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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tcatcttgtcatacacagctctgacaatattagatctttcatggtaaaattgcattttggggcgtttagattgcataacatgctttaattgaacttgcagCTATACACTAGGGATTCATCAAAAAGCTGGCGTCAGGCTGGATCAGATGGAAGTAGTCAGCTGACTTTAAAAGAACCATCAACCAATATGGTCTTAGCCG

Basic information

species Oryza sativa
transcript LOC_Os04g20230.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os04g20230.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G028730_T02 (Zea mays), 3'ss of exon 2
tcatcttgtcatacacagctctg----acaatattagatctttcatggtaaaattgcatt-ttggggcgtttagattgcataacatgctttaattgaacttgcagCTATACACTAGGGATTCATCAAAAAGCTGGCGTCAGGCTGGATCAGATGGAAGTAGTCAGCTGACTTTAAAAGAACCATCAACCAATATGGTCTTAGCCG
  |  |||| |  || |   ||     ||| |  | ||   ||| ||   | ||   ||  || |   |||| |||    |  |||| || | | | |  ||||| || |||| ||||||||||||||||| |||||||||||||||||||||||||| |||||||||| | |||||||||| || |||||| | ||| |||| |
-tactttgttactcataaagctagttcacattgatcgaagattcttgtagagataatatagttagtttgttttgatc---ttgcatggttca-tggcatatgcagTTACACACCAGGGATTCATCAAAAAGTTGGCGTCAGGCTGGATCAGATGGAAGCAGTCAGCTGATTCTAAAAGAACCTTCTACCAATGTTGTCCTAGCTG
















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|86861785|gb|CI329549.1|CI329549
EST:     AGAAGCTGGAGGAGGCAGTCAAGGGGAAGAGTCGCTAGCCAGTCGTTCAG                         CTATACACTAGGGATTCATCAAAAAGCTGGCGTCAGGCTGGATCAGATGGA
genomic: AGAAGCTGGAGGAGGCAGTCAAGGGGAAGAGTCGCGAGCCAGTCGTTCAGgtaatcgtcc ... gaacttgcagCTATACACTAGGGATTCATCAAAAAGCTGGCGTCAGGCTGGATCAGATGGA
EST: gi|88832118|gb|CI014677.1|CI014677
EST:     AGAAGCTGGAGGAGGCAGTCAAGGGGAAGAGTCGCGAGCCAGTCGTTCAG                         CTATACACTAGGGATTCATCAAAAAGCTGGCGTCAGGCCGGATCAGATGGA
genomic: AGAAGCTGGAGGAGGCAGTCAAGGGGAAGAGTCGCGAGCCAGTCGTTCAGgtaatcgtcc ... gaacttgcagCTATACACTAGGGATTCATCAAAAAGCTGGCGTCAGGCTGGATCAGATGGA
EST: gi|88546887|gb|CI477143.1|CI477143
EST:     GAAGAGTCGCGAGCCAGTCGTTCAG                         CTATACACTAGGGATTCATCAAAAAGCTGGCGTCAGGCTGGATCAGATGGA
genomic: GAAGAGTCGCGAGCCAGTCGTTCAGgtaatcgtcc ... gaacttgcagCTATACACTAGGGATTCATCAAAAAGCTGGCGTCAGGCTGGATCAGATGGA
EST: gi|86873136|gb|CI328516.1|CI328516
EST:     GAAGGCTGGAGGAGGCAGTCAAGGGGAAGAGTCGCGAGCCAGTCGTTCAG                         CTATACACTAGGGATTCATCAAAAAGCTGGCGTCAGGCTGGATCAGATGGA
genomic: GAA-GCTGGAGGAGGCAGTCAAGGGGAAGAGTCGCGAGCCAGTCGTTCAGgtaatcgtcc ... gaacttgcagCTATACACTAGGGATTCATCAAAAAGCTGGCGTCAGGCTGGATCAGATGGA
EST: gi|87034371|gb|CI188995.1|CI188995
EST:     AGAAGCTGGAGGAGGCAGTCAAGGGGAAGAGTCGCGAGCCAGTCGTTCAG                         CTATACACTAGGGATTCATCAAAAAGCTGGCGTCAGGCTGGATCAGATGGA
genomic: AGAAGCTGGAGGAGGCAGTCAAGGGGAAGAGTCGCGAGCCAGTCGTTCAGgtaatcgtcc ... gaacttgcagCTATACACTAGGGATTCATCAAAAAGCTGGCGTCAGGCTGGATCAGATGGA
EST: gi|87029911|gb|CI267924.1|CI267924
EST:     AGAAGCTGGAGGAGGCAGTCAAGGGGAAGAGTCGCGAGCCAGTCGTTCAG                         CTATACACTAGGGATTCATCAAAAAGCTGGCGTCAGGCTGGATCAGATGGA
genomic: AGAAGCTGGAGGAGGCAGTCAAGGGGAAGAGTCGCGAGCCAGTCGTTCAGgtaatcgtcc ... gaacttgcagCTATACACTAGGGATTCATCAAAAAGCTGGCGTCAGGCTGGATCAGATGGA
EST: gi|86511407|gb|CI154040.1|CI154040
EST:     AGAAGCTGGAGGAGGCAGTCAAGGGGAAGAGTCGCGAGCCAGTCGTTCAG                         CTATACACTAGGGATTCATCAAAAAGCTGGCGTCAGGCTGGATCAGATGGA
genomic: AGAAGCTGGAGGAGGCAGTCAAGGGGAAGAGTCGCGAGCCAGTCGTTCAGgtaatcgtcc ... gaacttgcagCTATACACTAGGGATTCATCAAAAAGCTGGCGTCAGGCTGGATCAGATGGA
EST: gi|86511306|gb|CI153939.1|CI153939
EST:     AGAAGCTGGAGGAGGCAGTCAAGGGGAAGAGTCGCGAGCCAGTCGTTCAG                         CTATACACTAGGGATTCATCAAAAAGCTGGCGTCAGGCTGGATCAGATGGA
genomic: AGAAGCTGGAGGAGGCAGTCAAGGGGAAGAGTCGCGAGCCAGTCGTTCAGgtaatcgtcc ... gaacttgcagCTATACACTAGGGATTCATCAAAAAGCTGGCGTCAGGCTGGATCAGATGGA
EST: gi|86595452|gb|CI264549.1|CI264549
EST:     AGAAGCTGGAGGAGGCAGTCAAGGGGAAGAGTCGCGAGCCAGTCGTTCAG                         CTATACACTAGGGATTCATCAAAAAGCTGGCGTCAGGCTGGATCAGATGGA
genomic: AGAAGCTGGAGGAGGCAGTCAAGGGGAAGAGTCGCGAGCCAGTCGTTCAGgtaatcgtcc ... gaacttgcagCTATACACTAGGGATTCATCAAAAAGCTGGCGTCAGGCTGGATCAGATGGA
EST: gi|86505090|gb|CI147723.1|CI147723
EST:     AGAAGCTGGAGGAGGCAGTCAAGGGGAAGAGTCGCGAGCCAGTCGTTCAG                         CTATACACTAGGGATTCATCAAAAAGCTGGCGTCAGGCTGGATCAGATGGA
genomic: AGAAGCTGGAGGAGGCAGTCAAGGGGAAGAGTCGCGAGCCAGTCGTTCAGgtaatcgtcc ... gaacttgcagCTATACACTAGGGATTCATCAAAAAGCTGGCGTCAGGCTGGATCAGATGGA
EST: gi|88531548|gb|CI460031.1|CI460031
EST:     TCAAGGGGAAGAGTCGCGAGCCAGTCGTTCAG                         CTATACAGTAGGGATTCATCAAAAAGCTGGCGTCAGGCTGGATCAGATGGA
genomic: TCAAGGGGAAGAGTCGCGAGCCAGTCGTTCAGgtaatcgtcc ... gaacttgcagCTATACACTAGGGATTCATCAAAAAGCTGGCGTCAGGCTGGATCAGATGGA
EST: gi|88848172|gb|CI086694.1|CI086694
EST:     AGAGGCTGGAGGAGGCAGTCAAGGGGAAGAGTCGCGAGCCAGTCGTTCAG                         CTATACACTAGGGATTCATCAAAAAGCNGGCGTCAGGCTGGATCAGATGGA
genomic: AGAAGCTGGAGGAGGCAGTCAAGGGGAAGAGTCGCGAGCCAGTCGTTCAGgtaatcgtcc ... gaacttgcagCTATACACTAGGGATTCATCAAAAAGCTGGCGTCAGGCTGGATCAGATGGA
EST: gi|87009322|gb|CI313795.1|CI313795
EST:     AGAAGCTGGAGGAGGCAGTCAA-GGGAAGAGTCGCGAGCCAATCTTTCAG                         CTATACACTAGGGATTCATCAGAAAGCTGGCGTCAGGCT-GATCAGATGGA
genomic: AGAAGCTGGAGGAGGCAGTCAAGGGGAAGAGTCGCGAGCCAGTCGTTCAGgtaatcgtcc ... gaacttgcagCTATACACTAGGGATTCATCAAAAAGCTGGCGTCAGGCTGGATCAGATGGA
EST: gi|88205861|gb|CI205710.1|CI205710
EST:     AGAAGCTGGAGGAGGCAGTCAAGGGGAAGAGTCGCGAGCCAGTCGTTCAG                         CTATACACTAGGGATTCATCAAAAAGCTGGCGTCAGGCTGGATCAGATGGA
genomic: AGAAGCTGGAGGAGGCAGTCAAGGGGAAGAGTCGCGAGCCAGTCGTTCAGgtaatcgtcc ... gaacttgcagCTATACACTAGGGATTCATCAAAAAGCTGGCGTCAGGCTGGATCAGATGGA
EST: gi|86428529|gb|CI075210.1|CI075210
EST:     AGAAGCTGGAGGAGGCAGTCAAGGGGAAGAGTCGCGAGCCAGTCGTTCAG                         CTATACACTAGGGATTCATCAAAAAGCTGGCGTCAGGCTGGATCAGATGGA
genomic: AGAAGCTGGAGGAGGCAGTCAAGGGGAAGAGTCGCGAGCCAGTCGTTCAGgtaatcgtcc ... gaacttgcagCTATACACTAGGGATTCATCAAAAAGCTGGCGTCAGGCTGGATCAGATGGA
EST: gi|88531862|gb|CI458380.1|CI458380
EST:     GGAAGATTCNCGAGCCAGTCGTTCAG                         GTATACACTAGGGATTCATCGGAAAGCTGGCGTCAGGCTGGATCAGATGGA
genomic: GGAAGAGTCGCGAGCCAGTCGTTCAGgtaatcgtcc ... gaacttgcagCTATACACTAGGGATTCATCAAAAAGCTGGCGTCAGGCTGGATCAGATGGA
EST: gi|86509598|gb|CI152231.1|CI152231
EST:     TGGAGGAGGCAGTCAAGGGGAAGAGTCGCGAGCCAGTCGTTCAG                         CTATACACTAGGGATTCATCAAAAAGCTGGCGTCAGGCTGGATCAGATGGA
genomic: TGGAGGAGGCAGTCAAGGGGAAGAGTCGCGAGCCAGTCGTTCAGgtaatcgtcc ... gaacttgcagCTATACACTAGGGATTCATCAAAAAGCTGGCGTCAGGCTGGATCAGATGGA
EST: gi|87034259|gb|CI188883.1|CI188883
EST:     AGAAGCTGGAGGAGGCAGTCAAGGGGAAGAGTCGCGAGCCAGTCGTTCAG                         CTATACACTAGGGATTCATCAAAAAGCTGGCGTCAGGCTGGATCAGATGGA
genomic: AGAAGCTGGAGGAGGCAGTCAAGGGGAAGAGTCGCGAGCCAGTCGTTCAGgtaatcgtcc ... gaacttgcagCTATACACTAGGGATTCATCAAAAAGCTGGCGTCAGGCTGGATCAGATGGA

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: 73 (upstream exon), 46 (downstream exon)
Score: 10

CTTGATAACAAGAAGCTGGAGGAGGCAGTCAAGGGGAAGAGTCGCGAGCCAGTCGTTCAGgtaatcgtcc ... gaacttgcagCTATACACTAGGGATTCATCAAAAAGCTGGCGTCAGGCTGGATCAGATGGAAGTAGTCAGCTGACTTTAAAAGAACCATCAACCAATATGGTCTTAGCCG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaaattgcattttggggcgtttagattgcataacatgctttaattgaacttgcagCTATACACTAGGGATTCATCAAAAAGCTGGCGTCAGGCTGGATCAGATGGAAGTAGTCAGCTGACTTTAAAAGAACCATCAACCAATATGGTCTTAGCCG
                                      tttaattgaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tcatcttgtcatacacagctctgacaatattagatctttcatggtaaaattgcattttggggcgtttagattgcataacatgctttaattgaacttgcagCTATACACTAGGGATTCATCAAAAAGCTGGCGTCAGGCTGGATCAGATGGAAGTAGTCAGCTGACTTTAAAAGAACCATCAACCAATATGGTCTTAGCCG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC
- - - - -catacac
- - - - - - - - - - - - - - - - - - tttcatg
- - - - - - - - - - - - - - - - - - - - - - - - -ttgcatt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gattgca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aacatgc