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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGAGGTCTTCATTTGCGCCAGCACCTGCTGAACCTACAGCTGGATCATTTTCAAGATCCTATGGCGAGgtaagctgcttgactggtttatattgacatacccagcaaatcacaagacctgagattggtacccagtggatacctagttaaaagatgggaaactaattga...

Basic information

species Zea mays
transcript GRMZM2G363460_T05
intron # 9
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|31354170|gb|CD438527.1|CD438527
EST:     CAGCACCTGCTGAACCTACAGCTGGATCATTTTCAAGATCCTATGGCGAGCAG                       
genomic: CAGCACCTGCTGAACCTACAGCTGGATCATTTTCAAGATCCTATGGC--G-AGgtaagctgct ... cttttagc
EST: gi|110517843|gb|EE022430.1|EE022430
EST:     TCATTTTCAAGATCCTATGGCGAG                         CCGATGTCCACTGCACAACGAAGCGATAGGTCTTCTGGCAGTAAG
genomic: TCATTTTCAAGATCCTATGGCGAGgtaagctgct ... cttttagcagCCGATGTCCACTGCACAACGAAGCGATAGGTCTTCTGGCAGTAAG
EST: gi|20301072|gb|BQ164015.1|BQ164015
EST:     CTACAGCTGGATCATTTTCAAGATCCTATGGCGAG                         CCGATGTCCACTGCACAACGAAGCGATAGGTCTTCTGGCAGTAAG
genomic: CTACAGCTGGATCATTTTCAAGATCCTATGGCGAGgtaagctgct ... cttttagcagCCGATGTCCACTGCACAACGAAGCGATAGGTCTTCTGGCAGTAAG
EST: gi|76281031|gb|DV020599.1|DV020599
EST:     ATCATTTTCAAGATCCTATGGCGAG                         CCGATGTCCACTGCACAACGAAGCGATAGGTCTTCTGGCAGTAAG
genomic: ATCATTTTCAAGATCCTATGGCGAGgtaagctgct ... cttttagcagCCGATGTCCACTGCACAACGAAGCGATAGGTCTTCTGGCAGTAAG
EST: gi|31355282|gb|CD439639.1|CD439639
EST:     CAGCACCTGCTGAACCTACAGCTGGATCATTTTCAAGATCCTATGGCGAG                         CCGATGTCCACTGCACAACGAAGCGATAGGTCTTCTGGCAGTAAG
genomic: CAGCACCTGCTGAACCTACAGCTGGATCATTTTCAAGATCCTATGGCGAGgtaagctgct ... cttttagcagCCGATGTCCACTGCACAACGAAGCGATAGGTCTTCTGGCAGTAAG
EST: gi|78109255|gb|DV527671.1|DV527671
EST:     GATCATTTTCAAGATCCTATGGCGAGCAG                       
genomic: GATCATTTTCAAGATCCTATGGC--G-AGgtaagctgct ... cttttagc

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: 46 (upstream exon), 49 (downstream exon)
Score: 88

TGAGGTCTTCATTTGCGCCAGCACCTGCTGAACCTACAGCTGGATCATTTTCAAGATCCTATGGCGAGgtaagctgct ... cttttagcagCCGATGTCCACTGCACAACGAAGCGATAGGTCTTCTGGCAGTAAG


Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 232

TGAGGTCTTCATTTGCGCCAGCACCTGCTGAACCTACAGCTGGATCATTTTCAAGATCCTATGGCGAGgtaagctgct ... cttttagcagCCGATGTCCACTGCACAACGAAGCGATAGGTCTTCTGGCAGTAAG


Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 220

TGAGGTCTTCATTTGCGCCAGCACCTGCTGAACCTACAGCTGGATCATTTTCAAGATCCTATGGCGAGgtaagctgct ... cttttagcagCCGATGTCCACTGCACAACGAAGCGATAGGTCTTCTGGCAGTAAG


Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 119

TGAGGTCTTCATTTGCGCCAGCACCTGCTGAACCTACAGCTGGATCATTTTCAAGATCCTATGGCGAGgtaagctgct ... cttttagcagCCGATGTCCACTGCACAACGAAGCGATAGGTCTTCTGGCAGTAAG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGAGGTCTTCATTTGCGCCAGCACCTGCTGAACCTACAGCTGGATCATTTTCAAGATCCTATGGCGAGgtaagctgcttgactggtttatattgacatacccagcaaatcacaagacctgagattggtacccagtggatacctagttaaaagatgggaaactaattga

- - - - - - - - - - - - - - - - - - CAGCTG
- - - - - - - - - - - - - - - - - - - GCTGGA