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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatatcagtggaactgagcaaatacatttaccacaaactgatggttgaaactaataggtcttgattaattacagGGTCTGTGAAAACATCCCAATTGTGCTCTGTGGTAACAAGGTTGATGTGAAGAACAGGCAGGTTAAAGCAAAGCAGGTTACCTTCCATAGGAAGAAGAAC

Basic information

species Oryza sativa
transcript LOC_Os01g42530.1
intron # 5
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|87030406|gb|CI252683.1|CI252683
EST:     TCTCGGCTGACGTACAAGAATGTCCCAACTTGGCACCGTGATTTATGCAG                         GGTCTGTGAAAACATCCCAATTGTGCTCTGTGGTAACAAGGTTGATGTGAA
genomic: TCTCGGCTGACGTACAAGAATGTCCCAACTTGGCACCGTGATTTATGCAGgtatatcagt ... ttaattacagGGTCTGTGAAAACATCCCAATTGTGCTCTGTGGTAACAAGGTTGATGTGAA
EST: gi|58687745|gb|CK076432.1|CK076432
EST:     TCTCGGCTGACGTACAAGAATGTCCCAACTTGGCACCGTGATTTATGCAG                         GGTCTGTGAAAACATCCCAATTGTGCTCTGTGGTAACAAGGTTGATGTGAA
genomic: TCTCGGCTGACGTACAAGAATGTCCCAACTTGGCACCGTGATTTATGCAGgtatatcagt ... ttaattacagGGTCTGTGAAAACATCCCAATTGTGCTCTGTGGTAACAAGGTTGATGTGAA
EST: gi|38479329|gb|CF963460.1|CF963460
EST:     TCTCGGCTGACGTACAAGAATGTCCCAACTTGGCACCGTGATTTATGCAG                         GGTCTGTGAAAACATCCCAATTGTGCTCTGTGGTAACAAGGTTGATGTGAA
genomic: TCTCGGCTGACGTACAAGAATGTCCCAACTTGGCACCGTGATTTATGCAGgtatatcagt ... ttaattacagGGTCTGTGAAAACATCCCAATTGTGCTCTGTGGTAACAAGGTTGATGTGAA
EST: gi|218479973|gb|FG945844.1|FG945844
EST:     TCTCGGCTGACGTACAAGAATGTCCCAACTTGGCACCGTGATTTATGCAG                         GGTCTGTGAAAACATCCCAATTGTGCTCTGTGGTAACAAGGTTGATGTGAA
genomic: TCTCGGCTGACGTACAAGAATGTCCCAACTTGGCACCGTGATTTATGCAGgtatatcagt ... ttaattacagGGTCTGTGAAAACATCCCAATTGTGCTCTGTGGTAACAAGGTTGATGTGAA
EST: gi|88329358|gb|CI653273.1|CI653273
EST:     TCTCGGCTGACGTACAAGAATGTCCCAACTTGGCACCGTGATTTATGCAG                         GGTCTGTGAAAACATCCCA
genomic: TCTCGGCTGACGTACAAGAATGTCCCAACTTGGCACCGTGATTTATGCAGgtatatcagt ... ttaattacagGGTCTGTGAAAACATCCCA
EST: gi|88239222|gb|CI240384.1|CI240384
EST:     TGATTTATGCAG                         GGTCTGTGAAAACATCCCAATTGTGCTCTGTGGTAACAAGGTTGATGTGAA
genomic: TGATTTATGCAGgtatatcagt ... ttaattacagGGTCTGTGAAAACATCCCAATTGTGCTCTGTGGTAACAAGGTTGATGTGAA
EST: gi|86511798|gb|CI154431.1|CI154431
EST:     GCACCGTGATTTATGCAG                         GGTCTGTGAGAACATCCCAATTGTGCTCTGTGGTAACAAGGTTGATGTGAA
genomic: GCACCGTGATTTATGCAGgtatatcagt ... ttaattacagGGTCTGTGAAAACATCCCAATTGTGCTCTGTGGTAACAAGGTTGATGTGAA
EST: gi|11564790|gb|AU165426.1|AU165426
EST:     CTCGGNTGACGTACAAGAATGTCCCAAACTTGGCACCGTGATTTATGCAG                         GGTCTGTGAAAACATCCCAATTGTGCTCTGTGGTAACAAGGTTGATGTGAA
genomic: CTCGGCTGACGTACAAGAATGTCCC-AACTTGGCACCGTGATTTATGCAGgtatatcagt ... ttaattacagGGTCTGTGAAAACATCCCAATTGTGCTCTGTGGTAACAAGGTTGATGTGAA
EST: gi|25802747|gb|CA758708.1|CA758708
EST:     TCTCGGCTGACGTACAAGAATGTCCCAACTTGGCACCGTGATNTATGCAG                         GGTCTGTGAAAACATCCCAATTGTGCTCTGTGGTAACAAGGTTGATGTGAA
genomic: TCTCGGCTGACGTACAAGAATGTCCCAACTTGGCACCGTGATTTATGCAGgtatatcagt ... ttaattacagGGTCTGTGAAAACATCCCAATTGTGCTCTGTGGTAACAAGGTTGATGTGAA
EST: gi|86494370|gb|CI137003.1|CI137003
EST:     CCCAACTTGGCACCGTGATTTATGCAG                         GGTCTGTGAAAACATCCCAATTGTGCTCTGTGGTAACAAGGTTGATGTGAA
genomic: CCCAACTTGGCACCGTGATTTATGCAGgtatatcagt ... ttaattacagGGTCTGTGAAAACATCCCAATTGTGCTCTGTGGTAACAAGGTTGATGTGAA
EST: gi|55442434|gb|CV734535.1|CV734535
EST:     TCTCGGCTGACGTACAAGAATGTCCCAACTTGGCACCGTGATTTATGCAG                         GGTCTGTGAAAACATCCCAATTGTGCTCTGTGGTAACAAGGTTGATGTGAA
genomic: TCTCGGCTGACGTACAAGAATGTCCCAACTTGGCACCGTGATTTATGCAGgtatatcagt ... ttaattacagGGTCTGTGAAAACATCCCAATTGTGCTCTGTGGTAACAAGGTTGATGTGAA
EST: gi|14980874|gb|BI305552.1|BI305552
EST:     TCTCGGCTGACGTACAAGAATGTCCCAACTTGGCACCGTGATTTATGCAG                         GGTCTGTGAAAACATCCCAATTGTGCTCTGTGGTAACAAGGTTGATGTGAA
genomic: TCTCGGCTGACGTACAAGAATGTCCCAACTTGGCACCGTGATTTATGCAGgtatatcagt ... ttaattacagGGTCTGTGAAAACATCCCAATTGTGCTCTGTGGTAACAAGGTTGATGTGAA

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: 75 (upstream exon), 73 (downstream exon)
Score: 63

TATCCATGGGCAGTGTGCTATCATAATGTTCGATGTTACTTCTCGGCTGACGTACAAGAATGTCCCAACTTGGCACCGTGATTTATGCAGgtatatcagt ... ttaattacagGGTCTGTGAAAACATCCCAATTGTGCTCTGTGGTAACAAGGTTGATGTGAAGAACAGGCAGGTTAAAGCAAAGCAGGTTACCTTCCATAGGAAGAAGAAC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaatacatttaccacaaactgatggttgaaactaataggtcttgattaattacagGGTCTGTGAAAACATCCCAATTGTGCTCTGTGGTAACAAGGTTGATGTGAAGAACAGGCAGGTTAAAGCAAAGCAGGTTACCTTCCATAGGAAGAAGAAC
                                         ttgattaatta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatatcagtggaactgagcaaatacatttaccacaaactgatggttgaaactaataggtcttgattaattacagGGTCTGTGAAAACATCCCAATTGTGCTCTGTGGTAACAAGGTTGATGTGAAGAACAGGCAGGTTAAAGCAAAGCAGGTTACCTTCCATAGGAAGAAGAAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAC