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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...actgaaaatatatttcttaccaaagcacttaatgctaataatatcttgttgtttaccgttgccatctgtaaattcctgatcctttaagttcaattttcagGCACACATTGCACTTAATGACATTGATGCAGCCGTGGAGAGCTTTAAACAGGCATTGGAGTTGGAGCCAAATGATG

Basic information

species Zea mays
transcript GRMZM2G329306_T01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G329306_T01 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os06g11320.1 (Oryza sativa), 3'ss of exon 5
--actgaaaatatatttcttaccaaagcact-taatgctaataatatcttgttgtttaccgttgccatctgtaaattcctgatcctttaagttcaattttcagGCACACATTGCACTTAATGACATTGATGCAGCCGTGGAGAGCTTTAAACAGGCATTGGAGTTGGAGCCAAATGATG
  |||    | ||   | | | ||| ||| | |  | || |||   | || || ||  |   ||   ||||   |   |  ||    ||| | | |||| ||||||||||||||||| |||||||||||||| || ||||||||||| || || ||||||||||||||||||| |||||
aaactattgacat---tttaatcaatgcaatgtgctactcatatcgtattattattaccatctggtttctgcgcaactcatatggcataaatgccatttgcagGCACACATTGCACTCAATGACATTGATGCGGCAGTGGAGAGCTTCAAGCATGCATTGGAGTTGGAGCCAAGTGATG
















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|71329028|gb|DR801213.1|DR801213
EST:     CACTGCGTGAAAGGGAGGGAAATGCTAAAGCTTTTTTCCGACAAGGACAG                         GCACACATTGCACTTAATGACATTGATGCAGCCGTGGAGAGCTTTAAACAG
genomic: CACTGCGTGAAAGGGAGGGAAATGCTAAAGCTTTTTTCCGACAAGGACAGgttggcaact ... caattttcagGCACACATTGCACTTAATGACATTGATGCAGCCGTGGAGAGCTTTAAACAG
EST: gi|32930877|gb|CF035689.1|CF035689
EST:     CACTGCGTGAAAGGGAGGGAAATGCTAAAGCTTTTTTCCGACAAGGACAG                         GCACACATTGCACTTAATGACATTGATGCAGCCGTGGAGAGCTTTAAACAG
genomic: CACTGCGTGAAAGGGAGGGAAATGCTAAAGCTTTTTTCCGACAAGGACAGgttggcaact ... caattttcagGCACACATTGCACTTAATGACATTGATGCAGCCGTGGAGAGCTTTAAACAG
EST: gi|113703884|gb|EE681388.1|EE681388
EST:     CACTGCGTGAAAGGGAGGGAAATGCTAAAGCTTTTTTCCGACAAGGACAG                         GCACACATTGCACTTAATGACATTGATGCAGCCGTGGAGAGCTTTAAACAG
genomic: CACTGCGTGAAAGGGAGGGAAATGCTAAAGCTTTTTTCCGACAAGGACAGgttggcaact ... caattttcagGCACACATTGCACTTAATGACATTGATGCAGCCGTGGAGAGCTTTAAACAG
EST: gi|149051834|gb|EE155961.2|EE155961
EST:     ACTGCG-GAAAGGGGAGGGAAATGCTAAAGCTTTTTTCCGACAAGGACAG                         GCACACATTGCACTTAATGACATTGATGCAGCCGTGGAGAGCTTTAAACAG
genomic: ACTGCGTGAAA-GGGAGGGAAATGCTAAAGCTTTTTTCCGACAAGGACAGgttggcaact ... caattttcagGCACACATTGCACTTAATGACATTGATGCAGCCGTGGAGAGCTTTAAACAG
EST: gi|78124365|gb|DV542749.1|DV542749
EST:     CACTGCGTGAAAGGGAGGGAAATGCTAAAGCTTTTTTCCGACAAGGACAG                         GCACACATTGCACTTAATGACATTGATGCAGCCGTGGAGAGCTTTAAACAG
genomic: CACTGCGTGAAAGGGAGGGAAATGCTAAAGCTTTTTTCCGACAAGGACAGgttggcaact ... caattttcagGCACACATTGCACTTAATGACATTGATGCAGCCGTGGAGAGCTTTAAACAG
EST: gi|71443878|gb|DR824928.1|DR824928
EST:     CACTGCGTGAAAGGGAGGGAAATGCTAAAGCTTTTTTCCGACAAGGACAG                         GCACACATTGCACTTAATGACATTGATGCAGCCGTGGAGAGCTTTAAACAG
genomic: CACTGCGTGAAAGGGAGGGAAATGCTAAAGCTTTTTTCCGACAAGGACAGgttggcaact ... caattttcagGCACACATTGCACTTAATGACATTGATGCAGCCGTGGAGAGCTTTAAACAG
EST: gi|60350322|gb|DN217295.1|DN217295
EST:     CACTGCGTGAAAGGGAGGGAAATGCTAAAGCTTTTTTCCGACAAGGACAG                         GCACACATTGCACTTAATGACATTGATGCAGCCGTGGAGAGCTTTAAACAG
genomic: CACTGCGTGAAAGGGAGGGAAATGCTAAAGCTTTTTTCCGACAAGGACAGgttggcaact ... caattttcagGCACACATTGCACTTAATGACATTGATGCAGCCGTGGAGAGCTTTAAACAG
EST: gi|32930670|gb|CF035482.1|CF035482
EST:     CACTGCGTGAAAAGGAGGGAAATGCTAAAGCTTTTTTCCGACAAGGACAG                         GCACACATTGCACTTAATGACATTGATGCAGCCGTGGAGAGCTTTAAACAG
genomic: CACTGCGTGAAAGGGAGGGAAATGCTAAAGCTTTTTTCCGACAAGGACAGgttggcaact ... caattttcagGCACACATTGCACTTAATGACATTGATGCAGCCGTGGAGAGCTTTAAACAG
EST: gi|88756259|gb|DY540400.1|DY540400
EST:     CACTGCGTGAAAGGGAGGGAAATGCTAAAGCTTTTTTCCGACAAGGACAG                         GCACACATTGCACTTAATGACATTGATGCAGCCGTGGAGAGCTTTAAACAG
genomic: CACTGCGTGAAAGGGAGGGAAATGCTAAAGCTTTTTTCCGACAAGGACAGgttggcaact ... caattttcagGCACACATTGCACTTAATGACATTGATGCAGCCGTGGAGAGCTTTAAACAG
EST: gi|76017867|gb|DT945037.1|DT945037
EST:     CACTGCGTGAAAGGGAGGGAAATGCTAAAGCTTTTTTCCGACAAGGACAG                         GCACACATTGCACTTAATGACATTGATGCAGCCGTGGAGAGCTTTAAACAG
genomic: CACTGCGTGAAAGGGAGGGAAATGCTAAAGCTTTTTTCCGACAAGGACAGgttggcaact ... caattttcagGCACACATTGCACTTAATGACATTGATGCAGCCGTGGAGAGCTTTAAACAG
EST: gi|32930642|gb|CF035454.1|CF035454
EST:     CACTGCGTGAAAGGGAGGGAAATGCTAAAGCTTTTTTCCGACAAGGACAG                         GCACACATTGCACTTAATGACATTGATGCAGCCGTGGAGAGCTTTAAACAG
genomic: CACTGCGTGAAAGGGAGGGAAATGCTAAAGCTTTTTTCCGACAAGGACAGgttggcaact ... caattttcagGCACACATTGCACTTAATGACATTGATGCAGCCGTGGAGAGCTTTAAACAG
EST: gi|149012518|gb|EE042586.2|EE042586
EST:     CACTGCGTGAAAGGGAGGGAAATGCTAAAGCTTTTTTCCGACAAGGACAG                         GCACACATTGCACTTAATGACATTGATGCAGCCGTGGAGAGCTTTAAACAG
genomic: CACTGCGTGAAAGGGAGGGAAATGCTAAAGCTTTTTTCCGACAAGGACAGgttggcaact ... caattttcagGCACACATTGCACTTAATGACATTGATGCAGCCGTGGAGAGCTTTAAACAG
EST: gi|211145441|gb|FL467393.1|FL467393
EST:     CGACAAGGACAG                         GCACACATTGCACTTAATGACATTGATGCAGCCGTGGAGAGCTTTAAACAG
genomic: CGACAAGGACAGgttggcaact ... caattttcagGCACACATTGCACTTAATGACATTGATGCAGCCGTGGAGAGCTTTAAACAG

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: 49

CAAATTAAAGTTAGGAGATTCAAGTGGGGCTTTATTAGACGCAGATTTTGCACTGCGTGAAAGGGAGGGAAATGCTAAAGCTTTTTTCCGACAAGGACAGgttggcaact ... caattttcagGCACACATTGCACTTAATGACATTGATGCAGCCGTGGAGAGCTTTAAACAGGCATTGGAGTTGGAGCCAAATGATG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 83

CAAATTAAAGTTAGGAGATTCAAGTGGGGCTTTATTAGACGCAGATTTTGCACTGCGTGAAAGGGAGGGAAATGCTAAAGCTTTTTTCCGACAAGGACAGgttggcaact ... caattttcagGCACACATTGCACTTAATGACATTGATGCAGCCGTGGAGAGCTTTAAACAGGCATTGGAGTTGGAGCCAAATGATG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 97

CAAATTAAAGTTAGGAGATTCAAGTGGGGCTTTATTAGACGCAGATTTTGCACTGCGTGAAAGGGAGGGAAATGCTAAAGCTTTTTTCCGACAAGGACAGgttggcaact ... caattttcagGCACACATTGCACTTAATGACATTGATGCAGCCGTGGAGAGCTTTAAACAGGCATTGGAGTTGGAGCCAAATGATG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 127

CAAATTAAAGTTAGGAGATTCAAGTGGGGCTTTATTAGACGCAGATTTTGCACTGCGTGAAAGGGAGGGAAATGCTAAAGCTTTTTTCCGACAAGGACAGgttggcaact ... caattttcagGCACACATTGCACTTAATGACATTGATGCAGCCGTGGAGAGCTTTAAACAGGCATTGGAGTTGGAGCCAAATGATG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgttgtttaccgttgccatctgtaaattcctgatcctttaagttcaattttcagGCACACATTGCACTTAATGACATTGATGCAGCCGTGGAGAGCTTTAAACAGGCATTGGAGTTGGAGCCAAATGATG
                            tcctgat  putative branch site (score: 127)
                                                ttttc  putative PPT
                                     tttaagttcaatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
actgaaaatatatttcttaccaaagcacttaatgctaataatatcttgttgtttaccgttgccatctgtaaattcctgatcctttaagttcaattttcagGCACACATTGCACTTAATGACATTGATGCAGCCGTGGAGAGCTTTAAACAGGCATTGGAGTTGGAGCCAAATGATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - -atgctaa
- - - - - - - - - - - - - - - - - - - - - - - tgttgtt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -gttgcca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -attcctg