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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...agacggctagaggcccttttgcatcacgaagatagaactaactgttatgatatccttatactctgtgcagaccataacttccttgttgttgctttatcagGAAACCAAAATACTTCTGAAGCTTCAGCTGACGCAGATGAAG

Basic information

species Zea mays
transcript GRMZM2G086484_T02
intron # 6
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|19770206|gb|BQ034927.1|BQ034927
EST:     CCCACAGAGTCCACCTCTGTTTTCAATGAATCAACAATCAGTCCTCCCAG                         GAAACCAAAATACTTCTGAAGCTTCAGCTGACGCAGATGAAG
genomic: CCCACAGAGTCCACCTCTGTTTTCAATGAATCAACAATCAGTCCTCCCAGgtatcttttc ... gctttatcagGAAACCAAAATACTTCTGAAGCTTCAGCTGACGCAGATGAAG
EST: gi|71311912|gb|DR792439.1|DR792439
EST:     CCCACAGAGTCCACCTCTGTTTTCAATGAATCAACAATCAGTCCTCCCAG                         GAAACCAAAATACTTCTGAAGCTTCAGCTGACGCAGATGAAG
genomic: CCCACAGAGTCCACCTCTGTTTTCAATGAATCAACAATCAGTCCTCCCAGgtatcttttc ... gctttatcagGAAACCAAAATACTTCTGAAGCTTCAGCTGACGCAGATGAAG
EST: gi|71762836|gb|DR960773.1|DR960773
EST:     CCCACAGAGTCCACCTCTGTTTTCAATGAATCAACAATCAGTCCTCCCAG                         GAAACCAAAATACTTCTGAAGCTTCAGCTGACGCAGATGAAG
genomic: CCCACAGAGTCCACCTCTGTTTTCAATGAATCAACAATCAGTCCTCCCAGgtatcttttc ... gctttatcagGAAACCAAAATACTTCTGAAGCTTCAGCTGACGCAGATGAAG
EST: gi|71315320|gb|DR794272.1|DR794272
EST:     TCAATGAATCACCAATCAGTCCTCCCAG                         GAAACAAAAATATTTCTGAAGCTTCAGCTGACGCAGATGAAG
genomic: TCAATGAATCAACAATCAGTCCTCCCAGgtatcttttc ... gctttatcagGAAACCAAAATACTTCTGAAGCTTCAGCTGACGCAGATGAAG
EST: gi|19822448|gb|BQ048472.1|BQ048472
EST:     CCCACAGAGTCCACCTCTGTTTTCAATGAATCAACAATCAGTCCTCCCAG                         GAAACCAAAATACTTCTGATGCTTCAGCTGACGCAGATGAAG
genomic: CCCACAGAGTCCACCTCTGTTTTCAATGAATCAACAATCAGTCCTCCCAGgtatcttttc ... gctttatcagGAAACCAAAATACTTCTGAAGCTTCAGCTGACGCAGATGAAG

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: 6

TTGCCCAAAGTTTTAACCCACAGAGTCCACCTCTGTTTTCAATGAATCAACAATCAGTCCTCCCAGgtatcttttc ... gctttatcagGAAACCAAAATACTTCTGAAGCTTCAGCTGACGCAGATGAAG


Block sizes: 49 (upstream exon), 33 (downstream exon)
Score: 7

TTGCCCAAAGTTTTAACCCACAGAGTCCACCTCTGTTTTCAATGAATCAACAATCAGTCCTCCCAGgtatcttttc ... gctttatcagGAAACCAAAATACTTCTGAAGCTTCAGCTGACGCAGATGAAG


Block sizes: 49 (upstream exon), 38 (downstream exon)
Score: 5

TTGCCCAAAGTTTTAACCCACAGAGTCCACCTCTGTTTTCAATGAATCAACAATCAGTCCTCCCAGgtatcttttc ... gctttatcagGAAACCAAAATACTTCTGAAGCTTCAGCTGACGCAGATGAAG


Block sizes: 10 (upstream exon), 40 (downstream exon)
Score: 2

TTGCCCAAAGTTTTAACCCACAGAGTCCACCTCTGTTTTCAATGAATCAACAATCAGTCCTCCCAGgtatcttttc ... gctttatcagGAAACCAAAATACTTCTGAAGCTTCAGCTGACGCAGATGAAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatgatatccttatactctgtgcagaccataacttccttgttgttgctttatcagGAAACCAAAATACTTCTGAAGCTTCAGCTGACGCAGATGAAG
                          ccataac  putative branch site (score: 2)
                                           ttgcttt  putative PPT
          ttatact  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
agacggctagaggcccttttgcatcacgaagatagaactaactgttatgatatccttatactctgtgcagaccataacttccttgttgttgctttatcagGAAACCAAAATACTTCTGAAGCTTCAGCTGACGCAGATGAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGATG