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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gcgtgtttgacaaaaataaaaagagaagaaaaaaccaatatgcaagaccatttctggtagcactttttattgccaatcaattatattttttttaatgtagGAAGCATTGGTTTTGCTATTGGATGTTGGCCCATCCATGCATGGCGTTCTGCAAGAAGTTGAGAATATCTGCTCCACCCTTGTGCATAAGAAG

Basic information

species Oryza sativa
transcript LOC_Os03g63920.1
intron # 1
splice site 3'
intron type U2

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|88719413|gb|CI742923.1|CI742923
EST:     GAGCCGCGTCGTCGTCGACCTCCTTCAATTCCCTCATGGCTCGCAACAAG                         GAAGCATTGGTTTTGCTATTGGATGTTGGCCCATCCATGCATGGCGTTCTG
genomic: GAGCCGCGTCGTCGTCGACCTCCTTCAATTCCCTCATGGCTCGCAACAAGgtaacctcgc ... tttaatgtagGAAGCATTGGTTTTGCTATTGGATGTTGGCCCATCCATGCATGGCGTTCTG
EST: gi|88728604|gb|CI752114.1|CI752114
EST:     GAGCCGCGTCGTCGTCGACCTCCTTCAATTCCCTCATGGCTCGCAACAAG                         GAAGCATTGGTTTTGCTATTGGATGTTGGCCCATCCATGCATGGCGTTCTG
genomic: GAGCCGCGTCGTCGTCGACCTCCTTCAATTCCCTCATGGCTCGCAACAAGgtaacctcgc ... tttaatgtagGAAGCATTGGTTTTGCTATTGGATGTTGGCCCATCCATGCATGGCGTTCTG
EST: gi|88722274|gb|CI745784.1|CI745784
EST:     GAGCCGCGTCGTCGTCGACCTCCTTCAATTCCCTCATGGNTCGCAACAAG                         GAAGCATTGGTTTTGCTATTGGATGTTGGCCCATCCATGCATGGCGTTCTG
genomic: GAGCCGCGTCGTCGTCGACCTCCTTCAATTCCCTCATGGCTCGCAACAAGgtaacctcgc ... tttaatgtagGAAGCATTGGTTTTGCTATTGGATGTTGGCCCATCCATGCATGGCGTTCTG
EST: gi|86904459|gb|CI308669.1|CI308669
EST:     GAGCCGCGTCGTCGTCGACCTCCTTCAATTCCCTCATGGCTCGCAACAAG                         GAAGCATTGGTTTTGCTATTGGATGTTGGCCCATCCATGCATGGCGTTCTG
genomic: GAGCCGCGTCGTCGTCGACCTCCTTCAATTCCCTCATGGCTCGCAACAAGgtaacctcgc ... tttaatgtagGAAGCATTGGTTTTGCTATTGGATGTTGGCCCATCCATGCATGGCGTTCTG
EST: gi|86909601|gb|CI304706.1|CI304706
EST:     GAGCCGCGTCGTCGTCGACCTCCTTCAATTCCCTCATGGCTCGCAACAAG                         GAAGCATTGGTTTTGCTATTGGATGTTGGCCCATCCATGCATGGCGTTCTG
genomic: GAGCCGCGTCGTCGTCGACCTCCTTCAATTCCCTCATGGCTCGCAACAAGgtaacctcgc ... tttaatgtagGAAGCATTGGTTTTGCTATTGGATGTTGGCCCATCCATGCATGGCGTTCTG
EST: gi|88372362|gb|CI619692.1|CI619692
EST:     GAGCCGCGTCGTCGTCGACCTCCTTCAATTCCCTCATGGCTCGCAACAAG                         GAAGCATTGGTTTTGCTATTGGATGTTGGCCCATCCATGCATGGCGTTCTG
genomic: GAGCCGCGTCGTCGTCGACCTCCTTCAATTCCCTCATGGCTCGCAACAAGgtaacctcgc ... tttaatgtagGAAGCATTGGTTTTGCTATTGGATGTTGGCCCATCCATGCATGGCGTTCTG
EST: gi|88314922|gb|CI609981.1|CI609981
EST:     GAGCCGCGTCGTCGTCGACCTCCTTCAATTCCCTCATGGCTCGCAACAAG                         GAAGCATTGGTTTTGCTATTGGATGTTGGCCCATCCATGCATGGCGTTCTG
genomic: GAGCCGCGTCGTCGTCGACCTCCTTCAATTCCCTCATGGCTCGCAACAAGgtaacctcgc ... tttaatgtagGAAGCATTGGTTTTGCTATTGGATGTTGGCCCATCCATGCATGGCGTTCTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gaccatttctggtagcactttttattgccaatcaattatattttttttaatgtagGAAGCATTGGTTTTGCTATTGGATGTTGGCCCATCCATGCATGGCGTTCTGCAAGAAGTTGAGAATATCTGCTCCACCCTTGTGCATAAGAAG
                                            ttttaat  putative branch site (score: 3)
                                      tatttttttt  CT-rich tract
                  tttttattgccaatca  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gcgtgtttgacaaaaataaaaagagaagaaaaaaccaatatgcaagaccatttctggtagcactttttattgccaatcaattatattttttttaatgtagGAAGCATTGGTTTTGCTATTGGATGTTGGCCCATCCATGCATGGCGTTCTGCAAGAAGTTGAGAATATCTGCTCCACCCTTGTGCATAAGAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- -tgtttga
- - - - - -aaaaata
- - - - - - - - - aaaagaga
- - - - - - - - - - - - - -gaaaaaa
- - - - - - - - - - - - - - - - - - - -atgcaag