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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacgctttaagagtagcaatcgtactgtcaaatctttttagcaaatgcatgttggtgccttgttgttgatgaaaccatttgatttaattacactactgtaaggcccaattcatgcacaattttgatgcgtgtttattttggtagGTTCTTGAGGAAGGTGTCCTCAACCCAGAATCAACTGTCGTTGCAATCTTCCCCTCTCCAATGCATTATGCAGGGCCAACTGAAGTGCAATGGCATGCTA

Basic information

species Oryza sativa
transcript LOC_Os03g53230.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g53230.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G088348_T01 (Zea mays), 3'ss of exon 9
gtacgctttaagagtagcaatcgtactgtcaaatctttttagcaaatgcatgttggtgccttgt-tgttgatgaaaccatttgatttaattacactac-tgtaaggcccaattcatgcacaattttgatgcgtgtttattt-tggtagGTTCTTGAGGAAGGTGTCCTCAACCCAGAATCAACTGTCGTTGCAATCTTCCCCTCTCCAATGCATTATGCAGGGCCAACTGAAGTGCAATGGCATGCTA
                                               | ||| | |    || | |  |||   |     ||   |  | || ||||  |  |||  |  |||| || ||  || | |  | |||| |||| |  ||||||||||||||||| ||||||||||||||||||||||| ||||| || || |||||||||||||||||||| ||||||||||| ||||| ||||||||||
-----------------------------------------------gaatgatagctttttctgtaatgaaacaggtggtttggtggactatactatgttcaagttctgattcttgtactgttctaacac-tgttgatttctactagGTTCTTGAGGAAGGCGTCCTCAACCCAGAATCAACTGTTGTTGCGATTTTTCCCTCTCCAATGCATTATGCTGGGCCAACTGAGGTGCAGTGGCATGCTA

upper sequence: LOC_Os03g53230.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G051270_T02 (Zea mays), 3'ss of exon 3
gtacgctttaagagtagcaatcgtactgtcaaatctttttagcaaatgcatgttggtgccttgttgttgatgaaaccatttgatttaattacactac-tgtaaggcccaattcatgcacaattttgatgcgtgtttattt-tggtagGTTCTTGAGGAAGGTGTCCTCAACCCAGAATCAACTGTCGTTGCAATCTTCCCCTCTCCAATGCATTATGCAGGGCCAACTGAAGTGCAATGGCATGCTA
                                             ||    | |  |  | |||  |  |  |     ||||||   |||| ||||  |  |||  |  |||| || ||  || | |  | |||| |||| |  ||||||||||||||||||||||||||||||||||||||||| ||||| ||||| |||||||||||||||||||| ||||||||||| ||||| ||||||||||
---------------------------------------------ataatagcttttttcctgtaatgaaacaggtggtttgatg-gattatactatgttcaagttctgattcttgtactgttctaacac-tgttgatttctactagGTTCTTGAGGAAGGTGTCCTCAACCCAGAATCAACTGTTGTTGCGATCTTTCCCTCTCCAATGCATTATGCTGGGCCAACTGAGGTGCAGTGGCATGCTA

upper sequence: LOC_Os03g53230.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G302080_T01 (Zea mays), 3'ss of exon 9
gtacgctttaagagtagcaatcgtactgtcaaatctttttagcaaatgcatgttggtgccttgttgttgatgaaaccatttgattta---attacactac-tgtaaggcccaattcatgcacaattttgatgcgtgtttattt-tggtagGTTCTTGAGGAAGGTGTCCTCAACCCAGAATCAACTGTCGTTGCAATCTTCCCCTCTCCAATGCATTATGCAGGGCCAACTGAAGTGCAATGGCATGCTA---------
                                                          | || |   | |||||||   | | ||     | || ||||  |  |||  |  |||| || ||  || | |  | |||| |||| |  || |||||||||||||| ||||||||||||||||||||||| ||||| ||||| |||||||||||||||||||| ||||||||||| ||||| ||||||||||         
----------------------------------------------------------ctttttctgtaatgaaacaggtggtttggtggactatactatgttcaagttctgattcttgtactgttctaacac-tgttgatttctactatgttcttgagGAAGGCGTCCTCAACCCAGAATCAACTGTTGTTGCGATCTTTCCCTCTCCAATGCATTATGCTGGGCCAACTGAGGTGCAGTGGCATGCTAAGGCTCGTA

upper sequence: LOC_Os03g53230.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G149952_T01 (Zea mays), 3'ss of exon 2
gtacgctttaagagtagcaatcgtactgtcaaatctttttagcaaatgcatgttggtgccttgttgttgatgaaaccatttgatttaattacactactgta--aggcccaattcatgcacaattttgatgcgtgtttattt-tggtagGTTCTTGAGGAAGGTGTCCTCAACCCAGAATCAACTGTCGTTGCAATCTTCCCCTCTCCAATGCATTATGCAGGGCCAACTGAAGTGCAATGGCATGCTA
                                            | ||  || |||    ||  |||  ||||||  |  || ||| ||  ||| |||  |  | |  ||| |  || ||  || | |  | |||| |||| |   |||||||||||||||||||||||||||||||||||||||| ||||| |||||||||||||| ||||||||||| ||||||||||| || |||||||||||||
--------------------------------------------attgagtgatggc-tattcctgt-aatgaaat-aggtgttttgatggcaccactacactatgttcaacttctgtactgttctaacac-tgttgatttctaccagGTTCTTGAGGAAGGTGTCCTCAACCCAGAATCAACTGTTGTTGCGATCTTCCCCTCTCCTATGCATTATGCTGGGCCAACTGAGGTTCAATGGCATGCTA

upper sequence: LOC_Os03g53230.1 (Oryza sativa), 3'ss of exon 2
lower sequence: EFJ22935 (Selaginella moellendorffii), 3'ss of exon 2
gtacgctttaagagtagcaatcgtactgtcaaatctttttagcaaatgcatgttggtgccttgttgttgatgaaaccatttgatttaattacactactgtaaggcccaattcatgcacaattttgatgcgtgtttattttggtagGTTCTTGAGGAAGGTGTCCTCAACCCAGAATCAACTGTCGTTGCAATCTTCCCCTCTCCAATGCATTATGCAGGGCCAACTGAAGTGCAATGGCATGCTA
                                                                              ||||||||  |||   |   |    |     | | | |  |  ||||       | | |||  | |||||||  | | ||||||  |  | |||||  |||| || || |||||||||||||| ||||||||||| || |||||||| ||||| |||||||| || |
-----------------------------------------------------------------------------gtttgattt--ttattttcgcggcgtgttttctacgttcttacatttgtcat---tgtctttgtgaagGTTCTCAAAGCAGGTGTGTTGGATCCAGAGACAACGGTGGTGGCAATCTTCCCCTCGCCAATGCATTACGCCGGGCCAACGGAAGTCCAATGGCACGCCA

upper sequence: LOC_Os03g53230.1 (Oryza sativa), 3'ss of exon 2
lower sequence: EFJ32830 (Selaginella moellendorffii), 3'ss of exon 2
gtacgctttaagagtagcaatcgtactgtcaaatctttttagcaaatgcatgttggtgccttgttgttgatgaaaccatttgatttaattacactactgtaaggcccaattcatgcacaattttgatgcgtgtttattttggt--agGTTCTTGAGGAAGGTGTCCTCAACCCAGAATCAACTGTCGTTGCAATCTTCCCCTCTCCAATGCATTATGCAGGGCCAACTGAAGTGCAATGGCATGCTA
                                                                                   |||  ||    || |    |||    ||  | |     ||  ||  ||  || | || ||  |||||||  | | ||||||  |  | |||||  |||| || || |||||||| ||||| ||||||||||| || |||||||| ||||| |||||||| || |
----------------------------------------------------------------------------------gtttgttttt--tatttcgcggcgtgttttctacgtt-cttacatttgtcattgtctttgtgaagGTTCTCAAAGCAGGTGTGTTGGATCCAGAGACAACGGTGGTGGCAATCTTTCCCTCGCCAATGCATTACGCCGGGCCAACGGAAGTCCAATGGCACGCCA

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|29681905|gb|CB678180.1|CB678180
EST:     GCAGATGATGTGCTTC-TAGTTGGAGAATGAAGCAGCATGAAAAG                         G-TCTTGAGGAAGGTGTCCTCAACCCAGAATCAACTGTCGTTGCAATCTTC
genomic: GCAGATGATGTGCCTCTTAGTTGGAGAATGAAGCAGCATGAAAAGgtacgcttta ... attttggtagGTTCTTGAGGAAGGTGTCCTCAACCCAGAATCAACTGTCGTTGCAATCTTC
EST: gi|29614774|gb|CB619787.1|CB619787
EST:     AAGCAGATGATGTGCCTCTTAGTTGGAGAATGAAGCAGCATGAAAAG                         TTTCTTGAGGAAGGTGTCCTCAACCCAGAATCAACTGTCGTTGCAATCTTC
genomic: AAGCAGATGATGTGCCTCTTAGTTGGAGAATGAAGCAGCATGAAAAGgtacgcttta ... attttggtagGTTCTTGAGGAAGGTGTCCTCAACCCAGAATCAACTGTCGTTGCAATCTTC
EST: gi|33794987|gb|CF323373.1|CF323373
EST:     CAAAAGCAGATGATGTGCCTCTTAGTTGGAGAATGAAGCAGCATGAAAAG                         GTTCTTGAGGAAGGTGTCCTCAACCCAGAATCAACTGTCGTTGCAATCTTC
genomic: CAAAAGCAGATGATGTGCCTCTTAGTTGGAGAATGAAGCAGCATGAAAAGgtacgcttta ... attttggtagGTTCTTGAGGAAGGTGTCCTCAACCCAGAATCAACTGTCGTTGCAATCTTC
EST: gi|27577783|gb|CB000478.1|CB000478
EST:     CAAAAGCAGATGATGTGCCTCTTAGTTGGAGAATGAAGCAGCATGAAAAG                         GTTCTTGAGGAAGGTGTCCTCAACCCAGAATCAACTGTCGTTGCAATCTTC
genomic: CAAAAGCAGATGATGTGCCTCTTAGTTGGAGAATGAAGCAGCATGAAAAGgtacgcttta ... attttggtagGTTCTTGAGGAAGGTGTCCTCAACCCAGAATCAACTGTCGTTGCAATCTTC
EST: gi|1854170|gb|AA231798.1|AA231798
EST:     CAAAAGCAGATGATGTGCCTCTTAGTTGGAGAATGAAGCAGCATGAAAAG                         GTTCTTGAGGAAG-TGTCCTCAACCCAGAATCAACTGTCGTTGCAATCTTC
genomic: CAAAAGCAGATGATGTGCCTCTTAGTTGGAGAATGAAGCAGCATGAAAAGgtacgcttta ... attttggtagGTTCTTGAGGAAGGTGTCCTCAACCCAGAATCAACTGTCGTTGCAATCTTC
EST: gi|55410414|gb|CV722790.1|CV722790
EST:     CAAAAGCAGATGATGTGCCTCTTAGTTGGAGAATGAAGCAGCATGAAAAG                         GTTCTTGAGGAAGGTGTCCTCAACCCAGAATCAACTGTCGTTGCAATCTTC
genomic: CAAAAGCAGATGATGTGCCTCTTAGTTGGAGAATGAAGCAGCATGAAAAGgtacgcttta ... attttggtagGTTCTTGAGGAAGGTGTCCTCAACCCAGAATCAACTGTCGTTGCAATCTTC
EST: gi|163918481|gb|EG714843.1|EG714843
EST:     CAAAAGCAGATGATGTGCCTCTTAGTTGGAGAATGAAGCAGCATGAAAAG                         GTTCTTGAGGAAGGTGTCCTCAACCCAGAATCAACTGTCGTTGCAATCTTC
genomic: CAAAAGCAGATGATGTGCCTCTTAGTTGGAGAATGAAGCAGCATGAAAAGgtacgcttta ... attttggtagGTTCTTGAGGAAGGTGTCCTCAACCCAGAATCAACTGTCGTTGCAATCTTC
EST: gi|29656058|gb|CB652333.1|CB652333
EST:     CAAAAGCAGATGATGTGCCTCTTAGTTGGAGAATGAAGCAGCATGAAAAG                         GTTCTTGAGGAAGGTGTCCTCAACCCAGAATCAACTGTCGTTGCAATCTTC
genomic: CAAAAGCAGATGATGTGCCTCTTAGTTGGAGAATGAAGCAGCATGAAAAGgtacgcttta ... attttggtagGTTCTTGAGGAAGGTGTCCTCAACCCAGAATCAACTGTCGTTGCAATCTTC
EST: gi|66924054|gb|CX110902.1|CX110902
EST:     AGCAGCATGAAAAG                         GTTCTTGAGGAAGGTGTCCTCAACCCAGAATCAACTGTCGTTGCAATCTTC
genomic: AGCAGCATGAAAAGgtacgcttta ... attttggtagGTTCTTGAGGAAGGTGTCCTCAACCCAGAATCAACTGTCGTTGCAATCTTC
EST: gi|33812718|gb|CF332246.1|CF332246
EST:     CAAAAGCAGATGATGTGCCTCTTAGTTGGAGAATGAAGCAGCATGAAAAG                         GTTCTTGAGGAAGGTGTCCTCAACCCAGAATCAACTGTCGTTGCAATCTTC
genomic: CAAAAGCAGATGATGTGCCTCTTAGTTGGAGAATGAAGCAGCATGAAAAGgtacgcttta ... attttggtagGTTCTTGAGGAAGGTGTCCTCAACCCAGAATCAACTGTCGTTGCAATCTTC
EST: gi|29662144|gb|CB658419.1|CB658419
EST:     GCAGATGATGTGCCTCTTAGTTGGAGAATGAAGCAGCATGAAAAG                         TTTCTTGAGGAAGGTGTCCTCAACCCAGAATCAACTGTCGTTGCAATCTTC
genomic: GCAGATGATGTGCCTCTTAGTTGGAGAATGAAGCAGCATGAAAAGgtacgcttta ... attttggtagGTTCTTGAGGAAGGTGTCCTCAACCCAGAATCAACTGTCGTTGCAATCTTC
EST: gi|58683689|gb|CK072376.1|CK072376
EST:     CAAAAGCAGATGATGTGCCTCTTAGTTGGAGAATGAAGCAGCATGAAAAG                         GTTCTTGAGGAAGGTGTCCTCAACCCAGAATCAACTGTCGTTGCAATCTTC
genomic: CAAAAGCAGATGATGTGCCTCTTAGTTGGAGAATGAAGCAGCATGAAAAGgtacgcttta ... attttggtagGTTCTTGAGGAAGGTGTCCTCAACCCAGAATCAACTGTCGTTGCAATCTTC

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: 147

GATGGGTTACAAAAATCCTGTTCTTCTGCTTCATCCATTGGGAGGATTCACAAAAGCAGATGATGTGCCTCTTAGTTGGAGAATGAAGCAGCATGAAAAGgtacgcttta ... attttggtagGTTCTTGAGGAAGGTGTCCTCAACCCAGAATCAACTGTCGTTGCAATCTTCCCCTCTCCAATGCATTATGCAGGGCCAACTGAAGTGCAATGGCATGCTA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acactactgtaaggcccaattcatgcacaattttgatgcgtgtttattttggtagGTTCTTGAGGAAGGTGTCCTCAACCCAGAATCAACTGTCGTTGCAATCTTCCCCTCTCCAATGCATTATGCAGGGCCAACTGAAGTGCAATGGCATGCTA
                              ttttgat  putative branch site (score: 147)
                                          tttatttt  putative PPT
                                        tgtttatttt  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacgctttaagagtagcaatcgtactgtcaaatctttttagcaaatgcatgttggtgccttgttgttgatgaaaccatttgatttaattacactactgtaaggcccaattcatgcacaattttgatgcgtgtttattttggtagGTTCTTGAGGAAGGTGTCCTCAACCCAGAATCAACTGTCGTTGCAATCTTCCCCTCTCCAATGCATTATGCAGGGCCAACTGAAGTGCAATGGCATGCTA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG