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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacttaactaatagctcatctcttctcatttatttagattctatgtggtttaatataccctatatcacagtttttttttctttcagGGGATAATGGAGCAGATTCATTAGTTGAGCTCCTTCTTACTTACCAG

Basic information

species Zea mays
transcript GRMZM2G092497_T04
intron # 3
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|78088679|gb|DV517072.1|DV517072
EST:     GGACATGGGTTTCTCAGAAGAGATTGTTCTGAAGGCCATGAAGGACAATG                         GGGATAATGGAGCAGATTCATTAGTTGAGCTCCTTCTTACTTACCAG
genomic: GGACATGGGTTTCTCAGAAGAGATTGTTCTGAAGGCCATGAAGGACAATGgtacttaact ... tttctttcagGGGATAATGGAGCAGATTCATTAGTTGAGCTCCTTCTTACTTACCAG
EST: gi|78109829|gb|DV528245.1|DV528245
EST:     GGACATGGGTTTCTCAGAAGAGATTGTTCTGAAGGCCATGAAGGACAATG                         GGGATAATGGAGCAGATTCATTAGTTGAGCTCCTTCTTACTTACCAG
genomic: GGACATGGGTTTCTCAGAAGAGATTGTTCTGAAGGCCATGAAGGACAATGgtacttaact ... tttctttcagGGGATAATGGAGCAGATTCATTAGTTGAGCTCCTTCTTACTTACCAG
EST: gi|28873635|gb|CB329598.1|CB329598
EST:     GGACATGGGTTTCTCAGAAGAGATTGTTCTGAAGGCCATGAAGGACAATG                         GGGATAATGGAGCAGATTCATTAGTTGAGCTCCTTCTTACTTACCAG
genomic: GGACATGGGTTTCTCAGAAGAGATTGTTCTGAAGGCCATGAAGGACAATGgtacttaact ... tttctttcagGGGATAATGGAGCAGATTCATTAGTTGAGCTCCTTCTTACTTACCAG
EST: gi|211528668|gb|FL445662.1|FL445662
EST:     GGACATGGGTTTCTCAGAAGAGATTGTTCTGAAGGCCATGAAGGACAATG                         GGGATAATGGAGCAGATTCATTAGTTGAGCTCCTTCTTACTTACCAG
genomic: GGACATGGGTTTCTCAGAAGAGATTGTTCTGAAGGCCATGAAGGACAATGgtacttaact ... tttctttcagGGGATAATGGAGCAGATTCATTAGTTGAGCTCCTTCTTACTTACCAG
EST: gi|71325873|gb|DR799620.1|DR799620
EST:     GGACATGGGTTTCTCAGAAGAGATTGTTCTGAAGGCCATGAAGGACAATG                         GGGATAATGGAGCAGATTCATTAGTTGAGCTCCTTCTTACTTACCAG
genomic: GGACATGGGTTTCTCAGAAGAGATTGTTCTGAAGGCCATGAAGGACAATGgtacttaact ... tttctttcagGGGATAATGGAGCAGATTCATTAGTTGAGCTCCTTCTTACTTACCAG
EST: gi|76913046|gb|DV164985.1|DV164985
EST:     GGACATGGGTTTCTCAGAAGAGATTGTTCTGAAGGCCATGAAGGACAATG                         GGGATAATGGAGCAGATTCATTAGTTGAGCTCCTTCTTACTTACCAG
genomic: GGACATGGGTTTCTCAGAAGAGATTGTTCTGAAGGCCATGAAGGACAATGgtacttaact ... tttctttcagGGGATAATGGAGCAGATTCATTAGTTGAGCTCCTTCTTACTTACCAG
EST: gi|91873568|gb|EB403525.1|EB403525
EST:     GGACATGGGTTTCTCAGAAGAGATTGTTCTGAAGGCCATGAAGGACAATG                         GGGATAATGGAGCAGATTCATTATTTGAGCTCCTTCTT
genomic: GGACATGGGTTTCTCAGAAGAGATTGTTCTGAAGGCCATGAAGGACAATGgtacttaact ... tttctttcagGGGATAATGGAGCAGATTCATTAGTTGAGCTCCTTCTT
EST: gi|71447185|gb|DR828235.1|DR828235
EST:     GGACATGGGTTTCTCAGAAGAGATTGTTCTGAAGGCCATGAAGGACAATG                         GGGATAATGGAGCAGATTCATTAGTTGAGCTCCTTCTTACTTACCAG
genomic: GGACATGGGTTTCTCAGAAGAGATTGTTCTGAAGGCCATGAAGGACAATGgtacttaact ... tttctttcagGGGATAATGGAGCAGATTCATTAGTTGAGCTCCTTCTTACTTACCAG
EST: gi|74238865|gb|DT646779.1|DT646779
EST:     GGACATGGGTTTCTCAGAAGAGATTGTTCTGAAGGCCATGAAGGACAATG                         GGGATAATGGAGCAGATTCATTAGTTGAGCTCCTTCTTACTTACCAG
genomic: GGACATGGGTTTCTCAGAAGAGATTGTTCTGAAGGCCATGAAGGACAATGgtacttaact ... tttctttcagGGGATAATGGAGCAGATTCATTAGTTGAGCTCCTTCTTACTTACCAG
EST: gi|149074707|gb|EE163131.2|EE163131
EST:     GGACATGGGTTTCTCAGAAGAGATTGTTCTGAAGGCCATGAAGGACAATG                         GGGATAATGGAGCAGATTCATTAGTTGAGCTC
genomic: GGACATGGGTTTCTCAGAAGAGATTGTTCTGAAGGCCATGAAGGACAATGgtacttaact ... tttctttcagGGGATAATGGAGCAGATTCATTAGTTGAGCTC
EST: gi|89762158|gb|DY689885.1|DY689885
EST:     GGACATGGGTTTCTCAGAAGAGATTGTTCTGAAGGACATGAAGGACAATG                         GGGATAATGGAGCAGATTCATTAGTTGAGCTCCTTCTTACTTACCAG
genomic: GGACATGGGTTTCTCAGAAGAGATTGTTCTGAAGGCCATGAAGGACAATGgtacttaact ... tttctttcagGGGATAATGGAGCAGATTCATTAGTTGAGCTCCTTCTTACTTACCAG

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 3 RNA-Seq libraries.


Block sizes: 47 (upstream exon), 48 (downstream exon)
Score: 15

AATGGCAATGGGAAGGCTGGGCGATCTGCCTCTTTGGTTCAGAAGTATGTGGACATGGGTTTCTCAGAAGAGATTGTTCTGAAGGCCATGAAGGACAATGgtacttaact ... tttctttcagGGGATAATGGAGCAGATTCATTAGTTGAGCTCCTTCTTACTTACCAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 32

AATGGCAATGGGAAGGCTGGGCGATCTGCCTCTTTGGTTCAGAAGTATGTGGACATGGGTTTCTCAGAAGAGATTGTTCTGAAGGCCATGAAGGACAATGgtacttaact ... tttctttcagGGGATAATGGAGCAGATTCATTAGTTGAGCTCCTTCTTACTTACCAG


Block sizes: 45 (upstream exon), 48 (downstream exon)
Score: 45

AATGGCAATGGGAAGGCTGGGCGATCTGCCTCTTTGGTTCAGAAGTATGTGGACATGGGTTTCTCAGAAGAGATTGTTCTGAAGGCCATGAAGGACAATGgtacttaact ... tttctttcagGGGATAATGGAGCAGATTCATTAGTTGAGCTCCTTCTTACTTACCAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atttagattctatgtggtttaatataccctatatcacagtttttttttctttcagGGGATAATGGAGCAGATTCATTAGTTGAGCTCCTTCTTACTTACCAG
                gtttaat  putative branch site (score: 45)
                                    cagtttttttttcttt  putative PPT
                                     agtttttttttcttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacttaactaatagctcatctcttctcatttatttagattctatgtggtttaatataccctatatcacagtttttttttctttcagGGGATAATGGAGCAGATTCATTAGTTGAGCTCCTTCTTACTTACCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGAT