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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tataatatggaatggaacgagtagggtttaagctatcctttttagcatattttgaaatgcatacggctttgctgacaaagtctaccatcttgttatgaagGCACACCATGTATCACGGATTGTGTTATGGCGGAGCTTGAAAAGCTGGGACAAAAGTATCGTGTAGCATTGAG

Basic information

species Oryza sativa
transcript LOC_Os06g06410.2
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os06g06410.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G016330_T03 (Zea mays), 3'ss of exon 4
-tataatatggaatggaacgagtagggtttaagctatcctttttagcatattttgaaatgcatacggctttgctgacaaagtctaccatcttgttatgaagGCACACCATGTATCACGGATTGTGTTATGGCGGAGCTTGAAAAGCTGGGACAAAAGTATCGTGTAGCATTGAG
 ||     |  | |        | |  ||     |||| ||||| |   | |  || |  | |      |  ||    || |||     ||||||||||||| || |||||||||||||| ||||||||||| |||||||||||| |||| || ||||||||||| || |||||
gtaagcatttaactctgttatcttgcattcccattatc-tttttggtgaactgagatacccctttaatat--cttttcaactctgatgccttgttatgaagGTACCCCATGTATCACGGACTGTGTTATGGCTGAGCTTGAAAAGATGGGGCAGAAGTATCGTGTGGCCTTGAG

upper sequence: LOC_Os06g06410.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G017761_T01 (Zea mays), 3'ss of exon 4
-tataatatggaatggaacgagtagggtttaagctatcctttttagcatattttgaaatgcatacggctttgctgacaaagtctaccatcttgttatgaagGCACACCATGTATCACGGATTGTGTTATGGCGGAGCTTGAAAAGCTGGGACAAAAGTATCGTGTAGCATTGAG
 ||     |  | |        | |  ||     |||| ||||| |   | |  || |  | |      |  ||    || |||     ||||||||||||| || |||||||||||||| ||||||||||| ||||||||||||||||| || ||||||||||| || |||||
gtaagcatttaactctgttatcttgcattcccattatc-tttttggtgaactgagatacccctttaatat--cttttcaactctgatgccttgttatgaagGTACCCCATGTATCACGGACTGTGTTATGGCTGAGCTTGAAAAGCTGGGGCAGAAGTATCGTGTGGCCTTGAG

upper sequence: LOC_Os06g06410.1 (Oryza sativa), 3'ss of exon 4
lower sequence: AT2G46230.2 (Arabidopsis thaliana), 3'ss of exon 4
tataatatggaatggaacgagtagggtttaagctatcctttttagcatattttgaaatgcatacggctttgctgacaaagtctacca--tcttgttatgaagGCACACCATGTATCACGGATTGTGTTATGGCGGAGCTTGAAAAGCTGGGACAAAAGTATCGTGTAGCATTGAG
                       | |  | |  ||    ||||   |  | |  | | |    |    ||| | || |  | ||     |  || | ||||||||| || ||||||||||||||||| ||||| ||| | || ||| | || || ||||||||||||||  | ||
-----------------------gtgagttacttaaagattttgataggtctatataggttctctctcttgttaaccacctgtaattgtttctggtttgaagGCACTCCTTGTATCACGGATTGTGTCATGGCTGAGTTAGAGAAGTTAGGTCAGAAGTATCGTGTAGCTCTAAG

upper sequence: LOC_Os06g06410.1 (Oryza sativa), 3'ss of exon 4
lower sequence: Vv15s0046g02690.t01 (Vitis vinifera), 3'ss of exon 4
tataatatggaatggaacgagtagggtttaagctatcctttttagcatattttgaaatgcatacggctttgctgacaaagtctaccatcttgttatgaagGCACACCATGTATCACGGATTGTGTTATGGCGGAGCTTGAAAAGCTGGGACAAAAGTATCGTGTAGCATTGAG
|| | | |  |    | | |   |    ||   |    |  |  |  | || |   ||      | ||||| ||      |||| | | |  || | ||||||| || ||||||||||||||||| ||||| |||||||| ||| | || || || || || || ||  ||||
taaattttttatcttatcaatctgaaagtatttttatgtgatgggattcttatattattttgttgtctttgttgcttccttctatcttttaattttaaagGCACTCCTTGTATCACGGATTGTGTGATGGCAGAGCTTGAGAAGTTAGGTCAGAAATACCGCGTGGCTCTGAG

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|86502684|gb|CI145317.1|CI145317
EST:     TTGGATTTGGAGAAAGGAATGATGGACTGCCTTTATGCAAAAT                         GCACACCATGTATCACGGATTGTGTTATGGCGGAGCTTGAAAAGCTGGGAC
genomic: TTGGATTTGGAGAAAGGAATGATGGACTGCCTTTATGCAAAATgtaagcatgc ... tgttatgaagGCACACCATGTATCACGGATTGTGTTATGGCGGAGCTTGAAAAGCTGGGAC
EST: gi|86828506|gb|CI278611.1|CI278611
EST:     TTGGATTTGGAGAAAGGAATGATGGACTGCCTTTATGCAAAAT                         GCACACCATGTATCACGGATTGTGTTATGGCGGAGCTTGAAAAGCTGGGAC
genomic: TTGGATTTGGAGAAAGGAATGATGGACTGCCTTTATGCAAAATgtaagcatgc ... tgttatgaagGCACACCATGTATCACGGATTGTGTTATGGCGGAGCTTGAAAAGCTGGGAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

catattttgaaatgcatacggctttgctgacaaagtctaccatcttgttatgaagGCACACCATGTATCACGGATTGTGTTATGGCGGAGCTTGAAAAGCTGGGACAAAAGTATCGTGTAGCATTGAG
                        tgctgac  putative branch site (score: 2)
                                       ccatctt  putative PPT
     tttgaaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tataatatggaatggaacgagtagggtttaagctatcctttttagcatattttgaaatgcatacggctttgctgacaaagtctaccatcttgttatgaagGCACACCATGTATCACGGATTGTGTTATGGCGGAGCTTGAAAAGCTGGGACAAAAGTATCGTGTAGCATTGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCTG