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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aaaaaaaaaaaaaaatcttttgcaaatctatatgctcattaactcattcattaggttcatcgatcatgcttatctgaagaaatctgtttactttatgcagCTCAAGGAAATGGTTGTTCCAGTCATCATTAGGAAAACGTCAGCACGAGATCTTAGAAGAACAAACTCGATGGAGTGGTAGACGTGAGCCAAGCTCAGTT

Basic information

species Oryza sativa
transcript LOC_Os01g64730.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g64730.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM5G858197_T02 (Zea mays), 3'ss of exon 3
aaaaaaaaaaaaaaatcttttgcaaatctatatgctcattaactcattcattaggt--tcatcgatcatgcttatctgaagaaatctgtttactttatgcagCTCAAGGAAATGGTTGTTCCAGTCATCATTAGGAAAACGTCAGCACGAGATCTTAGAAGAACAAACTCGATGGAGTGGTAGACGTGAGCCAAGCTCAGTT
 |            || |  ||         ||| |||||  ||  ||| |  |||   | |     ||| || ||| ||||| |   |||  || |||||||||  ||||  |||    ||||||||  | |||||||   || || |||||||||||||||| ||||| ||| |||||||||   |||||||||||||| 
cagtttggctttggatttactgacttgagcaatgttcatttgctt-ttcttggggtagccgttttatatgtttctctaaagaa-tacatttggttgatgcagCTCTTGGAACGGGTGACGCCAGTCATTCTGAGGAAAAAACCATCAGGAGATCTTAGAAGAACGAACTCAATGCAGTGGTAGATTGGAGCCAAGCTCAGTC
















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|88207103|gb|CI206952.1|CI206952
EST:     GAGGAGCAACATCAGAAACGACTTAAAGAG                         CTCAAGGAAATGGTTGTTCCAGTCATCATTAGGAAAACGTCAGCACGAGAT
genomic: GAGGAGCAACATCAGAAACGACTTAAAGAGgtaagctttg ... ctttatgcagCTCAAGGAAATGGTTGTTCCAGTCATCATTAGGAAAACGTCAGCACGAGAT
EST: gi|33364654|gb|BP432990.1|BP432990
EST:     GAGGAGCAACATCAGAAACGACTTAAAGAG                         CTCAAGGAAATGGTTGTTCCAGTCATCATTAGGAAAACGTCAGCACGAGAT
genomic: GAGGAGCAACATCAGAAACGACTTAAAGAGgtaagctttg ... ctttatgcagCTCAAGGAAATGGTTGTTCCAGTCATCATTAGGAAAACGTCAGCACGAGAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attcattaggttcatcgatcatgcttatctgaagaaatctgtttactttatgcagCTCAAGGAAATGGTTGTTCCAGTCATCATTAGGAAAACGTCAGCACGAGATCTTAGAAGAACAAACTCGATGGAGTGGTAGACGTGAGCCAAGCTCAGTT
                                         tttacttt  CT-rich tract
                                         tttactttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aaaaaaaaaaaaaaatcttttgcaaatctatatgctcattaactcattcattaggttcatcgatcatgcttatctgaagaaatctgtttactttatgcagCTCAAGGAAATGGTTGTTCCAGTCATCATTAGGAAAACGTCAGCACGAGATCTTAGAAGAACAAACTCGATGGAGTGGTAGACGTGAGCCAAGCTCAGTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTCA
aaaaaaa
- - - - - - - - -ttttgca
- - - - - - - - - - - - - - - - tgctcat
- - - - - - - - - - - - - - - - - - - - - - - - - - - gttcatc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - atcatgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gaagaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tctgttt