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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagttctgtatcaatctcattttccacacagtcctactcctctattgatccctttctcaaggcatgtatgagcttcattataaccctttttcttacagGTTTTAACAACTGACGCTCAAGTCAGCAGTGATGTTTGGAGAGAAATGGTCCGAACATCAGTGAGTAGAAGCTTCAATCAAATAACA

Basic information

species Oryza sativa
transcript LOC_Os03g17120.1
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g17120.2 (Oryza sativa), 3'ss of exon 9
lower sequence: GRMZM2G044237_T01 (Zea mays), 3'ss of exon 8
gtaagttctgtatcaatctcattttccacacagtcctactcctctattgatccctttctcaaggcatgtat--gagcttcattataaccctttttc-ttacagGTTTTAACAACTGACGCTCAAGTCAGCAGTGATGTTTGGAGAGAAATGGTCCGAACATCAGTGAGTAGAAGCTTCAATCAAATAACA
                    || |||| |||  ||    ||| |      | ||| | |  |||||||||    || || ||    |   ||||    |||||||||| || || || |||||||||||||||||||| |||||||||||| |||| |  |||||||||||||| ||||| ||||| |||
------------------gtatgttcc-caccctcaggttccccc-----ttcctctattgaggcatgtagcaaagtttgatggccatttttttctactacagGTTTTGACCACAGATGCTCAAGTCAGCAGTGATGTCTGGAGAGAAATGATCCGGATGTCAGTGAGTAGAAGTTTCAACCAAATTACA
















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|218494800|gb|FG943469.1|FG943469
EST:     TGGCCAAAGGTTCTGGGATGATTCATCCAAATATGGCAACAATGCTTGGT                         GTTTTAACAACTGACGCTCAAGTCAGCAGTGATGTTTGGAGAGAAATGGTC
genomic: TGGCCAAAGGTTCTGGGATGATTCATCCAAATATGGCAACAATGCTTGGTgtaagttctg ... tttcttacagGTTTTAACAACTGACGCTCAAGTCAGCAGTGATGTTTGGAGAGAAATGGTC
EST: gi|29670993|gb|CB667268.1|CB667268
EST:     TGGCCAAAGGTTCTGGGATGATTCATCCAAATATGGCAACAATGCTTGGT                         GTTTTAACAACTGACGCTCAAGTCAGCAGTGATGTTTGGAGAGAAATGGTC
genomic: TGGCCAAAGGTTCTGGGATGATTCATCCAAATATGGCAACAATGCTTGGTgtaagttctg ... tttcttacagGTTTTAACAACTGACGCTCAAGTCAGCAGTGATGTTTGGAGAGAAATGGTC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attgatccctttctcaaggcatgtatgagcttcattataaccctttttcttacagGTTTTAACAACTGACGCTCAAGTCAGCAGTGATGTTTGGAGAGAAATGGTCCGAACATCAGTGAGTAGAAGCTTCAATCAAATAACA
                                  ttataac  putative branch site (score: 2)
                                        ccctttttcttac  CT-rich tract
                              ttcattataa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagttctgtatcaatctcattttccacacagtcctactcctctattgatccctttctcaaggcatgtatgagcttcattataaccctttttcttacagGTTTTAACAACTGACGCTCAAGTCAGCAGTGATGTTTGGAGAGAAATGGTCCGAACATCAGTGAGTAGAAGCTTCAATCAAATAACA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC