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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cctcattatttacttgtatatttgagagtcaaacaatgtttcatgtcatcctttgacacaataatatggaaatataacctccaattctcctatattgcagGAAGTTGCTGGGCTTTCTCAGCAATAGCAGCTGTAGAAGGCATCAACCAGATTGTTACTGGCGACCTGATATCTTTGTCTGAGCAGGAGCTAGTTGACTG

Basic information

species Oryza sativa
transcript LOC_Os04g55650.1
intron # 1
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|29617445|gb|CB622457.1|CB622457
EST:     CTGGAGGACCAAGGGGGCCGTGGCTGAGATCAAGGACCAGGGAGGTTGCG                         GAAGTTGCTGGGCTTTCTCAGCAATAGCAGCTGTAGAAGGCATCAACCAGA
genomic: CTGGAGGACCAAGGGGGCCGTGGCTGAGATCAAGGACCAGG-AGGTTGCGgtaagcatcc ... tatattgcagGAAGTTGCTGGGCTTTCTCAGCAATAGCAGCTGTAGAAGGCATCAACCAGA
EST: gi|33797168|gb|CF324448.1|CF324448
EST:     CTGGAGGACCAAGGGGGCCGTGGCTGAGATCAAGGACCAGGGAGGTTGCG                         GAAGTTGCTGGGCTTTCTCAGCAATAGCAGCTGTAGAAGGCATCAACCAGA
genomic: CTGGAGGACCAAGGGGGCCGTGGCTGAGATCAAGGACCA-GGAGGTTGCGgtaagcatcc ... tatattgcagGAAGTTGCTGGGCTTTCTCAGCAATAGCAGCTGTAGAAGGCATCAACCAGA
EST: gi|29681379|gb|CB677654.1|CB677654
EST:     CTGGAGGACCAAGGGGGCCGTGGCTGAGATCAAGGACCAGGGAGGTTGCG                         GAAGTTGCTGGGCTTTCTCAGCAATAGCAGCTGTAGAAGGCATCAACCAGA
genomic: CTGGAGGACCAAGGGGGCCGTGGCTGAGATCAAGGACCAGG-AGGTTGCGgtaagcatcc ... tatattgcagGAAGTTGCTGGGCTTTCTCAGCAATAGCAGCTGTAGAAGGCATCAACCAGA
EST: gi|2800945|gb|AA754239.1|AA754239
EST:     CTGGAGGACCAAGGGGGCCGTGGCTGAGATCAAGGACCAGGGAGGTTGCG                         GAAGTTGCTGGGCTTTCTCAGCAATAGCAGCTGTAGAAGGCATCAACCAGA
genomic: CTGGAGGACCAAGGGGGCCGTGGCTGAGATCAAGGACCA-GGAGGTTGCGgtaagcatcc ... tatattgcagGAAGTTGCTGGGCTTTCTCAGCAATAGCAGCTGTAGAAGGCATCAACCAGA
EST: gi|58591175|gb|CF989483.1|CF989483
EST:     CTGGAGGACCAAGGGGGCCGTGGCTGAGATCAAGGACCAGGGAGGTTGCG                         GAAGTTGCTGGGCTTTCTCAGCAATAGCAGCTGTAGAAGGCATCAACCAGA
genomic: CTGGAGGACCAAGGGGGCCGTGGCTGAGATCAAGGACCA-GGAGGTTGCGgtaagcatcc ... tatattgcagGAAGTTGCTGGGCTTTCTCAGCAATAGCAGCTGTAGAAGGCATCAACCAGA
EST: gi|29686124|gb|CB682399.1|CB682399
EST:     CTGGAGGACCAAGGGGGCCGTGGCTGAGATCAAGGACCAGGGAGGTTGCG                         GAAGTTGCTGGGCTTTCTCATCAATAGCAGCTGTAGAAGGCATCAACCAGA
genomic: CTGGAGGACCAAGGGGGCCGTGGCTGAGATCAAGGACCAGG-AGGTTGCGgtaagcatcc ... tatattgcagGAAGTTGCTGGGCTTTCTCAGCAATAGCAGCTGTAGAAGGCATCAACCAGA
EST: gi|58611444|gb|CK039156.1|CK039156
EST:     CTGGAGGACCAAGGGGGCCGTGGCTGAGATCAAGGACCAGGGAGGTTGCG                         GAAGTTGCTGGGCTTTCTCAGCAATAGCAGCTGTAGAAGGCATCAACCAGA
genomic: CTGGAGGACCAAGGGGGCCGTGGCTGAGATCAAGGACCAGG-AGGTTGCGgtaagcatcc ... tatattgcagGAAGTTGCTGGGCTTTCTCAGCAATAGCAGCTGTAGAAGGCATCAACCAGA
EST: gi|15856080|gb|BI808892.1|BI808892
EST:     TGGAGGACCAAGGGGGCCGTGGCTGAGATCAAGGACCAGGGGAGGTTGCG                         GAAGTTGCTGGGCTTTCTCAGCAATAGCAGCTGTAGAAGGCATCAAC-AGA
genomic: TGGAGGACCAAGGGGGCCGTGGCTGAGATCAAGGACCAGG--AGGTTGCGgtaagcatcc ... tatattgcagGAAGTTGCTGGGCTTTCTCAGCAATAGCAGCTGTAGAAGGCATCAACCAGA
EST: gi|88385484|gb|CI564144.1|CI564144
EST:     CTGGAGGACCAAGGGGGCCGTGGCTGAGATCAAGGACCAGGGAGGTTGCG                         GAAGTTGCTGGGCTTTCTTCAGCAATAGCAGCTGTAGNAAGGCATCAACCA
genomic: CTGGAGGACCAAGGGGGCCGTGGCTGAGATCAAGGACCAGG-AGGTTGCGgtaagcatcc ... tatattgcagGAAGTTGCTGGGCTTTCT-CAGCAATAGCAGCTGTAG-AAGGCATCAACCA
EST: gi|14571289|gb|BI118657.1|BI118657
EST:     CTGGAGGACCAAGGGGGCCGTGGCTGAGATCAAGGACCAGGGAGGTTGCG                         GAAGTTGCTGGGCTTTCTCAGCAATAGCAGCTGTAGAAGGCATCAACCAGA
genomic: CTGGAGGACCAAGGGGGCCGTGGCTGAGATCAAGGACCA-GGAGGTTGCGgtaagcatcc ... tatattgcagGAAGTTGCTGGGCTTTCTCAGCAATAGCAGCTGTAGAAGGCATCAACCAGA
EST: gi|15857829|gb|BI810641.1|BI810641
EST:     TGGAGGACCAAGGGGGCCGTGGCTGAGATCAAGGACCAGGGGAGGTTGCG                         GAAGTTGCTGGGCTTTCTCAGCAATAGCAGCTGTAGAAGGCATCAACCAGA
genomic: TGGAGGACCAAGGGGGCCGTGGCTGAGATCAAGGACCAGG--AGGTTGCGgtaagcatcc ... tatattgcagGAAGTTGCTGGGCTTTCTCAGCAATAGCAGCTGTAGAAGGCATCAACCAGA
EST: gi|29641659|gb|CB646666.1|CB646666
EST:     CTGGAGGACCAAGGGGGCCGTGGCTGAGATCAAGGACCAGGGAGGTTGCG                         GAAGTTGCTGGGCTTTCTCAGCAATAGCAGCTGTAGAAGGCATCAACCAGA
genomic: CTGGAGGACCAAGGGGGCCGTGGCTGAGATCAAGGACCAGG-AGGTTGCGgtaagcatcc ... tatattgcagGAAGTTGCTGGGCTTTCTCAGCAATAGCAGCTGTAGAAGGCATCAACCAGA
EST: gi|58687243|gb|CK075930.1|CK075930
EST:     CTGGAGGACCAAGGGGGCCGTGGCTGAGATCAAGGACCAGGGAGGTTGCG                         GAAGTTGCTGGGCTTTCTCAGCAATAGCAGCTGTAGAAGG
genomic: CTGGAGGACCAAGGGGGCCGTGGCTGAGATCAAGGACCAGG-AGGTTGCGgtaagcatcc ... tatattgcagGAAGTTGCTGGGCTTTCTCAGCAATAGCAGCTGTAGAAGG
EST: gi|88263234|gb|CI367008.1|CI367008
EST:     CTGGAGGACCAAGGGGGCCGTGGCTGAGATCAAGGACCAGGGAGGTTGCG                         GAAGTTGCTGGGCTTTCTCAGCAATAGGCAGCTGTAGAAGGCATCAACCAG
genomic: CTGGAGGACCAAGGGGGCCGTGGCTGAGATCAAGGACCA-GGAGGTTGCGgtaagcatcc ... tatattgcagGAAGTTGCTGGGCTTTCTCAGCAATA-GCAGCTGTAGAAGGCATCAACCAG
EST: gi|14571385|gb|BI118753.1|BI118753
EST:     CTGGAGGACCAAGGGGGCCGTGGCTGAGATCAAGGACCAGGGAGGTTGCT                         GAAGTTGCCTGGGCTTTCTCAGCAATAGTAGCTGTAGAAGGCATCAACCAG
genomic: CTGGAGGACCAAGGGGGCCGTGGCTGAGATCAAGGACCA-GGAGGTTGCGgtaagcatcc ... tatattgcagGAAGTTG-CTGGGCTTTCTCAGCAATAGCAGCTGTAGAAGGCATCAACCAG

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), 75 (downstream exon)
Score: 127

CAGCGACAGGTACCTCGCCGCCGACAACGAGGCGCTGCCGGAGTCCGTTGACTGGAGGACCAAGGGGGCCGTGGCTGAGATCAAGGACCAGGAGGTTGCGgtaagcatcc ... tatattgcagGAAGTTGCTGGGCTTTCTCAGCAATAGCAGCTGTAGAAGGCATCAACCAGATTGTTACTGGCGACCTGATATCTTTGTCTGAGCAGGAGCTAGTTGACTG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcatcctttgacacaataatatggaaatataacctccaattctcctatattgcagGAAGTTGCTGGGCTTTCTCAGCAATAGCAGCTGTAGAAGGCATCAACCAGATTGTTACTGGCGACCTGATATCTTTGTCTGAGCAGGAGCTAGTTGACTG
                          atataac  putative branch site (score: 127)
                                cctccaattctcct  CT-rich tract
              aataatatggaaatat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cctcattatttacttgtatatttgagagtcaaacaatgtttcatgtcatcctttgacacaataatatggaaatataacctccaattctcctatattgcagGAAGTTGCTGGGCTTTCTCAGCAATAGCAGCTGTAGAAGGCATCAACCAGATTGTTACTGGCGACCTGATATCTTTGTCTGAGCAGGAGCTAGTTGACTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCT
- - - - - - cttgtat
- - - - - - - - - - - - - - tcaaaca
- - - - - - - - - - - - - - - - - - tgtttca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - cacaata
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - acctcca