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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...taatctagaaattgaaatctttttcaacggtggtagtaaaagatatttcttaaaaaaaaggaattaaccggaataatatggtgatgttttaaatctccagGAATTATGAGGCCGAGTCTGAGAGGAAGGAGACGGTGGAGGAGTTCTACCGGGTCAACCACATCAACCAGACATATGATTTC

Basic information

species Oryza sativa
transcript LOC_Os06g36560.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os06g36560.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G126900_T01 (Zea mays), 3'ss of exon 1
taatctagaaattgaaatctttttcaacggtggtagtaaaagatatttcttaaaaaaaaggaattaaccggaataatatggtgatgttttaaatctc----cagGAATTATGAGGCCGAGTCTGAGAGGAAGGAGACGGTGGAGGAGTTCTACCGGGTCAACCACATCAACCAGACATATGATTTC------------------
    |     | |||  | | |  |     ||    |   | | | |    ||  | || | |  | | |    |  |  | ||  |  | |  ||     |||| | || || || ||||| ||| ||||| ||||||| ||||||||||||||||| |||||| | |  |||||  | || |||                  
----ccttgcactgagctgtgtggccttaatgtccttgggaaaaaataaaaaatgagaacgcaggagctgatgaacgaccgggaactcctgacccttggtgcagGGACTACGACGCGGAGTCGGAGCGGAAGCAGACGGTAGAGGAGTTCTACCGGGTGAACCACGTGAGGCAGACGCACGAGTTCGTGGCGCGGATGCGGGCG
















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|86877114|gb|CI311430.1|CI311430
EST:     GACGGCGGCTTCGTCGTGCCGGACTCCAACGCCTTCGGCAACGCCTTCAG                         GAATTATGAGGCCGAGTCTGAGAGGAAGGAGACGGTGGAGGAGTTCTACCG
genomic: GACGGCGGCTTCGTCGTGCCGGACTCCAACGCCTTCGGCAACGCCTTCAGgtcagctaca ... aaatctccagGAATTATGAGGCCGAGTCTGAGAGGAAGGAGACGGTGGAGGAGTTCTACCG
EST: gi|38475187|gb|CF959320.1|CF959320
EST:     GACGGCGGCTTCGTCGTGCCGGACTCCAACGCCTTCGGCAACGCCTTCAG                         GAATTATGAGGCCGAGTCTGAGAGGAAGGAGACGGTGGAGGAGTTCTACCG
genomic: GACGGCGGCTTCGTCGTGCCGGACTCCAACGCCTTCGGCAACGCCTTCAGgtcagctaca ... aaatctccagGAATTATGAGGCCGAGTCTGAGAGGAAGGAGACGGTGGAGGAGTTCTACCG
EST: gi|86851034|gb|CI311252.1|CI311252
EST:     GACGGCGGCTTCGTCGTGCCGGACTCCAACGCCTTCGGCAACGCCTTCAG                         GAATTATGAGGCCGAGTCTGAGAGGAAGGAGACGGTGGAGGAGTTCTACCG
genomic: GACGGCGGCTTCGTCGTGCCGGACTCCAACGCCTTCGGCAACGCCTTCAGgtcagctaca ... aaatctccagGAATTATGAGGCCGAGTCTGAGAGGAAGGAGACGGTGGAGGAGTTCTACCG
EST: gi|88353796|gb|CI634587.1|CI634587
EST:     GACGGCGGCTTCGTCGTGCCGGACTCCAACGCCTTCGGCAACGCCTTCAG                         GAATTATGAGGCCGAGTCTGAGAGGAAGGAGACGGTGGAGGAGTTCTACCG
genomic: GACGGCGGCTTCGTCGTGCCGGACTCCAACGCCTTCGGCAACGCCTTCAGgtcagctaca ... aaatctccagGAATTATGAGGCCGAGTCTGAGAGGAAGGAGACGGTGGAGGAGTTCTACCG
EST: gi|58670144|gb|CK058830.1|CK058830
EST:     GACGGCGGCTTCGTCGTGCCGGACTCCAACGCCTTCGGCAACGCCTTCAG                         GAATTATGAGGCCGAGTCTGAGAGGAAGGAGACGGTGGAGGAGTTCTACCG
genomic: GACGGCGGCTTCGTCGTGCCGGACTCCAACGCCTTCGGCAACGCCTTCAGgtcagctaca ... aaatctccagGAATTATGAGGCCGAGTCTGAGAGGAAGGAGACGGTGGAGGAGTTCTACCG
EST: gi|87009635|gb|CI309156.1|CI309156
EST:     GCAACGCCTTCAG                         GAATTATGAGGCCGAGACTGAGAGGGAGGAGACGGTGGAGGAGTTCTACCG
genomic: GCAACGCCTTCAGgtcagctaca ... aaatctccagGAATTATGAGGCCGAGTCTGAGAGGAAGGAGACGGTGGAGGAGTTCTACCG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttcttaaaaaaaaggaattaaccggaataatatggtgatgttttaaatctccagGAATTATGAGGCCGAGTCTGAGAGGAAGGAGACGGTGGAGGAGTTCTACCGGGTCAACCACATCAACCAGACATATGATTTC
                aattaac  putative branch site (score: 2)
                                                tctcc  putative PPT
     taaaaaaaaggaatta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
taatctagaaattgaaatctttttcaacggtggtagtaaaagatatttcttaaaaaaaaggaattaaccggaataatatggtgatgttttaaatctccagGAATTATGAGGCCGAGTCTGAGAGGAAGGAGACGGTGGAGGAGTTCTACCGGGTCAACCACATCAACCAGACATATGATTTC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAG