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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGTACCATGAAGAGGTTGGTTTCGACCGCCCTCGCCGCGAGAGGGCTCCTGAGATCTCACGGACTGCCGACCACAACTTCTgtaaggttcacaaatccactccacgatggtcgccaatctccatacgtctttcttagcttcgagtgctaatgcagcgagattgttcgacacagccatgatg...

Basic information

species Zea mays
transcript GRMZM5G880300_T02
intron # 2
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|211324031|gb|FL418314.1|FL418314
EST:     TCGCCGCGAGAGGGCTCCTGAGATCTCACGGACTGCCGACCACAACTTCT                         GTTATGTACCAACCAGCATTCCAGCAATTTATGAACTATTCATCACCACAT
genomic: TCGCCGCGAGAGGGCTCCTGAGATCTCACGGACTGCCGACCACAACTTCTgtaaggttca ... ggaagagcagGTTATGTACCAACCAGCATTCCAGCAATTTATGAACTATTCATCACCACAT
EST: gi|211153335|gb|FL392722.1|FL392722
EST:     TCGCCGCGAGAGGGCTCCTGAGATCTCACGGACTGCCGACCACAACTTCT                         GTTATGTACCAACCAGCATTCCAGCAATTTATGAACTATTCATCACCACAT
genomic: TCGCCGCGAGAGGGCTCCTGAGATCTCACGGACTGCCGACCACAACTTCTgtaaggttca ... ggaagagcagGTTATGTACCAACCAGCATTCCAGCAATTTATGAACTATTCATCACCACAT
EST: gi|211071256|gb|FL399022.1|FL399022
EST:     TCGCCGCGAGAGGGCTCCTGAGATCTCACGGACTGCCGACCACAACTTCT                         GTTATGTACCAACCAGCATTCCAGCAATTTATGAACTATTCATCACCACAT
genomic: TCGCCGCGAGAGGGCTCCTGAGATCTCACGGACTGCCGACCACAACTTCTgtaaggttca ... ggaagagcagGTTATGTACCAACCAGCATTCCAGCAATTTATGAACTATTCATCACCACAT
EST: gi|74236784|gb|DT644698.1|DT644698
EST:     TCGCCGCGAGAGGGCTCCTGAGATCTCACGGACTGCCGACCACAACTTCT                         GTTATGTACCAACCAGCATTCCAGCAATTTATGAACTATTCATCACCACAT
genomic: TCGCCGCGAGAGGGCTCCTGAGATCTCACGGACTGCCGACCACAACTTCTgtaaggttca ... ggaagagcagGTTATGTACCAACCAGCATTCCAGCAATTTATGAACTATTCATCACCACAT
EST: gi|211479938|gb|FL425914.1|FL425914
EST:     TCGCCGCGAGAGGGCTCCTGAGATCTCACGGACTGCCGACCACAACTTCT                         GTTATGTACCAACCAGCATTCCAGCAATTTATGAACTATTCATCACCACAT
genomic: TCGCCGCGAGAGGGCTCCTGAGATCTCACGGACTGCCGACCACAACTTCTgtaaggttca ... ggaagagcagGTTATGTACCAACCAGCATTCCAGCAATTTATGAACTATTCATCACCACAT
EST: gi|91877551|gb|EB407508.1|EB407508
EST:     TCGCCGCGAGAGGGCTCCTGAGATCTCACGGACTGCCGACCACAACTTCT                         GTTATGTACCAACCAGCATTCCAGCAATTTATGAACTATTCATCACCACAT
genomic: TCGCCGCGAGAGGGCTCCTGAGATCTCACGGACTGCCGACCACAACTTCTgtaaggttca ... ggaagagcagGTTATGTACCAACCAGCATTCCAGCAATTTATGAACTATTCATCACCACAT
EST: gi|211159736|gb|FL393706.1|FL393706
EST:     TCGCCGCGAGAGGGCTCCTGAGATCTCACGGACTGCCGACCACAACTTCT                         GTTATGTACCAACCAGCATTCCAGCAATTTATGAACTATTCATCACCACAT
genomic: TCGCCGCGAGAGGGCTCCTGAGATCTCACGGACTGCCGACCACAACTTCTgtaaggttca ... ggaagagcagGTTATGTACCAACCAGCATTCCAGCAATTTATGAACTATTCATCACCACAT
EST: gi|93017644|gb|EB643164.1|EB643164
EST:     TCGCCGCGAGAGGGCTCCTGAGATCTCACGGACTGCCGACCACAACTTCT                         GTTATGTACCAACCAGCATTCCAGCAATTTATGAACTATTCATCACCACAT
genomic: TCGCCGCGAGAGGGCTCCTGAGATCTCACGGACTGCCGACCACAACTTCTgtaaggttca ... ggaagagcagGTTATGTACCAACCAGCATTCCAGCAATTTATGAACTATTCATCACCACAT
EST: gi|76281315|gb|DV020883.1|DV020883
EST:     TCGCCGCGAGAGGGCTCCTGAGATCTCACGGACTGCCGACCACAACTTCT                         GTTATGTACCAACCAGCATTCCAGCAATTTATGAACTATTCATCACCACAT
genomic: TCGCCGCGAGAGGGCTCCTGAGATCTCACGGACTGCCGACCACAACTTCTgtaaggttca ... ggaagagcagGTTATGTACCAACCAGCATTCCAGCAATTTATGAACTATTCATCACCACAT
EST: gi|211148655|gb|FL387728.1|FL387728
EST:     TCGCCGCGAGAGGGCTCCTGAGATCTCACGGACTGCCGACCACAACTTCT                         GTTATGTACCAACCAGCATTCCAGCAATTTATGAACTATTCATCACCACAT
genomic: TCGCCGCGAGAGGGCTCCTGAGATCTCACGGACTGCCGACCACAACTTCTgtaaggttca ... ggaagagcagGTTATGTACCAACCAGCATTCCAGCAATTTATGAACTATTCATCACCACAT
EST: gi|211243072|gb|FL400459.1|FL400459
EST:     TCGCCGCGAGAGGGCTCCTGAGATCTCACGGACTGCCGACCACAACTTCT                         GTTATGTACCAACCAGCATTCCAGCAATTTATGAACTATTCATCACCACAT
genomic: TCGCCGCGAGAGGGCTCCTGAGATCTCACGGACTGCCGACCACAACTTCTgtaaggttca ... ggaagagcagGTTATGTACCAACCAGCATTCCAGCAATTTATGAACTATTCATCACCACAT
EST: gi|84980275|gb|DW530624.1|DW530624
EST:     TCGCCGCGAGAGGGCTCCTGAGATCTCACGGACTGCCGACCACAACTTCT                         GTTATGTACCAACCAGCATTCCAGCAATTTATGAACTATTCATCACCACAT
genomic: TCGCCGCGAGAGGGCTCCTGAGATCTCACGGACTGCCGACCACAACTTCTgtaaggttca ... ggaagagcagGTTATGTACCAACCAGCATTCCAGCAATTTATGAACTATTCATCACCACAT
EST: gi|211069174|gb|FL417736.1|FL417736
EST:     TCGCCGCGAGAGGGCTCCTGAGATCTCACGGACTGCCGACCACAACTTCT                         GTTATGTACCAACCAGCATTCCAGCAATTTATGAACTATTCATCACCACAT
genomic: TCGCCGCGAGAGGGCTCCTGAGATCTCACGGACTGCCGACCACAACTTCTgtaaggttca ... ggaagagcagGTTATGTACCAACCAGCATTCCAGCAATTTATGAACTATTCATCACCACAT
EST: gi|101389214|gb|EB816562.1|EB816562
EST:     TCGCCGCGAGAGGGCTCCTGAGATCTCACGGACTGCCGACCACAACTTCT                         GTTATGTACCAACCAGCATTCCAGCAATTTATGAACTATTCATCACCACAT
genomic: TCGCCGCGAGAGGGCTCCTGAGATCTCACGGACTGCCGACCACAACTTCTgtaaggttca ... ggaagagcagGTTATGTACCAACCAGCATTCCAGCAATTTATGAACTATTCATCACCACAT
EST: gi|84980198|gb|DW530547.1|DW530547
EST:     TCGCCGCGAGAGGGCTCCTGAGATCTCACGGACTGCCGACCACAACTTCT                         GTTATGTACCAACCAGCATTCCAGCAATTTATGAACTATTCATCACCACAT
genomic: TCGCCGCGAGAGGGCTCCTGAGATCTCACGGACTGCCGACCACAACTTCTgtaaggttca ... ggaagagcagGTTATGTACCAACCAGCATTCCAGCAATTTATGAACTATTCATCACCACAT

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), 46 (downstream exon)
Score: 84

GGTACCATGAAGAGGTTGGTTTCGACCGCCCTCGCCGCGAGAGGGCTCCTGAGATCTCACGGACTGCCGACCACAACTTCTgtaaggttca ... ggaagagcagGTTATGTACCAACCAGCATTCCAGCAATTTATGAACTATTCATCACCACATGGTGGTGATCCCAATGCAAACACGAACTCAACTACAACACGAATAGCTG


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 44

GGTACCATGAAGAGGTTGGTTTCGACCGCCCTCGCCGCGAGAGGGCTCCTGAGATCTCACGGACTGCCGACCACAACTTCTgtaaggttca ... ggaagagcagGTTATGTACCAACCAGCATTCCAGCAATTTATGAACTATTCATCACCACATGGTGGTGATCCCAATGCAAACACGAACTCAACTACAACACGAATAGCTG


Block sizes: 47 (upstream exon), 46 (downstream exon)
Score: 63

GGTACCATGAAGAGGTTGGTTTCGACCGCCCTCGCCGCGAGAGGGCTCCTGAGATCTCACGGACTGCCGACCACAACTTCTgtaaggttca ... ggaagagcagGTTATGTACCAACCAGCATTCCAGCAATTTATGAACTATTCATCACCACATGGTGGTGATCCCAATGCAAACACGAACTCAACTACAACACGAATAGCTG


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 65

GGTACCATGAAGAGGTTGGTTTCGACCGCCCTCGCCGCGAGAGGGCTCCTGAGATCTCACGGACTGCCGACCACAACTTCTgtaaggttca ... ggaagagcagGTTATGTACCAACCAGCATTCCAGCAATTTATGAACTATTCATCACCACATGGTGGTGATCCCAATGCAAACACGAACTCAACTACAACACGAATAGCTG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGTACCATGAAGAGGTTGGTTTCGACCGCCCTCGCCGCGAGAGGGCTCCTGAGATCTCACGGACTGCCGACCACAACTTCTgtaaggttcacaaatccactccacgatggtcgccaatctccatacgtctttcttagcttcgagtgctaatgcagcgagattgttcgacacagccatgatg

- - - - - - - - - - - - - - - - - - - GAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - GAGATC