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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttgatcatcataaattcataacttttcttttcactcgactatttaacttctagggtccttacaaaattgaatttcccatcagGTACTGGTTTTTCTGTGTGTTAAATCAGTTCCAGTGCCACATGTTCAACCTGAAGAACGGTTTCTAGTGGGTCGCATTGGTCCAAAAGAGTACAGGCTAT

Basic information

species Oryza sativa
transcript LOC_Os02g49760.3
intron # 9
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|113930916|gb|DQ884017.1|DQ884017
EST:     GCCATCTTCTCCCACTTCGTCACTAATCTGCCTGCATTTCACCAG                         GTACTGGTTTTTCTGTGTGTT
genomic: GCCATCTTCTCCCACTTCGTCACTAATCTGCCTGCATTTCACCAGgttgatcatc ... ttcccatcagGTACTGGTTTTTCTGTGTGTT
EST: gi|29645721|gb|CB650728.1|CB650728
EST:     TTCCAGCCATCTTCTCCCACTTCGTCACTAATCTGCCTGCATTTCACCAG                         GTACTGGTTTTTCTGTGTGTTAAATCAGTTCCAGTGCCACATGTTCAACCT
genomic: TTCCAGCCATCTTCTCCCACTTCGTCACTAATCTGCCTGCATTTCACCAGgttgatcatc ... ttcccatcagGTACTGGTTTTTCTGTGTGTTAAATCAGTTCCAGTGCCACATGTTCAACCT
EST: gi|113930915|gb|DQ884016.1|DQ884016
EST:     GCCATCTTCTCCCACTTCGTCACTAATCTGCCTGCATTTCACCAG                         GTACTGGTTTTTCTGTGTGTTA
genomic: GCCATCTTCTCCCACTTCGTCACTAATCTGCCTGCATTTCACCAGgttgatcatc ... ttcccatcagGTACTGGTTTTTCTGTGTGTTA
EST: gi|38476805|gb|CF960938.1|CF960938
EST:     TTCCAGCCATCTTCTCCCACTTCGTCACTAATCTGCCTGCATTTCACCAG                         GTACTGGTTTTTCTGTGTGTTAAATCAGTTCCAGTGCCACATGTTCAACCT
genomic: TTCCAGCCATCTTCTCCCACTTCGTCACTAATCTGCCTGCATTTCACCAGgttgatcatc ... ttcccatcagGTACTGGTTTTTCTGTGTGTTAAATCAGTTCCAGTGCCACATGTTCAACCT
EST: gi|58678713|gb|CK067400.1|CK067400
EST:     TTCCAGCCATCTTCTCCCACTTCGTCACTAATCTGCCTGCATTTCACCAG                         GTACTGGTTTTTCTGTGTGTTAAATCAGTTCCAGTGCCACATGTTCAACCT
genomic: TTCCAGCCATCTTCTCCCACTTCGTCACTAATCTGCCTGCATTTCACCAGgttgatcatc ... ttcccatcagGTACTGGTTTTTCTGTGTGTTAAATCAGTTCCAGTGCCACATGTTCAACCT
EST: gi|58588951|gb|CF987259.1|CF987259
EST:     -TCCAGCCATCTTCTCCCACTTCGTCACTAATCTGCCTGCATTTCACCAG                         GTAGTGGTTTTTCTGTGTGTTAAATCAGTTCCAGTGCCACATGTTCAACCT
genomic: TTCCAGCCATCTTCTCCCACTTCGTCACTAATCTGCCTGCATTTCACCAGgttgatcatc ... ttcccatcagGTACTGGTTTTTCTGTGTGTTAAATCAGTTCCAGTGCCACATGTTCAACCT
EST: gi|58690775|gb|CK079462.1|CK079462
EST:     TTCCAGCCATCTTCTCCCACTTCGTCACTAATCTGCCTGCATTTCACCAG                         GTACTGGTTTTTCTGTGTGTTAAATCAGTTCCAGTGCCACATGTTCAACCT
genomic: TTCCAGCCATCTTCTCCCACTTCGTCACTAATCTGCCTGCATTTCACCAGgttgatcatc ... ttcccatcagGTACTGGTTTTTCTGTGTGTTAAATCAGTTCCAGTGCCACATGTTCAACCT
EST: gi|38478671|gb|CF962804.1|CF962804
EST:     TCTTCTCCCACTTCGTCACTAATCTGCCTGCATTTCACCAG                         GTACTGGTTTTTCTGTGTGTTAAATCAGTTGCCAGTGCCACATGTTCAACC
genomic: TCTTCTCCCACTTCGTCACTAATCTGCCTGCATTTCACCAGgttgatcatc ... ttcccatcagGTACTGGTTTTTCTGTGTGTTAAATCAGTT-CCAGTGCCACATGTTCAACC
EST: gi|113930917|gb|DQ884018.1|DQ884018
EST:     TTCCAGCCATCTTCTCCCACTTCGTCACTAATCTGCCTGCATTTCACCAG                         GTACTGGTTTTTCTGTG
genomic: TTCCAGCCATCTTCTCCCACTTCGTCACTAATCTGCCTGCATTTCACCAGgttgatcatc ... ttcccatcagGTACTGGTTTTTCTGTG
EST: gi|29626477|gb|CB631488.1|CB631488
EST:     TTCCAGCCATCTTCTCCCACTTCGTCACTAATCTGCCTGCATTTCACCAG                         GTACTGGTTTTTCTGTGTGTTAAATCAGTTCCAGTGCCACATGTTCAACCT
genomic: TTCCAGCCATCTTCTCCCACTTCGTCACTAATCTGCCTGCATTTCACCAGgttgatcatc ... ttcccatcagGTACTGGTTTTTCTGTGTGTTAAATCAGTTCCAGTGCCACATGTTCAACCT
EST: gi|58610060|gb|CK038093.1|CK038093
EST:     TTCCAGCCATCTTCTCCCACTTCGTCACTAATCTGCCTGCATTTCACCAG                         GTACTGGTTTTTCTGTGTGTTAAATCAGTTCCAGTGCCACATGTTCAACCT
genomic: TTCCAGCCATCTTCTCCCACTTCGTCACTAATCTGCCTGCATTTCACCAGgttgatcatc ... ttcccatcagGTACTGGTTTTTCTGTGTGTTAAATCAGTTCCAGTGCCACATGTTCAACCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttttcactcgactatttaacttctagggtccttacaaaattgaatttcccatcagGTACTGGTTTTTCTGTGTGTTAAATCAGTTCCAGTGCCACATGTTCAACCTGAAGAACGGTTTCTAGTGGGTCGCATTGGTCCAAAAGAGTACAGGCTAT
                            tccttac  putative branch site (score: 2)
                                            tttcccatc  putative PPT
                               ttacaaaattgaattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttgatcatcataaattcataacttttcttttcactcgactatttaacttctagggtccttacaaaattgaatttcccatcagGTACTGGTTTTTCTGTGTGTTAAATCAGTTCCAGTGCCACATGTTCAACCTGAAGAACGGTTTCTAGTGGGTCGCATTGGTCCAAAAGAGTACAGGCTAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAC