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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagtagttagctgcaagaaggaactcaaattgtttttgaccattttctctctcatttaagatgtttgacctatgttgctgtgttttgctatgaacacctgtctgtcgttttcttctttcagAATCGGCATGTTGTCTTGATCACGAATGTGAAGCCTGGAAAGCTGCGAGATGTAATGTCTGCTGGATTG

Basic information

species Zea mays
transcript GRMZM2G166345_T01
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G166345_T02 (Zea mays), 3'ss of exon 7
lower sequence: LOC_Os01g60660.2 (Oryza sativa), 3'ss of exon 7
gtgagtagttagctgcaagaaggaactcaaattgtttttgaccattttctctctcatttaagatgtttgacctatgttgctgtgttttgctatgaacacctgtctgtcgttttcttctttcagAATCGGCATGTTGTCTTGATCACGAATGTGAAGCCTGGAAAGCTGCGAGATGTAATGTCTGCTGGATTG
                || || | |||  |||| ||  ||  ||||||   |  |||  ||  ||||| | | | | | |||| || ||  || |||| ||| ||    ||| ||||   ||||||||||||||||| || |||||||||||||||||||| ||||||||||| ||||||||||| ||||||
----------------aacaatggacttgaattattcctgttcatttttcttgccatg-aaattgtttcatccaagattctgttttctgtaataaacaactgcct----tttccttca--cagAATCGGCATGTTGTATTAATCACGAATGTGAAGCCTGGGAAGCTGCGAGACGTAATGTCTGCCGGATTG

upper sequence: GRMZM2G166345_T02 (Zea mays), 3'ss of exon 7
lower sequence: LOC_Os01g60660.1 (Oryza sativa), 3'ss of exon 8
gtgagtagttagctgcaagaaggaactcaaattgtttttgaccattttctctctcatttaagatgtttgacctatgttgctgtgttttgctatgaacacctgtctgtcgttttcttctttcagAATCGGCATGTTGTCTTGATCACGAATGTGAAGCCTGGAAAGCTGCGAGATGTAATGTCTGCTGGATTG
||||||| ||| | |||| || | |||  |||| ||  ||  ||||||   |  |||  ||  ||||| | | | | | |||| || ||  || |||| ||| ||    ||| ||||   ||||||||||||||||| || |||||||||||||||||||| ||||||||||| ||||||||||| ||||||
gtgagtatttaacagcaacaatggacttgaattattcctgttcatttttcttgccatg-aaattgtttcatccaagattctgttttctgtaataaacaactgcct----tttccttca--cagAATCGGCATGTTGTATTAATCACGAATGTGAAGCCTGGGAAGCTGCGAGACGTAATGTCTGCCGGATTG
















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|12972445|gb|BG267985.1|BG267985
EST:     GTTGTTAGTGGTCTTGCAAAGTATTGCAGCCCAGATGATCTTACT                         AATCGGCATGTTGTCTTGATCACGAATGTGAAGCCTGGAAAGCTGCGAGAT
genomic: GTTGTTAGTGGTCTTGCAAAGTATTGCAGCCCAGATGATCTTACTgtgagtagtt ... cttctttcagAATCGGCATGTTGTCTTGATCACGAATGTGAAGCCTGGAAAGCTGCGAGAT
EST: gi|211244774|gb|FL481676.1|FL481676
EST:     GTTGTTAGTGGTCTTGCAAAGTATTGCAGCCCAGATGATCTTACT                         AATCGGCATGTTGTCTTGATCACGAATGTGAAGCCTGGAAAGCTGCGAGAT
genomic: GTTGTTAGTGGTCTTGCAAAGTATTGCAGCCCAGATGATCTTACTgtgagtagtt ... cttctttcagAATCGGCATGTTGTCTTGATCACGAATGTGAAGCCTGGAAAGCTGCGAGAT
EST: gi|33095166|gb|CF055160.1|CF055160
EST:     GTTGTTAGTGGTCTTGCAAAGTATTGCAGCCCAGATGATCTTACT                         AATCGGCATGTTGTCTTGATCACGAATGTGAAGCCTGGGAAGCTGCGAGAT
genomic: GTTGTTAGTGGTCTTGCAAAGTATTGCAGCCCAGATGATCTTACTgtgagtagtt ... cttctttcagAATCGGCATGTTGTCTTGATCACGAATGTGAAGCCTGGAAAGCTGCGAGAT
EST: gi|213173994|gb|FM188956.1|FM188956
EST:     GTTGTTAGTGGTCTTGCAAAGTATTGCAGCCCAGATGATCTTACT                         AATCGGCATGTTGTCTTGATCACGAATGTGAAGCCTGGGAAGCTGCGAGAT
genomic: GTTGTTAGTGGTCTTGCAAAGTATTGCAGCCCAGATGATCTTACTgtgagtagtt ... cttctttcagAATCGGCATGTTGTCTTGATCACGAATGTGAAGCCTGGAAAGCTGCGAGAT
EST: gi|89247315|gb|DY619101.1|DY619101
EST:     GTTGTTAGT-GTCTTTGCAAAGTATTGCAGCCCAGATGATCTTACT                         AATCGGCATGTTGTCTTGATCACGAATGTGAAGCCTGGAAAGCTGCGAGAT
genomic: GTTGTTAGTGGTC-TTGCAAAGTATTGCAGCCCAGATGATCTTACTgtgagtagtt ... cttctttcagAATCGGCATGTTGTCTTGATCACGAATGTGAAGCCTGGAAAGCTGCGAGAT
EST: gi|18173735|gb|BM349123.1|BM349123
EST:     GTTGTTAGTGGTCTTGCAAAGTATTGCAGCCCAGATGATCTTACT                         AATCGGCATGTTGTCTTGATCACGAATGTGAAGCCTGGAAAGCTGCGAGAT
genomic: GTTGTTAGTGGTCTTGCAAAGTATTGCAGCCCAGATGATCTTACTgtgagtagtt ... cttctttcagAATCGGCATGTTGTCTTGATCACGAATGTGAAGCCTGGAAAGCTGCGAGAT
EST: gi|33095762|gb|CF055756.1|CF055756
EST:     GTTGTTAGTGGTCTTGCAAAGTATTGCAGCCCAGATGATCTTACT                         AATCGGCATGTTGTCTTGATCACGAATGTGAAGCCTGGGAAGCTGCGAGAT
genomic: GTTGTTAGTGGTCTTGCAAAGTATTGCAGCCCAGATGATCTTACTgtgagtagtt ... cttctttcagAATCGGCATGTTGTCTTGATCACGAATGTGAAGCCTGGAAAGCTGCGAGAT
EST: gi|166465899|gb|EG190327.1|EG190327
EST:     TTGCAAAGTATTGCAGCCCAGATGATCTTACT                         AATCGGCATGTTGTCTTGATCACGAATGTGAAGCCTGGAAAGCTGCGAGAT
genomic: TTGCAAAGTATTGCAGCCCAGATGATCTTACTgtgagtagtt ... cttctttcagAATCGGCATGTTGTCTTGATCACGAATGTGAAGCCTGGAAAGCTGCGAGAT
EST: gi|91873662|gb|EB403619.1|EB403619
EST:     GTTGTTAGTGGTCTTGCAAAGTATTGCAGCCCAGATGATCTTACT                         AATCGGCATGTTGTCTTGATCACGAATGTGAAGCCTGGAAAGCTGCGAGAT
genomic: GTTGTTAGTGGTCTTGCAAAGTATTGCAGCCCAGATGATCTTACTgtgagtagtt ... cttctttcagAATCGGCATGTTGTCTTGATCACGAATGTGAAGCCTGGAAAGCTGCGAGAT
EST: gi|211165085|gb|FL207333.1|FL207333
EST:     AAAGTATTGCAGCCCAGATGATCTTACT                         AATCGSCATGTTGTCTTGATCACGAATGTGAAGCCTGGGAAGCTGCGAGAT
genomic: AAAGTATTGCAGCCCAGATGATCTTACTgtgagtagtt ... cttctttcagAATCGGCATGTTGTCTTGATCACGAATGTGAAGCCTGGAAAGCTGCGAGAT

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), 49 (downstream exon)
Score: 236

GTTGTTAGTGGTCTTGCAAAGTATTGCAGCCCAGATGATCTTACTgtgagtagtt ... cttctttcagAATCGGCATGTTGTCTTGATCACGAATGTGAAGCCTGGAAAGCTGCGAGATGTAATGTCTGCTGGATTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 189

GTTGTTAGTGGTCTTGCAAAGTATTGCAGCCCAGATGATCTTACTgtgagtagtt ... cttctttcagAATCGGCATGTTGTCTTGATCACGAATGTGAAGCCTGGAAAGCTGCGAGATGTAATGTCTGCTGGATTG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 225

GTTGTTAGTGGTCTTGCAAAGTATTGCAGCCCAGATGATCTTACTgtgagtagtt ... cttctttcagAATCGGCATGTTGTCTTGATCACGAATGTGAAGCCTGGAAAGCTGCGAGATGTAATGTCTGCTGGATTG


Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 160

GTTGTTAGTGGTCTTGCAAAGTATTGCAGCCCAGATGATCTTACTgtgagtagtt ... cttctttcagAATCGGCATGTTGTCTTGATCACGAATGTGAAGCCTGGAAAGCTGCGAGATGTAATGTCTGCTGGATTG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gacctatgttgctgtgttttgctatgaacacctgtctgtcgttttcttctttcagAATCGGCATGTTGTCTTGATCACGAATGTGAAGCCTGGAAAGCTGCGAGATGTAATGTCTGCTGGATTG
 gtttgac  putative branch site (score: 160)
                              cctgtctgtcgttttc  putative PPT
                                         ttttctt  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagtagttagctgcaagaaggaactcaaattgtttttgaccattttctctctcatttaagatgtttgacctatgttgctgtgttttgctatgaacacctgtctgtcgttttcttctttcagAATCGGCATGTTGTCTTGATCACGAATGTGAAGCCTGGAAAGCTGCGAGATGTAATGTCTGCTGGATTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGGA