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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ctcttcctaagaaagtgagagccatgtttaaaactgcaagctccatcattcattctattgtatttgtagcacatgaaatttacaaaacttttgtgtccagTTATCATCTTGCTGAGAAGAAGATCCCTTCCATCCATGGGTACGCAATGGGCTTGAAGCTTGAACAGTATATATTCGACGCGTTCAGTTACTCCCCATCC

Basic information

species Oryza sativa
transcript LOC_Os04g52370.1
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os04g52370.2 (Oryza sativa), 3'ss of exon 12
lower sequence: GRMZM2G044629_T02 (Zea mays), 3'ss of exon 11
-----------------------------ctcttcctaagaaagt-gagagccatgtttaaaactgcaagctccatcattcattctattgtatttgtagcacatgaaatttacaaaacttttgtgtccagTTATCATCTTGCTGAGAAGAAGATCCCTTCCATCCATGGGTACGCAATGGGCTTGAAGCTTGAACAGTATATATTCGACGCGTTCAGTTACTCCCCATCC
                             |||| |  ||    || |  || || |  |  | |   |   |     |     ||| ||| |  ||    |||      |  |     | |||||  ||| || ||||| ||||||||||||||||||||||||||||||| | | | |||| ||||||||||||||| |||||||||||| ||||  |||||||| |||
gtgagtgttgtctagtttgcctctgccttctctccaaaatgccgtcgccagtcaggccttgagcgatagagtaggcaaccgcatctgttggacctgcctgacagttgtgtgtcgtcgatcttgtgagcagATACCATCTAGCTGAGAAGAAGATCCCTTCCATCCATGGGTTCACGACGGGCCTGAAGCTTGAACAGTTTATATTCGACGCCTTCACATACTCCCCGTCC

upper sequence: LOC_Os04g52370.2 (Oryza sativa), 3'ss of exon 12
lower sequence: GRMZM2G019986_T04 (Zea mays), 3'ss of exon 12
---------------ctcttcctaagaaa-gtgagagccatgtttaaaactgcaagctccatcatt----cattctattgtatttgtagcacatgaaatttacaaaacttttgtgtccagTTATCATCTTGCTGAGAAGAAGATCCCTTCCATCCATGGGTACGCAATGGGCTTGAAGCTTGAACAGTATATATTCGACGCGTTCAGTTACTCCCCATCC
                ||||  |  |    ||   ||  || |  ||  | |  |||| || |  |     |  | |     |||||  ||   |   |||    | ||| |||| |||| || ||||| ||||||||||||||||||||||||||||||| | ||| |||| ||||||| ||||||| |||||||||||| |||| |||||||||||||
gtgagtatccccgtgttcttggttcgccttgtttcagagatttgcaagccaggcagcttcaacgatagagtaggcaaccacgtttgttacatgaggg-tttgtgtatcttgtgtgaccagATACCATCTAGCTGAGAAGAAGATCCCTTCCATCCATGGGTTCACAACGGGCCTGAAGCTGGAACAGTTTATATTCGACGCCTTCACTTACTCCCCATCC

upper sequence: LOC_Os04g52370.2 (Oryza sativa), 3'ss of exon 12
lower sequence: GLYMA05G26240.2 (Glycine max), 3'ss of exon 12
ctcttcctaagaaagtgagagccatgtttaa---aactgcaagctccatcattcattctattg--tatttgtagcacatgaaatt-tacaaaacttttgtgtccagTTATCATCTTGCTGAGAAGAAGATCCCTTCCATCCATGGGTACGCAATGGGCTTGAAGCTTGAACAGTATATATTCGACGCGTTCAGTTACTCCCCATCC
        |||   ||     |||  ||  |   |  || |   |  |   | || ||| ||   | |||   | | ||  |  | |  |    |||| | | ||||||||||||||| |||||||| || |||||||| ||||| ||  ||||||| || || |||||||||| |||||| || || ||    ||  | ||  | 
------aaaagggtgttgataccactttggacttatttgtatcatataatctgcaatcttttagctgttttatgaatattgatctgtggattgattttatatgcagTTATCATCTTGCAGAGAAGAAAATACCTTCCATACATGGATATACAATGGGATTAAAACTTGAACAGTTTATATTTGATGCATTTCCATATGCTCCTACA

upper sequence: LOC_Os04g52370.2 (Oryza sativa), 3'ss of exon 12
lower sequence: GLYMA08G09170.2 (Glycine max), 3'ss of exon 13
---ctcttcctaagaaagtgagagccatgtttaaaac-tgcaagctccatcattcattctattgtatttgtagcacatgaaatttacaaaacttttgtgtccagTTATCATCTTGCTGAGAAGAAGATCCCTTCCATCCATGGGTACGCAATGGGCTTGAAGCTTGAACAGTATATATTCGACGCGTTCAGTTACTCCCCATCC
      |    |||   ||     |||  |||  | | |  || || || | |||   || || | | | ||     ||| || |  |    |||| ||| ||||||||||||||| |||||||| || |||||||| ||||| ||  ||||||| || || |||||||||| |||||| || || ||    ||  | ||  | 
ataaagtcaaaaagggtgttgataccacttttgtatcatataatctgcaaccttctagctgttttgtatatat----tgatatgtggattgattttatgtgcagTTATCATCTTGCAGAGAAGAAAATACCTTCCATACATGGATATACAATGGGATTAAAACTTGAACAGTTTATATTTGATGCATTTCCATATGCTCCTACG

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|3768106|gb|AU032133.1|AU032133
EST:     ACTTTGGATTTTTTGAATCAAGTAGCANACAGCCTTGAGANGGACAGTAC                         TTATCATNTTGCTGAGAAGAAGATCCCTTCCATCCATGGGTACGCAATGGG
genomic: ACTTTGGATTTTTTGAATCAAGTAGCAAACAGCCTTGAGAAGGACAGTACgtgagtgctt ... ttgtgtccagTTATCATCTTGCTGAGAAGAAGATCCCTTCCATCCATGGGTACGCAATGGG
EST: gi|88389670|gb|CI603169.1|CI603169
EST:     ACTTTGGATTTTTTGAATCAAGTAGCAAACAGCCTTGAGAAGGACAGTAC                         TTATCATCTTGCTGAGAAGAAGATCCCTTCCATCCATGGGTACGCAATGGG
genomic: ACTTTGGATTTTTTGAATCAAGTAGCAAACAGCCTTGAGAAGGACAGTACgtgagtgctt ... ttgtgtccagTTATCATCTTGCTGAGAAGAAGATCCCTTCCATCCATGGGTACGCAATGGG
EST: gi|396941374|gb|HO188583.1|HO188583
EST:     ACTTTGGATTTTTTGAATCAAGTAGCAAACAGCCTTGAGAAAGACAGTAC                         TTATCATCTTGCTGA
genomic: ACTTTGGATTTTTTGAATCAAGTAGCAAACAGCCTTGAGAAGGACAGTACgtgagtgctt ... ttgtgtccagTTATCATCTTGCTGA
EST: gi|88961150|gb|CI096554.1|CI096554
EST:     AGCCTTGAGAAGGACAGTAC                         TTATCATCTTGCTGAGAAGAAGATCCCTTCCATCCATGGGTACGCAATGGG
genomic: AGCCTTGAGAAGGACAGTACgtgagtgctt ... ttgtgtccagTTATCATCTTGCTGAGAAGAAGATCCCTTCCATCCATGGGTACGCAATGGG
EST: gi|86831371|gb|CI297640.1|CI297640
EST:     ACTTTGGATTTTTTGAATCAAGTAGCAAACAGCCTTGAGAAGGACAGTAC                         TTATCATCTTGCTGAGAAGAAGATCCCTTCCATCCATGGGTACGCAATGGG
genomic: ACTTTGGATTTTTTGAATCAAGTAGCAAACAGCCTTGAGAAGGACAGTACgtgagtgctt ... ttgtgtccagTTATCATCTTGCTGAGAAGAAGATCCCTTCCATCCATGGGTACGCAATGGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcattcattctattgtatttgtagcacatgaaatttacaaaacttttgtgtccagTTATCATCTTGCTGAGAAGAAGATCCCTTCCATCCATGGGTACGCAATGGGCTTGAAGCTTGAACAGTATATATTCGACGCGTTCAGTTACTCCCCATCC
                                          cttttgt  CT-rich tract
                              aaatttacaaaacttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ctcttcctaagaaagtgagagccatgtttaaaactgcaagctccatcattcattctattgtatttgtagcacatgaaatttacaaaacttttgtgtccagTTATCATCTTGCTGAGAAGAAGATCCCTTCCATCCATGGGTACGCAATGGGCTTGAAGCTTGAACAGTATATATTCGACGCGTTCAGTTACTCCCCATCC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGC