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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...acggcgtcatatatttgtgaacggaggtagtattgtctaatgacacagttacaagtgtggcaaatgagtgaataacaatcaccatgtcctatttatgtagGTTGCAAGGCTGCTGGGCCTACAAGAAGCTGCTCTTCAGCCAAAGCGCGCGATCCAG

Basic information

species Zea mays
transcript GRMZM2G119248_T02
intron # 14
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|78023991|gb|DV492378.1|DV492378
EST:     CTAAGCTTGATGAACCTGTTGGAAGGGGTGACAAGAAGATCTTGAGAGAG                         GTTGCAAGGCTGCTGGGCCTACAAGAAGCTGCTCTTCAGCCAAAGCGCGCG
genomic: CTAAGCTTGATGAACCTGTTGGAAGGGGTGACAAGAAGATCTTGAGAGAGgttcgcgcat ... atttatgtagGTTGCAAGGCTGCTGGGCCTACAAGAAGCTGCTCTTCAGCCAAAGCGCGCG
EST: gi|60358033|gb|DN225006.1|DN225006
EST:     CTAAGCTTGATGAACCTGTTGGAAGGGGTGACAAGAAGATCTTGAGAGAG                         GTTGCAAGGCTGCTGGGCCTACAAGAAGCTGCTCTTCAGCCAAAGCGCGCG
genomic: CTAAGCTTGATGAACCTGTTGGAAGGGGTGACAAGAAGATCTTGAGAGAGgttcgcgcat ... atttatgtagGTTGCAAGGCTGCTGGGCCTACAAGAAGCTGCTCTTCAGCCAAAGCGCGCG
EST: gi|93011720|gb|EB637240.1|EB637240
EST:     CTAAGCTTGATGAACCTGTTGGAAGGGGTGACAAGAAGATCTTGAGAGAG                         GTTGCAAGGCTGCTGGGCCTACAAGAAGCTGCTCTTCAGCCAAAGCGCGCG
genomic: CTAAGCTTGATGAACCTGTTGGAAGGGGTGACAAGAAGATCTTGAGAGAGgttcgcgcat ... atttatgtagGTTGCAAGGCTGCTGGGCCTACAAGAAGCTGCTCTTCAGCCAAAGCGCGCG
EST: gi|6022275|gb|AW067203.1|AW067203
EST:     CTAAGCTTGATGAACCTGTTGGAAGGGGTGACAAGAAGATCTTGAGAGAG                         GTTGCAAGGCTGCTGGGCCTACAAGAAGCTGCTCTTCAGCCAAAGCGCGCG
genomic: CTAAGCTTGATGAACCTGTTGGAAGGGGTGACAAGAAGATCTTGAGAGAGgttcgcgcat ... atttatgtagGTTGCAAGGCTGCTGGGCCTACAAGAAGCTGCTCTTCAGCCAAAGCGCGCG
EST: gi|71324659|gb|DR799024.1|DR799024
EST:     CTAAGCTTGATGAACCTGTTGGAAGGGGTGACAAGAAGATCTTGAGAGAG                         GTTGCAAGGCTGCTGGGCCTACAAGAAGCTGCTCTTCAGCCAAAGCGCGCG
genomic: CTAAGCTTGATGAACCTGTTGGAAGGGGTGACAAGAAGATCTTGAGAGAGgttcgcgcat ... atttatgtagGTTGCAAGGCTGCTGGGCCTACAAGAAGCTGCTCTTCAGCCAAAGCGCGCG

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: 41 (upstream exon), 38 (downstream exon)
Score: 34

TGACGAGAACGTGATAAAAACTTTGTTGGAAATTCCGTTATGGGAAATTGCTAAGCTTGATGAACCTGTTGGAAGGGGTGACAAGAAGATCTTGAGAGAGgttcgcgcat ... atttatgtagGTTGCAAGGCTGCTGGGCCTACAAGAAGCTGCTCTTCAGCCAAAGCGCGCGATCCAG


Block sizes: 46 (upstream exon), 47 (downstream exon)
Score: 31

TGACGAGAACGTGATAAAAACTTTGTTGGAAATTCCGTTATGGGAAATTGCTAAGCTTGATGAACCTGTTGGAAGGGGTGACAAGAAGATCTTGAGAGAGgttcgcgcat ... atttatgtagGTTGCAAGGCTGCTGGGCCTACAAGAAGCTGCTCTTCAGCCAAAGCGCGCGATCCAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 32

TGACGAGAACGTGATAAAAACTTTGTTGGAAATTCCGTTATGGGAAATTGCTAAGCTTGATGAACCTGTTGGAAGGGGTGACAAGAAGATCTTGAGAGAGgttcgcgcat ... atttatgtagGTTGCAAGGCTGCTGGGCCTACAAGAAGCTGCTCTTCAGCCAAAGCGCGCGATCCAG


Block sizes: 28 (upstream exon), 48 (downstream exon)
Score: 8

TGACGAGAACGTGATAAAAACTTTGTTGGAAATTCCGTTATGGGAAATTGCTAAGCTTGATGAACCTGTTGGAAGGGGTGACAAGAAGATCTTGAGAGAGgttcgcgcat ... atttatgtagGTTGCAAGGCTGCTGGGCCTACAAGAAGCTGCTCTTCAGCCAAAGCGCGCGATCCAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cagttacaagtgtggcaaatgagtgaataacaatcaccatgtcctatttatgtagGTTGCAAGGCTGCTGGGCCTACAAGAAGCTGCTCTTCAGCCAAAGCGCGCGATCCAG
                        gaataac  putative branch site (score: 8)
                                         tcctattt  putative PPT
                                            tatttatgta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
acggcgtcatatatttgtgaacggaggtagtattgtctaatgacacagttacaagtgtggcaaatgagtgaataacaatcaccatgtcctatttatgtagGTTGCAAGGCTGCTGGGCCTACAAGAAGCTGCTCTTCAGCCAAAGCGCGCGATCCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGCT