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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gcatgtcatgttgcctacaattggatctcttttcttcattccaacactgttttctccatatactgttcctttactgataaccgtttgttttgcaagtcagATTTTACTATTTGCTGTTGCAAGCGAGTCCACCAAATTTCTGCCCATCTTTAAGGAAGCAGCAAAACCATTTAAGGGAAAG

Basic information

species Zea mays
transcript GRMZM2G134889_T01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G134889_T01 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os02g01010.1 (Oryza sativa), 3'ss of exon 4
gcatgtcatgttgcctacaattgg-atctcttttcttcattccaacactgttttctccatatac-tgttcctttactgataaccgtttgttttgcaagtcagATTTTACTATTTGCTGTTGCAAGCGAGTCCACCAAATTTCTGCCCATCTTTAAGGAAGCAGCAAAACCATTTAAGGGAAAG
               |  |||||  ||  ||| | | |||| |     | |||  ||||| ||    || ||   ||| ||||  ||| |||| |||  |||||||||||||||| |||||||| ||| ||  | ||||||||||||||||||||||||||| ||||| |||| ||||| |||
----------gcatgtctaattgatattgcttctgtacatttctcacttttttggtccatttatacattactgggctgctaact-tttatttttcaaaccagATTTTACTATTTGTTGTTGCAAACGAATCGTCGAAATTTCTGCCCATCTTTAAGGAAGCATCAAAATCATTCAAGGGGAAG
















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|148974381|gb|EE025158.2|EE025158
EST:     TAACTCAAGAAACTTCCCCTTCTATTTTTGGCAATCCAATCAAGAAGCAG                         ATTTTACTATTTGCTGTTGNCA-GCGAGTCCACCAAATTTCTGCCCATCTT
genomic: TAACTCAAGAAACTTCCCCTTCTATTTTTGGCAATCCAATCAAGAAGCAGgcatgtcatg ... tgcaagtcagATTTTACTATTTGCTGTTG-CAAGCGAGTCCACCAAATTTCTGCCCATCTT
EST: gi|31909789|gb|CD651094.1|CD651094
EST:     TAACTCAAGAAACTTCCCCTTCTATTTTGGGCAATCCAATCAAGAAGCAG                         ATTTTACTATTTGCTGTTGCAAGCGAGTCCACCAAATTTCTGCCCATCTTT
genomic: TAACTCAAGAAACTTCCCCTTCTATTTTTGGCAATCCAATCAAGAAGCAGgcatgtcatg ... tgcaagtcagATTTTACTATTTGCTGTTGCAAGCGAGTCCACCAAATTTCTGCCCATCTTT
EST: gi|19057888|gb|BM736555.1|BM736555
EST:     TAACTCAAGAAACTTCCCCTTCTATTTTTGGCAATCCAATCAAGAAGCAG                         ATTTTACTATTTGCTGTTGCAAGCGAGTCCACCAAATTTCTGCCCATCTTT
genomic: TAACTCAAGAAACTTCCCCTTCTATTTTTGGCAATCCAATCAAGAAGCAGgcatgtcatg ... tgcaagtcagATTTTACTATTTGCTGTTGCAAGCGAGTCCACCAAATTTCTGCCCATCTTT
EST: gi|67020721|gb|CO449470.1|CO449470
EST:     TAACTCAAAAAACTTCCCCTTCTATTTTTGGCAATCCAATCAAGAAGCAG                         ATTTTACTATTTGCTGTTGCAAGCGAGTCCACCAAATTTCTGCCCATCTTT
genomic: TAACTCAAGAAACTTCCCCTTCTATTTTTGGCAATCCAATCAAGAAGCAGgcatgtcatg ... tgcaagtcagATTTTACTATTTGCTGTTGCAAGCGAGTCCACCAAATTTCTGCCCATCTTT
EST: gi|211496710|gb|FL402045.1|FL402045
EST:     TAACTCAAGAAACTTCCCCTTCTATTTTTGGCAATCCAATCAAGAAGCAG                         ATTTTACTATTTGCTGTTGCAAGCGAGTCCACCAAATTTMTGCMCATCTTT
genomic: TAACTCAAGAAACTTCCCCTTCTATTTTTGGCAATCCAATCAAGAAGCAGgcatgtcatg ... tgcaagtcagATTTTACTATTTGCTGTTGCAAGCGAGTCCACCAAATTTCTGCCCATCTTT
EST: gi|19855080|gb|BQ060132.1|BQ060132
EST:     TAACTCAAGAAACTTCCCCTTCTATTTTTGGCAATCCAATCAAGAAGCAG                         ATTTTACTATTTGCTGTTGCAAGCGAGTCCACCAAATTTCTGCCCATCTTT
genomic: TAACTCAAGAAACTTCCCCTTCTATTTTTGGCAATCCAATCAAGAAGCAGgcatgtcatg ... tgcaagtcagATTTTACTATTTGCTGTTGCAAGCGAGTCCACCAAATTTCTGCCCATCTTT

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: 47 (upstream exon), 48 (downstream exon)
Score: 123

AGCCATTGCTGGTTTTGTGTCTGCTAACAAGCTTCCTTTGGTGACCACACTAACTCAAGAAACTTCCCCTTCTATTTTTGGCAATCCAATCAAGAAGCAGgcatgtcatg ... tgcaagtcagATTTTACTATTTGCTGTTGCAAGCGAGTCCACCAAATTTCTGCCCATCTTTAAGGAAGCAGCAAAACCATTTAAGGGAAAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 174

AGCCATTGCTGGTTTTGTGTCTGCTAACAAGCTTCCTTTGGTGACCACACTAACTCAAGAAACTTCCCCTTCTATTTTTGGCAATCCAATCAAGAAGCAGgcatgtcatg ... tgcaagtcagATTTTACTATTTGCTGTTGCAAGCGAGTCCACCAAATTTCTGCCCATCTTTAAGGAAGCAGCAAAACCATTTAAGGGAAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 189

AGCCATTGCTGGTTTTGTGTCTGCTAACAAGCTTCCTTTGGTGACCACACTAACTCAAGAAACTTCCCCTTCTATTTTTGGCAATCCAATCAAGAAGCAGgcatgtcatg ... tgcaagtcagATTTTACTATTTGCTGTTGCAAGCGAGTCCACCAAATTTCTGCCCATCTTTAAGGAAGCAGCAAAACCATTTAAGGGAAAG


Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 150

AGCCATTGCTGGTTTTGTGTCTGCTAACAAGCTTCCTTTGGTGACCACACTAACTCAAGAAACTTCCCCTTCTATTTTTGGCAATCCAATCAAGAAGCAGgcatgtcatg ... tgcaagtcagATTTTACTATTTGCTGTTGCAAGCGAGTCCACCAAATTTCTGCCCATCTTTAAGGAAGCAGCAAAACCATTTAAGGGAAAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

actgttttctccatatactgttcctttactgataaccgtttgttttgcaagtcagATTTTACTATTTGCTGTTGCAAGCGAGTCCACCAAATTTCTGCCCATCTTTAAGGAAGCAGCAAAACCATTTAAGGGAAAG
                             tgataac  putative branch site (score: 150)
                                      tttgtttt  putative PPT
                                      tttgtttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gcatgtcatgttgcctacaattggatctcttttcttcattccaacactgttttctccatatactgttcctttactgataaccgtttgttttgcaagtcagATTTTACTATTTGCTGTTGCAAGCGAGTCCACCAAATTTCTGCCCATCTTTAAGGAAGCAGCAAAACCATTTAAGGGAAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAA