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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tttgttttttcatgtctcagtttatcagtttctttatccagtatatatctgcctctgtgtcgattgttctaatatgctgtcatttccttttttttttcagAACTTGGTTGATCAAAATGAGAATGGTACCATTGCCTTGCCAGTTTCTGACAATTCAAACAACAGCAACCATTCTGAAGACGTGGATGGAAATTCAGGGG

Basic information

species Oryza sativa
transcript LOC_Os08g44820.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os08g44820.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G125777_T02 (Zea mays), 3'ss of exon 2
-tttgttttttcat--gtc---tcagtttatcagtttctttatccagtatatatctgcctctgtgtcgattgttctaat-atgctgtcatttccttttttttttcagAACTTGGTTGATCAAAATGAGAATGGTACCATTGCCTTGCCAGTTTCTGACAATTCAAACAACAGCAACCATTCTGAAGACGTGGATGGAAATTCAGGGG
  || |||||| ||  |||   ||| || |    | |   |||| | |||| |  |     |   |  || |||||||| |||| || |||| ||     |||||||   |||| |||||||||||  ||||||||   |   |||||||||||||| | |||||| || |||||||||||||||||||| ||||||||||| ||||
tcttttttttttattagtcaagtcatttcaatgatattggtatcaaatatacacat--tggtagattcatggttctaattatgccgttattttct-----ttttcagGGTTTGGATGATCAAAATGGAAATGGTACACCTAGTTTGCCAGTTTCTGATACTTCAAATAATAGCAACCATTCTGAAGACGTAGATGGAAATTCTGGGG
















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|33794906|gb|CF323333.1|CF323333
EST:     TGAGTGACCTCGTTCAG                         AACTTGGTTGATCAAAATGAGAATGGTACCATTGCCTTGCCAGTTTCTGAC
genomic: TGAGTGACCTCGTTCAGgtacagtttc ... tttttttcagAACTTGGTTGATCAAAATGAGAATGGTACCATTGCCTTGCCAGTTTCTGAC
EST: gi|29629364|gb|CB634375.1|CB634375
EST:     TTTCTGGTGCTATGGAGAAGGGCTATCTCCAGATGAGTGACCTCGTTCAG                         AACTTGGTTGATCAAAATGAGAATGGTACCATTGCCTTGCCAGTTTCTGAC
genomic: TTTCTGGTGCTATGGAGAAGGGCTATCTCCAGATGAGTGACCTCGTTCAGgtacagtttc ... tttttttcagAACTTGGTTGATCAAAATGAGAATGGTACCATTGCCTTGCCAGTTTCTGAC
EST: gi|58691437|gb|CK080124.1|CK080124
EST:     TTTCTGGTGCTATGGAGAAGGGCTATCTCCAGATGAGTGACCTCGTTCAG                         AACTTGGTTGATCAAAATGAGAATGGTACCATTGCCTTGCCAGTTTCTGAC
genomic: TTTCTGGTGCTATGGAGAAGGGCTATCTCCAGATGAGTGACCTCGTTCAGgtacagtttc ... tttttttcagAACTTGGTTGATCAAAATGAGAATGGTACCATTGCCTTGCCAGTTTCTGAC
EST: gi|29661739|gb|CB658014.1|CB658014
EST:     TTTCTGGTGCTATGGAGAAGGGCTATCTCCAGATGAGTGACCTCGTTCAG                         AACTTGGTTGATCAAAATGAGAATGGTACCATTGCCTTGCCAGTTTCTGAC
genomic: TTTCTGGTGCTATGGAGAAGGGCTATCTCCAGATGAGTGACCTCGTTCAGgtacagtttc ... tttttttcagAACTTGGTTGATCAAAATGAGAATGGTACCATTGCCTTGCCAGTTTCTGAC
EST: gi|29676092|gb|CB672367.1|CB672367
EST:     TTTCTGGTGCTATGGAGAAGGGCTATCTCCAGATGAGTGACCTCGTTCAG                         AACTTGGTTGATCAAAATGAGAATGGTACCATTGCCTTGCCAGTTTCTGAC
genomic: TTTCTGGTGCTATGGAGAAGGGCTATCTCCAGATGAGTGACCTCGTTCAGgtacagtttc ... tttttttcagAACTTGGTTGATCAAAATGAGAATGGTACCATTGCCTTGCCAGTTTCTGAC
EST: gi|29673244|gb|CB669519.1|CB669519
EST:     TTTCTGGTGCTATGGAGAAGGGCTATCTCCAGATGAGTGACCTCGTTCAG                         AACTTGGTTGATCAAAATGAGAATGGTACCATTGCCTTGCCAGTTTCTGAC
genomic: TTTCTGGTGCTATGGAGAAGGGCTATCTCCAGATGAGTGACCTCGTTCAGgtacagtttc ... tttttttcagAACTTGGTTGATCAAAATGAGAATGGTACCATTGCCTTGCCAGTTTCTGAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatctgcctctgtgtcgattgttctaatatgctgtcatttccttttttttttcagAACTTGGTTGATCAAAATGAGAATGGTACCATTGCCTTGCCAGTTTCTGACAATTCAAACAACAGCAACCATTCTGAAGACGTGGATGGAAATTCAGGGG
                     ttctaat  putative branch site (score: 2)
                             tgctgtcatttccttt  CT-rich tract
                                    atttcctttttttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tttgttttttcatgtctcagtttatcagtttctttatccagtatatatctgcctctgtgtcgattgttctaatatgctgtcatttccttttttttttcagAACTTGGTTGATCAAAATGAGAATGGTACCATTGCCTTGCCAGTTTCTGACAATTCAAACAACAGCAACCATTCTGAAGACGTGGATGGAAATTCAGGGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA