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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttggtttttgtttcttgtattctctaataactttgtttttcgaatgtatatatcggtttaaagtgtacaatttgttgatgtagTTCAACATGGGTGATGTACTGGTTGATGGAAAGTCCACTG

Basic information

species Zea mays
transcript GRMZM2G001713_T01
intron # 2
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|211224723|gb|FL222441.1|FL222441
EST:     ACAAGGGCGATCACACGTTTGTCCCAGTCACTCGGAAGGGATACTGGCAG                         TTCAACATGGGTGATGTCCTGGTTGATGGAAAGTCCACTG
genomic: ACAAGGGTGATCACACGTTTGTCCCAGTCACTCGGAAGGGATACTGGCAGgttggttttt ... gttgatgtagTTCAACATGGGTGATGTACTGGTTGATGGAAAGTCCACTG
EST: gi|31361595|gb|CD445952.1|CD445952
EST:     GTCCCAGTCACTCGGAAGGGATACTGGCAG                         TTCAACATGGGTGATGTCCTGGTTGATGGAAAGTCCACTG
genomic: GTCCCAGTCACTCGGAAGGGATACTGGCAGgttggttttt ... gttgatgtagTTCAACATGGGTGATGTACTGGTTGATGGAAAGTCCACTG
EST: gi|211222666|gb|FL222431.1|FL222431
EST:     ACAAGGGCGATCACACGTTTGTCCCAGTCACTCGGAAGGGATACTGGCAG                         TTCAACATGGGTGATGTCCTGGTTGATGGAAAGTCCACTG
genomic: ACAAGGGTGATCACACGTTTGTCCCAGTCACTCGGAAGGGATACTGGCAGgttggttttt ... gttgatgtagTTCAACATGGGTGATGTACTGGTTGATGGAAAGTCCACTG
EST: gi|32807856|gb|CD960090.1|CD960090
EST:     ACAAGGGTGATCACACGTTTGTCCCAGTCACTCGGAAGGGATACTGGCAG                         TTCAACATGGGTGATGTCCTGGTTGATGGAAAGTCCACTG
genomic: ACAAGGGTGATCACACGTTTGTCCCAGTCACTCGGAAGGGATACTGGCAGgttggttttt ... gttgatgtagTTCAACATGGGTGATGTACTGGTTGATGGAAAGTCCACTG
EST: gi|211224720|gb|FL222438.1|FL222438
EST:     ACAAGGGCGATCACACGTTTGTCCCAGTCACTCGGAAGGGATACTGGCAG                         TTCAACATGGGTGATGTCCTGGTTGATGGAAAGTCCACTG
genomic: ACAAGGGTGATCACACGTTTGTCCCAGTCACTCGGAAGGGATACTGGCAGgttggttttt ... gttgatgtagTTCAACATGGGTGATGTACTGGTTGATGGAAAGTCCACTG

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), 17 (downstream exon)
Score: 334

TGAAGGAGAAGGTGGTGAAATTGTATTTGGTGGAATGGATTCTAGCCACTACAAGGGTGATCACACGTTTGTCCCAGTCACTCGGAAGGGATACTGGCAGgttggttttt ... gttgatgtagTTCAACATGGGTGATGTACTGGTTGATGGAAAGTCCACTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 707

TGAAGGAGAAGGTGGTGAAATTGTATTTGGTGGAATGGATTCTAGCCACTACAAGGGTGATCACACGTTTGTCCCAGTCACTCGGAAGGGATACTGGCAGgttggttttt ... gttgatgtagTTCAACATGGGTGATGTACTGGTTGATGGAAAGTCCACTG


Block sizes: 49 (upstream exon), 17 (downstream exon)
Score: 453

TGAAGGAGAAGGTGGTGAAATTGTATTTGGTGGAATGGATTCTAGCCACTACAAGGGTGATCACACGTTTGTCCCAGTCACTCGGAAGGGATACTGGCAGgttggttttt ... gttgatgtagTTCAACATGGGTGATGTACTGGTTGATGGAAAGTCCACTG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 351

TGAAGGAGAAGGTGGTGAAATTGTATTTGGTGGAATGGATTCTAGCCACTACAAGGGTGATCACACGTTTGTCCCAGTCACTCGGAAGGGATACTGGCAGgttggttttt ... gttgatgtagTTCAACATGGGTGATGTACTGGTTGATGGAAAGTCCACTG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aactttgtttttcgaatgtatatatcggtttaaagtgtacaatttgttgatgtagTTCAACATGGGTGATGTACTGGTTGATGGAAAGTCCACTG
                                            tgttgat  putative branch site (score: 351)
              aatgtatatat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttggtttttgtttcttgtattctctaataactttgtttttcgaatgtatatatcggtttaaagtgtacaatttgttgatgtagTTCAACATGGGTGATGTACTGGTTGATGGAAAGTCCACTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA