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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...catacaacactcatctccatgcatcttgctcatttaaatttactgacaaattaaaagggcctttttctgactatttatttatttatgctacctggcgcagGTGTACAGTGATTTGACCGTTGACTACCTAAAGATGTTCCTGCTAAATGTTCCAGCAACTACTCTTGCTCTAGGACT

Basic information

species Oryza sativa
transcript LOC_Os03g64020.2
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g64020.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM5G896082_T01 (Zea mays), 3'ss of exon 5
catacaacactcatctccatgcatcttgctc--atttaaatttactgacaa---attaaaagggcctttttctgactatttatttatttatgctacctggcgcagGTGTACAGTGATTTGACCGTTGACTACCTAAAGATGTTCCTGCTAAATGTTCCAGCAACTACTCTTGCTCTAGGACT
  || |  | |  | |  ||  ||         | |||  | | |  ||      |||       || | |   | ||||    |||   | |||  | |   ||||||||||||| ||||  ||||||||||||||||||||||| |||||||||||||| || ||  | ||||| |||||
-gtaaattagtgttttaaatctattagaactggagttatgtgttccaacggctggttaccttttactctgtgcaagtattctgatatgcgtcctatatcgtatagGTGTACAGTGACTTGAATGTTGACTACCTAAAGATGTTCCTCCTAAATGTTCCAGCCACCACCGTAGCTCTGGGACT

upper sequence: LOC_Os03g64020.1 (Oryza sativa), 3'ss of exon 3
lower sequence: AC203966.5_FGT002 (Zea mays), 3'ss of exon 4
catacaacactcatctccatgcatctt--gctcatttaaatttactgacaaattaaaagggc-ctttttctgactatttatttatttatgctacctggcgcagGTGTACAGTGATTTGACCGTTGACTACCTAAAGATGTTCCTGCTAAATGTTCCAGCAACTACTCTTGCTCTAGGACT
  || |  | |  | |  ||| ||     ||  | |||  | | |  ||   | |  |     || | |   | ||||    |||   | |||  | |  |||||||||||||| ||||  ||||||||| |||||||||| ||||||||||||||||| || ||  | ||||| |||||
-gtaaataagtgttttaaatgtattagaagcggagttatgtattccaactgctgattaccttactctgtgcaagtattctgatatgcgtcctatatcgtacagGTGTACAGTGACTTGAATGTTGACTACATAAAGATGTTTCTGCTAAATGTTCCAGCCACCACCGTAGCTCTGGGACT
















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|38475301|gb|CF959434.1|CF959434
EST:     GAAGTGACATTGTCACCGAAGGTCCCAGGTGCAGTCTACGCAGCCGAAAG                         GTGTACAGTGATTTGACCGTTGACTACCTAAAGATGTTCCTGCTAAATGTT
genomic: GAAGTGACATTGTCACCGAAGGTCCCAGGTGCAGTCTACGCAGCCGAAAGgtaataaaaa ... cctggcgcagGTGTACAGTGATTTGACCGTTGACTACCTAAAGATGTTCCTGCTAAATGTT
EST: gi|117243743|gb|CT843209.1|CT843209
EST:     GAAGTGACATTGTCACCGAAGGTCCCAGGTGCAGTCTACGCAGCCGAAAG                         GTGTACAGTGATTTGACCGTTGACTACCTAAAGATGTTCCTGCTAAATGTT
genomic: GAAGTGACATTGTCACCGAAGGTCCCAGGTGCAGTCTACGCAGCCGAAAGgtaataaaaa ... cctggcgcagGTGTACAGTGATTTGACCGTTGACTACCTAAAGATGTTCCTGCTAAATGTT
EST: gi|218487328|gb|FG968259.1|FG968259
EST:     GAAGTGACATTGTCACCGAAGGTCCCAGGTGCAGTCTACGCAGCCGAAAG                         GTGTACAGTGATTTGACCGTTGACTACCTAAAGATGTTTCTGCTAAATGTT
genomic: GAAGTGACATTGTCACCGAAGGTCCCAGGTGCAGTCTACGCAGCCGAAAGgtaataaaaa ... cctggcgcagGTGTACAGTGATTTGACCGTTGACTACCTAAAGATGTTCCTGCTAAATGTT
EST: gi|58030632|gb|CX728175.1|CX728175
EST:     AGGTCCCAGGTGCAGTCTACGCAGCCGAAAG                         GTGTACAGTGATTTGACCGTTGACTACCTAAAGATGTTCCTGCTAAATGTT
genomic: AGGTCCCAGGTGCAGTCTACGCAGCCGAAAGgtaataaaaa ... cctggcgcagGTGTACAGTGATTTGACCGTTGACTACCTAAAGATGTTCCTGCTAAATGTT
EST: gi|38475842|gb|CF959975.1|CF959975
EST:     GAAGTGACATT-TCACCGAAGGTCCCAGGTGCAGTCTACGCAGCCGAAAG                         GTGTACAGTGATTTGACCGTGGGCTACCTAAAGATGTTCCTGCTAAATGTT
genomic: GAAGTGACATTGTCACCGAAGGTCCCAGGTGCAGTCTACGCAGCCGAAAGgtaataaaaa ... cctggcgcagGTGTACAGTGATTTGACCGTTGACTACCTAAAGATGTTCCTGCTAAATGTT
EST: gi|33801214|gb|CF326480.1|CF326480
EST:     GAAGTGACATTGTCACCGAAGGTCCCAGGTGCAGTCTACGCAGCCGAAAG                         GTGTACAGTGATTTGACCGTTGACTACCTAAAGATGTTCCTGCTAAATGTT
genomic: GAAGTGACATTGTCACCGAAGGTCCCAGGTGCAGTCTACGCAGCCGAAAGgtaataaaaa ... cctggcgcagGTGTACAGTGATTTGACCGTTGACTACCTAAAGATGTTCCTGCTAAATGTT
EST: gi|29687940|gb|CB684215.1|CB684215
EST:     GAAGTGACATTGTCACCGAAGGTCCCAGGTGCAGTCTACGCAGCCGAAAG                         GTGTACAGTGATTTGACCGTTGACTACCTAAAGATGTTCCTGCTAAATGTT
genomic: GAAGTGACATTGTCACCGAAGGTCCCAGGTGCAGTCTACGCAGCCGAAAGgtaataaaaa ... cctggcgcagGTGTACAGTGATTTGACCGTTGACTACCTAAAGATGTTCCTGCTAAATGTT
EST: gi|29687939|gb|CB684214.1|CB684214
EST:     GAAGTGACATTGTCACCGAAGGTCCCAGGTGCAGTCTACGCAGCCGAAAG                         GTGTACAGTGATTTGACCGTTGACTACCTAAAGATGTTCCTGCTAAATGTT
genomic: GAAGTGACATTGTCACCGAAGGTCCCAGGTGCAGTCTACGCAGCCGAAAGgtaataaaaa ... cctggcgcagGTGTACAGTGATTTGACCGTTGACTACCTAAAGATGTTCCTGCTAAATGTT
EST: gi|29682412|gb|CB678687.1|CB678687
EST:     GAAGGTCCCAGGTGCCTTCTACGCAGCCGAAAG                         GTGTACAGTGATTTGACCGTTGACTACCTAAAGATGTTCCTGCTAAATGTT
genomic: GAAGGTCCCAGGTGCAGTCTACGCAGCCGAAAGgtaataaaaa ... cctggcgcagGTGTACAGTGATTTGACCGTTGACTACCTAAAGATGTTCCTGCTAAATGTT

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), 49 (downstream exon)
Score: 58

AAAGACGGAAGTGACATTGTCACCGAAGGTCCCAGGTGCAGTCTACGCAGCCGAAAGgtaataaaaa ... cctggcgcagGTGTACAGTGATTTGACCGTTGACTACCTAAAGATGTTCCTGCTAAATGTTCCAGCAACTACTCTTGCTCTAGGACT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acaaattaaaagggcctttttctgactatttatttatttatgctacctggcgcagGTGTACAGTGATTTGACCGTTGACTACCTAAAGATGTTCCTGCTAAATGTTCCAGCAACTACTCTTGCTCTAGGACT
                tttttctgactattta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
catacaacactcatctccatgcatcttgctcatttaaatttactgacaaattaaaagggcctttttctgactatttatttatttatgctacctggcgcagGTGTACAGTGATTTGACCGTTGACTACCTAAAGATGTTCCTGCTAAATGTTCCAGCAACTACTCTTGCTCTAGGACT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG