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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagaacagtatgaagctcattgcaattaagtgtcttatgtagttttgcaatgacattcctaggcagctcctacatgttttctgtcatcccattttttatccaccacatgtatgaaatgttaattctacatttttgtgttattagGACGAAATCTGTCCCCAATGTGGGACAAATTGGTATTTAACAAAATAAAAGCTAGGCTTGGTGGACGTGTGAGGCTTATGTCTTCAGGTGCTTCTCCATT

Basic information

species Oryza sativa
transcript LOC_Os11g04980.2
intron # 14
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os11g04980.2 (Oryza sativa), 3'ss of exon 14
lower sequence: GRMZM2G176546_T01 (Zea mays), 3'ss of exon 5
gtaagaacagtatgaagctcattgcaattaagtgtcttatgtagttttgcaatgacattcctaggcagctcctacatgttttctgtcatcccatttt--ttatccaccacatgt---atgaaatgttaattctacatttttgtgttattagGACGAAATCTGTCCCCAATGTGGGACAAATTGGTATTTAACAAAATAAAAGCTAGGCTTGGTGGACGTGTGAGGCTTATGTCTTCAGGTGCTTCTCCATT
                                                 ||     |  ||||| | | |  |  |   | | |   |||| |||||  |  ||     |||||   || |||||| | ||||| | ||| ||||||| |||   |||||  |||||| ||||||| || |||||||||||||||||||||||||||||||||||||| ||||| ||||||  |||||||||||||||| |
-------------------------------------------------caccccaaaccctagacgggtagtctaacatctttaa-atccaattttgatcgtcacatgcatgtgcaataaaatgtcacttctatacttt-gtgttatcagGGAAAAATCCATCCCCAGTGTGGGATAAGTTGGTATTTAACAAAATAAAAGCTAGGCTTGGTGGACGAGTGAGACTTATGAGTTCAGGTGCTTCTCCACT

upper sequence: LOC_Os11g04980.2 (Oryza sativa), 3'ss of exon 14
lower sequence: Vv05s0020g03080.t01 (Vitis vinifera), 3'ss of exon 14
gtaagaacagtatgaagctcattgcaattaagtgtcttatgtagttttgcaatgacattcctaggcagctcctacatgttttctgtcatccc-attttttatccaccacatgtatgaaatgttaattctacatttttgtgttattagGACGAAATCTGTCCCCAATGTGGGACAAATTGGTATTTAACAAAATAAAAGCTAGGCTTGGTGGACGTGTGAGGCTTATGTCTTCAGGTGCTTCTCCATT
                                          | ||||    |     |||||  || |   | | || ||  | | ||    |||| || |    |   ||| |  | || | ||  || || ||  |||| | |||    ||||  || || |||||||||| |||||||||||| ||||||||||  | |||||| || || ||  |  |||||  ||| ||||| || || ||
-----------------------------------------cactttt----tcttgctcctac-caccagatgcttgcttctttttatttttatttatttttattcttttgtctttattggttatgttatatattattgtt-tcagGTAAGAATCCATCTCCCATGTGGGACAGATTGGTATTTAATAAAATAAAAGAAAAGCTTGGAGGCCGAGTTCGATTTATGGTTTCGGGTGCCTCACCCTT
















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|29679209|gb|CB675484.1|CB675484
EST:     AAGATTTTTTCATGCTGCATACAATGCTAAGAGGCAAGCCATTATGAATG                         GACGAAATCTGTCCCCAATGTGGGACAAATTGGTATTTAACAAAATAAAAG
genomic: AAGATTTTTTCATGCTGCATACAATGCTAAGAGGCAAGCCATTATGAATGgtaagaacag ... gtgttattagGACGAAATCTGTCCCCAATGTGGGACAAATTGGTATTTAACAAAATAAAAG
EST: gi|29679207|gb|CB675482.1|CB675482
EST:     AAGATTTTTTCATGCTGCATACAATGCTAAGAGGCAAGCCATTATGAATG                         GACGAAATCTGTCCCCAATGTGGGACAAATTGGTATTTAACAAAATAAAAG
genomic: AAGATTTTTTCATGCTGCATACAATGCTAAGAGGCAAGCCATTATGAATGgtaagaacag ... gtgttattagGACGAAATCTGTCCCCAATGTGGGACAAATTGGTATTTAACAAAATAAAAG
EST: gi|29671403|gb|CB667678.1|CB667678
EST:     AAGATTTTTTCATGCTGCATACAATGCTAAGAGGCAAGCCATTATGAATG                         GACGAAATCTGTCCCCAATGTGGGACAAATTGGTATTTAACAAAATAAAAG
genomic: AAGATTTTTTCATGCTGCATACAATGCTAAGAGGCAAGCCATTATGAATGgtaagaacag ... gtgttattagGACGAAATCTGTCCCCAATGTGGGACAAATTGGTATTTAACAAAATAAAAG
EST: gi|109974356|gb|DT806865.1|DT806865
EST:     AAGATTGTTTCATGCTGCATACAATGCTAAGAGGCAAGCCATTATGAATG                         GACGAAATCCGTCCCCAATGTGGGACAAATTGGTATTTAACAAAATAAAAG
genomic: AAGATTTTTTCATGCTGCATACAATGCTAAGAGGCAAGCCATTATGAATGgtaagaacag ... gtgttattagGACGAAATCTGTCCCCAATGTGGGACAAATTGGTATTTAACAAAATAAAAG
EST: gi|29670550|gb|CB666825.1|CB666825
EST:     AAGATTTTTTCATGCTGCATACAATGCTAAGAGGCAAGCCATTATGAATG                         GACGAAATCTGTCCCCAATGTGGGACAAATTGGTATTTAACAAAATAAAAG
genomic: AAGATTTTTTCATGCTGCATACAATGCTAAGAGGCAAGCCATTATGAATGgtaagaacag ... gtgttattagGACGAAATCTGTCCCCAATGTGGGACAAATTGGTATTTAACAAAATAAAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cattttttatccaccacatgtatgaaatgttaattctacatttttgtgttattagGACGAAATCTGTCCCCAATGTGGGACAAATTGGTATTTAACAAAATAAAAGCTAGGCTTGGTGGACGTGTGAGGCTTATGTCTTCAGGTGCTTCTCCATT
                           tgttaat  putative branch site (score: 3)
                                        tttttgt  putative PPT
                        aaatgttaattctaca  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagaacagtatgaagctcattgcaattaagtgtcttatgtagttttgcaatgacattcctaggcagctcctacatgttttctgtcatcccattttttatccaccacatgtatgaaatgttaattctacatttttgtgttattagGACGAAATCTGTCCCCAATGTGGGACAAATTGGTATTTAACAAAATAAAAGCTAGGCTTGGTGGACGTGTGAGGCTTATGTCTTCAGGTGCTTCTCCATT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGTGGA