCATCTTCGAGgtaataattt ... tttcattcagGCTGCGAGCTTTGGCGGAACAAACATCGATCCGACGGCGTGGGAGGACAAG
EST: gi|29682521|gb|CB678796.1|CB678796
EST:     CCCTCTTCCTCTACAACTACTCCACCCACCAGCTCCACGGCATCTTCGAG                         GCTGCGAGCTTTGGCGGAACAAACATCGATCCGACGGCGTGGGAGGACAAG
genomic: CCCTCTTCCTCTACAACTACTCCACCCACCAGCTCCACGGCATCTTCGAGgtaataattt ... tttcattcagGCTGCGAGCTTTGGCGGAACAAACATCGATCCGACGGCGTGGGAGGACAAG
EST: gi|86538667|gb|CI178873.1|CI178873
EST:     AGCTCCACGGCATCTTCGAG                         GCTGCGAGCTTTGGCGGAACAAACATCGATCCGACGGCGTGGGAGGACAAG
genomic: AGCTCCACGGCATCTTCGAGgtaataattt ... tttcattcagGCTGCGAGCTTTGGCGGAACAAACATCGATCCGACGGCGTGGGAGGACAAG
EST: gi|29671749|gb|CB668024.1|CB668024
EST:     CCCTCTTCCTTTACAACTACTCCACCCACCAGCTCCACGGCATCTTCGAG                         GCTGCGAGCTTTGGCGGAACAAACATCGATCCGACGGCGTGGGAGGACAAG
genomic: CCCTCTTCCTCTACAACTACTCCACCCACCAGCTCCACGGCATCTTCGAGgtaataattt ... tttcattcagGCTGCGAGCTTTGGCGGAACAAACATCGATCCGACGGCGTGGGAGGACAAG
EST: gi|29682522|gb|CB678797.1|CB678797
EST:     CCCTCTTCCTCTACAAATACTCCACCCACCAGCTCCACGGCATCTTCGAG                         GCTGCGAGCTTTGGCGGAACAAACATCGATCCGACGGCGTGGGAGGACAAG
genomic: CCCTCTTCCTCTACAACTACTCCACCCACCAGCTCCACGGCATCTTCGAGgtaataattt ... tttcattcagGCTGCGAGCTTTGGCGGAACAAACATCGATCCGACGGCGTGGGAGGACAAG
EST: gi|29668873|gb|CB665148.1|CB665148
EST:     CCACCCACCAGCTCCACGGCATCTTCGAG                         GCTGCGAGCTTTGGCGGAACAAACATCGATCCGACGGCGTGGGAGGACAAG
genomic: CCACCCACCAGCTCCACGGCATCTTCGAGgtaataattt ... tttcattcagGCTGCGAGCTTTGGCGGAACAAACATCGATCCGACGGCGTGGGAGGACAAG
EST: gi|87030339|gb|CI252616.1|CI252616
EST:     CCCTCTTCCTCTACAACTACTCCACCCACCAGCTCCACGGCATCTTCGAG                         GCTGCGAGCTTTGGCGGAACAAACATCGATCCGACGGCGTGGGAGGACAAG
genomic: CCCTCTTCCTCTACAACTACTCCACCCACCAGCTCCACGGCATCTTCGAGgtaataattt ... tttcattcagGCTGCGAGCTTTGGCGGAACAAACATCGATCCGACGGCGTGGGAGGACAAG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCTTCCATCGAGATACAGGGATTCAGTGAGGGCGATCAGGCCAGGGCTGCCCCTCTTCCTCTACAACTACTCCACCCACCAGCTCCACGGCATCTTCGAGgtaataattttgggtgtagctatatctatgacgccatatttttcactaaaaaatagtcgacatgtatttacattctaatttcctaaagtacatatgtgat

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTC