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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aataaaacatttaatttgttttgtcttctgcttttacttttgcatgaactttcttatcatttttttgtcacaacaaatatctgctgcttttgctttccagGTTTCACCCTTCTTGCATTGGAATGACTATTAAAGATGCAAAAAAACTAGAGCATTTTTTCTGCCAGAGCTGTACTGCGGAAAATGGAAAGATGGCTGAG

Basic information

species Oryza sativa
transcript LOC_Os07g08880.2
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os07g08880.2 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G097726_T02 (Zea mays), 3'ss of exon 3
aataaaacatttaatttgttttgtct-tctgcttttacttttgcatgaactttcttatcatttttttgtcacaacaaatatctgctgcttttgctttccagGTTTCACCCTTCTTGCATTGGAATGACTATTAAAGATGCAAAAAAACTAGAGCATTTTTTCTGCCAGAGCTGTACTGCGGAAAATGGAAAGATGGCTGAG
|     |  |     ||| || ||   |  |||  |   | | ||   ||||| |   | |||     |   |  | |  ||   |    |    || ||||||||||||| |||||||||| ||||| || ||||| ||||| ||||| ||||||||||||||||||| |||||| || |||||||| ||||||| ||||
atctttatctgagcattgattggttcatgggctcatggctattcagtcactttgt-gccctttgagactgttagtatacttcctataacctcctctttcagGTTTCACCCTGCTTGCATTGGGATGACAATCAAAGAAGCAAAGAAACTCGAGCATTTTTTCTGCCAGACCTGTACAGCTGAAAATGGTAAGATGGTTGAG
















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|218504563|gb|FG952376.1|FG952376
EST:     CCATACAATCCTGATGACCTTATGATCCAATGTGAGGAATGCTCTGATTG                         GTTTCACCCTTCTTGCATTGGAATGACTATTAAAGATGCNNNNNNNCTAGA
genomic: CCATACAATCCTGATGACCTTATGATCCAATGTGAGGAATGCTCTGATTGgtgagtaatg ... tgctttccagGTTTCACCCTTCTTGCATTGGAATGACTATTAAAGATGCAAAAAAACTAGA
EST: gi|3462559|gb|AF074797.1|AF074797
EST:     CATACAATCCTGATGACCTTATGATCCAATGTTGAGGAATGCTCTGATTG                         GTTTCACCCTTCTTGCATTGGAATGACTATTAAAGATGCNAAAAAACTANA
genomic: CATACAATCCTGATGACCTTATGATCCAATGT-GAGGAATGCTCTGATTGgtgagtaatg ... tgctttccagGTTTCACCCTTCTTGCATTGGAATGACTATTAAAGATGCAAAAAAACTAGA
EST: gi|86261244|gb|CI014311.1|CI014311
EST:     CCATACAATCCTGATGACCTTATGATCCAATGTGAGGAATGCTCTGATTG                         GTTTCACCCTTCTTGCATTGGAATGACTATTAAAGATGCNNNNNNNCTAGA
genomic: CCATACAATCCTGATGACCTTATGATCCAATGTGAGGAATGCTCTGATTGgtgagtaatg ... tgctttccagGTTTCACCCTTCTTGCATTGGAATGACTATTAAAGATGCAAAAAAACTAGA
EST: gi|218497932|gb|FG957265.1|FG957265
EST:     CCATACAATCCTGATGACCTTATGATCCAATGTGAGGAATGCTCTGATTG                         GTTTCACCCTTCTTGCATTGGAATGACTATTAAAGATGCAAAAAA-CTAGA
genomic: CCATACAATCCTGATGACCTTATGATCCAATGTGAGGAATGCTCTGATTGgtgagtaatg ... tgctttccagGTTTCACCCTTCTTGCATTGGAATGACTATTAAAGATGCAAAAAAACTAGA
EST: gi|88201730|gb|CI202085.1|CI202085
EST:     CATACAATCCTGATGACCTTATGATCCAATGTGAGGAATGCTCTGATTG                         GTTTCACCCTTCTTGCATTGGAATGACTATTAAAGATGCNNNNNNNCTAGA
genomic: CATACAATCCTGATGACCTTATGATCCAATGTGAGGAATGCTCTGATTGgtgagtaatg ... tgctttccagGTTTCACCCTTCTTGCATTGGAATGACTATTAAAGATGCAAAAAAACTAGA
EST: gi|86498011|gb|CI140644.1|CI140644
EST:     CCATACAATCCTGATGACCTTATGATCCAATGTGAGGAATGCTCTGATTG                         GTTTCACCCTTCTTGCATTGGAATGACTATTAAAGATGCNNNNNNNCTAGA
genomic: CCATACAATCCTGATGACCTTATGATCCAATGTGAGGAATGCTCTGATTGgtgagtaatg ... tgctttccagGTTTCACCCTTCTTGCATTGGAATGACTATTAAAGATGCAAAAAAACTAGA
EST: gi|29686487|gb|CB682762.1|CB682762
EST:     CCATACAATCCTGATGACCTTATGATCCAATGTGAGGAATGCTCTGATTG                         GTTTCACCCTTCTTGCATTGGAATGACTATTAAAGATGCNNNNNNNCTAGA
genomic: CCATACAATCCTGATGACCTTATGATCCAATGTGAGGAATGCTCTGATTGgtgagtaatg ... tgctttccagGTTTCACCCTTCTTGCATTGGAATGACTATTAAAGATGCAAAAAAACTAGA
EST: gi|88964512|gb|CI055208.1|CI055208
EST:     GAGGAATGCTCTGATTG                         GTTTCACCCTTCTTGCATTGGAATGACTATTAAAGATGCCAAAAAACTAGA
genomic: GAGGAATGCTCTGATTGgtgagtaatg ... tgctttccagGTTTCACCCTTCTTGCATTGGAATGACTATTAAAGATGCAAAAAAACTAGA
EST: gi|38471848|gb|CF955979.1|CF955979
EST:     CCATACAATCCTGATGACCTTATGATCCAATGTGAGGAATGCTCTGATTG                         GTTTCACCCTTTTTGCAT
genomic: CCATACAATCCTGATGACCTTATGATCCAATGTGAGGAATGCTCTGATTGgtgagtaatg ... tgctttccagGTTTCACCCTTCTTGCAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gaactttcttatcatttttttgtcacaacaaatatctgctgcttttgctttccagGTTTCACCCTTCTTGCATTGGAATGACTATTAAAGATGCAAAAAAACTAGAGCATTTTTTCTGCCAGAGCTGTACTGCGGAAAATGGAAAGATGGCTGAG
                                      ctgcttttgctttcc  CT-rich tract
     ttcttatcattttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aataaaacatttaatttgttttgtcttctgcttttacttttgcatgaactttcttatcatttttttgtcacaacaaatatctgctgcttttgctttccagGTTTCACCCTTCTTGCATTGGAATGACTATTAAAGATGCAAAAAAACTAGAGCATTTTTTCTGCCAGAGCTGTACTGCGGAAAATGGAAAGATGGCTGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG