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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatggattgatttttcatttatacataatgtcaaaactcaaatcactgcatttctgttccttgatcatttctctgttggatggaccaaacagGCAGAGCATGAAACAGCAGAAACTGGTCGCAAAGGATGTCTTCTCTTTCTGGCTTAATCGTGACCCTGATGCATCTTCTGGAGGAGGCGAGCTTGTCTTT

Basic information

species Zea mays
transcript GRMZM2G077233_T05
intron # 5
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|76291015|gb|DV030583.1|DV030583
EST:     CTTGGTCTCGGATTTCCTGAAATTTCTGTAGGAGGAGCCCCTCCAATTTG                         GCAGAGCATGAAACAGCAGAAACTGGTCGCAAAGGATGTCTTCTCTTTCTG
genomic: CTTGGTCTCGGATTTCCTGAAATTTCTGTAGGAGGAGCCCCTCCAATTTGgtatggattg ... gaccaaacagGCAGAGCATGAAACAGCAGAAACTGGTCGCAAAGGATGTCTTCTCTTTCTG
EST: gi|1298575|gb|W21639.1|W21639
EST:     TTGGTCTCGGATTTCCTGAAATTTCTGTAGGAGGAGCCCCTCCAATTTG                         GCAGANNATGAAACAGCAGAAACTGGTCGCAAAGGATGTCTTCTCTTTCTG
genomic: TTGGTCTCGGATTTCCTGAAATTTCTGTAGGAGGAGCCCCTCCAATTTGgtatggattg ... gaccaaacagGCAGAGCATGAAACAGCAGAAACTGGTCGCAAAGGATGTCTTCTCTTTCTG
EST: gi|13125876|gb|BG316446.1|BG316446
EST:     TTGG-CTCGGA-TTCCTGAAA-TTCTGTAGGAGGAGCCCCTCCAATTTG                         GCAGAGCATGAAACAGCAGAAACTGGTCGCAAAGGATGTCTTCTGTTTCTG
genomic: TTGGTCTCGGATTTCCTGAAATTTCTGTAGGAGGAGCCCCTCCAATTTGgtatggattg ... gaccaaacagGCAGAGCATGAAACAGCAGAAACTGGTCGCAAAGGATGTCTTCTCTTTCTG
EST: gi|211373714|gb|FL377783.1|FL377783
EST:     CTTGGTCTCGGATTTTCTGAAATTTCTGTAGGAGGAGCCCCTCCAATTTG                         GCAGAGCATGAAACAGCAGAAACTGGTCGCAAAGGATGTCTTTCTCTTTCT
genomic: CTTGGTCTCGGATTTCCTGAAATTTCTGTAGGAGGAGCCCCTCCAATTTGgtatggattg ... gaccaaacagGCAGAGCATGAAACAGCAGAAACTGGTCGCAAAGGATGTCTT-CTCTTTCT
EST: gi|76289740|gb|DV029308.1|DV029308
EST:     CTTGGTCTCGGATTTCCTGAAATTTCTGTAGGAGGAGCCCCTCCAATTTG                         GCAGAGCATGAAACAGCAGAAACTGGTCGCAAAGGATGTCTTCTCTTTCTG
genomic: CTTGGTCTCGGATTTCCTGAAATTTCTGTAGGAGGAGCCCCTCCAATTTGgtatggattg ... gaccaaacagGCAGAGCATGAAACAGCAGAAACTGGTCGCAAAGGATGTCTTCTCTTTCTG
EST: gi|101393193|gb|EB818527.1|EB818527
EST:     CTTGGTCTCGGATTTCCTGAAATTTCTGTAGGAGGAGCCCCTCCAATTTG                         GCAGAGCATGAAACAGCAGAAACTGGTCGCAAAGGATGTCTTCTCTTTCTG
genomic: CTTGGTCTCGGATTTCCTGAAATTTCTGTAGGAGGAGCCCCTCCAATTTGgtatggattg ... gaccaaacagGCAGAGCATGAAACAGCAGAAACTGGTCGCAAAGGATGTCTTCTCTTTCTG
EST: gi|67034446|gb|CO462996.1|CO462996
EST:     CTTGGTCTCGGATTTCCTGAAATTTCTGTAGGAGGAGCCCCTCCAATTTG                         GCAGAGTATGAAACAGCAGAAACTGGTCGCAAAGGATGTCTTCTCTTTCTG
genomic: CTTGGTCTCGGATTTCCTGAAATTTCTGTAGGAGGAGCCCCTCCAATTTGgtatggattg ... gaccaaacagGCAGAGCATGAAACAGCAGAAACTGGTCGCAAAGGATGTCTTCTCTTTCTG

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), 49 (downstream exon)
Score: 452

CAACTCGAGAAACCAGCCCTACTTTCATCATTGGGAAGTTTGATGGAATTCTTGGTCTCGGATTTCCTGAAATTTCTGTAGGAGGAGCCCCTCCAATTTGgtatggattg ... gaccaaacagGCAGAGCATGAAACAGCAGAAACTGGTCGCAAAGGATGTCTTCTCTTTCTGGCTTAATCGTGACCCTGATGCATCTTCTGGAGGAGGCGAGCTTGTCTTT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 485

CAACTCGAGAAACCAGCCCTACTTTCATCATTGGGAAGTTTGATGGAATTCTTGGTCTCGGATTTCCTGAAATTTCTGTAGGAGGAGCCCCTCCAATTTGgtatggattg ... gaccaaacagGCAGAGCATGAAACAGCAGAAACTGGTCGCAAAGGATGTCTTCTCTTTCTGGCTTAATCGTGACCCTGATGCATCTTCTGGAGGAGGCGAGCTTGTCTTT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 591

CAACTCGAGAAACCAGCCCTACTTTCATCATTGGGAAGTTTGATGGAATTCTTGGTCTCGGATTTCCTGAAATTTCTGTAGGAGGAGCCCCTCCAATTTGgtatggattg ... gaccaaacagGCAGAGCATGAAACAGCAGAAACTGGTCGCAAAGGATGTCTTCTCTTTCTGGCTTAATCGTGACCCTGATGCATCTTCTGGAGGAGGCGAGCTTGTCTTT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 557

CAACTCGAGAAACCAGCCCTACTTTCATCATTGGGAAGTTTGATGGAATTCTTGGTCTCGGATTTCCTGAAATTTCTGTAGGAGGAGCCCCTCCAATTTGgtatggattg ... gaccaaacagGCAGAGCATGAAACAGCAGAAACTGGTCGCAAAGGATGTCTTCTCTTTCTGGCTTAATCGTGACCCTGATGCATCTTCTGGAGGAGGCGAGCTTGTCTTT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcaaatcactgcatttctgttccttgatcatttctctgttggatggaccaaacagGCAGAGCATGAAACAGCAGAAACTGGTCGCAAAGGATGTCTTCTCTTTCTGGCTTAATCGTGACCCTGATGCATCTTCTGGAGGAGGCGAGCTTGTCTTT
                     ccttgat  putative branch site (score: 557)
                          atcattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatggattgatttttcatttatacataatgtcaaaactcaaatcactgcatttctgttccttgatcatttctctgttggatggaccaaacagGCAGAGCATGAAACAGCAGAAACTGGTCGCAAAGGATGTCTTCTCTTTCTGGCTTAATCGTGACCCTGATGCATCTTCTGGAGGAGGCGAGCTTGTCTTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCTT