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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttcttccattttttaagctgtaatgagatcatttctgattgttgttgttgtttgccgcttacgccgtatatattctctctttcagGTTATGGCAGTAACTAGAAGTACAATCTGCAAAAAAGGAATAGAGTCCCTTCCCAGGGGAGGTGCCATCATCTATTATGTCTGTGTTTTCCTGTACTTCT

Basic information

species Zea mays
transcript GRMZM2G018356_T02
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G018356_T02 (Zea mays), 3'ss of exon 10
lower sequence: LOC_Os07g04210.1 (Oryza sativa), 3'ss of exon 14
gttcttccatttttta-agctgtaatgagatc---atttctgattgttgttgttgtttgccgcttacgccgtatatattctctctttcagGTTATGGCAGTAACTAGAAGTACAATCTGCAAAAAAGGAATAGAGTCCCTTCCCAGGGGAGGTGCCATCATCTATTATGTCTGTGTTTTCCTGTACTTCT
        ||| || | |  | ||     |||   |||||||| |     |    ||| |  |    |   | ||||||  || ||||||||||||||||| || || || |||||||||| |||||||||||||||||||||  | ||||| || |||||||| ||||| || || ||||||||||| |
-----gttattcttcataaatataccagaatcgctatttctgagttcctgtaccattttcaaccc-tgtaatgtatatttgctatttcagGTTATGGCAGTTACGAGGAGCACAATCTGCAGAAAAGGAATAGAGTCCCTTCCTCGAGGAGGAGCGATCATCTACTATGTTTGCGTCTTCCTGTACTTTT
















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|211277902|gb|FL449020.1|FL449020
EST:     TTT-CCCTGCATGTA-TAAGTACCTCATGTCTGCATTCGACATCCCAGAG                         GTTATGGCAGTAACTAGAAGTACAATCTGCAAAAAAGGAATAGAGTCCCTT
genomic: TTTACCCTGCATGTATTAAGTACCTCATGTCTGCATTCGACATCCCAGAGgttcttccat ... tctctttcagGTTATGGCAGTAACTAGAAGTACAATCTGCAAAAAAGGAATAGAGTCCCTT
EST: gi|67013703|gb|CO442452.1|CO442452
EST:     TTTACCCTGCATGTATTAAGTACCTCATGTCTGCATTCGACATCCCAGAG                         GTTATGGCAGTAACTAGAAGTACAATCTGCAAAAAAGGAATAGAGTCCCTT
genomic: TTTACCCTGCATGTATTAAGTACCTCATGTCTGCATTCGACATCCCAGAGgttcttccat ... tctctttcagGTTATGGCAGTAACTAGAAGTACAATCTGCAAAAAAGGAATAGAGTCCCTT

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: 42 (upstream exon), 49 (downstream exon)
Score: 34

TCCTGATCCCACAGGACTTCGCGCTCGTCTCGAGCATTGGACCTTTGGACTTTACCCTGCATGTATTAAGTACCTCATGTCTGCATTCGACATCCCAGAGgttcttccat ... tctctttcagGTTATGGCAGTAACTAGAAGTACAATCTGCAAAAAAGGAATAGAGTCCCTTCCCAGGGGAGGTGCCATCATCTATTATGTCTGTGTTTTCCTGTACTTCT


Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 78

TCCTGATCCCACAGGACTTCGCGCTCGTCTCGAGCATTGGACCTTTGGACTTTACCCTGCATGTATTAAGTACCTCATGTCTGCATTCGACATCCCAGAGgttcttccat ... tctctttcagGTTATGGCAGTAACTAGAAGTACAATCTGCAAAAAAGGAATAGAGTCCCTTCCCAGGGGAGGTGCCATCATCTATTATGTCTGTGTTTTCCTGTACTTCT


Block sizes: 45 (upstream exon), 49 (downstream exon)
Score: 87

TCCTGATCCCACAGGACTTCGCGCTCGTCTCGAGCATTGGACCTTTGGACTTTACCCTGCATGTATTAAGTACCTCATGTCTGCATTCGACATCCCAGAGgttcttccat ... tctctttcagGTTATGGCAGTAACTAGAAGTACAATCTGCAAAAAAGGAATAGAGTCCCTTCCCAGGGGAGGTGCCATCATCTATTATGTCTGTGTTTTCCTGTACTTCT


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 37

TCCTGATCCCACAGGACTTCGCGCTCGTCTCGAGCATTGGACCTTTGGACTTTACCCTGCATGTATTAAGTACCTCATGTCTGCATTCGACATCCCAGAGgttcttccat ... tctctttcagGTTATGGCAGTAACTAGAAGTACAATCTGCAAAAAAGGAATAGAGTCCCTTCCCAGGGGAGGTGCCATCATCTATTATGTCTGTGTTTTCCTGTACTTCT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atttctgattgttgttgttgtttgccgcttacgccgtatatattctctctttcagGTTATGGCAGTAACTAGAAGTACAATCTGCAAAAAAGGAATAGAGTCCCTTCCCAGGGGAGGTGCCATCATCTATTATGTCTGTGTTTTCCTGTACTTCT
                         cgcttac  putative branch site (score: 37)
                                      tatattctctctttc  putative PPT
                                    tatatattct  TA-rich tract