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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tttctccttaaggagattatgtgctgacttacaaattaagattctgaactttatccatccacatgtatgtttatttttcttacaaatggcactttatcagACCTGATGGGCAGCCATGTGTCGAGGCTCAAGAGTTTGGATTGATCCGGAACATGCTCATTGCAGCTGTTGAAGAGAGATACAAAGATGCTG

Basic information

species Oryza sativa
transcript LOC_Os08g26870.3
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os08g26870.3 (Oryza sativa), 3'ss of exon 8
lower sequence: GRMZM2G006468_T04 (Zea mays), 3'ss of exon 8
---tttctccttaaggagattatgtgctgacttacaaattaagattctgaacttta-tccatccacatgtatgtttatttttcttacaaatggcactttatcagACCTGATGGGCAGCCATGTGTCGAGGCTCAAGAGTTTGGATTGATCCGGAACATGCTCATTGCAGCTGTTGAAGAGAGATACAAAGATGCTG
     | || |  |   || ||| | |||   | ||  ||||||| | |||||  | |  ||  |  |||||||| |||||| |||||  ||    ||| | ||||| ||||| ||| ||| ||| ||||||||||||||||||||| |   |||||||||||||||||| || |||||||||||||| |||||||
actggtttcgtacattcgagtatattctg---tgcat-ttaagatccagaactccaatatatgaatctgtatgttaatttttgttacacttgcatttttgttagACCCGATGGACAGGCATCTGTTGAGGCTCAAGAGTTTGGATTGGTGAAGAACATGCTCATTGCAGCCGTAGAAGAGAGATACAAGGATGCTG

upper sequence: LOC_Os08g26870.3 (Oryza sativa), 3'ss of exon 8
lower sequence: GRMZM2G053531_T02 (Zea mays), 3'ss of exon 8
-------------------------------------------------------tttctccttaaggagattatgtgctgacttacaaattaagattctgaactttatc-catccacatgtatgtt-tatttttcttacaaatggcactttatcagACCTGATGGGCAGCCATGTGTCGAGGCTCAAGAGTTTGGATTGATCCGGAACATGCTCATTGCAGCTGTTGAAGAGAGATACAAAGATGCTG
                                                       ||| |  || |   |         |  |||      ||| |         || |   ||  |  | |||||| | |||||||||||  || || ||| | ||||||||||| ||||||||||| |||||||||||||||||| || |  |||||||||||||||||||| | |||||||||||||| |||||||
gtattctagaaggcgaataagaattatacaatggttgtaggatttcttttaaatattttttgttgatctgcccccaactttgcttggggtctaaaagaagctttgttgttatatgaatctatatgttatttttttcttacacttg-catttttttagACCTGATGGACAGCCATGTGTGGAGGCTCAAGAGTTTGGACTGGTGAGGAACATGCTCATTGCAGCTATCGAAGAGAGATACAAGGATGCTG
















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|86436048|gb|CI107281.1|CI107281
EST:     GCGATAGCAGCCGGCATGTCTGACGGGTTGTTGTTTACAGAACTTGACAG                         ACCTGATGGGCAGCCATGTGTCGAGGCTCAAGAGTTTGGATTGATCCGGAA
genomic: GCGATAGCAGCCGGCATGTCTGACGGGTTGTTGTTTACAGAACTTGACAGgtattgttat ... actttatcagACCTGATGGGCAGCCATGTGTCGAGGCTCAAGAGTTTGGATTGATCCGGAA
EST: gi|109974602|gb|DT806998.1|DT806998
EST:     GCGATAGCAGCCGGCATGTCTGACGGGTTGTTGTTTACAGAACTTGACAG                         ACCTGATGGGCAGCCATGTGTCGAGGCTCAAGAGTTTGGATTGATCCGGAA
genomic: GCGATAGCAGCCGGCATGTCTGACGGGTTGTTGTTTACAGAACTTGACAGgtattgttat ... actttatcagACCTGATGGGCAGCCATGTGTCGAGGCTCAAGAGTTTGGATTGATCCGGAA
EST: gi|84117164|gb|CD150931.1|CD150931
EST:     GCGATAGCAGCCGGCATGTCTGACGGGTTGTTGTTTACAGAACTTGACAG                         ACCTGATGGGCAGCCATGTGTCGAGGCTCAAGAGTTTGGATTGATCCGGAA
genomic: GCGATAGCAGCCGGCATGTCTGACGGGTTGTTGTTTACAGAACTTGACAGgtattgttat ... actttatcagACCTGATGGGCAGCCATGTGTCGAGGCTCAAGAGTTTGGATTGATCCGGAA
EST: gi|29629366|gb|CB634377.1|CB634377
EST:     GCGATAGCAGCCGGCATGTCTGACGGGTTGTTGTTTACAGAACTTGACAG                         ACCTGATGGGCAGCCATGTGTCGAGGCTCAAGAGTTTGGATTGATC
genomic: GCGATAGCAGCCGGCATGTCTGACGGGTTGTTGTTTACAGAACTTGACAGgtattgttat ... actttatcagACCTGATGGGCAGCCATGTGTCGAGGCTCAAGAGTTTGGATTGATC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gaactttatccatccacatgtatgtttatttttcttacaaatggcactttatcagACCTGATGGGCAGCCATGTGTCGAGGCTCAAGAGTTTGGATTGATCCGGAACATGCTCATTGCAGCTGTTGAAGAGAGATACAAAGATGCTG
                               ttcttac  putative branch site (score: 2)
                                              ctttatc  putative PPT
                    tatgtttatttttctt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tttctccttaaggagattatgtgctgacttacaaattaagattctgaactttatccatccacatgtatgtttatttttcttacaaatggcactttatcagACCTGATGGGCAGCCATGTGTCGAGGCTCAAGAGTTTGGATTGATCCGGAACATGCTCATTGCAGCTGTTGAAGAGAGATACAAAGATGCTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG