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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTGTTGTAGCATATGCTTCGGATCTACTATATTCTGGTGTCAGCCTAAATCCTCATAGGGAGAAGGGTCTGAAGACATACTCACTCAGTCTTGATCACTCgtatgtttcagcaaaccgcacccagtactgcgattttaattaatacaactcgctagtaaaccgtttgtttgttactgttctgcag

Basic information

species Oryza sativa
transcript LOC_Os04g47120.1
intron # 14
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|88974436|gb|CI021977.1|CI021977
EST:     GACATACTCACTCAGTCTTGATCACTC                         GATTTGGTTCCACAAGCCTGTGAAAGCTGATGATTGGCTTTTATATGTG
genomic: GACATACTCACTCAGTCTTGATCACTCgtatgtttca ... tgttctgcagGATTTGGTTCCACAAGCCTGTGAAAGCTGATGATTGGCTTTTATATGTG
EST: gi|86430173|gb|CI082596.1|CI082596
EST:     GAAGACATACTCACTCAGTCTTGATCACTC                         GATTTGGTTCCACAAGCCTGTGAAAGCTGATGATTGGCTTTTATATGTG
genomic: GAAGACATACTCACTCAGTCTTGATCACTCgtatgtttca ... tgttctgcagGATTTGGTTCCACAAGCCTGTGAAAGCTGATGATTGGCTTTTATATGTG
EST: gi|87005717|gb|CI316136.1|CI316136
EST:     ACTCACTCAGTCTTGATCACTC                         GATTTGGTTCCACAAGCCTGTGAAAGCTGATGATTGGCTTTTATATGTG
genomic: ACTCACTCAGTCTTGATCACTCgtatgtttca ... tgttctgcagGATTTGGTTCCACAAGCCTGTGAAAGCTGATGATTGGCTTTTATATGTG
EST: gi|163927283|gb|EG710270.1|EG710270
EST:     CCTCATAGGGAGAAGGGTCTGAAGACATACTCACTCAGTCTTGATCACTC                         GATTTGGTTCCACAAGCCTGTGAAAGCTGATGATTGGCTTTTATATGTG
genomic: CCTCATAGGGAGAAGGGTCTGAAGACATACTCACTCAGTCTTGATCACTCgtatgtttca ... tgttctgcagGATTTGGTTCCACAAGCCTGTGAAAGCTGATGATTGGCTTTTATATGTG
EST: gi|89177316|gb|CI250765.1|CI250765
EST:     CCTCATAGGGAGAGGGGTCTGAAGACATACTCACTCAGTCTTGATCACTC                         GATTTGGTTCCACAAGCCTGTGAAAGCTGATGATTGGCTTTTATATGTG
genomic: CCTCATAGGGAGAAGGGTCTGAAGACATACTCACTCAGTCTTGATCACTCgtatgtttca ... tgttctgcagGATTTGGTTCCACAAGCCTGTGAAAGCTGATGATTGGCTTTTATATGTG
EST: gi|58609050|gb|CK037083.1|CK037083
EST:     CCTCATAGGGAGAAGGGTCTGAAGACATACTCACTCAGTCTTGATCACTC                         GATTTGGTTCCACAAGCCTGTGAAAGCTGATGATTGGCTTTTATATGTG
genomic: CCTCATAGGGAGAAGGGTCTGAAGACATACTCACTCAGTCTTGATCACTCgtatgtttca ... tgttctgcagGATTTGGTTCCACAAGCCTGTGAAAGCTGATGATTGGCTTTTATATGTG
EST: gi|88829709|gb|CI074579.1|CI074579
EST:     AAGACATACTCACTCAGTCTNGATCACTC                         GATTTGGTTCCACAAGCCTGTGAAAGCTGATGATTGGCTTTTATATGTG
genomic: AAGACATACTCACTCAGTCTTGATCACTCgtatgtttca ... tgttctgcagGATTTGGTTCCACAAGCCTGTGAAAGCTGATGATTGGCTTTTATATGTG
EST: gi|88250752|gb|CI348982.1|CI348982
EST:     CCTCATAGGGAGAAGGGTCTGAAGACATACTCACTCAGTCTTGATCACTC                         GATTTGGTTCCACAAGCCTGTGAAAGCTGATGATTGGCTTTTATATGTG
genomic: CCTCATAGGGAGAAGGGTCTGAAGACATACTCACTCAGTCTTGATCACTCgtatgtttca ... tgttctgcagGATTTGGTTCCACAAGCCTGTGAAAGCTGATGATTGGCTTTTATATGTG
EST: gi|88218896|gb|CI216894.1|CI216894
EST:     CCTCATAGGGAGAAGGGTCTGAAGACATACTCACTCAGTCTTGATCACTC                         GATTTGGTTCCACAAGCCTGTGAAAGCTGATGATTGGCTTTTATATGTG
genomic: CCTCATAGGGAGAAGGGTCTGAAGACATACTCACTCAGTCTTGATCACTCgtatgtttca ... tgttctgcagGATTTGGTTCCACAAGCCTGTGAAAGCTGATGATTGGCTTTTATATGTG
EST: gi|87026186|gb|CI278310.1|CI278310
EST:     CCTCATAGGGAGAAGGGTCTGAAGACATACTCACTCAGTCTTGATCACTC                         GATTTGGTTCCACAAGCCTGTGAAAGCTGATGATTGGCTTTTATATGTG
genomic: CCTCATAGGGAGAAGGGTCTGAAGACATACTCACTCAGTCTTGATCACTCgtatgtttca ... tgttctgcagGATTTGGTTCCACAAGCCTGTGAAAGCTGATGATTGGCTTTTATATGTG
EST: gi|86429359|gb|CI076040.1|CI076040
EST:     GAAGACATACTCACTCAGTCTTGATCACTC                         GATTTGGTTCCACAAGCCTGTGAAAGCTGATGATTGGCTTTTATATGTG
genomic: GAAGACATACTCACTCAGTCTTGATCACTCgtatgtttca ... tgttctgcagGATTTGGTTCCACAAGCCTGTGAAAGCTGATGATTGGCTTTTATATGTG
EST: gi|86878942|gb|CI315384.1|CI315384
EST:     GAAGACATACTCACTCAGTC-TGATCACTC                         GATTTGGTTCCACAAGCCTGTGAAAGCTGATGATTGGCTTTTATATGTG
genomic: GAAGACATACTCACTCAGTCTTGATCACTCgtatgtttca ... tgttctgcagGATTTGGTTCCACAAGCCTGTGAAAGCTGATGATTGGCTTTTATATGTG
EST: gi|29670926|gb|CB667201.1|CB667201
EST:     CCTCATAGGGAGAAGGGTCTGAAGACATACTCACTCAGTCTTGATCACTC                         GATTTGGTTCCACAAGCCTGTGAAAGCTGATGATTGGCTTTTATATGTG
genomic: CCTCATAGGGAGAAGGGTCTGAAGACATACTCACTCAGTCTTGATCACTCgtatgtttca ... tgttctgcagGATTTGGTTCCACAAGCCTGTGAAAGCTGATGATTGGCTTTTATATGTG
EST: gi|86434548|gb|CI105781.1|CI105781
EST:     GGTCTGAAGACATACTCACTCAGTCTTGATCACTC                         GATTTGGTTCCACAAGCCTGTGAAAGCTGATGGTTGGCTTTTATATGTG
genomic: GGTCTGAAGACATACTCACTCAGTCTTGATCACTCgtatgtttca ... tgttctgcagGATTTGGTTCCACAAGCCTGTGAAAGCTGATGATTGGCTTTTATATGTG
EST: gi|88843985|gb|CI008566.1|CI008566
EST:     CCTCATAGGGAGAAGGGTCTGAAGACATACTCACTCAGTCTTGATCACTC                         GATTTGGTTCCACAAGCCTGTGAAAGCTGATGATTGGCTTTTATATGTG
genomic: CCTCATAGGGAGAAGGGTCTGAAGACATACTCACTCAGTCTTGATCACTCgtatgtttca ... tgttctgcagGATTTGGTTCCACAAGCCTGTGAAAGCTGATGATTGGCTTTTATATGTG
EST: gi|33681707|gb|CF309946.1|CF309946
EST:     CCTCATAGG-AGAAGGGTCTGAAGACATACTCACTCAGTCTTGATCACTC                         GATTTGGTTCCACAAGCCTGTGAAAGCTGATGATTGGCTTTTATATGTG
genomic: CCTCATAGGGAGAAGGGTCTGAAGACATACTCACTCAGTCTTGATCACTCgtatgtttca ... tgttctgcagGATTTGGTTCCACAAGCCTGTGAAAGCTGATGATTGGCTTTTATATGTG
EST: gi|88971423|gb|CI017737.1|CI017737
EST:     CCTCATAGGGAGAAGGGTCTGAAGACATACTCACTCAGTCTTGATCACTC                         GATTTGGTTCCACAAGCCTGTGAAAGCTGATGATTGGCTTTTATATGTG
genomic: CCTCATAGGGAGAAGGGTCTGAAGACATACTCACTCAGTCTTGATCACTCgtatgtttca ... tgttctgcagGATTTGGTTCCACAAGCCTGTGAAAGCTGATGATTGGCTTTTATATGTG
EST: gi|86426203|gb|CI071300.1|CI071300
EST:     CCTCATAGGGAGAAGGGTCTGAAGACATACTCACTCAGTCTTGATCACTC                         GATTTGGTTCCACAAGCCTGTGAAAGCTGATGATTGGCTTTTATATGTG
genomic: CCTCATAGGGAGAAGGGTCTGAAGACATACTCACTCAGTCTTGATCACTCgtatgtttca ... tgttctgcagGATTTGGTTCCACAAGCCTGTGAAAGCTGATGATTGGCTTTTATATGTG
EST: gi|66920748|gb|CX107596.1|CX107596
EST:     CCTCATAGGGAGAAGGGTCTGAAGACATACTCACTCAGTCTTGATCACTC                         GATTTGGTTCCACAAGCCTGTGAAAGCTGATGATTGGCTTTTATATGTGAT
genomic: CCTCATAGGGAGAAGGGTCTGAAGACATACTCACTCAGTCTTGATCACTCgtatgtttca ... tgttctgcagGATTTGGTTCCACAAGCCTGTGAAAGCTGATGATTGGCTTTTATATGTGAT
EST: gi|86490744|gb|CI133377.1|CI133377
EST:     CCTCATAGGGAGAAGGGTCTGAAGACATACTCACTCAGTCTTGATCACTC                         GATTTGGTTCCACAAGCCTGTGAAAGCTGATGATTGGCTTTAATATGTG
genomic: CCTCATAGGGAGAAGGGTCTGAAGACATACTCACTCAGTCTTGATCACTCgtatgtttca ... tgttctgcagGATTTGGTTCCACAAGCCTGTGAAAGCTGATGATTGGCTTTTATATGTG
EST: gi|88959770|gb|CI002380.1|CI002380
EST:     CCTCATAGGGAGAAGGGTCTGAAGACATACTCACTCAGTCTTGATCACTC                         GATTTGGTTCCACAAGCCTGTGAAAGCTGATGATTGGCTTTTATATGTG
genomic: CCTCATAGGGAGAAGGGTCTGAAGACATACTCACTCAGTCTTGATCACTCgtatgtttca ... tgttctgcagGATTTGGTTCCACAAGCCTGTGAAAGCTGATGATTGGCTTTTATATGTG

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 1 RNA-Seqlibrary.


Block sizes: 69 (upstream exon), 49 (downstream exon)
Score: 24

GTGTTGTAGCATATGCTTCGGATCTACTATATTCTGGTGTCAGCCTAAATCCTCATAGGGAGAAGGGTCTGAAGACATACTCACTCAGTCTTGATCACTCgtatgtttca ... tgttctgcagGATTTGGTTCCACAAGCCTGTGAAAGCTGATGATTGGCTTTTATATGTG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTGTTGTAGCATATGCTTCGGATCTACTATATTCTGGTGTCAGCCTAAATCCTCATAGGGAGAAGGGTCTGAAGACATACTCACTCAGTCTTGATCACTCgtatgtttcagcaaaccgcacccagtactgcgattttaattaatacaactcgctagtaaaccgtttgtttgttactgttctgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA