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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CCACACCTGGAAGGTGGCGACAAAGgtatgtcttcagacccctcccccctcctctcacacacacaaacaattcaaaccgcatgccactgacattatattttatcatcatcaatgcag

Basic information

species Oryza sativa
transcript LOC_Os04g48770.1
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|88343864|gb|CI654900.1|CI654900
EST:     CCACACCTGGAAGGTGGCGACAAAG                         TAATTATGCCACCATCTGCTCTTGATCGGCTTG
genomic: CCACACCTGGAAGGTGGCGACAAAGgtatgtcttc ... atcaatgcagTAATTATGCCACCATCTGCTCTTGATCGGCTTG
EST: gi|88315253|gb|CI611917.1|CI611917
EST:     CCACACCTGGAAGGTGGCGACAAAG                         TAATTATGCCACCATCTGCTCTTGATCGGCTTG
genomic: CCACACCTGGAAGGTGGCGACAAAGgtatgtcttc ... atcaatgcagTAATTATGCCACCATCTGCTCTTGATCGGCTTG
EST: gi|88722801|gb|CI746311.1|CI746311
EST:     CCACACCTGGAAGGTGGCGACAAAG                         TAATTATGCCACCATCTGCTCTTGATCGGCTTG
genomic: CCACACCTGGAAGGTGGCGACAAAGgtatgtcttc ... atcaatgcagTAATTATGCCACCATCTGCTCTTGATCGGCTTG
EST: gi|88386212|gb|CI572829.1|CI572829
EST:     CCACACCTGGAAGGTGGCGACAAAG                         TAATTATGCCACCATCTGCTCTTGATCGGCTTG
genomic: CCACACCTGGAAGGTGGCGACAAAGgtatgtcttc ... atcaatgcagTAATTATGCCACCATCTGCTCTTGATCGGCTTG
EST: gi|88368046|gb|CI572767.1|CI572767
EST:     CCACACCTGGAAGGTGGCGACAAAG                         TAATTATGCCACCATCTGCTCTTGATCGGCTTG
genomic: CCACACCTGGAAGGTGGCGACAAAGgtatgtcttc ... atcaatgcagTAATTATGCCACCATCTGCTCTTGATCGGCTTG
EST: gi|88312012|gb|CI580177.1|CI580177
EST:     CCACACCTGGAAGGTGGCGACAAAG                         TAATTATGCCACCATCTGCTCTTGATCGGCTTG
genomic: CCACACCTGGAAGGTGGCGACAAAGgtatgtcttc ... atcaatgcagTAATTATGCCACCATCTGCTCTTGATCGGCTTG
EST: gi|88386211|gb|CI572828.1|CI572828
EST:     CCACAC-TGGAAGGTGGCGACAAAG                         TAATTATGCCACCATCTGCTCTTGATCGGCTTG
genomic: CCACACCTGGAAGGTGGCGACAAAGgtatgtcttc ... atcaatgcagTAATTATGCCACCATCTGCTCTTGATCGGCTTG
EST: gi|88361848|gb|CI682012.1|CI682012
EST:     CCACACCTGGAAGGTGGCGACAAAG                         TAATTATGCCACCATCTGCTCTTGATCGGCTTG
genomic: CCACACCTGGAAGGTGGCGACAAAGgtatgtcttc ... atcaatgcagTAATTATGCCACCATCTGCTCTTGATCGGCTTG
EST: gi|88393733|gb|CI621228.1|CI621228
EST:     CCACACCTGGAAGGTGGCGACAAAG                         TAATTATGCCACCATCTGCTCTTGATCGGCTTG
genomic: CCACACCTGGAAGGTGGCGACAAAGgtatgtcttc ... atcaatgcagTAATTATGCCACCATCTGCTCTTGATCGGCTTG
EST: gi|58588357|gb|CF986665.1|CF986665
EST:     CCACACCTGGAAGGTGGCGACAAAG                         TAATTATGCCACCATCTGCTCTTGATCGGCTTG
genomic: CCACACCTGGAAGGTGGCGACAAAGgtatgtcttc ... atcaatgcagTAATTATGCCACCATCTGCTCTTGATCGGCTTG
EST: gi|88738677|gb|CI762185.1|CI762185
EST:     CCACACCTGGAAGGTGGCGACAAAG                         TAATTATGCCACCATCTGCTCTTGATCGGCTTG
genomic: CCACACCTGGAAGGTGGCGACAAAGgtatgtcttc ... atcaatgcagTAATTATGCCACCATCTGCTCTTGATCGGCTTG
EST: gi|88582268|gb|CI699664.1|CI699664
EST:     CCACACCTGGAAGGTGGCGACAAAG                         TAATTATGCCACCATCTGCTCTTGATCGGCTTG
genomic: CCACACCTGGAAGGTGGCGACAAAGgtatgtcttc ... atcaatgcagTAATTATGCCACCATCTGCTCTTGATCGGCTTG
EST: gi|58595974|gb|CK006502.1|CK006502
EST:     CCACACCTGGAAGGTGGCGACAAAG                         TAATTATGCCACCATCTGCTCTTGATCGGCTTG
genomic: CCACACCTGGAAGGTGGCGACAAAGgtatgtcttc ... atcaatgcagTAATTATGCCACCATCTGCTCTTGATCGGCTTG
EST: gi|88359976|gb|CI679746.1|CI679746
EST:     CCACACCTGGAAGGTGGCGACAAAG                         TAATTATGCCACCATCTGCTCTTGATCGGCTTG
genomic: CCACACCTGGAAGGTGGCGACAAAGgtatgtcttc ... atcaatgcagTAATTATGCCACCATCTGCTCTTGATCGGCTTG
EST: gi|88335570|gb|CI642794.1|CI642794
EST:     CCACACCTGGAAGGTGGCGACAAAG                         TAATTATGCCACCATCTGCTCTTGATCGGCTTG
genomic: CCACACCTGGAAGGTGGCGACAAAGgtatgtcttc ... atcaatgcagTAATTATGCCACCATCTGCTCTTGATCGGCTTG
EST: gi|88314800|gb|CI608259.1|CI608259
EST:     CCACACCTGGAAGGTGGCGACAAAG                         TAATTATGCCACCATCTGCTCTTGATCGGCTTG
genomic: CCACACCTGGAAGGTGGCGACAAAGgtatgtcttc ... atcaatgcagTAATTATGCCACCATCTGCTCTTGATCGGCTTG
EST: gi|88349807|gb|CI634342.1|CI634342
EST:     CCACACCTGGAAGGTGGCGACAAAG                         TAATTATGCCACCATCTGCTCTTGATCGGCTTG
genomic: CCACACCTGGAAGGTGGCGACAAAGgtatgtcttc ... atcaatgcagTAATTATGCCACCATCTGCTCTTGATCGGCTTG
EST: gi|88330242|gb|CI658551.1|CI658551
EST:     CCACACCTGGAAGGTGGCGACAAAG                         TAATTATGCCACCATCTGCTCTTGATCGGCTTG
genomic: CCACACCTGGAAGGTGGCGACAAAGgtatgtcttc ... atcaatgcagTAATTATGCCACCATCTGCTCTTGATCGGCTTG
EST: gi|58689043|gb|CK077730.1|CK077730
EST:     CCACACCTGGAAGGTGGCGACAAAG                         TAATTATGCCACCATCTGCTCTTGATCGGCTTG
genomic: CCACACCTGGAAGGTGGCGACAAAGgtatgtcttc ... atcaatgcagTAATTATGCCACCATCTGCTCTTGATCGGCTTG
EST: gi|14191699|gb|AU183910.1|AU183910
EST:     CCACACCTGGAAGGTGGCGACAAAG                         TAATTATGCCACCATCTGCTCTTGATCGGCTTG
genomic: CCACACCTGGAAGGTGGCGACAAAGgtatgtcttc ... atcaatgcagTAATTATGCCACCATCTGCTCTTGATCGGCTTG

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: 25 (upstream exon), 33 (downstream exon)
Score: 8

CCACACCTGGAAGGTGGCGACAAAGgtatgtcttc ... atcaatgcagTAATTATGCCACCATCTGCTCTTGATCGGCTTG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CCACACCTGGAAGGTGGCGACAAAGgtatgtcttcagacccctcccccctcctctcacacacacaaacaattcaaaccgcatgccactgacattatattttatcatcatcaatgcag

- - -  TGGAAG