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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gacgttggattgaaaataaattccagagattttttcattggtgtgtttatggttgtttgatcatgtggtgagtggtgactatgcttgtatgtgaatgtagGACCTAAGTAAAAAGGAGAAAGAACTGCAGGCAAAGGAAGCTGAGCTAAACAAACGGGAAAGG

Basic information

species Zea mays
transcript GRMZM2G169773_T02
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G169773_T02 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os01g57220.2 (Oryza sativa), 3'ss of exon 2
-------gacgttggattgaaaata-aattccagagattttttcattggtgtgtttatggttgtttgatcatgtggtgagtggtgactatgcttgtatgtgaatgtagGACCTAAGTAAAAAGGAGAAAGAACTGCAGGCAAAGGAAGCTGAGCTAAACAAACGGGAAAGG
         | |||| ||| |  |   || ||| | ||| |||  ||| ||| ||| |||||| ||| | |||   |||||       ||| | |||||| |||  ||||| | |  ||||||||||||||||||||||||||||| ||||||||||||||||||||||| 
ttcactattccttggtttggatgtttgataccatatattcttttgttgctgtatttgtggttggttgcttatgcattgagt-------atgttcgtatgt-aattcagGACATGAAGAAAAAGGAGAAAGAACTGCAGGCAAAGGAGGCTGAGCTAAACAAACGGGAAAGC
















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|148980186|gb|EE026996.2|EE026996
EST:     TCTACAATGATCGTGGTGCAACAGTGGACATACCTCTTGATTCAACGAAG                         GACCTAAGTAAAAAGGAGAAAGAACTGCAGGCAAAGGAAGCTGAGCTAAAC
genomic: TCTACAATGATCGTGGTGCAACAGTGGACATACCTCTTGATTCAACGAAGgtaagcagac ... gtgaatgtagGACCTAAGTAAAAAGGAGAAAGAACTGCAGGCAAAGGAAGCTGAGCTAAAC
EST: gi|211370168|gb|FL333601.1|FL333601
EST:     TCTACAATGATCGTGGTGCAACAGTGGACATACCTCTTGATTCAACGAAG                         GACCTAAGTAAAAAGGAGAAAGAACTGCAGGCAAAGGAAGCTGAGCTAAAC
genomic: TCTACAATGATCGTGGTGCAACAGTGGACATACCTCTTGATTCAACGAAGgtaagcagac ... gtgaatgtagGACCTAAGTAAAAAGGAGAAAGAACTGCAGGCAAAGGAAGCTGAGCTAAAC
EST: gi|211274558|gb|FL349471.1|FL349471
EST:     TCTACAATGATCGTGGTGCAACAGTGGACATACCTCTTGATTCAACGAAG                         GACCTAAGTAAAAAGGAGAAAGAACTGCAGGCAAAGGAAGCTGAGCTAAAC
genomic: TCTACAATGATCGTGGTGCAACAGTGGACATACCTCTTGATTCAACGAAGgtaagcagac ... gtgaatgtagGACCTAAGTAAAAAGGAGAAAGAACTGCAGGCAAAGGAAGCTGAGCTAAAC
EST: gi|211265380|gb|FL345555.1|FL345555
EST:     TCTACAATGATCGTGGTGCAACAGTGGACATACCTCTTGATTCAACGAAG                         GACCTAAGTAAAAAGGAGAAAGAACTGCAGGCAAAGGAAGCTGAGCTAAAC
genomic: TCTACAATGATCGTGGTGCAACAGTGGACATACCTCTTGATTCAACGAAGgtaagcagac ... gtgaatgtagGACCTAAGTAAAAAGGAGAAAGAACTGCAGGCAAAGGAAGCTGAGCTAAAC
EST: gi|211534447|gb|FL327599.1|FL327599
EST:     TCTACAATGATCGTGGTGCAACAGTGGACATACCTCTTGATTCAACGAAG                         GACCTAAGTAAAAAGGAGAAAGAACTGCAGGCAAAGGAAGCTGAGCTAAAC
genomic: TCTACAATGATCGTGGTGCAACAGTGGACATACCTCTTGATTCAACGAAGgtaagcagac ... gtgaatgtagGACCTAAGTAAAAAGGAGAAAGAACTGCAGGCAAAGGAAGCTGAGCTAAAC
EST: gi|76293307|gb|DV032875.1|DV032875
EST:     TCTACAATGATCGTGGTGCAACAGTGGACATACCTCTTGATTCAACGAAG                         GACCTAAGTAAAAAGGAGAAAGAACTGCAGGCAAAGGAAGCTGAGCTAAAC
genomic: TCTACAATGATCGTGGTGCAACAGTGGACATACCTCTTGATTCAACGAAGgtaagcagac ... gtgaatgtagGACCTAAGTAAAAAGGAGAAAGAACTGCAGGCAAAGGAAGCTGAGCTAAAC
EST: gi|211525880|gb|FL340827.1|FL340827
EST:     TCTACAATGATCGTGGTGCAACAGTGGACATACCTCTTGATTCAACGAAG                         GACCTAAGTAAAAAGGAGAAAGAACTGCAGGCAAAGGAAGCTGAGCTAAAC
genomic: TCTACAATGATCGTGGTGCAACAGTGGACATACCTCTTGATTCAACGAAGgtaagcagac ... gtgaatgtagGACCTAAGTAAAAAGGAGAAAGAACTGCAGGCAAAGGAAGCTGAGCTAAAC
EST: gi|211278417|gb|FL366616.1|FL366616
EST:     TCTACAATGATCGTGGTGCAACAGTGGACATACCTCTTGATTCAACGAAG                         GACCTAAGTAAAAAGGAGAAAGAACTGCAGGCAAAGGAAGCTGAGCTAAAC
genomic: TCTACAATGATCGTGGTGCAACAGTGGACATACCTCTTGATTCAACGAAGgtaagcagac ... gtgaatgtagGACCTAAGTAAAAAGGAGAAAGAACTGCAGGCAAAGGAAGCTGAGCTAAAC
EST: gi|211425017|gb|FL340245.1|FL340245
EST:     TCTACAATGATCGTGGTGCAACAGTGGACATACCTCTTGATTCAACGAAG                         GACCTAAGTAAAAAGGAGAAAGAACTGCAGGCAAAGGAAGCTGAGCTAAAC
genomic: TCTACAATGATCGTGGTGCAACAGTGGACATACCTCTTGATTCAACGAAGgtaagcagac ... gtgaatgtagGACCTAAGTAAAAAGGAGAAAGAACTGCAGGCAAAGGAAGCTGAGCTAAAC
EST: gi|211404726|gb|FL347370.1|FL347370
EST:     TCTACAATGATCGTGGTGCAACAGTGGACATACCTCTTGATTCAACGAAG                         GACCTAAGTAAAAAGGAGAAAGAACTGCAGGCAAAGGAAGCTGAGCTAAA
genomic: TCTACAATGATCGTGGTGCAACAGTGGACATACCTCTTGATTCAACGAAGgtaagcagac ... gtgaatgtagGACCTAAGTAAAAAGGAGAAAGAACTGCAGGCAAAGGAAGCTGAGCTAAA
EST: gi|211465039|gb|FL331927.1|FL331927
EST:     TCTACAATGATCGTGGTGCAACAGTGGACATACCTCTTGATTCAACGAAG                         GACCTAAGTAAAAAGGAGAAAGAACTGCAGGCAAAGGAAGCTGAGCTAAAC
genomic: TCTACAATGATCGTGGTGCAACAGTGGACATACCTCTTGATTCAACGAAGgtaagcagac ... gtgaatgtagGACCTAAGTAAAAAGGAGAAAGAACTGCAGGCAAAGGAAGCTGAGCTAAAC
EST: gi|211196276|gb|FL364468.1|FL364468
EST:     TCTACAATGATCGTGGTGCAACAGTGGACATACCTCTTGATTCAACGAAG                         GACCTAAGTAAAAAGGAGAAAGAACTGCAGGCAAAGGAAGCTGAGCTAAAC
genomic: TCTACAATGATCGTGGTGCAACAGTGGACATACCTCTTGATTCAACGAAGgtaagcagac ... gtgaatgtagGACCTAAGTAAAAAGGAGAAAGAACTGCAGGCAAAGGAAGCTGAGCTAAAC
EST: gi|211433369|gb|FL360626.1|FL360626
EST:     TCTACAATGATCGTGGTGCAACAGTGGACATACCTCTTGATTCAACGAAG                         GACCTAAGTAAAAAGGAGAAAGAACTGCAGGCAAAGGAAGCTGAGCTAAAC
genomic: TCTACAATGATCGTGGTGCAACAGTGGACATACCTCTTGATTCAACGAAGgtaagcagac ... gtgaatgtagGACCTAAGTAAAAAGGAGAAAGAACTGCAGGCAAAGGAAGCTGAGCTAAAC
EST: gi|71429331|gb|DR810381.1|DR810381
EST:     TCTACAATGATCGTGGTGCAACAGTGGACATACCTCTTGATTCAACGAAG                         GACCTAAGTAAAAAGGAGAAAGAACTGCAGGCAAAGGAAGCTGAGCTAAAC
genomic: TCTACAATGATCGTGGTGCAACAGTGGACATACCTCTTGATTCAACGAAGgtaagcagac ... gtgaatgtagGACCTAAGTAAAAAGGAGAAAGAACTGCAGGCAAAGGAAGCTGAGCTAAAC
EST: gi|211015839|gb|FL346618.1|FL346618
EST:     TCTACAATGATCGTGGTGCAACAGTGGACATACCTCTTGATTCAACGAAG                         GACCTAAGTAAAAAGGAGAAAGAACTGCAGGCAAAGGAAGCTGAGCTAAAC
genomic: TCTACAATGATCGTGGTGCAACAGTGGACATACCTCTTGATTCAACGAAGgtaagcagac ... gtgaatgtagGACCTAAGTAAAAAGGAGAAAGAACTGCAGGCAAAGGAAGCTGAGCTAAAC
EST: gi|211537608|gb|FL330675.1|FL330675
EST:     TCTACAATGATCGTGGTGCAACAGTGGACATACCTCTTGATTCAACGAAG                         GACCTAAGTAAAAAGGAGAAAGAACTGCAGGCAAAGGAAGCTGAGCTAAAC
genomic: TCTACAATGATCGTGGTGCAACAGTGGACATACCTCTTGATTCAACGAAGgtaagcagac ... gtgaatgtagGACCTAAGTAAAAAGGAGAAAGAACTGCAGGCAAAGGAAGCTGAGCTAAAC
EST: gi|211231053|gb|FL343819.1|FL343819
EST:     TCTACAATGATCGTGGTGCAACAGTGGACATACCTCTTGATTCAACGAAG                         GACCTAAGTAAAAAGGAGAAAGAACTGCAGGCAAAGGAAGCTGAGCTAAAC
genomic: TCTACAATGATCGTGGTGCAACAGTGGACATACCTCTTGATTCAACGAAGgtaagcagac ... gtgaatgtagGACCTAAGTAAAAAGGAGAAAGAACTGCAGGCAAAGGAAGCTGAGCTAAAC
EST: gi|211211335|gb|FL360036.1|FL360036
EST:     TCTACAATGATCGTGGTGCAACAGTGGACATACCTCTTGATTCAACGAAG                         GACCTAAGTAAAAAGGAGAAAGAACTGCAGGCAAAGGAAG
genomic: TCTACAATGATCGTGGTGCAACAGTGGACATACCTCTTGATTCAACGAAGgtaagcagac ... gtgaatgtagGACCTAAGTAAAAAGGAGAAAGAACTGCAGGCAAAGGAAG
EST: gi|71449251|gb|DR830301.1|DR830301
EST:     TCTACAATGATCGTGGTGCAACAGTGGACATACCTCTTGATTCAACGAAG                         GACCTAAGTAAAAAGGAGAAAGAACTGCAGGCAAAGGAAGCTGAGCTAAAC
genomic: TCTACAATGATCGTGGTGCAACAGTGGACATACCTCTTGATTCAACGAAGgtaagcagac ... gtgaatgtagGACCTAAGTAAAAAGGAGAAAGAACTGCAGGCAAAGGAAGCTGAGCTAAAC
EST: gi|211012583|gb|FL327130.1|FL327130
EST:     TCTACAATGATCGTGGTGCAACAGTGGACATACCTCTTGATTCAACGAAG                         GACCTAAGTAAAAAGGAGAAAGAACTGCAGGCAAAGGAAGCTGAGCTAAAC
genomic: TCTACAATGATCGTGGTGCAACAGTGGACATACCTCTTGATTCAACGAAGgtaagcagac ... gtgaatgtagGACCTAAGTAAAAAGGAGAAAGAACTGCAGGCAAAGGAAGCTGAGCTAAAC
EST: gi|211224276|gb|FL315364.1|FL315364
EST:     TCTACAATGATCGTGGTGCAACAGTGGACATACCTCTTGATTCAACGAAG                         GACCTAAGTAAAAAGGAGAAAGAACTGCAGGCAAAGGAAG
genomic: TCTACAATGATCGTGGTGCAACAGTGGACATACCTCTTGATTCAACGAAGgtaagcagac ... gtgaatgtagGACCTAAGTAAAAAGGAGAAAGAACTGCAGGCAAAGGAAG
EST: gi|78115059|gb|DV533447.1|DV533447
EST:     TCTACAATGATCGTGGTGCAACAGTGGACATACCTCTTGATTCAACGAAG                         GACCTAAGTAAAAAGGAGAAAGAACTGCAGGCAAAGGAAGCTGAGCTAAAC
genomic: TCTACAATGATCGTGGTGCAACAGTGGACATACCTCTTGATTCAACGAAGgtaagcagac ... gtgaatgtagGACCTAAGTAAAAAGGAGAAAGAACTGCAGGCAAAGGAAGCTGAGCTAAAC
EST: gi|211067503|gb|FL350735.1|FL350735
EST:     TCTACAATGATCGTGGTGCAACAGTGGACATACCTCTTGATTCAACGAAG                         GACCTAAGTAAAAAGGAGAAAGAACTGCAGGCAAAGGAAGCTGAGCTAAAC
genomic: TCTACAATGATCGTGGTGCAACAGTGGACATACCTCTTGATTCAACGAAGgtaagcagac ... gtgaatgtagGACCTAAGTAAAAAGGAGAAAGAACTGCAGGCAAAGGAAGCTGAGCTAAAC
EST: gi|78077114|gb|DV505548.1|DV505548
EST:     TCTACAATGATCGTGGTGCAACAGTGGACATACCTCTTGATTCAACGAAG                         GACCTAAGTAAAAAGGAGAAAGAACTGCAGGCAAAGGAAGCTGAGCTAAAC
genomic: TCTACAATGATCGTGGTGCAACAGTGGACATACCTCTTGATTCAACGAAGgtaagcagac ... gtgaatgtagGACCTAAGTAAAAAGGAGAAAGAACTGCAGGCAAAGGAAGCTGAGCTAAAC
EST: gi|211146797|gb|FL347631.1|FL347631
EST:     TCTACAATGATCGTGGTGCAACAGTGGACATACCTCTTGATTCAACGAAG                         GACCTAAGTAAAAAGGAGAAAGAACTGCAGGCAAAGGAAGCTGAGCTAAAC
genomic: TCTACAATGATCGTGGTGCAACAGTGGACATACCTCTTGATTCAACGAAGgtaagcagac ... gtgaatgtagGACCTAAGTAAAAAGGAGAAAGAACTGCAGGCAAAGGAAGCTGAGCTAAAC

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: 49 (upstream exon), 49 (downstream exon)
Score: 75

TCCTGCTTCTAATTCTCGGATGTCAGCACTTCCTCATGAACCAGCTGGCTTCTACAATGATCGTGGTGCAACAGTGGACATACCTCTTGATTCAACGAAGgtaagcagac ... gtgaatgtagGACCTAAGTAAAAAGGAGAAAGAACTGCAGGCAAAGGAAGCTGAGCTAAACAAACGGGAAAGG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 112

TCCTGCTTCTAATTCTCGGATGTCAGCACTTCCTCATGAACCAGCTGGCTTCTACAATGATCGTGGTGCAACAGTGGACATACCTCTTGATTCAACGAAGgtaagcagac ... gtgaatgtagGACCTAAGTAAAAAGGAGAAAGAACTGCAGGCAAAGGAAGCTGAGCTAAACAAACGGGAAAGG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 188

TCCTGCTTCTAATTCTCGGATGTCAGCACTTCCTCATGAACCAGCTGGCTTCTACAATGATCGTGGTGCAACAGTGGACATACCTCTTGATTCAACGAAGgtaagcagac ... gtgaatgtagGACCTAAGTAAAAAGGAGAAAGAACTGCAGGCAAAGGAAGCTGAGCTAAACAAACGGGAAAGG


Block sizes: 49 (upstream exon), 45 (downstream exon)
Score: 112

TCCTGCTTCTAATTCTCGGATGTCAGCACTTCCTCATGAACCAGCTGGCTTCTACAATGATCGTGGTGCAACAGTGGACATACCTCTTGATTCAACGAAGgtaagcagac ... gtgaatgtagGACCTAAGTAAAAAGGAGAAAGAACTGCAGGCAAAGGAAGCTGAGCTAAACAAACGGGAAAGG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttatggttgtttgatcatgtggtgagtggtgactatgcttgtatgtgaatgtagGACCTAAGTAAAAAGGAGAAAGAACTGCAGGCAAAGGAAGCTGAGCTAAACAAACGGGAAAGG
         gtttgat  putative branch site (score: 112)
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gacgttggattgaaaataaattccagagattttttcattggtgtgtttatggttgtttgatcatgtggtgagtggtgactatgcttgtatgtgaatgtagGACCTAAGTAAAAAGGAGAAAGAACTGCAGGCAAAGGAAGCTGAGCTAAACAAACGGGAAAGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA
- - - - - - -aaataaa
- - - - - - - - - - - - - - - - tttcatt
- - - - - - - - - - - - - - - - - - - - -tgtgttt
- - - - - - - - - - - - - - - - - - - - - - - - - - ttgtttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgtggtg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tggtgac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgcttgt