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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atgggaattctgtgcttatttcttccatctacgaagagtgtgaaggttgaaatcgtcagcattaaactgatgtctgttctaccatttaacttgttttcagGTTGATCTTGGACTCGCGGTTCAACGGGCATGTGAGAGCCAGGCAGACCCTCTGAAATTTTTGTATCCTTTAGAATCTGGCATAAAGGAGAAGATTGAGT

Basic information

species Oryza sativa
transcript LOC_Os09g27420.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os09g27420.2 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM5G824944_T01 (Zea mays), 3'ss of exon 3
atgggaattctgtgcttatttcttccatct------acgaagagtgtgaaggttgaaatcgtcagcattaaactgatgtctgttctaccatttaacttgttttcagGTTGATCTTGGACTCGCGGTTCAACGGGCATGTGAGAGCCAGGCAGACCCTCTGAAATTTTTGTATCCTTTAGAATCTGGCATAAAGGAGAAGATTGAGT
      | ||| |  ||||||||||  |        |  || ||||||||       |  |  || ||| |||      || ||  |||||||||||| |||||||||||| |||||||| || |||||||| ||||| || ||||||||||| |||||||| ||||||||||| || |||||| |||||||||||||||||||||
------actctttatttatttcttcagtgctagaacaaaaacagtgtgaataacatgagtgcaagaatttaacctgaccctattgcaccatttaacttattttcagGTTGAGCTTGGACTTGCTGTTCAACGAGCATGCGAAAGCCAGGCAGAACCTCTGAAGTTTTTGTATCCCTTGGAATCTAGCATAAAGGAGAAGATTGAGT
















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|87010814|gb|CI312506.1|CI312506
EST:     GTAAAGGAGCG                         GTTGATCTTGGACTCGCGGTTCAACGNGCATGTGAGAGCCAGGCAGACCCT
genomic: GTAAAGGAGCGgttagttttc ... ttgttttcagGTTGATCTTGGACTCGCGGTTCAACGGGCATGTGAGAGCCAGGCAGACCCT
EST: gi|218480711|gb|FG957829.1|FG957829
EST:     CTTTTGATGCTGTTGTCTGCACTCACCATGCGCATGGTGGTAAAGGAGCG                         GTTGATCTTGGACTCGCGGTTCAACGGGCATGTGAGAGCCAGGCAGACCCT
genomic: CTTTTGATGCTGTTGTCTGCACTCACCATGCGCATGGTGGTAAAGGAGCGgttagttttc ... ttgttttcagGTTGATCTTGGACTCGCGGTTCAACGGGCATGTGAGAGCCAGGCAGACCCT
EST: gi|58666858|gb|CK055544.1|CK055544
EST:     CTTTTGATGCTGTTGTCTGCACTCACCATGCGCATGGTGGTAAAGGAGCG                         GTTGATCTTGGACTCGCGGTTCAACGGGCATGTGAGAGCCAGGCAGACCCT
genomic: CTTTTGATGCTGTTGTCTGCACTCACCATGCGCATGGTGGTAAAGGAGCGgttagttttc ... ttgttttcagGTTGATCTTGGACTCGCGGTTCAACGGGCATGTGAGAGCCAGGCAGACCCT
EST: gi|66914737|gb|CX101585.1|CX101585
EST:     CTTTTGATGCTGTTGTCTGCACTCACCATGCGCATGGTGGTAAAGGAGCG                         GTTGATCTTGGACTCGCGGTTCAACGGGCATGTGAGAGCCAGGCANGACCC
genomic: CTTTTGATGCTGTTGTCTGCACTCACCATGCGCATGGTGGTAAAGGAGCGgttagttttc ... ttgttttcagGTTGATCTTGGACTCGCGGTTCAACGGGCATGTGAGAGCCAGGCA-GACCC
EST: gi|87014954|gb|CI271553.1|CI271553
EST:     GTTGTCTGCACTCACCATGCGCATGGTGGTAAAGGAGCG                         GTTGATCTTGGACTCGCGGTTCAACGGGCATGTGAGAGCCAGGCAGACCCT
genomic: GTTGTCTGCACTCACCATGCGCATGGTGGTAAAGGAGCGgttagttttc ... ttgttttcagGTTGATCTTGGACTCGCGGTTCAACGGGCATGTGAGAGCCAGGCAGACCCT
EST: gi|86513763|gb|CI156396.1|CI156396
EST:     CTTTTGATGCTGTTGTCTGCACTCACCATGCGCATGGTGGTAAAGGAGCG                         GTCGATCTTGGACTCGCGGTTCAACGGGCATGTGAGAGCCAGGCAGACCCT
genomic: CTTTTGATGCTGTTGTCTGCACTCACCATGCGCATGGTGGTAAAGGAGCGgttagttttc ... ttgttttcagGTTGATCTTGGACTCGCGGTTCAACGGGCATGTGAGAGCCAGGCAGACCCT
EST: gi|86517622|gb|CI157828.1|CI157828
EST:     TGCGCATGGTGGTAAAGGAGCG                         GTTGATCTTGGACTCGCGGTTCAACGGGCATGTGAGAGCCAGGCAGACCCT
genomic: TGCGCATGGTGGTAAAGGAGCGgttagttttc ... ttgttttcagGTTGATCTTGGACTCGCGGTTCAACGGGCATGTGAGAGCCAGGCAGACCCT
EST: gi|58689176|gb|CK077863.1|CK077863
EST:     CTTTTGATGCTGTTGTCTGCACTCACCATGCGCATGGTGGTAAAGGAGCG                         GTTGATCTTGGACTCGCGGTTCAACGGGCATGTGAGAGCCAGGCAGACCCT
genomic: CTTTTGATGCTGTTGTCTGCACTCACCATGCGCATGGTGGTAAAGGAGCGgttagttttc ... ttgttttcagGTTGATCTTGGACTCGCGGTTCAACGGGCATGTGAGAGCCAGGCAGACCCT
EST: gi|86436750|gb|CI118472.1|CI118472
EST:     GATGCTGTTGTCTGCACTCACAATGCGCATGGTGGTAAAGGAGCG                         GTTGATCTTGGACTCGCGGTTCAACGGGCATGTGAGAGCCAGGCAGACCCT
genomic: GATGCTGTTGTCTGCACTCACCATGCGCATGGTGGTAAAGGAGCGgttagttttc ... ttgttttcagGTTGATCTTGGACTCGCGGTTCAACGGGCATGTGAGAGCCAGGCAGACCCT
EST: gi|90398849|gb|AJ608757.1|AJ608757
EST:     CTTTTGATGCTGTTGTCTGCACTCACCATGCGCATGGTGGTAAAGGAGCG                         GTTGATCTTGGACTCGCGGTTCAACAGGCAT-TGAGAGCCAGGCAGACCCT
genomic: CTTTTGATGCTGTTGTCTGCACTCACCATGCGCATGGTGGTAAAGGAGCGgttagttttc ... ttgttttcagGTTGATCTTGGACTCGCGGTTCAACGGGCATGTGAGAGCCAGGCAGACCCT
EST: gi|58691862|gb|CK080549.1|CK080549
EST:     CTTTTGATGCTGTTGTCTGCACTCACCATGCGCATGGTGGTAAAGGAGCG                         GTTGATCTTGGACTCGCGGTTCAACGGGCATGTGAGAG
genomic: CTTTTGATGCTGTTGTCTGCACTCACCATGCGCATGGTGGTAAAGGAGCGgttagttttc ... ttgttttcagGTTGATCTTGGACTCGCGGTTCAACGGGCATGTGAGAG
EST: gi|86517665|gb|CI157871.1|CI157871
EST:     GCTGTTGTCTGCACTCACCATGCGCATGGTGGTAAAGGAGCG                         GTTGATCTTGGACTCGCGGTTCAACGGGCATGTGAGAGCCAGGCAGACCCT
genomic: GCTGTTGTCTGCACTCACCATGCGCATGGTGGTAAAGGAGCGgttagttttc ... ttgttttcagGTTGATCTTGGACTCGCGGTTCAACGGGCATGTGAGAGCCAGGCAGACCCT
EST: gi|87040006|gb|CI194628.1|CI194628
EST:     ATGGTGGTAAAGGAGCG                         CTTGATCTTGGACTCGCGGTTCAACGGGCATGTGAGAGCCAGGCAGACCCT
genomic: ATGGTGGTAAAGGAGCGgttagttttc ... ttgttttcagGTTGATCTTGGACTCGCGGTTCAACGGGCATGTGAGAGCCAGGCAGACCCT
EST: gi|87014014|gb|CI273204.1|CI273204
EST:     CATGGTGGTAAAGGAGCG                         GTTGATCTTGGACTCGCGGTTCAACGGGCATGTGAGAGCCAGGCAGACCCT
genomic: CATGGTGGTAAAGGAGCGgttagttttc ... ttgttttcagGTTGATCTTGGACTCGCGGTTCAACGGGCATGTGAGAGCCAGGCAGACCCT
EST: gi|29685663|gb|CB681938.1|CB681938
EST:     CTTTTGATGCTGTTGTCTGCACTCACCATGCGCATGGTGGTAAAGGAGCG                         GTTGATCTTGGACTCGCGGTTCAACGGGCATGTGAGAGCCAGGCAGACCCT
genomic: CTTTTGATGCTGTTGTCTGCACTCACCATGCGCATGGTGGTAAAGGAGCGgttagttttc ... ttgttttcagGTTGATCTTGGACTCGCGGTTCAACGGGCATGTGAGAGCCAGGCAGACCCT
EST: gi|62936912|gb|AJ634725.1|AJ634725
EST:     CTTTTGATGCTGTTGTCTGCACTCACCATGCGCATGGTGGTAAAGGAGCG                         GTTGATCTTGGACTCGCGGTTCAACAGGCATGTGAGAGCCAGGCAGACCCT
genomic: CTTTTGATGCTGTTGTCTGCACTCACCATGCGCATGGTGGTAAAGGAGCGgttagttttc ... ttgttttcagGTTGATCTTGGACTCGCGGTTCAACGGGCATGTGAGAGCCAGGCAGACCCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gttgaaatcgtcagcattaaactgatgtctgttctaccatttaacttgttttcagGTTGATCTTGGACTCGCGGTTCAACGGGCATGTGAGAGCCAGGCAGACCCTCTGAAATTTTTGTATCCTTTAGAATCTGGCATAAAGGAGAAGATTGAGT
                                      atttaac  putative branch site (score: 3)
                                            cttgttttc  CT-rich tract
                                      atttaacttgtttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atgggaattctgtgcttatttcttccatctacgaagagtgtgaaggttgaaatcgtcagcattaaactgatgtctgttctaccatttaacttgttttcagGTTGATCTTGGACTCGCGGTTCAACGGGCATGTGAGAGCCAGGCAGACCCTCTGAAATTTTTGTATCCTTTAGAATCTGGCATAAAGGAGAAGATTGAGT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
- - - - - - tgcttat
- - - - - - - - - - - - -catctac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -actgatg