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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ctatttgactatatgtgcattcttggagagtcctctgatatcaactcctattggagtagagctgcatcatagtcttcataccatgtgtttatgctcgcagGTCCTGTTTGAGCAAAATCAGTGGGACAGCCTTGTGGACCAGTTTAAGCAGGAATTCTGCAAATTGTATGGCATGACATTGGAGCCGTTGCTGAACATCT

Basic information

species Oryza sativa
transcript LOC_Os05g06760.2
intron # 4
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|572123|gb|D41634.1|D41634
EST:     ACAGCAACATTGGTTTTTAGGANNCAGTACAAACTTGTGCTCCTTACAAG                         GTCCTGTTTGAGCAAAATCCAGTGGG
genomic: ACAGCAACATTGGTTTTTAGAAG-CAGTACAAACT-GTGCTCCTTACAAGgttagcagca ... atgctcgcagGTCCTGTTTGAGCAAAATC-AGTGGG
EST: gi|287145|gb|D15950.1|D15950
EST:     TCACAGCAACATTGGTTTTTAGAAGCAGTACAAACTGTGCTCCTTACAAG                         GTCCTGTTTGAGCAAAATCAGTGGGACAGCCTTGTGGACCAGTTTAAGCAG
genomic: TCACAGCAACATTGGTTTTTAGAAGCAGTACAAACTGTGCTCCTTACAAGgttagcagca ... atgctcgcagGTCCTGTTTGAGCAAAATCAGTGGGACAGCCTTGTGGACCAGTTTAAGCAG
EST: gi|58679080|gb|CK067767.1|CK067767
EST:     CACAGCAACATTGGTTTTTAGAAGCAGTACAAAACTGTGCTCCTTACAAG                         GTCCTGTTTGAGCAAAATCAGTGGGACAGCCTTGTGGACCAGTTTAAGCAG
genomic: CACAGCAACATTGGTTTTTAGAAGCAGTAC-AAACTGTGCTCCTTACAAGgttagcagca ... atgctcgcagGTCCTGTTTGAGCAAAATCAGTGGGACAGCCTTGTGGACCAGTTTAAGCAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcctattggagtagagctgcatcatagtcttcataccatgtgtttatgctcgcagGTCCTGTTTGAGCAAAATCAGTGGGACAGCCTTGTGGACCAGTTTAAGCAGGAATTCTGCAAATTGTATGGCATGACATTGGAGCCGTTGCTGAACATCT
                                        tgtttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ctatttgactatatgtgcattcttggagagtcctctgatatcaactcctattggagtagagctgcatcatagtcttcataccatgtgtttatgctcgcagGTCCTGTTTGAGCAAAATCAGTGGGACAGCCTTGTGGACCAGTTTAAGCAGGAATTCTGCAAATTGTATGGCATGACATTGGAGCCGTTGCTGAACATCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG