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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagattatatattttatcttgttatgatctgtttatcattttcataattttgctccagaacttaccttcagttgctcctgtttctagAGTTCTTGCCAAAGTTACATACATTGGTGCTTACAAACAATCGTCTTACAAATCTTGCGGAGATCGATCCCCTGGCATCTCTTCCAAAGCTTCAGTTTCT

Basic information

species Oryza sativa
transcript LOC_Os02g13990.3
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g13990.3 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G021742_T01 (Zea mays), 3'ss of exon 3
gtaagattatatattttatcttgttatgatctgtttatcattttcataattttgctccagaacttaccttcagttgctcctgtttcta----gAGTTCTTGCCAAAGTTACATACATTGGTGCTTACAAACAATCGTCTTACAAATCTTGCGGAGATCGATCCCCTGGCATCTCTTCCAAAGCTTCAGTTTCT
      | | |  |  | | || | |  |  ||||| ||    ||  |  |||||||||    | |||||   |      | |||| |    ||||| ||||||||| | |||||  ||||||| || || |||||||| ||||||||||| ||||| |||||||||||||||||||||||||| || || ||
-----gtaagaactcctgtattctcagcacttgttt-tctgactcccacatttgctccatgcttcaccttttttcttgtttttttccatgcagAGTTTTTGCCAAAGCTGCATACGCTGGTGCTCACGAATAATCGTCTGACAAATCTTGCAGAGATTGATCCCCTGGCATCTCTTCCAAAGCTACAATTCCT

upper sequence: LOC_Os02g13990.3 (Oryza sativa), 3'ss of exon 3
lower sequence: PP1S152_48V6.2 (Physcomitrella patens), 3'ss of exon 4
------------gtaagattatatattttatcttgttatgatctgtttatcattttcataattttgctccagaacttaccttca-gttgctcctgtttctagAGTTCTTGCCAAAGTTACATACATTGGTGCTTACAAACAATCGTCTTACAAATCTTGCGGAGATCGATCCCCTGGCATCTCTTCCAAAGCTTCAGTTTCT
            |       |  |||  |     ||    |   ||   | ||   ||| | |   ||  | || |   ||  | ||||    |||    || |   || |||||| |  | ||||||||||||||||||||||| ||| ||||||| | |||  | || |  ||     | |||   || || |||  | |
atccatacgtttgggttgcgaggtatccttctcagtgcacaggagtaattaataaacatgaatgctcttaataagtgttctgaaagttgtggttgtgc--agCGGCATTACCAAAGCTGGAGACATTGGTGCTTACAAACAATCGGCTTTCAAATCTGGTGGACCTTGACCATCTTCGGACACTTGTGAATCTGCAGAATTT
















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|218492413|gb|FG947005.1|FG947005
EST:     TCTGTTAGTTAACAATAACAGAATCACACGTATCAATCCCAATCTTGGTG                         AGTTCTTGCCAAAGTTACATACATTGGTGCTTACAAACAATCGTCTTACAA
genomic: TCTGTTAGTTAACAATAACAGAATCACACGTATCAATCCCAATCTTGGTGgtaagattat ... ctgtttctagAGTTCTTGCCAAAGTTACATACATTGGTGCTTACAAACAATCGTCTTACAA
EST: gi|29681478|gb|CB677753.1|CB677753
EST:     TCTGTTAGTTAACAATAACAGAATCACACGTATCAATCCCAATCTTGGTG                         AGTTCTTGCCAAAGTTACATACATTGGTGCTTACAAACAATCGTCTTACAA
genomic: TCTGTTAGTTAACAATAACAGAATCACACGTATCAATCCCAATCTTGGTGgtaagattat ... ctgtttctagAGTTCTTGCCAAAGTTACATACATTGGTGCTTACAAACAATCGTCTTACAA
EST: gi|86904173|gb|CI306591.1|CI306591
EST:     TCTGTTAGTTAACAATAACAGAATCACACGTATCAATCCCAATCTTGGTG                         AGTTCTTGCCAAAGTTACATACATTGGTGCTTACA
genomic: TCTGTTAGTTAACAATAACAGAATCACACGTATCAATCCCAATCTTGGTGgtaagattat ... ctgtttctagAGTTCTTGCCAAAGTTACATACATTGGTGCTTACA
EST: gi|58602112|gb|CK012640.1|CK012640
EST:     TCTGTTAGTTAACAATAACAGAATCACACGTATCAATCCCAATCTTGGTG                         AGTTCTTGCCAAAGTTACATACATTGGTGCTTACAAACAATCGTCTTACAA
genomic: TCTGTTAGTTAACAATAACAGAATCACACGTATCAATCCCAATCTTGGTGgtaagattat ... ctgtttctagAGTTCTTGCCAAAGTTACATACATTGGTGCTTACAAACAATCGTCTTACAA
EST: gi|58662231|gb|CK050911.1|CK050911
EST:     TCTGTTAGTTAACAATAACAGAATCACACGTATCAATCCCAATCTTGGTG                         AGTTCTTGCCAAAGTTACATACATAGGTGCTTACAAACAATCGTCTTACAA
genomic: TCTGTTAGTTAACAATAACAGAATCACACGTATCAATCCCAATCTTGGTGgtaagattat ... ctgtttctagAGTTCTTGCCAAAGTTACATACATTGGTGCTTACAAACAATCGTCTTACAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttatcattttcataattttgctccagaacttaccttcagttgctcctgtttctagAGTTCTTGCCAAAGTTACATACATTGGTGCTTACAAACAATCGTCTTACAAATCTTGCGGAGATCGATCCCCTGGCATCTCTTCCAAAGCTTCAGTTTCT
                          aacttac  putative branch site (score: 2)
                                       ttgctcctgtttct  putative PPT
     attttcataatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagattatatattttatcttgttatgatctgtttatcattttcataattttgctccagaacttaccttcagttgctcctgtttctagAGTTCTTGCCAAAGTTACATACATTGGTGCTTACAAACAATCGTCTTACAAATCTTGCGGAGATCGATCCCCTGGCATCTCTTCCAAAGCTTCAGTTTCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATC