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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagcaaacatttctgatttcttactggatgtaatgcacatatcaatgtctagtagagtttgtggttttggtcatctgaagccaaagctttgctcatgataaccaatgcagGTTGTTCCTGTCAAAAGCCAGCTTTCCAATGCAGCAGAGCAGATGCAAGTCACGCTTGCTCCTCACTCTTTCTCCTCATTCGATCTTGCGCTTGCCCAGT

Basic information

species Oryza sativa
transcript LOC_Os12g03470.5
intron # 16
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os12g03470.5 (Oryza sativa), 3'ss of exon 16
lower sequence: GRMZM2G006130_T03 (Zea mays), 3'ss of exon 17
gtaagcaaacatttctgatttcttactggatgtaatgcacatatcaatgtctagtagagtttgtggttttggtcatctgaagccaaagctttgctcatgataaccaatgcagGTTGTTCCTGTCAAAAGCCAGCTTTCCAATGCAGCAGAGCAGATGCAAGTCACGCTTGCTCCTCACTCTTTCTCCTCATTCGATCTTGCGCTTGCCCAGT
    | |  | |  |     |   |||     |  ||    | | ||||    |       |||||   | ||  |||||| || ||   |||||  |         |||||||||  || || |||||||||||   ||| || || ||||||||||| |||||||| ||||||||||| ||| || | |||||||| ||||| ||  || 
----gtatgcgtaccatgcatgc-actaagcttgttg-gtttctgaatggaaggagcgacgtgtggagcttgt--tctgaaccccaaagcttgctgct---------tgcagGTTGCGCCGGTGAAAAGCCAGCTGAGCAACGCCGCGGAGCAGATGCAGGTCACGCTGGCTCCTCACTCCTTCACCGCCTTCGATCTGGCGCTGGCTGAGC

upper sequence: LOC_Os12g03470.5 (Oryza sativa), 3'ss of exon 16
lower sequence: GRMZM2G006130_T04 (Zea mays), 3'ss of exon 17
gtaagcaaacatttctgatttcttactggatgtaatgcacatatcaatgtctagtagagtttgtggttttggtcatctgaagccaaagctttgctcatgataaccaatgcagGTTGTTCCTGTCAAAAGCCAGCTTTCCAATGCAGCAGAGCAGATGCAAGTCACGCTTGCTCCTCACTCTTTCTCCTCATTCGATCTTGCGCTTGCCCAGT
            | |         |||     |  ||    | | ||||    |       |||||   | ||  |||||| || ||   |||||  |         |||||||||  || || |||||||||||   ||| || || ||||||||||| |||||||| ||||||||||| ||| || | |||||||| ||||| ||  || 
-----------gtaccatgcatgcactaagcttgttg-gtttctgaatggaaggagcgacgtgtggagcttgt--tctgaaccccaaagcttgctgct---------tgcagGTTGCGCCGGTGAAAAGCCAGCTGAGCAACGCCGCGGAGCAGATGCAGGTCACGCTGGCTCCTCACTCCTTCACCGCCTTCGATCTGGCGCTGGCTGAGC

upper sequence: LOC_Os12g03470.5 (Oryza sativa), 3'ss of exon 16
lower sequence: GRMZM2G077299_T03 (Zea mays), 3'ss of exon 16
---------------------------------gtaagcaaacatttctgatttcttactggatgtaatgcacatatcaatg-tctagtagagtttgtggttttggtcatctgaagccaaagctttgctcatgataac--caatgcagGTTGTTCCTGTCAAAAGCCAGCTTTCCAATGCAGCAGAGCAGATGCAAGTCACGCTTGCTCCTCACTCTTTCTCCTCATTCGATCTTGCGCTTGCCCAGT
                                 |          |  |||| |  | |   | |     || |||||   || |||  |   | ||  | | |||    ||||||  | || | |  |     | ||   |   ||||||||| || || || ||| | ||   |||||| |||||||||||||| |||||||| ||||||| ||| |||  ||| |||||||| || || || ||||
gtaaatctgcccctttgtttgcgcttattacctgcgtctgtgtgtgcctgaatggtcatatgtttctcagcgcatatttgtgctctgttttcggtttcgatcttgtgattctgaatgcgaaacctgacggtgaacaattgcgcggcagGTTGTGCCGGTAAAGAGCGATCTGAGCAATGCTGCAGAGCAGATGCAGGTCACGCTGGCTCCTCGCTCCTTCAGCTCGTTCGATCTCGCCCTGGCTCAGT

upper sequence: LOC_Os12g03470.5 (Oryza sativa), 3'ss of exon 16
lower sequence: GRMZM2G006130_T05 (Zea mays), 3'ss of exon 16
gtaagcaaac--atttctgatttct-tactggatgtaatgcacatatcaatgtctagtagagtttgtggttttggtcatctgaagccaaagctttgctcatgataaccaatgcagGTTGTTCCTGTCAAAAGCCAGCTTTCCAATGCAGCAGAGCAGATGCAAGTCACGCTTGCTCCTCACTCTTTCTCCTCATTCGATCTTGCGCTTGCCCAGT
||| ||  ||  ||     ||   |  |||     |  ||    | | ||||    |       |||||   | ||  |||||| || ||   |||||  |         |||||||||  || || |||||||||||   ||| || || ||||||||||| |||||||| ||||||||||| ||| || | |||||||| ||||| ||  || 
gtatgcgtaccgatggtccatgcatgcactaagcttgttg-gtttctgaatggaaggagcgacgtgtggagcttgt--tctgaaccccaaagcttgctgct---------tgcagGTTGCGCCGGTGAAAAGCCAGCTGAGCAACGCCGCGGAGCAGATGCAGGTCACGCTGGCTCCTCACTCCTTCACCGCCTTCGATCTGGCGCTGGCTGAGC

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|88442211|gb|CI560452.1|CI560452
EST:     TCACATCCAGCAATGTGATGGATGAGAACTCTTTTAGTAACCCGAATAAG                         GTTGTTCCTTTCAAAAGCCAGCTTTCCAATGCAGCAGAGCAGATGCAAGTC
genomic: TCACATCCAGCAATGTGATGGATGAGAACTCTTTTAGTAACCCGAATAAGgtaagcaaac ... accaatgcagGTTGTTCCTGTCAAAAGCCAGCTTTCCAATGCAGCAGAGCAGATGCAAGTC
EST: gi|86886795|gb|CI334709.1|CI334709
EST:     TCACATCCAGCAATGTGATGGATGAGAACTCTTTTAGTAACCCGAATAAG                         GTTGTTCCTGTCAAAAGCCAGCTTTCCAATGCAGCAGAGCAGATGCAAGTC
genomic: TCACATCCAGCAATGTGATGGATGAGAACTCTTTTAGTAACCCGAATAAGgtaagcaaac ... accaatgcagGTTGTTCCTGTCAAAAGCCAGCTTTCCAATGCAGCAGAGCAGATGCAAGTC
EST: gi|29672406|gb|CB668681.1|CB668681
EST:     TCACATCCAGCAATGTGATGGATGAGAACTCTTTTAGTAACCCGAATAAG                         GTTGTTCCTGTCAAAAGCCAGCTTTCCAATGCAGCAGAGCAGATGCAAGTC
genomic: TCACATCCAGCAATGTGATGGATGAGAACTCTTTTAGTAACCCGAATAAGgtaagcaaac ... accaatgcagGTTGTTCCTGTCAAAAGCCAGCTTTCCAATGCAGCAGAGCAGATGCAAGTC
EST: gi|86864008|gb|CI332931.1|CI332931
EST:     TCACATCCAGCAATGTGATGGATGAGAACTCTTTTAGTAACCCGAATAAG                         GTTTTTCCTGTCAAAAGCCAGCTTTCCAATGCAGCAGAGCAGATGCAAGTC
genomic: TCACATCCAGCAATGTGATGGATGAGAACTCTTTTAGTAACCCGAATAAGgtaagcaaac ... accaatgcagGTTGTTCCTGTCAAAAGCCAGCTTTCCAATGCAGCAGAGCAGATGCAAGTC
EST: gi|86871078|gb|CI328280.1|CI328280
EST:     TCACATCCAGCAATGTGATGGATGAGAACTCTTTTAGTAACCCGAATAAG                         GTTGTTCCTGTCAAAAGCCAGCTTTCCAATGCAGCAGAGCAGATGCAAGTC
genomic: TCACATCCAGCAATGTGATGGATGAGAACTCTTTTAGTAACCCGAATAAGgtaagcaaac ... accaatgcagGTTGTTCCTGTCAAAAGCCAGCTTTCCAATGCAGCAGAGCAGATGCAAGTC
EST: gi|88275188|gb|CI395792.1|CI395792
EST:     TCACATCCAGCAATGTGATGGATGAGAACTCTTTTAGTAACCCGAATAAG                         GTTGTTCCTGTCAAAAGCCAGCTTTCCAATGCAGCAGAGCAGATGCAAGTC
genomic: TCACATCCAGCAATGTGATGGATGAGAACTCTTTTAGTAACCCGAATAAGgtaagcaaac ... accaatgcagGTTGTTCCTGTCAAAAGCCAGCTTTCCAATGCAGCAGAGCAGATGCAAGTC
EST: gi|88991325|gb|CI034660.1|CI034660
EST:     TCACATCCAGCAAT-TGATGGATGAGAACTCTTTTAGT-ACCCG-ATAAG                         GTTGTTCCTGTC-AAAGCCAGCTTTCCGATGCAGCAGAGCAGATGCAAGTC
genomic: TCACATCCAGCAATGTGATGGATGAGAACTCTTTTAGTAACCCGAATAAGgtaagcaaac ... accaatgcagGTTGTTCCTGTCAAAAGCCAGCTTTCCAATGCAGCAGAGCAGATGCAAGTC
EST: gi|86908591|gb|CI318942.1|CI318942
EST:     TCACATCCAGCAATTTGATGGATGAGAACTCTTTTAGTAACCCGAATAAG                         GTTGTTCCTGTCAAAAGCCAGCTTTCCAATGCAGCAGAGCAGATGCAAGTC
genomic: TCACATCCAGCAATGTGATGGATGAGAACTCTTTTAGTAACCCGAATAAGgtaagcaaac ... accaatgcagGTTGTTCCTGTCAAAAGCCAGCTTTCCAATGCAGCAGAGCAGATGCAAGTC
EST: gi|15852244|gb|BI805040.1|BI805040
EST:     TCACATCCAGCAATGTGATGGATGAGAACTCTTTTAGTAACCCGAATAAG                         GTTGTTCCTGTCACAAAGCCAGCTTTCCAATGCAGCAGAGCAGATGCAAGT
genomic: TCACATCCAGCAATGTGATGGATGAGAACTCTTTTAGTAACCCGAATAAGgtaagcaaac ... accaatgcagGTTGTTCCTGTCA-AAAGCCAGCTTTCCAATGCAGCAGAGCAGATGCAAGT
EST: gi|86895695|gb|CI315979.1|CI315979
EST:     TCACATCCAGCAATGTGATGGATGAGAACTCTTTTAGTAACCCGAATAAG                         GTTGTTCCTGTCAAAAGCCAGCTTTCCAATGCAGCAGAGCAGATGCAAGTC
genomic: TCACATCCAGCAATGTGATGGATGAGAACTCTTTTAGTAACCCGAATAAGgtaagcaaac ... accaatgcagGTTGTTCCTGTCAAAAGCCAGCTTTCCAATGCAGCAGAGCAGATGCAAGTC
EST: gi|88970064|gb|CI383566.1|CI383566
EST:     TCACATCCAGCAATGTGATGGATGAGAACTCTTTTAGTAACCCGAATAAG                         GTTGTTCCTGTCAAAAGCCAGCTTTCCAATGCAGCAGAGCAGATGCAAGTC
genomic: TCACATCCAGCAATGTGATGGATGAGAACTCTTTTAGTAACCCGAATAAGgtaagcaaac ... accaatgcagGTTGTTCCTGTCAAAAGCCAGCTTTCCAATGCAGCAGAGCAGATGCAAGTC
EST: gi|86853141|gb|CI324843.1|CI324843
EST:     TCACATCCAGCAATGTGATGGATGAGAACTCTTTTAGTAACCCGAATAAG                         GTTGTTCCTGTCAAAAGCCAGCTTTCCAATGCACCAGAGCAGATGTAAGTC
genomic: TCACATCCAGCAATGTGATGGATGAGAACTCTTTTAGTAACCCGAATAAGgtaagcaaac ... accaatgcagGTTGTTCCTGTCAAAAGCCAGCTTTCCAATGCAGCAGAGCAGATGCAAGTC
EST: gi|29672405|gb|CB668680.1|CB668680
EST:     TCACATCCAGCAATGTGATGGATGAGAACTCTTTTAGTAACCCGAATAAG                         GTTGTTCCTGTCAAAAGCCAGCTTTCCAATGCAGCAGAGCAGATGCAAGTC
genomic: TCACATCCAGCAATGTGATGGATGAGAACTCTTTTAGTAACCCGAATAAGgtaagcaaac ... accaatgcagGTTGTTCCTGTCAAAAGCCAGCTTTCCAATGCAGCAGAGCAGATGCAAGTC
EST: gi|88443457|gb|CI552200.1|CI552200
EST:     TCACATCCAGCAATGTGATGGATGAGAACTCTTTTAGTAACCCGAATAAG                         GTTGTTCCTGTCAAAAGCCAGCTTTCCAATGGAGCAGAGCAGATGCAAGTC
genomic: TCACATCCAGCAATGTGATGGATGAGAACTCTTTTAGTAACCCGAATAAGgtaagcaaac ... accaatgcagGTTGTTCCTGTCAAAAGCCAGCTTTCCAATGCAGCAGAGCAGATGCAAGTC
EST: gi|88431841|gb|CI560086.1|CI560086
EST:     TCACATCCAGCAATGTGATGGATGAGAACTCTTTTAGTAACCCGAATAAG                         GTTGTTCCTGTCAAAAGCCAGCTTTCCAATGCAGCAGAGCAGATGCAAGTC
genomic: TCACATCCAGCAATGTGATGGATGAGAACTCTTTTAGTAACCCGAATAAGgtaagcaaac ... accaatgcagGTTGTTCCTGTCAAAAGCCAGCTTTCCAATGCAGCAGAGCAGATGCAAGTC
EST: gi|86840456|gb|CI333774.1|CI333774
EST:     TCACATCCAGCAATTTGATGGATGAGAACTCTTTTATTAACCCGAATAAG                         TTTGTTCCTGTCAAAAGCCAGCTTTCCAATGCAGCAGAGCAGATGCAAGTC
genomic: TCACATCCAGCAATGTGATGGATGAGAACTCTTTTAGTAACCCGAATAAGgtaagcaaac ... accaatgcagGTTGTTCCTGTCAAAAGCCAGCTTTCCAATGCAGCAGAGCAGATGCAAGTC
EST: gi|86882978|gb|CI314236.1|CI314236
EST:     TCACATCCAGCAATGTGATGGATGAGAACTCTTTTAGTAACCCGAATAAG                         GTTGTTCCTGTCAAAAGCCAGCTTTCCAATGCAGCAGAGCAGATGCAAGTC
genomic: TCACATCCAGCAATGTGATGGATGAGAACTCTTTTAGTAACCCGAATAAGgtaagcaaac ... accaatgcagGTTGTTCCTGTCAAAAGCCAGCTTTCCAATGCAGCAGAGCAGATGCAAGTC
EST: gi|86852655|gb|CI321775.1|CI321775
EST:     TCACATCCAGCAATGTGATGGATGAGAACTCTTTTAGTAACCCGAATAAG                         GTTGTTCCTGTCAAAAGCCAGCTTTCCAATGCAGCAGAGCAGATGCAAGTC
genomic: TCACATCCAGCAATGTGATGGATGAGAACTCTTTTAGTAACCCGAATAAGgtaagcaaac ... accaatgcagGTTGTTCCTGTCAAAAGCCAGCTTTCCAATGCAGCAGAGCAGATGCAAGTC
EST: gi|86839190|gb|CI331473.1|CI331473
EST:     TCACATCCAGCAATGTGATGGATGAGAACTCTTTTAGTAACCCGAATAAG                         GTTGTTCCTGTCAAAAGCCAGCTTTCCAATGCAGCAGAGCAGATGCAAGTC
genomic: TCACATCCAGCAATGTGATGGATGAGAACTCTTTTAGTAACCCGAATAAGgtaagcaaac ... accaatgcagGTTGTTCCTGTCAAAAGCCAGCTTTCCAATGCAGCAGAGCAGATGCAAGTC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agtttgtggttttggtcatctgaagccaaagctttgctcatgataaccaatgcagGTTGTTCCTGTCAAAAGCCAGCTTTCCAATGCAGCAGAGCAGATGCAAGTCACGCTTGCTCCTCACTCTTTCTCCTCATTCGATCTTGCGCTTGCCCAGT
                                        tgataac  putative branch site (score: 2)
                                       atgataa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagcaaacatttctgatttcttactggatgtaatgcacatatcaatgtctagtagagtttgtggttttggtcatctgaagccaaagctttgctcatgataaccaatgcagGTTGTTCCTGTCAAAAGCCAGCTTTCCAATGCAGCAGAGCAGATGCAAGTCACGCTTGCTCCTCACTCTTTCTCCTCATTCGATCTTGCGCTTGCCCAGT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTCCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTCCTC