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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gcttaatccattattgatatatgtgcagaagacttccaagattgatatttctttacctttttagtttccatgttaatgatatgacacatgatttttgaagGTGGCACCAAAAGCATGTGGACATACTGAAGGAAGGAAAGTTATCTCAAGGGAGGATGCTATCATGCACATAAAAGCTGCCGTAGATGCTAGGAAAGAGA

Basic information

species Oryza sativa
transcript LOC_Os04g31700.1
intron # 2
splice site 3'
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|58599013|gb|CK009541.1|CK009541
EST:     TAAAAGGGTATATTAATGCTGGTTTTGCTGGAATCATGCTCGAAGATCAG                         GTGGCACCAAAAGCATGTGGACATACTGAAGGAAGGAAAGTTATCTCAAGG
genomic: TAAAAGGGTATATTAATGCTGGTTTTGCTGGAATCATGCTCGAAGATCAGgtatgcttcc ... atttttgaagGTGGCACCAAAAGCATGTGGACATACTGAAGGAAGGAAAGTTATCTCAAGG
EST: gi|58655722|gb|CK044402.1|CK044402
EST:     TAAAAGGGTATATTAATGCTGGTTTTGCTGGAATCATGCTCGAAGATCAG                         GTGGCACCAAAAGCATGTGGACATACTGAAGGAAGGAAAGTTATCTCAAGG
genomic: TAAAAGGGTATATTAATGCTGGTTTTGCTGGAATCATGCTCGAAGATCAGgtatgcttcc ... atttttgaagGTGGCACCAAAAGCATGTGGACATACTGAAGGAAGGAAAGTTATCTCAAGG
EST: gi|58657657|gb|CK046337.1|CK046337
EST:     TAAAAGGGTATATTAATGCTGGTTTTGCTGGAATCATGCTCGAAGATCAG                         GTGGCACCAAAAGCATGTGGACATACTGAAGGAAGGAAAGTTATCTCAAGG
genomic: TAAAAGGGTATATTAATGCTGGTTTTGCTGGAATCATGCTCGAAGATCAGgtatgcttcc ... atttttgaagGTGGCACCAAAAGCATGTGGACATACTGAAGGAAGGAAAGTTATCTCAAGG
EST: gi|58681690|gb|CK070377.1|CK070377
EST:     AAAGGGTACTATTAATGCTGGGTTTTGCTGGAATCATGCTCGAAGATCAG                         GTGGCACCAAAAGCATGTGGACATACTGAAGGAAGGAAAGTTATCTCAAGG
genomic: AAAGGGTA-TATTAATGCTGG-TTTTGCTGGAATCATGCTCGAAGATCAGgtatgcttcc ... atttttgaagGTGGCACCAAAAGCATGTGGACATACTGAAGGAAGGAAAGTTATCTCAAGG
EST: gi|58677255|gb|CK065942.1|CK065942
EST:     TAAAAGGGTATATTAATGCTGGTTTTGCTGGAATCATGCTCGAAGATCAG                         GTGGCACCAAAAGCATGTGGACATACTGAAGGAAGGAAAGTTA
genomic: TAAAAGGGTATATTAATGCTGGTTTTGCTGGAATCATGCTCGAAGATCAGgtatgcttcc ... atttttgaagGTGGCACCAAAAGCATGTGGACATACTGAAGGAAGGAAAGTTA
EST: gi|29686535|gb|CB682810.1|CB682810
EST:     TAAAAGGGTATATTAATGCTGGTTTTGCTGGAATCATGCTCGAAGATCAG                         GTGGCACCAAAAGCATGTGGACATACTGAAGGAAGGAAAGTTATCTCAAGG
genomic: TAAAAGGGTATATTAATGCTGGTTTTGCTGGAATCATGCTCGAAGATCAGgtatgcttcc ... atttttgaagGTGGCACCAAAAGCATGTGGACATACTGAAGGAAGGAAAGTTATCTCAAGG
EST: gi|58600134|gb|CK010662.1|CK010662
EST:     TAAAAGGGTATATTAATGCTGGTTTTGCTGGAATCATGCTCGAAGATCAG                         GTGGCACCAAAAGCATGTGGACATACTGAAGGAAGGAAAGTTATCTCAAGG
genomic: TAAAAGGGTATATTAATGCTGGTTTTGCTGGAATCATGCTCGAAGATCAGgtatgcttcc ... atttttgaagGTGGCACCAAAAGCATGTGGACATACTGAAGGAAGGAAAGTTATCTCAAGG
EST: gi|33675457|gb|CF303696.1|CF303696
EST:     TAAAAGGGTATATTAATGCTGGTTTTGCTGGAATCATGCTCGAAGATCAG                         GTGGCACCAAAAGCATGTGGACATACTGAAGGAAGGAAAGTTATCTCAAGG
genomic: TAAAAGGGTATATTAATGCTGGTTTTGCTGGAATCATGCTCGAAGATCAGgtatgcttcc ... atttttgaagGTGGCACCAAAAGCATGTGGACATACTGAAGGAAGGAAAGTTATCTCAAGG
EST: gi|58598367|gb|CK008895.1|CK008895
EST:     TAAAAGGGTATATTAATGCTGGTTTTGCTGGAATCATGCTCGAAGATCAG                         GTGGCACCAAAAGCATGTGGACATACTGAAGGAAGGAAAGTTATCTCAAGG
genomic: TAAAAGGGTATATTAATGCTGGTTTTGCTGGAATCATGCTCGAAGATCAGgtatgcttcc ... atttttgaagGTGGCACCAAAAGCATGTGGACATACTGAAGGAAGGAAAGTTATCTCAAGG
EST: gi|58686729|gb|CK075416.1|CK075416
EST:     TAAAAGGGTATATTAATGCTGGTTTTGCTGGAATCATGCTCGAAGATCAG                         GTGGCACCAAAAGC
genomic: TAAAAGGGTATATTAATGCTGGTTTTGCTGGAATCATGCTCGAAGATCAGgtatgcttcc ... atttttgaagGTGGCACCAAAAGC
EST: gi|29679221|gb|CB675496.1|CB675496
EST:     TAAAAGGGTATATTAATGCTGGTTTTGCTGGAATCATGCTCGAAGATCAG                         GTGGCACCAAAAGCATGTGGACATACTGAAGGAAGGAAAGTTATCTCAAGG
genomic: TAAAAGGGTATATTAATGCTGGTTTTGCTGGAATCATGCTCGAAGATCAGgtatgcttcc ... atttttgaagGTGGCACCAAAAGCATGTGGACATACTGAAGGAAGGAAAGTTATCTCAAGG
EST: gi|58675290|gb|CK063977.1|CK063977
EST:     TAAAAGGGTATATTAATGCTGGTTTTGCTGGAATCATGCTCGAAGATCAG                         GTGGCACCAAAAGCATGTGGACATACTGAAGGAAGGAAAGTTATCTCAAGG
genomic: TAAAAGGGTATATTAATGCTGGTTTTGCTGGAATCATGCTCGAAGATCAGgtatgcttcc ... atttttgaagGTGGCACCAAAAGCATGTGGACATACTGAAGGAAGGAAAGTTATCTCAAGG
EST: gi|58597777|gb|CK008305.1|CK008305
EST:     TAAAAGGGTATATTAATGCTGGTTTTGCTGGAATCATGCTCGAAGATCAG                         GTGGCACCAAAAGCATGTGGACATACTGAAGGAAGGAAAGTTATCTCAAGG
genomic: TAAAAGGGTATATTAATGCTGGTTTTGCTGGAATCATGCTCGAAGATCAGgtatgcttcc ... atttttgaagGTGGCACCAAAAGCATGTGGACATACTGAAGGAAGGAAAGTTATCTCAAGG

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: 39 (upstream exon), 70 (downstream exon)
Score: 76

CGGCGATGGTGATAATGGCTATGGAAATGCTATGAGCATTAAGAGAACCGTAAAAGGGTATATTAATGCTGGTTTTGCTGGAATCATGCTCGAAGATCAGgtatgcttcc ... atttttgaagGTGGCACCAAAAGCATGTGGACATACTGAAGGAAGGAAAGTTATCTCAAGGGAGGATGCTATCATGCACATAAAAGCTGCCGTAGATGCTAGGAAAGAGA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatttctttacctttttagtttccatgttaatgatatgacacatgatttttgaagGTGGCACCAAAAGCATGTGGACATACTGAAGGAAGGAAAGTTATCTCAAGGGAGGATGCTATCATGCACATAAAAGCTGCCGTAGATGCTAGGAAAGAGA
                         tgttaat  putative branch site (score: 76)
                                              ttttt  putative PPT
            tttttagttt  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gcttaatccattattgatatatgtgcagaagacttccaagattgatatttctttacctttttagtttccatgttaatgatatgacacatgatttttgaagGTGGCACCAAAAGCATGTGGACATACTGAAGGAAGGAAAGTTATCTCAAGGGAGGATGCTATCATGCACATAAAAGCTGCCGTAGATGCTAGGAAAGAGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA
- - - - - - - - - -tatgtgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -acacatg