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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CATGTGTCTCACTTGTTTGGTCTTTATCCTGGACATACTATGTCACTTGAGGAAACACCTGACCTCTGCAGAGCTGTTGCCAATAGTCTTTATAAAAGAGgtaccttttttttcttaaagtaaatgtgcataaggacatgttttagttttttgttttgctcggttctgcgtttgatgataattttatcttgattcgtgct...

Basic information

species Zea mays
transcript GRMZM2G019673_T05
intron # 4
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|37377099|gb|CF625124.1|CF625124
EST:     ACCTCTGCAGAGCTGTTGCCAATAGTCTTTATAAAAGAG                         GTGACGAAGGCCCAGGCTGGTCTACTTCATGGAAAATGGTCTTATGGGCTC
genomic: ACCTCTGCAGAGCTGTTGCCAATAGTCTTTATAAAAGAGgtaccttttt ... cattgctcagGTGACGAAGGCCCAGGCTGGTCTACTTCATGGAAAATGGTCCTATGGGCTC
EST: gi|211427630|gb|FL452061.1|FL452061
EST:     GGAAACACCTGACCTCTGCAGAGCTGTTGCCAATAGTCTTTATAAAAGAG                         GTGACGAAGGCCCAGGCTGGTCTACTTCATGGAAAATGGTCCTATGGGCTC
genomic: GGAAACACCTGACCTCTGCAGAGCTGTTGCCAATAGTCTTTATAAAAGAGgtaccttttt ... cattgctcagGTGACGAAGGCCCAGGCTGGTCTACTTCATGGAAAATGGTCCTATGGGCTC
EST: gi|211427631|gb|FL452062.1|FL452062
EST:     GGAAACACCTGACCTCTGCAGAGCTGTTGCCAATAGTCTTTATAAAAGAG                         GTGACGAAGGCCCAGGCTGGTCTACTTCATGGAAAATGGTCCTATGGGCTC
genomic: GGAAACACCTGACCTCTGCAGAGCTGTTGCCAATAGTCTTTATAAAAGAGgtaccttttt ... cattgctcagGTGACGAAGGCCCAGGCTGGTCTACTTCATGGAAAATGGTCCTATGGGCTC
EST: gi|67026471|gb|CO455220.1|CO455220
EST:     GGAAACACCTGACCTCTGCAGAGCTGTTGCCAATAGTCTTTATAAAAGAG                         GTGACGAAGGCCCAGGCTGGTCTACTTCATGGAAAATGGTCCTATGGGCTC
genomic: GGAAACACCTGACCTCTGCAGAGCTGTTGCCAATAGTCTTTATAAAAGAGgtaccttttt ... cattgctcagGTGACGAAGGCCCAGGCTGGTCTACTTCATGGAAAATGGTCCTATGGGCTC
EST: gi|60346394|gb|DN213367.1|DN213367
EST:     GGAAACACTTGACCTCTGCAGAGCTGTTGCCAATAGTCTTTATAAAAGAG                         GTGACGAAGGCCCAGGCTGGTCTACTTCATGGAAAATGGTCCTATGGGCTC
genomic: GGAAACACCTGACCTCTGCAGAGCTGTTGCCAATAGTCTTTATAAAAGAGgtaccttttt ... cattgctcagGTGACGAAGGCCCAGGCTGGTCTACTTCATGGAAAATGGTCCTATGGGCTC
EST: gi|78113504|gb|DV531895.1|DV531895
EST:     GGAAACACCTGACCTCTGCAGAGCTGTTGCCAATAGTCTTTATAAAAGAG                         GTGACGAAGGCCCAGGCTGGTCTACTTCATGGAAAATGGTCCTATGGGCTC
genomic: GGAAACACCTGACCTCTGCAGAGCTGTTGCCAATAGTCTTTATAAAAGAGgtaccttttt ... cattgctcagGTGACGAAGGCCCAGGCTGGTCTACTTCATGGAAAATGGTCCTATGGGCTC

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: 62

CATGTGTCTCACTTGTTTGGTCTTTATCCTGGACATACTATGTCACTTGAGGAAACACCTGACCTCTGCAGAGCTGTTGCCAATAGTCTTTATAAAAGAGgtaccttttt ... cattgctcagGTGACGAAGGCCCAGGCTGGTCTACTTCATGGAAAATGGTCCTATGGGCTCGCCTTCACAACAGTGACCATGCATACAAAATGATACTGCAGCTAATCAC


Block sizes: 47 (upstream exon), 48 (downstream exon)
Score: 70

CATGTGTCTCACTTGTTTGGTCTTTATCCTGGACATACTATGTCACTTGAGGAAACACCTGACCTCTGCAGAGCTGTTGCCAATAGTCTTTATAAAAGAGgtaccttttt ... cattgctcagGTGACGAAGGCCCAGGCTGGTCTACTTCATGGAAAATGGTCCTATGGGCTCGCCTTCACAACAGTGACCATGCATACAAAATGATACTGCAGCTAATCAC


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 77

CATGTGTCTCACTTGTTTGGTCTTTATCCTGGACATACTATGTCACTTGAGGAAACACCTGACCTCTGCAGAGCTGTTGCCAATAGTCTTTATAAAAGAGgtaccttttt ... cattgctcagGTGACGAAGGCCCAGGCTGGTCTACTTCATGGAAAATGGTCCTATGGGCTCGCCTTCACAACAGTGACCATGCATACAAAATGATACTGCAGCTAATCAC


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 35

CATGTGTCTCACTTGTTTGGTCTTTATCCTGGACATACTATGTCACTTGAGGAAACACCTGACCTCTGCAGAGCTGTTGCCAATAGTCTTTATAAAAGAGgtaccttttt ... cattgctcagGTGACGAAGGCCCAGGCTGGTCTACTTCATGGAAAATGGTCCTATGGGCTCGCCTTCACAACAGTGACCATGCATACAAAATGATACTGCAGCTAATCAC


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CATGTGTCTCACTTGTTTGGTCTTTATCCTGGACATACTATGTCACTTGAGGAAACACCTGACCTCTGCAGAGCTGTTGCCAATAGTCTTTATAAAAGAGgtaccttttttttcttaaagtaaatgtgcataaggacatgttttagttttttgttttgctcggttctgcgtttgatgataattttatcttgattcgtgct

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aaagtaaa