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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttattgcatctttacttattaagatgaacttatagctttcctctactggattttcaatttaattttaacgacataacagtgctttatattttgttttttaaccttgaagGCCTACTCGGCAATTCCACCGCATGGGTTCTTTCCACCTCCTGTTGCTGCAAGTCCCCAGGCTCATCCCTACATGTGGGGAGCTCAG

Basic information

species Oryza sativa
transcript LOC_Os02g03580.3
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g03580.3 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G019106_T01 (Zea mays), 3'ss of exon 3
gttattgcat-----------ctttacttattaagatgaacttatagctttcctctactggattttca--atttaattttaacgacataacagtgctttatattttgttttttaaccttgaagGCCTACTCGGCAATTCCACCGCATGGGTTCTTTCCACCTCCTGTTGCTGCAAGTCCCCAGGCTCATCCCTACATGTGGGGAGCTCAG
|||||| |||           | ||||| |||| || | |   ||        |    |  |||||||  |    ||| |     | |   |  | ||||| | ||||     | | | | |||||||||| |||||||||||||||| |||||| || ||| | |||||||||| ||| ||||| ||||| ||||||||||| ||||||
gttattccatataaaacatgcccttactaattaggaaggaaacattttccatataccttctattttcatcaagcgattctcctttcctt-tatggatttatctcttgtcaaaaatcttggtagGCCTACTCAGCAATTCCACCGCATGCGTTCTTCCCCCCTACCGTTGCTGCAAATCCACAGGCCCATCCATACATGTGGGGGGCTCAG

upper sequence: LOC_Os02g03580.3 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G153144_T01 (Zea mays), 3'ss of exon 3
-----------gttattgcatctttacttattaagatgaacttatagctttcctctac--tggattttca--atttaattttaacgacataacagtgctttatattttgttttttaaccttgaagGCCTACTCGGCAATTCCACCGCATGGGTTCTTTCCACCTCCTGTTGCTGCAAGTCCCCAGGCTCATCCCTACATGTGGGGAGCTCAG
              | |      || || |||||||  |||  | |  |||| | |||  |  ||||| |  |   |||| |     | |   |  ||||||| | |||||    |   | | |||| |||   ||||||||||| ||||||||||| || ||| | |||||||||| ||| ||||| ||| | ||||||||||||||||||
gttattccatataaaatatgctcttgctaattaaga--aacaaacaagtttcatttaccttatatttttatcaagcaattctccttgcctt-tatggctttatctcttgttaaaaattttggtagGCATACCAAGCAATTCCACCACATGGGTTCTTCCCCCCTACCGTTGCTGCAAATCCACAGGCCCATTCATACATGTGGGGAGCTCAG

upper sequence: LOC_Os02g03580.3 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G164848_T01 (Zea mays), 3'ss of exon 1
gttattgcat-----------ctttacttattaagatgaacttatagctttcctctactggattttcaatttaat--tttaacgacataacagtgctttatattttgttttttaaccttgaagGCCTACTCGGCAATTCCACCGCATGGGTTCTTTCCACCTCCTGTTGCTGCAAGTCCCCAGGCTCATCCCTACATGTGGGGAGCTCAG
|||||| |||           | || || |||| || | |   ||       ||    |   ||||  ||  |    ||   |        |  | ||||| | ||||     | | | | |||||||||| ||||||||||||||||  ||||| || ||| | |||||| ||| ||| ||||| ||||| |||||||||    |||||
gttattccatataaaacatgcccttgctaattaggaaggaaacattttccatctaccttctgtttttcatcaagcgattctcctttcctttatggatttatctcttgtcaaaaatcttggtagGCCTACTCAGCAATTCCACCGCATGCATTCTTCCC-CCTACCGTTGCTACAAATCCACAGGCCCATCCATACATGTGGAAGCCTCAG

upper sequence: LOC_Os02g03580.3 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G387310_T01 (Zea mays), 3'ss of exon 2
gttattgcat-----------ctttacttattaagatgaacttatagctttcctctactggattttcaatttaat--tttaacgacataacagtgctttatattttgttttttaaccttgaagGCCTACTCGGCAATTCCACCGCATGGGTTCTTTCCACCTCCTGTTGCTGCAAGTCCCCAGGCTCATCCCTACATGTGGGGAGCTCAG
|||||| |||           | || || |||| || | |   ||       ||    |   ||||  ||  |    |||  |        |  | ||||| | ||||     | | | | |||||||||| |||||||||||||||| |||||| || |||   ||| |||||| ||| ||||| ||||| |||||||||||  |||||
gttattccatataaaacatgcccttgctaattaggaaggaaacattttccatctaccttctgtttttcatcaagcgattttcctttcctttatggatttatctcttgtcaaaaatcttggtagGCCTACTCAGCAATTCCACCGCATGCGTTCTTCCCCCCTATCGTTCCTGCAAATCCACAGGCCCATCCATACATGTGGGGGCCTCAG

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|29670500|gb|CB666775.1|CB666775
EST:     CTCCAGTTTACCCTGAATGGCCTGGTTTTCAG                         GCCTACTCGGCAATTCCACCGCATGGGTTCTTTCCACCTCCTGTTGCTGCA
genomic: CTCCAGTTTACCCTGAATGGCCTGGTTTTCAGgttattgcat ... aaccttgaagGCCTACTCGGCAATTCCACCGCATGGGTTCTTTCCACCTCCTGTTGCTGCA
EST: gi|29665042|gb|CB661317.1|CB661317
EST:     CTACATCTGGCACTACAGCTCCAGTTTACCCTGAATGGCCTGGTTTTCAG                         GCCTACTCGGCAATTCCACCGCATGGGTTCTTTCC-CCTCCTGTTGCTGCA
genomic: CTACATCTGGCACTACAGCTCCAGTTTACCCTGAATGGCCTGGTTTTCAGgttattgcat ... aaccttgaagGCCTACTCGGCAATTCCACCGCATGGGTTCTTTCCACCTCCTGTTGCTGCA
EST: gi|32948307|gb|BP184879.1|BP184879
EST:     CTACATCTGGCACTACAGCTCCAGTTTACCCTGAATGGCCTGGTTTTCAG                         GCCTACTCGGCAATTCCACCGCATGGGTTCTTTCCACCTCCTGTTGCTGCA
genomic: CTACATCTGGCACTACAGCTCCAGTTTACCCTGAATGGCCTGGTTTTCAGgttattgcat ... aaccttgaagGCCTACTCGGCAATTCCACCGCATGGGTTCTTTCCACCTCCTGTTGCTGCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

caatttaattttaacgacataacagtgctttatattttgttttttaaccttgaagGCCTACTCGGCAATTCCACCGCATGGGTTCTTTCCACCTCCTGTTGCTGCAAGTCCCCAGGCTCATCCCTACATGTGGGGAGCTCAG
                                         ttttaac  putative branch site (score: 2)
                                       tttttta  CT-rich tract
                            tttatattttgttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttattgcatctttacttattaagatgaacttatagctttcctctactggattttcaatttaattttaacgacataacagtgctttatattttgttttttaaccttgaagGCCTACTCGGCAATTCCACCGCATGGGTTCTTTCCACCTCCTGTTGCTGCAAGTCCCCAGGCTCATCCCTACATGTGGGGAGCTCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTCA