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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatctccacgtttccattccaccagttaactgatatgtggtattgacaccttgtggatgtcatttcaaaatccctctattttgtttattacttatgattttttgggaagtgggaatgacccacttaaataaatattaaagtttgagaagatctatctgctaattactgttgccttgatcagGAAGCAAATAAGAGGAACAACAACTGGCTCCCACCTCCATGGGCACTTGCTGCAATGGCTATCCTTGGATTCAACGAGTTTATGACATTACTGAG

Basic information

species Zea mays
transcript AC196426.3_FGT007
intron # 19
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 19
lower sequence: LOC_Os01g39310.3 (Oryza sativa), 3'ss of exon 20
gtatctccacgtttccattccaccagttaactgatatgtggtattgacaccttgtggatgtcatttcaaaatccctctattttgtttattacttatgattttttgggaagtgggaatgacccacttaaataaatattaaagtttga--gaagatctatctgctaattactgttgccttgatcagGAAGCAAATAAGAGGAACAACAACTGGCTCCCACCTCCATGGGCACTTGCTGCAATGGCTATCCTTGGATTCAACGAGTTTATGACATTACTGAG-----
                                                | | |||  ||         |||||  |   ||| ||||  |||||   |  || |||  ||||||| ||||| | ||   || | | | | || |||  | |   ||| ||| |  ||||| || |||| ||||||| |||||||||||||||||||||||||| |||||||||||||||||||| ||||||||||||||||||||||||||||| ||||||||  | |      
----------------------------------------------gtatcctgttaat-------tgaaatctttaattttcgtttggtacttgaaacattgtgg--agtgggattgaccta-ttgggtataaaatgatgtatgattgtatgcctaactgtt--ttactttttccttcatcagGAGGCAAATAAGAGGAACAACAACTGGCTGCCACCTCCATGGGCACTTGCCGCAATGGCTATCCTTGGATTCAACGAGTTCATGACATTGTTAAAGTATT

upper sequence: AC196426.3_FGT007 (Zea mays), 3'ss of exon 19
lower sequence: LOC_Os01g39310.1 (Oryza sativa), 3'ss of exon 20
gtatctccacgtttccattccaccagttaactgatatgtggtattgacaccttgtggatgtcatttcaaaatccctctattttgtttattacttatgattttttgggaagtgggaatgacccacttaaataaatattaaagtttga--gaagatctatctgctaattactgttgccttgatcagGAAGCAAATAAGAGGAACAACAACTGGCTCCCACCTCCATGGGCACTTGCTGCAATGGCTATCCTTGGATTCAACGAGTTTATGACATTACTGAG
                                                | | |||  ||         |||||  |   ||| ||||  |||||   |  || |||  ||||||| ||||| | ||   || | | | | || |||  | |   ||| ||| |  ||||| || |||| ||||||| |||||||||||||||||||||||||| |||||||||||||||||||| ||||||||||||||||||||||||||||| ||||||||  | | 
----------------------------------------------gtatcctgttaat-------tgaaatctttaattttcgtttggtacttgaaacattgtgg--agtgggattgaccta-ttgggtataaaatgatgtatgattgtatgcctaactgtt--ttactttttccttcatcagGAGGCAAATAAGAGGAACAACAACTGGCTGCCACCTCCATGGGCACTTGCCGCAATGGCTATCCTTGGATTCAACGAGTTCATGACATTGTTAAA

upper sequence: AC196426.3_FGT007 (Zea mays), 3'ss of exon 19
lower sequence: Vv09s0002g02200.t01 (Vitis vinifera), 3'ss of exon 20
gtatctccacgtttccattccaccagttaactgatatgtggtattgacaccttgtggatgtcatttcaaaatccctctattttgtttattacttatgattttttgggaagtgggaatgacccacttaaataaatat------taaagtttgagaagatctatctgct---aattactgttgccttgatcagGAAGCAAATAAGAGGAACAACAACTGGCTCCCACCTCCATGGGCACTTGCTGCAATGGCTATCCTTGGATTCAACGAGTTTATGACATTACTGAG
                                                                                       | || ||     | |||| |||   | |   |   | || | |||  ||      | |   |  |    |||||  || |   | || || || |  | |||||||||| || ||| | || ||||||||| | ||||||||||||||| ||| ||| ||||   |||| |||||||| || ||||||||| | || ||
--------------------------------------------------------------------------------------caatattt-----tctttgagaaacagtatcaaaatatttcactaaccatgccccattaccgtcaatggtatctaattgttttcacttcctctttcaattatcagGAAGCCAACAAGCGTAATAACAACTGGTTACCACCTCCATGGGCAATTGTTGCTATGGTCGTCCTGGGATTCAATGAATTTATGACACTTCTAAG

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|18384778|gb|BM417977.1|BM417977
EST:     AATTCAAAGCTGAAACTGAATATACAGTCACTCAAGCCATAGCTGCTCAG                         GAAGCAAATAAGAGGAACAACAACTGGCTCCCACCTCCATGGGCACTTGCT
genomic: AATTCAAAGCTGAAACTGAATATACAGTCACTCAAGCCATAGCTGCTCAGgtatctccac ... ccttgatcagGAAGCAAATAAGAGGAACAACAACTGGCTCCCACCTCCATGGGCACTTGCT
EST: gi|88758420|gb|DY542789.1|DY542789
EST:     AATTCAAAGCTGAAACTGAATATACAGTCACTCAAGCCATAGCTGCTCAG                         GAAGCAAATAAGAGGAACAACAACTGGCTCCCACCTCCATGGGCACTTGCT
genomic: AATTCAAAGCTGAAACTGAATATACAGTCACTCAAGCCATAGCTGCTCAGgtatctccac ... ccttgatcagGAAGCAAATAAGAGGAACAACAACTGGCTCCCACCTCCATGGGCACTTGCT
EST: gi|17352581|gb|BM173695.1|BM173695
EST:     AATTCAAAGCTGAAACTGAATATACAGTCACTCAAGCCATAGCTGCTCAG                         GAAGCAAATAAGAGGAACAACAACTGGCTCCCACCTCCATGGGCACTTGCT
genomic: AATTCAAAGCTGAAACTGAATATACAGTCACTCAAGCCATAGCTGCTCAGgtatctccac ... ccttgatcagGAAGCAAATAAGAGGAACAACAACTGGCTCCCACCTCCATGGGCACTTGCT
EST: gi|18384779|gb|BM417978.1|BM417978
EST:     AATTCAAAGCTGAAACTGAATATACAGTCACTCAAGCCATAGCTGCTCAG                         GAAGCAAATAAGAGGAACAACAACTGGCTCCCACCTCCATGGGCACTTGCT
genomic: AATTCAAAGCTGAAACTGAATATACAGTCACTCAAGCCATAGCTGCTCAGgtatctccac ... ccttgatcagGAAGCAAATAAGAGGAACAACAACTGGCTCCCACCTCCATGGGCACTTGCT
EST: gi|18383908|gb|BM417108.1|BM417108
EST:     AATTCAAAGCTGAATCTGAATATACAGTCACTCAAGCCATAGCTGCTCAG                         GAAGCAAATAAGAGGAACAACAACTGGCTCCCACCTCCATGGGCACTTGCT
genomic: AATTCAAAGCTGAAACTGAATATACAGTCACTCAAGCCATAGCTGCTCAGgtatctccac ... ccttgatcagGAAGCAAATAAGAGGAACAACAACTGGCTCCCACCTCCATGGGCACTTGCT
EST: gi|22489182|gb|BU049105.1|BU049105
EST:     AATTCAAAGCTGAAACTGAATATACAGTCACTCAAGCCATAGCTGCTCAG                         GAAGCAAATAAGAGGAACAACAACTGGCTCCCACCTCCATGGGCACTTGCT
genomic: AATTCAAAGCTGAAACTGAATATACAGTCACTCAAGCCATAGCTGCTCAGgtatctccac ... ccttgatcagGAAGCAAATAAGAGGAACAACAACTGGCTCCCACCTCCATGGGCACTTGCT

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: 46 (upstream exon), 49 (downstream exon)
Score: 137

TGAGGAGAAGACTTTAATTACCCCTGTGCAGTGCAAAAATTTGTGGAGGCAATTCAAAGCTGAAACTGAATATACAGTCACTCAAGCCATAGCTGCTCAGgtatctccac ... ccttgatcagGAAGCAAATAAGAGGAACAACAACTGGCTCCCACCTCCATGGGCACTTGCTGCAATGGCTATCCTTGGATTCAACGAGTTTATGACATTACTGAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 170

TGAGGAGAAGACTTTAATTACCCCTGTGCAGTGCAAAAATTTGTGGAGGCAATTCAAAGCTGAAACTGAATATACAGTCACTCAAGCCATAGCTGCTCAGgtatctccac ... ccttgatcagGAAGCAAATAAGAGGAACAACAACTGGCTCCCACCTCCATGGGCACTTGCTGCAATGGCTATCCTTGGATTCAACGAGTTTATGACATTACTGAG


Block sizes: 45 (upstream exon), 49 (downstream exon)
Score: 104

TGAGGAGAAGACTTTAATTACCCCTGTGCAGTGCAAAAATTTGTGGAGGCAATTCAAAGCTGAAACTGAATATACAGTCACTCAAGCCATAGCTGCTCAGgtatctccac ... ccttgatcagGAAGCAAATAAGAGGAACAACAACTGGCTCCCACCTCCATGGGCACTTGCTGCAATGGCTATCCTTGGATTCAACGAGTTTATGACATTACTGAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 176

TGAGGAGAAGACTTTAATTACCCCTGTGCAGTGCAAAAATTTGTGGAGGCAATTCAAAGCTGAAACTGAATATACAGTCACTCAAGCCATAGCTGCTCAGgtatctccac ... ccttgatcagGAAGCAAATAAGAGGAACAACAACTGGCTCCCACCTCCATGGGCACTTGCTGCAATGGCTATCCTTGGATTCAACGAGTTTATGACATTACTGAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aataaatattaaagtttgagaagatctatctgctaattactgttgccttgatcagGAAGCAAATAAGAGGAACAACAACTGGCTCCCACCTCCATGGGCACTTGCTGCAATGGCTATCCTTGGATTCAACGAGTTTATGACATTACTGAG
                              tgctaat  putative branch site (score: 176)
                                          ttgcctt  putative PPT
     atattaaagtttga  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatctccacgtttccattccaccagttaactgatatgtggtattgacaccttgtggatgtcatttcaaaatccctctattttgtttattacttatgattttttgggaagtgggaatgacccacttaaataaatattaaagtttgagaagatctatctgctaattactgttgccttgatcagGAAGCAAATAAGAGGAACAACAACTGGCTCCCACCTCCATGGGCACTTGCTGCAATGGCTATCCTTGGATTCAACGAGTTTATGACATTACTGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC