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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTTCAGTGAAGGGGAAGAAACGTAAAAGTCAGCTTGGGACTGAGgtgactttaattccttaactttttgtgctatatgcctatccttccttgaatttcatattctttccactttcttgacccaaaatgataatacactatgcat...

Basic information

species Zea mays
transcript GRMZM2G484880_T04
intron # 6
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|76016791|gb|DT943961.1|DT943961
EST:     GGAAGAAACGTAAAAGTCAGCTTGGGACTGAG                         ATTCAGGACAAGGAAAAAAGATCATCACATAGTCTACTAGTGTTGCAGTTT
genomic: GGAAGAAACGTAAAAGTCAGCTTGGGACTGAGgtgactttaa ... atctctgaagATTCAGGACAAGGAAAAAAGATCATCACATAGTCTACTAGTGTTGCAGTTT
EST: gi|76912438|gb|DV164732.1|DV164732
EST:     TTTCAGTGAAGGGGAAGAAACGTAAAAGTCAGCTTGGGACTGAG                         -----G-ACAAGGAAAAAAGATCATCACATAGTCTACTAGTGTTGCAGTTT
genomic: TTTCAGTGAAGGGGAAGAAACGTAAAAGTCAGCTTGGGACTGAGgtgactttaa ... atctctgaagATTCAGGACAAGGAAAAAAGATCATCACATAGTCTACTAGTGTTGCAGTTT
EST: gi|71434326|gb|DR815376.1|DR815376
EST:     TTTCAGTGAAGGGGAAAGAAACGTAAAAGTCCAGCTTGGGACTGAG                         ATTCAGGACAAGGAAAAAAGATCATCACATAGTCTACTAGTGTTGCAGTTT
genomic: TTTCAGTGAAGGGGAA-GAAACGTAAAAGTC-AGCTTGGGACTGAGgtgactttaa ... atctctgaagATTCAGGACAAGGAAAAAAGATCATCACATAGTCTACTAGTGTTGCAGTTT
EST: gi|6031476|gb|AW076378.1|AW076378
EST:     TTTCAGTGAAGGGGAAGAAACGTAAAAGTCAGCTTGGGACTGAG                         ATTCAGGACAAGGAAAAAAGATCATCACATAGTCTACTAGTGTTGCAGTTT
genomic: TTTCAGTGAAGGGGAAGAAACGTAAAAGTCAGCTTGGGACTGAGgtgactttaa ... atctctgaagATTCAGGACAAGGAAAAAAGATCATCACATAGTCTACTAGTGTTGCAGTTT
EST: gi|60358481|gb|DN225454.1|DN225454
EST:     AAGGGGAAGAAACGTAAAAGTCAGCTTGGGACTGAG                         ATTCAGGACAAGGAAAAAAGATCATCACATAGTCTACTAGTGTTGCAGTTT
genomic: AAGGGGAAGAAACGTAAAAGTCAGCTTGGGACTGAGgtgactttaa ... atctctgaagATTCAGGACAAGGAAAAAAGATCATCACATAGTCTACTAGTGTTGCAGTTT
EST: gi|211058547|gb|FK994412.1|FK994412
EST:     TTTCAGTGAAGGGGAAGAAACGTAAAAGTCAGCTTGGGACTGAG                         AT-CAGGACAAGGAAAAA-GATCATCACATAGTCTACTA
genomic: TTTCAGTGAAGGGGAAGAAACGTAAAAGTCAGCTTGGGACTGAGgtgactttaa ... atctctgaagATTCAGGACAAGGAAAAAAGATCATCACATAGTCTACTA
EST: gi|32913308|gb|CF018120.1|CF018120
EST:     TTTCAGCGAAGGGGAAGAAACGTAAAAGTCAGCTTGGGACTGAG                         ATTCAGGACAAGGAAAAAAGATCATCACATAGTCTACTAGTGTTGCAGTTT
genomic: TTTCAGTGAAGGGGAAGAAACGTAAAAGTCAGCTTGGGACTGAGgtgactttaa ... atctctgaagATTCAGGACAAGGAAAAAAGATCATCACATAGTCTACTAGTGTTGCAGTTT
EST: gi|26456042|gb|CA827625.1|CA827625
EST:     TTTCAGTGAAGGGGAAGAAACGTAAAAGTCAGCTTGGGACTGAG                         ATTCAGGACAAGGAAAAAAGATCATCACATAGTCTACTAGTGTTGCAGTTT
genomic: TTTCAGTGAAGGGGAAGAAACGTAAAAGTCAGCTTGGGACTGAGgtgactttaa ... atctctgaagATTCAGGACAAGGAAAAAAGATCATCACATAGTCTACTAGTGTTGCAGTTT
EST: gi|71438521|gb|DR819571.1|DR819571
EST:     TTTCAGTGAAGGGGAAGAAACGTAAAAGTCAGCTTGGGACTGAG                         ATTCAGGACAAGGAAAAAAGATCATCACATAGTCTACTAGTGTTGCAGTTT
genomic: TTTCAGTGAAGGGGAAGAAACGTAAAAGTCAGCTTGGGACTGAGgtgactttaa ... atctctgaagATTCAGGACAAGGAAAAAAGATCATCACATAGTCTACTAGTGTTGCAGTTT
EST: gi|71331879|gb|DR802817.1|DR802817
EST:     TTTCAGTGAAGGGGAAGAAACGTAAAAGTCAGCTTGGGACTGAG                         ATTCAGGACAAGGAAAAAAGATCATCACATAGTCTACTAGTGTTGCAGTTT
genomic: TTTCAGTGAAGGGGAAGAAACGTAAAAGTCAGCTTGGGACTGAGgtgactttaa ... atctctgaagATTCAGGACAAGGAAAAAAGATCATCACATAGTCTACTAGTGTTGCAGTTT
EST: gi|32865668|gb|CF005350.1|CF005350
EST:     TTTCAGTGAAGGGGAAGAAACGTAAAAGTCAGCTTGGGACTGAG                         ATTCAGGACAAGGAAAAAAGATCATCACATAGTCTACTAGTGTTGCAGTTT
genomic: TTTCAGTGAAGGGGAAGAAACGTAAAAGTCAGCTTGGGACTGAGgtgactttaa ... atctctgaagATTCAGGACAAGGAAAAAAGATCATCACATAGTCTACTAGTGTTGCAGTTT

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: 44 (upstream exon), 46 (downstream exon)
Score: 284

TTTCAGTGAAGGGGAAGAAACGTAAAAGTCAGCTTGGGACTGAGgtgactttaa ... atctctgaagATTCAGGACAAGGAAAAAAGATCATCACATAGTCTACTAGTGTTGCAGTTTCCTTTGCCACTGAAGAAGCAACTTGTGGATGATTGGGAGTTTGTTACGC


Block sizes: 44 (upstream exon), 46 (downstream exon)
Score: 121

TTTCAGTGAAGGGGAAGAAACGTAAAAGTCAGCTTGGGACTGAGgtgactttaa ... atctctgaagATTCAGGACAAGGAAAAAAGATCATCACATAGTCTACTAGTGTTGCAGTTTCCTTTGCCACTGAAGAAGCAACTTGTGGATGATTGGGAGTTTGTTACGC


Block sizes: 44 (upstream exon), 46 (downstream exon)
Score: 147

TTTCAGTGAAGGGGAAGAAACGTAAAAGTCAGCTTGGGACTGAGgtgactttaa ... atctctgaagATTCAGGACAAGGAAAAAAGATCATCACATAGTCTACTAGTGTTGCAGTTTCCTTTGCCACTGAAGAAGCAACTTGTGGATGATTGGGAGTTTGTTACGC


Block sizes: 44 (upstream exon), 48 (downstream exon)
Score: 181

TTTCAGTGAAGGGGAAGAAACGTAAAAGTCAGCTTGGGACTGAGgtgactttaa ... atctctgaagATTCAGGACAAGGAAAAAAGATCATCACATAGTCTACTAGTGTTGCAGTTTCCTTTGCCACTGAAGAAGCAACTTGTGGATGATTGGGAGTTTGTTACGC


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TTTCAGTGAAGGGGAAGAAACGTAAAAGTCAGCTTGGGACTGAGgtgactttaattccttaactttttgtgctatatgcctatccttccttgaatttcatattctttccactttcttgacccaaaatgataatacactatgcat

- - - - - - GGAAGA
- - - - - - - AAGAAA
- - - - - - - - - - - - - - TCAGCT