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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagttcacttctgtaaaattgccgccctcggcacttatagaattgtattttctttctacacaaataaaactcattgcttcgtgactaataattaaggatttttcttttctgcatctttgttataattggcattcctgatgataactgagctatttctgcttgtaaagGTGACAGTAACTTAAACCTAGACTGGGTAATGCGCTTCGAGATCATTTTAGGAATAGCAAGAGGGCTAACTTATCTTCATGAGGAGTCAAGTGTACGCAT

Basic information

species Oryza sativa
transcript LOC_Os05g17604.3
intron # 20
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os05g17604.3 (Oryza sativa), 3'ss of exon 20
lower sequence: Vv00s0125g00090.t01 (Vitis vinifera), 3'ss of exon 21
gtgagttcacttctgtaaaattgccgccctcggcacttatagaattgtattttctttctacacaaataaaactcattgcttcgtgactaataattaaggatttttcttttctgcatctttgttataattggcattcctgatgataactgagctatttctgcttgtaaagGTGACAGTAACTTAAACCTAGACTGGGTAATGCGCTTCGAGATCATTTTAGGAATAGCAAGAGGGCTAACTTATCTTCATGAGGAGTCAAGTGTACGCAT
                                                                | | |  ||  |       ||| |   || |    | || |          | | ||   || |||    |  |||   ||| || | ||   ||  |||   |||  | | | | ||| | || || |||  ||  ||||   | ||   ||| |||| |||||||||| || |||||||||||||||| |||||     | ||
----------------------------------------------------------------acttattcttttctagaaatgattttgaactctaaagttcttacagtcaggtttatgacttatttgaaggttttgac--taaatggg-tagcactatttgc--agGGAAAATTGATTTACATCTTGATTGGCCAACCCGCTATAATATATGTTTGGGAACAGCAAGAGGGTTAGCTTATCTTCATGAGGAATCAAGGCCGAGAAT
















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|29680540|gb|CB676815.1|CB676815
EST:     GTTGGTTTATGAGTACCTTGAAAATGGAAGCTTAGATCGAGCAATCTTTG                         GTGACAGTAACTTAAACCTAGACTGGGTAATGCGCTTCGAGATCATTTTAG
genomic: GTTGGTTTATGAGTACCTTGAAAATGGAAGCTTAGATCGAGCAATCTTTGgtgagttcac ... gcttgtaaagGTGACAGTAACTTAAACCTAGACTGGGTAATGCGCTTCGAGATCATTTTAG
EST: gi|29676653|gb|CB672928.1|CB672928
EST:     GTTGGTTTATGAGTACCTTGAAAATGGAAGCTTAGATCGAGCAATCTTTG                         GTGACAGTAACTTAAACCTAGACTGGGTAATGCGCTTCGAGATCATTTTAG
genomic: GTTGGTTTATGAGTACCTTGAAAATGGAAGCTTAGATCGAGCAATCTTTGgtgagttcac ... gcttgtaaagGTGACAGTAACTTAAACCTAGACTGGGTAATGCGCTTCGAGATCATTTTAG
EST: gi|29624376|gb|CB629387.1|CB629387
EST:     GTTGGTTTATGAGTACCTTGAAAATGGAAGCTTAGATCGAGCAATCTTTG                         -T-A-A----CTTAAACCTAGACTGGGTAATGCGCTTCGAGATCATTTTAG
genomic: GTTGGTTTATGAGTACCTTGAAAATGGAAGCTTAGATCGAGCAATCTTTGgtgagttcac ... gcttgtaaagGTGACAGTAACTTAAACCTAGACTGGGTAATGCGCTTCGAGATCATTTTAG
EST: gi|29664574|gb|CB660849.1|CB660849
EST:     GTTGGTTTATGAGTACCTTGAAAATGGAAGCTTAGATCGAGCAATCTTTG                         GTGACAGTAACTTAAACCTAGACTGGGTAATGCGCTTCGAGATCATTTTAG
genomic: GTTGGTTTATGAGTACCTTGAAAATGGAAGCTTAGATCGAGCAATCTTTGgtgagttcac ... gcttgtaaagGTGACAGTAACTTAAACCTAGACTGGGTAATGCGCTTCGAGATCATTTTAG
EST: gi|29630956|gb|CB635965.1|CB635965
EST:     GTTGGTTTATGAGTACCTTGAAAATGGAAGCTTAGATCGAGCAATCTTTG                         GTGACAGTAACTTAAACCTAGACTGGGTAATGCGCTTCGAGATCATTTTAG
genomic: GTTGGTTTATGAGTACCTTGAAAATGGAAGCTTAGATCGAGCAATCTTTGgtgagttcac ... gcttgtaaagGTGACAGTAACTTAAACCTAGACTGGGTAATGCGCTTCGAGATCATTTTAG
EST: gi|29672836|gb|CB669111.1|CB669111
EST:     GTTGGTTTATGAGTACCTTGAAAATGGAAGCTTAGATCGAGCAATCTTTG                         GTGACAGTAACTTAAACCTAGACTGGGTAATGCGCTTCGAGATCATTTTAG
genomic: GTTGGTTTATGAGTACCTTGAAAATGGAAGCTTAGATCGAGCAATCTTTGgtgagttcac ... gcttgtaaagGTGACAGTAACTTAAACCTAGACTGGGTAATGCGCTTCGAGATCATTTTAG
EST: gi|29627532|gb|CB632543.1|CB632543
EST:     GTTGGTTTATGAGTACCTTGAAAATGGAAGCTTAGATCGAGCAATCTTTG                         GTGACAGTAACTTAAACCTAGACTGGGTAATGCGCTTCGAGATCATTTTAG
genomic: GTTGGTTTATGAGTACCTTGAAAATGGAAGCTTAGATCGAGCAATCTTTGgtgagttcac ... gcttgtaaagGTGACAGTAACTTAAACCTAGACTGGGTAATGCGCTTCGAGATCATTTTAG
EST: gi|29622648|gb|CB627659.1|CB627659
EST:     GTTGGTTTATGAGTACCTTGAAAATGGAAGCTTAGATCGAGCAATCTTTG                         -T-A-A----CTTAAACCTAGACTGGGTAATGCGCTTCGAGATCATTTTAG
genomic: GTTGGTTTATGAGTACCTTGAAAATGGAAGCTTAGATCGAGCAATCTTTGgtgagttcac ... gcttgtaaagGTGACAGTAACTTAAACCTAGACTGGGTAATGCGCTTCGAGATCATTTTAG
EST: gi|29675944|gb|CB672219.1|CB672219
EST:     GTTGGTTTATGAGTACCTTGAAAATGGAAGCTTAGATCGAGCAATCTTTG                         -T-A-A----CTTAAACCTAGACTGGGTAATGCGCTTCGAGATCATTTTAG
genomic: GTTGGTTTATGAGTACCTTGAAAATGGAAGCTTAGATCGAGCAATCTTTGgtgagttcac ... gcttgtaaagGTGACAGTAACTTAAACCTAGACTGGGTAATGCGCTTCGAGATCATTTTAG
EST: gi|29627200|gb|CB632211.1|CB632211
EST:     GTTGGTTTATGAGTACCTTGAAAATGGAAGCTTAGATCGAGCAATCTTTG                         GTGACAGTAACTTAAACCTAGACTGGGTAATGCGCTTCGAGATCATTTTAG
genomic: GTTGGTTTATGAGTACCTTGAAAATGGAAGCTTAGATCGAGCAATCTTTGgtgagttcac ... gcttgtaaagGTGACAGTAACTTAAACCTAGACTGGGTAATGCGCTTCGAGATCATTTTAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atctttgttataattggcattcctgatgataactgagctatttctgcttgtaaagGTGACAGTAACTTAAACCTAGACTGGGTAATGCGCTTCGAGATCATTTTAGGAATAGCAAGAGGGCTAACTTATCTTCATGAGGAGTCAAGTGTACGCAT
                          tgataac  putative branch site (score: 2)
                                        tttctgctt  putative PPT
     tgttataatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagttcacttctgtaaaattgccgccctcggcacttatagaattgtattttctttctacacaaataaaactcattgcttcgtgactaataattaaggatttttcttttctgcatctttgttataattggcattcctgatgataactgagctatttctgcttgtaaagGTGACAGTAACTTAAACCTAGACTGGGTAATGCGCTTCGAGATCATTTTAGGAATAGCAAGAGGGCTAACTTATCTTCATGAGGAGTCAAGTGTACGCAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAG