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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaattttcttcatttgtgcacaactgcatattcagttggtactgtttttccacatatttaacatctctcatttcagGGATGGTGTCAGTGAAGGACAGTTTTATCAGGTTCTGTTTTATGAGCTTGATGCCATTAGAAAG

Basic information

species Oryza sativa
transcript LOC_Os02g45070.1
intron # 17
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|38471881|gb|CF956012.1|CF956012
EST:     TCTTTCAAGAGGGCAACTGGACAGAAACCCCAGAGGATTATATTTTACAG                         GCATGGTGTCAGTGAAGGACAGTTTTATCAGGTTCTGTTTTATGAGCTTGA
genomic: TCTTTCAAGAGGGCAACTGGACAGAAACCCCAGAGGATTATATTTTACAGgtaattttct ... ctcatttcagGGATGGTGTCAGTGAAGGACAGTTTTATCAGGTTCTGTTTTATGAGCTTGA
EST: gi|218479705|gb|FG950878.1|FG950878
EST:     TCTTTCAAGAGGGCAACTGGACAGAAACCCCAGAGGATTATATTTTACAG                         GGATGGTGTCAGTGAAGGACAGTTTTATCAGGTTCTGTTTTATGAGCNTGA
genomic: TCTTTCAAGAGGGCAACTGGACAGAAACCCCAGAGGATTATATTTTACAGgtaattttct ... ctcatttcagGGATGGTGTCAGTGAAGGACAGTTTTATCAGGTTCTGTTTTATGAGCTTGA
EST: gi|58673688|gb|CK062374.1|CK062374
EST:     TCTTTCAAGAGGGCAACTGGACAGAAACCCCAGAGGATTATATTTTACAG                         GGATGGTGTCAGTGAAGGACAGTTTTATCAGGTTCTGTTTTATGAGCTTGA
genomic: TCTTTCAAGAGGGCAACTGGACAGAAACCCCAGAGGATTATATTTTACAGgtaattttct ... ctcatttcagGGATGGTGTCAGTGAAGGACAGTTTTATCAGGTTCTGTTTTATGAGCTTGA
EST: gi|14571449|gb|BI118817.1|BI118817
EST:     TCTTTCAAGAGGGCAACTGGACAGAAACCCCAGAGGATTATATTTTACAG                         GGATGGTGTCAGTGAAGGACAGTTTTATCAGGTTCTGTTTTATGAGCTTGA
genomic: TCTTTCAAGAGGGCAACTGGACAGAAACCCCAGAGGATTATATTTTACAGgtaattttct ... ctcatttcagGGATGGTGTCAGTGAAGGACAGTTTTATCAGGTTCTGTTTTATGAGCTTGA
EST: gi|38469760|gb|CF953891.1|CF953891
EST:     TCTTTCAAGAGGGCAACTGGACAGAAACCCCAGAGGATTATATTTTACAG                         GGATGGTGTCAGTGAAGGACAGTTTTATCAGGTTCTGTTTTATGAGCTTGA
genomic: TCTTTCAAGAGGGCAACTGGACAGAAACCCCAGAGGATTATATTTTACAGgtaattttct ... ctcatttcagGGATGGTGTCAGTGAAGGACAGTTTTATCAGGTTCTGTTTTATGAGCTTGA
EST: gi|58674483|gb|CK063170.1|CK063170
EST:     TCTTTCAAGAGGGCAACTGGACAGAAACCCCAGAGGATTATATTTTACAG                         GGATGGTGTCAGTGAAGGACAGTTTTATCAGGTTCTGTTTTATGAGCTTGA
genomic: TCTTTCAAGAGGGCAACTGGACAGAAACCCCAGAGGATTATATTTTACAGgtaattttct ... ctcatttcagGGATGGTGTCAGTGAAGGACAGTTTTATCAGGTTCTGTTTTATGAGCTTGA
EST: gi|58681274|gb|CK069961.1|CK069961
EST:     TCTTTCAAGAGGGCAACTGGACAGAAACCCCAGAGGATTATATTTTACAG                         GGATGGTGTCAGTGAAGGACAGTTTTATCAGGTTCTGTTTTATGAGCTTGA
genomic: TCTTTCAAGAGGGCAACTGGACAGAAACCCCAGAGGATTATATTTTACAGgtaattttct ... ctcatttcagGGATGGTGTCAGTGAAGGACAGTTTTATCAGGTTCTGTTTTATGAGCTTGA
EST: gi|14571456|gb|BI118824.1|BI118824
EST:     TCTTTCAAGAGGGCAACTGGACAGAAACCCCAGAGGATTATATTTTACAG                         GGATGGTGTCAGTGAAGGACAAGTTTTATCAGGTTCTGTTTTATGAGCTTG
genomic: TCTTTCAAGAGGGCAACTGGACAGAAACCCCAGAGGATTATATTTTACAGgtaattttct ... ctcatttcagGGATGGTGTCAGTGAAGGAC-AGTTTTATCAGGTTCTGTTTTATGAGCTTG
EST: gi|58599567|gb|CK010095.1|CK010095
EST:     TCTTTCAAGAGGGCAACTGGACAGAAACCCCAGAGGATTATATTTTACAG                         GGATGGTGTCAGTGAAGGACAGTTTTATCAGGTTCTGTTTTATGAGCTTGA
genomic: TCTTTCAAGAGGGCAACTGGACAGAAACCCCAGAGGATTATATTTTACAGgtaattttct ... ctcatttcagGGATGGTGTCAGTGAAGGACAGTTTTATCAGGTTCTGTTTTATGAGCTTGA
EST: gi|11544371|gb|BF475189.1|BF475189
EST:     TCTTTCAAGAGGGCAACTGGACAGAAACCCCAGAGGATTATATTTTACAG                         GGATGGTGTCAGTGAAGGACAGTTTTATCAGGTTCTGTTTTATGAGCTTGA
genomic: TCTTTCAAGAGGGCAACTGGACAGAAACCCCAGAGGATTATATTTTACAGgtaattttct ... ctcatttcagGGATGGTGTCAGTGAAGGACAGTTTTATCAGGTTCTGTTTTATGAGCTTGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aactgcatattcagttggtactgtttttccacatatttaacatctctcatttcagGGATGGTGTCAGTGAAGGACAGTTTTATCAGGTTCTGTTTTATGAGCTTGATGCCATTAGAAAG
                                  atttaac  putative branch site (score: 3)
                                          tctctcatttc  CT-rich tract
                                atatttaacat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaattttcttcatttgtgcacaactgcatattcagttggtactgtttttccacatatttaacatctctcatttcagGGATGGTGTCAGTGAAGGACAGTTTTATCAGGTTCTGTTTTATGAGCTTGATGCCATTAGAAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT