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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtctgctagcgctagctagctagagtttctgcgtttcatacctctgtttagctagctctgaactccagttaatctgcccttgacactgcatgcagACGGATCCACAGAGGGTGTGCAGCCAGGTTGGTCTGTGCGTGTTCGATGGCGCTCGATCTGTCAG

Basic information

species Zea mays
transcript GRMZM2G123029_T02
intron # 3
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|149100422|gb|EE186497.2|EE186497
EST:     AAGTTGTGAGCCAGTACGGAGAGATGATCCTCGACATGCTCATCGCACAG                         ACGGATCCACAGAGGGTGTGCAGCCAGGTTGGTCTGTGCGTGTTCGATGGC
genomic: AAGTTGTGAGCCAGTACGGAGAGATGATCCTCGACATGCTCATCGCACAGgtctgctagc ... ctgcatgcagACGGATCCACAGAGGGTGTGCAGCCAGGTTGGTCTGTGCGTGTTCGATGGC
EST: gi|149078277|gb|EE167036.2|EE167036
EST:     ATGCTCATGGCACAG                         ACGGATCCACAGAGGGGGTGCAGCCAGGTTGGTCTGTGGGTGTTTGATGGC
genomic: ATGCTCATCGCACAGgtctgctagc ... ctgcatgcagACGGATCCACAGAGGGTGTGCAGCCAGGTTGGTCTGTGCGTGTTCGATGGC
EST: gi|6827002|gb|AW330645.1|AW330645
EST:     AAGTTGTGAGCCAGTACGGAGAGATGATCCTCGACATGCTCATCGCACAG                         ACGGATCCACAGAGGGTGTGCAGCCAGGTTGGTCTGTGCGTGTTCGATGGC
genomic: AAGTTGTGAGCCAGTACGGAGAGATGATCCTCGACATGCTCATCGCACAGgtctgctagc ... ctgcatgcagACGGATCCACAGAGGGTGTGCAGCCAGGTTGGTCTGTGCGTGTTCGATGGC
EST: gi|110520668|gb|EE024852.1|EE024852
EST:     AAGTTGTGAGCCAGTACGGAGAGATGATCCTCGACATGCTCATCGCACAG                         ACGGATCCACAGAGGGTGTGCAGCCAGGTTGGTCTGTGCGTGTTCGATGGC
genomic: AAGTTGTGAGCCAGTACGGAGAGATGATCCTCGACATGCTCATCGCACAGgtctgctagc ... ctgcatgcagACGGATCCACAGAGGGTGTGCAGCCAGGTTGGTCTGTGCGTGTTCGATGGC
EST: gi|32844397|gb|CD984078.1|CD984078
EST:     TACGGAGAGATGATCCTCGACATGCTCATCGCACAG                         ACGGATCCACAGAGGGTGTGCAGCCAGGTTGGTCTGTGCGTGTTCGATGGC
genomic: TACGGAGAGATGATCCTCGACATGCTCATCGCACAGgtctgctagc ... ctgcatgcagACGGATCCACAGAGGGTGTGCAGCCAGGTTGGTCTGTGCGTGTTCGATGGC
EST: gi|32923207|gb|CF028019.1|CF028019
EST:     ACGGAGAGATGATCCTCGACATGCTCATCGCACAG                         ACGGATCCACAGAGGGTGTGCAGCCAGGTTGGTCTGTGCGTGTTCGATGGC
genomic: ACGGAGAGATGATCCTCGACATGCTCATCGCACAGgtctgctagc ... ctgcatgcagACGGATCCACAGAGGGTGTGCAGCCAGGTTGGTCTGTGCGTGTTCGATGGC
EST: gi|32844224|gb|CD983905.1|CD983905
EST:     ACGGAGAGATGATCCTCGACATGCTCATCGCACAG                         ACGGATCCACAGAGGGCGTGCAGCCAGGTTGGTCTGTGCGTGTTCGATGGC
genomic: ACGGAGAGATGATCCTCGACATGCTCATCGCACAGgtctgctagc ... ctgcatgcagACGGATCCACAGAGGGTGTGCAGCCAGGTTGGTCTGTGCGTGTTCGATGGC
EST: gi|32845458|gb|CD985139.1|CD985139
EST:     ACGGAGAGATGATCCTCGACATGCTCATCGCACAG                         ACGGATCCACAGAGGGTGTGCAGCCAGGTTGGTCTGTGCGTGTTCGATGGC
genomic: ACGGAGAGATGATCCTCGACATGCTCATCGCACAGgtctgctagc ... ctgcatgcagACGGATCCACAGAGGGTGTGCAGCCAGGTTGGTCTGTGCGTGTTCGATGGC
EST: gi|32844408|gb|CD984089.1|CD984089
EST:     ACGGAGAGATGATCCTCGACATGCTCATCGCACAG                         ACGGATCCACAGAGGGTGTGCAGCCAGGTTGGTCTGTGCGTGTTCGATGGC
genomic: ACGGAGAGATGATCCTCGACATGCTCATCGCACAGgtctgctagc ... ctgcatgcagACGGATCCACAGAGGGTGTGCAGCCAGGTTGGTCTGTGCGTGTTCGATGGC
EST: gi|148987680|gb|EE031561.2|EE031561
EST:     AAGTTTTGAGCCAGTACGGAGAGATGATCCTCGACATGCTCATCGCACAG                         ACGGATCCACAGAGGGTGTGCAGCCAGGTTGGTCTGTGCGTGTTCGATGGC
genomic: AAGTTGTGAGCCAGTACGGAGAGATGATCCTCGACATGCTCATCGCACAGgtctgctagc ... ctgcatgcagACGGATCCACAGAGGGTGTGCAGCCAGGTTGGTCTGTGCGTGTTCGATGGC

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: 48 (upstream exon), 48 (downstream exon)
Score: 194

GGTGAACGAAGCGATCGGGGCAGACGGGATCATCAGCACGGAGTGCAAGGAAGTTGTGAGCCAGTACGGAGAGATGATCCTCGACATGCTCATCGCACAGgtctgctagc ... ctgcatgcagACGGATCCACAGAGGGTGTGCAGCCAGGTTGGTCTGTGCGTGTTCGATGGCGCTCGATCTGTCAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 1813

GGTGAACGAAGCGATCGGGGCAGACGGGATCATCAGCACGGAGTGCAAGGAAGTTGTGAGCCAGTACGGAGAGATGATCCTCGACATGCTCATCGCACAGgtctgctagc ... ctgcatgcagACGGATCCACAGAGGGTGTGCAGCCAGGTTGGTCTGTGCGTGTTCGATGGCGCTCGATCTGTCAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 1382

GGTGAACGAAGCGATCGGGGCAGACGGGATCATCAGCACGGAGTGCAAGGAAGTTGTGAGCCAGTACGGAGAGATGATCCTCGACATGCTCATCGCACAGgtctgctagc ... ctgcatgcagACGGATCCACAGAGGGTGTGCAGCCAGGTTGGTCTGTGCGTGTTCGATGGCGCTCGATCTGTCAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 2207

GGTGAACGAAGCGATCGGGGCAGACGGGATCATCAGCACGGAGTGCAAGGAAGTTGTGAGCCAGTACGGAGAGATGATCCTCGACATGCTCATCGCACAGgtctgctagc ... ctgcatgcagACGGATCCACAGAGGGTGTGCAGCCAGGTTGGTCTGTGCGTGTTCGATGGCGCTCGATCTGTCAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cctctgtttagctagctctgaactccagttaatctgcccttgacactgcatgcagACGGATCCACAGAGGGTGTGCAGCCAGGTTGGTCTGTGCGTGTTCGATGGCGCTCGATCTGTCAG
                                     ccttgac  putative branch site (score: 2207)
                          agttaat  TA-rich tract