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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATGACTATCGCTTATTTTGTGGAGATCTGGGCAATGAAGTCAATGACGACGTCCTCTCAAAAGCTTTTTCACGGTTCCCCTCCTTCAACATGGCAAGGgtatggaaaagtttcgacatactctctacttccactccaagatcaaggacattaagctagctgggggttttgaaaatttacctgaggtagccttaactgt...

Basic information

species Oryza sativa
transcript LOC_Os08g45240.4
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os08g45240.4 (Oryza sativa), 5'ss of exon 2
lower sequence: GRMZM2G068255_T02 (Zea mays), 5'ss of exon 1
--ATGACTATCGCTTATTTTGTGGAGATCTGGGCAATGAAGTCAATGACGACGTCCTCTCAAAAGCTTTTTCACGGTTCCCCTCCTTCAACATGGCAAGGgtatggaaaagtttcgacatactctctacttccactccaagatcaaggacattaagctagctgggggtt--ttgaaaatttacctgaggtagccttaactgt-
  | ||||| ||  | || ||||||||||| ||||| ||||| ||||| || || ||||| ||||| ||||||||||| || |||||||||||||||||||||   ||  |        ||  |   |   |   |        ||    ||| | | | |      ||  |||  |  ||  ||||  |    |      | 
AGACGACTACCGGCTGTTCTGTGGAGATCTAGGCAACGAAGTTAATGATGATGTTCTCTCCAAAGCATTTTCACGGTTTCCATCCTTCAACATGGCAAGGgta---aacggcccatttttatccaaaaaagcttatttgtagcaaaacttattcaacgatccaattattgtttgccaggttctctgaaatttgttatgtaata

upper sequence: LOC_Os08g45240.4 (Oryza sativa), 5'ss of exon 2
lower sequence: GRMZM2G016106_T01 (Zea mays), 5'ss of exon 2
ATGACTATCGCTTATTTTGTGGAGATCTGGGCAATGAAGTCAATGACGACGTCCTCTCAAAAGCTTTTTCACGGTTCCCCTCCTTCAACATGGCAAGGgtatggaaaagtttcgacatactctctacttccactccaagatcaaggacattaagctagctgggggttttgaaaatttacc-tgaggtagccttaactgt
| ||||| ||  | || ||||||||||| ||||| ||||| ||||| || || || || ||||| || |||||||| || |||||||||||||||||||||   |    |||  |   |         |      ||| | |  |  ||  || | |  |   | | |  || |  ||   | |  |    |||   | 
ACGACTACCGGCTGTTCTGTGGAGATCTAGGCAACGAAGTTAATGATGATGTTCTATCCAAAGCATTCTCACGGTTTCCATCCTTCAACATGGCAAGGgtaaatatccctttttatccaaaaggcttatttgtagcaaaa-cttgttcaacaatccaattattgttatgcaatacctattgtcaaattcttttaggggc

upper sequence: LOC_Os08g45240.4 (Oryza sativa), 5'ss of exon 2
lower sequence: GRMZM2G068255_T01 (Zea mays), 5'ss of exon 2
ATGACTATCGCTTATTTTGTGGAGATCTGGGCAATGAAGTCAATGACGACGTCCTCTCAAAAGCTTTTTCACGGTTCCCCTCCTTCAACATGGCAAGGgtatggaaaagtttcgacatactctctacttccactccaagatcaaggacattaagctagctgggggtt--ttgaaaatttacctgaggtagccttaactgt-
| ||||| ||  | || ||||||||||| ||||| ||||| ||||| || || ||||| ||||| ||||||||||| || |||||||||||||||||||||   ||  |        ||  |   |   |   |        ||    ||| | | | |      ||  |||  |  ||  ||||  |    |      | 
ACGACTACCGGCTGTTCTGTGGAGATCTAGGCAACGAAGTTAATGATGATGTTCTCTCCAAAGCATTTTCACGGTTTCCATCCTTCAACATGGCAAGGgta---aacggcccatttttatccaaaaaagcttatttgtagcaaaacttattcaacgatccaattattgtttgccaggttctctgaaatttgttatgtaata

upper sequence: LOC_Os08g45240.4 (Oryza sativa), 5'ss of exon 2
lower sequence: GRMZM2G016106_T02 (Zea mays), 5'ss of exon 1
--ATGACTATCGCTTATTTTGTGGAGATCTGGGCAATGAAGTCAATGACGACGTCCTCTCAAAAGCTTTTTCACGGTTCCCCTCCTTCAACATGGCAAGGgtatggaaaagtttcgacatactctctacttccactccaagatcaaggacattaagctagctgggggttttgaaaatttacc-tgaggtagccttaactgt
  | ||||| ||  | || ||||||||||| ||||| ||||| ||||| || || || || ||||| || |||||||| || |||||||||||||||||||||   |    |||  |   |         |      ||| | |  |  ||  || | |  |   | | |  || |  ||   | |  |    |||   | 
AGACGACTACCGGCTGTTCTGTGGAGATCTAGGCAACGAAGTTAATGATGATGTTCTATCCAAAGCATTCTCACGGTTTCCATCCTTCAACATGGCAAGGgtaaatatccctttttatccaaaaggcttatttgtagcaaaa-cttgttcaacaatccaattattgttatgcaatacctattgtcaaattcttttaggggc

upper sequence: LOC_Os08g45240.4 (Oryza sativa), 5'ss of exon 2
lower sequence: Vv09s0018g01710.t01 (Vitis vinifera), 5'ss of exon 3
ATGACTATCGCTTATTTTGTGGAGATCTGGGCAATGAAGTCAATGACGACGTCCTCTCAAAAGCTTTTTCACGGTTCCCCTCCTTCAACATGGCAAGGgtatggaaaagtttcga-catactctctacttccactccaagatcaaggacattaa-gctagctgggggtt--ttgaaaatttacctgaggtagccttaactgt
|||| ||||| ||||||||||| ||||| |||||||| || || || || || || |||||||| |||||||| || || |||||||| ||||| || ||| |   |  ||||   ||   | | |||||    |     || | | ||  |||   ||| |   | ||  |||     ||        | || |   || |
ATGATTATCGTTTATTTTGTGGTGATCTTGGCAATGAGGTGAACGATGATGTTCTTTCAAAAGCATTTTCACGATTTCCTTCCTTCAATATGGCCAGAgtaagtttatatttccctcaagttttatactttttttt----attaggaactctaatattagatattgtttgcttggtgtattgttgttttttgcatatcctct

upper sequence: LOC_Os08g45240.4 (Oryza sativa), 5'ss of exon 2
lower sequence: Vv14s0036g00630.t01 (Vitis vinifera), 5'ss of exon 3
ATGACTATCGCTTATTTTGTGGAGATCTGGGCAATGAAGTCAATGACGACGTCCTCTCAAAAGCTTTTTCACGGTTCCCCTCCTTCAACATGGCAAGGgtatggaaaagtttcga-catactctctacttccactccaagatcaaggacattaagctagctgggggttttgaaaatttacctgaggtagccttaactgt---
|||| ||||| ||||||||||| ||||| |||||||| || ||||| || || || |||||||| |||||||| || || |||||||| ||||| |  ||| |      ||||   ||   ||| ||| |   ||  |  |  ||    ||||   ||| |     ||             |||| |    ||  |  |   
ATGATTATCGTTTATTTTGTGGTGATCTTGGCAATGAGGTGAATGATGATGTTCTTTCAAAAGCATTTTCACGATTTCCTTCCTTCAATATGGCTAAAgtaagtttctatttcattcaagttctttaccttttctttattaggaattctatta--ttagatatcatttgcttggtgcatggtgagct--ttttgcccattct

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|58599191|gb|CK009719.1|CK009719
EST:     ACGTCCTCTCAAAAGCTTTTTCACGGTTCCCCTCCTTCAACATGGCAAGG                         GTTGTTCGAGATAAGAGAACTGGCAAAACAAAAGGATATGGATTTGTGAG
genomic: ACGTCCTCTCAAAAGCTTTTTCACGGTTCCCCTCCTTCAACATGGCAAGGgtatggaaaa ... tttctttcagGTTGTTCGAGATAAGAGAACTGGCAAAACAAAAGGATATGGATTTGTGAG
EST: gi|88368173|gb|CI575055.1|CI575055
EST:     ACGTCCTCTCAAAAGCTTTTTCACGGTTCCCCTCCTTCAACATGGCAAGG                         GTTGTTCGAGATAAGAGAACTGGCAAAACAAAAGGATATGGATTTGTGAGC
genomic: ACGTCCTCTCAAAAGCTTTTTCACGGTTCCCCTCCTTCAACATGGCAAGGgtatggaaaa ... tttctttcagGTTGTTCGAGATAAGAGAACTGGCAAAACAAAAGGATATGGATTTGTGAGC
EST: gi|38475426|gb|CF959559.1|CF959559
EST:     ACGTCCTCTCAAAAGCTTTTTCACGGTTCCCCTCCTTCAACATGGCAAGG                         GTTGTTCGAGATAAGAGAACTGGCAAAACAAAAGGATATGGATTTGTGAGC
genomic: ACGTCCTCTCAAAAGCTTTTTCACGGTTCCCCTCCTTCAACATGGCAAGGgtatggaaaa ... tttctttcagGTTGTTCGAGATAAGAGAACTGGCAAAACAAAAGGATATGGATTTGTGAGC
EST: gi|33812852|gb|CF332314.1|CF332314
EST:     ACGTCCTCTCAAAAGCTTTTTCACGGTTCCCCTCCTTCAACATGGCAAGG                         GTTGTTCGAGATAAGAGAACTGGCAAAACAAAAGGATATGGATTTGTGAGC
genomic: ACGTCCTCTCAAAAGCTTTTTCACGGTTCCCCTCCTTCAACATGGCAAGGgtatggaaaa ... tttctttcagGTTGTTCGAGATAAGAGAACTGGCAAAACAAAAGGATATGGATTTGTGAGC
EST: gi|33684393|gb|CF312632.1|CF312632
EST:     ACGTCCTCTCAAAAGCTTTTTCACGGTTCCCCTCCTTCAACATGGCAAGG                         GTTGTTCGAGATAAGAGAACTGGCAAAACAAAAGGATATGGATTTGTGAGC
genomic: ACGTCCTCTCAAAAGCTTTTTCACGGTTCCCCTCCTTCAACATGGCAAGGgtatggaaaa ... tttctttcagGTTGTTCGAGATAAGAGAACTGGCAAAACAAAAGGATATGGATTTGTGAGC
EST: gi|29670352|gb|CB666627.1|CB666627
EST:     ACGTCCTCTCAAAAGCTTTTTCACGGTTCCCCTCCTTCAACATGGCAAGG                         GTTGTTCGAGATAAGAGAACTGGCAAAACAAAAGGATATGGATTTGTGAGC
genomic: ACGTCCTCTCAAAAGCTTTTTCACGGTTCCCCTCCTTCAACATGGCAAGGgtatggaaaa ... tttctttcagGTTGTTCGAGATAAGAGAACTGGCAAAACAAAAGGATATGGATTTGTGAGC
EST: gi|86829522|gb|CI286725.1|CI286725
EST:     ACGTCCTCTCAAAAGCTTTTTCACGGTTCCCCTCCTTCAACATGGCAAGG                         GTTGTTCGAGATAAGAGAACTGGCAAAACAAA
genomic: ACGTCCTCTCAAAAGCTTTTTCACGGTTCCCCTCCTTCAACATGGCAAGGgtatggaaaa ... tttctttcagGTTGTTCGAGATAAGAGAACTGGCAAAACAAA

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: 68 (upstream exon), 63 (downstream exon)
Score: 20

ATGACTATCGCTTATTTTGTGGAGATCTGGGCAATGAAGTCAATGACGACGTCCTCTCAAAAGCTTTTTCACGGTTCCCCTCCTTCAACATGGCAAGGgtatggaaaa ... tttctttcagGTTGTTCGAGATAAGAGAACTGGCAAAACAAAAGGATATGGATTTGTGAGCTTTTCAAACCCTACTGACCTTGCTGGAGCAATTAAAGAAATGAATG




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