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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaagcgttcccattgcggcatctgggtgttgctgcttatatctcagctgtatcctgtttatccagccattcccattcgcttgttttaaatttgggggcgcgcacacctgtagGGCTGGGGAACCTCCGTCATCGTCGGCGTCGCCGCCTCTGGCCAGGAGATCGCCACACGACCATTCCAGCTCGTGACTGGGCGTGTCTGGAAGGGAACCG

Basic information

species Zea mays
transcript GRMZM5G824600_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|113601628|gb|DW765886.1|DW765886
EST:     GCATTGGAAATGTTTCGGTTATGAGGGCTGCACTGGAATGCTGCCACAAG                         GGCTGGGGAACCTCCGTCATCGTCGGCGTCG
genomic: GCATTGGAAATGTTTCGGTTATGAGGGCTGCACTGGAATGCTGCCACAAGgtaaagcgtt ... acacctgtagGGCTGGGGAACCTCCGTCATCGTCGGCGTCG
EST: gi|60343794|gb|DN210767.1|DN210767
EST:     GCATTGGAAATGTTTCGGTTATGAGGGCTGCACTGGAATGCTGCCACAAG                         GGCTGGGGAACCTCCGTCATCGTCGGCGTCGCCGCCTCTGGCCAGGAGATC
genomic: GCATTGGAAATGTTTCGGTTATGAGGGCTGCACTGGAATGCTGCCACAAGgtaaagcgtt ... acacctgtagGGCTGGGGAACCTCCGTCATCGTCGGCGTCGCCGCCTCTGGCCAGGAGATC
EST: gi|74034792|gb|DT535283.1|DT535283
EST:     GCATTGGAAATGTTTCGGTTATGAGGGCTGCACTGGAATGCTGCCACAAG                         GGCTGGGGAACCTCCGTCATCGTCGGCGTCGCCGCCTCTGGCCAGGAGATC
genomic: GCATTGGAAATGTTTCGGTTATGAGGGCTGCACTGGAATGCTGCCACAAGgtaaagcgtt ... acacctgtagGGCTGGGGAACCTCCGTCATCGTCGGCGTCGCCGCCTCTGGCCAGGAGATC
EST: gi|78077865|gb|DV506290.1|DV506290
EST:     GCATTGGAAATGTTTCGGTTATGAGGGCTGCACTGGAATGCTGCCACAAG                         GGCTGGGGAACCTCCGTCATCGTCGGCGTCGCCGCCTCTGGCCAGGAGATC
genomic: GCATTGGAAATGTTTCGGTTATGAGGGCTGCACTGGAATGCTGCCACAAGgtaaagcgtt ... acacctgtagGGCTGGGGAACCTCCGTCATCGTCGGCGTCGCCGCCTCTGGCCAGGAGATC
EST: gi|211384473|gb|FL377381.1|FL377381
EST:     GCATTGGAAATGTTTCGGTTATGAGGGCTGCACTGGAATGCTGCCACAAG                         GGCTGGGGAACCTCCGTCATCGTCGGCGTCGCCGCCTCTGGCCAGGAGATC
genomic: GCATTGGAAATGTTTCGGTTATGAGGGCTGCACTGGAATGCTGCCACAAGgtaaagcgtt ... acacctgtagGGCTGGGGAACCTCCGTCATCGTCGGCGTCGCCGCCTCTGGCCAGGAGATC
EST: gi|61119600|gb|DN560561.1|DN560561
EST:     GCATTGGAAATGTTTCGGTTATGAGGGCTGCACTGGAATGCTGCCACAAG                         GGCTGGGGAACCTCCGTCATCGTCGGCGTCGCCGCCTCTGGCCAGGAGATC
genomic: GCATTGGAAATGTTTCGGTTATGAGGGCTGCACTGGAATGCTGCCACAAGgtaaagcgtt ... acacctgtagGGCTGGGGAACCTCCGTCATCGTCGGCGTCGCCGCCTCTGGCCAGGAGATC
EST: gi|60349074|gb|DN216047.1|DN216047
EST:     GCATTGGAAATGTTTCGGTTATGAGGGCTGCACTGGAATGCTGCCACAAG                         GGCTGGGGAACCTCCGTCATCGTCGGCGTCGCCGCCTCTGGCCAGGAGATC
genomic: GCATTGGAAATGTTTCGGTTATGAGGGCTGCACTGGAATGCTGCCACAAGgtaaagcgtt ... acacctgtagGGCTGGGGAACCTCCGTCATCGTCGGCGTCGCCGCCTCTGGCCAGGAGATC
EST: gi|78120687|gb|DV539071.1|DV539071
EST:     GCATTGGAAATGTTTCGGTTATGAGGGCTGCACTGGAATGCTGCCACAAG                         GGCTGGGGAACCTCCGTCATTGTCGGCGTCGCCGCCTCTGGCCAGGAGATC
genomic: GCATTGGAAATGTTTCGGTTATGAGGGCTGCACTGGAATGCTGCCACAAGgtaaagcgtt ... acacctgtagGGCTGGGGAACCTCCGTCATCGTCGGCGTCGCCGCCTCTGGCCAGGAGATC
EST: gi|211142580|gb|FL467371.1|FL467371
EST:     TTTCGGTTATGAGGGGCTGCACTGGAATGCTGCCACAAG                         GGCTGGGGAACCTCCGTCATCGNT-YGCGTCGCCGCYTCTGGCCAGGAGAT
genomic: TTTCGGTTATGA-GGGCTGCACTGGAATGCTGCCACAAGgtaaagcgtt ... acacctgtagGGCTGGGGAACCTCCGTCATCG-TCGGCGTCGCCGCCTCTGGCCAGGAGAT
EST: gi|78077864|gb|DV506289.1|DV506289
EST:     GCATTGGAAATGTTTCGGTTATGAGGGCTGCACTGGAATGCTGCCACAAG                         GGCTGGGGAACCTCCGTCATTGTTGGGGTCGCCGCCTCTGGCCAGGAGATC
genomic: GCATTGGAAATGTTTCGGTTATGAGGGCTGCACTGGAATGCTGCCACAAGgtaaagcgtt ... acacctgtagGGCTGGGGAACCTCCGTCATCGTCGGCGTCGCCGCCTCTGGCCAGGAGATC
EST: gi|71429707|gb|DR810757.1|DR810757
EST:     GCATTGGAAATGTTTCGGTTATGAGGGCTGCACTGGAATGCTGCCACAAG                         GGCTGGGGAACCTCCGTCATCGTCGGCGTCGCCGCCTCTGGCCAGGAGATC
genomic: GCATTGGAAATGTTTCGGTTATGAGGGCTGCACTGGAATGCTGCCACAAGgtaaagcgtt ... acacctgtagGGCTGGGGAACCTCCGTCATCGTCGGCGTCGCCGCCTCTGGCCAGGAGATC
EST: gi|78092172|gb|DV520546.1|DV520546
EST:     GCATTGGAAATGTTTCGGTTATGAGGGCTGCACTGGAATGCTGCCACAAG                         GGCTGGGGAACCTCCGTCATCGTCGGCGTCGCCGCCTCTGGCCAGGAGATC
genomic: GCATTGGAAATGTTTCGGTTATGAGGGCTGCACTGGAATGCTGCCACAAGgtaaagcgtt ... acacctgtagGGCTGGGGAACCTCCGTCATCGTCGGCGTCGCCGCCTCTGGCCAGGAGATC
EST: gi|110940376|gb|EE160533.1|EE160533
EST:     GCATTGGAAATGTTTCGGTTATGAGGGCTGCACTGGAATGCTGCCACAAG                         GGCTGGGGAACCTCCGTCATCGTCGGCGTCGCCGCCTCTGGCCAGGAGATC
genomic: GCATTGGAAATGTTTCGGTTATGAGGGCTGCACTGGAATGCTGCCACAAGgtaaagcgtt ... acacctgtagGGCTGGGGAACCTCCGTCATCGTCGGCGTCGCCGCCTCTGGCCAGGAGATC
EST: gi|60337655|gb|DN204628.1|DN204628
EST:     GCATTGGAAATGTTTCGGTTATGAGGGCTGCACTGGAATGCTGCCACAAG                         GGCTGGGGAACCTCCGTCATCGTCGGCGTCGCCGCCTCTGGCCAGGAGATC
genomic: GCATTGGAAATGTTTCGGTTATGAGGGCTGCACTGGAATGCTGCCACAAGgtaaagcgtt ... acacctgtagGGCTGGGGAACCTCCGTCATCGTCGGCGTCGCCGCCTCTGGCCAGGAGATC
EST: gi|31355047|gb|CD439404.1|CD439404
EST:     GCATTGGAAATGTTTCGGTTATGAGGGCTGCACTGGAATGCTGCCACAAG                         GGCTGGGGAACTTCCGTCATCGTTGGTGTCGCCGCCTCTGGCCAGGAGATC
genomic: GCATTGGAAATGTTTCGGTTATGAGGGCTGCACTGGAATGCTGCCACAAGgtaaagcgtt ... acacctgtagGGCTGGGGAACCTCCGTCATCGTCGGCGTCGCCGCCTCTGGCCAGGAGATC
EST: gi|30087007|gb|CB885215.1|CB885215
EST:     GCATTGGAAATGTTTCGGTTATGAGGGCTGCACTGGAATGCTGCCACAAG                         GGCTGGGGAACCTCCGTCATCGTCGGCGTCGCCGCCTCTGGCCAGGAGATC
genomic: GCATTGGAAATGTTTCGGTTATGAGGGCTGCACTGGAATGCTGCCACAAGgtaaagcgtt ... acacctgtagGGCTGGGGAACCTCCGTCATCGTCGGCGTCGCCGCCTCTGGCCAGGAGATC
EST: gi|60348372|gb|DN215345.1|DN215345
EST:     GCATTGGAAATGTTTCGGTTATGAGGGCTGCACTGGAATGCTGCCACAAG                         GGCTGGGGAACCTCCGTCATCGTCGGCGTCGCCGCCTCTGGCCAGGAGATC
genomic: GCATTGGAAATGTTTCGGTTATGAGGGCTGCACTGGAATGCTGCCACAAGgtaaagcgtt ... acacctgtagGGCTGGGGAACCTCCGTCATCGTCGGCGTCGCCGCCTCTGGCCAGGAGATC
EST: gi|211284800|gb|FL428470.1|FL428470
EST:     GCATTGGAAATGTTTCGGTTATGAGGGCTGCACTGGAATGCTGCCACAAG                         GGCTTGGGAACCTCCGTCATCGTCGGCGTCGC-GCCTCTGGCCAGGAGATC
genomic: GCATTGGAAATGTTTCGGTTATGAGGGCTGCACTGGAATGCTGCCACAAGgtaaagcgtt ... acacctgtagGGCTGGGGAACCTCCGTCATCGTCGGCGTCGCCGCCTCTGGCCAGGAGATC
EST: gi|60344516|gb|DN211489.1|DN211489
EST:     GCATTGGAAATGTTTCGGTTATGAGGGCTGCACTGGAATGCTGCCACAAG                         GGCTGGGGAACCTCCGTCATCGTCGGCGTCGCCGCCTCTGGCCAGGAGATC
genomic: GCATTGGAAATGTTTCGGTTATGAGGGCTGCACTGGAATGCTGCCACAAGgtaaagcgtt ... acacctgtagGGCTGGGGAACCTCCGTCATCGTCGGCGTCGCCGCCTCTGGCCAGGAGATC
EST: gi|110515671|gb|EE020259.1|EE020259
EST:     GCATTGGAAATGTTTCGGTTATGAGGGCTGCACTGGAATGCTGCCACAAG                         GGCTGGGGAACCTCCGTCATCGTCGGCGTCGCCGCCTCTGGCCAGGAGATC
genomic: GCATTGGAAATGTTTCGGTTATGAGGGCTGCACTGGAATGCTGCCACAAGgtaaagcgtt ... acacctgtagGGCTGGGGAACCTCCGTCATCGTCGGCGTCGCCGCCTCTGGCCAGGAGATC
EST: gi|110518190|gb|EE022777.1|EE022777
EST:     GCATTGGAAATGTTTCGGTTATGAGGGCTGCACTGGAATGCTGCCACAAG                         GGCTGGGGAACCTCCGTCATCGTCGGCGTCGCCGCCTCTGGCCAGGAGATC
genomic: GCATTGGAAATGTTTCGGTTATGAGGGCTGCACTGGAATGCTGCCACAAGgtaaagcgtt ... acacctgtagGGCTGGGGAACCTCCGTCATCGTCGGCGTCGCCGCCTCTGGCCAGGAGATC

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), 48 (downstream exon)
Score: 311

GCAGGTCCTGGTCGATCTTACAGATGGCGGCGTGGATTACAGCTTTGAGTGCATTGGAAATGTTTCGGTTATGAGGGCTGCACTGGAATGCTGCCACAAGgtaaagcgtt ... acacctgtagGGCTGGGGAACCTCCGTCATCGTCGGCGTCGCCGCCTCTGGCCAGGAGATCGCCACACGACCATTCCAGCTCGTGACTGGGCGTGTCTGGAAGGGAACCG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 345

GCAGGTCCTGGTCGATCTTACAGATGGCGGCGTGGATTACAGCTTTGAGTGCATTGGAAATGTTTCGGTTATGAGGGCTGCACTGGAATGCTGCCACAAGgtaaagcgtt ... acacctgtagGGCTGGGGAACCTCCGTCATCGTCGGCGTCGCCGCCTCTGGCCAGGAGATCGCCACACGACCATTCCAGCTCGTGACTGGGCGTGTCTGGAAGGGAACCG


Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 232

GCAGGTCCTGGTCGATCTTACAGATGGCGGCGTGGATTACAGCTTTGAGTGCATTGGAAATGTTTCGGTTATGAGGGCTGCACTGGAATGCTGCCACAAGgtaaagcgtt ... acacctgtagGGCTGGGGAACCTCCGTCATCGTCGGCGTCGCCGCCTCTGGCCAGGAGATCGCCACACGACCATTCCAGCTCGTGACTGGGCGTGTCTGGAAGGGAACCG


Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 173

GCAGGTCCTGGTCGATCTTACAGATGGCGGCGTGGATTACAGCTTTGAGTGCATTGGAAATGTTTCGGTTATGAGGGCTGCACTGGAATGCTGCCACAAGgtaaagcgtt ... acacctgtagGGCTGGGGAACCTCCGTCATCGTCGGCGTCGCCGCCTCTGGCCAGGAGATCGCCACACGACCATTCCAGCTCGTGACTGGGCGTGTCTGGAAGGGAACCG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttatccagccattcccattcgcttgttttaaatttgggggcgcgcacacctgtagGGCTGGGGAACCTCCGTCATCGTCGGCGTCGCCGCCTCTGGCCAGGAGATCGCCACACGACCATTCCAGCTCGTGACTGGGCGTGTCTGGAAGGGAACCG
                      ttgttttaaattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaagcgttcccattgcggcatctgggtgttgctgcttatatctcagctgtatcctgtttatccagccattcccattcgcttgttttaaatttgggggcgcgcacacctgtagGGCTGGGGAACCTCCGTCATCGTCGGCGTCGCCGCCTCTGGCCAGGAGATCGCCACACGACCATTCCAGCTCGTGACTGGGCGTGTCTGGAAGGGAACCG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAAG