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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaattgatgagtcatccgttgagaccatatgcaacctgatctgttgaagcatacatttcagtgattgtctgcatgttttgatcttgcagGTTGACACTACCATACTTGGCCTTGATACTGAGAGGGCAAAGGAATTGCCTTACATTGCTAGTATGGGAATCTATGTTTTTAGCAAAGATGTGATGCTTA

Basic information

species Oryza sativa
transcript LOC_Os09g12660.2
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os09g12660.2 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G106213_T02 (Zea mays), 3'ss of exon 3
----gtaattgatgagtcatccg--ttgagaccatatgcaacctgatctgttgaagca-----------tacattt---cagtgattgtctgcatgttttgatcttgcagGTTGACACTACCATACTTGGCCTTGATACTGAGAGGGCAAAGGAATTGCCTTACATTGCTAGTATGGGAATCTATGTTTTTAGCAAAGATGTGATGCTTA
      |  |||| |    |  |     ||  | ||||   |||||| ||||  |||            | |||||   |||| |   | ||| ||||||    || ||||| ||||| || ||| | ||||||||| |||| ||||| || ||| ||||||| ||||||||||||||||||||||||||||||||||||||||||||| 
gtacaaatgtgataaactttttgaccctagttcttatgtctcctgat-tgttagagctccttttgcgattgcattttttcagttaagttttgcttgttttaccttttcagGTAGACACCACTATATTGGGCCTTGATCCTGAAAGGGCCAAAGAACTGCCTTATATTGCTAGTATGGGAATCTATGTTTTTAGCAAAGATGTGATGCTTC

upper sequence: LOC_Os09g12660.2 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA02G47460.1 (Glycine max), 3'ss of exon 3
gtaattgatgagtc-atccgttgag-accatatgcaacctgatctgttgaagcatacatttcagtgattgtctgcatgttttgatcttgcagGTTGACACTACCATACTTGGCCTTGATACTGAGAGGGCAAAGGAATTGCCTTACATTGCTAGTATGGGAATCTATGTTTTTAGCAAAGATGTGATGCTTA
        | || | ||       | |  |||||        | | | |||      |  | ||  ||||  |  |  |     |     ||||||| ||||| ||  | || ||||||   ||||| ||||||||||||||||| |||||||| ||||| || |||||| |||||||| | |||||| |  
-------gtaagcccatataacatgtattatatgttgttatttatctggaaattattacctgagcaattgcttaaaaatgccact-----agGTTGATACTACAATTTTGGGTCTTGATGACGAGAGAGCAAAGGAATTGCCTTATATTGCTAGCATGGGTATATATGTTGTTAGCAAAAACGTGATGTTAG

upper sequence: LOC_Os09g12660.2 (Oryza sativa), 3'ss of exon 3
lower sequence: Vv12s0057g01480.t01 (Vitis vinifera), 3'ss of exon 3
-----------------------------gtaattgatgagtc---atccgttgagaccata----tgcaacct--gatctgttgaagcatacatttcagtgattgtctgcatgttttgatcttgcagGTTGACACTACCATACTTGGCCTTGATACTGAGAGGGCAAAGGAATTGCCTTACATTGCTAGTATGGGAATCTATGTTTTTAGCAAAGATGTGATGCTTA
                              ||||| |||  |     | | |  |  | | |    || |   |   |  || | ||| |  |   |  ||  |  | |      | |    ||  |||| || |||||||| || || ||||||  |||||| || || ||| |||||||||||||||||||||| || |||||  | ||||||||||||||| |  
gtagatgatatttgaaataaacattcgtattaatttatgcttttgtgttcctctattctacaattttgtagttttaaagttggttaagaaggctgatacgttttcctttctgaactgttccttttaagGTCGATACTACCATCCTGGGTCTTGATGATGAGAGAGCTAAAGAAATGCCTTACATTGCTAGTATGGGTATATATGTCGTCAGCAAAGATGTGATGTTAG

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|86517463|gb|CI157669.1|CI157669
EST:     TCATTGAATTTGCAGAAAAGCCAAAAGGAGAGAAGTTGAAATCAATGATG                         GTTGACACTACCATACTTGGCCTTGATACTGAGAGGGCAAAGGAATTGCCT
genomic: TCATTGAATTTGCAGAAAAGCCAAAAGGAGAGAAGTTGAAATCAATGATGgtaattgatg ... gatcttgcagGTTGACACTACCATACTTGGCCTTGATACTGAGAGGGCAAAGGAATTGCCT
EST: gi|86520775|gb|CI160981.1|CI160981
EST:     CCAAAAGGAGAGAAGTTGAAATCAATGATG                         GTTGACACTACCATACTTGGCCTTGATACTGAGAGGGCAAAGGAATTGCCT
genomic: CCAAAAGGAGAGAAGTTGAAATCAATGATGgtaattgatg ... gatcttgcagGTTGACACTACCATACTTGGCCTTGATACTGAGAGGGCAAAGGAATTGCCT
EST: gi|58674587|gb|CK063274.1|CK063274
EST:     TCATTGAATTTGCAGAAAAGCCAAAAGGAGAGAAGTTGAAATCAATGATG                         GTTGACACTACCATACTTGGCCTTGATACTGAGAGGGCAAAGGAATTGCCT
genomic: TCATTGAATTTGCAGAAAAGCCAAAAGGAGAGAAGTTGAAATCAATGATGgtaattgatg ... gatcttgcagGTTGACACTACCATACTTGGCCTTGATACTGAGAGGGCAAAGGAATTGCCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cctgatctgttgaagcatacatttcagtgattgtctgcatgttttgatcttgcagGTTGACACTACCATACTTGGCCTTGATACTGAGAGGGCAAAGGAATTGCCTTACATTGCTAGTATGGGAATCTATGTTTTTAGCAAAGATGTGATGCTTA
                                         ttttgat  putative branch site (score: 4)
                atacattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaattgatgagtcatccgttgagaccatatgcaacctgatctgttgaagcatacatttcagtgattgtctgcatgttttgatcttgcagGTTGACACTACCATACTTGGCCTTGATACTGAGAGGGCAAAGGAATTGCCTTACATTGCTAGTATGGGAATCTATGTTTTTAGCAAAGATGTGATGCTTA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGATG