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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gacttgcctcggtttatctgttttcagactccacttatgtgggtgtgtcctgcactaggtctgccctatcctataactaaataccttcccattttgtcagGTTGACACAACTACGGGGGAAGCTGATGAGGATGGTGTGGAGGATGAATACCAGTTAGAGGACTTTGAAATTGTTTCAGCTGATTATATGCTGAGGGTTG

Basic information

species Zea mays
transcript GRMZM2G012501_T02
intron # 14
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G012501_T02 (Zea mays), 3'ss of exon 14
lower sequence: LOC_Os03g12590.1 (Oryza sativa), 3'ss of exon 16
------gacttgcctcggtttatctgttttcagactccacttatgtgggtgtgtcctgcactaggtctgccctatcctataactaaataccttcccattttgtcagGTTGACACAACTACGGGGGAAGCTGATGAGGATGGTGTGGAGGATGAATACCAGTTAGAGGACTTTGAAATTGTTTCAGCTGATTATATGCTGAGGGTTG
       || | ||| |   |    ||  |||  ||| | ||| ||   |||  | ||  |||  |||      |   | ||  |   | | | ||| ||  ||||||||||||| |||| ||||||| ||||||||||||||||||||||||||||||| | || ||| | ||||||||||| |||||||| |||||||||||||
catcaacacgtaccttgtactggg-gtaatcattctctatttaagt---tgttccatg-gctatttctttttcttagaacaatgactaatcctgccaattc-tcagGTTGACACATCTACAGGGGAAGTTGATGAGGATGGTGTGGAGGATGAATACCAGATCGAAGACCTGGAAATTGTTTCGGCTGATTACATGCTGAGGGTTG

upper sequence: GRMZM2G012501_T02 (Zea mays), 3'ss of exon 14
lower sequence: Vv03s0063g02450.t01 (Vitis vinifera), 3'ss of exon 16
-------gacttgcctcggtttatctgttttcagactccacttatgtgggtgtgtcctgcactaggtctgccctatcctataactaaatacctt-cccattttgtcagGTTGACACAACTACGGGGGAAGCTGATGAGGATGGTGTGGAGGATGAATACCAGTTAGAGGACTTTGAAATTGTTTCAGCTGATTATATGCTGAGGGTTG
        | || |    |   |  || || ||      ||| |||      | |||  ||  |  |    | |    | | |  |  |   ||    || ||  ||||||||  ||||||| || ||  | || || |||||||| || || ||||||||| | |||||| ||||| ||||| ||||||||||| || ||| |||||
caaatagaaattacactagagga--tgcttcca-----tactgatgaactaatctccaacaaaaaattctacatggttt-tcatcatgtgttttgtttatatttccagGTTGATCCAACTACTGGTGAGACAGAGGAAGATGGTGTCGAAGACGAATACCAGCTGGAGGACCTTGAAGTTGTTGCAGCTGATTATGTGTTGAAGGTTG
















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|31350725|gb|CD435082.1|CD435082
EST:     TACCTGTTGTTGGGAAGTTTTTAAATTTGTTGAAGTTTACAGTTAAAGAG                         GTTGACACAACTACGGGGGAAGCTGATGAGGATGGTGTGGAGGATGAATAC
genomic: TACCTGTTGTTGGGAAGTTTTTAAATTTGTTGAAGTTTACAGTTAAAGAGgtaaacataa ... attttgtcagGTTGACACAACTACGGGGGAAGCTGATGAGGATGGTGTGGAGGATGAATAC
EST: gi|33093956|gb|CF053950.1|CF053950
EST:     ACCTGTTGTTGGGAAGTTTTTAAATTTGTTGAAGTTTACAGTTAAAGAG                         GTTGACACAACTACGGGGGAAGCTGATGAGGATGGTGTGGAGGATGAATAC
genomic: ACCTGTTGTTGGGAAGTTTTTAAATTTGTTGAAGTTTACAGTTAAAGAGgtaaacataa ... attttgtcagGTTGACACAACTACGGGGGAAGCTGATGAGGATGGTGTGGAGGATGAATAC
EST: gi|67021265|gb|CO450014.1|CO450014
EST:     TACCTGTTGTTGGGAAGTTTT-AAATTTGTTGAAGTT-ACAGTTAAAGAA                         GTTGACACAACTACGGGGGAANCTGATGAGGATGGTGTGGGAG-ATGAATA
genomic: TACCTGTTGTTGGGAAGTTTTTAAATTTGTTGAAGTTTACAGTTAAAGAGgtaaacataa ... attttgtcagGTTGACACAACTACGGGGGAAGCTGATGAGGATGGTGTGG-AGGATGAATA

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: 173

GTATAATTCACCTGGGCAAGTTTTTGTTGCTTTTGAAAAGCCAGAGCGTGTACCTGTTGTTGGGAAGTTTTTAAATTTGTTGAAGTTTACAGTTAAAGAGgtaaacataa ... attttgtcagGTTGACACAACTACGGGGGAAGCTGATGAGGATGGTGTGGAGGATGAATACCAGTTAGAGGACTTTGAAATTGTTTCAGCTGATTATATGCTGAGGGTTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 115

GTATAATTCACCTGGGCAAGTTTTTGTTGCTTTTGAAAAGCCAGAGCGTGTACCTGTTGTTGGGAAGTTTTTAAATTTGTTGAAGTTTACAGTTAAAGAGgtaaacataa ... attttgtcagGTTGACACAACTACGGGGGAAGCTGATGAGGATGGTGTGGAGGATGAATACCAGTTAGAGGACTTTGAAATTGTTTCAGCTGATTATATGCTGAGGGTTG


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 104

GTATAATTCACCTGGGCAAGTTTTTGTTGCTTTTGAAAAGCCAGAGCGTGTACCTGTTGTTGGGAAGTTTTTAAATTTGTTGAAGTTTACAGTTAAAGAGgtaaacataa ... attttgtcagGTTGACACAACTACGGGGGAAGCTGATGAGGATGGTGTGGAGGATGAATACCAGTTAGAGGACTTTGAAATTGTTTCAGCTGATTATATGCTGAGGGTTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 236

GTATAATTCACCTGGGCAAGTTTTTGTTGCTTTTGAAAAGCCAGAGCGTGTACCTGTTGTTGGGAAGTTTTTAAATTTGTTGAAGTTTACAGTTAAAGAGgtaaacataa ... attttgtcagGTTGACACAACTACGGGGGAAGCTGATGAGGATGGTGTGGAGGATGAATACCAGTTAGAGGACTTTGAAATTGTTTCAGCTGATTATATGCTGAGGGTTG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgtcctgcactaggtctgccctatcctataactaaataccttcccattttgtcagGTTGACACAACTACGGGGGAAGCTGATGAGGATGGTGTGGAGGATGAATACCAGTTAGAGGACTTTGAAATTGTTTCAGCTGATTATATGCTGAGGGTTG
                             aactaaa  putative branch site (score: 236)
                                      ccttcccattttgtc  putative PPT
                          tataactaaata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gacttgcctcggtttatctgttttcagactccacttatgtgggtgtgtcctgcactaggtctgccctatcctataactaaataccttcccattttgtcagGTTGACACAACTACGGGGGAAGCTGATGAGGATGGTGTGGAGGATGAATACCAGTTAGAGGACTTTGAAATTGTTTCAGCTGATTATATGCTGAGGGTTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG
- - tgcctcg
- - - - - - - - tctgttt
- - - - - - - - - - - - - - - - - - - - - - - gtcctgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aactaaa