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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaggagtaatataatacagcatttctagtcccagatttgaaaattcttaagctgtagtagctttgttgttattgacaccgttactaagctgatatactattcagTCAGTCAATTTACCTTATATGGAATCCTGAAGGGTAACAAGCCAGATTTTCATGTGGCTATGCCACCTGCTAAAGCAAAGCCATTCTATGCTTCTTTAGT

Basic information

species Oryza sativa
transcript LOC_Os01g14040.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g14040.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G100260_T03 (Zea mays), 3'ss of exon 4
gtaggagtaatataatacagcatttctagtcccagatttgaaaattcttaagctgtagtagctttgttgttattgacaccgttactaagctgatatactattcagTCAGTCAATTTACCTTATATGGAATCCTGAAGGGTAACAAGCCAGATTTTCATGTGGCTATGCCACCTGCTAAAGCAAAGCCATTCTATGCTTCTTTAGT
      ||||||| ||   |||    |   ||  |  |  || ||   ||  ||  | ||  | |||| |||   ||  | || || |  |||| |  | |||||||||||| || |||||||| || |||||||||||||| |||||||||||||| ||||||||| ||||||| ||||| || ||||||||||||||| ||||
------gtaatatgatgatgcagcctttcaccatgtgtaaaatataaatagcctccattaaatctgttattaaccactacatttctgacatgatgtcttcttcagTCAGTCAGTTCACCTTATACGGCATCCTGAAGGGTAATAAGCCAGATTTTCACGTGGCTATGTCACCTGCAAAAGCGAAACCATTCTATGCTTCTCTAGT

upper sequence: LOC_Os01g14040.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA13G30670.1 (Glycine max), 3'ss of exon 3
gtaggagtaatataatacagcatttctagtcccagatttgaaaattcttaagctgtagtagctttgttgttattgacaccgttactaagctgatatactattcagTCAGTCAATTTACCTTATATGGAATCCTGAAGGGTAACAAGCCAGATTTTCATGTGGCTATGCCACCTGCTAAAGCAAAGCCATTCTATGCTTCTTTAGT
      || |  |||   || |||   | |  ||   || |  ||   |  | || |  |      || |  || |     ||| |  |    | || |    ||| ||||| ||||| || |||||| |||||||||||||||| || |||||||| || || ||| |||||   | ||| |||||||||||||| ||||||||
------gtga-gtaagtgagtattcgcattttcaatcttaattatatattggatgcaaaaa-----ttatagtttattttattattttgtgcttttatttaatagTGAGTCAGTTTACGTTGTATGGATTCCTGAAGGGTAACAAACCGGATTTTCACGTTGCGATGGCACCTCAGAGAGCCAAGCCATTCTATGCCTCTTTAGT

upper sequence: LOC_Os01g14040.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA15G08610.1 (Glycine max), 3'ss of exon 2
gtaggagtaatataataca-gcatttctagtcccagatttgaaaattcttaagctgtagtagctttgttgttattgacaccgttactaagctgatatactattcagTCAGTCAATTTACCTTATATGGAATCCTGAAGGGTAACAAGCCAGATTTTCATGTGGCTATGCCACCTGCTAAAGCAAAGCCATTCTATGCTTCTTTAGT
    ||||||   | ||   |||||| |     |||  || |  ||   || | || |  |  | |  | |||||   |   ||          | |  |   |||| ||||| ||||| || |||||| |||||||||||||||| || |||||||| || || ||| | |||   | ||| ||||| |||||||| ||||||||
--gtgagtaagtgagtattcgcattttt-----cagtcttaattatatataggatgcaaaaattataat-ttatttttattattgt-------gtgtttttaacagTGAGTCAGTTTACGTTGTATGGATTCCTGAAGGGTAACAAACCGGATTTTCACGTAGCCATGGCGCCTCAGAGAGCCAAGCCCTTCTATGCCTCTTTAGT

upper sequence: LOC_Os01g14040.1 (Oryza sativa), 3'ss of exon 4
lower sequence: AT4G18460.1 (Arabidopsis thaliana), 3'ss of exon 3
----------gtaggagtaatata-atacagcattt--ctagtcccagatttgaa----aattcttaagctgtagtagctttgttgttattgacaccgttactaagctg-atatactatt-cagTCAGTCAATTTACCTTATATGGAATCCTGAAGGGTAACAAGCCAGATTTTCATGTGGCTATGCCACCTGCTAAAGCAAAGCCATTCTATGCTTCTTTAGT
           |     || |||  ||| | |||||   |||    || |||         ||  |   |||  ||   |||  | |  ||| |   ||   |        | |  || | |||| |||||||| || ||||| ||| || |||| |||||||| |||||||||||||| || |||||||||| |||||| || || || || || ||||||||
gtaatgatgcatctctttattattcatataccatttgattagagaaaggtttagcttgtggtttatgtactgaggtttgttttctttgcttgccctggtctttggatcatgtgtgttaatacagTTAGTCAATTCACATTATACGGATTCTTGAAAGGTAACAAACCAGATTTTCATGTCGCAATGCCACCTGATAAAGCGAAACCTTTTTACGCCTCTTTAGT

upper sequence: LOC_Os01g14040.1 (Oryza sativa), 3'ss of exon 4
lower sequence: Vv10s0003g00640.t01 (Vitis vinifera), 3'ss of exon 5
gtaggagtaatataatacagcatttctagtcccagatttgaaaattcttaa-gctgtagtagctttgttgttattgacaccgttactaagctgatatactatt-cagTCAGTCAATTTACCTTATATGGAATCCTGAAGGGTAACAAGCCAGATTTTCATGTGGCTATGCCACCTGCTAAAGCAAAGCCATTCTATGCTTCTTTAGT
     |||  || | | |  ||  | |  |   ||| |  |        || | | ||  ||    || |   || |||  |||   | |||| |    | || |||| ||||| ||||| || ||||||||  ||||||||||||||||||||||||||||||| ||||| ||    ||||||||||| || |||||||| || ||
-----agttctaaattgcttcaagtatcatgaaagagtgaagggagaaaaatgatatacaagtggagtggcattttaca--gttctaatgctgtttgggtgtttcagTGAGTCAGTTTACATTGTATGGAATTTTGAAGGGTAACAAGCCAGATTTTCATGTGGCAATGCCGCCCCAAAAAGCAAAGCCCTTTTATGCTTCGTTCGT

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|88395326|gb|CI611243.1|CI611243
EST:     GTTTTGCAGCGGAAATTTGAAGTTCTATTAG                         TCAGTCAATTTACCTTATATGGAATCCTGAAGGGTAACAAGCCAGATTTTC
genomic: GTTTTGCAGCGGAAATTTGAAGTTCTATTAGgtaggagtaa ... tactattcagTCAGTCAATTTACCTTATATGGAATCCTGAAGGGTAACAAGCCAGATTTTC
EST: gi|88692898|gb|CI736473.1|CI736473
EST:     GTTTTGCAGCGGAAATTTGAAGTTCTATTAG                         TCAGTCAATTTACCTTATATGGAATCCTGAAGGGTAAC
genomic: GTTTTGCAGCGGAAATTTGAAGTTCTATTAGgtaggagtaa ... tactattcagTCAGTCAATTTACCTTATATGGAATCCTGAAGGGTAAC
EST: gi|86854057|gb|CI252048.1|CI252048
EST:     GTTTTGCAGCGGAAATTTGAAGTTCTATTAG                         TCAGTCAATTTACCTTATATGGAATCCTGAAGGGTAACAAGCCAGATTTTC
genomic: GTTTTGCAGCGGAAATTTGAAGTTCTATTAGgtaggagtaa ... tactattcagTCAGTCAATTTACCTTATATGGAATCCTGAAGGGTAACAAGCCAGATTTTC
EST: gi|58690528|gb|CK079215.1|CK079215
EST:     GTTTTGCAGCGGAAATTTGAAGTTCTATTAG                         TCAGTCAATTTACCTTATATGGAATCCTGAAGGGTAACAAGCCAGATTTTC
genomic: GTTTTGCAGCGGAAATTTGAAGTTCTATTAGgtaggagtaa ... tactattcagTCAGTCAATTTACCTTATATGGAATCCTGAAGGGTAACAAGCCAGATTTTC
EST: gi|88422041|gb|CI611661.1|CI611661
EST:     GTTTTGCAGCGGAAATTTGAAGTTCTATTAG                         TCAGTCAATTTACCTTATATGGAATCCTGAAGGGTAACAAGCCAGA
genomic: GTTTTGCAGCGGAAATTTGAAGTTCTATTAGgtaggagtaa ... tactattcagTCAGTCAATTTACCTTATATGGAATCCTGAAGGGTAACAAGCCAGA

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), 31 (downstream exon)
Score: 17

GTTTTGCAGCGGAAATTTGAAGTTCTATTAGgtaggagtaa ... tactattcagTCAGTCAATTTACCTTATATGGAATCCTGAAGGGTAACAAGCCAGATTTTCATGTGGCTATGCCACCTGCTAAAGCAAAGCCATTCTATGCTTCTTTAGT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agctgtagtagctttgttgttattgacaccgttactaagctgatatactattcagTCAGTCAATTTACCTTATATGGAATCCTGAAGGGTAACAAGCCAGATTTTCATGTGGCTATGCCACCTGCTAAAGCAAAGCCATTCTATGCTTCTTTAGT
                                          atatactatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaggagtaatataatacagcatttctagtcccagatttgaaaattcttaagctgtagtagctttgttgttattgacaccgttactaagctgatatactattcagTCAGTCAATTTACCTTATATGGAATCCTGAAGGGTAACAAGCCAGATTTTCATGTGGCTATGCCACCTGCTAAAGCAAAGCCATTCTATGCTTCTTTAGT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAAG