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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CCTCCTCCCTTCTCTCGTCGTTCCCTCCACTCCTAGGCGGAAGCGGCCGGCGCAGAGTGGAGATCGACCCGGACTTTGAAATTGCCTCTTCCTTTTGATGgtaaggaaaaccatagccttgcttgattagtcactccacgcctaccagtttgtcgtgaatttgtcgttgtttcgagggcgacaataattccagtttattt...

Basic information

species Zea mays
transcript GRMZM5G880300_T02
intron # 1
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:     CGCAGAGTGGAGATCGACCCGGACTTTGAAATTGCCTCTTCCTTTTGATG                         GGTA-CATGAAGAGGTTGGTTTCGACCGCCCTCGCCGCGAGAGGGCTCCTG
genomic: CGCAGAGTGGAGATCGACCCGGACTTTGAAATTGCCTCTTCCTTTTGATGgtaaggaaaa ... ccgttcacagGGTACCATGAAGAGGTTGGTTTCGACCGCCCTCGCCGCGAGAGGGCTCCTG
EST: gi|211153335|gb|FL392722.1|FL392722
EST:     CGCAGAGTGGAGATCGACCCGGACTTTGAAATTGCCTCTTCCTTTTGATG                         GGTACCATGAAGAGGTTGGTTTCGACCGCCCTCGCCGCGAGAGGGCTCCTG
genomic: CGCAGAGTGGAGATCGACCCGGACTTTGAAATTGCCTCTTCCTTTTGATGgtaaggaaaa ... ccgttcacagGGTACCATGAAGAGGTTGGTTTCGACCGCCCTCGCCGCGAGAGGGCTCCTG
EST: gi|211071256|gb|FL399022.1|FL399022
EST:     CGCAGAGTGGAGATCGACCCGGACTTTGAAATTGCCTCTTCCTTTTGATG                         GGTACCATGAAGAGGTTGGTTTCGACCGCCCTCGCCGCGAGAGGGCTCCTG
genomic: CGCAGAGTGGAGATCGACCCGGACTTTGAAATTGCCTCTTCCTTTTGATGgtaaggaaaa ... ccgttcacagGGTACCATGAAGAGGTTGGTTTCGACCGCCCTCGCCGCGAGAGGGCTCCTG
EST: gi|74236784|gb|DT644698.1|DT644698
EST:     CGCAGAGTGGAGATCGACCCGGACTTTGAAATTGCCTCTTCCTTTTGATG                         GGTACCATGAAGAGGTTGGTTTCGACCGCCCTCGCCGCGAGAGGGCTCCTG
genomic: CGCAGAGTGGAGATCGACCCGGACTTTGAAATTGCCTCTTCCTTTTGATGgtaaggaaaa ... ccgttcacagGGTACCATGAAGAGGTTGGTTTCGACCGCCCTCGCCGCGAGAGGGCTCCTG
EST: gi|211479938|gb|FL425914.1|FL425914
EST:     CGCAGAGTGGAGATCGACCCGGACTTTGAAATTGCCTCTTCCTTTTGATG                         GGTACCATGAAGAGGTTGGTTTCGACCGCCCTCGCCGCGAGAGGGCTCCTG
genomic: CGCAGAGTGGAGATCGACCCGGACTTTGAAATTGCCTCTTCCTTTTGATGgtaaggaaaa ... ccgttcacagGGTACCATGAAGAGGTTGGTTTCGACCGCCCTCGCCGCGAGAGGGCTCCTG
EST: gi|91877551|gb|EB407508.1|EB407508
EST:     CGCAGAGTGGAGATCGACCCGGACTTTGAAATTGCCTCTTCCTTTTGATG                         GGTACCATGAAGAGGTTGGTTTCGACCGCCCTCGCCGCGAGAGGGCTCCTG
genomic: CGCAGAGTGGAGATCGACCCGGACTTTGAAATTGCCTCTTCCTTTTGATGgtaaggaaaa ... ccgttcacagGGTACCATGAAGAGGTTGGTTTCGACCGCCCTCGCCGCGAGAGGGCTCCTG
EST: gi|211159736|gb|FL393706.1|FL393706
EST:     CGCAGAGTGGAGATCGACCCGGACTTTGAAATTGCCTCTTCCTTTTGATG                         GGTA-CATGAAGAGGTTGGTTTCGACCGCCCTCGCCGCGAGAGGGCTCCTG
genomic: CGCAGAGTGGAGATCGACCCGGACTTTGAAATTGCCTCTTCCTTTTGATGgtaaggaaaa ... ccgttcacagGGTACCATGAAGAGGTTGGTTTCGACCGCCCTCGCCGCGAGAGGGCTCCTG
EST: gi|93017644|gb|EB643164.1|EB643164
EST:     CGCAGAGTGGAGATCGACCCGGACTTTGAAATTGCCTCTTCCTTTTGATG                         GGTACCATGAAGAGGTTGGTTTCGACCGCCCTCGCCGCGAGAGGGCTCCTG
genomic: CGCAGAGTGGAGATCGACCCGGACTTTGAAATTGCCTCTTCCTTTTGATGgtaaggaaaa ... ccgttcacagGGTACCATGAAGAGGTTGGTTTCGACCGCCCTCGCCGCGAGAGGGCTCCTG
EST: gi|76281315|gb|DV020883.1|DV020883
EST:     CGCAGAGTGGAGATCGACCCGGACTTTGAAATTGCCTCTTCCTTCTGATG                         GGTACCATGAAGAGGTTGGTTTCGACCGCCCTCGCCGCGAGAGGGCTCCTG
genomic: CGCAGAGTGGAGATCGACCCGGACTTTGAAATTGCCTCTTCCTTTTGATGgtaaggaaaa ... ccgttcacagGGTACCATGAAGAGGTTGGTTTCGACCGCCCTCGCCGCGAGAGGGCTCCTG
EST: gi|211148655|gb|FL387728.1|FL387728
EST:     CGCAGAGTGGAGATCGACCCGGACTTTGAAATTGCCTCTTCCTTTTGATG                         GGTACCATGAAGAGGTTGGTTTCGACCGCCCTCGCCGCGAGAGGGCTCCTG
genomic: CGCAGAGTGGAGATCGACCCGGACTTTGAAATTGCCTCTTCCTTTTGATGgtaaggaaaa ... ccgttcacagGGTACCATGAAGAGGTTGGTTTCGACCGCCCTCGCCGCGAGAGGGCTCCTG
EST: gi|211243072|gb|FL400459.1|FL400459
EST:     CGCAGAGTGGAGATCGACCCGGACTTTGAAATTGCCTCTTCCTTTTGATG                         GGTACCATGAAGAGGTTGGTTTCGACCGCCCTCGCCGCGAGAGGGCTCCTG
genomic: CGCAGAGTGGAGATCGACCCGGACTTTGAAATTGCCTCTTCCTTTTGATGgtaaggaaaa ... ccgttcacagGGTACCATGAAGAGGTTGGTTTCGACCGCCCTCGCCGCGAGAGGGCTCCTG
EST: gi|84980275|gb|DW530624.1|DW530624
EST:     CGCAGAGTGGAGATCGACCCGGACTTTGAAATTGCCTCTTCCTTTTGATG                         GGTACCATGAAGAGGTTGGTTTCGACCGCCCTCGCCGCGAGAGGGCTCCTG
genomic: CGCAGAGTGGAGATCGACCCGGACTTTGAAATTGCCTCTTCCTTTTGATGgtaaggaaaa ... ccgttcacagGGTACCATGAAGAGGTTGGTTTCGACCGCCCTCGCCGCGAGAGGGCTCCTG
EST: gi|211069174|gb|FL417736.1|FL417736
EST:     CGCAGAGTGGAGATCGACCCGGACTTTGAAATTGCCTCTTCCTTTTGATG                         GGTACCATGAAGAGGTTGGTTTCGACCGCCCTCGCCGCGAGAGGGCTCCTG
genomic: CGCAGAGTGGAGATCGACCCGGACTTTGAAATTGCCTCTTCCTTTTGATGgtaaggaaaa ... ccgttcacagGGTACCATGAAGAGGTTGGTTTCGACCGCCCTCGCCGCGAGAGGGCTCCTG
EST: gi|101389214|gb|EB816562.1|EB816562
EST:     CGCAGAGTGGAGATCGACCCGGACTTTGAAATTGCCTCTTCCTTTTGATG                         GGTACCATGAAGAGGTTGGTTTCGACCGCCCTCGCCGCGAGAGGGCTCCTG
genomic: CGCAGAGTGGAGATCGACCCGGACTTTGAAATTGCCTCTTCCTTTTGATGgtaaggaaaa ... ccgttcacagGGTACCATGAAGAGGTTGGTTTCGACCGCCCTCGCCGCGAGAGGGCTCCTG
EST: gi|84980198|gb|DW530547.1|DW530547
EST:     CGCAGAGTGGAGATCGACCCGGACTTTGAAATTGCCTCTTCCTTTTGATG                         GGTACCATGAAGAGGTTGGTTTCGACCGCCCTCGCCGCGAGAGGGCTCCTG
genomic: CGCAGAGTGGAGATCGACCCGGACTTTGAAATTGCCTCTTCCTTTTGATGgtaaggaaaa ... ccgttcacagGGTACCATGAAGAGGTTGGTTTCGACCGCCCTCGCCGCGAGAGGGCTCCTG

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), 47 (downstream exon)
Score: 143

CCTCCTCCCTTCTCTCGTCGTTCCCTCCACTCCTAGGCGGAAGCGGCCGGCGCAGAGTGGAGATCGACCCGGACTTTGAAATTGCCTCTTCCTTTTGATGgtaaggaaaa ... ccgttcacagGGTACCATGAAGAGGTTGGTTTCGACCGCCCTCGCCGCGAGAGGGCTCCTGAGATCTCACGGACTGCCGACCACAACTTCT


Block sizes: 47 (upstream exon), 48 (downstream exon)
Score: 103

CCTCCTCCCTTCTCTCGTCGTTCCCTCCACTCCTAGGCGGAAGCGGCCGGCGCAGAGTGGAGATCGACCCGGACTTTGAAATTGCCTCTTCCTTTTGATGgtaaggaaaa ... ccgttcacagGGTACCATGAAGAGGTTGGTTTCGACCGCCCTCGCCGCGAGAGGGCTCCTGAGATCTCACGGACTGCCGACCACAACTTCT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 114

CCTCCTCCCTTCTCTCGTCGTTCCCTCCACTCCTAGGCGGAAGCGGCCGGCGCAGAGTGGAGATCGACCCGGACTTTGAAATTGCCTCTTCCTTTTGATGgtaaggaaaa ... ccgttcacagGGTACCATGAAGAGGTTGGTTTCGACCGCCCTCGCCGCGAGAGGGCTCCTGAGATCTCACGGACTGCCGACCACAACTTCT


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 105

CCTCCTCCCTTCTCTCGTCGTTCCCTCCACTCCTAGGCGGAAGCGGCCGGCGCAGAGTGGAGATCGACCCGGACTTTGAAATTGCCTCTTCCTTTTGATGgtaaggaaaa ... ccgttcacagGGTACCATGAAGAGGTTGGTTTCGACCGCCCTCGCCGCGAGAGGGCTCCTGAGATCTCACGGACTGCCGACCACAACTTCT


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CCTCCTCCCTTCTCTCGTCGTTCCCTCCACTCCTAGGCGGAAGCGGCCGGCGCAGAGTGGAGATCGACCCGGACTTTGAAATTGCCTCTTCCTTTTGATGgtaaggaaaaccatagccttgcttgattagtcactccacgcctaccagtttgtcgtgaatttgtcgttgtttcgagggcgacaataattccagtttattt

- - - - - - - - - - - - - - - - - - - - - - - - - - -  AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gaaaacca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ccacgcc