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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...catgatatttgttggctcaatcctgttcttctgtagcttatgttatttaatgatttcaaaagatttcaattgttcatggacttctttttattgcttgcagCTGGCCAGGAAAGGTTTAGGGGAATCACAAGTTCTTACTACAGAGGTGCCCATGGCATCATTCTAG

Basic information

species Oryza sativa
transcript LOC_Os03g05280.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g05280.1 (Oryza sativa), 3'ss of exon 2
lower sequence: Vv13s0019g05280.t01 (Vitis vinifera), 3'ss of exon 3
catgatatttgttg--gctcaatcctgttcttctgtagcttatgttatttaatgatttcaaaagatttcaattgttcatggacttctttttattgcttgcagCTGGCCAGGAAAGGTTTAGGGGAATCACAAGTTCTTACTACAGAGGTGCCCATGGCATCATTCTAG
  ||  |  |  ||  | | |    |||  || | |   || | |||    |  |||  |   | ||   | || | ||    |||||||| ||| |||||||||| ||||| |||||| |   | | ||||   ||||||||||||||| ||||||||| |||||||
-ttgggaactagtgaaggtgacatttgtgtttttttttttttttttaaaagacaattcaagttgtttgttagtgat-attttgttcttttttttggttgcagCTGGACAGGAGAGGTTTGGAACATTGACAAACACTTACTACAGAGGTGTCCATGGCATTATTCTAG
















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|33654291|gb|CF276905.1|CF276905
EST:     ATTTCTCACTGTCAATGGGAAGAAACTGAAGCTAACAATATGGGACACTG                         CTGGCCGGGAAAGGTTTAGGGGAATCACAAGTTCTTACTACAGAGGTGCCC
genomic: ATTTCTCACTGTCAATGGGAAGAAACTGAAGCTAACAATATGGGACACTGgtaagttgtt ... ttgcttgcagCTGGCCAGGAAAGGTTTAGGGGAATCACAAGTTCTTACTACAGAGGTGCCC
EST: gi|86592468|gb|CI253149.1|CI253149
EST:     ATTTCTCACTGTCAATGGGAAGAAACTGAAGCTAACAATATGGGACACTG                         CTGGCCAGGAAAGGTTTAGGGGAATCACAAGTTCTTACTACAGAGGTGCCC
genomic: ATTTCTCACTGTCAATGGGAAGAAACTGAAGCTAACAATATGGGACACTGgtaagttgtt ... ttgcttgcagCTGGCCAGGAAAGGTTTAGGGGAATCACAAGTTCTTACTACAGAGGTGCCC
EST: gi|58592544|gb|CF990852.1|CF990852
EST:     ATTTCTCACTGTCAATGGGAAGAAACTGAAGCTAACAATATGGGACACTG                         CTGGCCAGGAAAGGTTTAGGGGAATCACAAGTTCTTACTACAGAGGTGCCC
genomic: ATTTCTCACTGTCAATGGGAAGAAACTGAAGCTAACAATATGGGACACTGgtaagttgtt ... ttgcttgcagCTGGCCAGGAAAGGTTTAGGGGAATCACAAGTTCTTACTACAGAGGTGCCC
EST: gi|33691502|gb|CF319741.1|CF319741
EST:     TGTCAATGGGAAGAAACTGAAGCTAACAATATGGGACACTG                         CTGGCCAGGAAAGGTTTAGGGGAATCACAAGTTCTTACTACAGAGGTGCCC
genomic: TGTCAATGGGAAGAAACTGAAGCTAACAATATGGGACACTGgtaagttgtt ... ttgcttgcagCTGGCCAGGAAAGGTTTAGGGGAATCACAAGTTCTTACTACAGAGGTGCCC
EST: gi|86910401|gb|CI293056.1|CI293056
EST:     ATTTCTCACTGTCAATGGGAAGAAACTGAAGCTAACAATATGGGACACTG                         CTGGCCAGGAAAGGTTTAGGGGAATCACAAGTTCTTACTACAGAGGTGCCC
genomic: ATTTCTCACTGTCAATGGGAAGAAACTGAAGCTAACAATATGGGACACTGgtaagttgtt ... ttgcttgcagCTGGCCAGGAAAGGTTTAGGGGAATCACAAGTTCTTACTACAGAGGTGCCC
EST: gi|33693314|gb|CF321553.1|CF321553
EST:     ATTTCTCACTGTCAATGGGAAGAAACTGAAGCTAACAATATGGGACACTG                         CTGGCCAGGAAAGGTTTAGGGGAATCACAAGTTCTTACTACAGAGGTGCCC
genomic: ATTTCTCACTGTCAATGGGAAGAAACTGAAGCTAACAATATGGGACACTGgtaagttgtt ... ttgcttgcagCTGGCCAGGAAAGGTTTAGGGGAATCACAAGTTCTTACTACAGAGGTGCCC
EST: gi|88401815|gb|CI591142.1|CI591142
EST:     ATTTCTCACTGTCAATGGGAAGAAACTGAAGCTAAAAATATGGGACACTG                         CTGGCCAGGAAAAGTTTAGGGGAATCACAAGTTCTTACTACAGAGGTGCCC
genomic: ATTTCTCACTGTCAATGGGAAGAAACTGAAGCTAACAATATGGGACACTGgtaagttgtt ... ttgcttgcagCTGGCCAGGAAAGGTTTAGGGGAATCACAAGTTCTTACTACAGAGGTGCCC
EST: gi|88401813|gb|CI591140.1|CI591140
EST:     ATTTCTCACTGTCAATGGGAAGAAACTGAAGCTAACAATATGGGACACTG                         CTGGCCAGGAAAAGTTTAGGGGAATCACAAGTTCTTACTACAGAGGTGCCC
genomic: ATTTCTCACTGTCAATGGGAAGAAACTGAAGCTAACAATATGGGACACTGgtaagttgtt ... ttgcttgcagCTGGCCAGGAAAGGTTTAGGGGAATCACAAGTTCTTACTACAGAGGTGCCC
EST: gi|88451481|gb|CI565534.1|CI565534
EST:     ATTTCTCACTGTCAATGGGAAGAAACTGAAGCTAACAATATGGGACACTG                         CTGGCCAGGAAAAGTTTAGGGGAATCACAAGTTCTTACTACAGAGGTGCCC
genomic: ATTTCTCACTGTCAATGGGAAGAAACTGAAGCTAACAATATGGGACACTGgtaagttgtt ... ttgcttgcagCTGGCCAGGAAAGGTTTAGGGGAATCACAAGTTCTTACTACAGAGGTGCCC

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), 57 (downstream exon)
Score: 17

GGGTTGACTTTAAAATCAAATTTCTCACTGTCAATGGGAAGAAACTGAAGCTAACAATATGGGACACTGgtaagttgtt ... ttgcttgcagCTGGCCAGGAAAGGTTTAGGGGAATCACAAGTTCTTACTACAGAGGTGCCCATGGCATCATTCTAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttaatgatttcaaaagatttcaattgttcatggacttctttttattgcttgcagCTGGCCAGGAAAGGTTTAGGGGAATCACAAGTTCTTACTACAGAGGTGCCCATGGCATCATTCTAG
 atttaat  putative branch site (score: 17)
                                   cttctttttattgctt  putative PPT
       atttcaaaagattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
catgatatttgttggctcaatcctgttcttctgtagcttatgttatttaatgatttcaaaagatttcaattgttcatggacttctttttattgcttgcagCTGGCCAGGAAAGGTTTAGGGGAATCACAAGTTCTTACTACAGAGGTGCCCATGGCATCATTCTAG

catgata
- - - - -tgttggc
- - - - - - - - - - -cctgttc
- - - - - - - - - - - - - - - ctgtagc
- - - - - - - - - - - - - - - - - - -ttatgtt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - caaaagat
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gttcatg