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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...catgtgcaatgctcaagttctgtatttgtatttttagattcagaaaaaagtattttatttttctccttaaatcaatgtcagttgtgattgtgatgttcagGTGGATGTTCCAATCAAGTACCTGAACTTCTTCCTTGAAGATGACAATGAGCTCGAGCACATAAAGAAG

Basic information

species Oryza sativa
transcript LOC_Os12g35570.2
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os12g35570.2 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G002687_T01 (Zea mays), 3'ss of exon 8
----catgtgcaatgctcaagttctgtatttgtatttttagattcagaaaaaagtattttatttttctccttaaatcaatgtcagttgtgattgtgatgttcagGTGGATGTTCCAATCAAGTACCTGAACTTCTTCCTTGAAGATGACAATGAGCTCGAGCACATAAAGAAG
      |    ||||| |  | | |     |  |||   | | ||     ||   |    |   |  |   | |||   ||    || |  ||| ||||   |||||||||| |||||||| ||||||||||||||||||||||||||  | ||||| | ||||||||| |||
tccatttccataatgcgcttggtattctggttaattaccatactcttctgaagtaacacaaaactagtttgtgaatggctggt--tttttgttgcgatga--agGTGGATGTCCCAATCAAATACCTGAACTTCTTCCTTGAAGATGATGACGAGCTTGCGCACATAAAAAAG
















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|86538796|gb|CI179002.1|CI179002
EST:     CATAGAAAACTTGGAGCTAACCTTGAT                         GTGGATGTTCCAATCAAGTACCTGAACTTCTTCCTTGAAGATGACAATGAG
genomic: CATAGAAAACTTGGAGCTAACCTTGATgtaagtcatt ... tgatgttcagGTGGATGTTCCAATCAAGTACCTGAACTTCTTCCTTGAAGATGACAATGAG
EST: gi|8527950|gb|AU092765.1|AU092765
EST:     GTGGCCGGGACTCAATTGAGCTCCATAGAAAACTTGGAGCTAACCTTGAT                         GTGGATGTTCCAATCAAGTACCTGAACTTCTTCCTTGAAGATGACAATGAG
genomic: GTGGCCGGGACTCAATTGAGCTCCATAGAAAACTTGGAGCTAACCTTGATgtaagtcatt ... tgatgttcagGTGGATGTTCCAATCAAGTACCTGAACTTCTTCCTTGAAGATGACAATGAG
EST: gi|38475276|gb|CF959409.1|CF959409
EST:     GTGGCCGGGACTCAATTGAGCTCCATAGAAAACTTGGAGCTAACCTTGAT                         GTGGATGTACCAATCAAGTACCTGAACTTCTTCCTTGAAGATGACAATGAG
genomic: GTGGCCGGGACTCAATTGAGCTCCATAGAAAACTTGGAGCTAACCTTGATgtaagtcatt ... tgatgttcagGTGGATGTTCCAATCAAGTACCTGAACTTCTTCCTTGAAGATGACAATGAG
EST: gi|3760141|gb|C97399.1|C97399
EST:     GGCCCGGGACTCAATTGAGCTCCCATAGAAAACTTGGAGCTAACCTTGAT                         GTGGATGTTCCAATCAAGTACCTGAACTTCTTCCTTGAAGATGACAATGAG
genomic: GG-CCGGGACTCAATTGAGCT-CCATAGAAAACTTGGAGCTAACCTTGATgtaagtcatt ... tgatgttcagGTGGATGTTCCAATCAAGTACCTGAACTTCTTCCTTGAAGATGACAATGAG
EST: gi|89183405|gb|CI045970.1|CI045970
EST:     GTGGCCGGGACTCAATTGAGCTCCATAGAAAACTTGGAGCTAACCTTGAT                         GTGGATGTTCCAATCAAGTACCTGAACTTCTTCCTTGAAGATGACAATGAG
genomic: GTGGCCGGGACTCAATTGAGCTCCATAGAAAACTTGGAGCTAACCTTGATgtaagtcatt ... tgatgttcagGTGGATGTTCCAATCAAGTACCTGAACTTCTTCCTTGAAGATGACAATGAG
EST: gi|86426769|gb|CI071866.1|CI071866
EST:     CCGGGACTCAATTGAGCTCCATAGAAAACTTGGAGCTAACCTTGAT                         GTGGATGTTCCAATCAGGTACCTGAACTTCTTCCTTGAAGATGACAATGAG
genomic: CCGGGACTCAATTGAGCTCCATAGAAAACTTGGAGCTAACCTTGATgtaagtcatt ... tgatgttcagGTGGATGTTCCAATCAAGTACCTGAACTTCTTCCTTGAAGATGACAATGAG
EST: gi|88248644|gb|CI248493.1|CI248493
EST:     TAGAAAACTTGGAGCTAACCTTGAT                         GTGGATGTTCCAATCAAGTACCTGAACTTCTTCCTTGAAGATGACAATGAG
genomic: TAGAAAACTTGGAGCTAACCTTGATgtaagtcatt ... tgatgttcagGTGGATGTTCCAATCAAGTACCTGAACTTCTTCCTTGAAGATGACAATGAG
EST: gi|86434156|gb|CI094499.1|CI094499
EST:     GCTAACCTTGAT                         GTGGATGTTCCAATCAAGTACCTGAACTTCTTCCTTGAAGATGACAATGAG
genomic: GCTAACCTTGATgtaagtcatt ... tgatgttcagGTGGATGTTCCAATCAAGTACCTGAACTTCTTCCTTGAAGATGACAATGAG
EST: gi|8527958|gb|AU092773.1|AU092773
EST:     GTGGCCGGGACTCAATTGAGCTCCATAGAAAACTTGGAGCTAACCTTGAT                         GTGGATGTTCCAATCAAGTACCTGAACTTCTTCCTTGAAGATGACAATGAG
genomic: GTGGCCGGGACTCAATTGAGCTCCATAGAAAACTTGGAGCTAACCTTGATgtaagtcatt ... tgatgttcagGTGGATGTTCCAATCAAGTACCTGAACTTCTTCCTTGAAGATGACAATGAG
EST: gi|218485927|gb|FG959165.1|FG959165
EST:     CCGGGACTCAATTGAGCTCCATAGTATACTTGGAGCTAACCTTGAT                         GTGGATGTTCCAATCAAGTACCTGAACTTCTTCCTTGAAGATGACAATGAG
genomic: CCGGGACTCAATTGAGCTCCATAGAAAACTTGGAGCTAACCTTGATgtaagtcatt ... tgatgttcagGTGGATGTTCCAATCAAGTACCTGAACTTCTTCCTTGAAGATGACAATGAG

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

CTGTCATTTATTTTACCATTTTTTCCAGGTGAACAAATATGCGTTCTCAGGTGGCCGGGACTCAATTGAGCTCCATAGAAAACTTGGAGCTAACCTTGATgtaagtcatt ... tgatgttcagGTGGATGTTCCAATCAAGTACCTGAACTTCTTCCTTGAAGATGACAATGAGCTCGAGCACATAAAGAAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaaagtattttatttttctccttaaatcaatgtcagttgtgattgtgatgttcagGTGGATGTTCCAATCAAGTACCTGAACTTCTTCCTTGAAGATGACAATGAGCTCGAGCACATAAAGAAG
     tattttatttttctcc  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
catgtgcaatgctcaagttctgtatttgtatttttagattcagaaaaaagtattttatttttctccttaaatcaatgtcagttgtgattgtgatgttcagGTGGATGTTCCAATCAAGTACCTGAACTTCTTCCTTGAAGATGACAATGAGCTCGAGCACATAAAGAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
catgtgc
- - - - -tgctcaa
- - - - - - - - -ttctgta
- - - - - - - - - - - - - - - - - - - - - gaaaaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aaatcaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ttgtgat