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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TCTGCAGAGAGCGGCGGTAGCACAGGAACGCACAAATAAGAAAGTGCAAGAGAGGGAAGATGCTTTGAGGGTAGAGCTTGCTAACCAACTATCTGAGAAGgtaattatttctctcaatgttatgttgcacactctttctcaatgttcaggaaaataaaattatggcatatttattgttaattttcttccaagttttgctatgtgcttcttggtcacttccatttgcttattatgtgtaaacag

Basic information

species Zea mays
transcript GRMZM2G031053_T01
intron # 11
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|87154018|gb|DY398807.1|DY398807
EST:     AGAGGGAAGATGCTTTGAGGGTAGAGCTTGCTAACCAACTATCTGAGAAG                         GAAGAGGAAATTGCAAGATTACATGCAAAACTTAGTCAAATGGAAATTCAT
genomic: AGAGGGAAGATGCTTTGAGGGTAGAGCTTGCTAACCAACTATCTGAGAAGgtaattattt ... gtgtaaacagGAAGAGGAAATTGCAAGATTACATGCAAAACGTAGTCAAATGGAAATTCAT
EST: gi|211025432|gb|FL195735.1|FL195735
EST:     AGAGGGAAGATGCTTTGAGGGTAGAGCTTGCTAACCGACTATCTGAGAAG                         GAAGAGAAAATTGCAAGATTACATGCAAAACTTAGTCAAATGGAAATTCAT
genomic: AGAGGGAAGATGCTTTGAGGGTAGAGCTTGCTAACCAACTATCTGAGAAGgtaattattt ... gtgtaaacagGAAGAGGAAATTGCAAGATTACATGCAAAACGTAGTCAAATGGAAATTCAT
EST: gi|18384448|gb|BM417647.1|BM417647
EST:     AGAGGGAAGATGCTTTGAGGGTAGAGCTTGCTAACCAACTATCTGAGAAG                         GAAGAGGAAATTGCAAGATTACATGCAAAACTTAGTCAAATGGAAATTCAT
genomic: AGAGGGAAGATGCTTTGAGGGTAGAGCTTGCTAACCAACTATCTGAGAAGgtaattattt ... gtgtaaacagGAAGAGGAAATTGCAAGATTACATGCAAAACGTAGTCAAATGGAAATTCAT
EST: gi|18649914|gb|BM498733.1|BM498733
EST:     AGAGGGAAGATGCTTTGAGGGTAGAGCTTGCTAACCAACTATCTGAGAAG                         GAAGAGGAAATTGCAAGATTACATGCAAAACTTAGTCAAATGGAAATTCAT
genomic: AGAGGGAAGATGCTTTGAGGGTAGAGCTTGCTAACCAACTATCTGAGAAGgtaattattt ... gtgtaaacagGAAGAGGAAATTGCAAGATTACATGCAAAACGTAGTCAAATGGAAATTCAT
EST: gi|211027876|gb|FL195737.1|FL195737
EST:     AGAGGGAAGATGCTTTGAGGGTAGAGCTTGCTAACCGACTATCTGAGAAG                         GAAGAGAAAATTGCAAGATTACATGCAAAACTTAGTCAAATGGAAATTCAT
genomic: AGAGGGAAGATGCTTTGAGGGTAGAGCTTGCTAACCAACTATCTGAGAAGgtaattattt ... gtgtaaacagGAAGAGGAAATTGCAAGATTACATGCAAAACGTAGTCAAATGGAAATTCAT
EST: gi|22489641|gb|BU049564.1|BU049564
EST:     AGAGGGAAGATGCTTTGAGGGTAGAGCTTGCTAACCAACTATCTGAGAAG                         GAAGAGGAAATTGCAAGATTACATGCAAAACTTAGTCAAATGGAAATTCAT
genomic: AGAGGGAAGATGCTTTGAGGGTAGAGCTTGCTAACCAACTATCTGAGAAGgtaattattt ... gtgtaaacagGAAGAGGAAATTGCAAGATTACATGCAAAACGTAGTCAAATGGAAATTCAT

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: 207

TCTGCAGAGAGCGGCGGTAGCACAGGAACGCACAAATAAGAAAGTGCAAGAGAGGGAAGATGCTTTGAGGGTAGAGCTTGCTAACCAACTATCTGAGAAGgtaattattt ... gtgtaaacagGAAGAGGAAATTGCAAGATTACATGCAAAACGTAGTCAAATGGAAATTCATGCTACAAGTTTGATCTCGAGGCTTGAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 91

TCTGCAGAGAGCGGCGGTAGCACAGGAACGCACAAATAAGAAAGTGCAAGAGAGGGAAGATGCTTTGAGGGTAGAGCTTGCTAACCAACTATCTGAGAAGgtaattattt ... gtgtaaacagGAAGAGGAAATTGCAAGATTACATGCAAAACGTAGTCAAATGGAAATTCATGCTACAAGTTTGATCTCGAGGCTTGAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 62

TCTGCAGAGAGCGGCGGTAGCACAGGAACGCACAAATAAGAAAGTGCAAGAGAGGGAAGATGCTTTGAGGGTAGAGCTTGCTAACCAACTATCTGAGAAGgtaattattt ... gtgtaaacagGAAGAGGAAATTGCAAGATTACATGCAAAACGTAGTCAAATGGAAATTCATGCTACAAGTTTGATCTCGAGGCTTGAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 95

TCTGCAGAGAGCGGCGGTAGCACAGGAACGCACAAATAAGAAAGTGCAAGAGAGGGAAGATGCTTTGAGGGTAGAGCTTGCTAACCAACTATCTGAGAAGgtaattattt ... gtgtaaacagGAAGAGGAAATTGCAAGATTACATGCAAAACGTAGTCAAATGGAAATTCATGCTACAAGTTTGATCTCGAGGCTTGAG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TCTGCAGAGAGCGGCGGTAGCACAGGAACGCACAAATAAGAAAGTGCAAGAGAGGGAAGATGCTTTGAGGGTAGAGCTTGCTAACCAACTATCTGAGAAGgtaattatttctctcaatgttatgttgcacactctttctcaatgttcaggaaaataaaattatggcatatttattgttaattttcttccaagttttgctatgtgcttcttggtcacttccatttgcttattatgtgtaaacag

- - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCTT