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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgggcatcttttgactcttcctaattaatcttgacagttcaatgcagccttttcaattttttaatttgtggccttcttttacagGATGTCTGTTGAGATGGTTGCTTGTATAGGTATAGAGGCCATCTCCATACTAGAGAAGATGCATGCTAAAGG

Basic information

species Oryza sativa
transcript LOC_Os01g10150.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g10150.2 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G045259_T01 (Zea mays), 3'ss of exon 5
gtgggcatcttttgactcttcctaattaatcttgacagtt-caatgcagccttttcaattttttaatttgtggccttcttttacagGATGTCTGTTGAGATGGTTGCTTGTATAGGTATAGAGGCCATCTCCATACTAGAGAAGATGCATGCTAAAGG
||||| ||||    | ||||   |||||  ||| || ||| | ||     |||| ||||  ||     || |    |||||||||||||||||||||||||||||||||| |||||||||||||| ||||||||||| || ||||||||  |||||||
gtgggtatctgcacattctttgcaattacacttcactgtttctatttgatctttccaatcattc---ctgagcttgtcttttacagGATGTCTGTTGAGATGGTTGCTTGCATAGGTATAGAGGCAATCTCCATACTGGAAAAGATGCACTCTAAAGG

upper sequence: LOC_Os01g10150.2 (Oryza sativa), 3'ss of exon 5
lower sequence: GLYMA06G09190.1 (Glycine max), 3'ss of exon 5
gtgggcatcttttgactcttcctaattaat-cttgacagttcaatgcagccttttcaattttttaatttgtggccttcttt----------tacagGATGTCTGTTGAGATGGTTGCTTGTATAGGTATAGAGGCCATCTCCATACTAGAGAAGATGCATGCTAAAGG
||| | |||| |  | | ||   |  |||| | |   | ||   |  |   | |  |   | || | | | | |  | |||          | ||||||||||  ||| |||||||| ||||| |  || ||||| ||||||||| |||||||||||||| ||| |||
gtgagtatctctgaaatgttgaaatgtaatgcatcttatttttcttaatgttatagagaatattgaatagcgactctttttccttttgggtttcagGATGTCTACTGAAATGGTTGCATGTATTGCAATTGAGGCTATCTCCATATTAGAGAAGATGCATTCTAGAGG

upper sequence: LOC_Os01g10150.2 (Oryza sativa), 3'ss of exon 5
lower sequence: GLYMA04G09080.1 (Glycine max), 3'ss of exon 5
----------------------------gtgggcatcttttgactcttcctaat-taatcttgacagttcaat-gcagccttttcaattttttaatttgtggccttcttttacagGATGTCTGTTGAGATGGTTGCTTGTATAGGTATAGAGGCCATCTCCATACTAGAGAAGATGCATGCTAAAGG
                             ||     | | | | | ||| |||| | ||   ||   || ||| ||   |||||   | ||||   || |||  |||      |||||||||  ||| |||||||| ||||| |  || ||||| ||||||||| |||||||||||||| ||| |||
gtgagtatctatctgaaatgatattgaaatgtaatgcatcttatttttcttaatgttatagagaatattgaatagctaacttttatttctttttccttttgggtttc------agGATGTCTACTGAAATGGTTGCATGTATTGCAATCGAGGCTATCTCCATATTAGAGAAGATGCATTCTAGAGG

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|29688778|gb|CB685053.1|CB685053
EST:     GATATGTTGGGACCGAGCCTGTGGGATGTTTGGAATAACAATTCCCACTC                         GATGTCTGTTGAGATGGTCGCTTGTATAGGTATAGAGGCCATCTCCATACT
genomic: GATATGTTGGGACCGAGCCTGTGGGATGTTTGGAATAACAATTCCCACTCgtgggcatct ... tcttttacagGATGTCTGTTGAGATGGTTGCTTGTATAGGTATAGAGGCCATCTCCATACT
EST: gi|29630440|gb|CB635449.1|CB635449
EST:     GATATGTTGGGACCGAGCCTGTGGGATGTTTGGAATAACAATTCCCACTC                         GATGTCTGTTGAGATGGTTGCTTGTATAGGTATAGAGGCCATCTCCATACT
genomic: GATATGTTGGGACCGAGCCTGTGGGATGTTTGGAATAACAATTCCCACTCgtgggcatct ... tcttttacagGATGTCTGTTGAGATGGTTGCTTGTATAGGTATAGAGGCCATCTCCATACT
EST: gi|88573975|gb|CI665744.1|CI665744
EST:     TGGGACCGAGCCTGTGGGATGTTTGGAATAACAATTCCCACTC                         GATGTCTGTTGAGATGGTTGCTTGTATAGGTATAGAGGCCATCTCCATACT
genomic: TGGGACCGAGCCTGTGGGATGTTTGGAATAACAATTCCCACTCgtgggcatct ... tcttttacagGATGTCTGTTGAGATGGTTGCTTGTATAGGTATAGAGGCCATCTCCATACT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttgacagttcaatgcagccttttcaattttttaatttgtggccttcttttacagGATGTCTGTTGAGATGGTTGCTTGTATAGGTATAGAGGCCATCTCCATACTAGAGAAGATGCATGCTAAAGG
                             ttttaat  putative branch site (score: 3)
                                          ccttcttttac  putative PPT
                    ttttcaattttttaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgggcatcttttgactcttcctaattaatcttgacagttcaatgcagccttttcaattttttaatttgtggccttcttttacagGATGTCTGTTGAGATGGTTGCTTGTATAGGTATAGAGGCCATCTCCATACTAGAGAAGATGCATGCTAAAGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG