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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ctgggcgagcgccccaggccagtctcccagccaagcatgccttagtctgtctctatttctatattatatccattttaatcttatatcaacttgatcttagATACTGTAAACGGGTTCTCGTTCCATCCATACCTTCCATTTGCTGTAACATCATCCGGGCACAGAAGATTTGGCATGCAAGATGAGTTTGAAGACGAGTT

Basic information

species Zea mays
transcript GRMZM2G133749_T02
intron # 11
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|71758651|gb|DR956588.1|DR956588
EST:     ATATGACCTTCAAGGTGGTCAATGGGTAACCGGCTACCAAGCAGCAGCTG                         ATACTGTAAACGGGTTCTCGTTCCATCCATACCTTCCATTTGCTGTAACAT
genomic: ATATGACCTTCAAGGTGGTCAATGGGTAACCGGCTACCAAGCAGCAGCTGgtatgtctct ... ttgatcttagATACTGTAAACGGGTTCTCGTTCCATCCATACCTTCCATTTGCTGTAACAT
EST: gi|60349571|gb|DN216544.1|DN216544
EST:     ATATGACCTTCAAGGTGGTCAATGGGTAACCGGCTACCAAGCAGCAGCTG                         ATACTGTAAACGGGTTCTCGTTCCATCCATACCTTCCATTTGCTGTAACAT
genomic: ATATGACCTTCAAGGTGGTCAATGGGTAACCGGCTACCAAGCAGCAGCTGgtatgtctct ... ttgatcttagATACTGTAAACGGGTTCTCGTTCCATCCATACCTTCCATTTGCTGTAACAT
EST: gi|78110506|gb|DV528916.1|DV528916
EST:     ATATGACCTTCAAGGTGGTCAATGGGTAACCGGCTACCAAGCAGCAGCTG                         ATACTGTAAACGGGTTCTCGTTCCATCCATACCTTCCATTTGCTGTAACAT
genomic: ATATGACCTTCAAGGTGGTCAATGGGTAACCGGCTACCAAGCAGCAGCTGgtatgtctct ... ttgatcttagATACTGTAAACGGGTTCTCGTTCCATCCATACCTTCCATTTGCTGTAACAT
EST: gi|78110507|gb|DV528917.1|DV528917
EST:     ATATGACCTTCAAGGTGGTCAATGGGTAACCGGCTACCAAGCAGCAGCTG                         ATACTGTAAACGGTTTCTCGTTCCCATC-ATACCCTTCCATTTGC
genomic: ATATGACCTTCAAGGTGGTCAATGGGTAACCGGCTACCAAGCAGCAGCTGgtatgtctct ... ttgatcttagATACTGTAAACGGGTTCTCGTTCC-ATCCATACC-TTCCATTTGC
EST: gi|78120249|gb|DV538633.1|DV538633
EST:     ATATGACCTTCAAGGTGGTCAATGGGTAACCGGCTACCAAGCAGCAGCTG                         ATACTGTAAACGGGTTCTCGTTCCATCCATACCTTCCATTTGCTGTAACAT
genomic: ATATGACCTTCAAGGTGGTCAATGGGTAACCGGCTACCAAGCAGCAGCTGgtatgtctct ... ttgatcttagATACTGTAAACGGGTTCTCGTTCCATCCATACCTTCCATTTGCTGTAACAT
EST: gi|60355334|gb|DN222307.1|DN222307
EST:     ATATGACCTTCAAGGTGGTCAATGGGTAACCGGCTACCAAGCAGCAGCTG                         ATACTGTAAACGGGTTCTCGTTCCATCCATACCTTCCATTTGCTGTAACAT
genomic: ATATGACCTTCAAGGTGGTCAATGGGTAACCGGCTACCAAGCAGCAGCTGgtatgtctct ... ttgatcttagATACTGTAAACGGGTTCTCGTTCCATCCATACCTTCCATTTGCTGTAACAT
EST: gi|76287081|gb|DV026649.1|DV026649
EST:     ATATGACCTTCAAGGTGGTCAATGGGTAACCGGCTACCAAGCAGCAGCTG                         ATACTGTAAACGGGTTCTCGTTCCATCCATACCTTCCATTTGCTGTAACAT
genomic: ATATGACCTTCAAGGTGGTCAATGGGTAACCGGCTACCAAGCAGCAGCTGgtatgtctct ... ttgatcttagATACTGTAAACGGGTTCTCGTTCCATCCATACCTTCCATTTGCTGTAACAT
EST: gi|5932732|gb|AW057093.1|AW057093
EST:     ATATGACCTTCAAGGTGGTCAATGGGTAACCGGCTACCAAGCAGCAGCTG                         ATACTGTAAACGGGTTCTCGTTCCATCCATACCTTCCATTTGCTGTAACAT
genomic: ATATGACCTTCAAGGTGGTCAATGGGTAACCGGCTACCAAGCAGCAGCTGgtatgtctct ... ttgatcttagATACTGTAAACGGGTTCTCGTTCCATCCATACCTTCCATTTGCTGTAACAT
EST: gi|31664125|gb|CD573305.1|CD573305
EST:     ATATGACCTTCAAGGTGGTCAATGGGTAACCGGCTACCAAGCAGCAGCTG                         ATACTGTAAACGGGTTCTCGTTCCATCCATACCTTCCATTTGCTGTAACAT
genomic: ATATGACCTTCAAGGTGGTCAATGGGTAACCGGCTACCAAGCAGCAGCTGgtatgtctct ... ttgatcttagATACTGTAAACGGGTTCTCGTTCCATCCATACCTTCCATTTGCTGTAACAT
EST: gi|213186763|gb|FM190552.1|FM190552
EST:     ATATGACCTTCAAGGTGGTCAATGGGTAACCGGCTACCAAGCAGCAGCTG                         ATACTGTAAACGGGTTCTCGTTCCATCCATACCTTCCATTTGCTGTAACAT
genomic: ATATGACCTTCAAGGTGGTCAATGGGTAACCGGCTACCAAGCAGCAGCTGgtatgtctct ... ttgatcttagATACTGTAAACGGGTTCTCGTTCCATCCATACCTTCCATTTGCTGTAACAT

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: 48 (upstream exon), 49 (downstream exon)
Score: 75

GATGGCATGGTCCATGTATATGACCTTCAAGGTGGTCAATGGGTAACCGGCTACCAAGCAGCAGCTGgtatgtctct ... ttgatcttagATACTGTAAACGGGTTCTCGTTCCATCCATACCTTCCATTTGCTGTAACATCATCCGGGCACAGAAGATTTGGCATGCAAGATGAGTTTGAAGACGAGTT


Block sizes: 48 (upstream exon), 47 (downstream exon)
Score: 66

GATGGCATGGTCCATGTATATGACCTTCAAGGTGGTCAATGGGTAACCGGCTACCAAGCAGCAGCTGgtatgtctct ... ttgatcttagATACTGTAAACGGGTTCTCGTTCCATCCATACCTTCCATTTGCTGTAACATCATCCGGGCACAGAAGATTTGGCATGCAAGATGAGTTTGAAGACGAGTT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 72

GATGGCATGGTCCATGTATATGACCTTCAAGGTGGTCAATGGGTAACCGGCTACCAAGCAGCAGCTGgtatgtctct ... ttgatcttagATACTGTAAACGGGTTCTCGTTCCATCCATACCTTCCATTTGCTGTAACATCATCCGGGCACAGAAGATTTGGCATGCAAGATGAGTTTGAAGACGAGTT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 20

GATGGCATGGTCCATGTATATGACCTTCAAGGTGGTCAATGGGTAACCGGCTACCAAGCAGCAGCTGgtatgtctct ... ttgatcttagATACTGTAAACGGGTTCTCGTTCCATCCATACCTTCCATTTGCTGTAACATCATCCGGGCACAGAAGATTTGGCATGCAAGATGAGTTTGAAGACGAGTT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tctgtctctatttctatattatatccattttaatcttatatcaacttgatcttagATACTGTAAACGGGTTCTCGTTCCATCCATACCTTCCATTTGCTGTAACATCATCCGGGCACAGAAGATTTGGCATGCAAGATGAGTTTGAAGACGAGTT
        tatttctatattatat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ctgggcgagcgccccaggccagtctcccagccaagcatgccttagtctgtctctatttctatattatatccattttaatcttatatcaacttgatcttagATACTGTAAACGGGTTCTCGTTCCATCCATACCTTCCATTTGCTGTAACATCATCCGGGCACAGAAGATTTGGCATGCAAGATGAGTTTGAAGACGAGTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - -ccaggcc
- - - - - - - - - - - - - ccagcca
- - - - - - - - - - - - - - - - -agcatgc