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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atgttatgggcatgcttccagcactttaaactcatgtcttgttctatattttgatttcatgatgcactacataagttttgacttgctttatgacttttagATATGGAGTTTCTGGCTATCCTACATTGAAGTTCTTCCCAAAGGGAAACAAAGCTGGTGAAGATTACGATGGCGGCAGGGAGTTGGATGACTTTGTCAAG

Basic information

species Oryza sativa
transcript LOC_Os01g23740.2
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g23740.2 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G128171_T04 (Zea mays), 3'ss of exon 6
----------------------------------------------------------------------------------atgttatgggcatgcttccagcactttaaactcatgtcttgttcta--------tattttgat-ttcatgatgcactacataagttttgacttgc-tttatgacttt----tagATATGGAGTTTCTGGCTATCCTACATTGAAGTTCTTCCCAAAGGGAAACAAAGCTGGTGAAGATTACGATGGCGGCAGGGAGTTGGATGACTTTGTCAAG
                                                                                  ||| | | |     |||  |  |||    |||  | | |  ||  |         |  ||  | ||  |||     |  ||| |   |    ||   |||| ||  |     || |||||||||  ||| | |||||| |||||||| |||||||||||||||||||||||||||||||| |||||||  ||||| |||| |||||||||||||
gtatgttctgtgtcttacattcacatatgctttatctgcatctgtttccctatttgtgttacctagcagctagcactggagcatgatcttgtttccctttgaatactagtcactagtatttgtttgcaacaaataacaccttattatttctgacttgttctatacgcaatatactgtacttatcacactacatcagGTATGGAGTTAGTGGATTTCCTACCTTGAAGTTTTTCCCAAAGGGAAACAAAGCTGGTGAAGATTATGATGGCGATAGGGACTTGGTTGACTTTGTCAAG

upper sequence: LOC_Os01g23740.2 (Oryza sativa), 3'ss of exon 7
lower sequence: GLYMA02G01750.3 (Glycine max), 3'ss of exon 7
atgttatgggcatgcttccagcactttaaactcat-gtcttgttctatattttgatttcatgatgcactacataagttttgacttgctttatgacttt-tagATATGGAGTTTCTGGCTATCCTACATTGAAGTTCTTCCCAAAGGGAAACAAAGCTGGTGAAGATTACGATGGCGGCAGGGAGTTGGATGACTTTGTCAAG
 |    |||  | |    ||  |  |  | |  |  |  |     |  | | | |   ||||||  |  |   ||||||   || |  | ||   | |  || ||||  ||   ||| | |||||| |||||||||||||||||||| ||||||||||||||||| ||||  || || || || ||||||||||||||    
ttacggtggttaagaaaacaaaaaatccagcgaagaggataaagatggaatattacaacatgataaataattgaagttt--gctggaataatatttatgcagGTATGATGTGAGTGGATTTCCTACCTTGAAGTTCTTCCCAAAGGGCAACAAAGCTGGTGAAGAGTACGGAGGTGGAAGAGACTTGGATGACTTTGTGGCT

upper sequence: LOC_Os01g23740.2 (Oryza sativa), 3'ss of exon 7
lower sequence: GLYMA10G01820.1 (Glycine max), 3'ss of exon 8
---atgttatgggcatgcttccagcactttaaactcatgtcttgttctatattttgatttcatgatgcactacataagttttgacttgctttatgacttt-tagATATGGAGTTTCTGGCTATCCTACATTGAAGTTCTTCCCAAAGGGAAACAAAGCTGGTGAAGATTACGATGGCGGCAGGGAGTTGGATGACTTTGTCAAG
      |  | | | | ||| ||      |||  | |||   | | | | ||  | |   ||||||  |  |   ||||||   || |  | ||   | |  || || |  ||   ||| | |||||| |||||||||||||||||||| ||||||||||||||||| ||||  || || || || ||||||||||||||    
tattcatagttgtcttcctttcaa-gtcataatgtgatggaatatacga-atcgttacaacatgataaataattgaagttt--gctggaataatatttatgcagGTACGACGTGAGTGGATTTCCTACCTTGAAGTTCTTCCCAAAGGGCAACAAAGCTGGTGAAGACTACGGAGGTGGAAGAGACTTGGATGACTTTGTGGCT

upper sequence: LOC_Os01g23740.2 (Oryza sativa), 3'ss of exon 7
lower sequence: GLYMA03G39130.1 (Glycine max), 3'ss of exon 7
atgt-tatgggcatgcttccagc-actttaaactcatgtcttgttctatattttgatttcatgatgcac-tacataagttttgacttgctttatgacttttagATATGGAGTTTCTGGCTATCCTACATTGAAGTTCTTCCCAAAGGGAAACAAAGCTGGTGAAGATTACGATGGCGGCAGGGAGTTGGATGACTTTGTCAAG
 ||  ||  |  |   ||  |   |  ||  | | |   || | |  ||||  |  ||     |||||  | | ||| ||   |  |  |  |  ||    |||||||| |||  ||||||||||||| ||||||| ||||||||| | ||||||||||||||||||||  |||| ||| | || |||||||| |||||    
gtgagtacagtgacattttgatttatcttctattta-aactaggtggatatcatatttaagaaatgcatgtgcctaatttagaaaattttccaatac----agATATGGTGTTAGTGGCTATCCTACACTGAAGTTTTTCCCAAAGAGCAACAAAGCTGGTGAAGATTATAATGGTGGCCGTGATTTGGATGATTTTGTAGCA

upper sequence: LOC_Os01g23740.2 (Oryza sativa), 3'ss of exon 7
lower sequence: GLYMA19G41690.1 (Glycine max), 3'ss of exon 7
atgttatgggcatgcttccagcactttaaactcatgtcttgttcta-tattttgatttcatgat---gcactacataagttttgacttgctttatgact--tttagATATGGAGTTTCTGGCTATCCTACATTGAAGTTCTTCCCAAAGGGAAACAAAGCTGGTGAAGATTACGATGGCGGCAGGGAGTTGGATGACTTTGTCAAG
      || | |   |  ||  | ||| |  |    ||| |||  | ||  ||| | ||||  |   | | | |||  |  |    | |     |  |   |  |||||||| |||  ||||||||||||| ||||||| ||||||||| | ||||||||||||||| |||| || || ||| | || |||||||| |||||    
-----gtgagtacagtggca-tattttgatttatcttctagttaaactaggttggtatcatatttaagaaatgcatgtgcctaatttagaaaatttgccaatacagATATGGTGTTAGTGGCTATCCTACACTGAAGTTTTTCCCAAAGAGCAACAAAGCTGGTGAAAATTATGACGGTGGCCGTGATTTGGATGATTTTGTAGCA

upper sequence: LOC_Os01g23740.2 (Oryza sativa), 3'ss of exon 7
lower sequence: GLYMA06G24520.1 (Glycine max), 3'ss of exon 9
atgttatgggcatgcttccagcactttaaactcat-gtcttgttctatattttgatttcatgatgcactacataagttttgacttgctttatgacttt-tagATATGGAGTTTCTGGCTATCCTACATTGAAGTTCTTCCCAAAGGGAAACAAAGCTGGTGAAGATTACGATGGCGGCAGGGAGTTGGATGACTTTGTCAAG
 |    |||  | |    ||  |  |  | |  |  |  |     |  | | | |   ||||||  |  |   ||||||   || |  | ||   | |  || ||||  ||   ||| | |||||| |||||||||||||||||||| ||||||||||||||||| ||||  || || || || ||||||||||||||    
ttacggtggttaagaaaacaaaaaatccagcgaagaggataaagatggaatattacaacatgataaataattgaagttt--gctagaataatatttatgcagGTATGATGTGAGTGGATTTCCTACCTTGAAGTTCTTCCCAAAGGGCAACAAAGCTGGTGAAGAGTACGGAGGTGGAAGAGACTTGGATGACTTTGTGGCT

upper sequence: LOC_Os01g23740.2 (Oryza sativa), 3'ss of exon 7
lower sequence: AT2G47470.3 (Arabidopsis thaliana), 3'ss of exon 7
atgttatgggcatgc-ttccagcactttaaactcatgtcttgttctatattttgatttcatgatgc-actacataagttttgacttgctttatgacttttagATATGGAGTTTCTGGCTATCCTACATTGAAGTTCTTCCCAAAGGGAAACAAAGCTGGTGAAGATTACGATGGCGGCAGGGAGTTGGATGACTTTGTCAAG
 |    ||| || || ||  |  | |    | |    | ||       ||||   |||||| |  | |  ||||||         | | ||||    || |||||||||||   ||| |  || |||||||| |||||||||||||  |||||||||||| | ||||| || || |||||||| || ||||||||||| |  
gtaagttggacaggcattttattaataccgattttactgtttaaagtcatttatgtttcataaaaccaaaacataaagacaag--taccttata---ttcagATATGGAGTGAGTGGATTCCCAACATTGAAATTCTTCCCAAAGGACAACAAAGCTGGTCACGATTATGACGGTGGCAGGGATTTAGATGACTTTGTAAGC

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|58666550|gb|CK055236.1|CK055236
EST:     GTTGTAATTGCTAACCTTGATGCTGACAAACACAAAGACTTGGCCGAAAA                         ATATGGAGTTTCTGGCTATCCTACATTGAAGTTCTTCCCAAAGGGAAACAA
genomic: GTTGTAATTGCTAACCTTGATGCTGACAAACACAAAGACTTGGCCGAAAAgtatgttctg ... tgacttttagATATGGAGTTTCTGGCTATCCTACATTGAAGTTCTTCCCAAAGGGAAACAA






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atattttgatttcatgatgcactacataagttttgacttgctttatgacttttagATATGGAGTTTCTGGCTATCCTACATTGAAGTTCTTCCCAAAGGGAAACAAAGCTGGTGAAGATTACGATGGCGGCAGGGAGTTGGATGACTTTGTCAAG
                              ttttgac  putative branch site (score: 3)
                                                ctttt  putative PPT
                         ataagtttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atgttatgggcatgcttccagcactttaaactcatgtcttgttctatattttgatttcatgatgcactacataagttttgacttgctttatgacttttagATATGGAGTTTCTGGCTATCCTACATTGAAGTTCTTCCCAAAGGGAAACAAAGCTGGTGAAGATTACGATGGCGGCAGGGAGTTGGATGACTTTGTCAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
-tgttatg
- - - - ggcatgc
- - - - - - - - -ccagcac
- - - - - - - - - - - - - - - - - tgtcttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgatgca