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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgttaactgactctttatcctcggtgatgcataacattaggcacttgttgattgcctgctgatgtgccttgttatctttctatcatcagGTGATCGCTGGACTCTGGATTCTGTCAGTTCTTGGTAGCAGCTGTAACTTTTTGACTTTGTTCTACATAGGTAATGATACCAGTGCTGCGAAGCTTAAGT

Basic information

species Oryza sativa
transcript LOC_Os01g53520.2
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|218484106|gb|FG945297.1|FG945297
EST:     CAACCTTGAGGGAGATTGGTCATGGCCGTGATCTGAAGAAGTTCCTCATT                         GTGATCGCTGGACTCTGGATTCTGTCAGTTCTTGGCAGCAGCTGCAACT
genomic: CAACCTTGAGGGAGATTGGTCATGGCCGTGATCTGAAGAAGTTCCTCATTgtatgttaac ... ctatcatcagGTGATCGCTGGACTCTGGATTCTGTCAGTTCTTGGTAGCAGCTGTAACT
EST: gi|33688621|gb|CF316860.1|CF316860
EST:     CAACCTTGAGGGAGATTGGTCATGGCCGTGATCTGAAGAAGTTCCTCATT                         GTGATCGCTGGACTCTGGATTCTGTCAGTTCTTGGTAGCAGCTGTAACTTT
genomic: CAACCTTGAGGGAGATTGGTCATGGCCGTGATCTGAAGAAGTTCCTCATTgtatgttaac ... ctatcatcagGTGATCGCTGGACTCTGGATTCTGTCAGTTCTTGGTAGCAGCTGTAACTTT
EST: gi|10109165|gb|AU065308.2|AU065308
EST:     CAACCTTGAGGGAGATTGGTCATGGCCGTGATCTGAAGAAGTTCCTCATT                         GTGATCGCTGGACTCTGGATTCTGTCA
genomic: CAACCTTGAGGGAGATTGGTCATGGCCGTGATCTGAAGAAGTTCCTCATTgtatgttaac ... ctatcatcagGTGATCGCTGGACTCTGGATTCTGTCA
EST: gi|58682578|gb|CK071265.1|CK071265
EST:     CAACCTTGAGGGAGATTGGTCATGGCCGTGATCTGAAGAAGTTCCTCATT                         GTGATCGCTGGACTCTGGATTCTGTCAGTTCTTG
genomic: CAACCTTGAGGGAGATTGGTCATGGCCGTGATCTGAAGAAGTTCCTCATTgtatgttaac ... ctatcatcagGTGATCGCTGGACTCTGGATTCTGTCAGTTCTTG
EST: gi|33678278|gb|CF306517.1|CF306517
EST:     CAACCTTGAGGGAGATTGGTCATGGCCGTGATCTGAAGAAGTTCCTCATT                         GTGATCGCTGGACTCTGGATTCTGTCAGTTCTTGGTAGCAGCT
genomic: CAACCTTGAGGGAGATTGGTCATGGCCGTGATCTGAAGAAGTTCCTCATTgtatgttaac ... ctatcatcagGTGATCGCTGGACTCTGGATTCTGTCAGTTCTTGGTAGCAGCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cattaggcacttgttgattgcctgctgatgtgccttgttatctttctatcatcagGTGATCGCTGGACTCTGGATTCTGTCAGTTCTTGGTAGCAGCTGTAACTTTTTGACTTTGTTCTACATAGGTAATGATACCAGTGCTGCGAAGCTTAAGT
                      tgctgat  putative branch site (score: 3)
                                ccttgttatctttct  putative PPT
                                     ttatcttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgttaactgactctttatcctcggtgatgcataacattaggcacttgttgattgcctgctgatgtgccttgttatctttctatcatcagGTGATCGCTGGACTCTGGATTCTGTCAGTTCTTGGTAGCAGCTGTAACTTTTTGACTTTGTTCTACATAGGTAATGATACCAGTGCTGCGAAGCTTAAGT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC