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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagactcactccatccgccatcttcttctcctccttactttcccatcttctagctagctaaacctttgatatggtagctcctcctcagGGCTTCTTGGACCTGGACTTGCTGCCTTTTTCTTCCTCGCCGGCATTACCTTTGCTGCCGTCTCTATCAGAAGCAGTGGCACCCACGCAGCTG

Basic information

species Zea mays
transcript GRMZM2G077222_T02
intron # 1
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|31361082|gb|CD445439.1|CD445439
EST:     CGCGGATGACGGCGCCGACAAATCTACTCTAGGGTTCGGCCGAGCAGGAG                         GGCTTCTTGGACCTGGACTTGCTGCCTTTTTCTTCCTCGCCGGCATTACCT
genomic: CGCGGATGACGGCGCCGACAAATCTACTCTAGGGTTCGGCCGAGCAGGAGgtgagactca ... tcctcctcagGGCTTCTTGGACCTGGACTTGCTGCCTTTTTCTTCCTCGCCGGCATTACCT
EST: gi|148965553|gb|EE016380.2|EE016380
EST:     CGCGGATGACGGCGCCGACAAATCTACTCTAGGGTTCGGCCGAGCAGGAG                         GGCTTCTTGGACCTGGACTTGCTGCCTTTTTCTTCCTCGCCGGCATTACCT
genomic: CGCGGATGACGGCGCCGACAAATCTACTCTAGGGTTCGGCCGAGCAGGAGgtgagactca ... tcctcctcagGGCTTCTTGGACCTGGACTTGCTGCCTTTTTCTTCCTCGCCGGCATTACCT
EST: gi|149097295|gb|EE183124.2|EE183124
EST:     CGCGGATGACGGCGCCGACAAATCTACTCTAGGGTTCGGCCGAGCAGGAG                         GGCTTCTTGGACCTGGACTTGCTGCCTTTTTCTTCCTCGCCGGCATTACCT
genomic: CGCGGATGACGGCGCCGACAAATCTACTCTAGGGTTCGGCCGAGCAGGAGgtgagactca ... tcctcctcagGGCTTCTTGGACCTGGACTTGCTGCCTTTTTCTTCCTCGCCGGCATTACCT
EST: gi|211124362|gb|FL103657.1|FL103657
EST:     CGCGGATGACGGCGCCGACAAATCTACTCTAGGGTTCGGCCGAGCAGGAG                         GGCTTCTTGGACCTGGACTTGCTGCCTTTTTCTTCCTCGCCGGCATTACCT
genomic: CGCGGATGACGGCGCCGACAAATCTACTCTAGGGTTCGGCCGAGCAGGAGgtgagactca ... tcctcctcagGGCTTCTTGGACCTGGACTTGCTGCCTTTTTCTTCCTCGCCGGCATTACCT
EST: gi|160481419|gb|EY254533.1|EY254533
EST:     CGCGGATGACGGCGCCGACAAATCTACTCTAGGGTTCGGCCGAGCAGGAG                         GGCTTCTTGGACCTGGACTTGCTGCCTTTTTCTTCCTCGCCGGCATTACCT
genomic: CGCGGATGACGGCGCCGACAAATCTACTCTAGGGTTCGGCCGAGCAGGAGgtgagactca ... tcctcctcagGGCTTCTTGGACCTGGACTTGCTGCCTTTTTCTTCCTCGCCGGCATTACCT
EST: gi|149074912|gb|EE163360.2|EE163360
EST:     CGCGGATGACGGCGCCGACAAATCTACTCTAGGGTTCGGCCGAGCAGGAG                         GGCTTCTTGGACCTGGACTTGCTGCCTTTTTCTTCCTCGCCGGCATTACCT
genomic: CGCGGATGACGGCGCCGACAAATCTACTCTAGGGTTCGGCCGAGCAGGAGgtgagactca ... tcctcctcagGGCTTCTTGGACCTGGACTTGCTGCCTTTTTCTTCCTCGCCGGCATTACCT
EST: gi|31354137|gb|CD438494.1|CD438494
EST:     CGCGGATGACGGCGCCGACAAATCTACTCTAGGGTTCGGCCGAGCAGGAG                         GGCTTCTTGGACCTGGACTTGCTGCCTTTTTCTTCCTCGCCGGCATTACCT
genomic: CGCGGATGACGGCGCCGACAAATCTACTCTAGGGTTCGGCCGAGCAGGAGgtgagactca ... tcctcctcagGGCTTCTTGGACCTGGACTTGCTGCCTTTTTCTTCCTCGCCGGCATTACCT

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: 47 (upstream exon), 49 (downstream exon)
Score: 62

GGCTCGTCCCCGCCCAACTCCTTCGCTGGCTGGTCCTCCGACTCCGACAGCGCGGATGACGGCGCCGACAAATCTACTCTAGGGTTCGGCCGAGCAGGAGgtgagactca ... tcctcctcagGGCTTCTTGGACCTGGACTTGCTGCCTTTTTCTTCCTCGCCGGCATTACCTTTGCTGCCGTCTCTATCAGAAGCAGTGGCACCCACGCAGCTG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 267

GGCTCGTCCCCGCCCAACTCCTTCGCTGGCTGGTCCTCCGACTCCGACAGCGCGGATGACGGCGCCGACAAATCTACTCTAGGGTTCGGCCGAGCAGGAGgtgagactca ... tcctcctcagGGCTTCTTGGACCTGGACTTGCTGCCTTTTTCTTCCTCGCCGGCATTACCTTTGCTGCCGTCTCTATCAGAAGCAGTGGCACCCACGCAGCTG


Block sizes: 42 (upstream exon), 49 (downstream exon)
Score: 61

GGCTCGTCCCCGCCCAACTCCTTCGCTGGCTGGTCCTCCGACTCCGACAGCGCGGATGACGGCGCCGACAAATCTACTCTAGGGTTCGGCCGAGCAGGAGgtgagactca ... tcctcctcagGGCTTCTTGGACCTGGACTTGCTGCCTTTTTCTTCCTCGCCGGCATTACCTTTGCTGCCGTCTCTATCAGAAGCAGTGGCACCCACGCAGCTG


Block sizes: 44 (upstream exon), 49 (downstream exon)
Score: 98

GGCTCGTCCCCGCCCAACTCCTTCGCTGGCTGGTCCTCCGACTCCGACAGCGCGGATGACGGCGCCGACAAATCTACTCTAGGGTTCGGCCGAGCAGGAGgtgagactca ... tcctcctcagGGCTTCTTGGACCTGGACTTGCTGCCTTTTTCTTCCTCGCCGGCATTACCTTTGCTGCCGTCTCTATCAGAAGCAGTGGCACCCACGCAGCTG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttactttcccatcttctagctagctaaacctttgatatggtagctcctcctcagGGCTTCTTGGACCTGGACTTGCTGCCTTTTTCTTCCTCGCCGGCATTACCTTTGCTGCCGTCTCTATCAGAAGCAGTGGCACCCACGCAGCTG
                                            ctcctcctc  CT-rich tract
                               tttgatat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagactcactccatccgccatcttcttctcctccttactttcccatcttctagctagctaaacctttgatatggtagctcctcctcagGGCTTCTTGGACCTGGACTTGCTGCCTTTTTCTTCCTCGCCGGCATTACCTTTGCTGCCGTCTCTATCAGAAGCAGTGGCACCCACGCAGCTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTG