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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttgctggtgtgtctacattgactggatgcatgcatgatctctgatttgtacttatgctattcttgttgccaattcattatcaactgaagGTTGGAAAGGTGGTTGATCAACTCCTCGCAGAACAAG

Basic information

species Zea mays
transcript GRMZM2G168858_T01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G168858_T01 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os09g38620.1 (Oryza sativa), 3'ss of exon 5
gtttgctggtgtgtctacattga--ctggatgcatgcatgatctctgatttgtacttatgctattcttgttgccaattcattatcaactgaagGTTGGAAAGGTGGTTGATCAACTCCTCGCAGAACAAG
|||||||||||  ||||||||||   ||      |  ||     |  |||||||       || |    ||| |  || |     ||||||||||||||||||||||||| ||||||||||| |||||||
gtttgctggtgcttctacattgatattgtgcttttatatagagcccaatttgta-------tacttacattgtcttttta-----aactgaagGTTGGAAAGGTGGTTGACCAACTCCTCGCTGAACAAG
















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|148931705|gb|EC874913.2|EC874913
EST:     GGTTTGGGGTGTTTGGCCTCGGACATAGACAGTATGAGCACTTTAACAAG                         GTTGGAAAGGTGGTTGATCAACTCCTCGCAGAACAAG
genomic: GGTTTGGGGTGTTTGGCCTCGGAAATAGACAGTATGAGCACTTTAACAAGgtttgctggt ... tcaactgaagGTTGGAAAGGTGGTTGATCAACTCCTCGCAGAACAAG
EST: gi|149075933|gb|EE164496.2|EE164496
EST:     GGTTTGGGGTGTTTGGCCTCGGAAATAGACAGTATGAGCACTTTAACAAG                         GTTGGAAAGGTGGTTGATCAACTCCTCGCAGAACAAG
genomic: GGTTTGGGGTGTTTGGCCTCGGAAATAGACAGTATGAGCACTTTAACAAGgtttgctggt ... tcaactgaagGTTGGAAAGGTGGTTGATCAACTCCTCGCAGAACAAG

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), 37 (downstream exon)
Score: 83

GGTAATGAGAGAGGCGAGTGGTTGAATAATCTTCGGTTTGGGGTGTTTGGCCTCGGAAATAGACAGTATGAGCACTTTAACAAGgtttgctggt ... tcaactgaagGTTGGAAAGGTGGTTGATCAACTCCTCGCAGAACAAG


Block sizes: 49 (upstream exon), 37 (downstream exon)
Score: 204

GGTAATGAGAGAGGCGAGTGGTTGAATAATCTTCGGTTTGGGGTGTTTGGCCTCGGAAATAGACAGTATGAGCACTTTAACAAGgtttgctggt ... tcaactgaagGTTGGAAAGGTGGTTGATCAACTCCTCGCAGAACAAG


Block sizes: 49 (upstream exon), 37 (downstream exon)
Score: 108

GGTAATGAGAGAGGCGAGTGGTTGAATAATCTTCGGTTTGGGGTGTTTGGCCTCGGAAATAGACAGTATGAGCACTTTAACAAGgtttgctggt ... tcaactgaagGTTGGAAAGGTGGTTGATCAACTCCTCGCAGAACAAG


Block sizes: 45 (upstream exon), 37 (downstream exon)
Score: 139

GGTAATGAGAGAGGCGAGTGGTTGAATAATCTTCGGTTTGGGGTGTTTGGCCTCGGAAATAGACAGTATGAGCACTTTAACAAGgtttgctggt ... tcaactgaagGTTGGAAAGGTGGTTGATCAACTCCTCGCAGAACAAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgatctctgatttgtacttatgctattcttgttgccaattcattatcaactgaagGTTGGAAAGGTGGTTGATCAACTCCTCGCAGAACAAG
    ctctgat  putative branch site (score: 139)
                                    aattcattat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtttgctggtgtgtctacattgactggatgcatgcatgatctctgatttgtacttatgctattcttgttgccaattcattatcaactgaagGTTGGAAAGGTGGTTGATCAACTCCTCGCAGAACAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTCCTC