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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gattgagcttttctttgatggtctttgctttgattcgccatggttgattgattgagaatttgaggtgagattgattcttgatgttcctgttttattgcagAGAGCTCGAGAAAGGGGATGGATGGCGCTTGTACAGTACTCGGCTACACTTCTGTCATGTACATTCATTTTTCTAGTTTTAAGTTAGTGATCTGATTACA

Basic information

species Oryza sativa
transcript LOC_Os02g10660.1
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|29644615|gb|CB649622.1|CB649622
EST:     GCCTCGTCCCTTCGTCGTCGTTGCCATCGTCGTCAATTATCTCATTCAAG                         AGAGCTCGAGAAAGGGGATGGATGGCGCTTGTACAGTACTCGGCTACACTT
genomic: GCCTCGTCCCTTCGTCGTCGTTGCCATCGTCGTCAATTATCTCATTCAAGgtacacttac ... tttattgcagAGAGCTCGAGAAAGGGGATGGATGGCGCTTGTACAGTACTCGGCTACACTT
EST: gi|86536128|gb|CI176334.1|CI176334
EST:     GCCTCGTCCCTTCGTCGTCGTTGCCATCGTCGTCAATTATCTCATTCAAG                         AGAGCTCGAGAAAGGGGATGGATGGCGCTTGTACAGTACTCGGCTACACTT
genomic: GCCTCGTCCCTTCGTCGTCGTTGCCATCGTCGTCAATTATCTCATTCAAGgtacacttac ... tttattgcagAGAGCTCGAGAAAGGGGATGGATGGCGCTTGTACAGTACTCGGCTACACTT
EST: gi|87019205|gb|CI277921.1|CI277921
EST:     GCCTCGTCCCTTCGTCGTCGTTGCCATCGTCGTCAATTATCTCATTCAAG                         AGAGCTCGAGAAAGGGGATGGATGGCGCTTGTACAGTACTCGGCTACACTT
genomic: GCCTCGTCCCTTCGTCGTCGTTGCCATCGTCGTCAATTATCTCATTCAAGgtacacttac ... tttattgcagAGAGCTCGAGAAAGGGGATGGATGGCGCTTGTACAGTACTCGGCTACACTT
EST: gi|89182542|gb|CI113911.1|CI113911
EST:     GCCTCGTCCCTTCGTCGTCGTTGCCATCGTCGTCAATTATCTCATTCAAG                         AGAGCTCGAGAAAGGGGATGGATGGCGCTTGTACAGTACTCGGCTACACTT
genomic: GCCTCGTCCCTTCGTCGTCGTTGCCATCGTCGTCAATTATCTCATTCAAGgtacacttac ... tttattgcagAGAGCTCGAGAAAGGGGATGGATGGCGCTTGTACAGTACTCGGCTACACTT
EST: gi|88993598|gb|CI110419.1|CI110419
EST:     GCCTCGTCCCTTTGTCGTCGTTGCCATTGTCGTCAATTATCTCATTCAAG                         AGAGCTCGAGAAAGGGGATGGATGGCGCTTGTACAGTACTCGGCTACACTT
genomic: GCCTCGTCCCTTCGTCGTCGTTGCCATCGTCGTCAATTATCTCATTCAAGgtacacttac ... tttattgcagAGAGCTCGAGAAAGGGGATGGATGGCGCTTGTACAGTACTCGGCTACACTT
EST: gi|86500676|gb|CI143309.1|CI143309
EST:     CCTCGTCCCTTCGTCGTCGTTGCCATCGTCGTCAATTATCTCATTCCAAG                         AGAGCTCGAGAAAGGGGATGGATGGCGCTTGTACAGTACTCGGCTACACT
genomic: CCTCGTCCCTTCGTCGTCGTTGCCATCGTCGTCAATTATCTCATTC-AAGgtacacttac ... tttattgcagAGAGCTCGAGAAAGGGGATGGATGGCGCTTGTACAGTACTCGGCTACACT
EST: gi|88247957|gb|CI247806.1|CI247806
EST:     GCCTCGTCCCTTCGTCGTCGTTGCCATCGTCGTCAATTATCTCATTCAAG                         AGAGCTCGAGAAAGGGGATGGATGGCGCTTGTACAGTACTCGGCTACACTT
genomic: GCCTCGTCCCTTCGTCGTCGTTGCCATCGTCGTCAATTATCTCATTCAAGgtacacttac ... tttattgcagAGAGCTCGAGAAAGGGGATGGATGGCGCTTGTACAGTACTCGGCTACACTT
EST: gi|88997388|gb|CI390054.1|CI390054
EST:     GCCTCGTCCCTTCGTCGTCGTTGCCATCGTCGTCAATTATCTCATTCAAG                         AGAGCTCGAGAAAGGGGATGGATGGCGCTTGTACAAGTACTCGGCTACACT
genomic: GCCTCGTCCCTTCGTCGTCGTTGCCATCGTCGTCAATTATCTCATTCAAGgtacacttac ... tttattgcagAGAGCTCGAGAAAGGGGATGGATGGCGCTTGTACA-GTACTCGGCTACACT
EST: gi|88246477|gb|CI246326.1|CI246326
EST:     GCCTCGTCCCTTCGTCGTCGTTGCCATCGTCGTCAATTATCTCATTCAAG                         AGAGCTCGAGAAAGGGGATGGATGGCGCTTGTACAGTACTCGGCTACACTT
genomic: GCCTCGTCCCTTCGTCGTCGTTGCCATCGTCGTCAATTATCTCATTCAAGgtacacttac ... tttattgcagAGAGCTCGAGAAAGGGGATGGATGGCGCTTGTACAGTACTCGGCTACACTT
EST: gi|109712660|gb|CI105268.1|CI105268
EST:     GCCTCGTCCCTTCGTCGTCGTTGCNATCGTCGTCAATTATCTCATTCAAG                         AGAGCTCGAGAAAGGGGATGGATGGCGCTTGTACAGTACTCGGCTACACTT
genomic: GCCTCGTCCCTTCGTCGTCGTTGCCATCGTCGTCAATTATCTCATTCAAGgtacacttac ... tttattgcagAGAGCTCGAGAAAGGGGATGGATGGCGCTTGTACAGTACTCGGCTACACTT
EST: gi|88250898|gb|CI248749.1|CI248749
EST:     GCCTCGTCCCTTCGTCGTCGTTGCCATCGTCGTCAATTATCTCATTCAAG                         AGAGCTCGAGAAAGGGGATGGATGGCGCTTGTACAGTACTCGGCTACACTT
genomic: GCCTCGTCCCTTCGTCGTCGTTGCCATCGTCGTCAATTATCTCATTCAAGgtacacttac ... tttattgcagAGAGCTCGAGAAAGGGGATGGATGGCGCTTGTACAGTACTCGGCTACACTT

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: 39 (upstream exon), 66 (downstream exon)
Score: 5

CGGCCTCTTCAAGCCCGACGGCAGCGTCTCGATCGATCTGGGGTTCAAGGGCCTCGTCCCTTCGTCGTCGTTGCCATCGTCGTCAATTATCTCATTCAAGgtacacttac ... tttattgcagAGAGCTCGAGAAAGGGGATGGATGGCGCTTGTACAGTACTCGGCTACACTTCTGTCATGTACATTCATTTTTCTAGTTTTAAGTTAGTGATCTGATTACA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gattgattgagaatttgaggtgagattgattcttgatgttcctgttttattgcagAGAGCTCGAGAAAGGGGATGGATGGCGCTTGTACAGTACTCGGCTACACTTCTGTCATGTACATTCATTTTTCTAGTTTTAAGTTAGTGATCTGATTACA
                              tcttgat  putative branch site (score: 5)
                                      ttcctgtttt  CT-rich tract
                                          tgttttatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gattgagcttttctttgatggtctttgctttgattcgccatggttgattgattgagaatttgaggtgagattgattcttgatgttcctgttttattgcagAGAGCTCGAGAAAGGGGATGGATGGCGCTTGTACAGTACTCGGCTACACTTCTGTCATGTACATTCATTTTTCTAGTTTTAAGTTAGTGATCTGATTACA

- - - - - - - ttgatgg
- - - - - - - - - - - - -tgctttg
- - - - - - - - - - - - - - - - - - gccatgg
- - - - - - - - - - - - - - - - - - - - - -ttgattg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgattct