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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGTATCGTCAGAGGCAAACTGGATCAGCTGAGAAGATGCTTTGAAgtaagatgcttgcagcctgtatctgcagcttcattatctatctgtccaatgatatttttatatgcatactgcattcgttttag

Basic information

species Zea mays
transcript GRMZM2G085670_T01
intron # 5
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|32927438|gb|CF032250.1|CF032250
EST:     GGTATCGTCAGAGGCAAACTGGATCAGCTGAGAAGATGCTTTGAA                         GTACAATTTGCAGCTGGAAGAGATCTTACACCTGATCAGCTAAACAACATG
genomic: GGTATCGTCAGAGGCAAACTGGATCAGCTGAGAAGATGCTTTGAAgtaagatgct ... ttcgttttagGTACAATTTGCAGCTGGAAGAGATCTTACACCTGATCAGCTAAACAACATG
EST: gi|50325881|gb|CO521007.1|CO521007
EST:     GGTATCGTCAGAGGCAAACTGGATCAGCTGAGAAGATGCTTTGAA                         GTACAATTTGCAGCTGGAAGAGATCTTACACCTGATCAGCTAAACAACATG
genomic: GGTATCGTCAGAGGCAAACTGGATCAGCTGAGAAGATGCTTTGAAgtaagatgct ... ttcgttttagGTACAATTTGCAGCTGGAAGAGATCTTACACCTGATCAGCTAAACAACATG
EST: gi|101390708|gb|EB817288.1|EB817288
EST:     GGTATCGTCAGAGGCAAACTGGATCAGCTGAGAAGATGCTTTGAA                         GTACAATTTGCAGCTGGAAGAGATCTTACACCTGATCAGCTAAACAACATG
genomic: GGTATCGTCAGAGGCAAACTGGATCAGCTGAGAAGATGCTTTGAAgtaagatgct ... ttcgttttagGTACAATTTGCAGCTGGAAGAGATCTTACACCTGATCAGCTAAACAACATG
EST: gi|32927905|gb|CF032717.1|CF032717
EST:     GGTATCGTCAGAGGCAAACTGGATCAGCTGAGAAGATGCTTTGAA                         GTACAATTTGCAGCTGGAAGAGATCTTACACCTGATCAGCTAAACAACATG
genomic: GGTATCGTCAGAGGCAAACTGGATCAGCTGAGAAGATGCTTTGAAgtaagatgct ... ttcgttttagGTACAATTTGCAGCTGGAAGAGATCTTACACCTGATCAGCTAAACAACATG
EST: gi|32927397|gb|CF032209.1|CF032209
EST:     GGTATCGTCAGAGGCAAACTGGATCAGCTGAGAAGATGCTTTGAA                         GTACAATTTGCAGCTGGAAGAGATCTTACACCTGATCAGCTAAACAACATG
genomic: GGTATCGTCAGAGGCAAACTGGATCAGCTGAGAAGATGCTTTGAAgtaagatgct ... ttcgttttagGTACAATTTGCAGCTGGAAGAGATCTTACACCTGATCAGCTAAACAACATG
EST: gi|71423346|gb|DR806010.1|DR806010
EST:     GGTATCGTCAGAGGCAAACTGGATCAGCTGAGAAGATGCTTTGAA                         GTACAATTTGCAGCTGGAAGAGATCTTACACCTGATCAGCTAAACAACATG
genomic: GGTATCGTCAGAGGCAAACTGGATCAGCTGAGAAGATGCTTTGAAgtaagatgct ... ttcgttttagGTACAATTTGCAGCTGGAAGAGATCTTACACCTGATCAGCTAAACAACATG
EST: gi|32927110|gb|CF031922.1|CF031922
EST:     GGTATCGTCAGAGGCAAACTGGATCAGCTGAGAAGATGCTTTGAA                         GTACAATTTGCAGCTGGAAGAGATCTTACACCTGATCAGC
genomic: GGTATCGTCAGAGGCAAACTGGATCAGCTGAGAAGATGCTTTGAAgtaagatgct ... ttcgttttagGTACAATTTGCAGCTGGAAGAGATCTTACACCTGATCAGC
EST: gi|71764777|gb|DR962714.1|DR962714
EST:     GGTATCGTCAGAGGCAAACTGGATCAGCTGAGAAGATGCTTTGAA                         GTACAATTTGCAGCTGGAAGAGATCTTACACCTGATCAGCTAAACAACATG
genomic: GGTATCGTCAGAGGCAAACTGGATCAGCTGAGAAGATGCTTTGAAgtaagatgct ... ttcgttttagGTACAATTTGCAGCTGGAAGAGATCTTACACCTGATCAGCTAAACAACATG
EST: gi|76936648|gb|DV174824.1|DV174824
EST:     GGTATCGTCAGAGGCAAACTGGATCAGCTGAGAAGATGCTTTGAA                         GTACAATTTGCAGCTGGAAGAGATCTTACACCTGATCAGCTAAACAACATG
genomic: GGTATCGTCAGAGGCAAACTGGATCAGCTGAGAAGATGCTTTGAAgtaagatgct ... ttcgttttagGTACAATTTGCAGCTGGAAGAGATCTTACACCTGATCAGCTAAACAACATG
EST: gi|211512615|gb|FL228208.1|FL228208
EST:     GGTATCGTCAGAGGCAAACTGGATCAGCTGAGAAGATGCTTTGAA                         GTACAATTTGCAGCTGGAAGAGATCTTAC
genomic: GGTATCGTCAGAGGCAAACTGGATCAGCTGAGAAGATGCTTTGAAgtaagatgct ... ttcgttttagGTACAATTTGCAGCTGGAAGAGATCTTAC
EST: gi|149000178|gb|EE037317.2|EE037317
EST:     GGTATCGTCAGAGGCAAACTGGATCAGCTGAGAAGATGCTTTGAA                         GTACAATTTGCAGCTGGAAGAGATCTTACACCTGATCAGCTAAACAACATG
genomic: GGTATCGTCAGAGGCAAACTGGATCAGCTGAGAAGATGCTTTGAAgtaagatgct ... ttcgttttagGTACAATTTGCAGCTGGAAGAGATCTTACACCTGATCAGCTAAACAACATG
EST: gi|32927326|gb|CF032138.1|CF032138
EST:     GGTATCGTCAGAGGCAAACTGGATCAGCTGAGAAGATGCTTTGAA                         GTACAATTTGCAGCTGGAAGAGATCTTACACCTGATCAGCTAAACAACATG
genomic: GGTATCGTCAGAGGCAAACTGGATCAGCTGAGAAGATGCTTTGAAgtaagatgct ... ttcgttttagGTACAATTTGCAGCTGGAAGAGATCTTACACCTGATCAGCTAAACAACATG
EST: gi|32927878|gb|CF032690.1|CF032690
EST:     TCAGCTGAGAAGATGCTTTGAA                         GTACAATTTGCAGCTGGAAGAGATCTTACACCTGATCAGCTAAACAACATG
genomic: TCAGCTGAGAAGATGCTTTGAAgtaagatgct ... ttcgttttagGTACAATTTGCAGCTGGAAGAGATCTTACACCTGATCAGCTAAACAACATG
EST: gi|76294401|gb|DV033969.1|DV033969
EST:     GGTATCGTCAGAGGCAAACTGGATCAGCTGAGAAGATGCTTTGAA                         GTACAATTTGCAGCTGGAAGAGATCTTA
genomic: GGTATCGTCAGAGGCAAACTGGATCAGCTGAGAAGATGCTTTGAAgtaagatgct ... ttcgttttagGTACAATTTGCAGCTGGAAGAGATCTTA
EST: gi|211512612|gb|FL228205.1|FL228205
EST:     GGTATCGTCAGAGGCAAACTGGATCAGCTGAGAAGATGCTTTGAA                         GTACAATTTGCAGCTGGAAGAGATCTTACACCTGATCAGCTAAACAACATG
genomic: GGTATCGTCAGAGGCAAACTGGATCAGCTGAGAAGATGCTTTGAAgtaagatgct ... ttcgttttagGTACAATTTGCAGCTGGAAGAGATCTTACACCTGATCAGCTAAACAACATG
EST: gi|89247571|gb|DY619357.1|DY619357
EST:     GGTATCGTCAGAGGCAAACTGGATCAGCTGAGAAGATGCTTTGAA                         GTACAATTTGCAGCTGGAAGAGATCTTACACCTGATCAGCTAAACAACATG
genomic: GGTATCGTCAGAGGCAAACTGGATCAGCTGAGAAGATGCTTTGAAgtaagatgct ... ttcgttttagGTACAATTTGCAGCTGGAAGAGATCTTACACCTGATCAGCTAAACAACATG
EST: gi|32928013|gb|CF032825.1|CF032825
EST:     GGTATCGGCAGAGGCAAACTGGATCAGCTGAGAAGATGCTTTGAA                         GTACAATTTGCAGCTGGAAGAGATCTTACACCTGATCAGCTAAACAACATG
genomic: GGTATCGTCAGAGGCAAACTGGATCAGCTGAGAAGATGCTTTGAAgtaagatgct ... ttcgttttagGTACAATTTGCAGCTGGAAGAGATCTTACACCTGATCAGCTAAACAACATG
EST: gi|32927819|gb|CF032631.1|CF032631
EST:     CAGCTGAGAAGATGCTTTGAA                         GTACAATTTGCAGCTGGAAGAGATCTTACACCTGATCAGCTAAACAACATG
genomic: CAGCTGAGAAGATGCTTTGAAgtaagatgct ... ttcgttttagGTACAATTTGCAGCTGGAAGAGATCTTACACCTGATCAGCTAAACAACATG
EST: gi|32927866|gb|CF032678.1|CF032678
EST:     AGAAGATGCTTTGAA                         GTACAATTTGCAGCTGGAAGAGATCTTACACCTGATCAGCTAAACAACATG
genomic: AGAAGATGCTTTGAAgtaagatgct ... ttcgttttagGTACAATTTGCAGCTGGAAGAGATCTTACACCTGATCAGCTAAACAACATG
EST: gi|31360706|gb|CD445063.1|CD445063
EST:     GGTATCGTCAGAGGCAAACTGGATCAGCTGAGAAGATGCTTTGAA                         GTACAATTTGCAGCTGGAAGAGATCTTACACCTGATCAGCTAAACAACATG
genomic: GGTATCGTCAGAGGCAAACTGGATCAGCTGAGAAGATGCTTTGAAgtaagatgct ... ttcgttttagGTACAATTTGCAGCTGGAAGAGATCTTACACCTGATCAGCTAAACAACATG
EST: gi|32927322|gb|CF032134.1|CF032134
EST:     GGTATCGTCAGAGGCAAACTGGATCAGCTGAGAAGATGCTTTGAA                         GTACAATTTGCAGCTGGAAGAGATCTTACACCTGATCAGCTAAACAACATG
genomic: GGTATCGTCAGAGGCAAACTGGATCAGCTGAGAAGATGCTTTGAAgtaagatgct ... ttcgttttagGTACAATTTGCAGCTGGAAGAGATCTTACACCTGATCAGCTAAACAACATG
EST: gi|32927641|gb|CF032453.1|CF032453
EST:     AGAAGATGCTTTGAA                         GTACAATTTGCAGCTGGAAGAGATCTTACACCTGATCAGCTAAACAACATG
genomic: AGAAGATGCTTTGAAgtaagatgct ... ttcgttttagGTACAATTTGCAGCTGGAAGAGATCTTACACCTGATCAGCTAAACAACATG
EST: gi|32927565|gb|CF032377.1|CF032377
EST:     ATCAGCTGAGAAGATGCTTTGAA                         GTACAATTTGCAGCTGGAAGAGATCTTACACCTGATCAGCTAAACAACATG
genomic: ATCAGCTGAGAAGATGCTTTGAAgtaagatgct ... ttcgttttagGTACAATTTGCAGCTGGAAGAGATCTTACACCTGATCAGCTAAACAACATG
EST: gi|101398140|gb|EB820944.1|EB820944
EST:     GGTATCGTCAGAGGCAAACTGGATCAGCTGAGAAGATGCTTTGAA                         GTACAATTTGCAGCTGGAAGAGATCTTACACCTGATCAGCTAAACAACATG
genomic: GGTATCGTCAGAGGCAAACTGGATCAGCTGAGAAGATGCTTTGAAgtaagatgct ... ttcgttttagGTACAATTTGCAGCTGGAAGAGATCTTACACCTGATCAGCTAAACAACATG
EST: gi|78090434|gb|DV518808.1|DV518808
EST:     GGTATCGTCAGAGGCAAACTGGATCAGCTGAGAAGATGCTTTGAA                         GTACAATTTGCAGCTGGAAGAGATCTTACACCTGATCAGCTAAACAACATG
genomic: GGTATCGTCAGAGGCAAACTGGATCAGCTGAGAAGATGCTTTGAAgtaagatgct ... ttcgttttagGTACAATTTGCAGCTGGAAGAGATCTTACACCTGATCAGCTAAACAACATG
EST: gi|32927333|gb|CF032145.1|CF032145
EST:     GGTATCGTCAGAGGCAAACTGGATCAGCTGAGAAGATGCTTTGAA                         GTACAATTTGCAGCTGGAAGAGATCTTACACCTGATCAGCTAAACAACATG
genomic: GGTATCGTCAGAGGCAAACTGGATCAGCTGAGAAGATGCTTTGAAgtaagatgct ... ttcgttttagGTACAATTTGCAGCTGGAAGAGATCTTACACCTGATCAGCTAAACAACATG
EST: gi|78090435|gb|DV518809.1|DV518809
EST:     GGTATCGTCAGAGGCAAACTGGATCAGCTGAGAAGATGCTTTGAA                         GTACAATTTGCAGCTGGAAGAGATCTTACACCTGATCAGCTAAACAACATG
genomic: GGTATCGTCAGAGGCAAACTGGATCAGCTGAGAAGATGCTTTGAAgtaagatgct ... ttcgttttagGTACAATTTGCAGCTGGAAGAGATCTTACACCTGATCAGCTAAACAACATG

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: 45 (upstream exon), 49 (downstream exon)
Score: 163

GGTATCGTCAGAGGCAAACTGGATCAGCTGAGAAGATGCTTTGAAgtaagatgct ... ttcgttttagGTACAATTTGCAGCTGGAAGAGATCTTACACCTGATCAGCTAAACAACATGATAGAGATCTTATCTGACTG


Block sizes: 45 (upstream exon), 49 (downstream exon)
Score: 103

GGTATCGTCAGAGGCAAACTGGATCAGCTGAGAAGATGCTTTGAAgtaagatgct ... ttcgttttagGTACAATTTGCAGCTGGAAGAGATCTTACACCTGATCAGCTAAACAACATGATAGAGATCTTATCTGACTG


Block sizes: 45 (upstream exon), 46 (downstream exon)
Score: 132

GGTATCGTCAGAGGCAAACTGGATCAGCTGAGAAGATGCTTTGAAgtaagatgct ... ttcgttttagGTACAATTTGCAGCTGGAAGAGATCTTACACCTGATCAGCTAAACAACATGATAGAGATCTTATCTGACTG


Block sizes: 45 (upstream exon), 49 (downstream exon)
Score: 97

GGTATCGTCAGAGGCAAACTGGATCAGCTGAGAAGATGCTTTGAAgtaagatgct ... ttcgttttagGTACAATTTGCAGCTGGAAGAGATCTTACACCTGATCAGCTAAACAACATGATAGAGATCTTATCTGACTG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGTATCGTCAGAGGCAAACTGGATCAGCTGAGAAGATGCTTTGAAgtaagatgcttgcagcctgtatctgcagcttcattatctatctgtccaatgatatttttatatgcatactgcattcgttttag

- - - - - - - - - - -  TCAGCT
- - - - - - - - - - - - CAGCTG
- - - - - - - - - - - -  AGCTGA
- - - - - - - - - - - - - - - - AAGATG