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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGGTTGTTGCTATGGCGAATTCTGGACTTGATTCTAATGGATCTCAGTTTTACATAACTACTATCAAGACAAGCTGgtgagttgtgttgtacaccacgtctcaccaatgattgacttggaagctgcagctcctgaaatggtagctttgtag

Basic information

species Zea mays
transcript GRMZM2G158237_T05
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G158237_T05 (Zea mays), 5'ss of exon 5
lower sequence: LOC_Os09g36670.1 (Oryza sativa), 5'ss of exon 6
GGGTTGTTGCTATGGCGAATTCTGGACTTGATTCTAATGGATCTCAGTTTTACATAACTACTATCAAGACAAGCTGgtgagttgtgttgtacaccacgtctcaccaatgattgacttggaagctgcagctcctgaaatggta-gctttgtag
| ||| |||| ||||| |||||||||| |||||| |||||||| ||||||||||| || || |||||||||||||||| |||||| || |||| | | |||| |||| | | || | | || |||||||||| || | | ||
GTGTTATTGCCATGGCAAATTCTGGACCTGATTCCAATGGATCGCAGTTTTACATTACCACAATCAAGACAAGCTGgtaagttgtatt--acactataagttaccagtgatcaatctagatggtacaactcctgaaattataagtaccgcag

upper sequence: GRMZM2G158237_T05 (Zea mays), 5'ss of exon 5
lower sequence: Vv03s0038g02200.t01 (Vitis vinifera), 5'ss of exon 6
GGGTTGTTGCTATGGCGAATTCTGGACTTGATTCTAATGGATCTCAGTTTTACATAACTACTATCAAGACAAGCTGgtgagttgtgttgta----caccacgtctcaccaatgattga--cttggaagctgcagctc---ctgaaatggtagctttgtag-----------------
| |||||| | |||| |||||| |||| |||||||||||| |||||||||| ||| || || ||||| | ||||||| || | || ||||| | | || || | | | | || || ||| || | | || ||
GTGTTGTTTCCATGGTGAATTCAGGACCTGATTCTAATGGCTCTCAGTTTTTCATCACCACAGTCAAGGCTAGCTGgtaagctactccatagaatcaccaaaacactggaaaattttagccattataatggcggcctgagctggaa-gatgatttcctaagaaacacaacctactct
















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|76926335|gb|DV170814.1|DV170814
EST:     CTTGATTTTAATGGATCTCAGTTTTACATAACTACTATCAAGACAAGCTG                         GTTGGATGGGGAGCATGTTGTCTTCGGCAGGGTGATCCAAGGAATGGATAC
genomic: CTTGATTCTAATGGATCTCAGTTTTACATAACTACTATCAAGACAAGCTGgtgagttgtg ... agctttgtagGTTGGATGGGGAGCATGTTGTCTTCGGCAGGGTGATCCAAGGAATGGATAC
EST: gi|87155387|gb|DY400176.1|DY400176
EST:     CTTGATTCTAATGGATCTCAGTTTTACATAACTACTATCAAGACAAGCTG                         GTTGGATGGGGAGCATGTTGTCTTCGGCAGGGTGATCCAAGGAATGGATAC
genomic: CTTGATTCTAATGGATCTCAGTTTTACATAACTACTATCAAGACAAGCTGgtgagttgtg ... agctttgtagGTTGGATGGGGAGCATGTTGTCTTCGGCAGGGTGATCCAAGGAATGGATAC
EST: gi|71434184|gb|DR815234.1|DR815234
EST:     CTTGATTCTAATGGATCTCAGTTTTACATAACTACTATCAAGACAAGCTG                         GTTGGATGGGGAGCATGTTGTCTTCGGCAGGGTGATCCAAGGAATGGATCC
genomic: CTTGATTCTAATGGATCTCAGTTTTACATAACTACTATCAAGACAAGCTGgtgagttgtg ... agctttgtagGTTGGATGGGGAGCATGTTGTCTTCGGCAGGGTGATCCAAGGAATGGATAC
EST: gi|30704816|gb|CD058610.1|CD058610
EST:     CTTGATTCTAATGGATCTCAGTTTTACATAACTACTATCAAGACAAGCTG                         GTTGGATGGGGAGCATGTTGTCTTCGGCAGGGTGATCCAAGGAATGGATAC
genomic: CTTGATTCTAATGGATCTCAGTTTTACATAACTACTATCAAGACAAGCTGgtgagttgtg ... agctttgtagGTTGGATGGGGAGCATGTTGTCTTCGGCAGGGTGATCCAAGGAATGGATAC
EST: gi|213175357|gb|FM185315.1|FM185315
EST:     CTTGATTCTAATGGATCTCAGTTTTACATAACTACTATCAAGACAAGCTG                         GTTGGATGGGGAGCATGTTGTCTTCGGCAGGGTGATCCAAGGAATGGATAC
genomic: CTTGATTCTAATGGATCTCAGTTTTACATAACTACTATCAAGACAAGCTGgtgagttgtg ... agctttgtagGTTGGATGGGGAGCATGTTGTCTTCGGCAGGGTGATCCAAGGAATGGATAC
EST: gi|16926545|gb|BM079613.1|BM079613
EST:     GTTTTACATAACTACTATCAAGACAAGCTG                         GTTGAATGGGGAGCATGTTGTCTTCGGCAGGGTGATCCAAGGAATGGATAC
genomic: GTTTTACATAACTACTATCAAGACAAGCTGgtgagttgtg ... agctttgtagGTTGGATGGGGAGCATGTTGTCTTCGGCAGGGTGATCCAAGGAATGGATAC
EST: gi|76922694|gb|DV169125.1|DV169125
EST:     CTTGATTCTAATGGATCTCAGTTTTACATAACTACTATCAAGACAAGCTG                         GTTGGATGGGGAGCATGTTGTCTTCGGCAGGGTGATCCAAGGAATGGATAC
genomic: CTTGATTCTAATGGATCTCAGTTTTACATAACTACTATCAAGACAAGCTGgtgagttgtg ... agctttgtagGTTGGATGGGGAGCATGTTGTCTTCGGCAGGGTGATCCAAGGAATGGATAC
EST: gi|32825245|gb|CD964967.1|CD964967
EST:     GATCTCAGTTTTACATAACTACTATCAAGACAAGCTG                         GTTGGATGGGGAGCATGTTGTCTTCGGCAGGGTGATCCAAGGAATGGATAC
genomic: GATCTCAGTTTTACATAACTACTATCAAGACAAGCTGgtgagttgtg ... agctttgtagGTTGGATGGGGAGCATGTTGTCTTCGGCAGGGTGATCCAAGGAATGGATAC
EST: gi|78024054|gb|DV492441.1|DV492441
EST:     CTTGATTTTAATGGATTTCAGTTTTACATAACTACTATCAAGACAAGCTG                         GTTGGATGGGGAGCATGTTGTCTTTGGCAGGGTGATCCAAGGAATGGATAC
genomic: CTTGATTCTAATGGATCTCAGTTTTACATAACTACTATCAAGACAAGCTGgtgagttgtg ... agctttgtagGTTGGATGGGGAGCATGTTGTCTTCGGCAGGGTGATCCAAGGAATGGATAC
EST: gi|76926341|gb|DV170815.1|DV170815
EST:     CTTGATTCTAATGGATCTCAGTTTTACATAACTACTATCAAGACAAGCTG                         GTTGGATGGGGAGCATGTTGTCTTCGGCAGGGTGATCCAAGGAATGGATAC
genomic: CTTGATTCTAATGGATCTCAGTTTTACATAACTACTATCAAGACAAGCTGgtgagttgtg ... agctttgtagGTTGGATGGGGAGCATGTTGTCTTCGGCAGGGTGATCCAAGGAATGGATAC
EST: gi|61118773|gb|DN559734.1|DN559734
EST:     CTTGATTCTAATGGATCTCAGTTTTACATAACTACTATCAAGACAAGCTG                         GTTGGATGGGGAGCATGTTGTCTTCGGCAGGGTGATCCAAGGAATGGATAC
genomic: CTTGATTCTAATGGATCTCAGTTTTACATAACTACTATCAAGACAAGCTGgtgagttgtg ... agctttgtagGTTGGATGGGGAGCATGTTGTCTTCGGCAGGGTGATCCAAGGAATGGATAC
EST: gi|60346388|gb|DN213361.1|DN213361
EST:     CTTGATTCTAATGGATCTCAGTTTTACATAACTACTATCAAGACAAGCTG                         GTTGGATGGGGAGCATGTTGTCTTCGGCAGGGTGATCCAAGGAATGGATAC
genomic: CTTGATTCTAATGGATCTCAGTTTTACATAACTACTATCAAGACAAGCTGgtgagttgtg ... agctttgtagGTTGGATGGGGAGCATGTTGTCTTCGGCAGGGTGATCCAAGGAATGGATAC
EST: gi|211328997|gb|FL454093.1|FL454093
EST:     CTTGATTCTAATGGATCTCAGTTTTACATAACTACTATCAAGACAAGCTG                         GTAGGATGGGGAGCATGTTGTCTTCGGCAGGGTGATCCAAGGAATGGATAC
genomic: CTTGATTCTAATGGATCTCAGTTTTACATAACTACTATCAAGACAAGCTGgtgagttgtg ... agctttgtagGTTGGATGGGGAGCATGTTGTCTTCGGCAGGGTGATCCAAGGAATGGATAC

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: 47 (upstream exon), 43 (downstream exon)
Score: 167

GGGTTGTTGCTATGGCGAATTCTGGACTTGATTCTAATGGATCTCAGTTTTACATAACTACTATCAAGACAAGCTGgtgagttgtg ... agctttgtagGTTGGATGGGGAGCATGTTGTCTTCGGCAGGGTGATCCAAGGAATGGATACCGTGTACGCCATAGAAGGGGGCGCTGGGACTTACAATGGCAAGCCAAGG


Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 94

GGGTTGTTGCTATGGCGAATTCTGGACTTGATTCTAATGGATCTCAGTTTTACATAACTACTATCAAGACAAGCTGgtgagttgtg ... agctttgtagGTTGGATGGGGAGCATGTTGTCTTCGGCAGGGTGATCCAAGGAATGGATACCGTGTACGCCATAGAAGGGGGCGCTGGGACTTACAATGGCAAGCCAAGG


Block sizes: 42 (upstream exon), 43 (downstream exon)
Score: 56

GGGTTGTTGCTATGGCGAATTCTGGACTTGATTCTAATGGATCTCAGTTTTACATAACTACTATCAAGACAAGCTGgtgagttgtg ... agctttgtagGTTGGATGGGGAGCATGTTGTCTTCGGCAGGGTGATCCAAGGAATGGATACCGTGTACGCCATAGAAGGGGGCGCTGGGACTTACAATGGCAAGCCAAGG


Block sizes: 39 (upstream exon), 48 (downstream exon)
Score: 65

GGGTTGTTGCTATGGCGAATTCTGGACTTGATTCTAATGGATCTCAGTTTTACATAACTACTATCAAGACAAGCTGgtgagttgtg ... agctttgtagGTTGGATGGGGAGCATGTTGTCTTCGGCAGGGTGATCCAAGGAATGGATACCGTGTACGCCATAGAAGGGGGCGCTGGGACTTACAATGGCAAGCCAAGG


Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGGTTGTTGCTATGGCGAATTCTGGACTTGATTCTAATGGATCTCAGTTTTACATAACTACTATCAAGACAAGCTGgtgagttgtgttgtacaccacgtctcaccaatgattgacttggaagctgcagctcctgaaatggtagctttgtag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG