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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATACCGTTGGTATTCTTGACAAGATATCTCCATGCTACGTTCAAGCATGTAATGgtacgctgtgtcaattatgtcctttttttcccattacctcttgccactacctaaccatcatcttcttatttggcag

Basic information

species Zea mays
transcript GRMZM2G169089_T01
intron # 15
splice site 5'
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|18164197|gb|BM334036.1|BM334036
EST:     CGTTGGTATTCTTGACAAGATATCTCCATGCTACGTTCAAGCATGTAATG                         GTGGGCAACATGATATTTTGGTTCTTCAGTATAGTCGGACAGCCGATGTGT
genomic: CGTTGGTATTCTTGACAAGATATCTCCATGCTACGTTCAAGCATGTAATGgtacgctgtg ... tatttggcagGTGGGCAACATGATATTTTGGTTCTTCAGTATAGTCGGACAGCCGATGTGT
EST: gi|17931277|gb|BM268237.1|BM268237
EST:     CGTTGGTATTCTTGACAAGATATCTCCATGCTACGTTCAAGCATGTAATG                         GTGGGCAACATGATATTTTGGTTCTTCAGTATAGTCGGACAAGCCGATGTG
genomic: CGTTGGTATTCTTGACAAGATATCTCCATGCTACGTTCAAGCATGTAATGgtacgctgtg ... tatttggcagGTGGGCAACATGATATTTTGGTTCTTCAGTATAGTCGGAC-AGCCGATGTG
EST: gi|17930011|gb|BM266971.1|BM266971
EST:     CGTTGGTATTCTTGACAAGATATCTCCATGCTACGTTCAAGCATGTAATG                         GTGGGCAACATGATATTTTGGTTCTTCAGTATAGTCGGACAGCCGATGTGT
genomic: CGTTGGTATTCTTGACAAGATATCTCCATGCTACGTTCAAGCATGTAATGgtacgctgtg ... tatttggcagGTGGGCAACATGATATTTTGGTTCTTCAGTATAGTCGGACAGCCGATGTGT
EST: gi|18165097|gb|BM334936.1|BM334936
EST:     CGTTGGTATTCTTGACAAGATATCTCCATGCTACGTTCAAGCATGTAATG                         GTGGGCAACATGATATTTTGGTTCTTCAGTATAGTCGGACAGCCGATGTGT
genomic: CGTTGGTATTCTTGACAAGATATCTCCATGCTACGTTCAAGCATGTAATGgtacgctgtg ... tatttggcagGTGGGCAACATGATATTTTGGTTCTTCAGTATAGTCGGACAGCCGATGTGT
EST: gi|32929949|gb|CF034761.1|CF034761
EST:     CGGTGGTATTCTTGACAAGATATCTCCATGCTACGTTCAAGCATGTAATG                         GTGGGCAACATGATATTTTGGTTCTTCAGTATAGTCGGACAGCCGATGTGT
genomic: CGTTGGTATTCTTGACAAGATATCTCCATGCTACGTTCAAGCATGTAATGgtacgctgtg ... tatttggcagGTGGGCAACATGATATTTTGGTTCTTCAGTATAGTCGGACAGCCGATGTGT
EST: gi|18172967|gb|BM348355.1|BM348355
EST:     CGTTGGTATTCTTGACAAGATATCTCCATGCTACGTTCAAGCATGTAATG                         GTGGGCAACATGATATTTTGGTTCTTCAGTATAGTCGGACAGCCGATGTGT
genomic: CGTTGGTATTCTTGACAAGATATCTCCATGCTACGTTCAAGCATGTAATGgtacgctgtg ... tatttggcagGTGGGCAACATGATATTTTGGTTCTTCAGTATAGTCGGACAGCCGATGTGT
EST: gi|113703224|gb|EE680728.1|EE680728
EST:     CGTTGGTATTCTTGACAAGATATCTCCATGCTACGTTCAAGCATGTAATG                         GTGGGCAACATGATATTTTGGTTCTTCAGTATAGTCGGACAGCCGATGTGT
genomic: CGTTGGTATTCTTGACAAGATATCTCCATGCTACGTTCAAGCATGTAATGgtacgctgtg ... tatttggcagGTGGGCAACATGATATTTTGGTTCTTCAGTATAGTCGGACAGCCGATGTGT
EST: gi|261490382|gb|GO359873.1|GO359873
EST:     CGTTGGTATTCTTGACAAGATATCTCCATGCTACGTTCAAGCATGTAATG                         GTGGGCAACATGATATTTTGGTTCTTCAGTATAGTCGGACAGCCGATGTGT
genomic: CGTTGGTATTCTTGACAAGATATCTCCATGCTACGTTCAAGCATGTAATGgtacgctgtg ... tatttggcagGTGGGCAACATGATATTTTGGTTCTTCAGTATAGTCGGACAGCCGATGTGT
EST: gi|18168645|gb|BM338485.1|BM338485
EST:     CGTTGGTATTCTTGACAAGATATCTCCATGCTACGTTCAAGCATGTAATG                         GTGGGCAACATGATATTTTGGTTCTTCAGTATAGTCGGACAGCCGATGTGT
genomic: CGTTGGTATTCTTGACAAGATATCTCCATGCTACGTTCAAGCATGTAATGgtacgctgtg ... tatttggcagGTGGGCAACATGATATTTTGGTTCTTCAGTATAGTCGGACAGCCGATGTGT
EST: gi|18171503|gb|BM341343.1|BM341343
EST:     CGTTGGTATTCTTGACAAGATATCTCCATGCTACGTTCAAGCATGTAATG                         GTGGGCAACATGATATTTTGGTTCTTCAGTATAGTCGGACAGNCCGATGTG
genomic: CGTTGGTATTCTTGACAAGATATCTCCATGCTACGTTCAAGCATGTAATGgtacgctgtg ... tatttggcagGTGGGCAACATGATATTTTGGTTCTTCAGTATAGTCGGACAG-CCGATGTG
EST: gi|18166786|gb|BM336625.1|BM336625
EST:     CGTTGGTATTCTTGACAGGATATCTCCATGGTACGTTCAAGCATGTAATG                         GTGGGCAACATAATATTTTGGTTCTTCAGTATAGTCGGACAGCCGATGTGT
genomic: CGTTGGTATTCTTGACAAGATATCTCCATGCTACGTTCAAGCATGTAATGgtacgctgtg ... tatttggcagGTGGGCAACATGATATTTTGGTTCTTCAGTATAGTCGGACAGCCGATGTGT
EST: gi|18171057|gb|BM340897.1|BM340897
EST:     CGTTGGTATTCTTGACAAGATATCTCCATGCTACGTTCAAGCATGTAATG                         GTGGGCAACATGATATTTTGGTTCTTCAGTATAGTCGGACAGCCGATGTGT
genomic: CGTTGGTATTCTTGACAAGATATCTCCATGCTACGTTCAAGCATGTAATGgtacgctgtg ... tatttggcagGTGGGCAACATGATATTTTGGTTCTTCAGTATAGTCGGACAGCCGATGTGT
EST: gi|18162243|gb|BM332082.1|BM332082
EST:     CGTTGGTATTCTTGACAAGATATCTCCATGCTACGTTCAAGCATGTAATG                         GTGGGCAACATGATATTTTGGTTCTTCAGTATAGTCGGACAGGCCGATGTG
genomic: CGTTGGTATTCTTGACAAGATATCTCCATGCTACGTTCAAGCATGTAATGgtacgctgtg ... tatttggcagGTGGGCAACATGATATTTTGGTTCTTCAGTATAGTCGGACA-GCCGATGTG
EST: gi|17929613|gb|BM266573.1|BM266573
EST:     CGTTGGTATTCTTGACAAGATATCTCCATGCTACGTTCAAGCATGTAATG                         GTGGGCAACATGATATTTTGGTTCTTCAGTATAGTCGGACAGCCGATGTGT
genomic: CGTTGGTATTCTTGACAAGATATCTCCATGCTACGTTCAAGCATGTAATGgtacgctgtg ... tatttggcagGTGGGCAACATGATATTTTGGTTCTTCAGTATAGTCGGACAGCCGATGTGT
EST: gi|18167925|gb|BM337765.1|BM337765
EST:     GTTGGTATTCTTGACAAGATATCTCCATGGTACGTTCAAGCATGTAATG                         GTGGGCAACATGATATTTTGGTTCTTCAGTATAGTCGGACAGCCGATGTGT
genomic: GTTGGTATTCTTGACAAGATATCTCCATGCTACGTTCAAGCATGTAATGgtacgctgtg ... tatttggcagGTGGGCAACATGATATTTTGGTTCTTCAGTATAGTCGGACAGCCGATGTGT
EST: gi|16921179|gb|BM075023.1|BM075023
EST:     CGTTGGTATTCTTGACAAGATATCTCCATGCTACGTTCAAGCATGTAATG                         GTGGGCAACATGATATTTTGGTTCTTCAGTATAGTCGGACAGCCGATGTGT
genomic: CGTTGGTATTCTTGACAAGATATCTCCATGCTACGTTCAAGCATGTAATGgtacgctgtg ... tatttggcagGTGGGCAACATGATATTTTGGTTCTTCAGTATAGTCGGACAGCCGATGTGT
EST: gi|16921463|gb|BM075161.1|BM075161
EST:     CGTTGGTATTCTTGACAAGATATCTCCATGCTACGTTCAAGCATGTAATG                         GTGGGCAACATGATATTTTGGTTCTTCAGTATAGTCGGACAGCCGATGTGT
genomic: CGTTGGTATTCTTGACAAGATATCTCCATGCTACGTTCAAGCATGTAATGgtacgctgtg ... tatttggcagGTGGGCAACATGATATTTTGGTTCTTCAGTATAGTCGGACAGCCGATGTGT
EST: gi|18166090|gb|BM335929.1|BM335929
EST:     CGTTGGTATTCTTGACAAGATATCTCCATGCTACGTTCAAGCATGTAATG                         GTGGGCAACATGATATTTTGGTTCTTCAGTATAGTCGGACAGCCGATGTGT
genomic: CGTTGGTATTCTTGACAAGATATCTCCATGCTACGTTCAAGCATGTAATGgtacgctgtg ... tatttggcagGTGGGCAACATGATATTTTGGTTCTTCAGTATAGTCGGACAGCCGATGTGT
EST: gi|18167616|gb|BM337456.1|BM337456
EST:     CGTTGGTATTCTTGACAAGATATCTCCATGCTACGTTCAAGCATGTAATG                         GTGGGCAACATGATATTTTGGTTCTTCAGTATAGTCGGACAGCGCGATGTG
genomic: CGTTGGTATTCTTGACAAGATATCTCCATGCTACGTTCAAGCATGTAATGgtacgctgtg ... tatttggcagGTGGGCAACATGATATTTTGGTTCTTCAGTATAGTCGGACAGC-CGATGTG
EST: gi|17930787|gb|BM267747.1|BM267747
EST:     CGTTGGTATTCTTGACAAGATATCTCCATGCTACGTTCAAGCATGTAATG                         GTGGGCAACATGATATTTTGGTTCTTCAGTATAGTCGGACAGCCGATGTGT
genomic: CGTTGGTATTCTTGACAAGATATCTCCATGCTACGTTCAAGCATGTAATGgtacgctgtg ... tatttggcagGTGGGCAACATGATATTTTGGTTCTTCAGTATAGTCGGACAGCCGATGTGT
EST: gi|18166675|gb|BM336514.1|BM336514
EST:     CGTTGGTATTCTTGACAAGATATCTCCATGCTACGTTCAAGCATGTAATG                         GTGGGCAACATAATATTTTGGTTCTTCAGTATAGTCGGACAGCCGATGTGT
genomic: CGTTGGTATTCTTGACAAGATATCTCCATGCTACGTTCAAGCATGTAATGgtacgctgtg ... tatttggcagGTGGGCAACATGATATTTTGGTTCTTCAGTATAGTCGGACAGCCGATGTGT

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), 47 (downstream exon)
Score: 26

ATACCGTTGGTATTCTTGACAAGATATCTCCATGCTACGTTCAAGCATGTAATGgtacgctgtg ... tatttggcagGTGGGCAACATGATATTTTGGTTCTTCAGTATAGTCGGACAGCCGATGTGTGTCCTTCTATACTACCATGACGTCATGAACAGGCAGGCCCAGGCAAGTA


Block sizes: 39 (upstream exon), 43 (downstream exon)
Score: 17

ATACCGTTGGTATTCTTGACAAGATATCTCCATGCTACGTTCAAGCATGTAATGgtacgctgtg ... tatttggcagGTGGGCAACATGATATTTTGGTTCTTCAGTATAGTCGGACAGCCGATGTGTGTCCTTCTATACTACCATGACGTCATGAACAGGCAGGCCCAGGCAAGTA


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 19

ATACCGTTGGTATTCTTGACAAGATATCTCCATGCTACGTTCAAGCATGTAATGgtacgctgtg ... tatttggcagGTGGGCAACATGATATTTTGGTTCTTCAGTATAGTCGGACAGCCGATGTGTGTCCTTCTATACTACCATGACGTCATGAACAGGCAGGCCCAGGCAAGTA


Block sizes: 47 (upstream exon), 48 (downstream exon)
Score: 15

ATACCGTTGGTATTCTTGACAAGATATCTCCATGCTACGTTCAAGCATGTAATGgtacgctgtg ... tatttggcagGTGGGCAACATGATATTTTGGTTCTTCAGTATAGTCGGACAGCCGATGTGTGTCCTTCTATACTACCATGACGTCATGAACAGGCAGGCCCAGGCAAGTA