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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgatttcatcttagtctgtatgatctctatagttttcttgctgtgtatccctacacattgctgatgcatatcaaattctctcactattttgtttttgcagTGATGGTTGGGACCGCACAACTCAGTTGGTTGCACTTGCTTGTTTGTTGCTTGATCCATATTATAGAACGTTCAATGGGTTCCAG

Basic information

species Oryza sativa
transcript LOC_Os08g44260.1
intron # 13
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os08g44260.1 (Oryza sativa), 3'ss of exon 13
lower sequence: GRMZM2G449163_T01 (Zea mays), 3'ss of exon 5
--tgatttcatcttagtctgtatgatctctatagttttcttgctgtgtatccctacacattgctgatgcatatcaaattctctcactattttgtttttgcagTGATGGTTGGGACCGCACAACTCAGTTGGTTGCACTTGCTTGTTTGTTGCTTGATCCATATTATAGAACGTTCAATGGGTTCCAG
  ||| |    |||  |  || | ||||    |   |   || | | |||  ||     ||  |      |     ||| | |  ||  | ||||| ||||||||||| |||||||||||||| ||||||||| ||||||||||||| ||||||||||| |||||| |||| |||| ||| ||||||
gatgaataatcctt--taggtgtcatctgaggatcctgtgtgatctctatagctttgtctttgtagcatctgaatgatttttttccttctctgtttctgcagTGATGGATGGGACCGCACAACCCAGTTGGTTTCACTTGCTTGTTTATTGCTTGATCCCTATTATCGAACTTTCAGTGGATTCCAG

upper sequence: LOC_Os08g44260.1 (Oryza sativa), 3'ss of exon 13
lower sequence: GRMZM2G046050_T01 (Zea mays), 3'ss of exon 1
-------tgatttcatcttag---tctgtatgatctctatagttttcttgctgtgtatccctacacattgctgatgcatatcaaattctctcactattttgtttttgcagTGATGGTTGGGACCGCACAACTCAGTTGGTTGCACTTGCTTGTTTGTTGCTTGATCCATATTATAGAACGTTCAATGGGTTCCAG
        | | |||||| ||    |||| |||||||||||| ||| | ||| ||| |   ||  |||      || ||     ||| |  | ||  ||||||| ||||||||||| |||||||||||||| ||||||||| ||||||||||||| ||||||||||| |||||| |||| |||| ||| ||||||
atcctttgggtgtcatctgaggatcctgtgtgatctctatagctttgtcgctttgtctttgta-gcatc-----tgaatg----atttttccccttctttgtttctgcagTGATGGATGGGACCGCACAACCCAGTTGGTTTCACTTGCTTGTTTATTGCTTGATCCCTATTATCGAACTTTCAGTGGATTCCAG

upper sequence: LOC_Os08g44260.1 (Oryza sativa), 3'ss of exon 13
lower sequence: GLYMA10G34510.1 (Glycine max), 3'ss of exon 7
------tgatttcatcttagtctgtatgatctctatagttttcttgctgtgtatccctacacat--tgctgatgcatatcaa-------------------attctctcactattttgttttt--gcagTGATGGTTGGGACCGCACAACTCAGTTGGTTGCACTTGCTTGTTTGTTGCTTGATCCATATTATAGAACGTTCAATGGGTTCCAG
      | || || | |    ||||   ||||  ||       || |  ||||| ||| || ||  |  | | |  | |                      |  | ||  |  ||||||||||  | |||||||| |||||  | ||||  ||||||||| ||||||||  |||||||||||||||||||||| | || ||||  ||||| |||
gtgctattatgtcttttctcactgtgaaatctaaatttaaaattttcaatgtattccttcatatgatattcaagtttgtttggcatctagcttggctccttaccccctgtcccttttgttttttggtagTGATGGATGGGATAGGACAAGCCAGTTGGTTTCACTTGCTAATTTGTTGCTTGATCCATATTATCGGACATTCACAGGGTTTCAG

upper sequence: LOC_Os08g44260.1 (Oryza sativa), 3'ss of exon 13
lower sequence: GLYMA20G33040.1 (Glycine max), 3'ss of exon 7
-----------------------------tgatttcatcttagtctgtatgatctctatagttttcttgctgtgtatccctacacattgctgatgcatatcaaattctctcactattttgtttttgcagTGATGGTTGGGACCGCACAACTCAGTTGGTTGCACTTGCTTGTTTGTTGCTTGATCCATATTATAGAACGTTCAATGGGTTCCAG
                             | | || |   |  ||  ||| |||  |    |  | ||   || | |   | ||  | ||   ||||  | |    ||    || || | |||| | |||||||| |||||  | ||||  ||||||||| ||||||||  |||||||||||||||||||||| | || ||||  ||||| |||
gtgctatgatgtattttctcactgaaatctaaattgaaaattttcaatataatccttcatatgatattcaggtttgttt-tgcatctagc-attgcaccttaccccctgcaccttttgttttttggtagTGATGGATGGGATAGGACAAGCCAGTTGGTTTCACTTGCTAATTTGTTGCTTGATCCATATTATCGGACATTCACAGGGTTTCAG

upper sequence: LOC_Os08g44260.1 (Oryza sativa), 3'ss of exon 13
lower sequence: AT3G10550.1 (Arabidopsis thaliana), 3'ss of exon 13
----------------------------------------tgatttc-atcttagtctgtatgatctctata-gttttcttgctgtgtatccctacacattgctgatgcatatcaaattctct----cactat-----tttgt------ttttgcagTGATGGTTGGGACCGCACAACTCAGTTGGTTGCACTTGCTTGTTTGTTGCTTGATCCATATTATAGAACGTTCAATGGGTTCCAG
                                          |||||  || | ||   || |||   |||| || |  |||  |   | |       ||       |   |  | ||| | |     |  ||     || ||      ||  |||||||||| |||||| | ||||||||| | ||| | ||||| || || |||||||||||||| || ||||| ||   |||||| |||
gttagctaccttgactcacatcaccggccaactgcttaaccaatttctgtcctcgtg-ataagatgaatatacgtctgtttgtagaaaaccttctattatcatcagggtgaaaaagattatttgttatatcatgactcttcgtatgtcattgcgcagTGATGGATGGGACAGAACAACTCAGCTTGTTTCTCTTGCGTGCTTATTGCTTGATCCATACTACAGAACTTTTGCTGGGTTTCAG

upper sequence: LOC_Os08g44260.1 (Oryza sativa), 3'ss of exon 13
lower sequence: AT5G04540.1 (Arabidopsis thaliana), 3'ss of exon 13
------------------------tgatttcatcttagtctgtatgatctctatagttttcttgctgtgtatccctacacattgctgatgcat-atcaaattct--ctcactattttgtttttgcagTGATGGTTGGGACCGCACAACTCAGTTGGTTGCACTTGCTTGTTTGTTGCTTGATCCATATTATAGAACGTTCAATGGGTTCCAG
                            | ||| ||  |         | || |  ||| | |   ||   |  |||  |   |  |||   |  | | || ||  ||    || |   | | |||||||||| |||||| | ||||||||| ||||| | ||||| || || ||||||||||| || || ||||| ||   |||||| |||
gttagctatatatgtgataagacaaagatgcat-ttgtttcaagcaggcacttttatttacatcaggtagttaactattctcagtagattttttgttatatcctgacttgtgatgtcactgt-gcagTGATGGATGGGACAGAACAACTCAGCTGGTTTCTCTTGCATGCTTATTGCTTGATCCTTACTACAGAACATTTTCTGGGTTTCAG

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|29675876|gb|CB672151.1|CB672151
EST:     ATTGCTGCACAAATTGTCCAAGAATCAGCTTCTGTTCTCGTCCATTGCAG                         TGATGGTTGGGACCGCACAACTCAGTTGGTTGCACTTGCTTGTTTGTTGCT
genomic: ATTGCTGCACAAATTGTCCAAGAATCAGCTTCTGTTCTCGTCCATTGCAGgttttttttt ... gtttttgcagTGATGGTTGGGACCGCACAACTCAGTTGGTTGCACTTGCTTGTTTGTTGCT






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatccctacacattgctgatgcatatcaaattctctcactattttgtttttgcagTGATGGTTGGGACCGCACAACTCAGTTGGTTGCACTTGCTTGTTTGTTGCTTGATCCATATTATAGAACGTTCAATGGGTTCCAG
                                ctctcac  putative branch site (score: 3)
                              ttctctcactattttg  CT-rich tract
                                     actattttgttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgatttcatcttagtctgtatgatctctatagttttcttgctgtgtatccctacacattgctgatgcatatcaaattctctcactattttgtttttgcagTGATGGTTGGGACCGCACAACTCAGTTGGTTGCACTTGCTTGTTTGTTGCTTGATCCATATTATAGAACGTTCAATGGGTTCCAG

- - - - - - - -ctgtatg
- - - - - - - - - - - - - - - - - - -ttgctgt
- - - - - - - - - - - - - - - - - - - - - - - - ccctaca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgctgat