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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgagctatattttccaattgaaaatcaagttcttgatatctgcacatatatgtcagacgtgtctgggataattgacttgatttccattcaaacaattgtagGAGGTTGCTTCGTGGAGGGTGAATGGTTAAGAAACGCATTCAGGTGGAGGGAATCTATTGGTCCATGGGAAGAGAGGCCTGGACACTTTGGGGATGTTTG

Basic information

species Oryza sativa
transcript LOC_Os12g03470.5
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os12g03470.5 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G006130_T01 (Zea mays), 3'ss of exon 7
gtatgagctatattttccaattgaaaatcaagttcttgatatctgcacatatatg------tcagacgtgtctgggataattgacttgatttccattcaaacaattgtagGAGGTTGCTTCGTGGAGGGTGAATGGTTAAGAAACGCATTCAGGTGGAGGGAATCTATTGGTCCATGGGAAGAGAGGCCTGGACACTTTGGGGATGTTTG
|||||  || | |||||  ||| |||||||||||||| || | || ||||||||       ||| |  ||| |  |||| ||||  |   |||||| | | | | |||||||||||| || || || ||||| ||| ||||||| |||||||| ||||| || || |||||||||||||||||||||||||||||||| |||||||||||
gtatgcactgtgttttcacatttaaaatcaagttcttcatgtttggacatatattatgtgttcatagatgtttcagatatttga--tagattccatgcga-ctactgtagGAGGTTGTTTTGTAGAAGGTGACTGGCTAAGAAATGCATTCAGATGGAGAGAGTCAATTGGTCCATGGGAAGAGAGGCCTGGACACTTCGGGGATGTTTG

upper sequence: LOC_Os12g03470.5 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G006130_T02 (Zea mays), 3'ss of exon 7
gtatgagctatattttccaattgaaaatcaagttcttgatatctgcacatatatg------tcagacgtgtctgggataattgacttgatttccattcaaacaattgtagGAGGTTGCTTCGTGGAGGGTGAATGGTTAAGAAACGCATTCAGGTGGAGGGAATCTATTGGTCCATGGGAAGAGAGGCCTGGACACTTTGGGGATGTTTG
       || | |||||  ||| |||||||||||||| || | || ||||||||       ||| |  ||| |  |||| ||||  |   |||||| | | | | |||||||||||| || || || ||||| ||| ||||||| |||||||| ||||| ||||| |||||||||||||||||||||||||||||||| |||||||||||
-------ctgtgttttcacatttaaaatcaagttcttcatgtttggacatatattacgtgttcatagatgtttcagatatttga--tagattccatgcga-ctactgtagGAGGTTGTTTTGTAGAAGGTGACTGGCTAAGAAATGCATTCAGATGGAGAGAATCAATTGGTCCATGGGAAGAGAGGCCTGGACACTTCGGGGATGTTTG

upper sequence: LOC_Os12g03470.5 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G393002_T01 (Zea mays), 3'ss of exon 16
gtatgagctatattttccaa-------ttgaaaatcaagttcttgatatctgcacatatatg-tcagacgtgtctgggataattgacttgatttccattcaaacaattgtagGAGGTTGCTTCGTGGAGGGTGAATGGTTAAGAAACGCATTCAGGTGGAGGGAATCTATTGGTCCATGGGAAGAGAGGCCTGGACACTTTGGGGATGTTTG
   |  ||| | |||   |        ||||  ||        ||| || |     |||||| ||| |  | | ||  | |||  ||  |  |  |||  ||| | || |||| |||||||| ||||| ||||  ||| |||||||||||||||| |||||  |||| ||||||||||||||||||||||| |||||||| || |||  |||
--gtacgctgtgtttataagagggttcttgacgattggacctatgaaatgtattgttatatgctcaaatatctttgaaacaatctacgcg--tggcatggaaata-ttttagGGGGTTGCTTTGTGGAAGGTGGTTGGCTAAGAAACGCATTCAGATGGAGACAATCCATTGGTCCATGGGAAGAGAGGCCAGGACACTTCGGAGATTGTTG

upper sequence: LOC_Os12g03470.5 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G006130_T05 (Zea mays), 3'ss of exon 19
gtatgagctatattttccaattgaaaatcaagttcttgatatctgcacatatatg------tcagacgtgtctgggataattgacttgatttccattcaaacaattgtagGAGGTTGCTTCGTGGAGGGTGAATGGTTAAGAAACGCATTCAGGTGGAGGGAATCTATTGGTCCATGGGAAGAGAGGCCTGGACACTTTGGGGATGTTTG
|||||  || | |||||  ||| |||||||||||||| || | || ||||||||       ||| |  ||| |  |||| ||||  |   |||||| | | | | |||||||||||| || || || ||||| ||| ||||||| |||||||| ||||| ||||| |||||||||||||||||||||||||||||||| |||||||||||
gtatgcactgtgttttcacatttaaaatcaagttcttcatgtttggacatatattacgtgttcatagatgtttcagatatttga--tagattccatgcga-ctactgtagGAGGTTGTTTTGTAGAAGGTGACTGGCTAAGAAATGCATTCAGATGGAGAGAATCAATTGGTCCATGGGAAGAGAGGCCTGGACACTTCGGGGATGTTTG

upper sequence: LOC_Os12g03470.5 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G077299_T03 (Zea mays), 3'ss of exon 6
gtatgagctatattttccaattgaaaatcaagttcttgatatctgcacatatatgtca--------------gacgtgtctg-ggataattgacttgatttccattcaaacaattgtagGAGGTTGCTTCGTGGAGGGTGAATGGTTAAGAAACGCATTCAGGTGGAGGGAATCTATTGGTCCATGGGAAGAGAGGCCTGGACACTTTGGGGATGTTTG
|||||  |  | |||||  ||| | ||||| ||||   ||      |  ||||||  |               |    | |  ||||||| |||| |||| |   | |  | ||||||||||| ||||| || || ||||  ||||||||||| || || |||||||| |||||||||||||||||||||||||| ||||||||||| |||||||||||
gtatgctccgtgttttcttatttagaatcaggttcccaatgctaagatgtatatgatatattgcaatatattaatacatttaaggataatggactagattgc--atgatgctattgtagGAGGCTGCTTTGTAGAAGGTGGCTGGTTAAGAAATGCCTTTAGGTGGAGAGAATCTATTGGTCCATGGGAAGAGAGACCTGGACACTTCGGGGATGTTTG

upper sequence: LOC_Os12g03470.5 (Oryza sativa), 3'ss of exon 7
lower sequence: GLYMA03G27460.3 (Glycine max), 3'ss of exon 7
gtatgagctatattttccaattgaaaatcaagttcttgatatctgcacatatatgtcagacgtgtctgggataattgacttgatttccattcaaacaattgtagGAGGTTGCTTCGTGGAGGGTGAATGGTTAAGAAACGCATTCAGGTGGAGGGAATCTATTGGTCCATGGGAAGAGAGGCCTGGACACTTTGGGGATGTTTG
|| ||||   ||     || |||| ||| | ||  |  |  | | | | | ||  |   | ||  ||    |||       || |   |||  |       |||| ||||| || || || || |||||||||||||| |||||  | ||||  | |||| |||| |||||||| ||||| ||||| |||||||| ||||||||
gtttgag---taagcatcatttgataataacgtgttcta-gtttactcttctagtttgtatgtaactcaactaacatctaggaatgttattttacattgcatagGCGGTTGTTTTGTTGAAGGAGAATGGTTAAGAAATGCATTTCGATGGAAAGCATCTGTTGGACCATGGGAGGAGAGACCTGGGCACTTTGGTGATGTTTG

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|29667817|gb|CB664092.1|CB664092
EST:     ACTAATATCTATGATGTTGGACTTAAAACCACGATTCTTGAGATTCCCTG                         GAGGTTGCTTCGTGGAGGGTGAATGGTTAAGAAACGCATTCAGGTGGAGGG
genomic: ACTAATATCTATGATGTTGGACTTAAAACCACGATTCTTGAGATTCCCTGgtatgagcta ... acaattgtagGAGGTTGCTTCGTGGAGGGTGAATGGTTAAGAAACGCATTCAGGTGGAGGG
EST: gi|29627933|gb|CB632944.1|CB632944
EST:     ACTAATATCTATGATGTTGGACTTAAAACCACGATTCTTGAGATTCCCTG                         GAGGTTGCTTCGTGGAGGGTGAATGGTTAAGAAACGCATTCAGGTGGAGGG
genomic: ACTAATATCTATGATGTTGGACTTAAAACCACGATTCTTGAGATTCCCTGgtatgagcta ... acaattgtagGAGGTTGCTTCGTGGAGGGTGAATGGTTAAGAAACGCATTCAGGTGGAGGG
EST: gi|33677669|gb|CF305908.1|CF305908
EST:     ACTAATATCTATGATGTTGGACTTAAAACCACGATTCTTGAGATTCCCTG                         GAGGTTGCTTCGTGGAGGGTGAATGGTTAAGAAACGCATTCAGGTGGAGGG
genomic: ACTAATATCTATGATGTTGGACTTAAAACCACGATTCTTGAGATTCCCTGgtatgagcta ... acaattgtagGAGGTTGCTTCGTGGAGGGTGAATGGTTAAGAAACGCATTCAGGTGGAGGG
EST: gi|55410431|gb|CV722807.1|CV722807
EST:     CTAATATCTATGATGTTGGACTTATATTCCACGATTCTTGAGATTCCCTG                         GAGGTTGCTTCGTGGAGGGTGAATGGTTAAGAAACGCATTCAGGTGGAGGG
genomic: CTAATATCTATGATGTTGGACTTA-AAACCACGATTCTTGAGATTCCCTGgtatgagcta ... acaattgtagGAGGTTGCTTCGTGGAGGGTGAATGGTTAAGAAACGCATTCAGGTGGAGGG
EST: gi|29630007|gb|CB635016.1|CB635016
EST:     ACTAATATCTATGATGTTGGACTTAAAACCACGATTCTTGAGATTCCCTG                         GAGGTTGCTTCGTGGAGGGTGAATGGTTAAGAAACGCATTCAGGTGGAGGG
genomic: ACTAATATCTATGATGTTGGACTTAAAACCACGATTCTTGAGATTCCCTGgtatgagcta ... acaattgtagGAGGTTGCTTCGTGGAGGGTGAATGGTTAAGAAACGCATTCAGGTGGAGGG
EST: gi|33675310|gb|CF303549.1|CF303549
EST:     ACTAATATCTATGATGTTGGACTTAAAACCACGATTCTTGAGATTCCCTG                         GAGGTTGCTTCGTGGAGGGTGAATGGTTAAGAAACGCATTCAGGTGGAGGG
genomic: ACTAATATCTATGATGTTGGACTTAAAACCACGATTCTTGAGATTCCCTGgtatgagcta ... acaattgtagGAGGTTGCTTCGTGGAGGGTGAATGGTTAAGAAACGCATTCAGGTGGAGGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatatgtcagacgtgtctgggataattgacttgatttccattcaaacaattgtagGAGGTTGCTTCGTGGAGGGTGAATGGTTAAGAAACGCATTCAGGTGGAGGGAATCTATTGGTCCATGGGAAGAGAGGCCTGGACACTTTGGGGATGTTTG
                     ataattga  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgagctatattttccaattgaaaatcaagttcttgatatctgcacatatatgtcagacgtgtctgggataattgacttgatttccattcaaacaattgtagGAGGTTGCTTCGTGGAGGGTGAATGGTTAAGAAACGCATTCAGGTGGAGGGAATCTATTGGTCCATGGGAAGAGAGGCCTGGACACTTTGGGGATGTTTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGAGG