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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagattgattgacatttcctccactgcgcatgttagaagaggcttctgatgattagCAAGATTTATTTCCTGTTATGTAGATCCTTCCACCACCAATCTCAAGGACAGATTTCGAGAAAGTCCTCGCCAGGCAGAGACCGACAGTGAGCAAGAAAG

Basic information

species Oryza sativa
transcript LOC_Os01g04814.4
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g04814.4 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G126860_T01 (Zea mays), 3'ss of exon 7
gtaagattgattgacatttcctccactgcgcatgttagaagaggcttctgat--gattagCAAGATTTA--TTTCCTGTT----ATGTAGATCCTTCCACCACCAATCTCAAGGACAGATTTCGAGAAAGTCCTCGCCAGGCAGAGACCGACAGTGAGCAAGAAAG------------------------
||||       || |  |||   || |||  |||| |||   ||||||   |    ||   ||| || |  | |  ||||    |||||||| ||||||||||| ||||||||||| ||||| ||||| ||| |  | |||||||| |||||||| |||||||| |                        
gtaacgaaagatgccgattctatcattgca-atgtgagagagggcttccagttgagttgttaaggttaaggtgttttgttttgaatgtagATTCTTCCACCACCTATCTCAAGGACGGATTTTGAGAAGGTCTTGTCGAGGCAGAGGCCGACAGTTAGCAAGAAGGATCTGGAGGTGCATGAGAGGTTCA

upper sequence: LOC_Os01g04814.4 (Oryza sativa), 3'ss of exon 7
lower sequence: Vv13s0106g00490.t01 (Vitis vinifera), 3'ss of exon 7
-------------------gtaagattgattgacatttcctccactgcgcatgttagaagaggcttctgatgattagCAAGATTTATTTCCTGTTATGTAGATCCTTCCACCACCAATCTCAAGGACAGATTTCGAGAAAGTCCTCGCCAGGCAGAGACCGACAGTGAGCAAGAAAG------------------------
                    ||   |    | |    |      ||   |||  |  |||  |  |    | ||         ||| |      |  | ||||||| || || || ||||||||||| ||||| || ||||| || || || |||||||| |||||||||||   ||                        
ttctaaagaactgcaatttctagcttcagctaattgcttgggttcttt-catcctgaaaggtgactgaatttatccttgttggttactgatgacttggcagATCCTCCCTCCGCCCATCTCAAGGACTGATTTTGAAAAAGTACTAGCAAGACAGAGACCAACAGTGAGCAAAGCAGATCTGGAGGTGCACAATAGATTCA
















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|58594912|gb|CF993220.1|CF993220
EST:     CCGTACAAACAACCATGCAGGAGCTCGCATCCAAGGGCCTTGCAGCAAAG                         CAAGATTTATTTCCTGTTATGTAGATCCTTCCACCACCAATCTCAAGGACA
genomic: CCGTACAAACAACCATGCAGGAGCTCGCATCCAAGGGCCTTGCAGCAAAGgtaagattga ... tgatgattagCAAGATTTATTTCCTGTTATGTAGATCCTTCCACCACCAATCTCAAGGACA
EST: gi|58588110|gb|CF986418.1|CF986418
EST:     CCGTACAAACAACCATGCAGGAGCTCGCATCCAAGGGCCTTGCAGCAAAG                         CAAGATTTATTTCCTGTTATGTA
genomic: CCGTACAAACAACCATGCAGGAGCTCGCATCCAAGGGCCTTGCAGCAAAGgtaagattga ... tgatgattagCAAGATTTATTTCCTGTTATGTA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agattgattgacatttcctccactgcgcatgttagaagaggcttctgatgattagCAAGATTTATTTCCTGTTATGTAGATCCTTCCACCACCAATCTCAAGGACAGATTTCGAGAAAGTCCTCGCCAGGCAGAGACCGACAGTGAGCAAGAAAG
                                          ttctgat  putative branch site (score: 3)
                                         cttct  CT-rich tract
                                               atgatta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagattgattgacatttcctccactgcgcatgttagaagaggcttctgatgattagCAAGATTTATTTCCTGTTATGTAGATCCTTCCACCACCAATCTCAAGGACAGATTTCGAGAAAGTCCTCGCCAGGCAGAGACCGACAGTGAGCAAGAAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA