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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttagtaattcatcttatgccttttacctgcaacattttatccgtgtgtactggaggtagtcgtggacttcttttgacggttgggacttggggctgcataagattctctattctatactagtaatagaatgtcacaatatcagcatgagataacaagaacctttaaacagATTTGAGGAACATGAAGCACCTGGATCAAGATCCTTCTTTACAGAGATAATCGCATCAATATCGGATATAAAATTTTCAAGGGATGGAAGATACATCCTT

Basic information

species Oryza sativa
transcript LOC_Os06g36770.2
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os06g36770.2 (Oryza sativa), 3'ss of exon 8
lower sequence: GRMZM2G165418_T02 (Zea mays), 3'ss of exon 9
gttagtaattcatcttatgccttttacctgcaacattttatccgtgtgtactggaggtagtcgtggacttcttttgacggttgggacttggggct--gcataagattctctattctatactagtaatagaatgtcacaatat-cagcatgagataacaagaacctttaaacagATTTGAGGAACATGAAGCACCTGGATCAAGATCCTTCTTTACAGAGATAATCGCATCAATATCGGATATAAAATTTTCAAGGGATGGAAGATACATCCTT
                                                                         | |||   |  | ||   | ||  | |||| ||   ||| |  ||     |   |||| || |  ||||     ||||| ||||||   |||  ||||||||||||||||||||||||||||||||||||||||||||||||||| || || |||||||| || |||||||| ||||||||| |||| | ||| || |||
-----------------------------------------------------------------------cctagacaactaaggctgtagcctatgtataacatatgctaata-atttatattgcagaa-gttattatatgttttatgagttaacaaaggcctaaaaacagATTTGAGGAACATGAAGCACCTGGATCAAGATCCTTCTTTACAGAAATTATTGCATCAATTTCTGATATAAAGTTTTCAAGGAATGGCAAATATATTCTT

upper sequence: LOC_Os06g36770.2 (Oryza sativa), 3'ss of exon 8
lower sequence: GLYMA08G20830.2 (Glycine max), 3'ss of exon 8
gttagtaattcatcttatgccttttacctgcaacattttatccgtgtgtactggaggtagtcgtggacttcttttgacggttgggacttggggctgcataagattctctattctatactagtaatagaatgtcacaatatcagcatgagataacaagaacctttaaacagATTTGAGGAACATGAAGCACCTGGATCAAGATCCTTCTTTACAGAGATAATCGCATCAATATCGGATATAAAATTTTCAAGGGATGGAAGATACATCCTT
                                            ||  |||  |    |  | |     | || ||  |  |   |  |     || ||    || | |  | | |  | |   || | |  || ||||| | |                 |||  |||||||||||||||| ||||| ||||| || ||||| || || |||||||| ||||| ||||| || || |||||||||   | |||||||||||| || |||
-------------------------------------------ttgcatacaaggaa-aaccat-----ttttctggagcctattatata----tgtattcatttatgtgatttgt-tttgcggtaaactcacagaatattacc----------------ttttgtacagATTTGAGGAACAAGAAGCCCCTGGGTCCAGATCATTTTTCACAGAGATTATCGCTTCAATCTCAGACATAAAATTTGGGAAGGATGGAAGATATATACTT

upper sequence: LOC_Os06g36770.2 (Oryza sativa), 3'ss of exon 8
lower sequence: GLYMA07G01440.1 (Glycine max), 3'ss of exon 8
gttagtaattcatcttatgccttttacctgcaacattttatccgtgtgtactggaggtagtcgtggacttcttttgacggttgggacttggggctgcataagattctctattctatact-agtaatagaatgtcaca-atatcagcatgagataacaagaacctttaaacagATTTGAGGAACATGAAGCACCTGGATCAAGATCCTTCTTTACAGAGATAATCGCATCAATATCGGATATAAAATTTTCAAGGGATGGAAGATACATCCTT
                                                                        |||  |            |   |      ||| || |  | | || | | | ||   || ||         ||  | | | || |  |   | |  |||||||||||||||| ||||| ||||| ||| |||| || || |||||||| || || ||||| || || |||||||||   | |||||||||||| || |||
------------------------------------------------------------------------ttttgcatacaaagaaaagcatttttctggatcctattatatttattcatttatgtgatttcttttgcggtagactcacagaaaattattttctgtacagATTTGAGGAACAAGAAGCCCCTGGGTCACGATCATTTTTCACAGAGATTATTGCCTCAATCTCAGACATAAAATTTGGGAAGGATGGAAGATATATACTT

upper sequence: LOC_Os06g36770.2 (Oryza sativa), 3'ss of exon 8
lower sequence: AT1G17720.2 (Arabidopsis thaliana), 3'ss of exon 8
--------------gttagtaattcatctta--tgccttttacctgcaacattttatccgtgtgtactggaggtagt--cgtggacttctttt-gacggttgggacttggggctgcataagattctctattctatactagtaa--tagaatgtcacaatatcagcatgagataacaagaacctttaaacagATTTGAGGAACATGAAGCACCTGGATCAAGATCCTTCTTTACAGAGATAATCGCATCAATATCGGATATAAAATTTTCAAGGGATGGAAGATACATCCTT
                |  |  || |||  |  ||    || | ||   || | ||| | |  | |  |||  |     |||||  |  |||   |   ||     ||   |    | | || |    | |  | | || ||   || | | ||  |  |    |    | |       | |     |||||||||| ||||  ||||||||||| |||||||| || || ||||||||||| || ||||| || ||||| ||||| |||| |||||| |||||||| |||
gtaagttctgttctcatcatcctttatcggaaatggtagttgcatgtttcaatatatacttaagaaggggatatgaatacgtgggttcatttccaatttttctcttttcttgtcagaaatgacttggaaatgaagattaataggctaaagtttctgaccactgaccattgttgcttcatatc-----acagATTTGAAGAACCGGAAGCACCTGGTTCAAGATCATTTTTCACAGAGATAATTGCCTCAATTTCAGATATTAAATTCTCAAAGGATGGGAGATACATACTT

upper sequence: LOC_Os06g36770.2 (Oryza sativa), 3'ss of exon 8
lower sequence: Vv04s0008g00840.t01 (Vitis vinifera), 3'ss of exon 8
gttagtaattcatcttatgccttttacctgcaacattttatc-cgtgtgtactggaggtagtcgtggacttcttttgacggttggg-act-tggggctgcataagattctctattctatactagtaatagaatgtcacaatatcagcatgagataacaagaacctttaa----acagATTTGAGGAACATGAAGCACCTGGATCAAGATCCTTCTTTACAGAGATAATCGCATCAATATCGGATATAAAATTTTCAAGGGATGGAAGATACATCCTT
    || | | ||||| ||   |||  ||  |   || | || ||| | |  |  |  |  ||  | |  || ||||      |   ||| | || | |||   || | | |  |  ||| |  |  | |||| | |   | | |   |    | | | |  | ||| |    |||| ||||||||||  || ||| ||   |||||||| || |||||||||||||| || ||||| || |||||||| ||||||| |||||||||| |  | |||
----gtgagtgatcttttggtctttgtct--agttttgtgtctcgtttcttgtttacatgatctagaagatcctttggtttcagaacactctaggtcagcaatggagttttttgtagatagttatg-tggaattttaatttctgatattctttttaaatgctcatttgatcatacagGTTTGAGGAACTGGAGGCATCTACTTCAAGATCTTTTTTTACAGAGATAATTGCCTCAATTTCTGATATAAAGTTTTCAAAGGATGGAAGACATTTACTT

upper sequence: LOC_Os06g36770.2 (Oryza sativa), 3'ss of exon 8
lower sequence: Vv09s0002g02470.t01 (Vitis vinifera), 3'ss of exon 8
gttagtaattcatcttatgccttttacctgcaacattttatccgtgtgtactggaggtagtcgtggacttcttttgacggttgggacttggggctgcat--aagattctctattctatactagtaatagaatgtcacaatatcagcatgagataacaagaacctttaaacagATTTGAGGAACATGAAGCACCTGGATCAAGATCCTTCTTTACAGAGATAATCGCATCAATATCGGATATAAAATTTTCAAGGGATGGAAGATACATCCTT
                                                               || | |  |   |      |  |            |  ||| |   |  || |||  ||||  |      |  |   |||||   | ||||  |    | |  |  ||| ||||||||||| || |||||||| |||||||| || || ||||||||||| || ||||| || || || |||||||| | |||||||||||  || || 
---------------------------------------------------------------tgcattgatcagggaaaaagaaaaaaaaaatcattttgaaggtaaacgtttttat-ttagtgct----ctttcctggatcagtcagtgatagta----cttgcatgcagGTTTGAGGAACAAGAGGCACCTGGTTCAAGATCATTTTTCACAGAGATAATTGCCTCAATTTCAGACATTAAATTTTCCAAGGATGGAAGATTTATACTC

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|58675521|gb|CK064208.1|CK064208
EST:     CGACTCATTGATCTGCGACAATCAGCTTTGTGTGACAACCATTCCAAGAT                         ATTTGAGGAACATGAAGCACCTGGATCAAGATCCTTCTTTACAGAGATAAT
genomic: CGACTCATTGATCTGCGACAATCAGCTTTGTGTGACAACCATTCCAAGATgttagtaatt ... ctttaaacagATTTGAGGAACATGAAGCACCTGGATCAAGATCCTTCTTTACAGAGATAAT
EST: gi|58687462|gb|CK076149.1|CK076149
EST:     CGACTCATTGATCTGCGACAATCAGCTTTGTGTGACAACCATTCCAAGAT                         ATTTGAGGAACATGAAGCACCTGGATCAAGATCCTTCTTTACAGAGATAAT
genomic: CGACTCATTGATCTGCGACAATCAGCTTTGTGTGACAACCATTCCAAGATgttagtaatt ... ctttaaacagATTTGAGGAACATGAAGCACCTGGATCAAGATCCTTCTTTACAGAGATAAT
EST: gi|218499339|gb|FG949286.1|FG949286
EST:     CGACTCATTGATCTGCGACAATCAGCTTTGTGTGACAACCATTCCAAGAT                         ATTTGAGGAACATGAAGCACCTGGATCAAGATCCTTCTTTACAGAGATAAT
genomic: CGACTCATTGATCTGCGACAATCAGCTTTGTGTGACAACCATTCCAAGATgttagtaatt ... ctttaaacagATTTGAGGAACATGAAGCACCTGGATCAAGATCCTTCTTTACAGAGATAAT
EST: gi|58658882|gb|CK047562.1|CK047562
EST:     CGACTCATTGATCGGCGAGAATCAGCTTTGTGTGACAACCATTCCAAGAT                         ATTTGAGGAACATGAAGCACCTGGATCAAGATCCTTCTTTACAGAGATAAT
genomic: CGACTCATTGATCTGCGACAATCAGCTTTGTGTGACAACCATTCCAAGATgttagtaatt ... ctttaaacagATTTGAGGAACATGAAGCACCTGGATCAAGATCCTTCTTTACAGAGATAAT
EST: gi|58593657|gb|CF991965.1|CF991965
EST:     CGACTCATTGATCTGCGACAATCAGCTTTGTGTGACAACCATTCCAAGAT                         ATTTGAGGAACATGAAGCACCTGGATCAAGATCCTTCTTTACAGAGATAAT
genomic: CGACTCATTGATCTGCGACAATCAGCTTTGTGTGACAACCATTCCAAGATgttagtaatt ... ctttaaacagATTTGAGGAACATGAAGCACCTGGATCAAGATCCTTCTTTACAGAGATAAT
EST: gi|66912957|gb|CX099805.1|CX099805
EST:     CGACTCATTGATCTGCGACAATCAACTTTGTGTGACAACCATTCCAAGAT                         ATTTGAGGAACATGAAGCACCTGGATCAAGATCCTTCTTTACAGAGATAAT
genomic: CGACTCATTGATCTGCGACAATCAGCTTTGTGTGACAACCATTCCAAGATgttagtaatt ... ctttaaacagATTTGAGGAACATGAAGCACCTGGATCAAGATCCTTCTTTACAGAGATAAT
EST: gi|58674786|gb|CK063473.1|CK063473
EST:     CGACTCATTGATCTGCGACAATCAGCTTTGTGTGACAACCATTCCAAGAT                         ATTTGAGGAACATGAAGCACCTGGATCAAGATCCTTCTTTACAGAGATAAT
genomic: CGACTCATTGATCTGCGACAATCAGCTTTGTGTGACAACCATTCCAAGATgttagtaatt ... ctttaaacagATTTGAGGAACATGAAGCACCTGGATCAAGATCCTTCTTTACAGAGATAAT
EST: gi|58688813|gb|CK077500.1|CK077500
EST:     CGACTCATTGATCTGCGACAATCAGCTTTGTGTGACAACCATTCCAAGAT                         ATTTGAGGAACATGAAGCACCTGGATCAAGATCCTTCTTTACAGAGATAAT
genomic: CGACTCATTGATCTGCGACAATCAGCTTTGTGTGACAACCATTCCAAGATgttagtaatt ... ctttaaacagATTTGAGGAACATGAAGCACCTGGATCAAGATCCTTCTTTACAGAGATAAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tactagtaatagaatgtcacaatatcagcatgagataacaagaacctttaaacagATTTGAGGAACATGAAGCACCTGGATCAAGATCCTTCTTTACAGAGATAATCGCATCAATATCGGATATAAAATTTTCAAGGGATGGAAGATACATCCTT
                                agataac  putative branch site (score: 3)
                                            ccttt  putative PPT
      taatagaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttagtaattcatcttatgccttttacctgcaacattttatccgtgtgtactggaggtagtcgtggacttcttttgacggttgggacttggggctgcataagattctctattctatactagtaatagaatgtcacaatatcagcatgagataacaagaacctttaaacagATTTGAGGAACATGAAGCACCTGGATCAAGATCCTTCTTTACAGAGATAATCGCATCAATATCGGATATAAAATTTTCAAGGGATGGAAGATACATCCTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA