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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atctctggtctggttgccccattgcatctcctaatgaagccattgctgcaaggatgtcctctctgtggttttaacttagaatggtgttcttttattccagTTGTCAGGTCGCATGAGGGCACTGCTGAATTATGAAGCTCCTGAAATCCATGAAGCTGGGACTTTTACCTACCGAAGTGATGTTTACAGTTTTGGCGTGG

Basic information

species Oryza sativa
transcript LOC_Os02g07960.2
intron # 14
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g07960.2 (Oryza sativa), 3'ss of exon 14
lower sequence: GRMZM2G335638_T01 (Zea mays), 3'ss of exon 14
atctctggtctggttgccccattgcatctcctaatgaagccattgctgcaaggatgtcctctctgtggttttaacttagaatggtgttc--ttttattccagTTGTCAGGTCGCATGAGGGCACTGCTGAATTATGAAGCTCCTGAAATCCATGAAGCTGGGACTTTTACCTACCGAAGTGATGTTTACAGTTTTGGCGTGG
     |     | || |    ||     |  || |     | || || |   |      |    ||     |   ||| ||| || |||  ||||||  ||| | ||||| || ||||| || || || ||||||||||| ||||||||||||||| ||| | |||||||    | ||| || || || ||||| || ||||
-gacttacctagattacttggttatcattaatattttcttctttacttctttgggagtatgaacgtaaaactt-tttataatagtattcccttttatctcagCTATCAGGCCGTATGAGAGCTCTACTCAATTATGAAGCACCTGAAATCCATGAATCTGAGCCTTTTACTCGTCAAAGCGACGTATATAGTTTGGGTGTGG
















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|58669825|gb|CK058511.1|CK058511
EST:     TCGCTGAATGTGGACTGGCAGAATTGACGCTGTCAGGTTCTGTTACACAG                         TTGTCAGGTCGCATGAGGGCACTGCTGAATTATGAAGCTCCTGAAATCCAT
genomic: TCGCTGAATGTGGACTGGCAGAATTGACGCTGTCAGGTTCTGTTACACAGgtaacatcta ... tttattccagTTGTCAGGTCGCATGAGGGCACTGCTGAATTATGAAGCTCCTGAAATCCAT
EST: gi|29621906|gb|CB626917.1|CB626917
EST:     TCGCTGAATGTGGACTGGCAGAATTGACGCTGTCAGGTTCTGTTACACAG                         TTGTCAGGTCGCATGAGGGCACTGCTGAATTATGAAGCTCCTGAAATCCAT
genomic: TCGCTGAATGTGGACTGGCAGAATTGACGCTGTCAGGTTCTGTTACACAGgtaacatcta ... tttattccagTTGTCAGGTCGCATGAGGGCACTGCTGAATTATGAAGCTCCTGAAATCCAT
EST: gi|29656568|gb|CB652843.1|CB652843
EST:     TCGCTGAATGTGGACTGGCAGAATTGACGCTGTCAGGTTCTGTTACACAG                         TTGTCAGGTCGCATGAGGGCACTGCTGAATTATGAAGCTCCTGAAATCCAT
genomic: TCGCTGAATGTGGACTGGCAGAATTGACGCTGTCAGGTTCTGTTACACAGgtaacatcta ... tttattccagTTGTCAGGTCGCATGAGGGCACTGCTGAATTATGAAGCTCCTGAAATCCAT
EST: gi|58611356|gb|CK039068.1|CK039068
EST:     TCGCTGAATGTGGACTGGCAGAATTGACGCTGTCAGGTTCTGTTACACAG                         TTGTCAGGTCGCATGAGGGCACTGCTGAATTATGAAGCTCCTGAAATCCAT
genomic: TCGCTGAATGTGGACTGGCAGAATTGACGCTGTCAGGTTCTGTTACACAGgtaacatcta ... tttattccagTTGTCAGGTCGCATGAGGGCACTGCTGAATTATGAAGCTCCTGAAATCCAT
EST: gi|29626065|gb|CB631076.1|CB631076
EST:     TCGCTGAATGTGGACTGGCAGAATTGACGCTGTCAGGTTCTGTTACACAG                         TTGTCAGGTCGCATGAGGGCACTGCTGAATTATGAAGCTCCTGAAATCCAT
genomic: TCGCTGAATGTGGACTGGCAGAATTGACGCTGTCAGGTTCTGTTACACAGgtaacatcta ... tttattccagTTGTCAGGTCGCATGAGGGCACTGCTGAATTATGAAGCTCCTGAAATCCAT
EST: gi|29626028|gb|CB631039.1|CB631039
EST:     GCAGAATTGACGCTGTCAGGTTCTGTTACACAG                         TCGTCAGGTCGCATGAGGGCACTGCTGAATTATGAAGCTCCTGAAATCCAT
genomic: GCAGAATTGACGCTGTCAGGTTCTGTTACACAGgtaacatcta ... tttattccagTTGTCAGGTCGCATGAGGGCACTGCTGAATTATGAAGCTCCTGAAATCCAT
EST: gi|29640907|gb|CB645914.1|CB645914
EST:     CAGAATTGACGCTGTCAGGTTCTGTTACACAG                         TTGTCAGGTCGCATGAGGGCACTGCTGAATTATGAAGCTCCTGAAATCCAT
genomic: CAGAATTGACGCTGTCAGGTTCTGTTACACAGgtaacatcta ... tttattccagTTGTCAGGTCGCATGAGGGCACTGCTGAATTATGAAGCTCCTGAAATCCAT
EST: gi|66927345|gb|CX114193.1|CX114193
EST:     GGTTCTGTTACACAG                         TTGTCAGGTCGCATGAGGGCACTGCTGAATTATGAAGCTCCTGAAATCCAT
genomic: GGTTCTGTTACACAGgtaacatcta ... tttattccagTTGTCAGGTCGCATGAGGGCACTGCTGAATTATGAAGCTCCTGAAATCCAT
EST: gi|29674397|gb|CB670672.1|CB670672
EST:     TCGCTGAATGTGGACTGGCAGAATTGACGCTGTCAGGTTCTGTTACACAG                         TTGTCAGGTCGCATGAGGGCACTGCTGAATTATGAAGCTCCTGAAATCCAT
genomic: TCGCTGAATGTGGACTGGCAGAATTGACGCTGTCAGGTTCTGTTACACAGgtaacatcta ... tttattccagTTGTCAGGTCGCATGAGGGCACTGCTGAATTATGAAGCTCCTGAAATCCAT
EST: gi|29671438|gb|CB667713.1|CB667713
EST:     TCGCTGAATGTGGACTGGCAGAATTGACGCTGTCAGGTTCTGTTACACAG                         TTGTCAGGTCGCATGAGGGCACTGCTGAATTATGAAGCTCCTGAAATCCAT
genomic: TCGCTGAATGTGGACTGGCAGAATTGACGCTGTCAGGTTCTGTTACACAGgtaacatcta ... tttattccagTTGTCAGGTCGCATGAGGGCACTGCTGAATTATGAAGCTCCTGAAATCCAT
EST: gi|29638004|gb|CB643013.1|CB643013
EST:     TCGCTGAATGTGGACTGGCAGAATTGACGCTGTCAGGTTCTGTTACACAG                         TTGTCAGGTCGCATGAGGGCACTGCTGAATTATGAAGCTCCTGAAATCCAT
genomic: TCGCTGAATGTGGACTGGCAGAATTGACGCTGTCAGGTTCTGTTACACAGgtaacatcta ... tttattccagTTGTCAGGTCGCATGAGGGCACTGCTGAATTATGAAGCTCCTGAAATCCAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctgcaaggatgtcctctctgtggttttaacttagaatggtgttcttttattccagTTGTCAGGTCGCATGAGGGCACTGCTGAATTATGAAGCTCCTGAAATCCATGAAGCTGGGACTTTTACCTACCGAAGTGATGTTTACAGTTTTGGCGTGG
                       ttttaac  putative branch site (score: 2)
                                       tgttcttttattcc  putative PPT
                       ttttaacttagaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atctctggtctggttgccccattgcatctcctaatgaagccattgctgcaaggatgtcctctctgtggttttaacttagaatggtgttcttttattccagTTGTCAGGTCGCATGAGGGCACTGCTGAATTATGAAGCTCCTGAAATCCATGAAGCTGGGACTTTTACCTACCGAAGTGATGTTTACAGTTTTGGCGTGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG