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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGCAGCTCCCCCCCAAAAACCCTAGCTCAGGCTTCGGCACCGCCTCTCCCCCCCTCGCCTTCCTCCCCCCACCAGGCGCCTCCAAGATGAAGCTCGTCAGgtaatccgcggctcccgcttcgctctccccttcccagatttgtttttttttctcctttttttgtggttaactggttcgtttcccgtgcgatttctcccgccgaattcgggtgcag

Basic information

species Oryza sativa
transcript LOC_Os02g37430.1
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g37430.1 (Oryza sativa), 5'ss of exon 1
lower sequence: GRMZM2G416061_T01 (Zea mays), 5'ss of exon 1
-GGCAGCTCCCCCCCAAAAACCCTAGCTCAGGCTTCGGCACCGCCTCTCCCCCCCTCGCCTTCCTCCCCCCACCAGGCGCCTCCAAGATGAAGCTCGTCAGgtaatcc-gcggctccc-gcttcgctctccccttcccagatttgttttttttt-ctcctttttttgtggttaactggttcgtttcccgtgcgatttctcccgccgaattcggg----tgcag
 | |  ||| ||| |    |  |      |||   | || || ||        ||    |||   | |||||| | ||||||||||||||||||||||||||||| || ||  | ||| | ||| | |    |  ||   ||| ||||   | | ||  ||  ||||  |  |  |    |     | |||||  || |  ||| | | | | |    | |||
TGTCTCCTCGCCCGCTCCGAATCAGCTCGAGGTAGCAGCTCCCCCCGCAAAAACCCTAGCTTTACCTCCCCAC-AAGCGCCTCCAAGATGAAGCTCGTCAGgtaagccagcatccccctgtttctcccctttccccctccattcgtttcagtctgctgattcgtttggtgcaattttcgcccgaatcggtgcggattttggcgcgggaattgcgcttttacag
















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|4880073|gb|AU064372.1|AU064372
EST:     CTCCCCCCACCAGGCGCCTCCAAGATGAAGCTCGTCAG                         GTTCTTGATGAAGCTGAACAACGAGACGGTAACGATCGAGCTCAAGAACGG
genomic: CTCCCCCCACCAGGCGCCTCCAAGATGAAGCTCGTCAGgtaatccgcg ... tcgggtgcagGTTCTTGATGAAGCTGAACAACGAGACGGTAACGATCGAGCTCAAGAACGG
EST: gi|8956556|gb|BE230471.1|BE230471
EST:     CCCCTCGCCTTCCTCCCCCCACCAGGCGCCTCCAAGATGAAGCTCGTCAG                         GTTCTTGATGAAGCTGAACAACGAGACGGTAACGATCGAGCTCAAGAACGG
genomic: CCCCTCGCCTTCCTCCCCCCACCAGGCGCCTCCAAGATGAAGCTCGTCAGgtaatccgcg ... tcgggtgcagGTTCTTGATGAAGCTGAACAACGAGACGGTAACGATCGAGCTCAAGAACGG
EST: gi|58686818|gb|CK075505.1|CK075505
EST:     CCCCTCGCCTTCCTCCCCCCACCAGGCGCCTCCAAGATGAAGCTCGTCAG                         GTTCTTGATGAAGCTGAACAACGAGACGGTAACGATCGAGCTCAAGAACGG
genomic: CCCCTCGCCTTCCTCCCCCCACCAGGCGCCTCCAAGATGAAGCTCGTCAGgtaatccgcg ... tcgggtgcagGTTCTTGATGAAGCTGAACAACGAGACGGTAACGATCGAGCTCAAGAACGG
EST: gi|88211519|gb|CI211159.1|CI211159
EST:     CAGGCGCCTCCAAGATGAAGCTCGTCAG                         GTTCTTGATGAAGCTGAACAACGAGACGGTAACGATCGAGCTCAAGAACGG
genomic: CAGGCGCCTCCAAGATGAAGCTCGTCAGgtaatccgcg ... tcgggtgcagGTTCTTGATGAAGCTGAACAACGAGACGGTAACGATCGAGCTCAAGAACGG
EST: gi|12622937|gb|AU173150.1|AU173150
EST:     NNNNTCGCCTTCCTCCCCCCACCAGGCGCCTCCAAGATGAAGCTCGTCAG                         GTTCTTGATGAAGCTGAACAACGAGACGGTAACGATCGAGCTCAAGAACGG
genomic: CCCCTCGCCTTCCTCCCCCCACCAGGCGCCTCCAAGATGAAGCTCGTCAGgtaatccgcg ... tcgggtgcagGTTCTTGATGAAGCTGAACAACGAGACGGTAACGATCGAGCTCAAGAACGG
EST: gi|88832522|gb|CI019463.1|CI019463
EST:     TCCAAGATGAAGCTCGTCAG                         GTTCTTGATGAAGCTGAACAACGAGACGGTAACGATCGAGCTCAAGAACGG
genomic: TCCAAGATGAAGCTCGTCAGgtaatccgcg ... tcgggtgcagGTTCTTGATGAAGCTGAACAACGAGACGGTAACGATCGAGCTCAAGAACGG
EST: gi|8956550|gb|BE230465.1|BE230465
EST:     CCCCTCGCCTTCCTCCCCCCACCAGGCGCCTCCAAGATGAAGCTCGTCAG                         GTTCTTGATGAAGCTGAACAACGAGACGGTAACGATCGAGCTCAAGAACGG
genomic: CCCCTCGCCTTCCTCCCCCCACCAGGCGCCTCCAAGATGAAGCTCGTCAGgtaatccgcg ... tcgggtgcagGTTCTTGATGAAGCTGAACAACGAGACGGTAACGATCGAGCTCAAGAACGG
EST: gi|11610356|gb|AU166032.1|AU166032
EST:     GATGAAGCTCGTCAG                         GTTCTTGATGAAGCTGAACAACGAGACGGTAACGATCGAGCTCAAGAACGG
genomic: GATGAAGCTCGTCAGgtaatccgcg ... tcgggtgcagGTTCTTGATGAAGCTGAACAACGAGACGGTAACGATCGAGCTCAAGAACGG
EST: gi|87013601|gb|CI267302.1|CI267302
EST:     CCAGGCGCCTCCAAGATGAAGCTCGTCAG                         GTTCTTGATGAAGCTGAACAACGAGACGGTAACGATCGAGCTCAAGAACGG
genomic: CCAGGCGCCTCCAAGATGAAGCTCGTCAGgtaatccgcg ... tcgggtgcagGTTCTTGATGAAGCTGAACAACGAGACGGTAACGATCGAGCTCAAGAACGG
EST: gi|58695967|gb|CK084654.1|CK084654
EST:     CCCTCGCGCTTCCTCCCCCCACCAGGCGCCTCCAAGATGAAGCTCGTCAG                         GTTCTTGATGAAGCTGAACAACGAGACGGTAACGATCGAGCTCAAGAACGG
genomic: CCCTCGC-CTTCCTCCCCCCACCAGGCGCCTCCAAGATGAAGCTCGTCAGgtaatccgcg ... tcgggtgcagGTTCTTGATGAAGCTGAACAACGAGACGGTAACGATCGAGCTCAAGAACGG
EST: gi|86423420|gb|CI062181.1|CI062181
EST:     TCGCCTTCCTCCCCCCACCAGGCGCCTCCAAGATGAAGCTCGTCAG                         GTTCTTGATGAAGCTGAACAACGAGACGGTAACGATCGAGCTCAAGAACGG
genomic: TCGCCTTCCTCCCCCCACCAGGCGCCTCCAAGATGAAGCTCGTCAGgtaatccgcg ... tcgggtgcagGTTCTTGATGAAGCTGAACAACGAGACGGTAACGATCGAGCTCAAGAACGG
EST: gi|88743395|gb|CI766903.1|CI766903
EST:     NNNNTCGCCTTCCTCCCCCCACCAGGCGCCTCCAAGATGAAGCTCGTCAG                         GTTCTTGATGAAGCTGAACAACGAGACGGTAACGATCGAGCTCAAGAACGG
genomic: CCCCTCGCCTTCCTCCCCCCACCAGGCGCCTCCAAGATGAAGCTCGTCAGgtaatccgcg ... tcgggtgcagGTTCTTGATGAAGCTGAACAACGAGACGGTAACGATCGAGCTCAAGAACGG
EST: gi|29689672|gb|CB685947.1|CB685947
EST:     NNNTCGCCTTCCTCCCCCCACCACGGCGCCTCCAAGATGAAGCTCGTCAG                         GTTCTTGATGAAGCTGAACAACGAGACGGTAACGATCGAGCTCAAGAACGG
genomic: CCCTCGCCTTCCTCCCCCCACCA-GGCGCCTCCAAGATGAAGCTCGTCAGgtaatccgcg ... tcgggtgcagGTTCTTGATGAAGCTGAACAACGAGACGGTAACGATCGAGCTCAAGAACGG
EST: gi|87013532|gb|CI267233.1|CI267233
EST:     CCAGGCGCCTCCAAGATGAAGCTCGTCAG                         GTTCTTGATGAAGCTGAACAACGAGACGGTAACGATCGAGCTCAAGAACGG
genomic: CCAGGCGCCTCCAAGATGAAGCTCGTCAGgtaatccgcg ... tcgggtgcagGTTCTTGATGAAGCTGAACAACGAGACGGTAACGATCGAGCTCAAGAACGG
EST: gi|3762685|gb|AU029437.1|AU029437
EST:     TCGCCTTCCTCCCCCCACCAGGCGCCTCCAAGATGAAGCTCNTCAG                         NTTCTTGATGAAGCTGAACAACGAGACGGTAACGATCGAGCTCAAGAACGG
genomic: TCGCCTTCCTCCCCCCACCAGGCGCCTCCAAGATGAAGCTCGTCAGgtaatccgcg ... tcgggtgcagGTTCTTGATGAAGCTGAACAACGAGACGGTAACGATCGAGCTCAAGAACGG
EST: gi|86824350|gb|CI262903.1|CI262903
EST:     AAGCTCGTCAG                         GTTCTTGATGAAGCTGAACAACGAGACGGTAACGATCGAGCTCAAGAACGG
genomic: AAGCTCGTCAGgtaatccgcg ... tcgggtgcagGTTCTTGATGAAGCTGAACAACGAGACGGTAACGATCGAGCTCAAGAACGG
EST: gi|38474190|gb|CF958322.1|CF958322
EST:     CCCCTCGCCTTCCTCCCCCCACCAGGCGCCTCCAAGATGAAGCTCGTCAG                         GTTCTTGATGAAGCTGAACAACGAGACGGTAACGATCGAGCTCAAGAACGG
genomic: CCCCTCGCCTTCCTCCCCCCACCAGGCGCCTCCAAGATGAAGCTCGTCAGgtaatccgcg ... tcgggtgcagGTTCTTGATGAAGCTGAACAACGAGACGGTAACGATCGAGCTCAAGAACGG
EST: gi|87013602|gb|CI267303.1|CI267303
EST:     CAGGCGCCTCCAAGATGAAGCTCGTCAG                         GTTCTTGATGAAGCTGAACAACGAGACGGTAACGATCGAGCTCAAGAACGG
genomic: CAGGCGCCTCCAAGATGAAGCTCGTCAGgtaatccgcg ... tcgggtgcagGTTCTTGATGAAGCTGAACAACGAGACGGTAACGATCGAGCTCAAGAACGG
EST: gi|86593782|gb|CI266462.1|CI266462
EST:     ACCAGGCGCCTCCAAGATGAAGCTCGTCAG                         GTTCTTGATGAAGCTGAACAACGAGACGGTAACGATCGAGCTCAAGAACGG
genomic: ACCAGGCGCCTCCAAGATGAAGCTCGTCAGgtaatccgcg ... tcgggtgcagGTTCTTGATGAAGCTGAACAACGAGACGGTAACGATCGAGCTCAAGAACGG
EST: gi|8857519|gb|AU094837.1|AU094837
EST:     CTTCCTCCCCCCACCAGGCGCCTCCAAGATGAAGCTCGTCAG                         GTTCTTGATGAAGCTGAACAACGAGACGGTAACGATCGAGCTCAAGAACGG
genomic: CTTCCTCCCCCCACCAGGCGCCTCCAAGATGAAGCTCGTCAGgtaatccgcg ... tcgggtgcagGTTCTTGATGAAGCTGAACAACGAGACGGTAACGATCGAGCTCAAGAACGG
EST: gi|25802948|gb|CA758909.1|CA758909
EST:     CCCCTCGCCTTCCTCCCCCCACCAGGCGCCTCCAAGATGAAGCTCGTCAG                         GTTCTTGATGAAGCTGAACAACGAGACGGTAACGATCGAGCTCAAGAACGG
genomic: CCCCTCGCCTTCCTCCCCCCACCAGGCGCCTCCAAGATGAAGCTCGTCAGgtaatccgcg ... tcgggtgcagGTTCTTGATGAAGCTGAACAACGAGACGGTAACGATCGAGCTCAAGAACGG
EST: gi|2442320|gb|C74091.1|C74091
EST:     NNNNTCGCCTNCCTCCCCCCACCAGGCGCCTCCAAGATGAAGCTCGTCAG                         GTTCTTGATGAAGCTGAACAACGAGACGGTAACGATCGAGCTCAAGAACGG
genomic: CCCCTCGCCTTCCTCCCCCCACCAGGCGCCTCCAAGATGAAGCTCGTCAGgtaatccgcg ... tcgggtgcagGTTCTTGATGAAGCTGAACAACGAGACGGTAACGATCGAGCTCAAGAACGG

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 1 RNA-Seqlibrary.


Block sizes: 63 (upstream exon), 74 (downstream exon)
Score: 39

GGCAGCTCCCCCCCAAAAACCCTAGCTCAGGCTTCGGCACCGCCTCTCCCCCCCTCGCCTTCCTCCCCCCACCAGGCGCCTCCAAGATGAAGCTCGTCAGgtaatccgcg ... tcgggtgcagGTTCTTGATGAAGCTGAACAACGAGACGGTAACGATCGAGCTCAAGAACGGCACCACCGTCCATGGCACCATCACTG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGCAGCTCCCCCCCAAAAACCCTAGCTCAGGCTTCGGCACCGCCTCTCCCCCCCTCGCCTTCCTCCCCCCACCAGGCGCCTCCAAGATGAAGCTCGTCAGgtaatccgcggctcccgcttcgctctccccttcccagatttgtttttttttctcctttttttgtggttaactggttcgtttcccgtgcgatttctcccgccgaattcgggtgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGC