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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgattacaatacatatcatacatgatttgtggatcatagattccttcaagaactgattctatatgatttctgtgtgaagGAATGGCAACAATTTGAGGAGGCTGTCCAACATGACTTTGTTACTGGGTTTGGGAAGAAGCTCAGCAGCCTTCTGGATAGATGTTTATCAGA

Basic information

species Zea mays
transcript AC196426.3_FGT007
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AC196426.3_FGT007 (Zea mays), 3'ss of exon 11
lower sequence: LOC_Os01g39310.3 (Oryza sativa), 3'ss of exon 12
gtgattacaatacatatcatacatgatttgtggatcatagattccttcaag-aactgattctatatgatttctgtgt---gaagGAATGGCAACAATTTGAGGAGGCTGTCCAACATGACTTTGTTACTGGGTTTGGGAAGAAGCTCAGCAGCCTTCTGGATAGATGTTTATCAGA
|||||| |||||||| |  | | |||  |        | |||      ||  | ||||| || |||   || ||| |    ||||| ||||||||||||||||| ||||| |||||||| |  ||  ||||||||||||||||| |||||| |||||| || ||||| ||||||||
gtgattgcaatacatgttgtgcttgacctacactaatttgatcgaagaaatcagctgatactttatatgttttgtatttaaaagGAGTGGCAACAATTTGAGGAAGCTGTTCAACATGATTACGTGCCTGGGTTTGGGAAGAAGATCAGCAACCTTCTTGACAGATGCTTATCAGA
















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|211457038|gb|FK967316.1|FK967316
EST:     GTTGTGAGGAAATTGGTAATGAGAAAGTTACCAGCTTTATAGCTGATGAG                         GAATGGCAACAATTTGAGGAGGCTGTCCAACATGACTTTGTTACTGGGTTT
genomic: GTTGTGAGGAAATTGGTAATGAGAAAGTTACCAGCTTTATAGCTGATGAGgtgattacaa ... ctgtgtgaagGAATGGCAACAATTTGAGGAGGCTGTCCAACATGACTTTGTTACTGGGTTT
EST: gi|211043098|gb|FK967329.1|FK967329
EST:     GTTGTGAGGAAATTGGTAATGAGAAAGTTACCAGCTTTATAGCTGATGAG                         GAATGGCAACAATTTGAGGAGGCTGTCCAACATGACTTTGTTACTGGGTTT
genomic: GTTGTGAGGAAATTGGTAATGAGAAAGTTACCAGCTTTATAGCTGATGAGgtgattacaa ... ctgtgtgaagGAATGGCAACAATTTGAGGAGGCTGTCCAACATGACTTTGTTACTGGGTTT
EST: gi|211454906|gb|FK967300.1|FK967300
EST:     GTTGTGAGGAAATTGGTAATGAGAAAGTTACCAGCTTTATAGCTGATGAG                         GAATGGCAACAATTTGAGGAGGCTGTCCAACATGACTTTGTTACTGGGTTT
genomic: GTTGTGAGGAAATTGGTAATGAGAAAGTTACCAGCTTTATAGCTGATGAGgtgattacaa ... ctgtgtgaagGAATGGCAACAATTTGAGGAGGCTGTCCAACATGACTTTGTTACTGGGTTT
EST: gi|211457037|gb|FK967315.1|FK967315
EST:     GTTGTGAGGAAATTGGTAATGAGAAAGTTACCAGCTTTATAGCTGATGAG                         GAATGGCAACAATTTGAGGAGGCTGTCCAACATGACTTTGTTACTGGGTTT
genomic: GTTGTGAGGAAATTGGTAATGAGAAAGTTACCAGCTTTATAGCTGATGAGgtgattacaa ... ctgtgtgaagGAATGGCAACAATTTGAGGAGGCTGTCCAACATGACTTTGTTACTGGGTTT
EST: gi|211454909|gb|FK967303.1|FK967303
EST:     GTTGTGAGGAAATTGGTAATGAGAAAGTTACCAGCTTTATAGCTGATGAG                         GAATGGCAACAATTTGAGGAGGCTGTCCAACATGACTTTGTTACTGGGTTT
genomic: GTTGTGAGGAAATTGGTAATGAGAAAGTTACCAGCTTTATAGCTGATGAGgtgattacaa ... ctgtgtgaagGAATGGCAACAATTTGAGGAGGCTGTCCAACATGACTTTGTTACTGGGTTT
EST: gi|211454913|gb|FK967307.1|FK967307
EST:     GTTGTGAGGAAATTGGTAATGAGAAAGTTACCAGCTTTATAGCTGATGAG                         GAATGGCAACAATTTGAGGAGGCTGTCCAACATGACTTTGTTACTGGGTTT
genomic: GTTGTGAGGAAATTGGTAATGAGAAAGTTACCAGCTTTATAGCTGATGAGgtgattacaa ... ctgtgtgaagGAATGGCAACAATTTGAGGAGGCTGTCCAACATGACTTTGTTACTGGGTTT
EST: gi|211454904|gb|FK967298.1|FK967298
EST:     GTTGTGAGGAAATTGGTAATGAGAAAGTTACCAGCTTTATAGCTGATGAG                         GAATGGCAACAATTTGAGGAGGCTGTCCAACATGACTTTGTTACTGGGTTT
genomic: GTTGTGAGGAAATTGGTAATGAGAAAGTTACCAGCTTTATAGCTGATGAGgtgattacaa ... ctgtgtgaagGAATGGCAACAATTTGAGGAGGCTGTCCAACATGACTTTGTTACTGGGTTT
EST: gi|211043097|gb|FK967328.1|FK967328
EST:     GTTGTGAGGAAATTGGTAATGAGAAAGTTACCAGCTTTATAGCTGATGAG                         GAATGGCAACAATTTGAGGAGGCTGTCCAACATGACTTTGTTACTGGGTTT
genomic: GTTGTGAGGAAATTGGTAATGAGAAAGTTACCAGCTTTATAGCTGATGAGgtgattacaa ... ctgtgtgaagGAATGGCAACAATTTGAGGAGGCTGTCCAACATGACTTTGTTACTGGGTTT
EST: gi|211457040|gb|FK967318.1|FK967318
EST:     GTTGTGAGGAAATTGGTAATGAGAAAGTTACCAGCTTTATAGCTGATGAG                         GAATGGCAACAATTTGAGGAGGCTGTCCAACATGACTTTGTTACTGGGTTT
genomic: GTTGTGAGGAAATTGGTAATGAGAAAGTTACCAGCTTTATAGCTGATGAGgtgattacaa ... ctgtgtgaagGAATGGCAACAATTTGAGGAGGCTGTCCAACATGACTTTGTTACTGGGTTT
EST: gi|211457033|gb|FK967311.1|FK967311
EST:     GTTGTGAGGAAATTGGTAATGAGAAAGTTACCAGCTTTATAGCTGATGAG                         GAATGGCAACAATTTGAGGAGGCTGTCCAACATGACTTTGTTACTGGGTTT
genomic: GTTGTGAGGAAATTGGTAATGAGAAAGTTACCAGCTTTATAGCTGATGAGgtgattacaa ... ctgtgtgaagGAATGGCAACAATTTGAGGAGGCTGTCCAACATGACTTTGTTACTGGGTTT
EST: gi|211454911|gb|FK967305.1|FK967305
EST:     GTTGTGAGGAAATTGGTAATGAGAAAGTTACCAGCTTTATAGCTGATGAG                         GAATGGCAACAATTTGAGGAGGCTGTCCAACATGACTTTGTTACTGGGTTT
genomic: GTTGTGAGGAAATTGGTAATGAGAAAGTTACCAGCTTTATAGCTGATGAGgtgattacaa ... ctgtgtgaagGAATGGCAACAATTTGAGGAGGCTGTCCAACATGACTTTGTTACTGGGTTT
EST: gi|211457034|gb|FK967312.1|FK967312
EST:     GTTGTGAGGAAATTGGTAATGAGAAAGTTACCAGCTTTATAGCTGATGAG                         GAATGGCAACAATTTGAGGAGGCTGTCCAACATGACTTTGTTACTGGGTTT
genomic: GTTGTGAGGAAATTGGTAATGAGAAAGTTACCAGCTTTATAGCTGATGAGgtgattacaa ... ctgtgtgaagGAATGGCAACAATTTGAGGAGGCTGTCCAACATGACTTTGTTACTGGGTTT
EST: gi|211457046|gb|FK967324.1|FK967324
EST:     GTTGTGAGGAAATTGGTAATGAGAAAGTTACCAGCTTTATAGCTGATGAG                         GAATGGCAACAATTTGAGGAGGCTGTCCAACATGACTTTGTTACTGGGTTT
genomic: GTTGTGAGGAAATTGGTAATGAGAAAGTTACCAGCTTTATAGCTGATGAGgtgattacaa ... ctgtgtgaagGAATGGCAACAATTTGAGGAGGCTGTCCAACATGACTTTGTTACTGGGTTT

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 4 RNA-Seq libraries.


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 265

GTTATGGTGGCTACTGTACGTTGTGAGGAAATTGGTAATGAGAAAGTTACCAGCTTTATAGCTGATGAGgtgattacaa ... ctgtgtgaagGAATGGCAACAATTTGAGGAGGCTGTCCAACATGACTTTGTTACTGGGTTTGGGAAGAAGCTCAGCAGCCTTCTGGATAGATGTTTATCAGA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 258

GTTATGGTGGCTACTGTACGTTGTGAGGAAATTGGTAATGAGAAAGTTACCAGCTTTATAGCTGATGAGgtgattacaa ... ctgtgtgaagGAATGGCAACAATTTGAGGAGGCTGTCCAACATGACTTTGTTACTGGGTTTGGGAAGAAGCTCAGCAGCCTTCTGGATAGATGTTTATCAGA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 190

GTTATGGTGGCTACTGTACGTTGTGAGGAAATTGGTAATGAGAAAGTTACCAGCTTTATAGCTGATGAGgtgattacaa ... ctgtgtgaagGAATGGCAACAATTTGAGGAGGCTGTCCAACATGACTTTGTTACTGGGTTTGGGAAGAAGCTCAGCAGCCTTCTGGATAGATGTTTATCAGA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 400

GTTATGGTGGCTACTGTACGTTGTGAGGAAATTGGTAATGAGAAAGTTACCAGCTTTATAGCTGATGAGgtgattacaa ... ctgtgtgaagGAATGGCAACAATTTGAGGAGGCTGTCCAACATGACTTTGTTACTGGGTTTGGGAAGAAGCTCAGCAGCCTTCTGGATAGATGTTTATCAGA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atttgtggatcatagattccttcaagaactgattctatatgatttctgtgtgaagGAATGGCAACAATTTGAGGAGGCTGTCCAACATGACTTTGTTACTGGGTTTGGGAAGAAGCTCAGCAGCCTTCTGGATAGATGTTTATCAGA
                          aactgat  putative branch site (score: 400)
                                          tttctgt  putative PPT
                               attctatatgattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgattacaatacatatcatacatgatttgtggatcatagattccttcaagaactgattctatatgatttctgtgtgaagGAATGGCAACAATTTGAGGAGGCTGTCCAACATGACTTTGTTACTGGGTTTGGGAAGAAGCTCAGCAGCCTTCTGGATAGATGTTTATCAGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTCA