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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagagctcaaaacttggttatactcttcatttttttttatgcattgttttgatctcccgtttcgttacttgcagAGATTTGAGCAACAACAACTTGCATGGTTCAATTCCTTACCAGCTGCCACCGAATCTCACATATCT

Basic information

species Oryza sativa
transcript LOC_Os02g09740.2
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g09740.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G103070_T02 (Zea mays), 3'ss of exon 3
gtgagagctcaaaacttggttata--ctcttcatttttttttatgcattgttttgatctcccgtttcgttacttgcagAGATTTGAGCAACAACAACTTGCATGGTTCAATTCCTTACCAGCTGCCACCGAATCTCACATATCT
  | |||||   ||||||  | ||  |  ||  |||| || ||  ||  || ||||||  |  |||| | || ||||||||||||||||| |||||||||||||||||||| ||||||||||||||||| ||||||||  ||||
--gtgagct-gcaacttgtctgtagcccttttcttttcttctagtcaccgtgttgatccacaatttcataacatgcagAGATTTGAGCAATAACAACTTGCATGGTTCAATCCCTTACCAGCTGCCACCTAATCTCACTAATCT
















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|88310800|gb|CI659403.1|CI659403
EST:     GATGGCTCTCTGGGATATGAACTCTCCAGTCTATTCTCATTGAAGACATT                         AGATTTGAGCAACAACAACTTGCATGGTTCAATTCCTTACCAGCTGCCACC
genomic: GATGGCTCTCTGGGATATGAACTCTCCAGTCTATTCTCATTGAAGACATTgtgagagctc ... ttacttgcagAGATTTGAGCAACAACAACTTGCATGGTTCAATTCCTTACCAGCTGCCACC
EST: gi|88721234|gb|CI744533.1|CI744533
EST:     GATGGCTCTCTGGGATATGAACTCTCCAGTCTATTCTCATTGAAGACATT                         AGATTTGAGCAACAACAACTTGCATGGTTCAATTCCT
genomic: GATGGCTCTCTGGGATATGAACTCTCCAGTCTATTCTCATTGAAGACATTgtgagagctc ... ttacttgcagAGATTTGAGCAACAACAACTTGCATGGTTCAATTCCT
EST: gi|88575273|gb|CI669418.1|CI669418
EST:     GATGGCTCTCTGGGATATGAACTCTCCAGTCTATTCTCATCGAAGACATT                         AGATTTGAGCAACAACAACTTGCATGGTTCAATTCCTTACCAGCTGCCACC
genomic: GATGGCTCTCTGGGATATGAACTCTCCAGTCTATTCTCATTGAAGACATTgtgagagctc ... ttacttgcagAGATTTGAGCAACAACAACTTGCATGGTTCAATTCCTTACCAGCTGCCACC
EST: gi|88726154|gb|CI749809.1|CI749809
EST:     GATGGCTCTCTGGGATATGAACTCTCCAGTCTATTCTCATTGAAGACATT                         AGATTTGAGCAACAACAACTTGCATGGTTCAATTCCTTACCAGCTGCCACC
genomic: GATGGCTCTCTGGGATATGAACTCTCCAGTCTATTCTCATTGAAGACATTgtgagagctc ... ttacttgcagAGATTTGAGCAACAACAACTTGCATGGTTCAATTCCTTACCAGCTGCCACC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atactcttcatttttttttatgcattgttttgatctcccgtttcgttacttgcagAGATTTGAGCAACAACAACTTGCATGGTTCAATTCCTTACCAGCTGCCACCGAATCTCACATATCT
                           ttttgat  putative branch site (score: 4)
                                 tctcccgtttcgtt  CT-rich tract
         atttttttttatgcat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagagctcaaaacttggttatactcttcatttttttttatgcattgttttgatctcccgtttcgttacttgcagAGATTTGAGCAACAACAACTTGCATGGTTCAATTCCTTACCAGCTGCCACCGAATCTCACATATCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGC