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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagatcttcagacatgtttctactgattttctgtggctgatgcgagatgcactaacagacttttatcttgtagACAATCACTATAAAATGGATCTGGCCCCAAAGAAAGAAGCCATCAAAGTTATGATCCAAGACGAGTTAACCAAGTTATCAGAGGAGGACGAAGGAGAGGG

Basic information

species Zea mays
transcript GRMZM5G859592_T01
intron # 3
splice site 3'
intron type U2

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|20512968|gb|BQ280154.1|BQ280154
EST:     GCAACTTTCAGTGACATCCTTAAGAAGCTTG                         GCAATCACTATAAAATGGATCTGGCCCCAAAGAAAGAAGCCATCAAAGTTA
genomic: GCAACTTTCAGTGACATCCTTAAGAAGCTTGgtaagatctt ... tatcttgtagACAATCACTATAAAATGGATCTGGCCCCAAAGAAAGAAGCCATCAAAGTTA
EST: gi|60352017|gb|DN218990.1|DN218990
EST:     GCAACTTTCAGTGACATCCTTAAGAAGCTTG                         ACAATCACTATAAAATGGATCTGGCCCCAAAGAAAGAAGCCATCAAAGTTA
genomic: GCAACTTTCAGTGACATCCTTAAGAAGCTTGgtaagatctt ... tatcttgtagACAATCACTATAAAATGGATCTGGCCCCAAAGAAAGAAGCCATCAAAGTTA
EST: gi|60357734|gb|DN224707.1|DN224707
EST:     GCAACTTTCAGTGACATCCTTAAGAAGCTTG                         ACAATCACTATAAAATGGATCTGGCCCCAAAGAAAGAAGCCATCAAAGTTA
genomic: GCAACTTTCAGTGACATCCTTAAGAAGCTTGgtaagatctt ... tatcttgtagACAATCACTATAAAATGGATCTGGCCCCAAAGAAAGAAGCCATCAAAGTTA
EST: gi|60394022|gb|DN226892.1|DN226892
EST:     GCAACTTTCAGTGACATCCTTAAGAAGCTTG                         ACAATCACTATAAAATGGATCTGGCCCCAAAGAAAGAAGCCATCAAAGTTA
genomic: GCAACTTTCAGTGACATCCTTAAGAAGCTTGgtaagatctt ... tatcttgtagACAATCACTATAAAATGGATCTGGCCCCAAAGAAAGAAGCCATCAAAGTTA
EST: gi|5791276|gb|AI978068.1|AI978068
EST:     GCAACTTTCAGTGACATCCTTAAGAAGCTTG                         CCAATCCCTATAAAATGGATCTGGCCCCAAAGAAAGAAGCCATCAAAGTTA
genomic: GCAACTTTCAGTGACATCCTTAAGAAGCTTGgtaagatctt ... tatcttgtagACAATCACTATAAAATGGATCTGGCCCCAAAGAAAGAAGCCATCAAAGTTA
EST: gi|32840442|gb|CD980123.1|CD980123
EST:     GCAACTTTCAGTGACATCCTTAAGAAGCTTG                         ACAATCACTATAAAATGGATCTGGCCCCAAAGAAAGAAGCCATCAAAGTTA
genomic: GCAACTTTCAGTGACATCCTTAAGAAGCTTGgtaagatctt ... tatcttgtagACAATCACTATAAAATGGATCTGGCCCCAAAGAAAGAAGCCATCAAAGTTA
EST: gi|60359543|gb|DN226516.1|DN226516
EST:     GCAACTTTCAGTGACATCCTTAAGAAGCTTG                         ACAATCACTATAAAATGGATCTGGCCCCAAAGAAAGAAGCCATCAAAGTTA
genomic: GCAACTTTCAGTGACATCCTTAAGAAGCTTGgtaagatctt ... tatcttgtagACAATCACTATAAAATGGATCTGGCCCCAAAGAAAGAAGCCATCAAAGTTA
EST: gi|60342848|gb|DN209821.1|DN209821
EST:     GCAACTTTCAGTGACATCCTTAAGAAGCTTG                         ACAATCACTATAAAATGGATCTGGCCCCAAAGAAAGAAGCCATCAAAGTTA
genomic: GCAACTTTCAGTGACATCCTTAAGAAGCTTGgtaagatctt ... tatcttgtagACAATCACTATAAAATGGATCTGGCCCCAAAGAAAGAAGCCATCAAAGTTA
EST: gi|61118457|gb|DN559418.1|DN559418
EST:     GCAACTTTCAGTGACATCCTTAAGAAGCTTG                         ACAATCACTATAAAATGGATCTGGCCCCAAAGAAAGAAGCCATCAAAGTTA
genomic: GCAACTTTCAGTGACATCCTTAAGAAGCTTGgtaagatctt ... tatcttgtagACAATCACTATAAAATGGATCTGGCCCCAAAGAAAGAAGCCATCAAAGTTA
EST: gi|31360388|gb|CD444745.1|CD444745
EST:     GCAACTTTCAGTGACATCCTTAAGAAGCTTG                         ACAATCACTATAAAATGGATCTGGCCCCAAAGAAAGAAGCCATCAAAGTTA
genomic: GCAACTTTCAGTGACATCCTTAAGAAGCTTGgtaagatctt ... tatcttgtagACAATCACTATAAAATGGATCTGGCCCCAAAGAAAGAAGCCATCAAAGTTA
EST: gi|60340221|gb|DN207194.1|DN207194
EST:     GCAACTTTCAGTGACATCCTTAAGAAGCTTG                         ACAATCACTATAAAATGGATCTGGCCCCAAAGAAAGAAGCCATCAAAGTTA
genomic: GCAACTTTCAGTGACATCCTTAAGAAGCTTGgtaagatctt ... tatcttgtagACAATCACTATAAAATGGATCTGGCCCCAAAGAAAGAAGCCATCAAAGTTA
EST: gi|213192952|gb|FM183710.1|FM183710
EST:     GCAACTTTCAGTGACATCCTTAAGAAGCTTG                         ACAATCACTATAAAATGGATCTGGCCCCAAAGAAAGAAGCCATCAAAGTTA
genomic: GCAACTTTCAGTGACATCCTTAAGAAGCTTGgtaagatctt ... tatcttgtagACAATCACTATAAAATGGATCTGGCCCCAAAGAAAGAAGCCATCAAAGTTA
EST: gi|60344920|gb|DN211893.1|DN211893
EST:     GCAACTTTCAGTGACATCCTTAAGAAGCTTG                         ACAATCACTATAAAATGGATCTGGCCCCAAAGAAAGAAGCCATCAAAGTTA
genomic: GCAACTTTCAGTGACATCCTTAAGAAGCTTGgtaagatctt ... tatcttgtagACAATCACTATAAAATGGATCTGGCCCCAAAGAAAGAAGCCATCAAAGTTA
EST: gi|67015164|gb|CO443913.1|CO443913
EST:     GCAACTTTCAGTGACATCCTTAAGAAGCTTG                         ACAATCACTATAAAATGGATCTGGCCCCAAAGAAAGAAGCCATCAAAGTTA
genomic: GCAACTTTCAGTGACATCCTTAAGAAGCTTGgtaagatctt ... tatcttgtagACAATCACTATAAAATGGATCTGGCCCCAAAGAAAGAAGCCATCAAAGTTA
EST: gi|211463894|gb|FL171640.1|FL171640
EST:     GCAACTTTCAGTGACATCCTTAAGAAGCTTG                         ATAATCACTATAAAATGGATCTGGCCCCAAAGAAAGAAGCCATCAAAGTTA
genomic: GCAACTTTCAGTGACATCCTTAAGAAGCTTGgtaagatctt ... tatcttgtagACAATCACTATAAAATGGATCTGGCCCCAAAGAAAGAAGCCATCAAAGTTA
EST: gi|211463893|gb|FL171639.1|FL171639
EST:     GCAACTTTCAGTGACATCCTTAAGAAGCTTG                         ACAATCACTATAAAATGGATCTGGCCCCAAAGAAAGAAGCCATCAAAGTTA
genomic: GCAACTTTCAGTGACATCCTTAAGAAGCTTGgtaagatctt ... tatcttgtagACAATCACTATAAAATGGATCTGGCCCCAAAGAAAGAAGCCATCAAAGTTA
EST: gi|30087353|gb|CB885559.1|CB885559
EST:     GCAACTTTCAGTGACATCCTTAAGAAGCTTG                         ACAATCACTATAAAATGGATCTGGCCCCAAAGAAAGAAGCCATCAAAGTTA
genomic: GCAACTTTCAGTGACATCCTTAAGAAGCTTGgtaagatctt ... tatcttgtagACAATCACTATAAAATGGATCTGGCCCCAAAGAAAGAAGCCATCAAAGTTA

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: 1068

GCAACTTTCAGTGACATCCTTAAGAAGCTTGgtaagatctt ... tatcttgtagACAATCACTATAAAATGGATCTGGCCCCAAAGAAAGAAGCCATCAAAGTTATGATCCAAGACGAGTTAACCAAGTTATCAGAGGAGGACGAAGGAGAGGG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 384

GCAACTTTCAGTGACATCCTTAAGAAGCTTGgtaagatctt ... tatcttgtagACAATCACTATAAAATGGATCTGGCCCCAAAGAAAGAAGCCATCAAAGTTATGATCCAAGACGAGTTAACCAAGTTATCAGAGGAGGACGAAGGAGAGGG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 579

GCAACTTTCAGTGACATCCTTAAGAAGCTTGgtaagatctt ... tatcttgtagACAATCACTATAAAATGGATCTGGCCCCAAAGAAAGAAGCCATCAAAGTTATGATCCAAGACGAGTTAACCAAGTTATCAGAGGAGGACGAAGGAGAGGG


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 394

GCAACTTTCAGTGACATCCTTAAGAAGCTTGgtaagatctt ... tatcttgtagACAATCACTATAAAATGGATCTGGCCCCAAAGAAAGAAGCCATCAAAGTTATGATCCAAGACGAGTTAACCAAGTTATCAGAGGAGGACGAAGGAGAGGG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tctactgattttctgtggctgatgcgagatgcactaacagacttttatcttgtagACAATCACTATAAAATGGATCTGGCCCCAAAGAAAGAAGCCATCAAAGTTATGATCCAAGACGAGTTAACCAAGTTATCAGAGGAGGACGAAGGAGAGGG
                               cactaac  putative branch site (score: 394)
                                         cttttatctt  putative PPT
                                          ttttatctt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagatcttcagacatgtttctactgattttctgtggctgatgcgagatgcactaacagacttttatcttgtagACAATCACTATAAAATGGATCTGGCCCCAAAGAAAGAAGCCATCAAAGTTATGATCCAAGACGAGTTAACCAAGTTATCAGAGGAGGACGAAGGAGAGGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGAGG