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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaaccttctgtcactctccatgttcatatgtggtcatgacctgatgcgctgccatcttgactaacccaatttgcaattgccagGGTAACAAGCGAATGAGAGCACACTTCCAATTTGCGGTCGGAGCTTTGGTTGTTTACACGGGACATTCCTGTGCGCTCCCAGCAATGGAGTTGTGGAGAC

Basic information

species Zea mays
transcript GRMZM2G057408_T02
intron # 8
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|71428976|gb|DR810026.1|DR810026
EST:     GAAGCCATGGAAAATCTTGGATCTCCTCAGAGTGGCCATCTTCCATCCCT                         GGTAACAAGCGAATGAGAGCACACTTCCAATTTGCGGTCGGAGCTTTGGTT
genomic: GAAGCCATGGAAAATCTTGGATCTCCTCAGAGTGGCCATCTTCCATCCCTgtaaaccttc ... caattgccagGGTAACAAGCGAATGAGAGCACACTTCCAATTTGCGGTCGGAGCTTTGGTT
EST: gi|78118281|gb|DV536668.1|DV536668
EST:     GAAGCCATGGAAAATCTTGGATCTCCTCAGAGTGGCCATCTTCCATCCCT                         GGTAACAAGCGAATGAGAGCACACTTCCAATTTGCGGTCGGAGCTTTGGTT
genomic: GAAGCCATGGAAAATCTTGGATCTCCTCAGAGTGGCCATCTTCCATCCCTgtaaaccttc ... caattgccagGGTAACAAGCGAATGAGAGCACACTTCCAATTTGCGGTCGGAGCTTTGGTT
EST: gi|148939135|gb|EC883572.2|EC883572
EST:     GAAGCCATGGAAAATCTTGGATCTCCTCAGAGTGGCCATCTTCCATCCCT                         GGTAACAAGCGAATGAGAGCACACTTCCAATTTGCGGTCGGAGCTTTGGTT
genomic: GAAGCCATGGAAAATCTTGGATCTCCTCAGAGTGGCCATCTTCCATCCCTgtaaaccttc ... caattgccagGGTAACAAGCGAATGAGAGCACACTTCCAATTTGCGGTCGGAGCTTTGGTT
EST: gi|60336979|gb|DN203952.1|DN203952
EST:     GAAGCCATGGAAAATCTTGGATCTCCTCAGAGTGGCCATCTTCCATCCCT                         GGTAACAAGCGAATGAGAGCACACTTCCAATTTGCGGTCGGAGCTTTGGTT
genomic: GAAGCCATGGAAAATCTTGGATCTCCTCAGAGTGGCCATCTTCCATCCCTgtaaaccttc ... caattgccagGGTAACAAGCGAATGAGAGCACACTTCCAATTTGCGGTCGGAGCTTTGGTT
EST: gi|91876491|gb|EB406448.1|EB406448
EST:     GAAGCCATGGAAAATCTTGGATCTCCTCAGAGTGGCCATCTTCCATCCCT                         GGTAACAAGCGAATGAGAGCACACTTCCAATTTGCGGTCGGAGCTTTGGTT
genomic: GAAGCCATGGAAAATCTTGGATCTCCTCAGAGTGGCCATCTTCCATCCCTgtaaaccttc ... caattgccagGGTAACAAGCGAATGAGAGCACACTTCCAATTTGCGGTCGGAGCTTTGGTT
EST: gi|60397572|gb|DN230388.1|DN230388
EST:     GAAGCCATGGAAAATCTTGGATCTCCTCAGAGTGGCCATCTTCCATCCCT                         GGTAACAAGCGAATGAGAGCACACTTCCAATTTGCGGTCGGAGCTTTGGTT
genomic: GAAGCCATGGAAAATCTTGGATCTCCTCAGAGTGGCCATCTTCCATCCCTgtaaaccttc ... caattgccagGGTAACAAGCGAATGAGAGCACACTTCCAATTTGCGGTCGGAGCTTTGGTT
EST: gi|78076507|gb|DV504941.1|DV504941
EST:     GAAGCCATGGAAAATCTTGGATCTCCTCAGAGTGGCCATCTTCCATCCCT                         GGTAACAAGCGAATGAGAGCACACTTCCAATTTGCGGTCGGAGCTTTGGTT
genomic: GAAGCCATGGAAAATCTTGGATCTCCTCAGAGTGGCCATCTTCCATCCCTgtaaaccttc ... caattgccagGGTAACAAGCGAATGAGAGCACACTTCCAATTTGCGGTCGGAGCTTTGGTT
EST: gi|110220916|gb|EC902814.1|EC902814
EST:     GAAGCCATGGAAAATCTTGGATCTCTTCAGAGTGGCCATCTTCCATCCCT                         GGTAACAAGCGAATGAGAGCACACTTCCAATTTGCGGTCGGAGCTTTGGTT
genomic: GAAGCCATGGAAAATCTTGGATCTCCTCAGAGTGGCCATCTTCCATCCCTgtaaaccttc ... caattgccagGGTAACAAGCGAATGAGAGCACACTTCCAATTTGCGGTCGGAGCTTTGGTT
EST: gi|50322593|gb|CO517719.1|CO517719
EST:     GAAGCCATGGAAAATTTTGGATCTCCTCAGAGTGGCCATCTTCCATCCCT                         GGTAACAAGCGAATGAGAGCACACTTCCAATTTGCGGTCGGAGCTTTGGTT
genomic: GAAGCCATGGAAAATCTTGGATCTCCTCAGAGTGGCCATCTTCCATCCCTgtaaaccttc ... caattgccagGGTAACAAGCGAATGAGAGCACACTTCCAATTTGCGGTCGGAGCTTTGGTT
EST: gi|71763063|gb|DR961000.1|DR961000
EST:     GAAGCCATGGAAAATCTTGGATCTCCTCAGAGTGGCCATCTTCCATCCCT                         GGTAACAAGCGAATGAGAGCACACTTCCAATTTGCGGTCGGAGCTTTGGTT
genomic: GAAGCCATGGAAAATCTTGGATCTCCTCAGAGTGGCCATCTTCCATCCCTgtaaaccttc ... caattgccagGGTAACAAGCGAATGAGAGCACACTTCCAATTTGCGGTCGGAGCTTTGGTT

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: 127

GGAGGTTGCTATCATCATATAGCTATGGTGGCGCGGACCATGTCAAATCTGAAGCCATGGAAAATCTTGGATCTCCTCAGAGTGGCCATCTTCCATCCCTgtaaaccttc ... caattgccagGGTAACAAGCGAATGAGAGCACACTTCCAATTTGCGGTCGGAGCTTTGGTTGTTTACACGGGACATTCCTGTGCGCTCCCAGCAATGGAGTTGTGGAGAC


Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 79

GGAGGTTGCTATCATCATATAGCTATGGTGGCGCGGACCATGTCAAATCTGAAGCCATGGAAAATCTTGGATCTCCTCAGAGTGGCCATCTTCCATCCCTgtaaaccttc ... caattgccagGGTAACAAGCGAATGAGAGCACACTTCCAATTTGCGGTCGGAGCTTTGGTTGTTTACACGGGACATTCCTGTGCGCTCCCAGCAATGGAGTTGTGGAGAC


Block sizes: 48 (upstream exon), 45 (downstream exon)
Score: 30

GGAGGTTGCTATCATCATATAGCTATGGTGGCGCGGACCATGTCAAATCTGAAGCCATGGAAAATCTTGGATCTCCTCAGAGTGGCCATCTTCCATCCCTgtaaaccttc ... caattgccagGGTAACAAGCGAATGAGAGCACACTTCCAATTTGCGGTCGGAGCTTTGGTTGTTTACACGGGACATTCCTGTGCGCTCCCAGCAATGGAGTTGTGGAGAC


Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 117

GGAGGTTGCTATCATCATATAGCTATGGTGGCGCGGACCATGTCAAATCTGAAGCCATGGAAAATCTTGGATCTCCTCAGAGTGGCCATCTTCCATCCCTgtaaaccttc ... caattgccagGGTAACAAGCGAATGAGAGCACACTTCCAATTTGCGGTCGGAGCTTTGGTTGTTTACACGGGACATTCCTGTGCGCTCCCAGCAATGGAGTTGTGGAGAC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgtggtcatgacctgatgcgctgccatcttgactaacccaatttgcaattgccagGGTAACAAGCGAATGAGAGCACACTTCCAATTTGCGGTCGGAGCTTTGGTTGTTTACACGGGACATTCCTGTGCGCTCCCAGCAATGGAGTTGTGGAGAC
                              gactaac  putative branch site (score: 117)
                                       aattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaaccttctgtcactctccatgttcatatgtggtcatgacctgatgcgctgccatcttgactaacccaatttgcaattgccagGGTAACAAGCGAATGAGAGCACACTTCCAATTTGCGGTCGGAGCTTTGGTTGTTTACACGGGACATTCCTGTGCGCTCCCAGCAATGGAGTTGTGGAGAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA