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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cctgtaagttagaaatgctattaccactttccgtaattaaagtattttctgatatttcattgtcatttttcatatctttctatcatttcttttcttacagGTGCAACCATTGTTGTGTCTGGTGATGGCCGCTATTTCTCGAAGGATGCTGTTCAG

Basic information

species Oryza sativa
transcript LOC_Os03g50480.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g50480.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G109383_T01 (Zea mays), 3'ss of exon 2
cctgtaagttagaaatgctattaccactttccgtaattaaagtattttctgatatttcattgtcatt-tttcatatctttc-tatcatttcttttcttac---agGTGCAACCATTGTTGTGTCTGGTGATGGCCGCTATTTCTCGAAGGATGCTGTTCAG
  ||||| |  ||||||   || |||          | |   | |   ||| ||||||  ||   || || |  ||  |||   || |||||||| ||     ||||||||| |||||||| ||||||||||||||||||||||| || ||||||||||||
attgtaa-tgggaaatgtagttcccaaaaatt----tcatgatctcccctgttatttctctgctgttgttccccattgttcacgtcttttcttttttttttttagGTGCAACAATTGTTGTCTCTGGTGATGGCCGCTATTTCTCAAAAGATGCTGTTCAG

upper sequence: LOC_Os03g50480.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G023289_T03 (Zea mays), 3'ss of exon 2
cctgtaagttagaaatgctattaccactttccgtaattaaagtattttctgatatttcatt---gtcatttttcat-atctttctatcatttcttttcttacagGTGCAACCATTGTTGTGTCTGGTGATGGCCGCTATTTCTCGAAGGATGCTGTTCAG
  ||||| |  ||||||   || |||  |  |  ||||    |    || | | | || ||   ||  ||  | || |    | | || |||| ||||||| |||||||||||||||||| ||||||||||||||||||||||| || ||||||||||||
--tgtaaatgggaaatgtagttgcca--tagccaaatttttatgacctccgttctctcttttcagttgttgctaattagtcatgtctcctttcctttcttatagGTGCAACCATTGTTGTCTCTGGTGATGGCCGCTATTTCTCAAAAGATGCTGTTCAG

upper sequence: LOC_Os03g50480.1 (Oryza sativa), 3'ss of exon 2
lower sequence: Vv01s0011g05370.t01 (Vitis vinifera), 3'ss of exon 3
cctgtaagttagaaatgctattaccactttccgtaattaaagtattttctgatatttcattgtcatttttcatatctttctatcatttcttttcttacagGTGCAACCATTGTTGTGTCTGGTGATGGCCGCTATTTCTCGAAGGATGCTGTTCAG
| | |   | | |  |   || |    | |    |  |||  |||| |||| ||  |   |   ||||    | |   |   | || | | | | | ||||    ||  ||||||| ||||||||||||||||||||||||||||||||  |||||
cttttgtttcatacctcacatgatttttgttttgatctaatttattatctgttaaatgggtcagatttactcttttcctagtttatgtttgtgcatgcagGCATGACACTTGTTGTTTCTGGTGATGGCCGCTATTTCTCGAAGGATGCCATTCAG

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|33675938|gb|CF304177.1|CF304177
EST:     GAACTTTGTGCAATCCACATTTAATGCCCTTCCTGCCGACAAAGTAAAAG                         GTGCAACCATTGTTGTGTCTGGTGATGGCCGCTATTTCTCGAAGGATGCTG
genomic: GAACTTTGTGCAATCCACATTTAATGCCCTTCCTGCCGACAAAGTAAAAGgttagctact ... tttcttacagGTGCAACCATTGTTGTGTCTGGTGATGGCCGCTATTTCTCGAAGGATGCTG
EST: gi|11863329|gb|AU066043.2|AU066043
EST:     GAACTTTGTGCAATCCACATTTAATGCCCTTCCTGCCGACAAAGTAAAAG                         GTGCA-CCATTGTTGTGTCTGGTGATGGCCGCTATTTCTCGAAGGATGCTG
genomic: GAACTTTGTGCAATCCACATTTAATGCCCTTCCTGCCGACAAAGTAAAAGgttagctact ... tttcttacagGTGCAACCATTGTTGTGTCTGGTGATGGCCGCTATTTCTCGAAGGATGCTG
EST: gi|58688355|gb|CK077042.1|CK077042
EST:     GAACTTTGTGCAATCCACATTTAATGCCCTTCCTGCCGACAAAGTAAAAG                         GTGCAACCATTGTTGTGTCTGGTGATGGCCGCTATTTCTCGAAGGATGCTG
genomic: GAACTTTGTGCAATCCACATTTAATGCCCTTCCTGCCGACAAAGTAAAAGgttagctact ... tttcttacagGTGCAACCATTGTTGTGTCTGGTGATGGCCGCTATTTCTCGAAGGATGCTG
EST: gi|58675297|gb|CK063984.1|CK063984
EST:     TGCCCTTCCTGCCGACAAAGTAAAAG                         GTGCAACCATTGTTGTGTCTGGTGATGGCCGCTATTTCTCGAAGGATGCTG
genomic: TGCCCTTCCTGCCGACAAAGTAAAAGgttagctact ... tttcttacagGTGCAACCATTGTTGTGTCTGGTGATGGCCGCTATTTCTCGAAGGATGCTG
EST: gi|29612833|gb|CB617846.1|CB617846
EST:     GAACTTTGTGCAATCCACATTTAATGCCCTTCCTGCCGACAAAGTAAAAG                         GTGCAACCATTGTTGTGTCTGGTGATGGCCGCTATTTCTCGAAGGATGCTG
genomic: GAACTTTGTGCAATCCACATTTAATGCCCTTCCTGCCGACAAAGTAAAAGgttagctact ... tttcttacagGTGCAACCATTGTTGTGTCTGGTGATGGCCGCTATTTCTCGAAGGATGCTG
EST: gi|29689598|gb|CB685873.1|CB685873
EST:     GAACTTTGTGCAATCCACATTTAATGCCCTTCCTGCCGACAAAGTAAAAG                         GTGCAACCATTGTTGTGTCTGGTGATGGCCGCTATTTCTCGAAGGATGCTG
genomic: GAACTTTGTGCAATCCACATTTAATGCCCTTCCTGCCGACAAAGTAAAAGgttagctact ... tttcttacagGTGCAACCATTGTTGTGTCTGGTGATGGCCGCTATTTCTCGAAGGATGCTG
EST: gi|29671540|gb|CB667815.1|CB667815
EST:     GAACTTTGTGCAATCCACATTTAATGCCCTTCCTGCCGACAAAGTAAAAG                         GTGCAACCATTGTTGTGTCTGGTGATGGCCGCTATTTCTCGAAGGATGCTG
genomic: GAACTTTGTGCAATCCACATTTAATGCCCTTCCTGCCGACAAAGTAAAAGgttagctact ... tttcttacagGTGCAACCATTGTTGTGTCTGGTGATGGCCGCTATTTCTCGAAGGATGCTG
EST: gi|29664693|gb|CB660968.1|CB660968
EST:     ACATTTAATGCCCTTCCTGCCGACAAAGTAAAAG                         GTGCAACCATTGTTGTGTCTGGTGATGGCCGCTATTTCTCGAAGGATGCTG
genomic: ACATTTAATGCCCTTCCTGCCGACAAAGTAAAAGgttagctact ... tttcttacagGTGCAACCATTGTTGTGTCTGGTGATGGCCGCTATTTCTCGAAGGATGCTG
EST: gi|58670502|gb|CK059188.1|CK059188
EST:     GAACTTTGTGCAATCCACATTTAATGCCCTTCCTGCCGACAAAGTAAAAG                         GTGCAACCATTGTTGTGTCTGGTGATGGCCGCTATTTCTCGAAGGATGCTG
genomic: GAACTTTGTGCAATCCACATTTAATGCCCTTCCTGCCGACAAAGTAAAAGgttagctact ... tttcttacagGTGCAACCATTGTTGTGTCTGGTGATGGCCGCTATTTCTCGAAGGATGCTG
EST: gi|29682384|gb|CB678659.1|CB678659
EST:     GAACTTTGTGCAATCCACATTTAATGCCCTTCCTGCCGACAAAGTAAAAG                         GTGCAACCATTGTTGTGTCTGGTGATGGCCGCTATTTCTCGAAGGATGCTG
genomic: GAACTTTGTGCAATCCACATTTAATGCCCTTCCTGCCGACAAAGTAAAAGgttagctact ... tttcttacagGTGCAACCATTGTTGTGTCTGGTGATGGCCGCTATTTCTCGAAGGATGCTG
EST: gi|33676013|gb|CF304252.1|CF304252
EST:     GAACTTTGTGCAATCCACATTTAATGCCCTTCCTGCCGACAAAGTAAAAG                         GTGCAACCATTGTTGTGTCTGGTGATGGCCGCTATTTCTCGAAGGATGCTG
genomic: GAACTTTGTGCAATCCACATTTAATGCCCTTCCTGCCGACAAAGTAAAAGgttagctact ... tttcttacagGTGCAACCATTGTTGTGTCTGGTGATGGCCGCTATTTCTCGAAGGATGCTG
EST: gi|87015499|gb|CI303105.1|CI303105
EST:     GAACTTTGTGCAATCCACATTTAATGCCCTTCCTGCCGACAAAGTAAAAG                         GTGCAACCATTGTTGTGTCTGGTGATGGCCGCTATTTCTCGAAGGATGCTG
genomic: GAACTTTGTGCAATCCACATTTAATGCCCTTCCTGCCGACAAAGTAAAAGgttagctact ... tttcttacagGTGCAACCATTGTTGTGTCTGGTGATGGCCGCTATTTCTCGAAGGATGCTG
EST: gi|58667231|gb|CK055917.1|CK055917
EST:     GAACTTTGTGCAATCCACATTTAATGCCCTTCCTGCCGACAAAGTAAAAG                         GTGCAACCATTGTTGTGTCTGGTGATGGCCGCTATTTCTCGAAGGATGCTG
genomic: GAACTTTGTGCAATCCACATTTAATGCCCTTCCTGCCGACAAAGTAAAAGgttagctact ... tttcttacagGTGCAACCATTGTTGTGTCTGGTGATGGCCGCTATTTCTCGAAGGATGCTG
EST: gi|58667790|gb|CK056476.1|CK056476
EST:     CGACAAAGTAAAAG                         GTGCAACCATTG-TGTGTCTGGTGATGGCCGCTATTTCTCGAAGGATGCTG
genomic: CGACAAAGTAAAAGgttagctact ... tttcttacagGTGCAACCATTGTTGTGTCTGGTGATGGCCGCTATTTCTCGAAGGATGCTG
EST: gi|58666319|gb|CK055005.1|CK055005
EST:     GAACTTTGTGCAATCCACATTTAATGCCCTTCCTGCCGACAAAGTAAAAA                         GTGCAACCATTGTTGTGTCTGGTGATGGCCGCTATTTCTCGAAGGATGCTG
genomic: GAACTTTGTGCAATCCACATTTAATGCCCTTCCTGCCGACAAAGTAAAAGgttagctact ... tttcttacagGTGCAACCATTGTTGTGTCTGGTGATGGCCGCTATTTCTCGAAGGATGCTG
EST: gi|29614791|gb|CB619804.1|CB619804
EST:     GAACTTTGTGCAATCCACATTTAATGCCCTTCCTGCCGACAAAGTAAAAG                         GTGCAACCATTGTTGTGTCTGGTGATGGCCGCTATTTCTCGAAGGATGCTG
genomic: GAACTTTGTGCAATCCACATTTAATGCCCTTCCTGCCGACAAAGTAAAAGgttagctact ... tttcttacagGTGCAACCATTGTTGTGTCTGGTGATGGCCGCTATTTCTCGAAGGATGCTG
EST: gi|29671584|gb|CB667859.1|CB667859
EST:     GAACTTTGTGCAATCCACATTTAATGCCCTTCCTGCCGACAAAGTAAAAG                         GTGCAACCATTGTTGTGTCTGGTGATGGCCGCTATTTCTCGAAGGATGCTG
genomic: GAACTTTGTGCAATCCACATTTAATGCCCTTCCTGCCGACAAAGTAAAAGgttagctact ... tttcttacagGTGCAACCATTGTTGTGTCTGGTGATGGCCGCTATTTCTCGAAGGATGCTG
EST: gi|58668595|gb|CK057281.1|CK057281
EST:     GAACTTTGTGCAATCCACATTTAATGCCCTTCCTGCCGACAAAGTAAAAG                         GTGCAACCATTGTTGTGTCTGGTGATGGCCGCTATTTCTCGAAGGATGCTG
genomic: GAACTTTGTGCAATCCACATTTAATGCCCTTCCTGCCGACAAAGTAAAAGgttagctact ... tttcttacagGTGCAACCATTGTTGTGTCTGGTGATGGCCGCTATTTCTCGAAGGATGCTG
EST: gi|33675599|gb|CF303838.1|CF303838
EST:     GAACTTTGTGCAATCCACATTTAATGCCCTTCCTGCCGACAAAGTAAAAG                         GTGCAACCATTGTTGTGTCTGGTGATGGCCGCTATTTCTCGAAGGATGCTG
genomic: GAACTTTGTGCAATCCACATTTAATGCCCTTCCTGCCGACAAAGTAAAAGgttagctact ... tttcttacagGTGCAACCATTGTTGTGTCTGGTGATGGCCGCTATTTCTCGAAGGATGCTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttctgatatttcattgtcatttttcatatctttctatcatttcttttcttacagGTGCAACCATTGTTGTGTCTGGTGATGGCCGCTATTTCTCGAAGGATGCTGTTCAG
 ttctgat  putative branch site (score: 3)
                 tcatttttcatatctt  putative PPT
                   atttttcatatcttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cctgtaagttagaaatgctattaccactttccgtaattaaagtattttctgatatttcattgtcatttttcatatctttctatcatttcttttcttacagGTGCAACCATTGTTGTGTCTGGTGATGGCCGCTATTTCTCGAAGGATGCTGTTCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGTT
- - - - - - - -tgctatt
- - - - - - - - - - - - - - - - - - - - - - - ttctgat
- - - - - - - - - - - - - - - - - - - - - - - - - - - tttcatt