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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ggatatattttgaccctaaagtttaaattaaggggtctaggcagctttgatttaattttctgattgttgaggtttgctattatattttgttgatcctcagGTTTGGGAGGTGAAAGCTGCTGATTTGAGCATTAGTCCTGTGCATCGTGCTGCCAATGGTATAGTTGATCCGAACAAG

Basic information

species Oryza sativa
transcript LOC_Os10g34750.1
intron # 14
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os10g34750.2 (Oryza sativa), 3'ss of exon 14
lower sequence: GRMZM2G071304_T01 (Zea mays), 3'ss of exon 14
ggatatattttgaccctaaagtttaaattaaggggtctaggcagctttgatttaattttctgattgttgaggtttgcta--ttatattttgttgatcctca--gGTTTGGGAGGTGAAAGCTGCTGATTTGAGCATTAGTCCTGTGCATCGTGCTGCCAATGGTATAGTTGATCCGAACAAG
   |  |  ||  |||| ||| ||   |  |      |||   |    |       ||   |  |||||  |||   ||  |||| |||| ||| |  |||  ||| |||||||| |||||||| ||| ||||||| || ||||| ||||||||||||||||||||||| ||||| || |||
---ttcacatttgccctgaagattgcttgtaacacagtagatgggaaagggcgcggttaa-gcctgttgcagttaattaaattattttttcttgcttttcacagGTCTGGGAGGTCAAAGCTGCCGATCTGAGCATAAGCCCTGTACATCGTGCTGCCAATGGTATAGTCGATCCAAATAAG

upper sequence: LOC_Os10g34750.2 (Oryza sativa), 3'ss of exon 14
lower sequence: GLYMA12G08600.1 (Glycine max), 3'ss of exon 14
ggatatattttgaccctaaagtttaaattaaggggtctaggcagctttgatttaattttctgattgttgaggtttgct--attatattttg--ttgatcc--tcagGTTTGGGAGGTGAAAGCTGCTGATTTGAGCATTAGTCCTGTGCATCGTGCTGCCAATGGTATAGTTGATCCGAACAAG
  ||   |||| |     |  |||  ||        | |   |  |    | | ||  |   |     ||  ||| ||   |||||| ||   ||  | |   ||||| ||||||||||||||||| ||  ||| |||||| ||||| || ||||||||    || ||||| ||||||||||||
caatgccttttcatttatatatttttatc------ccgacaaaattgcattatgatcgttgtagcaaagatatttacttagttatatgttaccttatttcatccagGTGTGGGAGGTGAAAGCTGCCGACCTGACCATTAGCCCTGTTCACCGTGCTGCAGTGGGCATAGTAGATCCGAACAAG

upper sequence: LOC_Os10g34750.2 (Oryza sativa), 3'ss of exon 14
lower sequence: Vv06s0061g00690.t01 (Vitis vinifera), 3'ss of exon 14
ggatatattttgaccctaaagtttaaattaaggggtctaggcagctt-tgatttaattttctgattgttgaggtttgctattatattttgttgatcct-cagGTTTGGGAGGTGAAAGCTGCTGATTTGAGCATTAGTCCTGTGCATCGTGCTGCCAATGGTATAGTTGATCCGAACAAG
   || || | ||     ||   |   ||   | | |  ||||  |  | ||   | |   |   |  |      ||  | ||||   |  |  |  | ||||||||||||||||||||||| || |||| |||||| ||||| |||||||||||   ||| ||||| ||||| ||||||
-agta-atctggatgaataaacatctgttctcgagacatggcatttgatcatcagagtgcatatgttatattaaatgtaaatataaagtaattcttttgcagGTTTGGGAGGTGAAAGCTGCAGACTTGACCATTAGCCCTGTTCATCGTGCTGCAGTTGGAATAGTGGATCCTAACAAG

upper sequence: LOC_Os10g34750.2 (Oryza sativa), 3'ss of exon 14
lower sequence: PP1S223_54V6.2 (Physcomitrella patens), 3'ss of exon 16
-------ggatatattttgaccctaaagtttaaattaaggggtctaggcagctttgatttaattttctg-attgttgaggtttgctattatattttgttgatcctcagGTTTGGGAGGTGAAAGCTGCTGATTTGAGCATTAGTCCTGTGCATCGTGCTGCCAATGGTATAGTTGATCCGAACAAG
           | | || ||   |  |    | ||| ||   || |||    ||  |||   ||| | | ||  |  | | |   |||| ||||| |||  ||  ||||| ||||||||||| |||||||||||||| ||||| ||||| ||||| || ||    ||  | |||||||| || |||
aagcttcaagaacacttggaaagtgca--caagatttagttatcgaggtcttttctattc--tttacagtatcatctatgctca-tatt-tatttggtt--tcggcagGTCTGGGAGGTGAAGGCTGCTGATTTGAGTATTAGCCCTGTCCATCGAGCAGCTGTGGGATTGGTTGATCCCAATAAG

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|8857707|gb|AU095025.1|AU095025
EST:     GCTGACACAATGGACCCAGATGTGTGGTTTGAGCCTTCAGAG                         GTTTGGGAGGTGAAAGCTGCTGATTTGAGCATTAGTCCTGTGCATCGTGCT
genomic: GCTGACACAATGGACCCAGATGTGTGGTTTGAGCCTTCAGAGgtaatgccca ... tgatcctcagGTTTGGGAGGTGAAAGCTGCTGATTTGAGCATTAGTCCTGTGCATCGTGCT
EST: gi|29629335|gb|CB634346.1|CB634346
EST:     ATAGGTTTGCTGACACAATGGACCCAGATGTGTGGTTTGAGCCTTCAGAG                         GTTTGGGAGGTGAAAGCTGCTGATTTGAGCATTAGTCCTGTGCATCGTGCT
genomic: ATAGGTTTGCTGACACAATGGACCCAGATGTGTGGTTTGAGCCTTCAGAGgtaatgccca ... tgatcctcagGTTTGGGAGGTGAAAGCTGCTGATTTGAGCATTAGTCCTGTGCATCGTGCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttgatttaattttctgattgttgaggtttgctattatattttgttgatcctcagGTTTGGGAGGTGAAAGCTGCTGATTTGAGCATTAGTCCTGTGCATCGTGCTGCCAATGGTATAGTTGATCCGAACAAG
                                       ttttgtt  CT-rich tract
                                tattatattttgttga  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ggatatattttgaccctaaagtttaaattaaggggtctaggcagctttgatttaattttctgattgttgaggtttgctattatattttgttgatcctcagGTTTGGGAGGTGAAAGCTGCTGATTTGAGCATTAGTCCTGTGCATCGTGCTGCCAATGGTATAGTTGATCCGAACAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC