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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtactgtatttttgtagttcacaaattacaagtagtgaagtcattaactcatttttcctttttttttcccttttatgtattctacttttttctcttggcagATTGTTCCTATGAAATACAATCCAAGAGATGTGGATTCAATTAAGGCTGTCATGGCCAAATCCAATGTGGTCATTAACCTAATAG

Basic information

species Oryza sativa
transcript LOC_Os02g57180.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g57180.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G143651_T01 (Zea mays), 3'ss of exon 4
gtactgtatttttgtagttcacaaattaca-agtagtgaagtcattaactcatttttcctttttttttcccttttatgtattctacttttttctcttggcagATTGTTCCTATGAAATACAATCCAAGAGATGTGGATTCAATTAAGGCTGTCATGGCCAAATCCAATGTGGTCATTAACCTAATAG
                         | | | ||||   ||||   | |||   |||    |||   |    ||||||  || ||  ||||  ||  ||||||||||| || ||||||||| |||| |||||||| ||||||||||||||||| |||||||| || |||||||| |||||||| ||||
------------------------gtgaaacagtaagcaagtagattactatatttagtatttaaatcattttttattcatcct--ttttggcttctggcagATTGTGCCCATGAAATACCATCCGAGAGATGTTGATTCAATTAAGGCTGTTATGGCCAAGTCAAATGTGGTTATTAACCTCATAG
















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|58603608|gb|CK014136.1|CK014136
EST:     GTTCTGAGGATTGTCACCGACACCTGAAGTTGATGGGTGACCTGGGTCAG                         ATTGTTCCTATGAAATACAATCCAAGAGATGTGGATTCAATTAAGGCTGTC
genomic: GTTCTGAGGATTGTCACCGACACCTGAAGTTGATGGGTGACCTGGGTCAGgtactgtatt ... ctcttggcagATTGTTCCTATGAAATACAATCCAAGAGATGTGGATTCAATTAAGGCTGTC
EST: gi|58690755|gb|CK079442.1|CK079442
EST:     GTTCTGAGGATTGTCACCGACACCTGAAGTTGATGGGTGACCTGGGTCAG                         ATTGTTCCTATGAAATACAATCCAAGAGATGTGGATTCAATTAAGGCTGTC
genomic: GTTCTGAGGATTGTCACCGACACCTGAAGTTGATGGGTGACCTGGGTCAGgtactgtatt ... ctcttggcagATTGTTCCTATGAAATACAATCCAAGAGATGTGGATTCAATTAAGGCTGTC
EST: gi|38565625|gb|CK085078.1|CK085078
EST:     GTTCTGAGGATTGTCACCGACACCTGAAGTTGATGGGTGACCTGGGTCAG                         ATTGTTCCTATGAAATACAACCCAAGAGATGTGGATTCAATTAAGGCTGTC
genomic: GTTCTGAGGATTGTCACCGACACCTGAAGTTGATGGGTGACCTGGGTCAGgtactgtatt ... ctcttggcagATTGTTCCTATGAAATACAATCCAAGAGATGTGGATTCAATTAAGGCTGTC
EST: gi|29673108|gb|CB669383.1|CB669383
EST:     GTTCTGAGGATTGTCACCGACACCTGAAGTTGATGGGTGACCTGGGTCAG                         ATTGTTCCTATGAAATACAATCCAAGAGATGTGGATTCAATTAAGGCTGTC
genomic: GTTCTGAGGATTGTCACCGACACCTGAAGTTGATGGGTGACCTGGGTCAGgtactgtatt ... ctcttggcagATTGTTCCTATGAAATACAATCCAAGAGATGTGGATTCAATTAAGGCTGTC
EST: gi|29671358|gb|CB667633.1|CB667633
EST:     GTTCTGAGGATTGTCACCGACACCTGAAGTTGATGGGTGACCTGGGTCAG                         ATTGTTCCTATGAAATACAATCCAAGAGATGTGGATTCAATTAAGGCTGTC
genomic: GTTCTGAGGATTGTCACCGACACCTGAAGTTGATGGGTGACCTGGGTCAGgtactgtatt ... ctcttggcagATTGTTCCTATGAAATACAATCCAAGAGATGTGGATTCAATTAAGGCTGTC
EST: gi|58663529|gb|CK052215.1|CK052215
EST:     TTCTGAGGATTGTCACCGACACCTGAAGTTGATGGGTTGACCTGGGTCAG                         ATTGTTCCTATGAAATACAATCCAAGAGATGTGGATTCAATTAAGGCTGTC
genomic: TTCTGAGGATTGTCACCGACACCTGAAGTTGATGGGT-GACCTGGGTCAGgtactgtatt ... ctcttggcagATTGTTCCTATGAAATACAATCCAAGAGATGTGGATTCAATTAAGGCTGTC
EST: gi|58597371|gb|CK007899.1|CK007899
EST:     GTTCTGAGGATTGTCACCGACACCTGAAGTTGATGGGTGACCTGGGTCAG                         ATTGTTCCTATGAAATACAATCCAAGAGATGTGGATTCAATTAAGGCTGTC
genomic: GTTCTGAGGATTGTCACCGACACCTGAAGTTGATGGGTGACCTGGGTCAGgtactgtatt ... ctcttggcagATTGTTCCTATGAAATACAATCCAAGAGATGTGGATTCAATTAAGGCTGTC
EST: gi|33657303|gb|CF279917.1|CF279917
EST:     GTTCTGAGGATTGTCACCGACACCTGAAGTTGATGGGTGACCTGGGTCAG                         ATTGTTCCTATGAAATACAATCCAAGAGATGTGGATTCAATTAAGGCTGTC
genomic: GTTCTGAGGATTGTCACCGACACCTGAAGTTGATGGGTGACCTGGGTCAGgtactgtatt ... ctcttggcagATTGTTCCTATGAAATACAATCCAAGAGATGTGGATTCAATTAAGGCTGTC
EST: gi|58652884|gb|CK041564.1|CK041564
EST:     GTTCTGAGGATTGTCACCGACACCTGAAGTTGATGGGTGACCTGGGTCAG                         ATTGTTCCTATGAAATACAATCCAAGAGATGTGGATTCAATTAAGGCTGTC
genomic: GTTCTGAGGATTGTCACCGACACCTGAAGTTGATGGGTGACCTGGGTCAGgtactgtatt ... ctcttggcagATTGTTCCTATGAAATACAATCCAAGAGATGTGGATTCAATTAAGGCTGTC

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: 74 (upstream exon), 70 (downstream exon)
Score: 37

CAAAGATGGGGTCTCAAGTGCTTGTACCATTCAGAGGTTCTGAGGATTGTCACCGACACCTGAAGTTGATGGGTGACCTGGGTCAGgtactgtatt ... ctcttggcagATTGTTCCTATGAAATACAATCCAAGAGATGTGGATTCAATTAAGGCTGTCATGGCCAAATCCAATGTGGTCATTAACCTAATAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

actcatttttcctttttttttcccttttatgtattctacttttttctcttggcagATTGTTCCTATGAAATACAATCCAAGAGATGTGGATTCAATTAAGGCTGTCATGGCCAAATCCAATGTGGTCATTAACCTAATAG
 cattaac  putative branch site (score: 37)
       tttcctttttttttcc  putative PPT
                        ttttatgtattctact  TA-rich tract