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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagttaatatgatcatattttttttactttattatatgcaaggtttatcccgtgatcagattatgattacttttatatttaatgatttgaaacaatttccatcacttttaatttattatgtttttgcagTTCATCCGGAATCTTGGAATCCTATGTGGTCTGTGGCAAG

Basic information

species Oryza sativa
transcript LOC_Os06g09330.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os06g09330.2 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G177276_T01 (Zea mays), 3'ss of exon 5
gtaagttaatatgatcatattttttttactttattatatgcaaggttt-atcccgtgatcagattatgattacttttatatttaatgatt-tgaaacaatttccatcacttttaatttattatgtttttgcagTTCATCCGGAATCTTGGAATCCTATGTGGTCTGTGGCAAG
                                       | ||| | | | |  |      ||||||   | ||||| |  ||| |   | ||||| |||   ||| |        |||  ||||||| ||||||||||| |||||||||||||| ||||||||||| |||||
---------------------------------------gtaagttctgaacttgcttgtggattatagatgcttttgttattattagctctgaaataatgctcatta--------ttacaatgtttt-gcagTTCATCCTGAATCTTGGAATCCAATGTGGTCTGTTGCAAG

upper sequence: LOC_Os06g09330.2 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G116919_T02 (Zea mays), 3'ss of exon 5
gtaagttaatatgatcatattttttttactttattatatgc--aaggtttatcccgtgatcagattatgattacttttatatttaatgatttgaaacaatttccatcacttttaatttattatgtttttgcagTTCATCCGGAATCTTGGAATCCTATGTGGTCTGTGGCAAG------------------------------------------------------------
                           ||      | ||||  |  |  |     |      |    |  | | |     |  ||    ||||||| ||    ||| | ||       |||  | ||||||||||||||| |||||||||||||| ||||||||||| |||||                                                            
-------------------------ccaccccggcaaatgcggagaggctgctttgaacctgggacctagtgattcagtgagatagctctttgaaataacgctcattatttc------att--gcttttgcagTTCATCCTGAATCTTGGAATCCGATGTGGTCTGTTGCAAGGTACACATATACCAATAACTAGCTTATTACATGAACAGTAATGTTTTTTTGGAAGACATA

upper sequence: LOC_Os06g09330.2 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G116919_T01 (Zea mays), 3'ss of exon 5
gtaagttaatatgatcatattttttttactttattatatgc--aaggtttatcccgtgatcagattatgattacttttatatttaatgatttgaaacaatttccatcacttttaatttattatgtttttgcagTTCATCCGGAATCTTGGAATCCTATGTGGTCTGTGGCAAG
                           ||      | ||||  |  |  |     |      |    |  | | |     |  ||    ||||||| ||    ||| | ||       |||  | ||||||||||||||| |||||||||||||| ||||||||||| |||||
-------------------------ccaccccggcaaatgcggagaggctgctttgaacctgggacctagtgattcagtgagatagctctttgaaataacgctcattatttc------att--gcttttgcagTTCATCCTGAATCTTGGAATCCGATGTGGTCTGTTGCAAG

upper sequence: LOC_Os06g09330.2 (Oryza sativa), 3'ss of exon 2
lower sequence: GLYMA16G01680.1 (Glycine max), 3'ss of exon 6
gtaagttaatatgatcatattttttttactttattatatgcaaggtttatcccgtgatcagattatgattacttttatatttaatgatttgaaacaatttccatcacttttaatttattatgtttttgcagTTCATCCGGAATCTTGGAATCCTATGTGGTCTGTGGCAAG
                 ||  || | |  | | || || |||      |    ||      || |||| |      |||||  |  |||| | |    || |  |||     ||||  ||   ||||||||||||||| |||  ||||||||| |||||||||||  ||||
----------------gtaagttctcttttctgttgta-gcacaaaacaattagt------atcatgagttaacccatatt--acaatttaata----tttctgcac----gatttgcta--cttttgcagTTCATCCAGAAAGTTGGAATCCCATGTGGTCTGTATCAAG

upper sequence: LOC_Os06g09330.2 (Oryza sativa), 3'ss of exon 2
lower sequence: GLYMA07G05170.1 (Glycine max), 3'ss of exon 6
gtaagttaatatgatcatattttttttactttattatatgcaaggtttatcccgtgatcagattatgattacttttatatttaatgatttgaaacaatttccatcacttttaatttattatgtttttgcagTTCATCCGGAATCTTGGAATCCTATGTGGTCTGTGGCAAG
                                    || || |  |||        | || |  |  |||| | | ||   |||     |   |||||||        |      | |  |  ||||||||||||||| |||  ||||||||| |||||||||||  ||||
-----------------------------------gtaagctattttttctgttgtagcacaaaacaattagtatcatgagtaacc-catattacaatttaatatttctgcgggatttgctacttttgcagTTCATCCAGAAAGTTGGAATCCCATGTGGTCTGTATCAAG

upper sequence: LOC_Os06g09330.2 (Oryza sativa), 3'ss of exon 2
lower sequence: GLYMA07G05170.2 (Glycine max), 3'ss of exon 5
gtaagttaatatgatcatattttttttactttattatatgcaaggtttatcccgtgatcagattatgattacttttatatttaatgatttgaaacaatttccatcacttttaatttattatgtttttgcagTTCATCCGGAATCTTGGAATCCTATGTGGTCTGTGGCAAG
                              | | | || || |  |||        | || |  |  |||| | | ||   |||     |   |||||||        |      | |  |  ||||||||||||||| |||  ||||||||| |||||||||||  ||||
------------------------------tgactgtaagctattttttctgttgtagcacaaaacaattagtatcatgagtaacc-catattacaatttaatatttctgcgggatttgctacttttgcagTTCATCCAGAAAGTTGGAATCCCATGTGGTCTGTATCAAG

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|87015788|gb|CI279540.1|CI279540
EST:     TAGCGGAAGGTTTGCCCCTCACAAAAGAATATGCCTATCAATGAGTGACT                         TTCATCCGGAATCTTGGAATCCTATGTGGTCTGTGGCAAG
genomic: TAGCGGAAGGTTTGCCCCTCACAAAAGAATATGCCTATCAATGAGTGACTgtaagttaat ... gtttttgcagTTCATCCGGAATCTTGGAATCCTATGTGGTCTGTGGCAAG
EST: gi|87010686|gb|CI312378.1|CI312378
EST:     AGCGGAAGGTTTGCCCTTCACAAAAGAATAGGCCTATCAATGAGTGACT                         TTCATCCGGAATCTTGGAATCCTATGTGGTCTGTGGCAAG
genomic: AGCGGAAGGTTTGCCCCTCACAAAAGAATATGCCTATCAATGAGTGACTgtaagttaat ... gtttttgcagTTCATCCGGAATCTTGGAATCCTATGTGGTCTGTGGCAAG
EST: gi|86599367|gb|CI251325.1|CI251325
EST:     AATATGCCTATCAATGAGTGACT                         TTCATCCGGAATCTTGGAATCCTATGTGGTCTGTGGCAAG
genomic: AATATGCCTATCAATGAGTGACTgtaagttaat ... gtttttgcagTTCATCCGGAATCTTGGAATCCTATGTGGTCTGTGGCAAG
EST: gi|86514651|gb|CI157284.1|CI157284
EST:     TCAATGAGTGACT                         TTCATCCGGAATCTTGGAATCCTATGTGGTCTGTGGCAAG
genomic: TCAATGAGTGACTgtaagttaat ... gtttttgcagTTCATCCGGAATCTTGGAATCCTATGTGGTCTGTGGCAAG
EST: gi|87035496|gb|CI190118.1|CI190118
EST:     TAGCGGAAGGTTTGCCCCTCACAAAAGAATATGCCTATCAATGAGTGACT                         TTCATCCGGAATCTTGGAATCCTATGTGGTCTGTGGCAAG
genomic: TAGCGGAAGGTTTGCCCCTCACAAAAGAATATGCCTATCAATGAGTGACTgtaagttaat ... gtttttgcagTTCATCCGGAATCTTGGAATCCTATGTGGTCTGTGGCAAG
EST: gi|88206366|gb|CI206215.1|CI206215
EST:     TGCCCCTCACAAAAGAATATGCCTATCAATGAGTGACT                         TTCATCCGGAATCTTGGAATCCTATGTGGTCTGTGGCAAG
genomic: TGCCCCTCACAAAAGAATATGCCTATCAATGAGTGACTgtaagttaat ... gtttttgcagTTCATCCGGAATCTTGGAATCCTATGTGGTCTGTGGCAAG
EST: gi|86495662|gb|CI138295.1|CI138295
EST:     TAGCGGAAGGTTTGCCCCTCACAAAAGAATATGCCTATCAATGAGTGACT                         TTCATCCGGAATCTTGGAATCCTATGTGGTCTGTGGCAAG
genomic: TAGCGGAAGGTTTGCCCCTCACAAAAGAATATGCCTATCAATGAGTGACTgtaagttaat ... gtttttgcagTTCATCCGGAATCTTGGAATCCTATGTGGTCTGTGGCAAG
EST: gi|8956608|gb|BE230283.1|BE230283
EST:     TAGCGGAAGGTTTGCCCCTCACAAAAGAATATGCCTATCAATGAGTGACT                         TTCATCCGGAATCTTGGAATCCTATGTGGTCTGTGGCAAG
genomic: TAGCGGAAGGTTTGCCCCTCACAAAAGAATATGCCTATCAATGAGTGACTgtaagttaat ... gtttttgcagTTCATCCGGAATCTTGGAATCCTATGTGGTCTGTGGCAAG
EST: gi|7134934|gb|AU082746.1|AU082746
EST:     TAGCGGAAGGTTTGCCCCTCACAAAAGAATATGCCTATCAATGAGTGACT                         TTCATCCGGAATCTTGGAATCCTATGTGGTCTGTGGCAAG
genomic: TAGCGGAAGGTTTGCCCCTCACAAAAGAATATGCCTATCAATGAGTGACTgtaagttaat ... gtttttgcagTTCATCCGGAATCTTGGAATCCTATGTGGTCTGTGGCAAG
EST: gi|218487817|gb|FG955497.1|FG955497
EST:     TAGCGGAAGGTTTGCCCCTCACAAAAGAATATGCCTATCAATGAGTGACT                         TTCATCCGGAATCTTGGAATCCTATGTGGTCTGTGGCAAG
genomic: TAGCGGAAGGTTTGCCCCTCACAAAAGAATATGCCTATCAATGAGTGACTgtaagttaat ... gtttttgcagTTCATCCGGAATCTTGGAATCCTATGTGGTCTGTGGCAAG
EST: gi|218490255|gb|FG953556.1|FG953556
EST:     TAGCGGAAGGTTTGCCCCTCACAAAAGAATATGCCTATCAATGAGTGACT                         TTCATCCGGAATCTTGGAATCCTATGTGGTCTGTGGCAAG
genomic: TAGCGGAAGGTTTGCCCCTCACAAAAGAATATGCCTATCAATGAGTGACTgtaagttaat ... gtttttgcagTTCATCCGGAATCTTGGAATCCTATGTGGTCTGTGGCAAG
EST: gi|218494998|gb|FG948724.1|FG948724
EST:     TAGCGGAAGGTTTGCCCCTCACAAAAGAATATGCCTATCAATGAGTGACT                         TTCATCCGGAATCTTGGAATCCTATGTGGTCTGTGGCAAG
genomic: TAGCGGAAGGTTTGCCCCTCACAAAAGAATATGCCTATCAATGAGTGACTgtaagttaat ... gtttttgcagTTCATCCGGAATCTTGGAATCCTATGTGGTCTGTGGCAAG

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 1 RNA-Seqlibrary.


Block sizes: 62 (upstream exon), 64 (downstream exon)
Score: 98

CATGACAACTCCTAGCGGAAGGTTTGCCCCTCACAAAAGAATATGCCTATCAATGAGTGACTgtaagttaat ... gtttttgcagTTCATCCGGAATCTTGGAATCCTATGTGGTCTGTGGCAAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atatttaatgatttgaaacaatttccatcacttttaatttattatgtttttgcagTTCATCCGGAATCTTGGAATCCTATGTGGTCTGTGGCAAG
                               ttttaat  putative branch site (score: 98)
                                            tgttttt  putative PPT
                          atcacttttaatttat  TA-rich tract