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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...actagttaatgctagtttcctttcatatgatttggaactgcctgaacagccgccatatgctatcatcgttaatgcaagcatactactacttttttttcagGTGAAGGCTGAAGCCATATATCCTGTAAGTAACGCGCCAAATACCTTTTGAGACTTAATAATCTTGTTTTGTTCCGCCTGTCTCAAGCCGGGTTCCTTCA

Basic information

species Zea mays
transcript GRMZM2G143356_T02
intron # 12
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|211269252|gb|FK955991.1|FK955991
EST:     TTATCTAATAGTTGCTGCCAGTTTCTTTGTTCACGTTGATCCACAATCAA                         GTGAAGGCTGAAGCCATATATCCTGTAAGTAACGCGCCAAATACCTTTTGA
genomic: TTATCTAATAGTTGCTGCCAGTTTCTTTGTTCACGTTGATCCACAATCAAgtgagtagga ... tttttttcagGTGAAGGCTGAAGCCATATATCCTGTAAGTAACGCGCCAAATACCTTTTGA
EST: gi|211145245|gb|FL448473.1|FL448473
EST:     TTATCTAATAGTTGCTGCCAGTTTCTTTGTTCACGTTGATCCACAATCAA                         GTGAAGGCTGAAGCCATATATCCTGTAAGTAACGCGCCAAATACCTTTTGA
genomic: TTATCTAATAGTTGCTGCCAGTTTCTTTGTTCACGTTGATCCACAATCAAgtgagtagga ... tttttttcagGTGAAGGCTGAAGCCATATATCCTGTAAGTAACGCGCCAAATACCTTTTGA
EST: gi|60357296|gb|DN224269.1|DN224269
EST:     TTATCTAATAGTTGCTGCCAGTTTCTTTGTTCACGTTGATCCACAATCAA                         GTGAAGGCTGAAGCCATATATCCTGTAAGTAACGCGCCAAATACCTTTTGA
genomic: TTATCTAATAGTTGCTGCCAGTTTCTTTGTTCACGTTGATCCACAATCAAgtgagtagga ... tttttttcagGTGAAGGCTGAAGCCATATATCCTGTAAGTAACGCGCCAAATACCTTTTGA
EST: gi|148952029|gb|EC897815.2|EC897815
EST:     TTATTTAATAGTTGCTGCCAGTTTCTTTGTTCACGTTGATCCACAATCAA                         GTGAAGGCTGAAGCCATATATCCTGTAAGTAACGCGCCAAATACCTTTTGA
genomic: TTATCTAATAGTTGCTGCCAGTTTCTTTGTTCACGTTGATCCACAATCAAgtgagtagga ... tttttttcagGTGAAGGCTGAAGCCATATATCCTGTAAGTAACGCGCCAAATACCTTTTGA
EST: gi|211269251|gb|FK955990.1|FK955990
EST:     TTATCTAATAGTTGCTGCCAGTTTCTTTGTTCACGTTGATCCACAATCAA                         GTGAAGGCTGAAGCCATATATCCTGTAAGTAACGCGCCAAATACCTTTTGA
genomic: TTATCTAATAGTTGCTGCCAGTTTCTTTGTTCACGTTGATCCACAATCAAgtgagtagga ... tttttttcagGTGAAGGCTGAAGCCATATATCCTGTAAGTAACGCGCCAAATACCTTTTGA
EST: gi|12968375|gb|BG265321.1|BG265321
EST:     TTATCTAATAGTTGCTGCCAGTTTCTTTGTTCACGTTGATCCACAATCAA                         GTGAAGGCTGAAGCCATATATCCTGTAAGTAACGCGCCAAATACCTTTTGA
genomic: TTATCTAATAGTTGCTGCCAGTTTCTTTGTTCACGTTGATCCACAATCAAgtgagtagga ... tttttttcagGTGAAGGCTGAAGCCATATATCCTGTAAGTAACGCGCCAAATACCTTTTGA
EST: gi|91870161|gb|EB400733.1|EB400733
EST:     TTATCTAATAGTTGCTGCCAGTTTCTTTGTTCACGTTGATCCACAATCAA                         GTGAAGGCTGAAGCCATATATC
genomic: TTATCTAATAGTTGCTGCCAGTTTCTTTGTTCACGTTGATCCACAATCAAgtgagtagga ... tttttttcagGTGAAGGCTGAAGCCATATATC
EST: gi|60351533|gb|DN218506.1|DN218506
EST:     TTATCTAATAGTTGCTGCCAGTTTCTTTGTTCACGTTGATCCACAATCAA                         GTGAAGGCTGAAGCCATATATCCTGTAAGTAACGCGCCAAATACCTTTTGA
genomic: TTATCTAATAGTTGCTGCCAGTTTCTTTGTTCACGTTGATCCACAATCAAgtgagtagga ... tttttttcagGTGAAGGCTGAAGCCATATATCCTGTAAGTAACGCGCCAAATACCTTTTGA
EST: gi|110949660|gb|EE169817.1|EE169817
EST:     TTATTTAATAGTTGCTGCCAGTTTCTTTGTTCACGTTGATCCACAATCAA                         GTGAAGGCTGAAGCCATATATCCTGTAAGTAACGCGCCAAATACCTTTTGA
genomic: TTATCTAATAGTTGCTGCCAGTTTCTTTGTTCACGTTGATCCACAATCAAgtgagtagga ... tttttttcagGTGAAGGCTGAAGCCATATATCCTGTAAGTAACGCGCCAAATACCTTTTGA
EST: gi|211269249|gb|FK955988.1|FK955988
EST:     TTATCTAATAGTTGCTGCCAGTTTCTTTGTTCACGTTGATCCACAATCAA                         GTGAAGGCTGAAGCCATATATCCTGTAAGTAACGCGCCAAATACCTTTTGA
genomic: TTATCTAATAGTTGCTGCCAGTTTCTTTGTTCACGTTGATCCACAATCAAgtgagtagga ... tttttttcagGTGAAGGCTGAAGCCATATATCCTGTAAGTAACGCGCCAAATACCTTTTGA
EST: gi|211269248|gb|FK955987.1|FK955987
EST:     TTATCTAATAGTTGCTGCCAGTTTCTTTGTTCACGTTGATCCACAATCAA                         GTGAAGGCTGAAGCCATATATCCTGTAAGTAACGCGCCAAATACCTTTTGA
genomic: TTATCTAATAGTTGCTGCCAGTTTCTTTGTTCACGTTGATCCACAATCAAgtgagtagga ... tttttttcagGTGAAGGCTGAAGCCATATATCCTGTAAGTAACGCGCCAAATACCTTTTGA
EST: gi|148951917|gb|EC897693.2|EC897693
EST:     TTATTTAATAGTTGCTGCCAGTTTCTTTGTTCACGTTGATCCACAATCAA                         GTGAAGGCTGAAGCCATATATCCTGTAAGTAACGCGCCAAATACCTTTTGA
genomic: TTATCTAATAGTTGCTGCCAGTTTCTTTGTTCACGTTGATCCACAATCAAgtgagtagga ... tttttttcagGTGAAGGCTGAAGCCATATATCCTGTAAGTAACGCGCCAAATACCTTTTGA

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), 46 (downstream exon)
Score: 61

GATGGCACTGCGAACTACTTGAAAGGACTTATGCTGATCCTATGTTATCTAATAGTTGCTGCCAGTTTCTTTGTTCACGTTGATCCACAATCAAgtgagtagga ... tttttttcagGTGAAGGCTGAAGCCATATATCCTGTAAGTAACGCGCCAAATACCTTTTGAGACTTAATAATCTTGTTTTGTTCCGCCTGTCTCAAGCCGGGTTCCTTCA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 113

GATGGCACTGCGAACTACTTGAAAGGACTTATGCTGATCCTATGTTATCTAATAGTTGCTGCCAGTTTCTTTGTTCACGTTGATCCACAATCAAgtgagtagga ... tttttttcagGTGAAGGCTGAAGCCATATATCCTGTAAGTAACGCGCCAAATACCTTTTGAGACTTAATAATCTTGTTTTGTTCCGCCTGTCTCAAGCCGGGTTCCTTCA


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 133

GATGGCACTGCGAACTACTTGAAAGGACTTATGCTGATCCTATGTTATCTAATAGTTGCTGCCAGTTTCTTTGTTCACGTTGATCCACAATCAAgtgagtagga ... tttttttcagGTGAAGGCTGAAGCCATATATCCTGTAAGTAACGCGCCAAATACCTTTTGAGACTTAATAATCTTGTTTTGTTCCGCCTGTCTCAAGCCGGGTTCCTTCA


Block sizes: 49 (upstream exon), 45 (downstream exon)
Score: 106

GATGGCACTGCGAACTACTTGAAAGGACTTATGCTGATCCTATGTTATCTAATAGTTGCTGCCAGTTTCTTTGTTCACGTTGATCCACAATCAAgtgagtagga ... tttttttcagGTGAAGGCTGAAGCCATATATCCTGTAAGTAACGCGCCAAATACCTTTTGAGACTTAATAATCTTGTTTTGTTCCGCCTGTCTCAAGCCGGGTTCCTTCA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acagccgccatatgctatcatcgttaatgcaagcatactactacttttttttcagGTGAAGGCTGAAGCCATATATCCTGTAAGTAACGCGCCAAATACCTTTTGAGACTTAATAATCTTGTTTTGTTCCGCCTGTCTCAAGCCGGGTTCCTTCA
                     cgttaat  putative branch site (score: 106)
                                     ctactacttttttttc  putative PPT
                                      tactactttttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
actagttaatgctagtttcctttcatatgatttggaactgcctgaacagccgccatatgctatcatcgttaatgcaagcatactactacttttttttcagGTGAAGGCTGAAGCCATATATCCTGTAAGTAACGCGCCAAATACCTTTTGAGACTTAATAATCTTGTTTTGTTCCGCCTGTCTCAAGCCGGGTTCCTTCA

- - - taatgct
- - - - - - - - - -ctttcat
- - - - - - - - - - - - - -tgatttg
- - - - - - - - - - - - - - - - - - - -gcctgaa
- - - - - - - - - - - - - - - - - - - - - - - cagccgc
- - - - - - - - - - - - - - - - - - - - - - - - - - -catatgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgcaagc