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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gtatataggacaactattgagctacattggtagatgttggatctaatattccaaaagcattctgttgtagcctttgaaacatttccatttcaaattgcagGCTGGATTTTTCCTTGTTCAGTATGCTCACTTGTGGCAAGATCATCTTAACAAACTTTTTGACCTGTATGCCTCTGGAAAGCTAAAG

Basic information

species Zea mays
transcript GRMZM2G147191_T02
intron # 15
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G147191_T02 (Zea mays), 3'ss of exon 15
lower sequence: LOC_Os09g28570.2 (Oryza sativa), 3'ss of exon 15
--gtatataggacaactat-tgagctac--attggtagatgttggatctaatattccaaaagcattctgttgtagcctttgaaacatttccatttcaaattgcagGCTGGATTTTTCCTTGTTCAGTATGCTCACTTGTGGCAAGATCATCTTAACAAACTTTTTGACCTGTATGCCTCTGGAAAGCTAAAG-------------
    |   |    || | | ||||| |   ||||  |  |  |  ||   ||  | |   |   | ||        |   ||    ||||| | |||| || |||||||| ||||||||  | |||||||||||||||||||||||||||||| ||||||||||||||||||||||||||||||||||||||             
tgtcaagcaaatgaattgtatgagccagtgattgtgatgtacta-atacgattcttctggaatgtcctaacactaac---gagttctttccttgtcaactt-cagGCTGGTTTTTTCCTAATCCAGTATGCTCACTTGTGGCAAGATCATCTTGACAAACTTTTTGACCTGTATGCCTCTGGAAAGCTAAAGGTATGCCTCGAGC

upper sequence: GRMZM2G147191_T02 (Zea mays), 3'ss of exon 15
lower sequence: LOC_Os09g28570.1 (Oryza sativa), 3'ss of exon 15
--gtatataggacaactat-tgagctac--attggtagatgttggatctaatattccaaaagcattctgttgtagcctttgaaacatttccatttcaaattgcagGCTGGATTTTTCCTTGTTCAGTATGCTCACTTGTGGCAAGATCATCTTAACAAACTTTTTGACCTGTATGCCTCTGGAAAGCTAAAG
    |   |    || | | ||||| |   ||||  |  |  |  ||   ||  | |   |   | ||        |   ||    ||||| | |||| || |||||||| ||||||||  | |||||||||||||||||||||||||||||| ||||||||||||||||||||||||||||||||||||||
tgtcaagcaaatgaattgtatgagccagtgattgtgatgtacta-atacgattcttctggaatgtcctaacactaac---gagttctttccttgtcaactt-cagGCTGGTTTTTTCCTAATCCAGTATGCTCACTTGTGGCAAGATCATCTTGACAAACTTTTTGACCTGTATGCCTCTGGAAAGCTAAAG

upper sequence: GRMZM2G147191_T02 (Zea mays), 3'ss of exon 15
lower sequence: GLYMA02G15070.1 (Glycine max), 3'ss of exon 15
--------gtatataggacaactattgagctacattggtagatgttggatctaatattccaaaagcattctgttgtagcctttgaaacatttccatttcaaattgcagGCTGGATTTTTCCTTGTTCAGTATGCTCACTTGTGGCAAGATCATCTTAACAAACTTTTTGACCTGTATGCCTCTGGAAAGCTAAAG
         | |  |   |||  ||||   |     |  | |  ||   | | || || | |    |||   || |   | ||   | | |||||    ||||| ||| |||| |||||||| || || |||| ||||||||||||||| |||||| ||| ||| ||| | || ||  | || ||||||||||||
agtgaactcttttcattccaagcattgcaatctcccgtgaaaatttccgttttatttttctatg--atttacttatgttcgttc--ataattcca----aaatttcagTCTGGCTTTTTCCTGGTGCAATATGGTCACTTGTGGCAAGAACATCTTGACAGACTATTTAATCTTTACTCTTCGGGAAAGCTAAAG

upper sequence: GRMZM2G147191_T02 (Zea mays), 3'ss of exon 15
lower sequence: GLYMA07G33380.1 (Glycine max), 3'ss of exon 5
gtatataggacaactattgagctacattggtagatgttgg-atctaatattccaaaagcattctgttgtagcctttgaaacatttccatttc--aaattgcagGCTGGATTTTTCCTTGTTCAGTATGCTCACTTGTGGCAAGATCATCTTAACAAACTTTTTGACCTGTATGCCTCTGGAAAGCTAAAG
   ||   || | || || |     |    |  ||  |    |  ||  || ||      || | |  |   |||     | |   || |||  ||||| ||| |||| |||||||| || || |||| ||||||||||||||| |||||| ||   || ||| | || ||  |  | ||||||||||||
---taagtgaaatcttttcattccaagaattgcattctcccgtgcaaagtttcattttatttttctgatttacttatgttcgtacacaattccaaaatttcagTCTGGCTTTTTCCTGGTGCAATATGGTCACTTGTGGCAAGAACATCTTGACGGGCTATTTAATCTTTACTCTACGGGAAAGCTAAAG

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|76282583|gb|DV022151.1|DV022151
EST:     AGAACTACACTGGACTATGTGAGAAGATTCTAGCTAAAAGTCAAACTGTG                         GCTGGATTTTTCCTTGTTCAGTATGCTCACTTGTGGCAAGATCATCTTAAC
genomic: AGAACTACACTGGACTATGTGAGAAGATTCTAGCTAAAAGTCAAACTGTGgtatgtctca ... caaattgcagGCTGGATTTTTCCTTGTTCAGTATGCTCACTTGTGGCAAGATCATCTTAAC
EST: gi|211530862|gb|FL078323.1|FL078323
EST:     AGAACTACACTGGACTATGTGAGAAGATTCTAGCTAAAAGTCAAACTGTG                         GCTGGATTTTTCCTTGTTCAGTATGCTCACTTGTGGCAAGATCATCTTAAC
genomic: AGAACTACACTGGACTATGTGAGAAGATTCTAGCTAAAAGTCAAACTGTGgtatgtctca ... caaattgcagGCTGGATTTTTCCTTGTTCAGTATGCTCACTTGTGGCAAGATCATCTTAAC
EST: gi|76282582|gb|DV022150.1|DV022150
EST:     AGAACTACACTGGACTATGTGAGAAGATTCTAGCTAAAAGTCAAACTGTG                         GCTGGATTTTTCCTTGTTCAGTATGCTCACTTGTGGCAAGATCATCTTAAC
genomic: AGAACTACACTGGACTATGTGAGAAGATTCTAGCTAAAAGTCAAACTGTGgtatgtctca ... caaattgcagGCTGGATTTTTCCTTGTTCAGTATGCTCACTTGTGGCAAGATCATCTTAAC
EST: gi|211538275|gb|FL465653.1|FL465653
EST:     AGAACTACACTGGACTATGTGAGAAGATTCTAGCTAAAAGTCAAACTGTG                         GCTGGATTTTTCCTTGTTCAGTATGCTCACTTGTGGCAAGATCATCTTAAC
genomic: AGAACTACACTGGACTATGTGAGAAGATTCTAGCTAAAAGTCAAACTGTGgtatgtctca ... caaattgcagGCTGGATTTTTCCTTGTTCAGTATGCTCACTTGTGGCAAGATCATCTTAAC
EST: gi|211530863|gb|FL078324.1|FL078324
EST:     AGAACTACACTGGACTATGTGAGAAGATTCTAGCTAAAAGTCAAACTGTG                         GCTGGATTTTTCCTTGTTCAGTATGCTCACTTGTGGCAAGATCATCTTAAC
genomic: AGAACTACACTGGACTATGTGAGAAGATTCTAGCTAAAAGTCAAACTGTGgtatgtctca ... caaattgcagGCTGGATTTTTCCTTGTTCAGTATGCTCACTTGTGGCAAGATCATCTTAAC
EST: gi|58029381|gb|CX724808.1|CX724808
EST:     AGAACTACACTGGACTATGTGAGAAGATTCTAGCTGAAAGTCAAACTGTG                         GCTGGATTTTTCCTTGTTCAGTATGCTCACTTGTGGCAAGATCATCTTAAC
genomic: AGAACTACACTGGACTATGTGAGAAGATTCTAGCTAAAAGTCAAACTGTGgtatgtctca ... caaattgcagGCTGGATTTTTCCTTGTTCAGTATGCTCACTTGTGGCAAGATCATCTTAAC
EST: gi|6672154|gb|AW282329.1|AW282329
EST:     TCTAGCTAAAAGTC-AACTGTG                         GCTGGATTTTTCCTTGTTCAGTATGCTCACTTGTGGCAAGATCATCTTANC
genomic: TCTAGCTAAAAGTCAAACTGTGgtatgtctca ... caaattgcagGCTGGATTTTTCCTTGTTCAGTATGCTCACTTGTGGCAAGATCATCTTAAC
EST: gi|67018859|gb|CO447608.1|CO447608
EST:     AGAACTACACTGGACTATGTGAGAAGATTCTAGCTAAAAGTCAAACTGTG                         GCTGGGATTTT-CCTTGTTCAATATGCTCACTTGTGGCAAGATCATCTTAA
genomic: AGAACTACACTGGACTATGTGAGAAGATTCTAGCTAAAAGTCAAACTGTGgtatgtctca ... caaattgcagGCTGG-ATTTTTCCTTGTTCAGTATGCTCACTTGTGGCAAGATCATCTTAA
EST: gi|13557631|gb|BG548987.1|BG548987
EST:     AGAACTACACTGGACTATGTGAGAAGATTCTAGCTAAAAGTCAAACTGTG                         GCTGGATTTTTCCTTGTTCAGTATGCTCACTTGTGGCAAGATCATCTTAAC
genomic: AGAACTACACTGGACTATGTGAGAAGATTCTAGCTAAAAGTCAAACTGTGgtatgtctca ... caaattgcagGCTGGATTTTTCCTTGTTCAGTATGCTCACTTGTGGCAAGATCATCTTAAC
EST: gi|91868064|gb|EB399901.1|EB399901
EST:     AGAACTACACTGGACTATGTGAGAAGATTTTAGCTAAAAGTCAAACTGTG                         GCTGGATTTTTCCTTGTTCAGTATGCTCACTTGTGGCAAGATCATCTTAAC
genomic: AGAACTACACTGGACTATGTGAGAAGATTCTAGCTAAAAGTCAAACTGTGgtatgtctca ... caaattgcagGCTGGATTTTTCCTTGTTCAGTATGCTCACTTGTGGCAAGATCATCTTAAC
EST: gi|60357940|gb|DN224913.1|DN224913
EST:     AGAACTACACTGGACTATGTGAGAAGATTCTAGCTAAAAGTCAAACTGTG                         GCTGGATTTTTCCTTGTTCAGTATGCTCACTTGTGGCAAGATCATCTTAAC
genomic: AGAACTACACTGGACTATGTGAGAAGATTCTAGCTAAAAGTCAAACTGTGgtatgtctca ... caaattgcagGCTGGATTTTTCCTTGTTCAGTATGCTCACTTGTGGCAAGATCATCTTAAC
EST: gi|16380053|gb|BI993288.1|BI993288
EST:     AGAACTACACTGGACTATGTGAGAAGATTCTAGCTAAAAGTCAAACTGTG                         GCTGGATTTTTCCTTGTTCAGTATGCTCACTTGTGGCAAGATCATCTTAAC
genomic: AGAACTACACTGGACTATGTGAGAAGATTCTAGCTAAAAGTCAAACTGTGgtatgtctca ... caaattgcagGCTGGATTTTTCCTTGTTCAGTATGCTCACTTGTGGCAAGATCATCTTAAC

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), 47 (downstream exon)
Score: 98

TATCAAGGAGAGGATGGCTGGAAGCCAAAGAACTACACTGGACTATGTGAGAAGATTCTAGCTAAAAGTCAAACTGTGgtatgtctca ... caaattgcagGCTGGATTTTTCCTTGTTCAGTATGCTCACTTGTGGCAAGATCATCTTAACAAACTTTTTGACCTGTATGCCTCTGGAAAGCTAAAG


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 161

TATCAAGGAGAGGATGGCTGGAAGCCAAAGAACTACACTGGACTATGTGAGAAGATTCTAGCTAAAAGTCAAACTGTGgtatgtctca ... caaattgcagGCTGGATTTTTCCTTGTTCAGTATGCTCACTTGTGGCAAGATCATCTTAACAAACTTTTTGACCTGTATGCCTCTGGAAAGCTAAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 152

TATCAAGGAGAGGATGGCTGGAAGCCAAAGAACTACACTGGACTATGTGAGAAGATTCTAGCTAAAAGTCAAACTGTGgtatgtctca ... caaattgcagGCTGGATTTTTCCTTGTTCAGTATGCTCACTTGTGGCAAGATCATCTTAACAAACTTTTTGACCTGTATGCCTCTGGAAAGCTAAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 380

TATCAAGGAGAGGATGGCTGGAAGCCAAAGAACTACACTGGACTATGTGAGAAGATTCTAGCTAAAAGTCAAACTGTGgtatgtctca ... caaattgcagGCTGGATTTTTCCTTGTTCAGTATGCTCACTTGTGGCAAGATCATCTTAACAAACTTTTTGACCTGTATGCCTCTGGAAAGCTAAAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atattccaaaagcattctgttgtagcctttgaaacatttccatttcaaattgcagGCTGGATTTTTCCTTGTTCAGTATGCTCACTTGTGGCAAGATCATCTTAACAAACTTTTTGACCTGTATGCCTCTGGAAAGCTAAAG
 atctaat  putative branch site (score: 380)
                                    tttccatttc  putative PPT
                                         atttcaaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatataggacaactattgagctacattggtagatgttggatctaatattccaaaagcattctgttgtagcctttgaaacatttccatttcaaattgcagGCTGGATTTTTCCTTGTTCAGTATGCTCACTTGTGGCAAGATCATCTTAACAAACTTTTTGACCTGTATGCCTCTGGAAAGCTAAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGATCA
- - - - - - - - - -agctaca
- - - - - - - - - - - - - - - - gatgttg
- - - - - - - - - - - - - - - - - - - - - - - - - -caaaagca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctgttgt