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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagttagtgttctatcaaaatctctgtttatcaagctaatggtgaaacgagcatatattgaacttacgattttccaaaaaacacttatttgcagGTTCCTCGTGGTTCTGGTGGTTCACGTGAGTACATGGGAAGAGGACCTCCACCAGGAACAGGTCGTTGTTTTAACTGTGGAATGGATGGTCACTGGGCAA

Basic information

species Zea mays
transcript GRMZM2G099186_T03
intron # 5
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|6431785|gb|AW171989.1|AW171989
EST:     ATGGCAGGGAAGTCGATGGAAGCCGTATTATTGTTGAATTTGCTAAAGGA                         GTTCCTCGTGGTTCTGGTGGTTCACGTGAGTACATGGGAAGAGGACCTCCA
genomic: ATGGCAGGGAAGTCGATGGAAGCCGTATTATTGTTGAATTTGCTAAAGGAgtaagttagt ... ttatttgcagGTTCCTCGTGGTTCTGGTGGTTCACGTGAGTACATGGGAAGAGGACCTCCA
EST: gi|19057891|gb|BM736558.1|BM736558
EST:     ATGGCAGGGAAGTCGATGGAAGCCGTATTATTGGTGAATTTGCTAAAGGA                         GTTCCTCGTGGTTCTGGTGGTTCACGTGAGTACATGGGAAGAGGACCTCCA
genomic: ATGGCAGGGAAGTCGATGGAAGCCGTATTATTGTTGAATTTGCTAAAGGAgtaagttagt ... ttatttgcagGTTCCTCGTGGTTCTGGTGGTTCACGTGAGTACATGGGAAGAGGACCTCCA
EST: gi|71309062|gb|DR790796.1|DR790796
EST:     ATGGCAGGGAAGTCGATGGAAGCCGTATTATTGTTGAATTTGCTAAAGGA                         GTTCCTCGTGGTTCTGGTGGTTCACGTGAGTACATGGGAAGAGGACCTCCA
genomic: ATGGCAGGGAAGTCGATGGAAGCCGTATTATTGTTGAATTTGCTAAAGGAgtaagttagt ... ttatttgcagGTTCCTCGTGGTTCTGGTGGTTCACGTGAGTACATGGGAAGAGGACCTCCA
EST: gi|31351638|gb|CD435995.1|CD435995
EST:     ATGGCAGGGAAGTCGATGGAAGCCGTATTATTGTTGAATTTGCTAAAGGA                         GTTCCTCGTGGTTCTGGTGGTTCACGTGAGTACATGGGAAGAGGACCTCCA
genomic: ATGGCAGGGAAGTCGATGGAAGCCGTATTATTGTTGAATTTGCTAAAGGAgtaagttagt ... ttatttgcagGTTCCTCGTGGTTCTGGTGGTTCACGTGAGTACATGGGAAGAGGACCTCCA
EST: gi|32835126|gb|CD974804.1|CD974804
EST:     ATGGCAGGGAAGTCGATGGAAGCCGTATTATTGTTGAATTTGCTAAAGGA                         GTTCCTCGTGGTTCTGGTGGTTCACGTGAGT
genomic: ATGGCAGGGAAGTCGATGGAAGCCGTATTATTGTTGAATTTGCTAAAGGAgtaagttagt ... ttatttgcagGTTCCTCGTGGTTCTGGTGGTTCACGTGAGT

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: 40 (upstream exon), 40 (downstream exon)
Score: 42

GAATTCAGTGACCCCCGTGATGCTGATGATGCGCAGTACAACCTAGATGGCAGGGAAGTCGATGGAAGCCGTATTATTGTTGAATTTGCTAAAGGAgtaagttagt ... ttatttgcagGTTCCTCGTGGTTCTGGTGGTTCACGTGAGTACATGGGAAGAGGACCTCCACCAGGAACAGGTCGTTGTTTTAACTGTGGAATGGATGGTCACTGGGCAA


Block sizes: 40 (upstream exon), 49 (downstream exon)
Score: 88

GAATTCAGTGACCCCCGTGATGCTGATGATGCGCAGTACAACCTAGATGGCAGGGAAGTCGATGGAAGCCGTATTATTGTTGAATTTGCTAAAGGAgtaagttagt ... ttatttgcagGTTCCTCGTGGTTCTGGTGGTTCACGTGAGTACATGGGAAGAGGACCTCCACCAGGAACAGGTCGTTGTTTTAACTGTGGAATGGATGGTCACTGGGCAA


Block sizes: 40 (upstream exon), 49 (downstream exon)
Score: 95

GAATTCAGTGACCCCCGTGATGCTGATGATGCGCAGTACAACCTAGATGGCAGGGAAGTCGATGGAAGCCGTATTATTGTTGAATTTGCTAAAGGAgtaagttagt ... ttatttgcagGTTCCTCGTGGTTCTGGTGGTTCACGTGAGTACATGGGAAGAGGACCTCCACCAGGAACAGGTCGTTGTTTTAACTGTGGAATGGATGGTCACTGGGCAA


Block sizes: 40 (upstream exon), 47 (downstream exon)
Score: 59

GAATTCAGTGACCCCCGTGATGCTGATGATGCGCAGTACAACCTAGATGGCAGGGAAGTCGATGGAAGCCGTATTATTGTTGAATTTGCTAAAGGAgtaagttagt ... ttatttgcagGTTCCTCGTGGTTCTGGTGGTTCACGTGAGTACATGGGAAGAGGACCTCCACCAGGAACAGGTCGTTGTTTTAACTGTGGAATGGATGGTCACTGGGCAA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tggtgaaacgagcatatattgaacttacgattttccaaaaaacacttatttgcagGTTCCTCGTGGTTCTGGTGGTTCACGTGAGTACATGGGAAGAGGACCTCCACCAGGAACAGGTCGTTGTTTTAACTGTGGAATGGATGGTCACTGGGCAA
                     aacttac  putative branch site (score: 59)
                                            cttattt  putative PPT
                                    aaaaaacacttattt  TA-rich tract