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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagaaccctttgtctctgtattaacgagtgcatgttttccattattggaagtcctaatccctgtgcaatgcatcttccttcagTGAGTTTTGCAGGATGGTGAAAAGGATTTACATTTACACATACGAGGAGGCAAAGAAGCTGACATCCAAGTCAAAGTTACCGGTTAGCAGTGACAGCAGC

Basic information

species Zea mays
transcript GRMZM2G017187_T02
intron # 13
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|22546670|gb|BU098981.1|BU098981
EST:     TTCACTGATGATGAGGATGACATGATGCTTGTTGGAGATGATCCTTGGGA                         TGAGTTTTGCAGGATGGTGAAAAGGATTTACATTTACACATAC-AGGAGGC
genomic: TTCACTGATGATGAGGATGACATGATGCTTGTTGGAGATGATCCTTGGGAgtaagaaccc ... cttccttcagTGAGTTTTGCAGGATGGTGAAAAGGATTTACATTTACACATACGAGGAGGC
EST: gi|20506801|gb|BQ279347.1|BQ279347
EST:     TTCACTGATGATGAGGATGACATGATGCTTGTTGGAGATGATCCTTGGGA                         TGAGTTTTGCAGGATGGTGAAAAGGATTTACATTTACACATACGAGGAGGC
genomic: TTCACTGATGATGAGGATGACATGATGCTTGTTGGAGATGATCCTTGGGAgtaagaaccc ... cttccttcagTGAGTTTTGCAGGATGGTGAAAAGGATTTACATTTACACATACGAGGAGGC
EST: gi|76011838|gb|DT939008.1|DT939008
EST:     TTCACTGATGATGAGGATGACATGATGCTTGTTGGAGATGATCCTTGGGA                         TGAGTTTTGCAGGATGGTGAAAAGGATTTACATTTACACATACGAGGAGGC
genomic: TTCACTGATGATGAGGATGACATGATGCTTGTTGGAGATGATCCTTGGGAgtaagaaccc ... cttccttcagTGAGTTTTGCAGGATGGTGAAAAGGATTTACATTTACACATACGAGGAGGC
EST: gi|71761940|gb|DR959877.1|DR959877
EST:     TTCACTGATGATGAGGATGACATGATGCTTGTTGGAGATGATCCTTGGGA                         TGAGTTTTGCAGGATGGTGAAAAGGATTTACATTTACACATACGAGGAGGC
genomic: TTCACTGATGATGAGGATGACATGATGCTTGTTGGAGATGATCCTTGGGAgtaagaaccc ... cttccttcagTGAGTTTTGCAGGATGGTGAAAAGGATTTACATTTACACATACGAGGAGGC
EST: gi|76016628|gb|DT943798.1|DT943798
EST:     TTCACTGATGATGAGGATGACATGATGCTTGTTGGAGATGATCCTTGGGA                         TGAGTTTTGCAGGATGGTGAAAAGGATTTACATTTACACATACGAGGAGGC
genomic: TTCACTGATGATGAGGATGACATGATGCTTGTTGGAGATGATCCTTGGGAgtaagaaccc ... cttccttcagTGAGTTTTGCAGGATGGTGAAAAGGATTTACATTTACACATACGAGGAGGC
EST: gi|211002036|gb|FL118778.1|FL118778
EST:     TTCACTGATGATGAGGATGACATGATGCTTGTTGGAGATGATCCTTGGGA                         TGAGTTTTGCAGGATGGTGAAAAGGATTTACATTTACACATACGAGGAGGC
genomic: TTCACTGATGATGAGGATGACATGATGCTTGTTGGAGATGATCCTTGGGAgtaagaaccc ... cttccttcagTGAGTTTTGCAGGATGGTGAAAAGGATTTACATTTACACATACGAGGAGGC
EST: gi|47962491|gb|CN845200.1|CN845200
EST:     TTCACTGATGATGAGGATGACATGATGCTTGTTGGAGATGATCCTTGGGA                         TGAGTTTTGCAGGATGGTGAAAAGGATTTACATTTACACATACGAGGAGGC
genomic: TTCACTGATGATGAGGATGACATGATGCTTGTTGGAGATGATCCTTGGGAgtaagaaccc ... cttccttcagTGAGTTTTGCAGGATGGTGAAAAGGATTTACATTTACACATACGAGGAGGC
EST: gi|211002035|gb|FL118777.1|FL118777
EST:     TTCACTGATGATGAGGATGACATGATGCTTGTTGGAGATGATCCTTGGGA                         TGAGTTTTGCAGGATGGTGAAAAGGATTTACATTTACACATACGAGGAGGC
genomic: TTCACTGATGATGAGGATGACATGATGCTTGTTGGAGATGATCCTTGGGAgtaagaaccc ... cttccttcagTGAGTTTTGCAGGATGGTGAAAAGGATTTACATTTACACATACGAGGAGGC
EST: gi|76016629|gb|DT943799.1|DT943799
EST:     TTCACTGATGATGAGGATGACATGATGCTTGTTGGAGATGATCCTTGGGA                         TGAGTTTTGCAGGATGGTGAAAAGGATTTACATTTACACATACGAGGAGGC
genomic: TTCACTGATGATGAGGATGACATGATGCTTGTTGGAGATGATCCTTGGGAgtaagaaccc ... cttccttcagTGAGTTTTGCAGGATGGTGAAAAGGATTTACATTTACACATACGAGGAGGC
EST: gi|78087330|gb|DV515723.1|DV515723
EST:     TTCACTGATGATGAGGATGACATGATGCTTGTTGGAGATGATCCTTGGGA                         TGAGTTTTGCAGGATGGTGAAAAGGATTTACATTTACACATACGAGGAGGC
genomic: TTCACTGATGATGAGGATGACATGATGCTTGTTGGAGATGATCCTTGGGAgtaagaaccc ... cttccttcagTGAGTTTTGCAGGATGGTGAAAAGGATTTACATTTACACATACGAGGAGGC
EST: gi|213177991|gb|FM192832.1|FM192832
EST:     TTCACTGATGATGAGGATGACATGATGCTTGTTGGAGATGATCCTTGGGA                         TGAGTTTTGCAGGATGGTGAAAAGGATTTACATTTACACATACGAGGAGGC
genomic: TTCACTGATGATGAGGATGACATGATGCTTGTTGGAGATGATCCTTGGGAgtaagaaccc ... cttccttcagTGAGTTTTGCAGGATGGTGAAAAGGATTTACATTTACACATACGAGGAGGC
EST: gi|26456680|gb|CA828263.1|CA828263
EST:     TTCACTGATGATGAGGATGACATGATGCTTGTTGGAGATGATCCTTGGGA                         TGAGTTTTGCAGGATGGTGAAAAGGATTTACATTTACACATACGAGGAGGC
genomic: TTCACTGATGATGAGGATGACATGATGCTTGTTGGAGATGATCCTTGGGAgtaagaaccc ... cttccttcagTGAGTTTTGCAGGATGGTGAAAAGGATTTACATTTACACATACGAGGAGGC
EST: gi|87155859|gb|DY400648.1|DY400648
EST:     TTCACTGATGATGAGGATGACATGATGCTTGTTGGAGATGATCCTTGGGA                         TGAGTTTTGCAGGATGGTGAAAAGGATTTACATTTACACATAC-AGGAGGC
genomic: TTCACTGATGATGAGGATGACATGATGCTTGTTGGAGATGATCCTTGGGAgtaagaaccc ... cttccttcagTGAGTTTTGCAGGATGGTGAAAAGGATTTACATTTACACATACGAGGAGGC

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: 759

TTGACATCCAGGGGGAGCTGGGTTCCACACTAAAGAAATGGCGGGTCATTTTCACTGATGATGAGGATGACATGATGCTTGTTGGAGATGATCCTTGGGAgtaagaaccc ... cttccttcagTGAGTTTTGCAGGATGGTGAAAAGGATTTACATTTACACATACGAGGAGGCAAAGAAGCTGACATCCAAGTCAAAGTTACCGGTTAGCAGTGACAGCAGC


Block sizes: 49 (upstream exon), 44 (downstream exon)
Score: 82

TTGACATCCAGGGGGAGCTGGGTTCCACACTAAAGAAATGGCGGGTCATTTTCACTGATGATGAGGATGACATGATGCTTGTTGGAGATGATCCTTGGGAgtaagaaccc ... cttccttcagTGAGTTTTGCAGGATGGTGAAAAGGATTTACATTTACACATACGAGGAGGCAAAGAAGCTGACATCCAAGTCAAAGTTACCGGTTAGCAGTGACAGCAGC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 105

TTGACATCCAGGGGGAGCTGGGTTCCACACTAAAGAAATGGCGGGTCATTTTCACTGATGATGAGGATGACATGATGCTTGTTGGAGATGATCCTTGGGAgtaagaaccc ... cttccttcagTGAGTTTTGCAGGATGGTGAAAAGGATTTACATTTACACATACGAGGAGGCAAAGAAGCTGACATCCAAGTCAAAGTTACCGGTTAGCAGTGACAGCAGC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 130

TTGACATCCAGGGGGAGCTGGGTTCCACACTAAAGAAATGGCGGGTCATTTTCACTGATGATGAGGATGACATGATGCTTGTTGGAGATGATCCTTGGGAgtaagaaccc ... cttccttcagTGAGTTTTGCAGGATGGTGAAAAGGATTTACATTTACACATACGAGGAGGCAAAGAAGCTGACATCCAAGTCAAAGTTACCGGTTAGCAGTGACAGCAGC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgcatgttttccattattggaagtcctaatccctgtgcaatgcatcttccttcagTGAGTTTTGCAGGATGGTGAAAAGGATTTACATTTACACATACGAGGAGGCAAAGAAGCTGACATCCAAGTCAAAGTTACCGGTTAGCAGTGACAGCAGC
                       tcctaat  putative branch site (score: 130)
                                          catcttccttc  putative PPT
            attatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagaaccctttgtctctgtattaacgagtgcatgttttccattattggaagtcctaatccctgtgcaatgcatcttccttcagTGAGTTTTGCAGGATGGTGAAAAGGATTTACATTTACACATACGAGGAGGCAAAGAAGCTGACATCCAAGTCAAAGTTACCGGTTAGCAGTGACAGCAGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGA