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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagaaacaaaggtctactgcctccaccccacattatgattcacttatattattcttttgaagagtaggctgagattattcatattggttagcattacttacttttctcaatgtgggaagttccaaataatgataaactgtgaatcagGGTAAATCCCGAAGTGACATGACAGTTGAAGAGAGGATTGCAGCTGCAGACAGGAGAAAGATTGAGGGCAATGCATATTTCAAAGAAAAGAAGCTTGAGG

Basic information

species Zea mays
transcript GRMZM2G133624_T01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G133624_T01 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os12g05090.1 (Oryza sativa), 3'ss of exon 4
gtaagaaacaaaggtctactgcctccaccccacattatgattcacttatattattcttttgaagagtaggctgagattattcatattggttagcattacttacttttctcaatgtgggaagttccaaataatgataaactgtgaatcagGGTAAATCCCGAAGTGACATGACAGTTGAAGAGAGGATTGCAGCTGCAGACAGGAGAAAGATTGAGGGCAATGCATATTTCAAAGAAAAGAAGCTTGAGG
                               |   ||    || ||  ||| |  |||     || |    |||  || || | |    |     | |   |    |  | |   || |  || || ||||||  |||||      ||||| ||| |||||||||| |||||||| ||||| ||||||| ||| ||||||||||| |||||||| ||||||| ||||||||||||||||||| | ||||
-----------------------------gtaggataaatatccctcttatcaccctt-----gatt---ttgattttttttaaaaaaatatttgtgaaccaaaggttccta---ggaagcttacagataatgtaaaacta-----cagGGAAAAGCCCGAAGTGATATGACAGTGGAAGAAAGGATTGAAGCAGCAGACAGGAGGAAGATTGAAGGCAATGAATATTTCAAAGAAAAGAAGTTCGAGG
















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|71765927|gb|DR963864.1|DR963864
EST:     CAGACCTTGTTTATGAAGTTGAACTCATTGGATTTGATGATGTTAAAGAG                         GGTAAATCCCGAAGTGACATGACAGTTGAAGAGAGGATTGCAGCTGCAGAC
genomic: CAGACCTTGTTTATGAAGTTGAACTCATTGGATTTGATGATGTTAAAGAGgtaagaaaca ... tgtgaatcagGGTAAATCCCGAAGTGACATGACAGTTGAAGAGAGGATTGCAGCTGCAGAC
EST: gi|71299220|gb|DR785608.1|DR785608
EST:     ATTTGATGATGTTAAAGAG                         GGTAAATCCCGAAGTGACATGACAGTTGAAGAGAGGATTGCAGCTGCAGAC
genomic: ATTTGATGATGTTAAAGAGgtaagaaaca ... tgtgaatcagGGTAAATCCCGAAGTGACATGACAGTTGAAGAGAGGATTGCAGCTGCAGAC
EST: gi|71438300|gb|DR819350.1|DR819350
EST:     CAGACCTTGTTTATGAAGTTGAACTCATTGGATTTGATGATGTTAAAGAG                         GGTAAATCCCGAAGTGACATGACAGTTGAAGAGAGGATTGCAGCTGCAGAC
genomic: CAGACCTTGTTTATGAAGTTGAACTCATTGGATTTGATGATGTTAAAGAGgtaagaaaca ... tgtgaatcagGGTAAATCCCGAAGTGACATGACAGTTGAAGAGAGGATTGCAGCTGCAGAC
EST: gi|71435151|gb|DR816201.1|DR816201
EST:     CAGACCTTGTTTATGAAGTTGAACTCATTGGATTTGATGATGTTAAAGAG                         GGTAAATCCCGAAGTGACATGACAGTTGAAGAGAGGATTGCAGCTGCAGAC
genomic: CAGACCTTGTTTATGAAGTTGAACTCATTGGATTTGATGATGTTAAAGAGgtaagaaaca ... tgtgaatcagGGTAAATCCCGAAGTGACATGACAGTTGAAGAGAGGATTGCAGCTGCAGAC
EST: gi|32864226|gb|CF003908.1|CF003908
EST:     CAGACCTTGTTTATGAAGTTGAACTCATTGGATTTGATGATGTTAAAGAG                         GGTAAATCCCGAAGTGACATGACAGTTGAAGAGAGGATTGCAGCTGCAGAC
genomic: CAGACCTTGTTTATGAAGTTGAACTCATTGGATTTGATGATGTTAAAGAGgtaagaaaca ... tgtgaatcagGGTAAATCCCGAAGTGACATGACAGTTGAAGAGAGGATTGCAGCTGCAGAC
EST: gi|71768316|gb|DR966253.1|DR966253
EST:     GACCTTGTTTATGAAGTTGAACTCATTGGATTTGATGATGTTAAAGAG                         GGTAAATCCCGAAGTGACATGACAGTTGAAGAGAGGATTGCAGCTGCAGAC
genomic: GACCTTGTTTATGAAGTTGAACTCATTGGATTTGATGATGTTAAAGAGgtaagaaaca ... tgtgaatcagGGTAAATCCCGAAGTGACATGACAGTTGAAGAGAGGATTGCAGCTGCAGAC
EST: gi|78089641|gb|DV518015.1|DV518015
EST:     CAGACCTTGTTTATGAAGTTGAACTCATTGGATTTGATGATGTTAAAGAG                         GGTAAATCCCGAAGTGACATGACAGTTGAAGAGAGGATTGCAGCTGCAGAC
genomic: CAGACCTTGTTTATGAAGTTGAACTCATTGGATTTGATGATGTTAAAGAGgtaagaaaca ... tgtgaatcagGGTAAATCCCGAAGTGACATGACAGTTGAAGAGAGGATTGCAGCTGCAGAC
EST: gi|33104053|gb|CF064013.1|CF064013
EST:     CAGACCTTGTTTATGAAGTTGAACTCATTGGATTTGATGATGTTAAAGAG                         GGTAAATCCCGAAGTGACATGACAGTTGAAGAGAGGATTGCAGCTGCAGAC
genomic: CAGACCTTGTTTATGAAGTTGAACTCATTGGATTTGATGATGTTAAAGAGgtaagaaaca ... tgtgaatcagGGTAAATCCCGAAGTGACATGACAGTTGAAGAGAGGATTGCAGCTGCAGAC
EST: gi|76021435|gb|DT948605.1|DT948605
EST:     CAGACCTTGTTTATGAAGTTGAACTCATTGGATTTGATGATGTTAAAGAG                         GGTAAATCCCGAAGGGACATGACAGTTGAAGAGAGGATGGCAGCTGCAGAC
genomic: CAGACCTTGTTTATGAAGTTGAACTCATTGGATTTGATGATGTTAAAGAGgtaagaaaca ... tgtgaatcagGGTAAATCCCGAAGTGACATGACAGTTGAAGAGAGGATTGCAGCTGCAGAC
EST: gi|71306393|gb|DR789338.1|DR789338
EST:     CAGACCTTGTTTATGAAGTTGAACTCATTGGATTTGATGATGTTAAAGAG                         GGTAAATCCCGAAGTGACATGACAGTTGAAGAGAGGATTGCAGCTGCAGAC
genomic: CAGACCTTGTTTATGAAGTTGAACTCATTGGATTTGATGATGTTAAAGAGgtaagaaaca ... tgtgaatcagGGTAAATCCCGAAGTGACATGACAGTTGAAGAGAGGATTGCAGCTGCAGAC
EST: gi|149015212|gb|EE044997.2|EE044997
EST:     CAGACCTTGTTTATGAAGTTGAACTCATTGGATTTGATGATGTTAAAGAG                         GGTAAATCCCGAAGTGACATGACAGTTGAAGAGAGGATTGCAGCTGCAGAC
genomic: CAGACCTTGTTTATGAAGTTGAACTCATTGGATTTGATGATGTTAAAGAGgtaagaaaca ... tgtgaatcagGGTAAATCCCGAAGTGACATGACAGTTGAAGAGAGGATTGCAGCTGCAGAC
EST: gi|71299221|gb|DR785609.1|DR785609
EST:     CAGACCTTGTTTATGAAGTTGAACTCATTGGATTTGATGATGTTAAAGAG                         GGTAAATCCCGAAGTGACATGACAGTTGAAGAGAGGATTGCAGCTGCAGAC
genomic: CAGACCTTGTTTATGAAGTTGAACTCATTGGATTTGATGATGTTAAAGAGgtaagaaaca ... tgtgaatcagGGTAAATCCCGAAGTGACATGACAGTTGAAGAGAGGATTGCAGCTGCAGAC
EST: gi|78108738|gb|DV527155.1|DV527155
EST:     CAGACCTTGTTTATGAAGTTGAACTCATTGGATTTGATGATGTTAAAGAG                         GGTAAATCCCGAAGTGACATGACAGTTGAAGAGAGGATTGCAGCTGCAGAC
genomic: CAGACCTTGTTTATGAAGTTGAACTCATTGGATTTGATGATGTTAAAGAGgtaagaaaca ... tgtgaatcagGGTAAATCCCGAAGTGACATGACAGTTGAAGAGAGGATTGCAGCTGCAGAC
EST: gi|149076434|gb|EE165057.2|EE165057
EST:     CAGACCTTGTTTATGAAGTTGAACTCATTGGATTTGATGATGTTAAAGAG                         GGTAAATCCCGAAGTGACATGACAGTTGAAGAGAGGATTGCAGCTGCAGAC
genomic: CAGACCTTGTTTATGAAGTTGAACTCATTGGATTTGATGATGTTAAAGAGgtaagaaaca ... tgtgaatcagGGTAAATCCCGAAGTGACATGACAGTTGAAGAGAGGATTGCAGCTGCAGAC
EST: gi|76021436|gb|DT948606.1|DT948606
EST:     CAGACCTTGTTTATGAAGTTGAACTCATTGGATTTGATGATGTTAAAGAG                         GGTAAATCCCGAAGTGACATGACAGTTGAAGAGAGGATTGCAGCTGCAGAC
genomic: CAGACCTTGTTTATGAAGTTGAACTCATTGGATTTGATGATGTTAAAGAGgtaagaaaca ... tgtgaatcagGGTAAATCCCGAAGTGACATGACAGTTGAAGAGAGGATTGCAGCTGCAGAC
EST: gi|71435313|gb|DR816363.1|DR816363
EST:     CAGACCTTGTTTATGAAGTTGAACTCATTGGATTTGATGATGTTAAAGAG                         GGTAAATCCCGAAGTGACATGACAGTTGAAGAGAGGATTGCAGCTGCAGAC
genomic: CAGACCTTGTTTATGAAGTTGAACTCATTGGATTTGATGATGTTAAAGAGgtaagaaaca ... tgtgaatcagGGTAAATCCCGAAGTGACATGACAGTTGAAGAGAGGATTGCAGCTGCAGAC
EST: gi|9794264|gb|BE552572.1|BE552572
EST:     CAGACCTTGTTTATGAAGTTGAACTCATTGGATTTGATGATGTTAAAGAG                         GGTAAATCCCGAAGTGACATGACAGTTGAAGAGAGGATTGCAGCTGC
genomic: CAGACCTTGTTTATGAAGTTGAACTCATTGGATTTGATGATGTTAAAGAGgtaagaaaca ... tgtgaatcagGGTAAATCCCGAAGTGACATGACAGTTGAAGAGAGGATTGCAGCTGC
EST: gi|71321226|gb|DR797322.1|DR797322
EST:     CAGACCTTGTTTATGAAGTTGAACTCATTGGATTTGATGATGTTAAAGAG                         GGTAAATCCCGAAGTGACATGACAGTTGAAGAGAGGATTGCAGCTGCAGAC
genomic: CAGACCTTGTTTATGAAGTTGAACTCATTGGATTTGATGATGTTAAAGAGgtaagaaaca ... tgtgaatcagGGTAAATCCCGAAGTGACATGACAGTTGAAGAGAGGATTGCAGCTGCAGAC

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: 48 (upstream exon), 49 (downstream exon)
Score: 167

AGGCTATGGCAAAGAAGGAAGTTTTTCATTCCCAAATGTCCCTCCAATGGCAGACCTTGTTTATGAAGTTGAACTCATTGGATTTGATGATGTTAAAGAGgtaagaaaca ... tgtgaatcagGGTAAATCCCGAAGTGACATGACAGTTGAAGAGAGGATTGCAGCTGCAGACAGGAGAAAGATTGAGGGCAATGCATATTTCAAAGAAAAGAAGCTTGAGG


Block sizes: 47 (upstream exon), 48 (downstream exon)
Score: 43

AGGCTATGGCAAAGAAGGAAGTTTTTCATTCCCAAATGTCCCTCCAATGGCAGACCTTGTTTATGAAGTTGAACTCATTGGATTTGATGATGTTAAAGAGgtaagaaaca ... tgtgaatcagGGTAAATCCCGAAGTGACATGACAGTTGAAGAGAGGATTGCAGCTGCAGACAGGAGAAAGATTGAGGGCAATGCATATTTCAAAGAAAAGAAGCTTGAGG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 58

AGGCTATGGCAAAGAAGGAAGTTTTTCATTCCCAAATGTCCCTCCAATGGCAGACCTTGTTTATGAAGTTGAACTCATTGGATTTGATGATGTTAAAGAGgtaagaaaca ... tgtgaatcagGGTAAATCCCGAAGTGACATGACAGTTGAAGAGAGGATTGCAGCTGCAGACAGGAGAAAGATTGAGGGCAATGCATATTTCAAAGAAAAGAAGCTTGAGG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 113

AGGCTATGGCAAAGAAGGAAGTTTTTCATTCCCAAATGTCCCTCCAATGGCAGACCTTGTTTATGAAGTTGAACTCATTGGATTTGATGATGTTAAAGAGgtaagaaaca ... tgtgaatcagGGTAAATCCCGAAGTGACATGACAGTTGAAGAGAGGATTGCAGCTGCAGACAGGAGAAAGATTGAGGGCAATGCATATTTCAAAGAAAAGAAGCTTGAGG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attacttacttttctcaatgtgggaagttccaaataatgataaactgtgaatcagGGTAAATCCCGAAGTGACATGACAGTTGAAGAGAGGATTGCAGCTGCAGACAGGAGAAAGATTGAGGGCAATGCATATTTCAAAGAAAAGAAGCTTGAGG
  tacttac  putative branch site (score: 113)
                               aaataatgataaact  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagaaacaaaggtctactgcctccaccccacattatgattcacttatattattcttttgaagagtaggctgagattattcatattggttagcattacttacttttctcaatgtgggaagttccaaataatgataaactgtgaatcagGGTAAATCCCGAAGTGACATGACAGTTGAAGAGAGGATTGCAGCTGCAGACAGGAGAAAGATTGAGGGCAATGCATATTTCAAAGAAAAGAAGCTTGAGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGC