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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ccgagacatgatccatctgcacgcatgacttagcaaaattttgtactactacatttggaaactgacaggcaagtaactaaactggtttttgtcttttcagGTGAAAGGGCTCCTGAAAGAGAAGAAGGTGGAGATGCTGGTGGACCCGGACCTCCAGAGCGGCTTCGTGGAGCATGAGGTGGAGTCACTCATCCAGGTGG

Basic information

species Oryza sativa
transcript LOC_Os04g38480.1
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os04g38480.1 (Oryza sativa), 3'ss of exon 10
lower sequence: GRMZM5G870959_T01 (Zea mays), 3'ss of exon 10
----------------------------------ccgagacatgatccatctgcacgcatgacttagc-----aaaattttgtactactacatttggaaactgacag-gcaagtaactaaactggt---------ttttgtcttttcagGTGAAAGGGCTCCTGAAAGAGAAGAAGGTGGAGATGCTGGTGGACCCGGACCTCCAGAGCGGCTTCGTGGAGCATGAGGTGGAGTCACTCATCCAGGTGG
                                    |||  |   |  | ||   | |    || ||       |      | |  |  | ||   ||| |||     ||   |   ||  || ||         || |||  || |||||||| | ||| ||||| ||||||||| |||||  |||||||||||||||||| ||| || | | |||||| || ||||||||||| || ||||||||||
gtaggtggagtcgatctttgagtatgagtacactatgaggtaccttgtacctagcctcggtgctaaggcctgagagggagggaagaaagaaatgaagaagctgctgctgctgctgcatatgcttgtggcggggtgttgtgtgcttgcagGTGAAGGCGCTGCTGAAGGAGAAGAAGCTGGAGCAGCTGGTGGACCCGGACCTGCAGGGCCGGTACGTGGACCAGGAGGTGGAGTCGCTGATCCAGGTGG

upper sequence: LOC_Os04g38480.1 (Oryza sativa), 3'ss of exon 10
lower sequence: AT1G34210.1 (Arabidopsis thaliana), 3'ss of exon 10
ccgagacatgatccatctgcacgcatgacttagcaaaattttgtactactacatttggaaa-ctgacaggcaagtaactaaactggt--ttttgtcttttcagGTGAAAGGGCTCCTGAAAGAGAAGAAGGTGGAGATGCTGGTGGACCCGGACCTCCAGAGCGGCTTCGTGGAGCATGAGGTGGAGTCACTCATCCAGGTGG
                      | || ||  ||    || || ||  || | || |||  | ||  ||   |  | | | | ||| |  ||| ||||| |||||||||||||||  |||| ||||||||| |||||||||| ||||| || ||||| || |||   | |   ||    || || ||    ||||| || ||||
----------------------gtataacacag----atcttttagcac-atatctggctatctctcaaaaagctgatttatctgttcatttggtcttctcagGTGAAAGGGCTTTTGAAGGAGAAGAAGCTGGAGATGCTTGTGGATCCTGACCTGCAAAGCAATTACACAGAAGCAGAAGTAGAACAGCTCATACAAGTGG
















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|86482096|gb|CI124729.1|CI124729
EST:     TGATGTGATGTTGCTCGATTGG                         GTGAAAGGGCTCCTGAAAGAGAAGAAGGTGGAGATGCTGGTGGACCCGGAC
genomic: TGATGTGATGTTGCTCGATTGGgtaagtacca ... gtcttttcagGTGAAAGGGCTCCTGAAAGAGAAGAAGGTGGAGATGCTGGTGGACCCGGAC
EST: gi|44670535|gb|CR283969.1|CR283969
EST:     TGTGATGTTGCTTGATTGG                         GTGAAAGGGCTCCTGAAAGAGAAGAAGGTGGAGATGCTGGTGGACCCGGAC
genomic: TGTGATGTTGCTCGATTGGgtaagtacca ... gtcttttcagGTGAAAGGGCTCCTGAAAGAGAAGAAGGTGGAGATGCTGGTGGACCCGGAC
EST: gi|41883645|gb|BX928529.1|BX928529
EST:     TTGATCTTGCTCGTCTTGCAAACGATGATCATGTGATGTTGCTCGATTGG                         GTGAAAGGGCTCCTGAAAGAGAAGAAGGTGGAGATGCTGGTGGACCCGGAC
genomic: TTGATCTTGCTCGTCTTGCAAACGATGATGATGTGATGTTGCTCGATTGGgtaagtacca ... gtcttttcagGTGAAAGGGCTCCTGAAAGAGAAGAAGGTGGAGATGCTGGTGGACCCGGAC
EST: gi|29675544|gb|CB671819.1|CB671819
EST:     TTGATCTTGCTCGTCTTGCAAACGATGATGATGTGATGTTGCTCGATTGG                         GTGAAAGGGCTCCTGAAAGAGAAGAAGGTGGAGATGCTGGTGGACCCGGAC
genomic: TTGATCTTGCTCGTCTTGCAAACGATGATGATGTGATGTTGCTCGATTGGgtaagtacca ... gtcttttcagGTGAAAGGGCTCCTGAAAGAGAAGAAGGTGGAGATGCTGGTGGACCCGGAC
EST: gi|87035916|gb|CI190538.1|CI190538
EST:     TTGCTCGTCTTGCGAACGATGATGATGTGATGTTGCTCGATT-G                         GTGAAAGGGCTCCTGAAAGAGAAGAAGCTGGAAATGCTGGTGGACCCGGAC
genomic: TTGCTCGTCTTGCAAACGATGATGATGTGATGTTGCTCGATTGGgtaagtacca ... gtcttttcagGTGAAAGGGCTCCTGAAAGAGAAGAAGGTGGAGATGCTGGTGGACCCGGAC
EST: gi|29675502|gb|CB671777.1|CB671777
EST:     TTGATCTTGCTCGTCTTGCAAACGATGATGATGTGATGTTGCTCGATTGG                         GTGAAAGGGCTCCTGAAAGAGAAGAAGGTGGAGATGCTGGTGGACCCGGAC
genomic: TTGATCTTGCTCGTCTTGCAAACGATGATGATGTGATGTTGCTCGATTGGgtaagtacca ... gtcttttcagGTGAAAGGGCTCCTGAAAGAGAAGAAGGTGGAGATGCTGGTGGACCCGGAC
EST: gi|87039761|gb|CI194383.1|CI194383
EST:     TTGATCTTGCTCGTCTTGCAAACGATGATGATGTGATGTTGCTCGATTGG                         GTGAAAGGGCTCCTGAAAGAGAAGAAGGTGGAGATGCTGGTGGACCCGGAC
genomic: TTGATCTTGCTCGTCTTGCAAACGATGATGATGTGATGTTGCTCGATTGGgtaagtacca ... gtcttttcagGTGAAAGGGCTCCTGAAAGAGAAGAAGGTGGAGATGCTGGTGGACCCGGAC
EST: gi|29614688|gb|CB619701.1|CB619701
EST:     TTGATCTTGCTCGTCTTGCAAACGATGATGATGTGATGTTGCTCGATTGG                         GTGAAAGGGCTCCTGAAAGAGAAGAAGGTGGAGATGCTGGTGGACCCGGAC
genomic: TTGATCTTGCTCGTCTTGCAAACGATGATGATGTGATGTTGCTCGATTGGgtaagtacca ... gtcttttcagGTGAAAGGGCTCCTGAAAGAGAAGAAGGTGGAGATGCTGGTGGACCCGGAC
EST: gi|29614453|gb|CB619466.1|CB619466
EST:     TTGATCTTGCTCGTCTTGCAAACGATGATGATGTGATGTTGCTCGATTGG                         GTGAAAGGGCTCCTGAAAGAGAAGAAGGTGGAGATGCTGGTGGACCCGGAC
genomic: TTGATCTTGCTCGTCTTGCAAACGATGATGATGTGATGTTGCTCGATTGGgtaagtacca ... gtcttttcagGTGAAAGGGCTCCTGAAAGAGAAGAAGGTGGAGATGCTGGTGGACCCGGAC
EST: gi|86903581|gb|CI300435.1|CI300435
EST:     TTGATCTTGCTCGTCTTGCAAACGATGATGATGTGATGTTGCTCGATTGG                         GTGAAAGGGCTCCTGAAAGAGAAGAAGGTGGAGATGCTGGTGGACCCGGAC
genomic: TTGATCTTGCTCGTCTTGCAAACGATGATGATGTGATGTTGCTCGATTGGgtaagtacca ... gtcttttcagGTGAAAGGGCTCCTGAAAGAGAAGAAGGTGGAGATGCTGGTGGACCCGGAC
EST: gi|88964773|gb|CI084771.1|CI084771
EST:     TTGATCTTGCTCGTCTTGCAAACGATGATGATGTGATGTTGCTCGATTGG                         GTGAAAGGGCTCCTGAAAGAGAAGAAGGTGGAGATGCTGGTGGACCCGGAC
genomic: TTGATCTTGCTCGTCTTGCAAACGATGATGATGTGATGTTGCTCGATTGGgtaagtacca ... gtcttttcagGTGAAAGGGCTCCTGAAAGAGAAGAAGGTGGAGATGCTGGTGGACCCGGAC
EST: gi|29623135|gb|CB628146.1|CB628146
EST:     TTGATCTTGCTCGTCTTGCAAACGATGATGATGTGATGTTGCTCGATTGG                         GTGAAAGGGCTCCTGAAAGAGAAGAAGGTGGAGATGCTGGTGGACCCGGAC
genomic: TTGATCTTGCTCGTCTTGCAAACGATGATGATGTGATGTTGCTCGATTGGgtaagtacca ... gtcttttcagGTGAAAGGGCTCCTGAAAGAGAAGAAGGTGGAGATGCTGGTGGACCCGGAC
EST: gi|29626769|gb|CB631780.1|CB631780
EST:     TTGATCTTGCTCGTCTTGCAAACGATGATGATGTGATGTTGCTCGATTGG                         GTGAAAGGGCTCCTGAAAGAGAAGAAGGTGGAGATGCTGGTGGACCCGGAC
genomic: TTGATCTTGCTCGTCTTGCAAACGATGATGATGTGATGTTGCTCGATTGGgtaagtacca ... gtcttttcagGTGAAAGGGCTCCTGAAAGAGAAGAAGGTGGAGATGCTGGTGGACCCGGAC
EST: gi|87040035|gb|CI193244.1|CI193244
EST:     TTGATCTTGCTCGTCTTGCAAACGATGATGATGTGATGTTGCTCGATTGG                         GTGAAAGGGCTCCTGAAAGAGAAGAAGGTGGAGATGCTGGTGGACCCGGAC
genomic: TTGATCTTGCTCGTCTTGCAAACGATGATGATGTGATGTTGCTCGATTGGgtaagtacca ... gtcttttcagGTGAAAGGGCTCCTGAAAGAGAAGAAGGTGGAGATGCTGGTGGACCCGGAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctactacatttggaaactgacaggcaagtaactaaactggtttttgtcttttcagGTGAAAGGGCTCCTGAAAGAGAAGAAGGTGGAGATGCTGGTGGACCCGGACCTCCAGAGCGGCTTCGTGGAGCATGAGGTGGAGTCACTCATCCAGGTGG
                             aactaaa  putative branch site (score: 2)
                                        tttttgtcttttc  putative PPT
                            taactaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ccgagacatgatccatctgcacgcatgacttagcaaaattttgtactactacatttggaaactgacaggcaagtaactaaactggtttttgtcttttcagGTGAAAGGGCTCCTGAAAGAGAAGAAGGTGGAGATGCTGGTGGACCCGGACCTCCAGAGCGGCTTCGTGGAGCATGAGGTGGAGTCACTCATCCAGGTGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - -acatgat
- - - - - - - - -tgcacgc
- - - - - - - - - - - - - - - -agcaaaa
- - - - - - - - - - - - - - - - - - - - - - - - - acatttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -caggcaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aactaaa