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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gtcataccaatttctgtctgcttatgcatgagaatatgttgtctaatttttgtttatttcttattttcttctgtggtacctaaactgtttcacttgacagGCATTTTCAGTTATTGCGAATTCACCTCTACGTATTGATCTCTCGTGTGTCCTGGATCATGTTGTTTCTGAGCTCACAGCTTTCCTTCGCAAG

Basic information

species Zea mays
transcript GRMZM2G168629_T05
intron # 17
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G168629_T01 (Zea mays), 3'ss of exon 17
lower sequence: LOC_Os02g07120.1 (Oryza sativa), 3'ss of exon 17
gtcataccaatttctgtctgcttatgcatgagaatatgttgtctaatttttgtttatttcttattttcttctgtggtacctaaactgttt---cacttgacagGCATTTTCAGTTATTGCGAATTCACCTCTACGTATTGATCTCTCGTGTGTCCTGGATCATGTTGTTTCTGAGCTCACAGCTTTCCTTCGCAAG
 | | |     || | |||   | ||| |||   | |    || | |   | ||| |||  | ||    |    ||||| |||| |||||   | ||| |||||| ||| |||| ||||| || |||||||| || |||||||| ||||||||||| || |||||  ||||||||||||| ||||||||||| |||
attagaagttcttttttctatatttgcctgatttttt-caatcgagtgcctatttgttt--tgttgatctgctcggtacataaaatgtttttcccctttacagGCGTTTGCAGTGATTGCTAAATCACCTCTTCGCATTGATCTTTCGTGTGTCCTAGACCATGTCATTTCTGAGCTCACGGCTTTCCTTCGAAAG
















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|18383962|gb|BM417162.1|BM417162
EST:     TACTCGTTGACAGGATGGGTAATGAAATTACAAGACTTACAGCTGTCAAG                         GCATTTTCAGTTATTGCGAATTCACCTCTACGTATTGATCTCTCGTGTGTC
genomic: TACTCGTTGACAGGATGGGTAATGAAATTACAAGACTTACAGCTGTCAAGgtaagttttt ... cacttgacagGCATTTTCAGTTATTGCGAATTCACCTCTACGTATTGATCTCTCGTGTGTC
EST: gi|22489194|gb|BU049130.1|BU049130
EST:     TACTCGTTGACAGGATGGGTAATGAAATTACAAGACTTACAGCTGTCAAG                         GCATTTTCAGTTATTGCGAATTCACCTCTACGTATTGATCTCTCGTGTGTC
genomic: TACTCGTTGACAGGATGGGTAATGAAATTACAAGACTTACAGCTGTCAAGgtaagttttt ... cacttgacagGCATTTTCAGTTATTGCGAATTCACCTCTACGTATTGATCTCTCGTGTGTC
EST: gi|211432450|gb|FL213954.1|FL213954
EST:     TACTCGTTGACAGGATGGGTAATGAAATTACAAGACTTACAGCTGTCAAG                         GCATTTTCAGTTATTGCGAATTCACCTCTACGTATTGATCTCTCGTGTGTC
genomic: TACTCGTTGACAGGATGGGTAATGAAATTACAAGACTTACAGCTGTCAAGgtaagttttt ... cacttgacagGCATTTTCAGTTATTGCGAATTCACCTCTACGTATTGATCTCTCGTGTGTC
EST: gi|87298767|gb|DY470770.1|DY470770
EST:     TACTCGTTGACAGGATGGGTAATGAAATTACAAGACTTACAGCTGTCAAG                         GCATTTTCAGTTATTGCGAATTCACCTCTACGTATTGATCTCTCGTGTGTC
genomic: TACTCGTTGACAGGATGGGTAATGAAATTACAAGACTTACAGCTGTCAAGgtaagttttt ... cacttgacagGCATTTTCAGTTATTGCGAATTCACCTCTACGTATTGATCTCTCGTGTGTC
EST: gi|61118518|gb|DN559479.1|DN559479
EST:     TACTCGTTGACAGGATGGGTAATGAAATTACAAGACTTACAGCTGTCAAG                         GCATTTTCAGTTATTG
genomic: TACTCGTTGACAGGATGGGTAATGAAATTACAAGACTTACAGCTGTCAAGgtaagttttt ... cacttgacagGCATTTTCAGTTATTG
EST: gi|32859371|gb|CD999052.1|CD999052
EST:     TACTCGTTGACAGGATGGGTAATGAAATTACAAGACTTACAGCTGTCAAG                         GCATTTTCAGGTATTGCGAATTCACCTCTACGTATTGATCTCTCGTGTGTC
genomic: TACTCGTTGACAGGATGGGTAATGAAATTACAAGACTTACAGCTGTCAAGgtaagttttt ... cacttgacagGCATTTTCAGTTATTGCGAATTCACCTCTACGTATTGATCTCTCGTGTGTC
EST: gi|211432451|gb|FL213955.1|FL213955
EST:     TACTCGTTGACAGGATGGGTAATGAAATTACAAGACTTACAGCTGTCAAG                         GCATTTTCAGTTATTGCGAATTCACCTCTACGTATTGATCTCTCGTGTGTC
genomic: TACTCGTTGACAGGATGGGTAATGAAATTACAAGACTTACAGCTGTCAAGgtaagttttt ... cacttgacagGCATTTTCAGTTATTGCGAATTCACCTCTACGTATTGATCTCTCGTGTGTC

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), 49 (downstream exon)
Score: 397

CTCTACTTTTGGTGATGGTCTTGAAAGAGAATTACCAGCATGCCTTCCCATACTCGTTGACAGGATGGGTAATGAAATTACAAGACTTACAGCTGTCAAGgtaagttttt ... cacttgacagGCATTTTCAGTTATTGCGAATTCACCTCTACGTATTGATCTCTCGTGTGTCCTGGATCATGTTGTTTCTGAGCTCACAGCTTTCCTTCGCAAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 206

CTCTACTTTTGGTGATGGTCTTGAAAGAGAATTACCAGCATGCCTTCCCATACTCGTTGACAGGATGGGTAATGAAATTACAAGACTTACAGCTGTCAAGgtaagttttt ... cacttgacagGCATTTTCAGTTATTGCGAATTCACCTCTACGTATTGATCTCTCGTGTGTCCTGGATCATGTTGTTTCTGAGCTCACAGCTTTCCTTCGCAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 184

CTCTACTTTTGGTGATGGTCTTGAAAGAGAATTACCAGCATGCCTTCCCATACTCGTTGACAGGATGGGTAATGAAATTACAAGACTTACAGCTGTCAAGgtaagttttt ... cacttgacagGCATTTTCAGTTATTGCGAATTCACCTCTACGTATTGATCTCTCGTGTGTCCTGGATCATGTTGTTTCTGAGCTCACAGCTTTCCTTCGCAAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 164

CTCTACTTTTGGTGATGGTCTTGAAAGAGAATTACCAGCATGCCTTCCCATACTCGTTGACAGGATGGGTAATGAAATTACAAGACTTACAGCTGTCAAGgtaagttttt ... cacttgacagGCATTTTCAGTTATTGCGAATTCACCTCTACGTATTGATCTCTCGTGTGTCCTGGATCATGTTGTTTCTGAGCTCACAGCTTTCCTTCGCAAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atttttgtttatttcttattttcttctgtggtacctaaactgtttcacttgacagGCATTTTCAGTTATTGCGAATTCACCTCTACGTATTGATCTCTCGTGTGTCCTGGATCATGTTGTTTCTGAGCTCACAGCTTTCCTTCGCAAG
                                acctaaa  putative branch site (score: 164)
                                          tttcactt  putative PPT
       tttatttcttattttc  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtcataccaatttctgtctgcttatgcatgagaatatgttgtctaatttttgtttatttcttattttcttctgtggtacctaaactgtttcacttgacagGCATTTTCAGTTATTGCGAATTCACCTCTACGTATTGATCTCTCGTGTGTCCTGGATCATGTTGTTTCTGAGCTCACAGCTTTCCTTCGCAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTCA