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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttctttccctctatgacatgctaccaccattttctctgttcccagtcttcatgtttcttttctgaatcctttgtttcagGGTCTAAGGGAAAGGTTTTCGCATTGTAACTCAAACATGGACGCAGGCCAG

Basic information

species Zea mays
transcript GRMZM2G141873_T06
intron # 8
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|32837832|gb|CD977510.1|CD977510
EST:     CTGGGAGGAGGACAATGCACTCTTTCTACAGTGATGTTGTGCGCCTTCAG                         GGTCTAAGGGAAAGGTTTTCACATTGTAACTCAAACATGGACGCAGGCCAG
genomic: CTGGGAGGAGGACAATGCACTCTTTCTACAGTGATATTGTGCGCCTTCAGgtttctttcc ... tttgtttcagGGTCTAAGGGAAAGGTTTTCGCATTGTAACTCAAACATGGACGCAGGCCAG
EST: gi|149011848|gb|EE042455.2|EE042455
EST:     CTGGGAGGAGGACAATGCACTCTTTCTACAGTGATATTGTGCGCCTTCAG                         GGTCTAAGGGAAAGGTTTTCGCATTGTAACTCAAACATGGACGCAGGCCAG
genomic: CTGGGAGGAGGACAATGCACTCTTTCTACAGTGATATTGTGCGCCTTCAGgtttctttcc ... tttgtttcagGGTCTAAGGGAAAGGTTTTCGCATTGTAACTCAAACATGGACGCAGGCCAG
EST: gi|211526768|gb|FL028557.1|FL028557
EST:     CTGGGAGGAGGACAATGCACTCTTTCTACAGTGATATTGTGCGCCTTCAG                         GGTCTAAGGGAAAGGTTTTCGCATTGTAACTCAAACATGGACGCAGGCCAG
genomic: CTGGGAGGAGGACAATGCACTCTTTCTACAGTGATATTGTGCGCCTTCAGgtttctttcc ... tttgtttcagGGTCTAAGGGAAAGGTTTTCGCATTGTAACTCAAACATGGACGCAGGCCAG
EST: gi|71423226|gb|DR805987.1|DR805987
EST:     CTGGGAGGAGGACAATGCACTCTTTCTACAGTGATATTGTGCGCCTTCAG                         GGTCTAAGGGAAAGGTTTTCGCATTGTAACTCAAACATGGACGCAGGCCAG
genomic: CTGGGAGGAGGACAATGCACTCTTTCTACAGTGATATTGTGCGCCTTCAGgtttctttcc ... tttgtttcagGGTCTAAGGGAAAGGTTTTCGCATTGTAACTCAAACATGGACGCAGGCCAG
EST: gi|71417999|gb|DR804277.1|DR804277
EST:     CTGGGAGGAGGACAATGCACTCTTTCTACAGTGATATTGTGCGCCTTCAG                         GGTCTAAGGGAAAGGTTTTCGCATTGTAACTCAAACATGGACGCAGGCCAG
genomic: CTGGGAGGAGGACAATGCACTCTTTCTACAGTGATATTGTGCGCCTTCAGgtttctttcc ... tttgtttcagGGTCTAAGGGAAAGGTTTTCGCATTGTAACTCAAACATGGACGCAGGCCAG
EST: gi|78087078|gb|DV515471.1|DV515471
EST:     CTGGGAGGAGGACAATGCACTCTTTCTACAGTGATATTGTGCGCCTTCAG                         GGTCTAAGGGAAAGGTTTTCGCATTGTAACTCAAACATGGACGCAGGCCAG
genomic: CTGGGAGGAGGACAATGCACTCTTTCTACAGTGATATTGTGCGCCTTCAGgtttctttcc ... tttgtttcagGGTCTAAGGGAAAGGTTTTCGCATTGTAACTCAAACATGGACGCAGGCCAG

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), 46 (downstream exon)
Score: 29

AGAAGACATTTCTGGGAGGAGGACAATGCACTCTTTCTACAGTGATATTGTGCGCCTTCAGgtttctttcc ... tttgtttcagGGTCTAAGGGAAAGGTTTTCGCATTGTAACTCAAACATGGACGCAGGCCAG


Block sizes: 42 (upstream exon), 48 (downstream exon)
Score: 22

AGAAGACATTTCTGGGAGGAGGACAATGCACTCTTTCTACAGTGATATTGTGCGCCTTCAGgtttctttcc ... tttgtttcagGGTCTAAGGGAAAGGTTTTCGCATTGTAACTCAAACATGGACGCAGGCCAG


Block sizes: 45 (upstream exon), 49 (downstream exon)
Score: 32

AGAAGACATTTCTGGGAGGAGGACAATGCACTCTTTCTACAGTGATATTGTGCGCCTTCAGgtttctttcc ... tttgtttcagGGTCTAAGGGAAAGGTTTTCGCATTGTAACTCAAACATGGACGCAGGCCAG


Block sizes: 48 (upstream exon), 47 (downstream exon)
Score: 37

AGAAGACATTTCTGGGAGGAGGACAATGCACTCTTTCTACAGTGATATTGTGCGCCTTCAGgtttctttcc ... tttgtttcagGGTCTAAGGGAAAGGTTTTCGCATTGTAACTCAAACATGGACGCAGGCCAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

caccattttctctgttcccagtcttcatgtttcttttctgaatcctttgtttcagGGTCTAAGGGAAAGGTTTTCGCATTGTAACTCAAACATGGACGCAGGCCAG
                                          tcctttgtttc  CT-rich tract
                             tttctttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtttctttccctctatgacatgctaccaccattttctctgttcccagtcttcatgtttcttttctgaatcctttgtttcagGGTCTAAGGGAAAGGTTTTCGCATTGTAACTCAAACATGGACGCAGGCCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA