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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagtcgatgagtttatctccttccggccttacctattctcgatcttctctgctcccttagttcttgttcctttattttccttgttccccactgtctcttcctgattagtgttatttcgcttgagtcagAGATCCCTAAGTTTCGATCCACTGTCCCAGTGGATTTGGGACTGCGATGGAGGAGCAGTTCATCCTCCGCGTGCCGCCATCCGTCGCAGAGCGGATCGAG

Basic information

species Zea mays
transcript GRMZM2G147614_T05
intron # 1
splice site 3'
intron type U2

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:     GGGGGAGAAAATCAGCGGCACAGCGTGGGTCTCGCGACCTCCAGCGAACG                         AGATCCCTAAGTTTCGATCCACTGTCCCAGTGGATTTGGGACTGCGATGGA
genomic: AGTGGAGAAAATCAGCGGCACAGCGTGGGTCTCGCGACCTCCAGCGAACGgtgagtcgat ... cttgagtcagAGATCCCTAAGTTTCGATCCACTGTCCCAGTGGATTTGGGACTGCGATGGA
EST: gi|211322003|gb|FL424973.1|FL424973
EST:     AGTGGAGAAAATCAGCGGCACAGCGTGGGTCTCGCGACCTCCAGCGAACG                         AGATCCCTAAGTTTCGATCCACTGTCCCAGTGGATTTGGGACTGCGATGGA
genomic: AGTGGAGAAAATCAGCGGCACAGCGTGGGTCTCGCGACCTCCAGCGAACGgtgagtcgat ... cttgagtcagAGATCCCTAAGTTTCGATCCACTGTCCCAGTGGATTTGGGACTGCGATGGA
EST: gi|9254486|gb|BE344954.1|BE344954
EST:     GGTGGAGAAAATCAGCGGCACAGCGTGGGTCTCGCGACCTCCAGCGAACG                         AGATCCCTAAGTTTCGATCCACTGTCCCAGTGGATTTGGGACTGCGATGGA
genomic: AGTGGAGAAAATCAGCGGCACAGCGTGGGTCTCGCGACCTCCAGCGAACGgtgagtcgat ... cttgagtcagAGATCCCTAAGTTTCGATCCACTGTCCCAGTGGATTTGGGACTGCGATGGA
EST: gi|116819180|gb|EC862277.1|EC862277
EST:     AGTGGAGAAAATCAGCGGCACAGCGTGGGTCTCGCGACCTCCAGCGAACG                         AGATCCCTAAGTTTCGATCCACTGTCCCAGTGGATTTGGGACTGCGATGGA
genomic: AGTGGAGAAAATCAGCGGCACAGCGTGGGTCTCGCGACCTCCAGCGAACGgtgagtcgat ... cttgagtcagAGATCCCTAAGTTTCGATCCACTGTCCCAGTGGATTTGGGACTGCGATGGA
EST: gi|211005527|gb|FL375718.1|FL375718
EST:     AGTGGAGAAAATCAGCGGCACAGCGTGGGTCTCGCGACCTCCAGCGAACG                         AGATCCCTAAGTTTCGATCCACTGTCCCAGTGGATTTGGGACTGCGATGGA
genomic: AGTGGAGAAAATCAGCGGCACAGCGTGGGTCTCGCGACCTCCAGCGAACGgtgagtcgat ... cttgagtcagAGATCCCTAAGTTTCGATCCACTGTCCCAGTGGATTTGGGACTGCGATGGA
EST: gi|211416221|gb|FL415023.1|FL415023
EST:     AGTGGAGAAAATCAGCGGCACAGCGTGGGTCTCGCGACCTCCAGCGAACG                         AGATCCCTAAGTTTCGATCCACTGTCCCAGT-GATTTGGGACTGCGATGGA
genomic: AGTGGAGAAAATCAGCGGCACAGCGTGGGTCTCGCGACCTCCAGCGAACGgtgagtcgat ... cttgagtcagAGATCCCTAAGTTTCGATCCACTGTCCCAGTGGATTTGGGACTGCGATGGA
EST: gi|89764296|gb|DY691155.1|DY691155
EST:     AGTGGAGAAAATCAGCGGCACAGCGTGGGTCTCGCGACCTCCAGCGAACG                         AGATCCCTAAGTTTCGATCCACTGTCCCAGTGGATTTGGGACTGCGATGGA
genomic: AGTGGAGAAAATCAGCGGCACAGCGTGGGTCTCGCGACCTCCAGCGAACGgtgagtcgat ... cttgagtcagAGATCCCTAAGTTTCGATCCACTGTCCCAGTGGATTTGGGACTGCGATGGA
EST: gi|211526828|gb|FL377016.1|FL377016
EST:     AGTGGAGAAAATCAGCGGCACAGCGTGGGTCTCGCGACCTCCAGCGAACG                         AGATCCCTAAGTTTCGATCCACTGTCCCAGTGGATTTGGGACTGCGATGGA
genomic: AGTGGAGAAAATCAGCGGCACAGCGTGGGTCTCGCGACCTCCAGCGAACGgtgagtcgat ... cttgagtcagAGATCCCTAAGTTTCGATCCACTGTCCCAGTGGATTTGGGACTGCGATGGA
EST: gi|211161653|gb|FL415254.1|FL415254
EST:     AGTGGAGAAAATCAGCGGCACAGCGTGGGTCTCGCGACCTCCAGCGAACG                         AGATCCCTAAGTTTCGATCCACTGTCCCAGTGGATTTGGGACTGCGATGGA
genomic: AGTGGAGAAAATCAGCGGCACAGCGTGGGTCTCGCGACCTCCAGCGAACGgtgagtcgat ... cttgagtcagAGATCCCTAAGTTTCGATCCACTGTCCCAGTGGATTTGGGACTGCGATGGA

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), 48 (downstream exon)
Score: 105

CTGCTGCTCCGCGCGAGAAGAGCCACCACGGAGTCTGCGTGACTCGGGACAGTGGAGAAAATCAGCGGCACAGCGTGGGTCTCGCGACCTCCAGCGAACGgtgagtcgat ... cttgagtcagAGATCCCTAAGTTTCGATCCACTGTCCCAGTGGATTTGGGACTGCGATGGAGGAGCAGTTCATCCTCCGCGTGCCGCCATCCGTCGCAGAGCGGATCGAG


Block sizes: 47 (upstream exon), 48 (downstream exon)
Score: 145

CTGCTGCTCCGCGCGAGAAGAGCCACCACGGAGTCTGCGTGACTCGGGACAGTGGAGAAAATCAGCGGCACAGCGTGGGTCTCGCGACCTCCAGCGAACGgtgagtcgat ... cttgagtcagAGATCCCTAAGTTTCGATCCACTGTCCCAGTGGATTTGGGACTGCGATGGAGGAGCAGTTCATCCTCCGCGTGCCGCCATCCGTCGCAGAGCGGATCGAG


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 162

CTGCTGCTCCGCGCGAGAAGAGCCACCACGGAGTCTGCGTGACTCGGGACAGTGGAGAAAATCAGCGGCACAGCGTGGGTCTCGCGACCTCCAGCGAACGgtgagtcgat ... cttgagtcagAGATCCCTAAGTTTCGATCCACTGTCCCAGTGGATTTGGGACTGCGATGGAGGAGCAGTTCATCCTCCGCGTGCCGCCATCCGTCGCAGAGCGGATCGAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 182

CTGCTGCTCCGCGCGAGAAGAGCCACCACGGAGTCTGCGTGACTCGGGACAGTGGAGAAAATCAGCGGCACAGCGTGGGTCTCGCGACCTCCAGCGAACGgtgagtcgat ... cttgagtcagAGATCCCTAAGTTTCGATCCACTGTCCCAGTGGATTTGGGACTGCGATGGAGGAGCAGTTCATCCTCCGCGTGCCGCCATCCGTCGCAGAGCGGATCGAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attttccttgttccccactgtctcttcctgattagtgttatttcgcttgagtcagAGATCCCTAAGTTTCGATCCACTGTCCCAGTGGATTTGGGACTGCGATGGAGGAGCAGTTCATCCTCCGCGTGCCGCCATCCGTCGCAGAGCGGATCGAG
                         tcctgat  putative branch site (score: 182)
                                        tttcgctt  putative PPT
                                   tgttattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagtcgatgagtttatctccttccggccttacctattctcgatcttctctgctcccttagttcttgttcctttattttccttgttccccactgtctcttcctgattagtgttatttcgcttgagtcagAGATCCCTAAGTTTCGATCCACTGTCCCAGTGGATTTGGGACTGCGATGGAGGAGCAGTTCATCCTCCGCGTGCCGCCATCCGTCGCAGAGCGGATCGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCAG