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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cttgtcatatttacatttccaatataatccttattacacaacactgcctttaactttgccgccgctcactgtgcactgctttgcttataacatggttcagGTGGCATTCGTGGCCATTGGAGCAACAATGGTTGGAAGCATCGAGTTCTTGAAAGAAGAGGGTGACTACGTCCACAAAGGAGATGAG

Basic information

species Oryza sativa
transcript LOC_Os01g72940.1
intron # 16
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g72940.1 (Oryza sativa), 3'ss of exon 16
lower sequence: GRMZM2G133885_T02 (Zea mays), 3'ss of exon 3
--cttgtcatatttacatttccaatataatc--cttattaca----caacactgcctttaactttgccgccgctcactgtgcactgctttgcttataacatggttcagGTGGCATTCGTGGCCATTGGAGCAACAATGGTTGGAAGCATCGAGTTCTTGAAAGAAGAGGGTGACTACGTCCACAAAGGAGATGAG
   ||||    |||||  || |  |   ||   || |  |||    ||| |  ||||  | ||| || | |  |   ||| | ||| |  ||       ||||||||||| ||||| || || ||||||||||| ||||| |||||||||  |||||||||| |||||||||||||||||| |||||||||||||
tttttgtgtggtttaccgtttctttgagatgaactgacaacaaagtcaataaagcctgaagcttagctgacttttcttgttc-ctgatgggc-------atggttcagGTAGCATTTGTTGCGATTGGAGCAACCATGGTAGGAAGCATCACGTTCTTGAAAAAAGAGGGTGACTACGTCCGCAAAGGAGATGAG

upper sequence: LOC_Os01g72940.1 (Oryza sativa), 3'ss of exon 16
lower sequence: GLYMA08G19310.2 (Glycine max), 3'ss of exon 17
---------------------------------------------------------------cttgtcatatttacatttccaatataatccttattac--acaac--actgcctttaactttgccgccgctcactgt-gcactgctttg-----------cttataacatggttcagGTGGCATTCGTGGCCATTGGAGCAACAATGGTTGGAAGCATCGAGTTCTTGAAAGAAGAGGGTGACTACGTCCACAAAGGAGATGAG
                                                                || |   ||     | |  | ||| |||    ||||  | ||   ||||||| ||  ||       ||| |  || |||   ||||            |||||||  |  ||||||||||||| || || |||||||| ||||||||||| |||||    ||    ||  || |||| ||||| ||  | || |||||||||
gttggtcattgcaattaatttctttgtctgaattgttgagttcatgactatatcctgctgaaatttataccataagtttgtgaattattatctgagttacctataatctactgcctctactttcatttttgcttatagttgcagacctttattgaccagtatcttataattttattcagGTGGCATTTGTTGCAATTGGAGCTACAATGGTTGGTAGCATTACTTTTACAAAGAAAAAGGGCGACTATGTTAAGAAGGGAGATGAG

upper sequence: LOC_Os01g72940.1 (Oryza sativa), 3'ss of exon 16
lower sequence: EFJ07899 (Selaginella moellendorffii), 3'ss of exon 17
cttgtcatatttacatttccaatataatccttattacacaacactgcctttaactttgccgccgctcactgtgcactgctttgcttataacatggttcagGTGGCATTCGTGGCCATTGGAGCAACAATGGTTGGAAGCATCGAGTTCTTGAAAGAAGAGGGTGACTACGTCCACAAAGGAGATGAG
                                             |  |   |  || ||   |      ||  ||  || |  ||| ||     |  |||||||||||||||| || |||||||||||||| || |||||   ||||   ||| |||| ||   |  |||| | || || || |||
---------------------------------------------gtatgcgatcttccctttg------gtaaacc-ctctatttaaaattaaatgtagGTGGCATTCGTGGCAATCGGAGCAACAATGGTGGGCAGCATTACGTTCACTAAAAAAGAAGGATCCGTCGTCAAGAAGGGCGACGAG

upper sequence: LOC_Os01g72940.1 (Oryza sativa), 3'ss of exon 16
lower sequence: EFJ07241 (Selaginella moellendorffii), 3'ss of exon 17
cttgtcatatttacatttccaatataatccttattacacaacactgcctttaactttgccgccgctcactgtgcactgctttgcttataacatggttcagGTGGCATTCGTGGCCATTGGAGCAACAATGGTTGGAAGCATCGAGTTCTTGAAAGAAGAGGGTGACTACGTCCACAAAGGAGATGAG
                                             |  |   |  || ||   |      ||  ||  || |  ||| ||     |  |||||||||||||||| || |||||||||||||| || |||||   ||||   ||| |||| ||   |  |||| | || || || |||
---------------------------------------------gtatgcgatcttccctttg------gtaaacc-ctctatttagaattaaatgtagGTGGCATTCGTGGCAATCGGAGCAACAATGGTGGGCAGCATTACGTTCACTAAAAAAGAAGGATCCGTCGTCAAGAAGGGCGACGAG

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|33655366|gb|CF277980.1|CF277980
EST:     CCGAGAACAAACGAGTTGTTTCAATAATCTCAACTTCAGAGTTTGGAAAG                         GTGGCATTCGTGGCCATTGGAGCAACAATGGTTGGAAGCATCGAGTTCTTG
genomic: CCGAGAACAAACGAGTTGTTTCAATAATCTCAACTTCAGAGTTTGGAAAGgtttgtactt ... catggttcagGTGGCATTCGTGGCCATTGGAGCAACAATGGTTGGAAGCATCGAGTTCTTG
EST: gi|86492670|gb|CI135303.1|CI135303
EST:     CCGAGAACAAACGAGTTGTTTCAATAATCTCAACTTCAGAGTTTGGAAAG                         GTGGCATTCGTGGCCATTGGAGCAACAATGGTTGGAAGCATCGAGTTCTTG
genomic: CCGAGAACAAACGAGTTGTTTCAATAATCTCAACTTCAGAGTTTGGAAAGgtttgtactt ... catggttcagGTGGCATTCGTGGCCATTGGAGCAACAATGGTTGGAAGCATCGAGTTCTTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gcctttaactttgccgccgctcactgtgcactgctttgcttataacatggttcagGTGGCATTCGTGGCCATTGGAGCAACAATGGTTGGAAGCATCGAGTTCTTGAAAGAAGAGGGTGACTACGTCCACAAAGGAGATGAG
                                       ttataac  putative branch site (score: 2)
                                       ttataacat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cttgtcatatttacatttccaatataatccttattacacaacactgcctttaactttgccgccgctcactgtgcactgctttgcttataacatggttcagGTGGCATTCGTGGCCATTGGAGCAACAATGGTTGGAAGCATCGAGTTCTTGAAAGAAGAGGGTGACTACGTCCACAAAGGAGATGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATG
- - - - - - - - - - - - - - - - - - cacaaca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - tgccgcc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ctgtgca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctgcttt