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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtattgatttgtgttttttttccttctctggttctccatattcatggtatcatctgactcccaaatggttcactgtccttccccaagTGTAAAGCAGGTTAGCTTTTATGATGATGATGTTCGCTTTTGGCAACATTGGCGCAATTGCTCTGCTGCTGCTGAGGCTCCAACTGCGGTCAATCAACAA

Basic information

species Oryza sativa
transcript LOC_Os01g46510.2
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g46510.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G000177_T01 (Zea mays), 3'ss of exon 3
---------------------------------------------gtattgatt--tgtgttttttttccttctctggttctccatattcatggta---tcatctgactcccaaatggttcactgtccttccccaagTGTAAAGCAGGTTAGCTTTTATGATGATGATGTTCGCTTTTGGCAACATTGGCGCAATTGCTCTGCTGCTGCTGAGGCTCCAACTGCGGTCAATCAACAA
                                             |  || | |  | |||| || ||  |  |   | |   ||| | |||  ||   ||| ||||||||| |  |||  ||||| |||| ||||||||||||||||||  ||||||||||||||||||||||||||||||||||||||||||||| ||||||||||||||||| |||||||| |||||||| |||
gtatgtcccttaattatgatgatcatgctaccctaacttgcttgggacttaaatgctttgttgttattgttaattatgatgatcatgtgcatattaccttcacctgactcccgatgggtctactgttcttctccaagTGTAAAGCAGGTTTCCTTTTATGATGATGATGTTCGCTTTTGGCAACATTGGCGCAATTGTTCTGCTGCTGCTGAGGCCCCAACTGCAGTCAATCAGCAA

upper sequence: LOC_Os01g46510.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA19G41130.1 (Glycine max), 3'ss of exon 3
-------gtatt-gatttgtgttttttttccttctctggttctccatattcatggtatcatctgactcccaaatggttcactgtccttccccaagTGTAAAGCAGGTTAGCTTTTATGATGATGATGTTCGCTTTTGGCAACATTGGCGCAATTGCTCTGCTGCTGCTGAGGCTCCAACTGCGGTCAATCAACAA
       |  || | |||||| |||| |  ||| |   |   |  || || ||||| |||| |   | |||   |  ||  |      |   |||||| |||||||| |  ||||||||||||||||| ||||||||||||| |||||  ||| ||||||  |||||||| |||||||| || ||| ||     |
gtaatatgcgtttgctttgtgattttatatctttttctggcttttat-tttatggt-tcatttacttacca--cgactcgttactggccttaaagTGTTAAGCAGGTGAATTTTTATGATGATGATGTACGCTTTTGGCAACTTTGGCATAATCGCTCTGTGGCTGCTGAAGCTCCAACAGCTGTCCATACTTCA

upper sequence: LOC_Os01g46510.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA03G38530.1 (Glycine max), 3'ss of exon 3
-------gtatt-gatttgtgttttttttccttctctggttctccatattcatggtatcatctgactcccaaatggttcactgtccttccccaagTGTAAAGCAGGTTAGCTTTTATGATGATGATGTTCGCTTTTGGCAACATTGGCGCAATTGCTCTGCTGCTGCTGAGGCTCCAACTGCGGTCAATCAACAA
       || || | |||||| |||| |  ||| |   |   |  || || ||||| |||| |   | |||  ||  ||  |  |   |   |||||| |||||||| |  ||||||||||||||||| ||||||||||||| |||||  ||  ||||||| ||||||||||||||||| || ||| ||     |
gtaatatgtgtttgctttgtgattttatatctttttccggcttttat-tttatggt-tcatttacttacca--tgactctttaccggccttaaagTGTCAAGCAGGTGAATTTTTATGATGATGATGTACGCTTTTGGCAACTTTGGCATAACCGCTCTGCCGCTGCTGAGGCTCCAACAGCTGTCCATACTTCA

upper sequence: LOC_Os01g46510.1 (Oryza sativa), 3'ss of exon 3
lower sequence: Vv08s0056g00040.t01 (Vitis vinifera), 3'ss of exon 4
---------gtattgatttgtgttttttt-tccttctctggttctccatattcat--ggtatcatctgactcccaaatggttcactgtccttccccaagTGTAAAGCAGGTTAGCTTTTATGATGATGATGTTCGCTTTTGGCAACATTGGCGCAATTGCTCTGCTGCTGCTGAGGCTCCAACTGCGGTCAATCAACAA
          | |  |  ||  ||||  | | ||| |||  |||||    ||| |  |||   | |||        ||||  ||      | |   ||| || ||||||||   |||||||||||||||||| ||||||||||||| |||||||||  | ||||| |||||||| |||||  | || || |||||    
gtaattgatatgtatacctgccttttcatattcttttctacttctctggtttcctaaggtgaaacctggactgactatggggcatatgtttccttgaagCGTTAAGCAGGTGGACTTTTATGATGATGATGTACGCTTTTGGCAACTTTGGCGCAACCGATCTGCAGCTGCTGAAGCTCCCTCAGCTGTTAATCATGTT

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|88301497|gb|CI597190.1|CI597190
EST:     ATTCAAAAGGAAGGCCCACTGAAGCCATCCGAGGTGGAAG                         TGTAAAGCAGGTTAGCTTTTATGATGATGATGTT-GCTTTTGGCACCATTG
genomic: ATTCAAAAGGAAAGCCCACTGAAGCCATCCGAGGTGGAAGgtattgattt ... cttccccaagTGTAAAGCAGGTTAGCTTTTATGATGATGATGTTCGCTTTTGGCAACATTG
EST: gi|88315291|gb|CI613560.1|CI613560
EST:     ATTCAAAAGGAAAGCCCACTGAAGCCATCCGAGGTGGAAG                         TGTAAAGCAGGTTAGCTTTTATG
genomic: ATTCAAAAGGAAAGCCCACTGAAGCCATCCGAGGTGGAAGgtattgattt ... cttccccaagTGTAAAGCAGGTTAGCTTTTATG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tctccatattcatggtatcatctgactcccaaatggttcactgtccttccccaagTGTAAAGCAGGTTAGCTTTTATGATGATGATGTTCGCTTTTGGCAACATTGGCGCAATTGCTCTGCTGCTGCTGAGGCTCCAACTGCGGTCAATCAACAA
                   atctgac  putative branch site (score: 3)
                                    ttcactgtccttcccc  putative PPT
     atattcat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtattgatttgtgttttttttccttctctggttctccatattcatggtatcatctgactcccaaatggttcactgtccttccccaagTGTAAAGCAGGTTAGCTTTTATGATGATGATGTTCGCTTTTGGCAACATTGGCGCAATTGCTCTGCTGCTGCTGAGGCTCCAACTGCGGTCAATCAACAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT