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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGACATCCAAGGCAATACATTTGCTTTTGGAGTGATTTTGCTGGAGATCATCAGTGGACGGCTTCCTTATTGCAAGGACAAAGGCTATTTGATTGACTGGgtgaggcattctactctttctctatctcattgtgacaaagaagtaaatattttagaaattgactctgaagtctgctcaagaggaccagagcctagttcca...

Basic information

species Oryza sativa
transcript LOC_Os04g58700.2
intron # 12
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os04g58700.1 (Oryza sativa), 5'ss of exon 12
lower sequence: GRMZM2G119759_T04 (Zea mays), 5'ss of exon 10
AGACATCCAAGGCAATACATTTGCTTTTGGAGTGATTTTGCTGGAGATCATCAGTGGACGGCTTCCTTATTGCAAGGACAAAGGCTATTTGATTGACTGGgtgaggcattctactctttctctatctcattgtgacaaagaagtaaatattttagaaattgactctgaagtctgctcaagaggaccagagcctagttcca
 || ||||| | ||| || || ||||| ||||||||||| |||||||||||||| || |||||||| || |||||||| |||||||||||| | ||||||||||| |  ||   || |  |  | || |  |   | |  || |   | |    |||  |     |   |  |||                         
TGATATCCAGGCCAACACCTTCGCTTTCGGAGTGATTTTACTGGAGATCATCAGCGGGCGGCTTCCATACTGCAAGGATAAAGGCTATTTGGTCGACTGGgtgagccgatcg--tcatcttggacctgaa-gcagctataaaatgtctgtcgctgaagct--tctttgtgcatgcag-----------------------
















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|87020795|gb|CI269512.1|CI269512
EST:     TCAGTGGACGGCTTCCTTATTGCAAGGACAAAGGCTATTTGATTGACTGG                         GCCATCAAGTATCTGCAGCAGACAGAGGAGATCGGTAAGCTTGTCGATCCT
genomic: TCAGTGGACGGCTTCCTTATTGCAAGGACAAAGGCTATTTGATTGACTGGgtgaggcatt ... cattgttcagGCCATCAAGTATCTGCAGCAGACAGAGGAGATCGGTAAGCTTGTCGATCCT
EST: gi|86479202|gb|CI121835.1|CI121835
EST:     TCAGTGGACGGCTTCCTTATTGCAAGGACAAAGGCTATTTGATTGACTGG                         GCCATCAAGTATCTGCAGCAGACAGAGGAGATCGGTAAGCTTGTCGATCCT
genomic: TCAGTGGACGGCTTCCTTATTGCAAGGACAAAGGCTATTTGATTGACTGGgtgaggcatt ... cattgttcagGCCATCAAGTATCTGCAGCAGACAGAGGAGATCGGTAAGCTTGTCGATCCT
EST: gi|86834224|gb|CI343984.1|CI343984
EST:     TCAGTGGACGGCTTCCTTATTGCAAGGACAAAGGCTATTTTATTGACTGG                         GCCATCAAGTATCTGCAGCAGACAGAGGAGATCGGTAAGCTTGTCGATCCT
genomic: TCAGTGGACGGCTTCCTTATTGCAAGGACAAAGGCTATTTGATTGACTGGgtgaggcatt ... cattgttcagGCCATCAAGTATCTGCAGCAGACAGAGGAGATCGGTAAGCTTGTCGATCCT
EST: gi|86493569|gb|CI136202.1|CI136202
EST:     TCAGTGGACGGCTTCCTTATTGCAAGGACAAAGGCTATTTGATTGACTGG                         GCCATCAAGTATCTGCAGCAGACAGAGGAGATCGGTAAGCTTGTCGATCCT
genomic: TCAGTGGACGGCTTCCTTATTGCAAGGACAAAGGCTATTTGATTGACTGGgtgaggcatt ... cattgttcagGCCATCAAGTATCTGCAGCAGACAGAGGAGATCGGTAAGCTTGTCGATCCT
EST: gi|86418514|gb|CI032723.1|CI032723
EST:     TCAGTGGACGGCTTCCTTATTGCAAGGACAAAGGCTATTTGATTGACTGG                         GCCATCAAGTATCTGCAGCAGACAGAGGAGATCGGTAAGCTTGTCGATCCT
genomic: TCAGTGGACGGCTTCCTTATTGCAAGGACAAAGGCTATTTGATTGACTGGgtgaggcatt ... cattgttcagGCCATCAAGTATCTGCAGCAGACAGAGGAGATCGGTAAGCTTGTCGATCCT
EST: gi|7212756|gb|AU066074.2|AU066074
EST:     TCAGTGGACGGCTTCCTTATTGCAAGGACAAAGGCTATTTGATTGACTGG                         GCCATCAAGTATCTGCAGCAGACAGAGGAGATCGGTAAGCTTGTCGATCCT
genomic: TCAGTGGACGGCTTCCTTATTGCAAGGACAAAGGCTATTTGATTGACTGGgtgaggcatt ... cattgttcagGCCATCAAGTATCTGCAGCAGACAGAGGAGATCGGTAAGCTTGTCGATCCT
EST: gi|89192799|gb|CI050097.1|CI050097
EST:     TCAGTGGACGGCTTCCTTATTGCAAGGACAAAGGCTATTTGATTGACTGG                         GCCATCAAGTATCTGCAGCAGACAGAGGAGATCGGTAAGCTTGTCGATCCT
genomic: TCAGTGGACGGCTTCCTTATTGCAAGGACAAAGGCTATTTGATTGACTGGgtgaggcatt ... cattgttcagGCCATCAAGTATCTGCAGCAGACAGAGGAGATCGGTAAGCTTGTCGATCCT
EST: gi|86901194|gb|CI297428.1|CI297428
EST:     TCAGTGGACGGCTTCCTTATTGCAAGGACAAAGGCTATTTGATTGACTGG                         GCCATCAAGTATCTGCAGCAGACAGAGGAGATCGGTAAGCTTGTCGATCCT
genomic: TCAGTGGACGGCTTCCTTATTGCAAGGACAAAGGCTATTTGATTGACTGGgtgaggcatt ... cattgttcagGCCATCAAGTATCTGCAGCAGACAGAGGAGATCGGTAAGCTTGTCGATCCT
EST: gi|88270634|gb|CI385892.1|CI385892
EST:     TGATTGACTGG                         GCCATCAAGTATCTGCAGCAGACAGAGGAGATCGGTAAGCTTGTCGATCCT
genomic: TGATTGACTGGgtgaggcatt ... cattgttcagGCCATCAAGTATCTGCAGCAGACAGAGGAGATCGGTAAGCTTGTCGATCCT
EST: gi|88991542|gb|CI019720.1|CI019720
EST:     TCAGTGGACGGCTTCCTTATTGCAAGGACCAAGGCTATTTGATTGACTGG                         GCCATCAAGTATCTGCAGCAGACAGAGGAGATCGGTAAGCTTGTCGATCCT
genomic: TCAGTGGACGGCTTCCTTATTGCAAGGACAAAGGCTATTTGATTGACTGGgtgaggcatt ... cattgttcagGCCATCAAGTATCTGCAGCAGACAGAGGAGATCGGTAAGCTTGTCGATCCT
EST: gi|88907127|gb|CI089921.1|CI089921
EST:     TCAGTGGACGGCTTCCTTATTGCAAGGACAAAGGCTATTTGATTGACTGG                         GCCATCAAGTATCTGCAGCAGACAGAGGAGATCGGTAAGCTTGTCGATCCT
genomic: TCAGTGGACGGCTTCCTTATTGCAAGGACAAAGGCTATTTGATTGACTGGgtgaggcatt ... cattgttcagGCCATCAAGTATCTGCAGCAGACAGAGGAGATCGGTAAGCTTGTCGATCCT

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
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---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGACATCCAAGGCAATACATTTGCTTTTGGAGTGATTTTGCTGGAGATCATCAGTGGACGGCTTCCTTATTGCAAGGACAAAGGCTATTTGATTGACTGGgtgaggcattctactctttctctatctcattgtgacaaagaagtaaatattttagaaattgactctgaagtctgctcaagaggaccagagcctagttcca

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