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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tatcatgctgtgtgttgtcgcctgcgcttgtgtctatgtctgtgatttctagtttttttttccggtaatttttgttgttctctcctgtttctcatttcagTCTCTGGAATGGATCATGTTCGCGTGCACCCTAGATTTCTGCACTCAAACGCAACAAGTCACAAGTGGGCTCTAGGTG

Basic information

species Zea mays
transcript GRMZM2G161087_T01
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|211002749|gb|FL375709.1|FL375709
EST:     TGGGGACTACGACGGAAAGCCGCTCGGTGATGGGGTGGCTCAGCAGTCAG                         TCTCTGGAATGGATCATGTTCGCGTGCACCCTANATTTCTGCACTCAAACG
genomic: TGGGGACTACGACGGAAAGCCGCTCGGTGATGGGGTGGCTCAGCAGTCAGgtaccatcct ... ctcatttcagTCTCTGGAATGGATCATGTTCGCGTGCACCCTAGATTTCTGCACTCAAACG
EST: gi|78121690|gb|DV540074.1|DV540074
EST:     TGGGGACTACGACGGAAAGCCGCTCGGTGATGGGGTGGCTCAGCAGTCAG                         TCTCTGGAATGGATCATGTTCGCGTGCACCCTAGATTTCTGCACTCAAACG
genomic: TGGGGACTACGACGGAAAGCCGCTCGGTGATGGGGTGGCTCAGCAGTCAGgtaccatcct ... ctcatttcagTCTCTGGAATGGATCATGTTCGCGTGCACCCTAGATTTCTGCACTCAAACG
EST: gi|71772592|gb|DR970521.1|DR970521
EST:     TGGGGACTACGACGGAAAGCCGCTCGGTGATGGGGTGGCTCAGCAGTCAG                         TCTCTGGAATGGATCATGTTCGCGTGCACCCTAGATTTCTGCACTCAAACG
genomic: TGGGGACTACGACGGAAAGCCGCTCGGTGATGGGGTGGCTCAGCAGTCAGgtaccatcct ... ctcatttcagTCTCTGGAATGGATCATGTTCGCGTGCACCCTAGATTTCTGCACTCAAACG

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: 244

CCGGTGCCGGTGCCATTGGCAGCTTGTGCGACGAAGCAGTTCTGGAAGGCTGGGGACTACGACGGAAAGCCGCTCGGTGATGGGGTGGCTCAGCAGTCAGgtaccatcct ... ctcatttcagTCTCTGGAATGGATCATGTTCGCGTGCACCCTAGATTTCTGCACTCAAACGCAACAAGTCACAAGTGGGCTCTAGGTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 105

CCGGTGCCGGTGCCATTGGCAGCTTGTGCGACGAAGCAGTTCTGGAAGGCTGGGGACTACGACGGAAAGCCGCTCGGTGATGGGGTGGCTCAGCAGTCAGgtaccatcct ... ctcatttcagTCTCTGGAATGGATCATGTTCGCGTGCACCCTAGATTTCTGCACTCAAACGCAACAAGTCACAAGTGGGCTCTAGGTG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 76

CCGGTGCCGGTGCCATTGGCAGCTTGTGCGACGAAGCAGTTCTGGAAGGCTGGGGACTACGACGGAAAGCCGCTCGGTGATGGGGTGGCTCAGCAGTCAGgtaccatcct ... ctcatttcagTCTCTGGAATGGATCATGTTCGCGTGCACCCTAGATTTCTGCACTCAAACGCAACAAGTCACAAGTGGGCTCTAGGTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 194

CCGGTGCCGGTGCCATTGGCAGCTTGTGCGACGAAGCAGTTCTGGAAGGCTGGGGACTACGACGGAAAGCCGCTCGGTGATGGGGTGGCTCAGCAGTCAGgtaccatcct ... ctcatttcagTCTCTGGAATGGATCATGTTCGCGTGCACCCTAGATTTCTGCACTCAAACGCAACAAGTCACAAGTGGGCTCTAGGTG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttctagtttttttttccggtaatttttgttgttctctcctgtttctcatttcagTCTCTGGAATGGATCATGTTCGCGTGCACCCTAGATTTCTGCACTCAAACGCAACAAGTCACAAGTGGGCTCTAGGTG
                       tttttgttgttctctc  CT-rich tract
                    taatttttgttgtt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tatcatgctgtgtgttgtcgcctgcgcttgtgtctatgtctgtgatttctagtttttttttccggtaatttttgttgttctctcctgtttctcatttcagTCTCTGGAATGGATCATGTTCGCGTGCACCCTAGATTTCTGCACTCAAACGCAACAAGTCACAAGTGGGCTCTAGGTG

- -catgctg
- - - - - tgtgttg
- - - - - - - - - -gcctgcg
- - - - - - - - - - - - - - - - - - - - tgtgatt