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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaactacaggtgcagatccttaatcatgttataatgttatcgcattttggcatgcacctaaaagttctacctttctgcatgattcacatctctgaagATTGGTGAGTCAGCTGGCCCTGAATGCAAAGCAGCACTACAAGAAACAACAAAACTTGTTGACGGACAACTTCAGTCTGGTCGCAATGCAGTTAAACAAC

Basic information

species Oryza sativa
transcript LOC_Os10g36760.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os10g36760.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G031572_T01 (Zea mays), 3'ss of exon 4
gtaactacaggtgcagatccttaatcatgttataa-tgttatcgcattttggcatgcacctaaa-------agttctacctttctgcatgattcacatctctgaagATTGGTGAGTCAGCTGGCCCTGAATGCAAAGCAGCACTACAAGAAACAACAAAACTTGTTGACGGACAACTTCAGTCTGGTCGCAATGCAGTTAAACAAC
||   | |||| ||||||| | | | || |  |||   |||  |||||   |  | ||||| ||       |||||||| | | || |||||| ||||||||| |||||||    || ||||| ||||||||||| |||||||| ||||||| ||||  ||||||||| ||||| ||||||||||| || ||  | |||||  |  
gtttgtgcaggagcagatcttgatttatttattaaacattaaagcattcaagtctacacctgaactcctgaagttctacttctgtgtatgatttacatctctgtagATTGGGATCTCTGCTGGTCCTGAATGCAAGGCAGCACTTCAAGAAATAACAGGACTTGTTGATGGACAGCTTCAGTCTGGCCGTAACTCGGTTAAGGAGT

upper sequence: LOC_Os10g36760.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA16G24270.1 (Glycine max), 3'ss of exon 5
------------------------------------gtaactacaggtgcagatccttaatcatgttataatgttatcgcattttggcatgcacctaaaagttctacctttctgcatgattcacatctctga-----agATTGGTGAGTCAGCTGGCCCTGAATGCAAAGCAGCACTACAAGAAACAACAAAACTTGTTGACGGACAACTTCAGTCTGGTCGCAATGCAGTTAAACAAC
                                    ||   | |   |  |||| || ||  | ||   || |||  |   | ||    | ||   |||  ||  |  |   ||  ||| |   |||| | |     |||||||||||||||| ||  ||||||| ||||||| | |||||||||| ||  ||||  ||||     |||||    |   | | || | | | ||   | 
gtgaacatagttatttttgtttcacatacatcttttgttttttctattctagatgctaaaataagtc--aaagttcccttttattcaatttcagtcaaattttgaatttagttgagtgagttctatctttcacatgcagATTGGTGAGTCAGCAGGTGCTGAATGTAAAGCAGTATTACAAGAAACTACTCAACTCATTGAGCACAAACTTGCAACCAATGGAAAGGAACTAAAGGCAT
















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|29667887|gb|CB664162.1|CB664162
EST:     GTTCAGGAGTTGTTCTTTCTGTTTACAACTATACTGACTTTGACAAACAG                         ATTGGTGAGTCAGCTGGCCCTGAATGC
genomic: GTTCAGGAGTTGTTCTTTCTGTTTACAACTATACTGACTTTGACAAACAGgtaactacag ... atctctgaagATTGGTGAGTCAGCTGGCCCTGAATGC
EST: gi|5056122|gb|AU075501.1|AU075501
EST:     GTTCAGGAGTTGTTCTTTCTGTTTACAACTATACTGACTTTGACAAACAG                         ATTGGTGAGTCAGCTGGCCCTGAATGCAAAGCAGCACTACAAGAAACAACA
genomic: GTTCAGGAGTTGTTCTTTCTGTTTACAACTATACTGACTTTGACAAACAGgtaactacag ... atctctgaagATTGGTGAGTCAGCTGGCCCTGAATGCAAAGCAGCACTACAAGAAACAACA
EST: gi|29678499|gb|CB674774.1|CB674774
EST:     GTTCAGGAGTTGTTCTTTCTGTTTACAACTATACTGACTTTGACAAACAG                         ATTGGTGAGTCAGCTGGCCCTGAATGCAAAGCAGCACTAC
genomic: GTTCAGGAGTTGTTCTTTCTGTTTACAACTATACTGACTTTGACAAACAGgtaactacag ... atctctgaagATTGGTGAGTCAGCTGGCCCTGAATGCAAAGCAGCACTAC
EST: gi|163918133|gb|EG713999.1|EG713999
EST:     TTGACAAACAG                         ATTGGTGAGTCAGCTGGCCCTGAATGCAAAGCAGCACTAGAAGAAACAACA
genomic: TTGACAAACAGgtaactacag ... atctctgaagATTGGTGAGTCAGCTGGCCCTGAATGCAAAGCAGCACTACAAGAAACAACA
EST: gi|33796974|gb|CF324350.1|CF324350
EST:     GTTCAGGAGTTGTTCTTTCTGTTTACAACTATACTGACTTTGACAAACAG                         ATTGGTGAGTCAGCTGGCCCTGAATGCAAAGCAGCACTACAAGAAACAACA
genomic: GTTCAGGAGTTGTTCTTTCTGTTTACAACTATACTGACTTTGACAAACAGgtaactacag ... atctctgaagATTGGTGAGTCAGCTGGCCCTGAATGCAAAGCAGCACTACAAGAAACAACA
EST: gi|33794179|gb|CF322980.1|CF322980
EST:     GTTCAGGAGTTGTTCTTTCTGTTTACAACTATACTGACTTTGACAAACAG                         ATTGGTGAGTCAGCTGGCCCTGAATGCAAAGCAGCACTACAAGAAACAACA
genomic: GTTCAGGAGTTGTTCTTTCTGTTTACAACTATACTGACTTTGACAAACAGgtaactacag ... atctctgaagATTGGTGAGTCAGCTGGCCCTGAATGCAAAGCAGCACTACAAGAAACAACA

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: 75 (upstream exon), 75 (downstream exon)
Score: 26

TGCTTGGTTCAGATTGAAGTTCCCTCACTTGACATGTGGAAGTCTTGCGAGTTCAGGAGTTGTTCTTTCTGTTTACAACTATACTGACTTTGACAAACAGgtaactacag ... atctctgaagATTGGTGAGTCAGCTGGCCCTGAATGCAAAGCAGCACTACAAGAAACAACAAAACTTGTTGACGGACAACTTCAGTCTGGTCGCAATGCAGTTAAACAAC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cattttggcatgcacctaaaagttctacctttctgcatgattcacatctctgaagATTGGTGAGTCAGCTGGCCCTGAATGCAAAGCAGCACTACAAGAAACAACAAAACTTGTTGACGGACAACTTCAGTCTGGTCGCAATGCAGTTAAACAAC
             acctaaa  putative branch site (score: 26)
                                            catctct  putative PPT
                taaaagtt  TA-rich tract