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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CAAATCCTAAACGTGCAGCACTGTTTTACGATCAATCTCTGTCTGGTGAAGATATTTATGAGCCTTTCTTAAGttaagtgtactatgtttgtttaattcttttattttttgtcttattaatttaaggaatctgctcatttcgttattcaacaaatagattgacatatattgcc...

Basic information

species Zea mays
transcript GRMZM2G163233_T04
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G163233_T04 (Zea mays), 5'ss of exon 5
lower sequence: Vv16s0039g01610.t01 (Vitis vinifera), 5'ss of exon 4
CAAATCCTAAACGTGCAGCACTGTTTTACGATCAATCTCTGTCTGGTGAAGATATTTATGAGCCTTTCTTAAGttaagtgtactatgtttgtttaattcttttattttttgtcttattaatttaaggaa--tctgctcatttcgttattcaacaaatagattgacatata--ttgcc
||||||| ||| | ||   ||| ||  | ||| | |||||  ||  |||||||| |||||| |||||||||||||||||     || |  |   ||||  || ||||| |||  |  |  || ||      | |  ||||  | | | | || | | | ||| |  | |   ||| |
CAAATCCAAAAAGAGCCAAACTATTCCATGATAAGTCTCTTGCTAATGAAGATACTTATGAACCTTTCTTAAgttaagt-----atctaagcaaaatttgttaattttgtgtaattgtgtttgaaactccttttattcatagcataaatgaatatagaaattcatttgtcccttgtc
















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|32864578|gb|CF004260.1|CF004260
EST:     TTTTACGACCAATCTCTGTCTGGTGAAGATATTTATGAGCCTTTCTTAAG                         GTTGTTATGGAAAGGCAACTGGTTTGTACAAGAAAAAAGTTGTAAGATATT
genomic: TTTTACGATCAATCTCTGTCTGGTGAAGATATTTATGAGCCTTTCTTAAGttaagtgtac ... tagttttcagGTTGTTATGGAAAGGCAACTGGTTTGTACAAGAAAAAAGTTGTAAGATATT
EST: gi|5439388|gb|AI820309.1|AI820309
EST:     ATATTTATGAGCCTTTCTTAAG                         GTTGTTATGGAAAGGCAACTGGTTTGTACAAGAAAAAAGTTGTAAGATATT
genomic: ATATTTATGAGCCTTTCTTAAGttaagtgtac ... tagttttcagGTTGTTATGGAAAGGCAACTGGTTTGTACAAGAAAAAAGTTGTAAGATATT
EST: gi|67023139|gb|CO451888.1|CO451888
EST:     TTTTACGACCAATCTCTGTCTGGTGAAGATATTTATGAGCCTTTCTTAAG                         GTTGTTATGGAAAGGCAACTGGTTTGTACAAGAAAAAAGTTGTAAGATATT
genomic: TTTTACGATCAATCTCTGTCTGGTGAAGATATTTATGAGCCTTTCTTAAGttaagtgtac ... tagttttcagGTTGTTATGGAAAGGCAACTGGTTTGTACAAGAAAAAAGTTGTAAGATATT
EST: gi|71757599|gb|DR955536.1|DR955536
EST:     TTTTACGATCAATCTCTGTCTGGTGAAGATATTTATGAGCCTTTCTTAAG                         GTTGTTATGGAAAGGCAACTGGTTTGTACAAGAAAAAAGTTGTAAGATATT
genomic: TTTTACGATCAATCTCTGTCTGGTGAAGATATTTATGAGCCTTTCTTAAGttaagtgtac ... tagttttcagGTTGTTATGGAAAGGCAACTGGTTTGTACAAGAAAAAAGTTGTAAGATATT
EST: gi|211460866|gb|FL363678.1|FL363678
EST:     TTTTACGATCAATCTCTGTCTGGTGAAGATATTTATGAGCCTTTCTTAAG                         GTTGTTATGGAAAGGCAACTGGTTTGTACAAGAAAAAAGTTGTAAGATATT
genomic: TTTTACGATCAATCTCTGTCTGGTGAAGATATTTATGAGCCTTTCTTAAGttaagtgtac ... tagttttcagGTTGTTATGGAAAGGCAACTGGTTTGTACAAGAAAAAAGTTGTAAGATATT

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: 178

CAAATCCTAAACGTGCAGCACTGTTTTACGATCAATCTCTGTCTGGTGAAGATATTTATGAGCCTTTCTTAAGttaagtgtac ... tagttttcagGTTGTTATGGAAAGGCAACTGGTTTGTACAAGAAAAAAGTTGTAAGATATTGACTGCTATAATCAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 253

CAAATCCTAAACGTGCAGCACTGTTTTACGATCAATCTCTGTCTGGTGAAGATATTTATGAGCCTTTCTTAAGttaagtgtac ... tagttttcagGTTGTTATGGAAAGGCAACTGGTTTGTACAAGAAAAAAGTTGTAAGATATTGACTGCTATAATCAG


Block sizes: 45 (upstream exon), 49 (downstream exon)
Score: 153

CAAATCCTAAACGTGCAGCACTGTTTTACGATCAATCTCTGTCTGGTGAAGATATTTATGAGCCTTTCTTAAGttaagtgtac ... tagttttcagGTTGTTATGGAAAGGCAACTGGTTTGTACAAGAAAAAAGTTGTAAGATATTGACTGCTATAATCAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 330

CAAATCCTAAACGTGCAGCACTGTTTTACGATCAATCTCTGTCTGGTGAAGATATTTATGAGCCTTTCTTAAGttaagtgtac ... tagttttcagGTTGTTATGGAAAGGCAACTGGTTTGTACAAGAAAAAAGTTGTAAGATATTGACTGCTATAATCAG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CAAATCCTAAACGTGCAGCACTGTTTTACGATCAATCTCTGTCTGGTGAAGATATTTATGAGCCTTTCTTAAGttaagtgtactatgtttgtttaattcttttattttttgtcttattaatttaaggaatctgctcatttcgttattcaacaaatagattgacatatattgcc

- - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aacaaata