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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaagtatgagtcttgtccatttctggagcatgttttgttttctgccagggtcctggcactttgccatttaagagttgtgattcaaagaattagcatgtaaaatatttggcattgcagATTTATGTCCACAGTAAGTTGATGATAATTGATGACCGCATCACATTGATTGGATCAGCTAACATAAATGATAGAAGCTTGCTTGGATCAAGAGATTCTG

Basic information

species Oryza sativa
transcript LOC_Os05g29050.1
intron # 14
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os05g29050.1 (Oryza sativa), 3'ss of exon 14
lower sequence: GRMZM2G066485_T01 (Zea mays), 3'ss of exon 14
gtaaagtatgagtcttgtccatttctggagcatgttttgttttctgccagggtcctggcactttgccatttaagagttgtgattcaaagaattagcatgtaaaatatttggcattgcagATTTATGTCCACAGTAAGTTGATGATAATTGATGACCGCATCACATTGATTGGATCAGCTAACATAAATGATAGAAGCTTGCTTGGATCAAGAGATTCTG
              ||| || ||     |    |   ||| || |   |  | |  ||        ||| ||| |  ||| |||||    |  |   |  | ||| |      || ||||||||||| || || ||||| |||||| ||||||||||||||||||||||||| |||||||| || ||||||||||||||||||||||||||||| || |
-------------tttgacccttgacata-tgcgaaatgtcttataaaatagactgggaggagcagcatataaaa--tgt-attcaggataccattcta-acaatgtcccat-ttccagATTTATGTACATAGCAAGTTAATGATAGTTGATGACCGCATCACATTGATTGGCTCAGCTAATATTAATGATAGAAGCTTGCTTGGATCAAGAGACTCCG

upper sequence: LOC_Os05g29050.1 (Oryza sativa), 3'ss of exon 14
lower sequence: GLYMA20G38200.1 (Glycine max), 3'ss of exon 16
------------------------------------------------------------------------gtaaagtatgagtcttgtccatttctggagcatgttttgttttctgccagggtcctggcacttt--gccatttaagagtt---gtgattcaaagaattagcatgtaaaatatttggcattgcagATTTATGTCCACAGTAAGTTGATGATAATTGATGACCGCATCACATTGATTGGATCAGCTAACATAAATGATAGAAGCTTGCTTGGATCAAGAGATTCTG
                                                                           |  | |  |    || || || |||| | |  |   | || |||     |  |  |  ||      |||||| || |    |  ||     | || |  | |||      |     | ||| | ||||| |||||||| |||||||||||||||||||| ||  | || ||||||||| |||| ||||||||  | || |||||||||| |||||| ||||
gtatcttaccatatatattgaaacatcttttgattttgcttttaaaacatcaaatatttttctctgagccaaaagagatcttggaaaagtgcaatt-tggatc-tcctagatcttgtgcacaacttttaacttttataatgatttaacagctcaaatatttgtcttatttggtgtataattcccatattgatacagGTATATGTGCACAGTAAATTGATGATAATTGATGACCGTATAGCTTTTATTGGATCATCTAATATAAATGACCGTAGTTTGCTTGGATTAAGAGACTCTG

upper sequence: LOC_Os05g29050.1 (Oryza sativa), 3'ss of exon 14
lower sequence: GLYMA15G16270.1 (Glycine max), 3'ss of exon 15
gtaaagtatgagtcttgtccatttctggagcatgttttgttttctgccagggtcctggcactttgccatttaagagttgtgattcaaagaattagcatgtaaaatatttggcattgcagATTTATGTCCACAGTAAGTTGATGATAATTGATGACCGCATCACATTGATTGGATCAGCTAACATAAATGATAGAAGCTTGCTTGGATCAAGAGATTCTG
                                      || ||||  | |  ||     |   |   ||  |   || ||  ||||   |  |   |||  |   | ||    |||||| | ||||| ||||||||  | |||||  |||||||  | || || ||||||||||| ||||| || |||||||| ||||| ||||| || ||||||||||
--------------------------------------gtattctttc-gcatctgtctatggtcatatacagaggtagt--ttcagtcagctta-atgatatgcactt---tttgcagGTGTATGTTCACAGTAAAATCATGATTGTTGATGATTGTATTACTTTGATTGGATCTGCTAATATTAATGATAGGAGCTTACTTGGCTCCAGAGATTCTG

upper sequence: LOC_Os05g29050.1 (Oryza sativa), 3'ss of exon 14
lower sequence: GLYMA09G04620.1 (Glycine max), 3'ss of exon 15
gtaaagtatgagtcttgtccatttctggagcatgttttgttttctgccagggtcctggcactttgccatttaagagttgtgattcaaagaattagcatgtaaaatatttggcattgcagATTTATGTCCACAGTAAGTTGATGATAATTGATGACCGCATCACATTGATTGGATCAGCTAACATAAATGATAGAAGCTTGCTTGGATCAAGAGATTCTG
                                 || || ||||    | |  | | | || | | |      ||||||  | ||||   |  |   |||  |   | ||    |||||| | ||||| ||||||||  | |||||  |||||||  | || || ||||||||||| ||||| || |||||||| ||||| ||||| || ||||||||||
---------------------------------gtattcttttgcatctgtctacagtca-tatac------agagtta-gtttcagtcagctta-atgatatgcactt---tttgcagGTGTATGTTCACAGTAAAATCATGATTGTTGATGATTGTATTACTTTGATTGGATCTGCTAATATTAATGATAGGAGCTTACTTGGCTCCAGAGATTCTG

upper sequence: LOC_Os05g29050.1 (Oryza sativa), 3'ss of exon 14
lower sequence: Vv05s0077g01830.t01 (Vitis vinifera), 3'ss of exon 16
------------------------------------------------------------------gtaaagtatgagtcttgtccatttctggagcatgttttgttttctgccagggtcctggcactttgccatttaa--gag-ttgtgattcaaagaattagcatgtaaaatatt----------tggcattgcagATTTATGTCCACAGTAAGTTGATGATAATTGATGACCGCATCACATTGATTGGATCAGCTAACATAAATGATAGAAGCTTGCTTGGATCAAGAGATTCTG
                                                                    ||| | | | |  | | ||| | |      | |||| ||||         |  |||   |  |  |   ||  ||| |||  | |||  |   || ||| |   | |||          ||    || || | ||||| || || ||  | |||||| |||||||| |||  || ||||||||||| |||||||| |||||||| || ||||||||||||||||||||||
gtattgtgttttgctgatgcacataatcacatatgtacatttattttcaatgttccctaatcaattacaaaatct-atttgtatgcatctttttcatgtttttttttttaaatttttataatggacatgggaaaaacaattgagcttggaactcagtggtatatcatttttcacattatattcctattgtttctgtagGTGTATGTGCATAGCAAAATCATGATAGTTGATGACTGCACAACCTTGATTGGATCCGCTAACATTAATGATAGGAGTTTGCTTGGATCAAGAGATTCTG

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|11442731|gb|BF430634.1|BF430634
EST:     TTAGAGCACATGGTAGACTATGCGAAGGAGGTCCCTTGGTCACTAATCAG                         ATTTATGTCCACAGTAAGTTGATGATAATTGATGACCGCATCACATTGATT
genomic: TTAGAGCACATGGTAGACTATGCGAAGGAGGTCCCTTGGTCACTAATCAGgtaaagtatg ... ggcattgcagATTTATGTCCACAGTAAGTTGATGATAATTGATGACCGCATCACATTGATT
EST: gi|33797063|gb|CF324398.1|CF324398
EST:     TTAGAGCACATGGTAGACTATGCGAAGGAGGTCCCTTGGTCACTAATCAG                         ATTTATGTCCACAGTAAGTTGATGATAATTGATGACCGCATCACATTGATT
genomic: TTAGAGCACATGGTAGACTATGCGAAGGAGGTCCCTTGGTCACTAATCAGgtaaagtatg ... ggcattgcagATTTATGTCCACAGTAAGTTGATGATAATTGATGACCGCATCACATTGATT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gccatttaagagttgtgattcaaagaattagcatgtaaaatatttggcattgcagATTTATGTCCACAGTAAGTTGATGATAATTGATGACCGCATCACATTGATTGGATCAGCTAACATAAATGATAGAAGCTTGCTTGGATCAAGAGATTCTG
                                atgtaaaatattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaagtatgagtcttgtccatttctggagcatgttttgttttctgccagggtcctggcactttgccatttaagagttgtgattcaaagaattagcatgtaaaatatttggcattgcagATTTATGTCCACAGTAAGTTGATGATAATTGATGACCGCATCACATTGATTGGATCAGCTAACATAAATGATAGAAGCTTGCTTGGATCAAGAGATTCTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA