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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgcgttgatccatccttataccaagtgtttccgcgtatttaagcttcggcctaatttagtgtttatggggacgggcggatttagattgtgcctctaagtggtgaggggaggctctgaaggggggaagggcgtgcgtgcttttaggtttcgtgcgtatttgatgatggttgattggtgtgtggtggtgttgcagAGGTTGTTGCGGCGACATCCATCGCCAGGCCTAGGGCGGATGTCGCCTACTGCATCCACGCGCTTGCCCGCCGTCTTGCCAAGACCCGCAACTGGATT

Basic information

species Zea mays
transcript GRMZM2G114513_T02
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|211095367|gb|FL067776.1|FL067776
EST:     GAAGGCGACTAATCACGTGGAGTGCCCACCCAAGGAGCGACACCTGCGAA                         AGGTTGTTGCGGCGACATCCATCGCCAGGCCTAGGGCGGATGTCGCCTACT
genomic: GAAGGCGACTAATCACGTGGAGTGCCCACCCAAGGAGCGACACCTGCGAAgtgcgttgat ... ggtgttgcagAGGTTGTTGCGGCGACATCCATCGCCAGGCCTAGGGCGGATGTCGCCTACT
EST: gi|211097837|gb|FL067788.1|FL067788
EST:     GAAGGCGACTAATCACGTGGAGTGCCCACCCAAGGAGCGACACCTGCGAA                         AGGTTGTTGCGGCGACATCCATCACCAGGCCTAGGGCGGATGTCGCCTACT
genomic: GAAGGCGACTAATCACGTGGAGTGCCCACCCAAGGAGCGACACCTGCGAAgtgcgttgat ... ggtgttgcagAGGTTGTTGCGGCGACATCCATCGCCAGGCCTAGGGCGGATGTCGCCTACT
EST: gi|211079577|gb|FL056323.1|FL056323
EST:     GAAGGCGACTAATCACGTGGAGTGCCCACCCAAGGAGCGACACCTGCGAA                         AGGTTGTTGCKGCGACATCCATCGCCAGGCCTAGGGCGGATGTCGCCTACT
genomic: GAAGGCGACTAATCACGTGGAGTGCCCACCCAAGGAGCGACACCTGCGAAgtgcgttgat ... ggtgttgcagAGGTTGTTGCGGCGACATCCATCGCCAGGCCTAGGGCGGATGTCGCCTACT
EST: gi|211097840|gb|FL067791.1|FL067791
EST:     GAAGGCGACTAATCACGTGGAGTGCCCACCCAAGGAGCGACACCTGCGAA                         AGGTTGTTGCGGCGACATCCATCGCCAGGCCTAGGGCGGATGTCGCCTACT
genomic: GAAGGCGACTAATCACGTGGAGTGCCCACCCAAGGAGCGACACCTGCGAAgtgcgttgat ... ggtgttgcagAGGTTGTTGCGGCGACATCCATCGCCAGGCCTAGGGCGGATGTCGCCTACT
EST: gi|21760018|gb|BQ635559.1|BQ635559
EST:     GAAGGCGACTAATCACGTGGAGTGCCCACCCAAGGAGCGACACCTGCGAA                         AGGTTGTTGCGGCGACATCCATCGCCAGGCCTAGGGCGGATGTCGCCTACT
genomic: GAAGGCGACTAATCACGTGGAGTGCCCACCCAAGGAGCGACACCTGCGAAgtgcgttgat ... ggtgttgcagAGGTTGTTGCGGCGACATCCATCGCCAGGCCTAGGGCGGATGTCGCCTACT
EST: gi|211095370|gb|FL067779.1|FL067779
EST:     GAAGGCGACTAATCACGTGGAGTGCCCACCCAAGGAGCGACACCTGCGAA                         AGGTTGTTGCGGCGACATCCATCGCCAGGCCTAGGGCGGATGTCGCCTACT
genomic: GAAGGCGACTAATCACGTGGAGTGCCCACCCAAGGAGCGACACCTGCGAAgtgcgttgat ... ggtgttgcagAGGTTGTTGCGGCGACATCCATCGCCAGGCCTAGGGCGGATGTCGCCTACT
EST: gi|211095362|gb|FL067771.1|FL067771
EST:     GAAGGCGACTAATCACGTGGAGTGCCCACCCAAGGAGCGACACCTGCGAA                         AGGTTGTTGCGGCGACATCCATCACCAGGCCTAGGGCGGATGTCGCCTACT
genomic: GAAGGCGACTAATCACGTGGAGTGCCCACCCAAGGAGCGACACCTGCGAAgtgcgttgat ... ggtgttgcagAGGTTGTTGCGGCGACATCCATCGCCAGGCCTAGGGCGGATGTCGCCTACT
EST: gi|211095368|gb|FL067777.1|FL067777
EST:     GAAGGCGACTAATCACGTGGAGTGCCCACCCAAGGAGCGACACCTGCGAA                         AGGTTGTTGCGGCGACATCCATCGCCAGGCCTAAGGGCG
genomic: GAAGGCGACTAATCACGTGGAGTGCCCACCCAAGGAGCGACACCTGCGAAgtgcgttgat ... ggtgttgcagAGGTTGTTGCGGCGACATCCATCGCCAGGCCTA-GGGCG
EST: gi|211092897|gb|FL067767.1|FL067767
EST:     GAAGGCGACTAATCACGTGGAGTGCCCACCCAAGGAGCGACACCTGCGAA                         AGGTTGTTGCGGCGACATCCATCGCCAGGCCTAGGGCGGATGTCGCCTACT
genomic: GAAGGCGACTAATCACGTGGAGTGCCCACCCAAGGAGCGACACCTGCGAAgtgcgttgat ... ggtgttgcagAGGTTGTTGCGGCGACATCCATCGCCAGGCCTAGGGCGGATGTCGCCTACT
EST: gi|211097835|gb|FL067786.1|FL067786
EST:     GAAGGCGACTAATCACGTGGAGTGCCCACCCAAGGAGCGACACCTGCGAA                         AGGTTGTTGCGGCGACATCCATCGCCAGGCCTAGGGCGGATGTCGCCTACT
genomic: GAAGGCGACTAATCACGTGGAGTGCCCACCCAAGGAGCGACACCTGCGAAgtgcgttgat ... ggtgttgcagAGGTTGTTGCGGCGACATCCATCGCCAGGCCTAGGGCGGATGTCGCCTACT
EST: gi|211095373|gb|FL067782.1|FL067782
EST:     GAAGGCGACTAATCACGTGGAGTGCCCACCCAAGGAGCGACACCTGCGAA                         AGGTTGTTGCGGCGACATCCATCGCCAGGCCTAGGGCGGATGTCGCCTACT
genomic: GAAGGCGACTAATCACGTGGAGTGCCCACCCAAGGAGCGACACCTGCGAAgtgcgttgat ... ggtgttgcagAGGTTGTTGCGGCGACATCCATCGCCAGGCCTAGGGCGGATGTCGCCTACT
EST: gi|211095375|gb|FL067784.1|FL067784
EST:     GAAGGCGACTAATCACGTGGAGTGCCCACCCAAGGAGCGACACCTGCGAA                         AGGTTGTTGCGGCGACATCCATCACCAGGCCTAGGGCGGATGTCGCCTACT
genomic: GAAGGCGACTAATCACGTGGAGTGCCCACCCAAGGAGCGACACCTGCGAAgtgcgttgat ... ggtgttgcagAGGTTGTTGCGGCGACATCCATCGCCAGGCCTAGGGCGGATGTCGCCTACT
EST: gi|9254928|gb|BE345396.1|BE345396
EST:     AAGGCGACTAATCACGTGGAGTGCCCACCCAAGGAGCGACACCTGCCGAA                         -GGTTGTTGCGGCGACATCCATCGCCAGGCCTAGGGCGGATGTCGCCTAC
genomic: AAGGCGACTAATCACGTGGAGTGCCCACCCAAGGAGCGACACCTGC-GAAgtgcgttgat ... ggtgttgcagAGGTTGTTGCGGCGACATCCATCGCCAGGCCTAGGGCGGATGTCGCCTAC
EST: gi|211097834|gb|FL067785.1|FL067785
EST:     GAAGGCGACTAATCACGTGGAGTGCCCACCCAAGGAGCGACACCTGCGAA                         AGGTTGTTGCGGCGACATCCATCGCCAGGCCTAGGGCGGATGTCGCCTACT
genomic: GAAGGCGACTAATCACGTGGAGTGCCCACCCAAGGAGCGACACCTGCGAAgtgcgttgat ... ggtgttgcagAGGTTGTTGCGGCGACATCCATCGCCAGGCCTAGGGCGGATGTCGCCTACT
EST: gi|211095371|gb|FL067780.1|FL067780
EST:     GAAGGCGACTAATCACGTGGAGTGCCCACCCAAGGAGCGACACCTGCGAA                         AGGTTGTTGCGGCGACATCCATCGCCAGGCCTAGGGCGGATGTCGCCTACT
genomic: GAAGGCGACTAATCACGTGGAGTGCCCACCCAAGGAGCGACACCTGCGAAgtgcgttgat ... ggtgttgcagAGGTTGTTGCGGCGACATCCATCGCCAGGCCTAGGGCGGATGTCGCCTACT
EST: gi|211092899|gb|FL067769.1|FL067769
EST:     GAAGGCGACTAATCACGTGGAGTGCCCACCCAAGGAGCGACACCTGCGAA                         AGGTTGTTGCGGCGACATCCATCACCAGGCCTAGGGCGGATGTCGCCTACT
genomic: GAAGGCGACTAATCACGTGGAGTGCCCACCCAAGGAGCGACACCTGCGAAgtgcgttgat ... ggtgttgcagAGGTTGTTGCGGCGACATCCATCGCCAGGCCTAGGGCGGATGTCGCCTACT
EST: gi|32823840|gb|CD963562.1|CD963562
EST:     GAAGGCGACTAATCACGTGGAGTGCCCACCCAAGGAGCGACACCTGCGAA                         AGGTTGTTGCGGCGACATCCATCGCCAGGCCTAGGGCGGATGTCGCCTACT
genomic: GAAGGCGACTAATCACGTGGAGTGCCCACCCAAGGAGCGACACCTGCGAAgtgcgttgat ... ggtgttgcagAGGTTGTTGCGGCGACATCCATCGCCAGGCCTAGGGCGGATGTCGCCTACT
EST: gi|211095369|gb|FL067778.1|FL067778
EST:     GAAGGCGACTAATCACGTGGAGTGCCCACCCAAGGAGCGACACCTGCGAA                         AGGTTGTTGCGGCGACATCCATCACCAGGCCTAGGGCGGATGTCGCCTACT
genomic: GAAGGCGACTAATCACGTGGAGTGCCCACCCAAGGAGCGACACCTGCGAAgtgcgttgat ... ggtgttgcagAGGTTGTTGCGGCGACATCCATCGCCAGGCCTAGGGCGGATGTCGCCTACT
EST: gi|211095366|gb|FL067775.1|FL067775
EST:     GAAGGCGACTAATCACGTGGAGTGCCCACCCAAGGAGCGACACCTGCGAA                         AGGTTGTTGCGGCGACATCCATCGCCAGGCCTAGGGCGGATGTCGCCTACT
genomic: GAAGGCGACTAATCACGTGGAGTGCCCACCCAAGGAGCGACACCTGCGAAgtgcgttgat ... ggtgttgcagAGGTTGTTGCGGCGACATCCATCGCCAGGCCTAGGGCGGATGTCGCCTACT

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: 47 (upstream exon), 48 (downstream exon)
Score: 238

GATCTGGATGTGGCGATCGTGAAGGCGACTAATCACGTGGAGTGCCCACCCAAGGAGCGACACCTGCGAAgtgcgttgat ... ggtgttgcagAGGTTGTTGCGGCGACATCCATCGCCAGGCCTAGGGCGGATGTCGCCTACTGCATCCACGCGCTTGCCCGCCGTCTTGCCAAGACCCGCAACTGGATT


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 177

GATCTGGATGTGGCGATCGTGAAGGCGACTAATCACGTGGAGTGCCCACCCAAGGAGCGACACCTGCGAAgtgcgttgat ... ggtgttgcagAGGTTGTTGCGGCGACATCCATCGCCAGGCCTAGGGCGGATGTCGCCTACTGCATCCACGCGCTTGCCCGCCGTCTTGCCAAGACCCGCAACTGGATT


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 210

GATCTGGATGTGGCGATCGTGAAGGCGACTAATCACGTGGAGTGCCCACCCAAGGAGCGACACCTGCGAAgtgcgttgat ... ggtgttgcagAGGTTGTTGCGGCGACATCCATCGCCAGGCCTAGGGCGGATGTCGCCTACTGCATCCACGCGCTTGCCCGCCGTCTTGCCAAGACCCGCAACTGGATT


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 151

GATCTGGATGTGGCGATCGTGAAGGCGACTAATCACGTGGAGTGCCCACCCAAGGAGCGACACCTGCGAAgtgcgttgat ... ggtgttgcagAGGTTGTTGCGGCGACATCCATCGCCAGGCCTAGGGCGGATGTCGCCTACTGCATCCACGCGCTTGCCCGCCGTCTTGCCAAGACCCGCAACTGGATT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttttaggtttcgtgcgtatttgatgatggttgattggtgtgtggtggtgttgcagAGGTTGTTGCGGCGACATCCATCGCCAGGCCTAGGGCGGATGTCGCCTACTGCATCCACGCGCTTGCCCGCCGTCTTGCCAAGACCCGCAACTGGATT
                           ggttgat  putative branch site (score: 151)
                tatttgat  TA-rich tract