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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATTTCCAGTCTTTCAGCAAGATTTCCAGGACTGAGGACCCTTAGAAGCTGTGATTTATCACCGCGAAGTTGGATATCTGTTGCTTGgtgagttctttttccattggcatggtagcagactagcagttatagagtatggtagtaactagttactgagttgcctacaacatcatgcag

Basic information

species Oryza sativa
transcript LOC_Os01g33000.1
intron # 4
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|218493642|gb|FG944469.1|FG944469
EST:     ACCCTTAGAAGCTGTGATTTATCACCGCGAAGTTGGATATCTGTTGCTTG                         GTATCCAATTTACCGTATCCCTACTGGCCCAACATTAAAAGATTTGGATGC
genomic: ACCCTTAGAAGCTGTGATTTATCACCGCGAAGTTGGATATCTGTTGCTTGgtgagttctt ... catcatgcagGTATCCAATTTACCGTATCCCTACTGGCCCAACATTAAAAGATTTGGATGC
EST: gi|87006610|gb|CI294993.1|CI294993
EST:     ACCCTTAGAAGCTGTGATTTATCACCGCGAAGTTGGATATCTGTTGCTTG                         GTATCCAATTTACCGTATCCCTACTGGCCCAACATTAAAAGATTTGGATGC
genomic: ACCCTTAGAAGCTGTGATTTATCACCGCGAAGTTGGATATCTGTTGCTTGgtgagttctt ... catcatgcagGTATCCAATTTACCGTATCCCTACTGGCCCAACATTAAAAGATTTGGATGC
EST: gi|33680042|gb|CF308281.1|CF308281
EST:     ACCCTTAGAAGCTGTGATTTATCACCGCGAAGTTGGATATCTGTTGCTTG                         GTATCCAATTTACCGTATCCCTACTGGCCCAACATTAAAAGATTTGGATGC
genomic: ACCCTTAGAAGCTGTGATTTATCACCGCGAAGTTGGATATCTGTTGCTTGgtgagttctt ... catcatgcagGTATCCAATTTACCGTATCCCTACTGGCCCAACATTAAAAGATTTGGATGC
EST: gi|29681976|gb|CB678251.1|CB678251
EST:     ACCCTTAGAAGCTGTGATTTATCACCGCGAAGTTGGATATCTGTTGCTTG                         GTATCCAATTTACCGTATCCCTACTGGCCCAACATTAAAAGATTTGGATGC
genomic: ACCCTTAGAAGCTGTGATTTATCACCGCGAAGTTGGATATCTGTTGCTTGgtgagttctt ... catcatgcagGTATCCAATTTACCGTATCCCTACTGGCCCAACATTAAAAGATTTGGATGC
EST: gi|33685867|gb|CF314106.1|CF314106
EST:     ACCCTTAGAAGCTGTGATTTATCACCGCGAAGTTGGATATCTGTTGCTTG                         GTATCCAATTTACCGTATCCCTACTGGCCCAACATTAAAAGATTTGGATGC
genomic: ACCCTTAGAAGCTGTGATTTATCACCGCGAAGTTGGATATCTGTTGCTTGgtgagttctt ... catcatgcagGTATCCAATTTACCGTATCCCTACTGGCCCAACATTAAAAGATTTGGATGC
EST: gi|87021808|gb|CI277975.1|CI277975
EST:     AAGTTGGATATCTGTTGCTTG                         GTATCCAATTTACCGTATCCCTACTGGCCCAACATTAAAAGATTTGGATGC
genomic: AAGTTGGATATCTGTTGCTTGgtgagttctt ... catcatgcagGTATCCAATTTACCGTATCCCTACTGGCCCAACATTAAAAGATTTGGATGC
EST: gi|218482382|gb|FG946501.1|FG946501
EST:     A-CCTTAGAAGCTGTGATTTATCACCGCGAAGTTGGATATCTGTTGCTTG                         GTATCCAATTTACCGTATCCCTACTGGCCCAACATTAAAAGATTTGGATGC
genomic: ACCCTTAGAAGCTGTGATTTATCACCGCGAAGTTGGATATCTGTTGCTTGgtgagttctt ... catcatgcagGTATCCAATTTACCGTATCCCTACTGGCCCAACATTAAAAGATTTGGATGC
EST: gi|218487332|gb|FG968263.1|FG968263
EST:     ACCCTTAGAAGCTGTGATTTATCACCGCGAAGTTGGATATCTGTTGCTTG                         GTATCCAATTTACCGTATCCCTACTGGCCCAACATTAAAAGATTTGGATGC
genomic: ACCCTTAGAAGCTGTGATTTATCACCGCGAAGTTGGATATCTGTTGCTTGgtgagttctt ... catcatgcagGTATCCAATTTACCGTATCCCTACTGGCCCAACATTAAAAGATTTGGATGC
EST: gi|218493643|gb|FG944470.1|FG944470
EST:     ACCCTTAGAAGCTGTGATTTATCACCGCGAAGTTGGATATCTGTTGCTTG                         GTATCCAATTTACCGTATCCCTACTGGCCCAACATTAAAAGATTTGGATGC
genomic: ACCCTTAGAAGCTGTGATTTATCACCGCGAAGTTGGATATCTGTTGCTTGgtgagttctt ... catcatgcagGTATCCAATTTACCGTATCCCTACTGGCCCAACATTAAAAGATTTGGATGC
EST: gi|33810073|gb|CF330924.1|CF330924
EST:     ACCCTTAAAAGCTGTGATTTATCACCGCGAAGTTGGATATCTGTTGCTTG                         GTATCCAATTTACCGTATCCCTACTGGCCCAACATTAAAAGATTTGGATGC
genomic: ACCCTTAGAAGCTGTGATTTATCACCGCGAAGTTGGATATCTGTTGCTTGgtgagttctt ... catcatgcagGTATCCAATTTACCGTATCCCTACTGGCCCAACATTAAAAGATTTGGATGC
EST: gi|218498668|gb|FG952677.1|FG952677
EST:     ACCCTTAGAAGCTGTGATTTATCACCGCGAAGTTGGATATCTGTTGCTTG                         GTATCCAATTTACCGTATCCCTACTGGCCCAACATTAAAAGATTTGGATGC
genomic: ACCCTTAGAAGCTGTGATTTATCACCGCGAAGTTGGATATCTGTTGCTTGgtgagttctt ... catcatgcagGTATCCAATTTACCGTATCCCTACTGGCCCAACATTAAAAGATTTGGATGC
EST: gi|33680411|gb|CF308650.1|CF308650
EST:     ACCCTTAGAAGCTGTGATTTATCACCGCGAAGTTGGATATCTGTTGCTTG                         GTATCCAATTTACCGTATCCCTACTGGCCCAACATTAAAAGATTTGGATGC
genomic: ACCCTTAGAAGCTGTGATTTATCACCGCGAAGTTGGATATCTGTTGCTTGgtgagttctt ... catcatgcagGTATCCAATTTACCGTATCCCTACTGGCCCAACATTAAAAGATTTGGATGC
EST: gi|218480683|gb|FG945057.1|FG945057
EST:     ACCCTTAGAAGCTGTGATTTATCACCGCGAAGTTGGATATCTGTTGCTTG                         GTATCCAATTTACCGTATCCCTACT
genomic: ACCCTTAGAAGCTGTGATTTATCACCGCGAAGTTGGATATCTGTTGCTTGgtgagttctt ... catcatgcagGTATCCAATTTACCGTATCCCTACT
EST: gi|86493867|gb|CI136500.1|CI136500
EST:     TCTGTTGCTTG                         GTATCCAATTTACCGTATCCCTACTGGCCCAACATTAAAAGATTTGGATGC
genomic: TCTGTTGCTTGgtgagttctt ... catcatgcagGTATCCAATTTACCGTATCCCTACTGGCCCAACATTAAAAGATTTGGATGC
EST: gi|87018091|gb|CI275905.1|CI275905
EST:     ACCCTTAGAAGCTGTGATTTATCACCGCGAAGTTGGATATCTGTTGCTTG                         GTATCCAATTTACCGTATCCCTACTGGCCCAACATTAAAAGATTTGGATGC
genomic: ACCCTTAGAAGCTGTGATTTATCACCGCGAAGTTGGATATCTGTTGCTTGgtgagttctt ... catcatgcagGTATCCAATTTACCGTATCCCTACTGGCCCAACATTAAAAGATTTGGATGC
EST: gi|87027175|gb|CI278207.1|CI278207
EST:     AGAAGCTGTGATTTATCACCGCGAAGTTGGATATCTGTTGCTTG                         GTATCCAATTTACCGTATCCCTACTGGCCCAACATTAAAAGATTTGGATGC
genomic: AGAAGCTGTGATTTATCACCGCGAAGTTGGATATCTGTTGCTTGgtgagttctt ... catcatgcagGTATCCAATTTACCGTATCCCTACTGGCCCAACATTAAAAGATTTGGATGC

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: 65 (upstream exon), 73 (downstream exon)
Score: 17

ATTTCCAGTCTTTCAGCAAGATTTCCAGGACTGAGGACCCTTAGAAGCTGTGATTTATCACCGCGAAGTTGGATATCTGTTGCTTGgtgagttctt ... catcatgcagGTATCCAATTTACCGTATCCCTACTGGCCCAACATTAAAAGATTTGGATGCATGCTTTCTCACCTTCCATCGGCTATCAACTGGGCCAGAAGAAG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATTTCCAGTCTTTCAGCAAGATTTCCAGGACTGAGGACCCTTAGAAGCTGTGATTTATCACCGCGAAGTTGGATATCTGTTGCTTGgtgagttctttttccattggcatggtagcagactagcagttatagagtatggtagtaactagttactgagttgcctacaacatcatgcag

- - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - - - - - - - - - - - - - - - - - - AAGCTG