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

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttgtgttacatgattgccaatggaatgaaatgcacccttttttttttccagttctctgagcttcttttccatcttagtctcactgactaacttttgtcagGTGATAACAAAGTTTTGCTCTGAGAGGATTGCCAAATATGCTTTTGAGTATGCTTACCTTAACAACCGAAAGAAAGTCACAGCAGTGCATAAAGCAAACA

Basic information

species Oryza sativa
transcript LOC_Os04g40310.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os04g40310.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G025366_T02 (Zea mays), 3'ss of exon 1
ttgtgttacatgatt-gccaatggaatgaaatgcacccttttttttttccagttctctgagcttcttttccatc-ttagtctcactgactaacttttgtcagGTGATAACAAAGTTTTGCTCTGAGAGGATTGCCAAATATGCTTTTGAGTATGCTTACCTTAACAACCGAAAGAAAGTCACAGCAGTGCATAAAGCAAACA------------
         |  ||   |  ||  ||||   ||    | |||    |||   || ||||| | | | ||||||  ||| ||| ||||| |   |||    ||||||| ||||||||||||||||||||||||||||||||||| || ||||||||||||||||||||||||||||||||||| |||||||||||||||||||            
---------agaatccactcatttaatgtt-tgtgatcctttacagttc---ttatctgaacctttcttccattattactcttactgaatggatttc-ctaggtgatcacaaagTTTTGCTCTGAGAGGATTGCCAAATATGCATTCGAGTATGCTTACCTTAACAACCGAAAGAAAGTCACTGCAGTGCATAAAGCAAACATTATGAAGCTTG

upper sequence: LOC_Os04g40310.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G025366_T01 (Zea mays), 3'ss of exon 1
ttgtgttacatgattgccaatggaatgaaatgcacccttttttttttccagttct---ctgagcttcttttccatc-ttagtctcactgactaacttttgtcagGTGATAACAAAGTTTTGCTCTGAGAGGATTGCCAAATATGCTTTTGAGTATGCTTACCTTAACAACCGAAAGAAAGTCACAGCAGTGCATAAAGCAAACA
|  ||||  |  |    | |   | | ||         |  |  ||| |||||||   |||| | | | ||||||  ||| ||| ||||| |   |||    ||||||| ||||||||||||||||||||||||||||||||||| || ||||||||||||||||||||||||||||||||||| |||||||||||||||||||
tgttgttgaaatagaatccactcatttaa---tgtttgtgatcctttacagttcttatctgaacctttcttccattattactcttactgaatggatttc-ctagGTGATCACAAAGTTTTGCTCTGAGAGGATTGCCAAATATGCATTCGAGTATGCTTACCTTAACAACCGAAAGAAAGTCACTGCAGTGCATAAAGCAAACA

upper sequence: LOC_Os04g40310.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GLYMA11G08920.1 (Glycine max), 3'ss of exon 1
ttgtgttacatgattgccaatggaatgaaatgcacccttttttttttccagttctctgagct-tcttttccatcttagtctcactgactaa-cttttgtcagGTGATAACAAAGTTTTGCTCTGAGAGGATTGCCAAATATGCTTTTGAGTATGCTTACCTTAACAACCGAAAGAAAGTCACAGCAGTGCATAAAGCAAACA
 | | | |  | ||   ||||   ||  |   ||     ||             | ||| || |   ||  || || |   | |  ||||| ||||||  |||| ||||||||||| ||||| ||| | ||||| |||||||||||||||||||||||||| || ||| ||||||| || || || ||||| ||||||||||
ctttttcatctaatcttcaat--tatatatctcatgaagttagcgccttgacattgtgaactgtgagttttatgtttgcacctcatactaatcttttgctagGTAATAACAAAGTTCTGCTCAGAGCGCATTGCTAAATATGCTTTTGAGTATGCTTACCTAAATAACAGAAAGAAGGTGACTGCTGTGCACAAAGCAAACA

upper sequence: LOC_Os04g40310.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GLYMA16G22640.1 (Glycine max), 3'ss of exon 1
-ttgtgttacatgattgcca-atggaatgaaatg--cacccttttttttttccagttc--tctgagcttcttttccatcttagtctcactgactaacttttgtcagGTGATAACAAAGTTTTGCTCTGAGAGGATTGCCAAATATGCTTTTGAGTATGCTTACCTTAACAACCGAAAGAAAGTCACAGCAGTGCATAAAGCAAACA
  |||| |   ||||    | |||  ||||| |   || | |  |  | | |   | |  | || | || | ||   | ||  ||         |  ||||   |||| ||||| ||||| || || ||| | ||||| |||||||| || |||||||||||||| || ||| ||||||| || || || ||||| |||||||| |
catgtgatctttgatgcatatatgtcatgaagttatcaacttgatactgtcctgatgcagtgtgggtttatgttttctgttgatcct------catattttactagGTAATAACGAAGTTCTGTTCAGAGCGAATTGCTAAATATGCATTCGAGTATGCTTACCTGAATAACAGAAAGAAGGTGACTGCCGTGCACAAAGCAAATA

upper sequence: LOC_Os04g40310.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GLYMA02G04780.1 (Glycine max), 3'ss of exon 1
-ttgtgttacatgat-tgccaatggaatgaaa-tgcacccttttttttttccagttctctgagcttcttttccatcttagtctcactgactaacttttgtcagGTGATAACAAAGTTTTGCTCTGAGAGGATTGCCAAATATGCTTTTGAGTATGCTTACCTTAACAACCGAAAGAAAGTCACAGCAGTGCATAAAGCAAACA
  |||| |   |||| |    |||  |||||  |    ||||  |  | ||| | |     ||  |   ||     ||  | |   |    |  ||||   |||| |||||||||||||| || ||| | ||||| |||||||| || |||||||||||||| || ||| ||||||| || || || ||||| |||||||| |
catgtgatctttgatgtatatatgtcatgaaggtatcaccttgatactgtcctgatgc---agtatgggtttatgtttgctgttgatactcatattttactagGTAATAACAAAGTTTTGTTCAGAGCGAATTGCTAAATATGCATTCGAGTATGCTTACCTGAATAACAGAAAGAAGGTGACTGCCGTGCACAAAGCAAATA

upper sequence: LOC_Os04g40310.1 (Oryza sativa), 3'ss of exon 1
lower sequence: AT4G35260.1 (Arabidopsis thaliana), 3'ss of exon 1
--------------ttgtgttacatgattgccaatggaatgaaat-----gcacccttttttttttccagttctctgagcttcttttccatc-ttagtctcactgactaacttttgtcagGTGATAACAAAGTTTTGCTCTGAGAGGATTGCCAAATATGCTTTTGAGTATGCTTACCTTAACAACCGAAAGAAAGTCACAGCAGTGCATAAAGCAAACA
              || || | |  | ||   | |  |     ||     | | | | ||  ||| | |||  |||  |  | || |   |  ||  ||| |     |  || |  | ||||||| || ||||| || || ||| | ||||| || ||||||||||||||||| ||||| |||||| | |||||||| ||||| |||||||| || ||||
gtgagaattccgatttctgctcctcgttttggattcaatctgtatttgtggaatcatcttcgtttgcaagtggtctttgtatgttatgtgtgattgttctgatcctatttctatgcttagGTGATCACGAAGTTCTGTTCGGAGCGTATTGCAAAGTATGCTTTTGAGTATGCCTACCTGAACAACAGGAAGAAAGTTACAGCGGTGCATAAGGCTAACA

upper sequence: LOC_Os04g40310.1 (Oryza sativa), 3'ss of exon 1
lower sequence: AT2G17130.2 (Arabidopsis thaliana), 3'ss of exon 1
--------------------ttgtgttacatgattgccaatggaatgaaatgcacccttttttttttccagttctctgagcttct--tttccatctta--------gtctcactga--ctaac-ttttgtcagGTGATAACAAAGTTTTGCTCTGAGAGGATTGCCAAATATGCTTTTGAGTATGCTTACCTTAACAACCGAAAGAAAGTCACAGCAGTGCATAAAGCAAACA------------
                    |||  |    || || | ||||  ||   || ||   |  |||  |   || | |   || |     | | ||| |||         | || ||||  ||||  |||||  ||||||| |||||||| || || ||| | ||||| || ||||| ||||||||||| ||| | |||||| | |||||||| ||||||||||| || || || |            
gtgcaatttctcagtttttgttgattgttttggttacaaatgtgatttgattcatagtgatttggtagtagatgtgaaagttggagatgttcatgttatatcaaagatgtctctgatgctaatgttttggtaggtgattacaaagTTCTGTTCAGAGCGTATTGCAAAGTATGCGTTTGAGTATGCCTACTTGAACAACAGGAAGAAAGTTACAGCAGTGCACAAGGCTAATATCATGAAATTGG

upper sequence: LOC_Os04g40310.1 (Oryza sativa), 3'ss of exon 1
lower sequence: AT4G35650.1 (Arabidopsis thaliana), 3'ss of exon 1
ttgtgttacatgattgccaatggaatgaaatgcacccttttttttttccagttctctgagcttcttttccatcttagtctcactgactaacttttgtcagGTGATAACAAAGTTTTGCTCTGAGAGGATTGCCAAATATGCTTTTGAGTATGCTTACCTTAACAACCGAAAGAAAGTCACAGCAGTGCATAAAGCAAACA
             |   | ||  |     ||      | |||||  ||||  | | ||| |   |||     | |  | |   ||| |   || ||| ||||||||||||||||||| |||||||| || || | |||||| ||||||||||| || || |||||  | |||||||| || || || |||||||| ||||
------------gtaaaccatatataattatagggattgtttttagtccaaat-tgtgatcccttttgtatacatgatgttgttgaattgtttgtgt-agGTGATAACAAAGTTTTGTTCTGAGAGAATAGCGAGATATGCATTTGAGTATGCGTATCTAAACAATAGGAAGAAAGTGACTGCTGTTCATAAAGCTAACA

upper sequence: LOC_Os04g40310.1 (Oryza sativa), 3'ss of exon 1
lower sequence: AT2G17130.1 (Arabidopsis thaliana), 3'ss of exon 1
--------------------ttgtgttacatgattgccaatggaatgaaatgcacccttttttttttccagttctctgagcttct--tttccatctta--------gtctcactga--ctaac-ttttgtcagGTGATAACAAAGTTTTGCTCTGAGAGGATTGCCAAATATGCTTTTGAGTATGCTTACCTTAACAACCGAAAGAAAGTCACAGCAGTGCATAAAGCAAACA
                    |||  |    || || | ||||  ||   || ||   |  |||  |   || | |   || |     | | ||| |||         | || ||||  ||||  |||||  ||||||| |||||||| || || ||| | ||||| || ||||| ||||||||||| ||| | |||||| | |||||||| ||||||||||| || || || |
gtgcaatttctcagtttttgttgattgttttggttacaaatgtgatttgattcatagtgatttggtagtagatgtgaaagttggagatgttcatgttatatcaaagatgtctctgatgctaatgttttggtagGTGATTACAAAGTTCTGTTCAGAGCGTATTGCAAAGTATGCGTTTGAGTATGCCTACTTGAACAACAGGAAGAAAGTTACAGCAGTGCACAAGGCTAATA

upper sequence: LOC_Os04g40310.1 (Oryza sativa), 3'ss of exon 1
lower sequence: Vv03s0038g03120.t01 (Vitis vinifera), 3'ss of exon 1
------ttgtgttacatgattgccaatggaatgaaatgcacccttttttttttccagttctctgagcttcttttccatcttagtctcactgactaacttttgtcagGTGATAACAAAGTTTTGCTCTGAGAGGATTGCCAAATATGCTTTTGAGTATGCTTACCTTAACAACCGAAAGAAAGTCACAGCAGTGCATAAAGCAAACA
      | |  ||| |   ||     |  |      |  |   | || |||||||     | ||   || | |    |  |  ||   |||       ||||  ||||||| |||||||| ||||| ||  | ||||| |||||||| ||||||||| ||||||| ||||||||||||||||| ||||| ||||| ||||| ||||
tttagatagcattataaatttagtgtttaagatttttataaagtgttgtttttccgacagtatggaattgtgtctgtttctgatccagctg------ctttgctagGTGATTACAAAGTTCTGCTCCGAACGAATTGCAAAATATGCCTTTGAGTATTCTTACCTAAACAACCGAAAGAAAGTGACAGCTGTGCACAAAGCCAACA

upper sequence: LOC_Os04g40310.1 (Oryza sativa), 3'ss of exon 1
lower sequence: Vv04s0210g00180.t01 (Vitis vinifera), 3'ss of exon 1
ttgtgttacatgattgc-caatggaatgaaatgcacccttttttttttccagttctctg-agcttcttttccatcttagtctcactgactaacttttgtcagGTGATAACAAAGTTTTGCTCTGAGAGGATTGCCAAATATGCTTTTGAGTATGCTTACCTTAACAACCGAAAGAAAGTCACAGCAGTGCATAAAGCAAACA
    ||||| |   |   |  ||  |||   | ||     ||   | |   |   |    ||  | |  |   | |  | |||| |||    | ||||  |||| ||||||||||| || || ||| | ||||| |||||||||||||||||||| ||||| |||||| |||||||||| ||||| ||||| ||||||||||
-gaggttaccttcctattctttgctatgcttttcatgaacttgcatcttgggcattgcacagtctgtagtatgtttgtggctca-tgatgctcatttgctagGTAATAACAAAGTTCTGTTCAGAGCGCATTGCAAAATATGCTTTTGAGTATGCATACCTAAACAACAGAAAGAAAGTGACAGCTGTGCACAAAGCAAACA

upper sequence: LOC_Os04g40310.1 (Oryza sativa), 3'ss of exon 1
lower sequence: PP1S212_85V6.2 (Physcomitrella patens), 3'ss of exon 2
----------ttgtgttacatgattgccaatggaatgaaatgcacccttttttttttccagttctctgagcttcttttccatcttagtctcactgactaacttttgtcagGTGATAACAAAGTTTTGCTCTGAGAGGATTGCCAAATATGCTTTTGAGTATGCTTACCTTAACAACCGAAAGAAAGTCACAGCAGTGCATAAAGCAAACA
           | | || ||| ||  ||  | ||||||  |||    |  ||| |  |  ||| ||  |     | |  | |    | ||||| |  | |   || |||||||||||| || || ||||| ||| | ||||| || || || |||||||||||||| || |||||||| |||| ||| |||||||| ||||| || ||||
gcgactctatgtatattgcataat-acctgtcgaatgacctgc----tggtttctgccttgttgtcaaa-----tatgtcgtggatgcctcacagtgttaagcttttcagGTGATAACCAAATTCTGCTCCGAGCGAATTGCAAAGTACGCCTTTGAGTATGCTTATCTCAACAACCGTAAGACAGTAACAGCAGTACATAAGGCCAACA

upper sequence: LOC_Os04g40310.1 (Oryza sativa), 3'ss of exon 1
lower sequence: PP1S101_151V6.1 (Physcomitrella patens), 3'ss of exon 1
ttgtgttacatgattgccaatggaatg-aaatgcacccttttttttttccagttctctgagcttcttttccatcttagtctcactgactaacttttgtcagGTGATAACAAAGTTTTGCTCTGAGAGGATTGCCAAATATGCTTTTGAGTATGCTTACCTTAACAACCGAAAGAAAGTCACAGCAGTGCATAAAGCAAACA
 | |  | | | ||     ||| | ||   |   |  ||| | |  | |  | |  |||        |||  |    | || || |    |   |  |||||| || || ||||| ||||| ||| | ||||| ||||| || |||||||||||||| || |||||||| |||| ||| ||||||||||| || || ||||
atctcct-cgtcatgcttcatgcattgtggaaataatcttatctactgcgtggtacctgtcaaataattctgtaagtgccttacagtgccaagatgttcagGTAATCACCAAGTTCTGCTCGGAGCGCATTGCGAAATACGCCTTTGAGTATGCTTATCTCAACAACCGCAAGACAGTAACAGCAGTGCACAAGGCCAACA

upper sequence: LOC_Os04g40310.1 (Oryza sativa), 3'ss of exon 1
lower sequence: PP1S152_81V6.1 (Physcomitrella patens), 3'ss of exon 1
-------ttgtgttacatgattgccaatggaatgaaatgcacccttttttttttccagttctctgagcttcttttccatcttagtctcactgactaacttttgtcagGTGATAACAAAGTTTTGCTCTGAGAGGATTGCCAAATATGCTTTTGAGTATGCTTACCTTAACAACCGAAAGAAAGTCACAGCAGTGCATAAAGCAAACA
          ||| |      ||   |||     |  ||||   ||  |  || |||  ||| |||| ||  |     || || |    |  |  ||   |||||||||||| ||||| || ||||| ||| | || || |||||||||||||| ||||| || ||||||||||| ||||  || ||||||||||| || || ||||
caagagggcttgtcagtgtcatgtgtatgatcgtatctgcaggtttcctacttgcca--tctatgagattgatgagattcctaatggtgccaa--aa---ttgtcagGTGATTACAAAATTCTGCTCCGAGCGCATAGCAAAATATGCTTTTGAATATGCATATCTTAACAACCGCAAGACGGTTACAGCAGTGCACAAGGCGAACA

upper sequence: LOC_Os04g40310.1 (Oryza sativa), 3'ss of exon 1
lower sequence: EFJ13705 (Selaginella moellendorffii), 3'ss of exon 1
ttgtgttacatgattgccaatggaatgaaatgcacccttttttttttccagttctctgagcttcttttccatcttagtctcactgactaacttttgtcagGTGATAACAAAGTTTTGCTCTGAGAGGATTGCCAAATATGCTTTTGAGTATGCTTACCTTAACAACCGAAAGAAAGTCACAGCAGTGCATAAAGCAAACA
                               | || |   ||| ||  |    |||||   | ||   ||     ||   |  |   |         |||||||| || ||||||||||| ||  |||||||||| || || |||||||| || ||||| |||||| ||||||  || || || ||||| || || ||||
-------------------------------gtactccaatttcttctc----ctctgctttgctcggccgctccagctacgtttcttcttgcgcaccagGTGATCACGAAGTTTTGCTCCGAACGGATTGCCAAGTACGCGTTTGAGTACGCCTACCTGAACAACAGAAAGACGGTGACGGCGGTGCACAAGGCCAACA

upper sequence: LOC_Os04g40310.1 (Oryza sativa), 3'ss of exon 1
lower sequence: EFJ29002 (Selaginella moellendorffii), 3'ss of exon 1
ttgtgttacatgattgccaatggaatgaaatgcacccttttttttttccagttctctgagcttcttttccatcttagtctcactgactaacttttgtcagGTGATAACAAAGTTTTGCTCTGAGAGGATTGCCAAATATGCTTTTGAGTATGCTTACCTTAACAACCGAAAGAAAGTCACAGCAGTGCATAAAGCAAACA
                               | || |   ||| ||  |    |||||   | ||   ||     ||   |  |   |         |||||||| || ||||||||||| ||| |||||||||| || || |||||||| || ||||| |||||| ||||||  || || || ||||| || || ||||
-------------------------------gtactccaatttcttctc----ctctgctttgctcggccgctccagctacgtttcttcttgcgcaccagGTGATCACGAAGTTTTGCTCCGAGCGGATTGCCAAGTACGCGTTTGAGTACGCCTACCTGAACAACAGAAAGACGGTGACGGCGGTGCACAAGGCCAACA

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|29687051|gb|CB683326.1|CB683326
EST:     ACTCGGGGCTCGAGCACGAGGTCGTGCCCGGCGTCGTCGAGAG-C-C---                         ----T--C-AAGTTTTGCTCTGAGAGGATTGCCAAATATGCTTTTGAGTAT
genomic: ACTCGGGGCTCGAGCACGAGGTCGTGCCCGGCGTCGTCGAGAGCCTCAAGgtacgggcca ... cttttgtcagGTGATAACAAAGTTTTGCTCTGAGAGGATTGCCAAATATGCTTTTGAGTAT
EST: gi|29662276|gb|CB658551.1|CB658551
EST:     ACTCGGGGCTCGAGCACGAGGTCGTGCCCGGCGTCGTCGAGAGCCTCAAG                         GTGATAACAAAGTTTTGCTCTGAGAGGATTGCCAAATATGCTTTTGAGTAT
genomic: ACTCGGGGCTCGAGCACGAGGTCGTGCCCGGCGTCGTCGAGAGCCTCAAGgtacgggcca ... cttttgtcagGTGATAACAAAGTTTTGCTCTGAGAGGATTGCCAAATATGCTTTTGAGTAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttccagttctctgagcttcttttccatcttagtctcactgactaacttttgtcagGTGATAACAAAGTTTTGCTCTGAGAGGATTGCCAAATATGCTTTTGAGTATGCTTACCTTAACAACCGAAAGAAAGTCACAGCAGTGCATAAAGCAAACA
                                       gactaac  putative branch site (score: 1)
                                             cttttgtc  CT-rich tract
                                          taactttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttgtgttacatgattgccaatggaatgaaatgcacccttttttttttccagttctctgagcttcttttccatcttagtctcactgactaacttttgtcagGTGATAACAAAGTTTTGCTCTGAGAGGATTGCCAAATATGCTTTTGAGTATGCTTACCTTAACAACCGAAAGAAAGTCACAGCAGTGCATAAAGCAAACA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCAA
ttgtgtt
- - - - - tgattgc
- - - - - - - - - - tggaatg
- - - - - - - - - - - - - - aatgcac