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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tattgtatcatgtgattttatttaacaatattgatattgaacacatgacctctcctatatgtcttgtgccttattatttttttattgttaactctggcagTATTGCAAAGCACCTGGAGTCAGCTAATACAATGTTCTCCTTCATATGGTGGATAATTGGATTTTATTGGATATCTGCTGGGGGTGAGGATGTTATCCGT

Basic information

species Oryza sativa
transcript LOC_Os04g48050.1
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|27577289|gb|CA999983.1|CA999983
EST:     CCGATTGCGTCAG                         TATTGCAAAGCACCTGGACTTAGCTAATACAATGTTCTCCTTCATATGGTG
genomic: CCGATTGCGTCAGgtaaatggaa ... actctggcagTATTGCAAAGCACCTGGAGTCAGCTAATACAATGTTCTCCTTCATATGGTG
EST: gi|38473211|gb|CF957343.1|CF957343
EST:     GATGATGTCACGGAGGACGATCGCCGTGGTAGCTGCACCGATTGCGTCAG                         TATTGCAAAGCACCTGGAGTCAGCTAATACAATGTTCTCCTTCATATGGTG
genomic: GATGATGTCACGGAGGACGATCGCCGTGGTAGCTGCACCGATTGCGTCAGgtaaatggaa ... actctggcagTATTGCAAAGCACCTGGAGTCAGCTAATACAATGTTCTCCTTCATATGGTG
EST: gi|29616405|gb|CB621417.1|CB621417
EST:     GATGATGTCACGGAGGACGATCGCCGTGGTAGCTGCACCGATTGCGTCAG                         TATTGCAAAGCACCTGGAGTCAGCTAATACAATGTTCTCCTTCATATGGTG
genomic: GATGATGTCACGGAGGACGATCGCCGTGGTAGCTGCACCGATTGCGTCAGgtaaatggaa ... actctggcagTATTGCAAAGCACCTGGAGTCAGCTAATACAATGTTCTCCTTCATATGGTG
EST: gi|88742881|gb|CI766389.1|CI766389
EST:     GATGATGTCACGGAGGACGATCGCCGTGGTAGCTGCACCGATTGCGTCAG                         TATTGCAAAGCACCTGGAGTCAGCTAATACAATGTTCTCCTTCATATGGTG
genomic: GATGATGTCACGGAGGACGATCGCCGTGGTAGCTGCACCGATTGCGTCAGgtaaatggaa ... actctggcagTATTGCAAAGCACCTGGAGTCAGCTAATACAATGTTCTCCTTCATATGGTG
EST: gi|58683789|gb|CK072476.1|CK072476
EST:     GTCACGGAGGACGATCGCCGTGGTAGCTGCACCGATTGCGTCAG                         TATTGCAAAGCACCTGGAGTCAGCTAATACAATGTTCTCCTTCATATGGTG
genomic: GTCACGGAGGACGATCGCCGTGGTAGCTGCACCGATTGCGTCAGgtaaatggaa ... actctggcagTATTGCAAAGCACCTGGAGTCAGCTAATACAATGTTCTCCTTCATATGGTG
EST: gi|88760780|gb|CI770336.1|CI770336
EST:     GATGATGTCACGGAGGACGATCGCCGTGGTAGCTGCACCGATTGCGTCAG                         TATTGCAAAGCACCTGGAGTCAGCTAATACAATGTTCTCCTTCATATGGTG
genomic: GATGATGTCACGGAGGACGATCGCCGTGGTAGCTGCACCGATTGCGTCAGgtaaatggaa ... actctggcagTATTGCAAAGCACCTGGAGTCAGCTAATACAATGTTCTCCTTCATATGGTG
EST: gi|88405109|gb|CI685558.1|CI685558
EST:     ACGGAGGACGATCGCCGTGGTAGCTGCACCGATTGCGTCAG                         TATTGCAAAGCACCTGGAGTCAGCTAATACAATGTTCTCCTTCATATGGTG
genomic: ACGGAGGACGATCGCCGTGGTAGCTGCACCGATTGCGTCAGgtaaatggaa ... actctggcagTATTGCAAAGCACCTGGAGTCAGCTAATACAATGTTCTCCTTCATATGGTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgacctctcctatatgtcttgtgccttattatttttttattgttaactctggcagTATTGCAAAGCACCTGGAGTCAGCTAATACAATGTTCTCCTTCATATGGTGGATAATTGGATTTTATTGGATATCTGCTGGGGGTGAGGATGTTATCCGT
                                        tgttaac  putative branch site (score: 2)
                         ttattatttttttatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tattgtatcatgtgattttatttaacaatattgatattgaacacatgacctctcctatatgtcttgtgccttattatttttttattgttaactctggcagTATTGCAAAGCACCTGGAGTCAGCTAATACAATGTTCTCCTTCATATGGTGGATAATTGGATTTTATTGGATATCTGCTGGGGGTGAGGATGTTATCCGT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG
- - - - catgtga
- - - - - - - - - - - -aacaata
- - - - - - - - - - - - - - - - - - ttgaaca
- - - - - - - - - - - - - - - - - - - - - -catgacc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgtcttg