Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgagcatataacttgaactctacgctagactagatatgtatttaagaattgaaattttgaactgttcccttgtgcgttgatgagatatttgttcttacagAGGATGGAAGAAATGGCACATTTATGATCGGTAATGAGAGCTTTCCTGCATCTCTCTTGGATCTACCTGCTGTGGTGGAGTCATACAAAACATATGATGA

Basic information

species Zea mays
transcript GRMZM2G147614_T05
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G147614_T05 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os05g28010.1 (Oryza sativa), 3'ss of exon 1
tgagcatataacttgaactctacgctagactagatatgtatttaagaattgaaattttgaactgttccct--------tgtgcgttgatgagatatttgttcttacagAGGATGGAAGAAATGGCACATTTATGATCGGTAATGAGAGCTTTCCTGCATCTCTCTTGGATCTACCTGCTGTGGTGGAGTCATACAAAACATATGATGA
       | ||||| || | ||   ||  || |   |||  | | ||  |||| |||| | ||  |   |        ||||  ||||||  || |||  |  || |||||||||||||||||||||||||||||| || ||||| |||||||||||||| ||||||||||| ||  |||| |||||||||||||| |||||||||||
------cacaacttaaattataa--taccctggtattgttatcaggatgtgaattttttatctaatatttgttgaacctgtggattgatggtatttttcatgctatagAGGATGGAAGAAATGGCACATTTATGATTGGGAATGAAAGCTTTCCTGCATCACTCTTGGATCTCCCAACTGTTGTGGAGTCATACAAGACATATGATGA

upper sequence: GRMZM2G147614_T05 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os05g28010.2 (Oryza sativa), 3'ss of exon 1
tgagcatataacttgaactctacgctagactagatatgtatttaagaattgaaattttgaactgttccct--------tgtgcgttgatgagatatttgttcttacagAGGATGGAAGAAATGGCACATTTATGATCGGTAATGAGAGCTTTCCTGCATCTCTCTTGGATCTACCTGCTGTGGTGGAGTCATACAAAACATATGATGA--
         ||||| || | ||   ||  || |   |||  | | ||  |||| |||| | ||  |   |        ||||  ||||||  || |||  |  || |||||||||||||||||||||||||||||| || ||||| |||||||||||||| ||||||||||| ||  |||| |||||||||||||| |||||||||||  
--------caacttaaattataa--taccctggtattgttatcaggatgtgaattttttatctaatatttgttgaacctgtggattgatggtatttttcatgctatagagGATGGAAGAAATGGCACATTTATGATTGGGAATGAAAGCTTTCCTGCATCACTCTTGGATCTCCCAACTGTTGTGGAGTCATACAAGACATATGATGATT

upper sequence: GRMZM2G147614_T05 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os01g46020.2 (Oryza sativa), 3'ss of exon 1
tgagcatataacttgaactcta-cgctagactagatatgtatttaagaattgaaattttgaactgttcccttgtgcgttgatgagatatttgt-tcttacagAGGATGGAAGAAATGGCACATTTATGATCGGTAATGAGAGCTTTCCTGCATCTCTCTTGGATCTACCTGCTGTGGTGGAGTCATACAAAACATATGATGA
   | ||| |||||| | | ||   ||  | ||    | |   | | | ||  | ||      | ||  ||||||  ||| ||   | |||   |  ||||||||||||||||| ||||||||||||||| || ||||| |||||||| ||||||||||| ||||| ||  ||||  ||||||||||||| |||||  ||||
--tggatacaacttgtattgtaatactctagtactgttatcactgaaattttcagttaatcttttttgacttgtggattggtgttcttttttcgtgctacagAGGATGGAAGAAGTGGCACATTTATGATTGGAAATGAAAGCTTTCCAGCATCTCTCTTAGATCTCCCAACTGTTATGGAGTCATACAAGACATACAATGA

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|26457225|gb|CA828808.1|CA828808
EST:     CTCCTCCTCCTCCAACCCCGACGAGGCCTCCCTGGACCTCTCCTTCTCAG                         AGGATGGAAGAAATGGCACATTTATGATCGGTAATGAGAGCTTTCCTGCAT
genomic: CGCCTCCTCCTCCAACCCCGACGAGGCCTCCCTGGACCTCTCCTTCTCAGgttagtttac ... gttcttacagAGGATGGAAGAAATGGCACATTTATGATCGGTAATGAGAGCTTTCCTGCAT
EST: gi|211322003|gb|FL424973.1|FL424973
EST:     CGCCTCCTCCTCCAACCCCGACGAGGCCTCCCTGGACCTCTCCTTCTCAG                         AGGATGGAAGAAATGGCACATTTATGATCGGTAATGAGAGCTTTCCTGCAT
genomic: CGCCTCCTCCTCCAACCCCGACGAGGCCTCCCTGGACCTCTCCTTCTCAGgttagtttac ... gttcttacagAGGATGGAAGAAATGGCACATTTATGATCGGTAATGAGAGCTTTCCTGCAT
EST: gi|9254486|gb|BE344954.1|BE344954
EST:     CTNCTCCTCCTCCAACCCCGACGAGGCCTCCCTGGACCTCTCCTTCTCAG                         AGGATGGAAGAAATGGCACATTTATGATCGGTAATGAGAGCTTTCCTGCAT
genomic: CGCCTCCTCCTCCAACCCCGACGAGGCCTCCCTGGACCTCTCCTTCTCAGgttagtttac ... gttcttacagAGGATGGAAGAAATGGCACATTTATGATCGGTAATGAGAGCTTTCCTGCAT
EST: gi|116819180|gb|EC862277.1|EC862277
EST:     CGCCTCCTCCTCCAACCCCGACGAGGCCTCCCTGGACCTCTCCTTCTCAG                         AGGATGGAAGACATGGCACATTTATGATCGGTAATGAGAGCTTTCCTGCTT
genomic: CGCCTCCTCCTCCAACCCCGACGAGGCCTCCCTGGACCTCTCCTTCTCAGgttagtttac ... gttcttacagAGGATGGAAGAAATGGCACATTTATGATCGGTAATGAGAGCTTTCCTGCAT
EST: gi|211005527|gb|FL375718.1|FL375718
EST:     CGCCTCCTCCTCCAACCCCGACGAGGCCTCCCTGGACCTCTCCTTCTCAG                         AGGATGGAAGAAATGGCACATTTATGATCGGTAATGAGAGCTTTCCTGCAT
genomic: CGCCTCCTCCTCCAACCCCGACGAGGCCTCCCTGGACCTCTCCTTCTCAGgttagtttac ... gttcttacagAGGATGGAAGAAATGGCACATTTATGATCGGTAATGAGAGCTTTCCTGCAT
EST: gi|211416221|gb|FL415023.1|FL415023
EST:     CGCCTCCTCCTCCAACCCCGACGAGGCCTCCCTGGACCTCTCCTTCTCAG                         AGGATGGAAGAAATGGCACATTTATGATCGGTAATGAGAGCTTTCCTGCAT
genomic: CGCCTCCTCCTCCAACCCCGACGAGGCCTCCCTGGACCTCTCCTTCTCAGgttagtttac ... gttcttacagAGGATGGAAGAAATGGCACATTTATGATCGGTAATGAGAGCTTTCCTGCAT
EST: gi|89764296|gb|DY691155.1|DY691155
EST:     CGCCTCCTCCTCCAACCCCGACGAGGCCTCCCTGGACCTCTCCTTCTCAG                         AGGATGGAAGAAATGGCACATTTATGATCGGTAATGAGAGCTTTCCTGCAT
genomic: CGCCTCCTCCTCCAACCCCGACGAGGCCTCCCTGGACCTCTCCTTCTCAGgttagtttac ... gttcttacagAGGATGGAAGAAATGGCACATTTATGATCGGTAATGAGAGCTTTCCTGCAT
EST: gi|211526828|gb|FL377016.1|FL377016
EST:     CGCCTCCTCCTCCAACCCCGACGAGGCCTCCCTGGACCTCTCCTTCTCAG                         AGGATGGAAGAAATGGCACATTTATGATCGGTAATGAGAGCTTTCCTGCAT
genomic: CGCCTCCTCCTCCAACCCCGACGAGGCCTCCCTGGACCTCTCCTTCTCAGgttagtttac ... gttcttacagAGGATGGAAGAAATGGCACATTTATGATCGGTAATGAGAGCTTTCCTGCAT
EST: gi|211161653|gb|FL415254.1|FL415254
EST:     CGCCTCCTCCTCCAACCCCGACGAGGCCTCCCTGGACCTCTCCTTCTCAG                         AGGATGGAAGAAATGGCACATTTATGATCGGTAATGAGAGCTTTCCTGCAT
genomic: CGCCTCCTCCTCCAACCCCGACGAGGCCTCCCTGGACCTCTCCTTCTCAGgttagtttac ... gttcttacagAGGATGGAAGAAATGGCACATTTATGATCGGTAATGAGAGCTTTCCTGCAT

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: 106

GTGCCGCCATCCGTCGCAGAGCGGATCGAGCGCCTCATGAATGAATCCGCCGCCTCCTCCTCCAACCCCGACGAGGCCTCCCTGGACCTCTCCTTCTCAGgttagtttac ... gttcttacagAGGATGGAAGAAATGGCACATTTATGATCGGTAATGAGAGCTTTCCTGCATCTCTCTTGGATCTACCTGCTGTGGTGGAGTCATACAAAACATATGATGA


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 52

GTGCCGCCATCCGTCGCAGAGCGGATCGAGCGCCTCATGAATGAATCCGCCGCCTCCTCCTCCAACCCCGACGAGGCCTCCCTGGACCTCTCCTTCTCAGgttagtttac ... gttcttacagAGGATGGAAGAAATGGCACATTTATGATCGGTAATGAGAGCTTTCCTGCATCTCTCTTGGATCTACCTGCTGTGGTGGAGTCATACAAAACATATGATGA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 51

GTGCCGCCATCCGTCGCAGAGCGGATCGAGCGCCTCATGAATGAATCCGCCGCCTCCTCCTCCAACCCCGACGAGGCCTCCCTGGACCTCTCCTTCTCAGgttagtttac ... gttcttacagAGGATGGAAGAAATGGCACATTTATGATCGGTAATGAGAGCTTTCCTGCATCTCTCTTGGATCTACCTGCTGTGGTGGAGTCATACAAAACATATGATGA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 95

GTGCCGCCATCCGTCGCAGAGCGGATCGAGCGCCTCATGAATGAATCCGCCGCCTCCTCCTCCAACCCCGACGAGGCCTCCCTGGACCTCTCCTTCTCAGgttagtttac ... gttcttacagAGGATGGAAGAAATGGCACATTTATGATCGGTAATGAGAGCTTTCCTGCATCTCTCTTGGATCTACCTGCTGTGGTGGAGTCATACAAAACATATGATGA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gaattgaaattttgaactgttcccttgtgcgttgatgagatatttgttcttacagAGGATGGAAGAAATGGCACATTTATGATCGGTAATGAGAGCTTTCCTGCATCTCTCTTGGATCTACCTGCTGTGGTGGAGTCATACAAAACATATGATGA
                             cgttgat  putative branch site (score: 95)
                                          tttgttctt  putative PPT
      aaattttgaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgagcatataacttgaactctacgctagactagatatgtatttaagaattgaaattttgaactgttcccttgtgcgttgatgagatatttgttcttacagAGGATGGAAGAAATGGCACATTTATGATCGGTAATGAGAGCTTTCCTGCATCTCTCTTGGATCTACCTGCTGTGGTGGAGTCATACAAAACATATGATGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG