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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtagctgtgcgtttttctttaaacagtttgctgcttactgaactttttacccaagtctgtgtcctgatgcagGCAGATATCTGGTCGTTAGGTATAACTGCTATTGAAATGGCAAAAGGTGAACCCCCTTTGGCAGATATCCATCCCATGAGAGTTCTTTTCATGATACCTC

Basic information

species Oryza sativa
transcript LOC_Os07g32400.2
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os07g32400.2 (Oryza sativa), 3'ss of exon 8
lower sequence: GRMZM2G027756_T02 (Zea mays), 3'ss of exon 5
gtagctgtgcgtttttctttaaacagtttgctgcttactgaactttt-tacccaagtctgtgtcctgatgcagGCAGATATCTGGTCGTTAGGTATAACTGCTATTGAAATGGCAAAAGGTGAACCCCCTTTGGCAGATATCCATCCCATGAGAGTTCTTTTCATGATACCTC
|||  ||||| |||     |||| |  ||  |   || ||| ||||| ||  |||| |||| ||   |||||||||||||||||||| |||||||| ||||| ||||||||||| ||||||||||||||| |||||||||| ||||||||||||||||||||||| |||||||
gtacttgtgcatttg---ctaaataaatttattagtagtgagcttttatagacaaggctgtttc--aatgcagGCAGATATCTGGTCTTTAGGTATCACTGCCATTGAAATGGCTAAAGGTGAACCCCCTCTGGCAGATATTCATCCCATGAGAGTTCTTTTCATCATACCTC

upper sequence: LOC_Os07g32400.2 (Oryza sativa), 3'ss of exon 8
lower sequence: GLYMA12G27300.1 (Glycine max), 3'ss of exon 9
----------------------------------------------gtagctgtgcgtttttctttaaacagtttgctgctt-actgaactt---tttaccc---aag---------tctgtgtcctg---atgcagGCAGATATCTGGTCGTTAGGTATAACTGCTATTGAAATGGCAAAAGGTGAACCCCCTTTGGCAGATATCCATCCCATGAGAGTTCTTTTCATGATACCTC
                                                | |    | | |||||||  |   | || | ||| | ||   ||   |||| ||   |||         ||||| || ||   || |||||||||||||||||  | || || ||||| ||||| ||||||||||| || || ||  | || ||| | ||||| |||||||| |||||||| ||||| |
gttatcttatagttactactcaaatcatttattatgctttctgagttcatcctaacatatttcttttcatcctctgttcctttattgtttttgtttttatcccctaagaatcatcactctgtatcttgtttatacagGCAGATATCTGGTCTCTGGGCATTACTGCGATTGAGATGGCAAAAGGGGAGCCTCCACTTGCTGATCTTCATCCAATGAGAGTGCTTTTCATCATACCCC

upper sequence: LOC_Os07g32400.2 (Oryza sativa), 3'ss of exon 8
lower sequence: Vv19s0014g02310.t01 (Vitis vinifera), 3'ss of exon 9
-----------------gtagctgtgcgtttttc-----tttaaacagtttgctgcttactga-actttt-----tacccaagtctgtgtcctgatgcagGCAGATATCTGGTCGTTAGGTATAACTGCTATTGAAATGGCAAAAGGTGAACCCCCTTTGGCAGATATCCATCCCATGAGAGTTCTTTTCATGATACCTC
                 ||   | | | |||||      |||   |  |||| ||||| ||   |||| |     ||        ||     |||||||||| ||||| |||||  | || |||||||| ||||| ||||||||||| || || ||  | |||||| ||||||| |||||||| ||||| || |||||||
tgaggtggtcagtatttgtgtttctccttttttgccatgttttgtccatttggtgcttcctcccacttctgatattattgggccatgaacaatgatgcagGCGGATATTTGGTCTCTGGGAATAACTGCAATTGAGATGGCAAAAGGGGAGCCTCCACTTGCAGATCTCCATCCAATGAGAGTGCTTTTTATAATACCTC

upper sequence: LOC_Os07g32400.2 (Oryza sativa), 3'ss of exon 8
lower sequence: PP1S98_82V6.1 (Physcomitrella patens), 3'ss of exon 8
-----------------------------------------gtagctgtgcgtttttctttaaacagtttgctgcttactga-acttttt-----acccaagtc--tgtgtcctgatgcagGCAGATATCTGGTCGTTAGGTATAACTGCTATTGAAATGGCAAAAGGTGAACCCCCTTTGGCAGATATCCATCCCATGAGAGTTCTTTTCATGATACCTC
                                             || | | | || || |      | |  | |||    | |||  ||      |  ||  |  || ||  |  ||||||||||||| ||||| || || || ||||| ||||||||||| ||||| ||||| ||||  || ||| | || || ||| | || || ||  | || ||  
gtaattatttaggttgtatcgacccttcgcttagaggagtaccgactcttcttcttcctctttttcttcttattcttgtcaatactccttcaatagctgaaagcagtgcgttttattgcagGCAGATATATGGTCATTGGGAATCACTGCCATTGAAATGGCGAAAGGGGAACCACCTTATGCTGATTTACACCCTATGCGGGTGCTCTTTCTAATTCCCA

upper sequence: LOC_Os07g32400.2 (Oryza sativa), 3'ss of exon 8
lower sequence: PP1S84_190V6.1 (Physcomitrella patens), 3'ss of exon 7
-------------------gtagctgtgcgtttttctttaaacagtttgctgcttact-gaacttttt----acccaagtct--gtgtcctga--tgcagGCAGATATCTGGTCGTTAGGTATAACTGCTATTGAAATGGCAAAAGGTGAACCCCCTTTGGCAGATATCCATCCCATGAGAGTTCTTTTCATGATACCTC
                   || |  | |  |  |  |    | |    |||  | | | | | |  ||    | |  ||     ||| | ||   ||||||||||||| || || || || || ||||||||||| ||||||||||| ||||    ||   ||        |                            
ttcacttcccgtcgtttgtgttgaagaggatgatggtagtgataaaaagctattcatttgtattccttcaatatctgagagcaagtggcttgcattgcagGCAGATATATGTTCATTGGGAATCACTGCTATTGAGATGGCAAAAGGGGAACTGTATTCTCCAAGAGATTTT----------------------------

upper sequence: LOC_Os07g32400.2 (Oryza sativa), 3'ss of exon 8
lower sequence: PP1S59_173V6.1 (Physcomitrella patens), 3'ss of exon 7
----------------------gtagctgtgcgtttttctt----taaacagtttgctgcttactgaactttttacccaagtc---tgtgtcctgatgcagGCAGATATCTGGTCGTTAGGTATAACTGCTATTGAAATGGCAAAAGGTGAACCCCCTTTGGCAGATATCCATCCCATGAGAGTTCTTTTCATGATACCTC
                      || |  | | ||| | |||    |  | || |   | || | | |     |  |  |   |   ||  |     ||||||||||||| ||||| || || || || |||||||| ||||||||||| || || ||||  |||||| | ||||| ||| | ||||||||  | || ||| 
atgctactttttgctcattcgtgttgaagggggttatgcttgtgatggaaagatcatt-ctcattcattcaatagctgagagcaggtgattttcattgcagGCAGATATATGGTCATTGGGGATCACCGCTATTGAGATGGCAAAAGGGGAGCCACCTTACGCAGATCTGCATCCTATGCGTGTTCTTTTTCTTATTCCTA

upper sequence: LOC_Os07g32400.2 (Oryza sativa), 3'ss of exon 8
lower sequence: EFJ32910 (Selaginella moellendorffii), 3'ss of exon 8
gtagctgtgcgtttttctttaaacagtttgctgcttactgaactttttacccaagtctgtgtcctgatg-cagGCAGATATCTGGTCGTTAGGTATAACTGCTATTGAAATGGCAAAAGGTGAACCCCCTTTGGCAGATATCCATCCCATGAGAGTTCTTTTCATGATACCTC
                         || || |   | ||     |    | ||    | |||     || ||||||||||| |||||  | || |||||| | || ||||||||||| |||||||| ||||| || ||| | ||||||||||||||||||||  |||| ||| 
-------------------------gtatgttatgttctagcagtacggctcattcatctgtttcattgacagGCAGATATATGGTCCCTTGGAATAACTACCATCGAAATGGCAAAGGGTGAACCGCCTTTTGCCGATTTACATCCCATGAGAGTTCTTTTTTTGATTCCTA

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|33796053|gb|CF323894.1|CF323894
EST:     TTTGGATGGCACCTGAGGTTATTCAAAACTCTGACGGGTACAATGAAAAG                         GCAGATATCTGGTCGTTAGGTATAACTGCTATTGAAATGGCAAAAGGTGAA
genomic: TTTGGATGGCACCTGAGGTTATTCAAAACTCTGACGGGTACAATGAAAAGgtagctgtgc ... cctgatgcagGCAGATATCTGGTCGTTAGGTATAACTGCTATTGAAATGGCAAAAGGTGAA
EST: gi|25799236|gb|CA755197.1|CA755197
EST:     TTTGGATGGCACCTGAGGTTATTCAAAACTCTGACGGGTACAATGAAAAG                         GCAGATATCTGGTCGTTAGGTATAACTGCTATTGAAATGGCAAAAGGTGAA
genomic: TTTGGATGGCACCTGAGGTTATTCAAAACTCTGACGGGTACAATGAAAAGgtagctgtgc ... cctgatgcagGCAGATATCTGGTCGTTAGGTATAACTGCTATTGAAATGGCAAAAGGTGAA
EST: gi|58665909|gb|CK054595.1|CK054595
EST:     TTTGGATGGCACCTGAGGTTATTCAAAACTCTGACGGGTACAATGAAAAG                         GCAGATATCTGGTCGTTAGGTATAACTGCTATTGAAATGGCAAAAGGTGAA
genomic: TTTGGATGGCACCTGAGGTTATTCAAAACTCTGACGGGTACAATGAAAAGgtagctgtgc ... cctgatgcagGCAGATATCTGGTCGTTAGGTATAACTGCTATTGAAATGGCAAAAGGTGAA
EST: gi|58669013|gb|CK057699.1|CK057699
EST:     TTTGGATGGCACCTGAGGTTATTCAAAACTCTGACGGGTACAATGAAAAG                         GCAGATATCTGGTCGTTAGGTATAACTGCTATTGAAATGGCAAAAGGTGAA
genomic: TTTGGATGGCACCTGAGGTTATTCAAAACTCTGACGGGTACAATGAAAAGgtagctgtgc ... cctgatgcagGCAGATATCTGGTCGTTAGGTATAACTGCTATTGAAATGGCAAAAGGTGAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttaaacagtttgctgcttactgaactttttacccaagtctgtgtcctgatgcagGCAGATATCTGGTCGTTAGGTATAACTGCTATTGAAATGGCAAAAGGTGAACCCCCTTTGGCAGATATCCATCCCATGAGAGTTCTTTTCATGATACCTC
                       aacttttta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtagctgtgcgtttttctttaaacagtttgctgcttactgaactttttacccaagtctgtgtcctgatgcagGCAGATATCTGGTCGTTAGGTATAACTGCTATTGAAATGGCAAAAGGTGAACCCCCTTTGGCAGATATCCATCCCATGAGAGTTCTTTTCATGATACCTC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGAT