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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...catggtgttggactgttggttgatattgcagttttcatatcactacattgtgctagaacaccttttagttacttgaacatctgttttgtccatggcgcagTCGAGGCAAAAGGCACTGGGGGACCTTCAAAGCCTACAGAACGACAAG

Basic information

species Zea mays
transcript GRMZM2G006428_T02
intron # 10
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|76281609|gb|DV021177.1|DV021177
EST:     CGCTTGAGAGATATACACATTATTATGAACGATGGGCAGCCAATCAGTCG                         TCGAGGCAAA-GGCACTGGGG
genomic: CGCTTGAGAGATATACACATTATTATGAACGATGGGCAGCCAATCAGTCGgtaagtattg ... catggcgcagTCGAGGCAAAAGGCACTGGGG
EST: gi|211292139|gb|FL375498.1|FL375498
EST:     CGCTTGAGAGATATACACATTATTATGAACGATGGGCAGCCAATCAGTCG                         TCGAGGCAAAAGGCACTGGNGGGACCTTCAAAGCCTACAGAACGACAAG
genomic: CGCTTGAGAGATATACACATTATTATGAACGATGGGCAGCCAATCAGTCGgtaagtattg ... catggcgcagTCGAGGCAAAAGGCACTGG-GGGACCTTCAAAGCCTACAGAACGACAAG
EST: gi|78080365|gb|DV508777.1|DV508777
EST:     CGCTTGAGAGATATACACATTATTATGAACGATGGGCAGCCAATCAGTCG                         TCGAGGCAAAAGGCACTGGGGGACCTTCAAAGCCTACAGAACGACAAG
genomic: CGCTTGAGAGATATACACATTATTATGAACGATGGGCAGCCAATCAGTCGgtaagtattg ... catggcgcagTCGAGGCAAAAGGCACTGGGGGACCTTCAAAGCCTACAGAACGACAAG

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), 48 (downstream exon)
Score: 327

TATGATGAATCTGAAAGGAGAAGAGAAATGGCAAAGAACTCGCTTGAGAGATATACACATTATTATGAACGATGGGCAGCCAATCAGTCGgtaagtattg ... catggcgcagTCGAGGCAAAAGGCACTGGGGGACCTTCAAAGCCTACAGAACGACAAG


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 306

TATGATGAATCTGAAAGGAGAAGAGAAATGGCAAAGAACTCGCTTGAGAGATATACACATTATTATGAACGATGGGCAGCCAATCAGTCGgtaagtattg ... catggcgcagTCGAGGCAAAAGGCACTGGGGGACCTTCAAAGCCTACAGAACGACAAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 323

TATGATGAATCTGAAAGGAGAAGAGAAATGGCAAAGAACTCGCTTGAGAGATATACACATTATTATGAACGATGGGCAGCCAATCAGTCGgtaagtattg ... catggcgcagTCGAGGCAAAAGGCACTGGGGGACCTTCAAAGCCTACAGAACGACAAG


Block sizes: 47 (upstream exon), 48 (downstream exon)
Score: 221

TATGATGAATCTGAAAGGAGAAGAGAAATGGCAAAGAACTCGCTTGAGAGATATACACATTATTATGAACGATGGGCAGCCAATCAGTCGgtaagtattg ... catggcgcagTCGAGGCAAAAGGCACTGGGGGACCTTCAAAGCCTACAGAACGACAAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cattgtgctagaacaccttttagttacttgaacatctgttttgtccatggcgcagTCGAGGCAAAAGGCACTGGGGGACCTTCAAAGCCTACAGAACGACAAG
                                      ttttgtcc  CT-rich tract
                 ttttagtta  TA-rich tract