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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtgtacacgcacacgaggtgttcgacggattgcctagcctgcaatgcgcgcaccttcttgcgctagtgtctctgaccattccaactgaaaagtgttgatcgtgtgattcagttatttttcctcttatctgatgagaaggcggagctaacacattacgtgctgacgcagGAAGATATATGACAAGGATGCAACTGGCCAGATACCAGGAGAGCTGCGGAACCTCACACATTTAACCCATCT

Basic information

species Oryza sativa
transcript LOC_Os04g52640.3
intron # 2
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|88410203|gb|CI575801.1|CI575801
EST:     AAGTGCGACTGCTCCGACCAGAACAACACAGTGTGCCACATCACCGGGCT                         GAAGATATATGACAAGGATGCAACTGGCCAGATACCAGGAGAGCTGCGGAA
genomic: AAGTGCGACTGCTCCGACCAGAACAACACAGTGTGCCACATCACCGGGCTgtaagtgtac ... gctgacgcagGAAGATATATGACAAGGATGCAACTGGCCAGATACCAGGAGAGCTGCGGAA
EST: gi|88360881|gb|CI625187.1|CI625187
EST:     AAGTGCGACTGCTCCGACCAGAACAACACAGTGTGCCACATCACCGGGCT                         GAAGATATATGACAAGGATGCAACTGGCCAGATACCAGGAGAGCTGGGGAA
genomic: AAGTGCGACTGCTCCGACCAGAACAACACAGTGTGCCACATCACCGGGCTgtaagtgtac ... gctgacgcagGAAGATATATGACAAGGATGCAACTGGCCAGATACCAGGAGAGCTGCGGAA
EST: gi|88347608|gb|CI634293.1|CI634293
EST:     AAGTGCGACTGCTCCGACCAGAACAACACAGTGTGCCACATCACCGGGCT                         GAAGATATATGANAAGGATGCAAGTGGCCAGATACCAGGAGAGCTGCGGAA
genomic: AAGTGCGACTGCTCCGACCAGAACAACACAGTGTGCCACATCACCGGGCTgtaagtgtac ... gctgacgcagGAAGATATATGACAAGGATGCAACTGGCCAGATACCAGGAGAGCTGCGGAA
EST: gi|88368820|gb|CI649411.1|CI649411
EST:     AAGTGCGACTGCTCCGACCAGAACAACACAGTGTGCCACATCACCGGGCT                         GAAGATATATGACAAGGATGCAACTGGCCAGATACCAGGAGAGCTGCGGAA
genomic: AAGTGCGACTGCTCCGACCAGAACAACACAGTGTGCCACATCACCGGGCTgtaagtgtac ... gctgacgcagGAAGATATATGACAAGGATGCAACTGGCCAGATACCAGGAGAGCTGCGGAA
EST: gi|88334354|gb|CI642599.1|CI642599
EST:     AAGTGCGACTGCTCCGACCAGAACAACACAGTGTGCCACATCACCGGGCT                         GAAGATATATGACAAGGATGCAACTGGCCAGATACCAGGAGAGCTGCGGAA
genomic: AAGTGCGACTGCTCCGACCAGAACAACACAGTGTGCCACATCACCGGGCTgtaagtgtac ... gctgacgcagGAAGATATATGACAAGGATGCAACTGGCCAGATACCAGGAGAGCTGCGGAA
EST: gi|88326454|gb|CI659885.1|CI659885
EST:     AAGTGCGACTGCTCCGACCAGAACAACACAGTGTGCCACATCACCGGGCT                         GAAGATATATGACAAGGATGCAACTGGCCAGATACCAGGAGAGCTGCGGAA
genomic: AAGTGCGACTGCTCCGACCAGAACAACACAGTGTGCCACATCACCGGGCTgtaagtgtac ... gctgacgcagGAAGATATATGACAAGGATGCAACTGGCCAGATACCAGGAGAGCTGCGGAA
EST: gi|88380887|gb|CI634912.1|CI634912
EST:     AAGTGCGACTGCTCCGACCAGAACAACACAGTGTGCCACATCACCGGGCT                         GAAGATATATGACAAGGATGCAACTGGCCAGATACCAGGAGAGCTGCGGAA
genomic: AAGTGCGACTGCTCCGACCAGAACAACACAGTGTGCCACATCACCGGGCTgtaagtgtac ... gctgacgcagGAAGATATATGACAAGGATGCAACTGGCCAGATACCAGGAGAGCTGCGGAA
EST: gi|88389754|gb|CI626523.1|CI626523
EST:     AAGTGCGACTGCTCCGACCAGAACAACACAGTGTGCCACATCACCGGGCT                         GAAGATATATGAAAAGGATGCAACTGGCCAGATACCAGGAGAGCTGCGGAA
genomic: AAGTGCGACTGCTCCGACCAGAACAACACAGTGTGCCACATCACCGGGCTgtaagtgtac ... gctgacgcagGAAGATATATGACAAGGATGCAACTGGCCAGATACCAGGAGAGCTGCGGAA
EST: gi|88396823|gb|CI577972.1|CI577972
EST:     AAGTGCGACTGCTCCGACCAGAACAACACAGTGTGCCACATCACCGGGCT                         GAAGATATATGACAAGGATGCAACTGGCCAGATAC-AGGAGAGCTGCGGAA
genomic: AAGTGCGACTGCTCCGACCAGAACAACACAGTGTGCCACATCACCGGGCTgtaagtgtac ... gctgacgcagGAAGATATATGACAAGGATGCAACTGGCCAGATACCAGGAGAGCTGCGGAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atttttcctcttatctgatgagaaggcggagctaacacattacgtgctgacgcagGAAGATATATGACAAGGATGCAACTGGCCAGATACCAGGAGAGCTGCGGAACCTCACACATTTAACCCATCT
                                            tgctgac  putative branch site (score: 2)
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagtgtacacgcacacgaggtgttcgacggattgcctagcctgcaatgcgcgcaccttcttgcgctagtgtctctgaccattccaactgaaaagtgttgatcgtgtgattcagttatttttcctcttatctgatgagaaggcggagctaacacattacgtgctgacgcagGAAGATATATGACAAGGATGCAACTGGCCAGATACCAGGAGAGCTGCGGAACCTCACACATTTAACCCATCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGC