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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTACCGGGATTTCAAGAGGTCTCTGCAACAAGCTCTAGACAGAAGGTGTGGTGAGGCTGCTCGACAAACTGTGGATTTTTTAATACAGgtgaagttctaacatgtcagttgcgtttttttaaccatatatcaacacttcgtgggccctagctggggaagtgccctcccctttctttgttttttcatac...

Basic information

species Zea mays
transcript GRMZM2G409430_T02
intron # 16
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|33094907|gb|CF054901.1|CF054901
EST:     ACAGAAGGTGTGGTGAGGCTGCTCGACAAACTGTGGATTTTTTAATACAG                         CTTATGAAAAACCCATCCACACCTCAACGTTTCTGGCTACCCCTTCTACAT
genomic: ACAGAAGGTGTGGTGAGGCTGCTCGACAAACTGTGGATTTTTTAATACAGgtgaagttct ... ttctttgcagCTTATGAAAAACCCATCCACACCTCAACGTTTCTGGCTACCCCTTCTACAT
EST: gi|71423078|gb|DR805944.1|DR805944
EST:     ACAGAAGGTGTGGTGAGGCTGCTCGACAAACTGTGGATTTTTTAATACAG                         CTTATGAAAAACCCATCCACACCTCAACGTTTCTGGCTACCCCTTCTACAT
genomic: ACAGAAGGTGTGGTGAGGCTGCTCGACAAACTGTGGATTTTTTAATACAGgtgaagttct ... ttctttgcagCTTATGAAAAACCCATCCACACCTCAACGTTTCTGGCTACCCCTTCTACAT
EST: gi|211246515|gb|FL461040.1|FL461040
EST:     AAGGTGTGGTGAGGCTGCTCGACAAACTGTGGATTTTTTAATACAG                         CTTATGAAAAACCCATCCACACCTCAACGTTTYTGGCTACCCCTTYTACAT
genomic: AAGGTGTGGTGAGGCTGCTCGACAAACTGTGGATTTTTTAATACAGgtgaagttct ... ttctttgcagCTTATGAAAAACCCATCCACACCTCAACGTTTCTGGCTACCCCTTCTACAT
EST: gi|24766432|gb|CA401586.1|CA401586
EST:     ACAGAAGGTGTGGTGAGGCTGCTCGACAAACTGTGGATTTTTTAATACAG                         CTTATGAAAAACCCATCCACACCTCAACGTTTCTGGCTACCCCTTCTACAT
genomic: ACAGAAGGTGTGGTGAGGCTGCTCGACAAACTGTGGATTTTTTAATACAGgtgaagttct ... ttctttgcagCTTATGAAAAACCCATCCACACCTCAACGTTTCTGGCTACCCCTTCTACAT
EST: gi|7304511|gb|AW600450.1|AW600450
EST:     AGAAGGTGTGGTGAGGCTGCTCGACAAACTGTGGATTTTTTAATACAG                         CTTATGAAAAACCCATCCNCACCTCAACGTTTCTGGGCTACCCCTTCTACA
genomic: AGAAGGTGTGGTGAGGCTGCTCGACAAACTGTGGATTTTTTAATACAGgtgaagttct ... ttctttgcagCTTATGAAAAACCCATCCACACCTCAACGTTTCT-GGCTACCCCTTCTACA
EST: gi|5929080|gb|AW056372.1|AW056372
EST:     GTGGATTTTTTAATACAG                         CTTATGAAAAACCCATNNNNNNNTCAACGTTTCTGGCTACCCCTTCTACAT
genomic: GTGGATTTTTTAATACAGgtgaagttct ... ttctttgcagCTTATGAAAAACCCATCCACACCTCAACGTTTCTGGCTACCCCTTCTACAT
EST: gi|71763805|gb|DR961742.1|DR961742
EST:     ACAGAAGGTGTGGTGAGGCTGCTCGACAAACTGTGGATTTTTTAATACAG                         CTTATGAAAAACCCATCCACACCTCAACGTTTCTGGCTACCCCTTCTACAT
genomic: ACAGAAGGTGTGGTGAGGCTGCTCGACAAACTGTGGATTTTTTAATACAGgtgaagttct ... ttctttgcagCTTATGAAAAACCCATCCACACCTCAACGTTTCTGGCTACCCCTTCTACAT

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: 49 (upstream exon), 47 (downstream exon)
Score: 100

GTACCGGGATTTCAAGAGGTCTCTGCAACAAGCTCTAGACAGAAGGTGTGGTGAGGCTGCTCGACAAACTGTGGATTTTTTAATACAGgtgaagttct ... ttctttgcagCTTATGAAAAACCCATCCACACCTCAACGTTTCTGGCTACCCCTTCTACATGATTCG


Block sizes: 43 (upstream exon), 49 (downstream exon)
Score: 25

GTACCGGGATTTCAAGAGGTCTCTGCAACAAGCTCTAGACAGAAGGTGTGGTGAGGCTGCTCGACAAACTGTGGATTTTTTAATACAGgtgaagttct ... ttctttgcagCTTATGAAAAACCCATCCACACCTCAACGTTTCTGGCTACCCCTTCTACATGATTCG


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

GTACCGGGATTTCAAGAGGTCTCTGCAACAAGCTCTAGACAGAAGGTGTGGTGAGGCTGCTCGACAAACTGTGGATTTTTTAATACAGgtgaagttct ... ttctttgcagCTTATGAAAAACCCATCCACACCTCAACGTTTCTGGCTACCCCTTCTACATGATTCG


Block sizes: 48 (upstream exon), 47 (downstream exon)
Score: 29

GTACCGGGATTTCAAGAGGTCTCTGCAACAAGCTCTAGACAGAAGGTGTGGTGAGGCTGCTCGACAAACTGTGGATTTTTTAATACAGgtgaagttct ... ttctttgcagCTTATGAAAAACCCATCCACACCTCAACGTTTCTGGCTACCCCTTCTACATGATTCG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTACCGGGATTTCAAGAGGTCTCTGCAACAAGCTCTAGACAGAAGGTGTGGTGAGGCTGCTCGACAAACTGTGGATTTTTTAATACAGgtgaagttctaacatgtcagttgcgtttttttaaccatatatcaacacttcgtgggccctagctggggaagtgccctcccctttctttgttttttcatac

- - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ccctccc