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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tggtcttcacattttcatagctttagctgctttctttgtttgcctcaaagaccttgatttgatttgcaatgattactgaagaactgtttatccctcttagAAAGAAGAATTTCAGCATACAGCATATGCAACCAATGCATATGTTGCCTTGGGACCACTGTGGAAGCCAGCACTACAAG

Basic information

species Oryza sativa
transcript LOC_Os11g48090.3
intron # 17
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os11g48090.4 (Oryza sativa), 3'ss of exon 17
lower sequence: GLYMA09G34860.1 (Glycine max), 3'ss of exon 17
tggtcttcacattttcatagctttagctgctttctttgtttgcctcaaagaccttgatttgat--ttgcaatgattactgaagaactgtttatccctct---tagAAAGAAGAATTTCAGCATACAGCATATGCAACCAATGCATATGTTGCCTTGGGACCACTGTGGAAGCCAGCACTACAAG
     || | |   ||| | | ||  | | |  | || |  |    |||     |  ||  ||  ||  | ||  |  |  ||| |      |  ||     |||||||||||||||||||||||| | ||||| || ||||| ||  ||||  ||||  || ||   |||| |  | | ||||
---attttaaagcatca-accattcacagttgaccttata-gtaaaaaaatatatacttcaatatttttagtgggtgatttagagccagccttttcttgatgtagAAAGAAGAATTTCAGCATACACCTTATGCCACAAATGCTTACATTGCTGTGGGGTCATTGGCCAAGCAAATATTGCAAG

upper sequence: LOC_Os11g48090.4 (Oryza sativa), 3'ss of exon 17
lower sequence: Vv02s0087g00070.t01 (Vitis vinifera), 3'ss of exon 17
tggtcttcacattttcatagctttagctgctttctttgtttgcctcaaagaccttgatt--tgatttgcaatg-attactgaagaactgtttatccct--cttagAAAGAAGAATTTCAGCATACAGCATATGCAACCAATGCATATGTTGCCTTGGGACCACTGTGGAAGCCAGCACTACAAG
     || |    | ||| |  ||   || || | |    |  || |    | ||  ||  |||  |   ||  | |   |||  |   ||| |  ||    |||||||||||||||||||||||||| ||||| || ||||| || ||  | ||||||| | ||||||||| || |   || |
-----ttgatcgatccatggaatttattgtttccgtgcaatttcttagcatcattttttgatgacctatcatataatttggaaccatgatttgtttctggtgtagAAAGAAGAATTTCAGCATACAGCTTATGCTACAAATGCTTACGTGACATTGGGACTATTGTGGAAGCAAGTATCGCATG
















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|29673291|gb|CB669566.1|CB669566
EST:     AAGAAGGCATTGAACAGTTGGTAGTTCAACTTATACTCGATCGGGTTTTG                         AAAGAAGAATTTCAGCATACAGCATATGCAACCAATGCATATGTTGCCTTG
genomic: AAGAAGGCATTGAACAGTTGGTAGTTCAACTTATACTCGATCGGGTTTTGgtatgtgtga ... tccctcttagAAAGAAGAATTTCAGCATACAGCATATGCAACCAATGCATATGTTGCCTTG
EST: gi|66918333|gb|CX105181.1|CX105181
EST:     AGGCATTGGAACAGTTGGTTAGTTCANACTTATTACTCGATCGGGTTTTG                         AAAGAAGAATTTCAGCATACAGCATATGCAACCAATGCATATGTTGCCTTG
genomic: AGGCATT-GAACAGTTGG-TAGTTCA-ACTTA-TACTCGATCGGGTTTTGgtatgtgtga ... tccctcttagAAAGAAGAATTTCAGCATACAGCATATGCAACCAATGCATATGTTGCCTTG
EST: gi|29639799|gb|CB644808.1|CB644808
EST:     AAGAAGGCATTGAACAGTTGGTAGTTCAACTTATACTCGATCGGGTTTTG                         AAAGAAGAATTTCAGCATACAGCATATGCAACCAATGCATATGTTGCCTTG
genomic: AAGAAGGCATTGAACAGTTGGTAGTTCAACTTATACTCGATCGGGTTTTGgtatgtgtga ... tccctcttagAAAGAAGAATTTCAGCATACAGCATATGCAACCAATGCATATGTTGCCTTG
EST: gi|29639599|gb|CB644608.1|CB644608
EST:     AAGAAGGCATTGAACAGTTGGTAGTTCAACTTATACTCGATCGGGTTTTG                         AAAGAAGAATTTCAGCATACAGCATATGCAACCAATGCATATGTTGCCTTG
genomic: AAGAAGGCATTGAACAGTTGGTAGTTCAACTTATACTCGATCGGGTTTTGgtatgtgtga ... tccctcttagAAAGAAGAATTTCAGCATACAGCATATGCAACCAATGCATATGTTGCCTTG
EST: gi|29626859|gb|CB631870.1|CB631870
EST:     AAGAAGGCATTGAACAGTTGGTAGTTCAACTTATACTCGATCGGGTTTTG                         AAAGAAGAATTTCAGCATACAGCATATGCAACCAATGCATATGTTGCCTTG
genomic: AAGAAGGCATTGAACAGTTGGTAGTTCAACTTATACTCGATCGGGTTTTGgtatgtgtga ... tccctcttagAAAGAAGAATTTCAGCATACAGCATATGCAACCAATGCATATGTTGCCTTG
EST: gi|86479042|gb|CI121675.1|CI121675
EST:     GTTCAACTTATACTCGATCGGGTTTTG                         AAAGAAGAATTTCAGCATACAGCATATGCAACCAATGCATATGTTGCCTTG
genomic: GTTCAACTTATACTCGATCGGGTTTTGgtatgtgtga ... tccctcttagAAAGAAGAATTTCAGCATACAGCATATGCAACCAATGCATATGTTGCCTTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

caaagaccttgatttgatttgcaatgattactgaagaactgtttatccctcttagAAAGAAGAATTTCAGCATACAGCATATGCAACCAATGCATATGTTGCCTTGGGACCACTGTGGAAGCCAGCACTACAAG
           atttgat  putative branch site (score: 5)
                                      ctgtttatccctctt  putative PPT
           atttgattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tggtcttcacattttcatagctttagctgctttctttgtttgcctcaaagaccttgatttgatttgcaatgattactgaagaactgtttatccctcttagAAAGAAGAATTTCAGCATACAGCATATGCAACCAATGCATATGTTGCCTTGGGACCACTGTGGAAGCCAGCACTACAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG