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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtgtatactttatttgcaggtcactgtatataatttttgtcaccaagttatttacacaattcccttaatactcctgcagGATGGGAAAATTGATTCAATGGAAGCTAAACAG

Basic information

species Zea mays
transcript GRMZM2G558539_T02
intron # 7
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|60339589|gb|DN206562.1|DN206562
EST:     AGAATATTGGTTCAGAAATCAAGAACATCAAAGAATTGGTTTGGGGTCTG                         GATGGGAAAATTGATTCAATGGAAGCTAAACAG
genomic: AGAATATTGGTTCAGAAATCAAGAACATCAAAGAATTGGTTTGGGGTCTGgtaagtgtat ... actcctgcagGATGGGAAAATTGATTCAATGGAAGCTAAACAG
EST: gi|60358480|gb|DN225453.1|DN225453
EST:     AGAATATTGGTTCAGAAATCAAGAACATCAAAGAATTGGTTTGGGGTCTG                         GATGGGAAAATTGATTCAATGGAAGCTAAACAG
genomic: AGAATATTGGTTCAGAAATCAAGAACATCAAAGAATTGGTTTGGGGTCTGgtaagtgtat ... actcctgcagGATGGGAAAATTGATTCAATGGAAGCTAAACAG
EST: gi|86471474|gb|DY237844.1|DY237844
EST:     AGAATATTGGTTCAGAAATCAAGAACATCAAAGAATTGGTTTGGGGTCTG                         GATGGGAAAATTGATTCAATGGAAGCTAAACAG
genomic: AGAATATTGGTTCAGAAATCAAGAACATCAAAGAATTGGTTTGGGGTCTGgtaagtgtat ... actcctgcagGATGGGAAAATTGATTCAATGGAAGCTAAACAG
EST: gi|5936814|gb|AW060082.1|AW060082
EST:     AGAATATTGGTTCAGAAATCAAGAACATCAAAGAATTGGTTTGGGGTCTG                         GATGGGAAAATTGATTCAATGGAAGCTAAACAG
genomic: AGAATATTGGTTCAGAAATCAAGAACATCAAAGAATTGGTTTGGGGTCTGgtaagtgtat ... actcctgcagGATGGGAAAATTGATTCAATGGAAGCTAAACAG
EST: gi|60354187|gb|DN221160.1|DN221160
EST:     GAATTGGTTGGGGGTCTG                         GATGGGAAAATTGATTCAATGGAAGCTAAACAG
genomic: GAATTGGTTTGGGGTCTGgtaagtgtat ... actcctgcagGATGGGAAAATTGATTCAATGGAAGCTAAACAG
EST: gi|76925222|gb|DV170325.1|DV170325
EST:     AGAATATTGGTTCAGAAATCAAGAACATCAAAGAATTGGTTTGGGGTCTG                         GATGGGAAAATTGATTCAATGGAAGCTAAACAG
genomic: AGAATATTGGTTCAGAAATCAAGAACATCAAAGAATTGGTTTGGGGTCTGgtaagtgtat ... actcctgcagGATGGGAAAATTGATTCAATGGAAGCTAAACAG
EST: gi|60398906|gb|DN231722.1|DN231722
EST:     CAAAGAATTGGTTTGGGGTCTG                         GATGGGAAAATTGATTCAATGGAAGCTAAACAG
genomic: CAAAGAATTGGTTTGGGGTCTGgtaagtgtat ... actcctgcagGATGGGAAAATTGATTCAATGGAAGCTAAACAG
EST: gi|71300395|gb|DR786266.1|DR786266
EST:     AGAATATTGGTTCAGAAATCAAGAACATCAAAGAATTGGTTTGGGGTCTG                         GATGGGAAAATTGATTCAATGGAAGCTAAACAG
genomic: AGAATATTGGTTCAGAAATCAAGAACATCAAAGAATTGGTTTGGGGTCTGgtaagtgtat ... actcctgcagGATGGGAAAATTGATTCAATGGAAGCTAAACAG
EST: gi|60340147|gb|DN207120.1|DN207120
EST:     AGAATATTGGTTCAGAAATCAAGAACATCAAAGAATTGGTTTGGGGTCTG                         GATGGGAAAATTGATTCAATGGAAGCTAAACAG
genomic: AGAATATTGGTTCAGAAATCAAGAACATCAAAGAATTGGTTTGGGGTCTGgtaagtgtat ... actcctgcagGATGGGAAAATTGATTCAATGGAAGCTAAACAG
EST: gi|86474502|gb|DY240872.1|DY240872
EST:     AGAATATTGGTTCAGAAATCAAGAACATCAAAGAATTGGTTTGGGGTCTG                         GATGGGAAAATTGATTCAATGGAAGCTAAACAG
genomic: AGAATATTGGTTCAGAAATCAAGAACATCAAAGAATTGGTTTGGGGTCTGgtaagtgtat ... actcctgcagGATGGGAAAATTGATTCAATGGAAGCTAAACAG
EST: gi|60354933|gb|DN221906.1|DN221906
EST:     GGTTCAGAAATCAAGAACATCAAAGAATTGGTTTGGGGTCTG                         GATGGGAAAATTGATTCAATGGAAGCTAAACAG
genomic: GGTTCAGAAATCAAGAACATCAAAGAATTGGTTTGGGGTCTGgtaagtgtat ... actcctgcagGATGGGAAAATTGATTCAATGGAAGCTAAACAG
EST: gi|110944775|gb|EE164932.1|EE164932
EST:     AGAATATTGGTTCAGAAATCAAGAACATCAAAGAATTGGTTTGGGGTCTG                         GATGGGAAAATTGATTCAATGGAAGCTAAACAG
genomic: AGAATATTGGTTCAGAAATCAAGAACATCAAAGAATTGGTTTGGGGTCTGgtaagtgtat ... actcctgcagGATGGGAAAATTGATTCAATGGAAGCTAAACAG
EST: gi|71329626|gb|DR801542.1|DR801542
EST:     AGAATATTGGTTCAGAAATCAAGAACATCAAAGAATTGGTTTGGGGTCTG                         GATGGGAAAATTGATTCAATGGAAGCTAAACAG
genomic: AGAATATTGGTTCAGAAATCAAGAACATCAAAGAATTGGTTTGGGGTCTGgtaagtgtat ... actcctgcagGATGGGAAAATTGATTCAATGGAAGCTAAACAG
EST: gi|211119819|gb|FL462976.1|FL462976
EST:     GAATATTGTTTCAGAAATC-AGAACCATCAAAGAAATGGTTTGGGTTCTG                         GATGGGAAAATTGATTCAATGGAAGCTAAACAG
genomic: GAATATTGGTTCAGAAATCAAGAA-CATCAAAGAATTGGTTTGGGGTCTGgtaagtgtat ... actcctgcagGATGGGAAAATTGATTCAATGGAAGCTAAACAG
EST: gi|93011741|gb|EB637261.1|EB637261
EST:     AGAATATTGGTTCAGAAATCAAGAACATCAAAGAATTGGTTTGGGGTCTG                         GATGGGAAAATTGATTCAATGGAAGCTAAACAG
genomic: AGAATATTGGTTCAGAAATCAAGAACATCAAAGAATTGGTTTGGGGTCTGgtaagtgtat ... actcctgcagGATGGGAAAATTGATTCAATGGAAGCTAAACAG
EST: gi|93282521|gb|EB674785.1|EB674785
EST:     AGAATATTGGTTCAGAAATCAAGAACATCAAAGAATTGGTTTGGGGTCTG                         GATGGGAAAATTGATTCAATGGAAGCTAAACAG
genomic: AGAATATTGGTTCAGAAATCAAGAACATCAAAGAATTGGTTTGGGGTCTGgtaagtgtat ... actcctgcagGATGGGAAAATTGATTCAATGGAAGCTAAACAG
EST: gi|71321373|gb|DR797399.1|DR797399
EST:     TGGTTTGGGGTCTG                         GAGGGGAAAATTGATTCAATGGAAGCTAAACAG
genomic: TGGTTTGGGGTCTGgtaagtgtat ... actcctgcagGATGGGAAAATTGATTCAATGGAAGCTAAACAG
EST: gi|32929416|gb|CF034228.1|CF034228
EST:     AGAATATTGGTTCAGAAATCAAGAACATCAAAGAATTGGGTTGGGGTCTG                         GATGGGAAAATTGATTCAATGGAAGCTAAACAG
genomic: AGAATATTGGTTCAGAAATCAAGAACATCAAAGAATTGGTTTGGGGTCTGgtaagtgtat ... actcctgcagGATGGGAAAATTGATTCAATGGAAGCTAAACAG
EST: gi|71332095|gb|DR802954.1|DR802954
EST:     AGAATATTGGTTCAGAAATCAAGAACATCAAAGAATTGGTTTGGGGTCTG                         GATGGGAAAATTGATTCAATGGAAGCTAAACAG
genomic: AGAATATTGGTTCAGAAATCAAGAACATCAAAGAATTGGTTTGGGGTCTGgtaagtgtat ... actcctgcagGATGGGAAAATTGATTCAATGGAAGCTAAACAG
EST: gi|166646694|gb|EG294487.1|EG294487
EST:     AGAATATTGGTTCAGAAATTAAGAACATCAAAGAATTAGTTTGGGGTCTG                         GATGGGAAAATTGATTCAATGGAAGCTAAACAG
genomic: AGAATATTGGTTCAGAAATCAAGAACATCAAAGAATTGGTTTGGGGTCTGgtaagtgtat ... actcctgcagGATGGGAAAATTGATTCAATGGAAGCTAAACAG

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: 568

GTCACTGATGCACGTCTGAAGCTTGAGAATATTGGTTCAGAAATCAAGAACATCAAAGAATTGGTTTGGGGTCTGgtaagtgtat ... actcctgcagGATGGGAAAATTGATTCAATGGAAGCTAAACAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 1035

GTCACTGATGCACGTCTGAAGCTTGAGAATATTGGTTCAGAAATCAAGAACATCAAAGAATTGGTTTGGGGTCTGgtaagtgtat ... actcctgcagGATGGGAAAATTGATTCAATGGAAGCTAAACAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 1070

GTCACTGATGCACGTCTGAAGCTTGAGAATATTGGTTCAGAAATCAAGAACATCAAAGAATTGGTTTGGGGTCTGgtaagtgtat ... actcctgcagGATGGGAAAATTGATTCAATGGAAGCTAAACAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 746

GTCACTGATGCACGTCTGAAGCTTGAGAATATTGGTTCAGAAATCAAGAACATCAAAGAATTGGTTTGGGGTCTGgtaagtgtat ... actcctgcagGATGGGAAAATTGATTCAATGGAAGCTAAACAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgtatataatttttgtcaccaagttatttacacaattcccttaatactcctgcagGATGGGAAAATTGATTCAATGGAAGCTAAACAG
                                      ccttaat  putative branch site (score: 746)
                                            tactcct  CT-rich tract
                       ttatttacacaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagtgtatactttatttgcaggtcactgtatataatttttgtcaccaagttatttacacaattcccttaatactcctgcagGATGGGAAAATTGATTCAATGGAAGCTAAACAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG