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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CCCCTCCCCTGCGGGCTTCTCTCACGAGCTCCCCCGGCCTCGCCGCCGCCGCCTGCTCCGGCGGGCGGGACCCAGCTCGCAGCGTCTCCCCTGCGGCGAGgtacgccttctcctctctgcgcctgcctctactctaccctcccttagtccctttgtcctcccagcctgccaattgggatgcgcgtctgggtgtttgagcc...

Basic information

species Zea mays
transcript GRMZM2G077278_T01
intron # 1
splice site 5'
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|91878198|gb|EB408155.1|EB408155
EST:     GCCTGCTCCGGCGGGCGGGACCCAGCTCGCAGCGTCTCCCCTGCGGCGAG                         GTACACGATGGAGGGAGCGGGAAGAGATGCCAACCCTTTGAGCGGTTACAG
genomic: GCCTGCTCCGGCGGGCGGGACCCAGCTCGCAGCGTCTCCCCTGCGGCGAGgtacgccttc ... tgtgattcagGTACACGATGGAGGGAGCGGGAAGAGATGCCAACCCTTTGAGCGGTTACAG
EST: gi|149109232|gb|EE190089.2|EE190089
EST:     GCCTGCTCCGGCGGGCGGGACCCAGCTCGCAGCGTCTCCCCTGCGGCGAG                         GTACACGATGGAGGGAGCGGGAAGAGATGCCAACCCTTTGAGCGGTTACAG
genomic: GCCTGCTCCGGCGGGCGGGACCCAGCTCGCAGCGTCTCCCCTGCGGCGAGgtacgccttc ... tgtgattcagGTACACGATGGAGGGAGCGGGAAGAGATGCCAACCCTTTGAGCGGTTACAG
EST: gi|71327271|gb|DR800259.1|DR800259
EST:     GCCTGCTCCGGCGGGCGGGACCCAGCTCGCAGCGTCTCCCCTGCGGCGAG                         GTACACGATGGAGGGAGCGGGAAGAGATGCCAACCCTTTGAGCGGTTACAG
genomic: GCCTGCTCCGGCGGGCGGGACCCAGCTCGCAGCGTCTCCCCTGCGGCGAGgtacgccttc ... tgtgattcagGTACACGATGGAGGGAGCGGGAAGAGATGCCAACCCTTTGAGCGGTTACAG
EST: gi|74240534|gb|DT648448.1|DT648448
EST:     GCCTGCTCCGGCGGGCGGGACCCAGCTCGCAGCGTCTCCCCTGCGGCGAG                         GTACACGATGGAGGGAGCGGGAAGAGATGCCAACCCTTTGAGCGGTTACAG
genomic: GCCTGCTCCGGCGGGCGGGACCCAGCTCGCAGCGTCTCCCCTGCGGCGAGgtacgccttc ... tgtgattcagGTACACGATGGAGGGAGCGGGAAGAGATGCCAACCCTTTGAGCGGTTACAG
EST: gi|149013919|gb|EE043417.2|EE043417
EST:     GCCTGCTCCGGCGGGCGGGACCCAGCTCGCAGCGTCTCCCCTGCGGCGAG                         GTACACGATGGAGGGAGCGGGAAGAGATGCCAACCCTTTGAGCGGTTACAG
genomic: GCCTGCTCCGGCGGGCGGGACCCAGCTCGCAGCGTCTCCCCTGCGGCGAGgtacgccttc ... tgtgattcagGTACACGATGGAGGGAGCGGGAAGAGATGCCAACCCTTTGAGCGGTTACAG
EST: gi|211110233|gb|FL282966.1|FL282966
EST:     GCAGCGTCTCCCCTGCGGCGAG                         GTACACGATGGAGGGAGCGGGAAGAGATGCCAACCCTTTGAGCGGTTACAG
genomic: GCAGCGTCTCCCCTGCGGCGAGgtacgccttc ... tgtgattcagGTACACGATGGAGGGAGCGGGAAGAGATGCCAACCCTTTGAGCGGTTACAG
EST: gi|211085855|gb|FL313546.1|FL313546
EST:     GCCTGCTCCGGCGGGCCGGACCCAGCTCGCAGCGTCTCCCCTGCGGCGAG                         GTACACGATGGAGGGAGCGGGAAGAGATGCCAACCCTTTGAGCGGTTACAG
genomic: GCCTGCTCCGGCGGGCGGGACCCAGCTCGCAGCGTCTCCCCTGCGGCGAGgtacgccttc ... tgtgattcagGTACACGATGGAGGGAGCGGGAAGAGATGCCAACCCTTTGAGCGGTTACAG
EST: gi|148954916|gb|EC900404.2|EC900404
EST:     GCCTGCTCCGGCGGGCGGGACCCAGCTCGCAGCGTCTCCCCTGCGGCGAG                         GTACACGATGGAGGGAGCGGGAAGAGATGCCAACCCTTTGAGCGGTTACAG
genomic: GCCTGCTCCGGCGGGCGGGACCCAGCTCGCAGCGTCTCCCCTGCGGCGAGgtacgccttc ... tgtgattcagGTACACGATGGAGGGAGCGGGAAGAGATGCCAACCCTTTGAGCGGTTACAG
EST: gi|78108756|gb|DV527173.1|DV527173
EST:     GCCTGCTCCGGCGGGCGGGACCCAGCTCGCAGCGTCTCCCCTGCGGCGAG                         GTACACGATGGAGGGAGCGGGAAGAGATGCCAACCCTTTGAGCGGTTACAG
genomic: GCCTGCTCCGGCGGGCGGGACCCAGCTCGCAGCGTCTCCCCTGCGGCGAGgtacgccttc ... tgtgattcagGTACACGATGGAGGGAGCGGGAAGAGATGCCAACCCTTTGAGCGGTTACAG
EST: gi|9255242|gb|BE345710.1|BE345710
EST:     GCCTGCTCCGGCGGGCGGGACCCAGCTCGCAGCGTCTCCCCTGCGGCGAG                         GTACACGATGGAGGGAGCGGGAAGAGATGCCAACCCTTTGAGCGGTTACAG
genomic: GCCTGCTCCGGCGGGCGGGACCCAGCTCGCAGCGTCTCCCCTGCGGCGAGgtacgccttc ... tgtgattcagGTACACGATGGAGGGAGCGGGAAGAGATGCCAACCCTTTGAGCGGTTACAG
EST: gi|9255371|gb|BE345839.1|BE345839
EST:     GCCTGCTCCGGCGGGCGGGACCCAGCTCGCAGCGTCTCCCCTGCGGCGAG                         GTACACGATGGAGGGAGCGGGAAGAGATGCCAACCCTTTGAGCGGTTACAG
genomic: GCCTGCTCCGGCGGGCGGGACCCAGCTCGCAGCGTCTCCCCTGCGGCGAGgtacgccttc ... tgtgattcagGTACACGATGGAGGGAGCGGGAAGAGATGCCAACCCTTTGAGCGGTTACAG
EST: gi|71316811|gb|DR795093.1|DR795093
EST:     CCGGCGGGCGGGACCCAGCTCGCAGCGTCTCCCCTGCGGCGAG                         GTACACGATGGAGGGAGCGGGAAGAGATGCCAACCCTTTGAGCGGTTACAG
genomic: CCGGCGGGCGGGACCCAGCTCGCAGCGTCTCCCCTGCGGCGAGgtacgccttc ... tgtgattcagGTACACGATGGAGGGAGCGGGAAGAGATGCCAACCCTTTGAGCGGTTACAG
EST: gi|76012620|gb|DT939790.1|DT939790
EST:     GCCTGCTCCGGCGGGCGGGACCCAGCTCGCAGCGTCTCCCCTGCGGCGAG                         GTACACGATGGAGGGAGCGGGAAGAGATGCCAACCCTTTGAGCGGTTACAG
genomic: GCCTGCTCCGGCGGGCGGGACCCAGCTCGCAGCGTCTCCCCTGCGGCGAGgtacgccttc ... tgtgattcagGTACACGATGGAGGGAGCGGGAAGAGATGCCAACCCTTTGAGCGGTTACAG
EST: gi|31352455|gb|CD436812.1|CD436812
EST:     CGGCGGGCGGGACCCAGGTCGCAGCGTCTCCCCTGCCTCGAG                         GTACACGATGGAGGGAGCGGGAAGAGATGCAAACCCTTTGAGCGGTTACAG
genomic: CGGCGGGCGGGACCCAGCTCGCAGCGTCTCCCCTGCGGCGAGgtacgccttc ... tgtgattcagGTACACGATGGAGGGAGCGGGAAGAGATGCCAACCCTTTGAGCGGTTACAG
EST: gi|211104121|gb|FL354108.1|FL354108
EST:     CCTGCTCCGGCGGGCGGGACCCAGCTCGCAGCGTCTCSCCCTGCGGCGAG                         GTACACGATGGAGGGAGCGGGAAGAGATGCCAACCCTTTGAGCGGTTACAG
genomic: CCTGCTCCGGCGGGCGGGACCCAGCTCGCAGCGTCTC-CCCTGCGGCGAGgtacgccttc ... tgtgattcagGTACACGATGGAGGGAGCGGGAAGAGATGCCAACCCTTTGAGCGGTTACAG

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), 47 (downstream exon)
Score: 57

CCCCTCCCCTGCGGGCTTCTCTCACGAGCTCCCCCGGCCTCGCCGCCGCCGCCTGCTCCGGCGGGCGGGACCCAGCTCGCAGCGTCTCCCCTGCGGCGAGgtacgccttc ... tgtgattcagGTACACGATGGAGGGAGCGGGAAGAGATGCCAACCCTTTGAGCGGTTACAGAATTGGCAAAACCCTGGGAATTGGGTCGTTCGGTAAAGTGAAGATCGCG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 55

CCCCTCCCCTGCGGGCTTCTCTCACGAGCTCCCCCGGCCTCGCCGCCGCCGCCTGCTCCGGCGGGCGGGACCCAGCTCGCAGCGTCTCCCCTGCGGCGAGgtacgccttc ... tgtgattcagGTACACGATGGAGGGAGCGGGAAGAGATGCCAACCCTTTGAGCGGTTACAGAATTGGCAAAACCCTGGGAATTGGGTCGTTCGGTAAAGTGAAGATCGCG


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 43

CCCCTCCCCTGCGGGCTTCTCTCACGAGCTCCCCCGGCCTCGCCGCCGCCGCCTGCTCCGGCGGGCGGGACCCAGCTCGCAGCGTCTCCCCTGCGGCGAGgtacgccttc ... tgtgattcagGTACACGATGGAGGGAGCGGGAAGAGATGCCAACCCTTTGAGCGGTTACAGAATTGGCAAAACCCTGGGAATTGGGTCGTTCGGTAAAGTGAAGATCGCG


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

CCCCTCCCCTGCGGGCTTCTCTCACGAGCTCCCCCGGCCTCGCCGCCGCCGCCTGCTCCGGCGGGCGGGACCCAGCTCGCAGCGTCTCCCCTGCGGCGAGgtacgccttc ... tgtgattcagGTACACGATGGAGGGAGCGGGAAGAGATGCCAACCCTTTGAGCGGTTACAGAATTGGCAAAACCCTGGGAATTGGGTCGTTCGGTAAAGTGAAGATCGCG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CCCCTCCCCTGCGGGCTTCTCTCACGAGCTCCCCCGGCCTCGCCGCCGCCGCCTGCTCCGGCGGGCGGGACCCAGCTCGCAGCGTCTCCCCTGCGGCGAGgtacgccttctcctctctgcgcctgcctctactctaccctcccttagtccctttgtcctcccagcctgccaattgggatgcgcgtctgggtgtttgagcc

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ccttctcc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ccctccc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cccagcc