Skip to another splice site:
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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaacactagcccttttgtagtatttcagtgtgatgctaattcaacatttgagagcattatttgagcaaatatttcttgttacagGTTGTACAATCTCACCAGTGTATGTTATCATTCTCTTTACCTTCCACTTCTCTATGTGACTTTCCTAGCAGACTTTTTCCAG

Basic information

species Oryza sativa
transcript LOC_Os03g54920.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g54920.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G123732_T01 (Zea mays), 3'ss of exon 3
gtaaacact-agcccttttgtagtatttcagtgtgatgctaattcaacatttgagagcattatttgagcaaatatttcttgttacagGTTGTACAATCTCACCAGTGTATGTTATCATTCTCTTTACCTTCCACTTCTCTATGTGACTTTCCTAGCAGACTTTTTCCAG
||| | ||  | | || |||| |||||| |            |||| | |   ||| |  |||||||  |      | ||| |  ||||| || |||||||| |  ||||| |||||||| ||||||||||| || || |||||||||||| |||| ||||||||||||
gtacatacagaacactcttgtggtatttta------------ttcaccgtc-aagaactatatttgatgatgacccttttgctgtagGTTATATAATCTCACAATCGTATGCTATCATTCGCTTTACCTTCCCCTCCTATATGTGACTTTCTTAGCGGACTTTTTCCAG

upper sequence: LOC_Os03g54920.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G086497_T02 (Zea mays), 3'ss of exon 2
----gtaaacactagcccttttgtagtat-ttcagtgtg-atgctaattca---acatttgagagcattatttgagca-aatatttcttgttacagGTTGTACAATCTCACCAGTGTATGTTATCATTCTCTTTACCTTCCACTTCTCTATGTGACTTTCCTAGCAGACTTTTTCCAG
     || | |  |    |||  |  | | ||||| ||  ||| ||| | |   || ||  |||||| | |||||  |  |    | ||| |  ||||| || |||||||| |  ||||| |||||||||||||||||||| || || |||||||||||| |||||||||| ||||||
gtacatacagaacactattttcttgatttcttcagagtttatggtaacttattaaccttcaagagcaatctttgatgatgaccccttttgctgtagGTTATATAATCTCACAACCGTATGCTATCATTCTCTTTACCTTCCCCTCCTATATGTGACTTTCTTAGCAGACTTCTTCCAG
















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|86490061|gb|CI132694.1|CI132694
EST:     TCACTGTTTGGATGTTTCCTTGTTGCAACTGGAGCTGGATTTGGTTTATG                         GTTGTACAATCTCACCAGTGTATGTTATCATTCTCTTTACCTTCCACTTCT
genomic: TCACTGTTTGGATGTTTCCTTGTTGCAACTGGAGCTGGATTTGGTTTATGgtaaacacta ... cttgttacagGTTGTACAATCTCACCAGTGTATGTTATCATTCTCTTTACCTTCCACTTCT
EST: gi|86835747|gb|CI348204.1|CI348204
EST:     TCACT-TTTGGATGTTTCCTTGTTGCAACTGGAGCTGGATTTGGTTTATG                         GTTGTACAATCTCACCAGTGTATGTTATCATTCTCTTTACCTTCCACTTCT
genomic: TCACTGTTTGGATGTTTCCTTGTTGCAACTGGAGCTGGATTTGGTTTATGgtaaacacta ... cttgttacagGTTGTACAATCTCACCAGTGTATGTTATCATTCTCTTTACCTTCCACTTCT
EST: gi|88543335|gb|CI473334.1|CI473334
EST:     TCACTGTTTGGATGTTTCCTTGTTGCAACTGGAGCTGGATTTGGTTTATG                         GTTGTACAATCTCACCAGTGTATGTTATCATTCTCTTTACCTTCCACTTCT
genomic: TCACTGTTTGGATGTTTCCTTGTTGCAACTGGAGCTGGATTTGGTTTATGgtaaacacta ... cttgttacagGTTGTACAATCTCACCAGTGTATGTTATCATTCTCTTTACCTTCCACTTCT
EST: gi|88202487|gb|CI200842.1|CI200842
EST:     TCACTGTTTGGATGTTTCCTTGTTGCAACTGGAGCTGGATTTGGTTTATG                         GTTGTACAATCTCACCAGTGTATGTTATCATTCTCTTTACCTTCCACTTCT
genomic: TCACTGTTTGGATGTTTCCTTGTTGCAACTGGAGCTGGATTTGGTTTATGgtaaacacta ... cttgttacagGTTGTACAATCTCACCAGTGTATGTTATCATTCTCTTTACCTTCCACTTCT
EST: gi|88554329|gb|CI484502.1|CI484502
EST:     TGTTTCCTTGTTGCAACTGGAGCTGGATTTGGTTTATG                         GTTGTACAATCTCACCAGTGTATGTTATCATTCTCTTTACCTTCCACTTCT
genomic: TGTTTCCTTGTTGCAACTGGAGCTGGATTTGGTTTATGgtaaacacta ... cttgttacagGTTGTACAATCTCACCAGTGTATGTTATCATTCTCTTTACCTTCCACTTCT
EST: gi|86542850|gb|CI183056.1|CI183056
EST:     TCACTGTTTGGATGTTTCCTTGTTGCAACTGGAGCTGGATTTGGTTTATG                         GTTGTACAATCTCACCAGTGTATGTTATCATTCTCTTTACCTTCCACTTCT
genomic: TCACTGTTTGGATGTTTCCTTGTTGCAACTGGAGCTGGATTTGGTTTATGgtaaacacta ... cttgttacagGTTGTACAATCTCACCAGTGTATGTTATCATTCTCTTTACCTTCCACTTCT
EST: gi|87008567|gb|CI315025.1|CI315025
EST:     TCACTGTTTGGATGTTTCCTTGTTGCAAC-GGAGCT-GATTTGGTTTATG                         GTTGTACAATCTCACCAGTGTATG-TATCATTCTCTTTACCTTCCACTTCT
genomic: TCACTGTTTGGATGTTTCCTTGTTGCAACTGGAGCTGGATTTGGTTTATGgtaaacacta ... cttgttacagGTTGTACAATCTCACCAGTGTATGTTATCATTCTCTTTACCTTCCACTTCT
EST: gi|86892806|gb|CI312118.1|CI312118
EST:     TCACTGTTTGGATGTTTCCTTGTTGCAACTGGAGCTGGATTTGGTTTATG                         GTTGTACAATCTCACCAGTGTATGTTATCATTCTCTTTACCTTCCACTTCT
genomic: TCACTGTTTGGATGTTTCCTTGTTGCAACTGGAGCTGGATTTGGTTTATGgtaaacacta ... cttgttacagGTTGTACAATCTCACCAGTGTATGTTATCATTCTCTTTACCTTCCACTTCT
EST: gi|55438101|gb|CV732344.1|CV732344
EST:     TCACTGTTTGGATGTTTCCTTGTTGCAACTGGAGCTGGATTTGGTTTATG                         GTTGTACAATCTCACCAGTGTATGTTATCATTCTCTTTACCTTCCACTTCT
genomic: TCACTGTTTGGATGTTTCCTTGTTGCAACTGGAGCTGGATTTGGTTTATGgtaaacacta ... cttgttacagGTTGTACAATCTCACCAGTGTATGTTATCATTCTCTTTACCTTCCACTTCT
EST: gi|88962251|gb|CI097404.1|CI097404
EST:     TCACTGTTTGGATGTTTCCTTGTTGCAACTGGAGCTGGATTTGGTTTATG                         GTTGTACAATCTCACCAGTGTATGTTATCATTCTCTTTACCTTCCACTTCT
genomic: TCACTGTTTGGATGTTTCCTTGTTGCAACTGGAGCTGGATTTGGTTTATGgtaaacacta ... cttgttacagGTTGTACAATCTCACCAGTGTATGTTATCATTCTCTTTACCTTCCACTTCT
EST: gi|86543258|gb|CI183464.1|CI183464
EST:     CACTGTTTTGGATGTTTCCTTGTTGCAACTGGAGCTGGATTTGGTTTATG                         GTTGTACAATCTCACCAGTGTATGTTATCATTCTCTTTACCTTCCACTTCT
genomic: CACTG-TTTGGATGTTTCCTTGTTGCAACTGGAGCTGGATTTGGTTTATGgtaaacacta ... cttgttacagGTTGTACAATCTCACCAGTGTATGTTATCATTCTCTTTACCTTCCACTTCT
EST: gi|88559941|gb|CI490561.1|CI490561
EST:     TTTGGATGTTTCCTTGTTGCAACTGGAGCTGGATTTGGTTTATG                         GTTGTACAATCTCACCAGTGTATG-TANTCATTCTCTTTACCTTCCACTTC
genomic: TTTGGATGTTTCCTTGTTGCAACTGGAGCTGGATTTGGTTTATGgtaaacacta ... cttgttacagGTTGTACAATCTCACCAGTGTATGTTA-TCATTCTCTTTACCTTCCACTTC
EST: gi|86863609|gb|CI345283.1|CI345283
EST:     TCACTGTTTGGATGTTTCCTTGTTGCAACTGGAGCTGGATTTGGTTTATG                         GTTGTACAATCTCACCAGTGTATGTTATCATTCTCTTTACCTTCCACTTCT
genomic: TCACTGTTTGGATGTTTCCTTGTTGCAACTGGAGCTGGATTTGGTTTATGgtaaacacta ... cttgttacagGTTGTACAATCTCACCAGTGTATGTTATCATTCTCTTTACCTTCCACTTCT
EST: gi|88522143|gb|CI449880.1|CI449880
EST:     TCACTGTTTGGATGTTTCCTTGTTGCAACTGGAGCTGGATTTGGTTTATG                         GTTGTACAATCTCACCAGTGTATGTTATCATTCTCTTTACCTTCCACTTCT
genomic: TCACTGTTTGGATGTTTCCTTGTTGCAACTGGAGCTGGATTTGGTTTATGgtaaacacta ... cttgttacagGTTGTACAATCTCACCAGTGTATGTTATCATTCTCTTTACCTTCCACTTCT

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: 72 (upstream exon), 66 (downstream exon)
Score: 42

AACCAGCATATTATAACTATGTCTGTGCGATGTTACTACTGAATGGCATATCACTGTTTGGATGTTTCCTTGTTGCAACTGGAGCTGGATTTGGTTTATGgtaaacacta ... cttgttacagGTTGTACAATCTCACCAGTGTATGTTATCATTCTCTTTACCTTCCACTTCTCTATGTGACTTTCCTAGCAGACTTTTTCCAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtgatgctaattcaacatttgagagcattatttgagcaaatatttcttgttacagGTTGTACAATCTCACCAGTGTATGTTATCATTCTCTTTACCTTCCACTTCTCTATGTGACTTTCCTAGCAGACTTTTTCCAG
    tgctaat  putative branch site (score: 42)
                                          tttcttgtt  putative PPT
                                     aaatatttcttgtta  TA-rich tract