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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gcatattagtatcagttggacatagttctgatgtttggtactataatataattttctatgattttcatccatcaataaatactatttttacctcttacagAATTGCAAAGGACCCTAGGTTCCAGAGATTAGCATGCACACACAAGGGAACTTATGCTGATGACTGTATCGTAGAGAGGGTTACTCAG

Basic information

species Oryza sativa
transcript LOC_Os06g06410.2
intron # 5
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 5
lower sequence: GRMZM2G016330_T01 (Zea mays), 3'ss of exon 6
gcatattagtatcagttggacatagttctgatgt--ttggtactataatataattttc--tatgattttcatccatcaata-aatactatttttacctcttacagAATTGCAAAGGACCCTAGGTTCCAGAGATTAGCATGCACACACAAGGGAACTTATGCTGATGACTGTATCGTAGAGAGGGTTACTCAG
      |   |  |    ||  | | |   ||||  ||| |  |||| |  | | |||   || | ||||||| |||   | |||   ||||    | || |||||||||| ||||||||||||||||| |||||||||||||||||||||||||| |||||||||||||| || || |||||||| ||||||
-----cttccactataaagatgtcgattgcatgtacttgctgttatactcaattcttcagcataactttcatctatctgcacaatctaatttacctccctcacagAATTGCCAAGGACCCTAGGTTCCAAAGATTAGCATGCACACACAAGGGAACCTATGCTGATGACTGCATTGTGGAGAGGGTCACTCAG

upper sequence: LOC_Os06g06410.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G017761_T01 (Zea mays), 3'ss of exon 5
---------------------------------------------------------------------------------------------------------------------gcatattagtatcagttggacatagttctgatgt--ttggtactataatataattttc--tatgattttcatccatcaata-aatactatttttacctcttacagAATTGCAAAGGACCCTAGGTTCCAGAGATTAGCATGCACACACAAGGGAACTTATGCTGATGACTGTATCGTAGAGAGGGTTACTCAG
                                                                                                                     |     |   |  |    ||  | | |   ||||  ||| |  |||| || | | |||   || | ||||||| |||   | |||   ||||    | || |||||||||| ||||||||||||||||| | |||||||||||||||||||||||| |||                                 
gtgtgctcctatccaatgctgttcccacattgtgttatttaatgtcttcttttggctttatctgcttcattgtatcaaatagaggttagattagtttttttatctatgcctcttgttgttatcttccactataaagatgtcgattgcatgtacttgctgttatactaaattcttcagCATAACTTTCATCTATCTGCACAATCTAATTTACCTCCCTCACAGAATTGCCAAGGACCCTAGGTTCCAAATATTAGCATGCACACACAAGGGAACCTAT---------------------------------

upper sequence: LOC_Os06g06410.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G174312_T01 (Zea mays), 3'ss of exon 5
gcatattagtatcagttggacatagttctgatgt--ttggtactataatataattttc--tatgattttcatccatcaata-aatactatttttacctcttacagAATTGCAAAGGACCCTAGGTTCCAGAGATTAGCATGCACACACAAGGGAACTTATGCTGATGACTGTATCGTAGAGAGGGTTACTCAG------------
      |   |  |    ||  | | |   ||||  ||| |  |||| |  | | |||   || | ||||||| |||   | |||   ||||    | || |||||||||| ||||||||||||||||| |||||||||||||||||||||||||| |||||||||||||| || || |||||||| ||||||            
-----cttccactataaagatgtcgattgcatgtacttgctgttatactcaattcttcagcataactttcatctatctgcacaatctaatttacctccctcacagAATTGCCAAGGACCCTAGGTTCCAAAGATTAGCATGCACACACAAGGGAACCTATGCTGATGACTGCATTGTGGAGAGGGTCACTCAGGTAAAAGCTCTC

upper sequence: LOC_Os06g06410.1 (Oryza sativa), 3'ss of exon 5
lower sequence: Vv15s0046g02690.t01 (Vitis vinifera), 3'ss of exon 5
gcatattagtatcagttggacatagttctgatgtttggtactataatat--aatttt-ctatgattttcatccatcaataaatactatttttacctctt--acagAATTGCAAAGGACCCTAGGTTCCAGAGATTAGCATGCACACACAAGGGAACTTATGCTGATGACTGTATCGTAGAGAGGGTTACTCAG
  | || | |||   ||   |  | ||       |||  ||  | ||||  | |||| | || |  |  |   || |       ||   | ||| |  |   ||| ||||||||||| ||| ||||  | ||||||   || || || |||||||||||||||||||||||||| || || || |||||||||
--agatgaatatttatt---cccaattgaagaaattgagacattgatatccagttttaccataaaatagaaagataagatgtctcttgatctactttcttggcagGATTGCAAAGGATCCTCGGTTTGAAAGATTACTCTGTACTCATAAGGGAACTTATGCTGATGACTGTATTGTTGATAGAGTTACTCAG

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|86483369|gb|CI126002.1|CI126002
EST:     GCTGGGACAAAAGTATCGTGTAGCATTGAG                         AATTGCAAAGGACCCTAGGTTCCAGAGATTAGCATGCACACACAAGGGAAC
genomic: GCTGGGACAAAAGTATCGTGTAGCATTGAGgtatgttcat ... cctcttacagAATTGCAAAGGACCCTAGGTTCCAGAGATTAGCATGCACACACAAGGGAAC
EST: gi|88251122|gb|CI349352.1|CI349352
EST:     GCTGGGACAAAAGTATCGTGTAGCATTGAG                         AATTGCAAAGGACCCTAGGTTCCAGAGATTAGCATGCACACACAAGGGAAC
genomic: GCTGGGACAAAAGTATCGTGTAGCATTGAGgtatgttcat ... cctcttacagAATTGCAAAGGACCCTAGGTTCCAGAGATTAGCATGCACACACAAGGGAAC
EST: gi|88970584|gb|CI385274.1|CI385274
EST:     AAGTATCGTGTAGCATTGAG                         AATTGCAAAGGACCCTAGGTTCCAGAGATTAGCATGCACACACAAGGGAAC
genomic: AAGTATCGTGTAGCATTGAGgtatgttcat ... cctcttacagAATTGCAAAGGACCCTAGGTTCCAGAGATTAGCATGCACACACAAGGGAAC
EST: gi|88847535|gb|CI016028.1|CI016028
EST:     TTGAAAAGCTGGGACAAAAGTATCGTGTAGCATTGAG                         AATTGCAAAGGACCCTAGGTTCCAGAGATTAGCATGCACACACAAGGGAAC
genomic: TTGAAAAGCTGGGACAAAAGTATCGTGTAGCATTGAGgtatgttcat ... cctcttacagAATTGCAAAGGACCCTAGGTTCCAGAGATTAGCATGCACACACAAGGGAAC
EST: gi|88846433|gb|CI373201.1|CI373201
EST:     AAGTATCGTGTAGCATTGAG                         AATTGCAAAGGACCCTAGGTTCCAGAGATTAGCATGCACACACAAGGGAAC
genomic: AAGTATCGTGTAGCATTGAGgtatgttcat ... cctcttacagAATTGCAAAGGACCCTAGGTTCCAGAGATTAGCATGCACACACAAGGGAAC
EST: gi|86502684|gb|CI145317.1|CI145317
EST:     GTTATGGCGGAGCTTGAAAAGCTGGGACAAAAGTATCGTGTAGCATTGAG                         AATTGCAAAGGACCCTAGGTTCCAGAGATTAGCATGCACACACCAAGGGAA
genomic: GTTATGGCGGAGCTTGAAAAGCTGGGACAAAAGTATCGTGTAGCATTGAGgtatgttcat ... cctcttacagAATTGCAAAGGACCCTAGGTTCCAGAGATTAGCATGCACACAC-AAGGGAA
EST: gi|87015953|gb|CI279705.1|CI279705
EST:     GTTATGGCGGAGCTTGAAAAGCTGGGACAAAAGTATCGTGTAGCATTGAG                         AATTGCAAAGGACCCTAGGTTCCAGAGATTAGCATGCACACACAAGGGAAC
genomic: GTTATGGCGGAGCTTGAAAAGCTGGGACAAAAGTATCGTGTAGCATTGAGgtatgttcat ... cctcttacagAATTGCAAAGGACCCTAGGTTCCAGAGATTAGCATGCACACACAAGGGAAC
EST: gi|86828506|gb|CI278611.1|CI278611
EST:     GTTATGGCGGAGCTTGAAAAGCTGGGACAAAAGTATCGTGTAGCATTGAG                         AATTGCAAAGGACCCTAGGTTCCAGAGATTAGCATGCACACACAAGGGAAC
genomic: GTTATGGCGGAGCTTGAAAAGCTGGGACAAAAGTATCGTGTAGCATTGAGgtatgttcat ... cctcttacagAATTGCAAAGGACCCTAGGTTCCAGAGATTAGCATGCACACACAAGGGAAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atataattttctatgattttcatccatcaataaatactatttttacctcttacagAATTGCAAAGGACCCTAGGTTCCAGAGATTAGCATGCACACACAAGGGAACTTATGCTGATGACTGTATCGTAGAGAGGGTTACTCAG
                                    ctatttttacctctt  CT-rich tract
                         atcaataaatactatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gcatattagtatcagttggacatagttctgatgtttggtactataatataattttctatgattttcatccatcaataaatactatttttacctcttacagAATTGCAAAGGACCCTAGGTTCCAGAGATTAGCATGCACACACAAGGGAACTTATGCTGATGACTGTATCGTAGAGAGGGTTACTCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGAGG