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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatcacaatggaaaatgctctgatcgatcgagttttgttgatttactgcttgaattaattactgatgaagaacagctaatgcacaagactgacattaagagtagttactgaacgctgatgatgcatatgggtaaattcaatttgcagGATCCCCAGAGGCCAGGAGAAGTTCGTCTGCATCGTGGATCTCAAGGGCTGGGGTTACTCCAACTGCGACATCAGAGCTTACATCGCGGCCATAGAGATC

Basic information

species Oryza sativa
transcript LOC_Os01g70210.1
intron # 3
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|33666128|gb|CF297095.1|CF297095
EST:     GTTATTGTGTCTACTTACTTGACAGCATCTGTGCAAG                         GATCCCCANAGGCCAGGAGAAGTTCGTCTGCATCGTGGATCTCAAGGGCTG
genomic: GTTATTGTGTCTACTTACTTGACAGCATCTGTGCAAGgtaatcacaa ... caatttgcagGATCCCCAGAGGCCAGGAGAAGTTCGTCTGCATCGTGGATCTCAAGGGCTG
EST: gi|33662283|gb|CF293250.1|CF293250
EST:     GTTATTGTGTCTACTTACTTGACAGCATCTGTGCAAG                         GATCCCCAGAGGCCAGGAGAAGTTCGTCTGCATCGTGGATCTCAAGGGCTG
genomic: GTTATTGTGTCTACTTACTTGACAGCATCTGTGCAAGgtaatcacaa ... caatttgcagGATCCCCAGAGGCCAGGAGAAGTTCGTCTGCATCGTGGATCTCAAGGGCTG
EST: gi|33663142|gb|CF294109.1|CF294109
EST:     GTTATTGTGTCTACTTACTTGACAGCATCTGTGCAAG                         GATCCCCAGAGGCCAGGAGAAGTTCGTCTGCATCGTGGATCTCAAGGGCTG
genomic: GTTATTGTGTCTACTTACTTGACAGCATCTGTGCAAGgtaatcacaa ... caatttgcagGATCCCCAGAGGCCAGGAGAAGTTCGTCTGCATCGTGGATCTCAAGGGCTG
EST: gi|1631918|gb|C19647.1|C19647
EST:     GTTATTGTGTCTACTTACTTGACAGCATCTTTNCAAG                         GATTCCCAGAGGCCAGGAGAAGTTCGTCTTCATCGTGGATCTNAAGGGCTT
genomic: GTTATTGTGTCTACTTACTTGACAGCATCTGTGCAAGgtaatcacaa ... caatttgcagGATCCCCAGAGGCCAGGAGAAGTTCGTCTGCATCGTGGATCTCAAGGGCTG
EST: gi|55438121|gb|CV732354.1|CV732354
EST:     GTTATTGTGTCTACTTACTTGACAGCATCTGTGCAAG                         GATCCCCAGAGGCCAGGAGAAGTTCG
genomic: GTTATTGTGTCTACTTACTTGACAGCATCTGTGCAAGgtaatcacaa ... caatttgcagGATCCCCAGAGGCCAGGAGAAGTTCG
EST: gi|33664298|gb|CF295265.1|CF295265
EST:     GTTATTGTGTCTACTTACTTGACAGCATCTGTGCAAG                         GATCCCCAGAGGCCAGGAGAAGTTCGTCTGCATCGTGGATCTCAAGGGCTG
genomic: GTTATTGTGTCTACTTACTTGACAGCATCTGTGCAAGgtaatcacaa ... caatttgcagGATCCCCAGAGGCCAGGAGAAGTTCGTCTGCATCGTGGATCTCAAGGGCTG
EST: gi|27577459|gb|CB000154.1|CB000154
EST:     GTTATTGTGTCTACTTACTTGACAGCATCTGTGCAAG                         GATCCCCAGAGGCCAGGAGAAGTTCGTCTGCATCGTGGATCTCAAGGGCTG
genomic: GTTATTGTGTCTACTTACTTGACAGCATCTGTGCAAGgtaatcacaa ... caatttgcagGATCCCCAGAGGCCAGGAGAAGTTCGTCTGCATCGTGGATCTCAAGGGCTG
EST: gi|55439749|gb|CV733184.1|CV733184
EST:     GTTATTGTGTCTACTTACTTGACAGCATCTGTGCAAG                         GATCCCCAGAGGCCAGGAGAAGTTCGTCTGCATCGTGGATCTCAAGGGCTG
genomic: GTTATTGTGTCTACTTACTTGACAGCATCTGTGCAAGgtaatcacaa ... caatttgcagGATCCCCAGAGGCCAGGAGAAGTTCGTCTGCATCGTGGATCTCAAGGGCTG
EST: gi|33677265|gb|CF305504.1|CF305504
EST:     GTTATTGTGTCTACTTACTTGACAGCATCTGTGCAAG                         GATCCCCAGAGGCCAGGAGAAGTTCGTCTGCATCGTGGATCTCAAGGGCTG
genomic: GTTATTGTGTCTACTTACTTGACAGCATCTGTGCAAGgtaatcacaa ... caatttgcagGATCCCCAGAGGCCAGGAGAAGTTCGTCTGCATCGTGGATCTCAAGGGCTG
EST: gi|33662282|gb|CF293249.1|CF293249
EST:     GTTATTGTGTCTACTTACTTGACAGCATCTGTGCAAG                         GATCCCCAGAGGCCAGGAGAAGTTCGTCTGCATCGTGGATCTCAAGGGCTG
genomic: GTTATTGTGTCTACTTACTTGACAGCATCTGTGCAAGgtaatcacaa ... caatttgcagGATCCCCAGAGGCCAGGAGAAGTTCGTCTGCATCGTGGATCTCAAGGGCTG
EST: gi|11565074|gb|AU165710.1|AU165710
EST:     GTTATTGTGTCTACTTACTTGACAGCATCTGTGCAAG                         GATCCCCAGAGGCCAGGAGAAGTTCGTCTGCATCGTGGATCTCAAGGGCTG
genomic: GTTATTGTGTCTACTTACTTGACAGCATCTGTGCAAGgtaatcacaa ... caatttgcagGATCCCCAGAGGCCAGGAGAAGTTCGTCTGCATCGTGGATCTCAAGGGCTG
EST: gi|18385341|gb|BM418540.1|BM418540
EST:     GTTATTGTGTCTACTTACTTGACAGCATCTGTGCAAG                         GATCCCCAGAGGCCAGGAGAAGTTCGTCTGCATCGTGGATCTCAAGGGCTG
genomic: GTTATTGTGTCTACTTACTTGACAGCATCTGTGCAAGgtaatcacaa ... caatttgcagGATCCCCAGAGGCCAGGAGAAGTTCGTCTGCATCGTGGATCTCAAGGGCTG

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: 37 (upstream exon), 74 (downstream exon)
Score: 44

GTTATTGTGTCTACTTACTTGACAGCATCTGTGCAAGgtaatcacaa ... caatttgcagGATCCCCAGAGGCCAGGAGAAGTTCGTCTGCATCGTGGATCTCAAGGGCTGGGGTTACTCCAACTGCGACATCAGAGCTTACATCGCGGCCATAGAGATC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cattaagagtagttactgaacgctgatgatgcatatgggtaaattcaatttgcagGATCCCCAGAGGCCAGGAGAAGTTCGTCTGCATCGTGGATCTCAAGGGCTGGGGTTACTCCAACTGCGACATCAGAGCTTACATCGCGGCCATAGAGATC
                    cgctgat  putative branch site (score: 44)
                                       taaattcaattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaatcacaatggaaaatgctctgatcgatcgagttttgttgatttactgcttgaattaattactgatgaagaacagctaatgcacaagactgacattaagagtagttactgaacgctgatgatgcatatgggtaaattcaatttgcagGATCCCCAGAGGCCAGGAGAAGTTCGTCTGCATCGTGGATCTCAAGGGCTGGGGTTACTCCAACTGCGACATCAGAGCTTACATCGCGGCCATAGAGATC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATC