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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagaaaaatgtgacattgaaataagataaccggataaaaagtcacatcaaatagtttgttgctcatttattttgtgtgaaagcatctgaatcattttttttttgttctctgcactgatagCCTTCAGATAAGCCTGTTCCGAATGCCACTCTACAAGTTACTGGTGCTGTTGGTTGGAGAAGAGAGGGTCTTATGTACAAGAAGAACGAG

Basic information

species Oryza sativa
transcript LOC_Os02g46510.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g46510.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G331032_T01 (Zea mays), 3'ss of exon 4
gtgagaaaaatgtgacattgaaataagata--accggataaaaagtcacatcaaatagtttgttgctcattta--ttttgtgtgaaagcatctgaatcattttttttttgttctctgcactgatagCCTTCAGATAAGCCTGTTCCGAATGCCACTCTA-CAAGTTACTGGTGCTGTTGGTTGGAGAAGAGAGGGTCTTATGTACAAGAAGAACGAG
|| ||||||||   ||  |||| |  ||||  |   | |||||| | || || ||| || || || |  |||   |||| | ||||| |||||||     |||| || |  | | |||||| | |||| ||||| ||||||||||| ||||| |||||  ||||| ||||| ||||||||||||||||||||||| ||| ||||||||||||| |||
gttagaaaaatcaaac-ctgaattttgatagaatgtgctaaaaatttacctcgaattgtatgatgatagttttgtttttctatgaaaccatctga-----ttttcttgtcatttatgcacttacagCCCTCAGAGAAGCCTGTTCCAAATGCGACTCTTTCAAGTCACTGGCGCTGTTGGTTGGAGAAGAGAGGGACTTGTGTACAAGAAGAATGAG

upper sequence: LOC_Os02g46510.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G331032_T02 (Zea mays), 3'ss of exon 5
gtgagaaaaatgtgacattgaaataagataaccggataaaaagtcacatcaaatagtttgttgctcatttattttgtgtgaaagcatctgaatcattttttttttgttctctgcactgatagCCTTCAGATAAGCCTGTTCCGAATGCCACTCTACAAGTTACTGGTGCTGTTGGTTGGAGAAGAGAGGGTCTTATGTACAAGAAGAACGAG
                                                                                                                                                           ||||| ||||| ||||||||||||||||||||||| ||| ||||||||||||| |||
----------------------------------------------------------------------------------------------------------------------------------------------------------tCAAGTCACTGGCGCTGTTGGTTGGAGAAGAGAGGGACTTGTGTACAAGAAGAATGAG

upper sequence: LOC_Os02g46510.1 (Oryza sativa), 3'ss of exon 4
lower sequence: AT5G46630.1 (Arabidopsis thaliana), 3'ss of exon 4
--------------------gtgagaaaaatgtgacattgaaataagataaccggataaaaagtcaca-tcaaatagtttgttgctcatttatt-----ttgtgtgaaagcatc--tgaatcattttttttttgt-----tctctgcactgatagCCTTCAGATAAGCCTGTTCCGAATGCCACTCTACAAGTTACTGGTGCTGTTGGTTGGAGAAGAGAGGGTCTTATGTACAAGAAGAACGAG
                    |||   | ||   ||  ||| |||    |    |  |      ||  | | ||  ||| | |  | || | | |     || |||     | ||  |  ||   |||   ||  |     ||| | || | | ||||   ||| || |||||||| ||||| ||  |||||||||| |||||||||||||||||||||||||| |||   ||||| ||||| |||
gtaaaggcatctatttgtttgtgtatacaaca-gattttgtaattgtgttggtgtgtggttcttcgaagttaagcagtatttcccgcaataaatagagattatgttgcttcttcactagatatgtttgcattcataagcttcttttcatt-acagCCAAAAGACAAACCTGTTCCAAATGCAACATTACAAGTTACAGGTGCTGTTGGTTGGAGAAGAGAGGGCCTTGCTTACAAAAAGAATGAG

upper sequence: LOC_Os02g46510.1 (Oryza sativa), 3'ss of exon 4
lower sequence: Vv02s0012g00910.t01 (Vitis vinifera), 3'ss of exon 4
-------------------------------------------------------------------gtgagaaaaatgtgac-attgaaataagataaccggataaaaagtcacatcaaatagtttgttgctc----atttattttgtgtgaaagcatctgaatcattttttttttgttctctgc------actgatagCCTTCAGATAAGCCTGTTCCGAATGCCACTCTACAAGTTACTGGTGCTGTTGGTTGGAGAAGAGAGGGTCTTATGTACAAGAAGAACGAG
                                                                    |    ||  |||    | ||   ||   |    | ||| |   | | |   || | |   ||         |  ||||| | |  |||  ||   |  | | ||||| | |  | |||      |   ||||||||||||||| || || || ||||| ||| |||||||||| ||||||||||||||||| |||||||| ||| | || || ||||| |||
gttagatgtttattttagctatacattttggaatctagtaatttgagcagatgaggcattaccgtggatttctaagttgtacttaatggtttatattttaagtatacattattaaaatgaagattcctttatattaaagtgaattttttattgaagattccttaatactatttttctttaatgtgccaaaatataaatagCCTTCAGATAAACCAGTCCCCAATGCAACTTTACAAGTTACAGGTGCTGTTGGTTGGAGGAGAGAGGGCCTTGTTTATAAAAAGAATGAG

upper sequence: LOC_Os02g46510.1 (Oryza sativa), 3'ss of exon 4
lower sequence: EFJ22278 (Selaginella moellendorffii), 3'ss of exon 4
gtgagaaaaatgtgacattgaaataagataaccggataaaaagtcacatcaaatagtttgttgctcatttattttgtgtgaaagcatctgaatcattttttttttgttctctgcactgatagCCTTCAGATAAGCCTGTTCCGAATGCCACTCTACAAGTTACTGGTGCTGTTGGTTGGAGAAGAGAGGGTCTTATGTACAAGAAGAACGAG
                                                     |||     || |   ||   | |   |  | ||   ||||   | | |||     |  |  |   |   ||  |||            | ||||| ||||| ||||| || ||||| || || |||||||||||||||||| | |||||||| || |||
----------------------------------------------------gtagcgatgtgttgcattgcctggctggttaaca---gaatttatctctttccagCCCATAGATACAAGACCCCCAG------------CAAATGCTACTCTCCAAGTCACCGGTGCAGTGGGATGGAGAAGAGAGGGTCTTGTTTACAAGAAAAATGAG

upper sequence: LOC_Os02g46510.1 (Oryza sativa), 3'ss of exon 4
lower sequence: EFJ25669 (Selaginella moellendorffii), 3'ss of exon 4
gtgagaaaaatgtgacattgaaataagataaccggataaaaagtcacatcaaatagtttgttgctcatttattttgtgtgaaagcatctgaatcattttttttttgttctctgcactgatagCCTTCAGATAAGCCTGTTCCGAATGCCACTCTACAAGTTACTGGTGCTGTTGGTTGGAGAAGAGAGGGTCTTATGTACAAGAAGAACGAG
                                                     |||     || |   ||   | |   |  | ||   ||||   | |||||     |  |  |   |   ||  |||            | ||||| ||||| ||||| || ||||| || || |||||||||||||||||| | |||||||| ||||||
----------------------------------------------------gtagcgatgtgttgcattgcctggctggttaaca---gaatttatctttttccagCCCATAGATACAAGACCCCCAG------------CAAATGCTACTCTTCAAGTCACCGGTGCAGTGGGATGGAGAAGAGAGGGTCTTGTTTACAAGAAAAACGAG

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|38469602|gb|CF953733.1|CF953733
EST:     CGCCATTTTCCTCCAAG                         CCTTCAGATAAGCCTGTTCCAAATGCCACTCTACAAGTTACTGGTGCTGTT
genomic: CGCCATTTTCCTCCAAGgtgagaaaaa ... gcactgatagCCTTCAGATAAGCCTGTTCCGAATGCCACTCTACAAGTTACTGGTGCTGTT
EST: gi|11565235|gb|AU165871.1|AU165871
EST:     TAAAATTGTATATAACTCAAGAAGGAGTTCGGTCGCCATTTTCCTCCAAG                         CCTTCAGATAAGCCTGTTCCGAATGCCACTCTACAAGTTACTGGTGCTGTT
genomic: TAAAATTGTATATAACTCAAGAAGGAGTTCGGTCGCCATTTTCCTCCAAGgtgagaaaaa ... gcactgatagCCTTCAGATAAGCCTGTTCCGAATGCCACTCTACAAGTTACTGGTGCTGTT
EST: gi|11565221|gb|AU165857.1|AU165857
EST:     TAAAATTGTATATAACTCAAGAAGGAGTTCGGTCGCCATTTTCCTCCAAG                         CCTTCAGATAAGCCTGTTCCGAATGCCACTCTACAAGTTACTGGTGCTGTT
genomic: TAAAATTGTATATAACTCAAGAAGGAGTTCGGTCGCCATTTTCCTCCAAGgtgagaaaaa ... gcactgatagCCTTCAGATAAGCCTGTTCCGAATGCCACTCTACAAGTTACTGGTGCTGTT
EST: gi|11565225|gb|AU165861.1|AU165861
EST:     TAAAATTGTATATAACTCAAGAAGGAGTTCGGTCGCCATTTTCCTCCAAG                         CCTTCAGATAAGCCTGTTCCGAATGCCACTCTACAAGTTACTGGTGCTGTT
genomic: TAAAATTGTATATAACTCAAGAAGGAGTTCGGTCGCCATTTTCCTCCAAGgtgagaaaaa ... gcactgatagCCTTCAGATAAGCCTGTTCCGAATGCCACTCTACAAGTTACTGGTGCTGTT
EST: gi|11025706|gb|AU162307.1|AU162307
EST:     TAAAATTGTATATAACTCAAGAAGGAGTTCGGTCGCCATTTTCCTCCAAG                         CCTTCAGATAAGCCTGTTCCGAATGCCACTCTACAAGTTACTGGTGCTGTT
genomic: TAAAATTGTATATAACTCAAGAAGGAGTTCGGTCGCCATTTTCCTCCAAGgtgagaaaaa ... gcactgatagCCTTCAGATAAGCCTGTTCCGAATGCCACTCTACAAGTTACTGGTGCTGTT
EST: gi|58679139|gb|CK067826.1|CK067826
EST:     CTCAAGAAGGAGTTCGGTCGCCATTTTCCTCCAAG                         CCTTCAGATAAGCCTGTTCCAAATGCCACTCTACAAGTTACTGGTGCTGTT
genomic: CTCAAGAAGGAGTTCGGTCGCCATTTTCCTCCAAGgtgagaaaaa ... gcactgatagCCTTCAGATAAGCCTGTTCCGAATGCCACTCTACAAGTTACTGGTGCTGTT
EST: gi|428998|gb|D25154.1|D25154
EST:     TCAAGAAGGAGTTCGGTCGCCATTTTCCTCCAAG                         CCTTCAGATAAGCCTGTTCCGAATGCCACTCTACAAGTTACTGGTGCTGTT
genomic: TCAAGAAGGAGTTCGGTCGCCATTTTCCTCCAAGgtgagaaaaa ... gcactgatagCCTTCAGATAAGCCTGTTCCGAATGCCACTCTACAAGTTACTGGTGCTGTT

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: 70 (upstream exon), 73 (downstream exon)
Score: 43

AAATTATGGACTTCGGTTACCCTCAAAACCTCTCACCTGAAATCTTAAAATTGTATATAACTCAAGAAGGAGTTCGGTCGCCATTTTCCTCCAAGgtgagaaaaa ... gcactgatagCCTTCAGATAAGCCTGTTCCGAATGCCACTCTACAAGTTACTGGTGCTGTTGGTTGGAGAAGAGAGGGTCTTATGTACAAGAAGAACGAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttattttgtgtgaaagcatctgaatcattttttttttgttctctgcactgatagCCTTCAGATAAGCCTGTTCCGAATGCCACTCTACAAGTTACTGGTGCTGTTGGTTGGAGAAGAGAGGGTCTTATGTACAAGAAGAACGAG
                         tcattttttttttgtt  CT-rich tract
                       aatcattttttttttg  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagaaaaatgtgacattgaaataagataaccggataaaaagtcacatcaaatagtttgttgctcatttattttgtgtgaaagcatctgaatcattttttttttgttctctgcactgatagCCTTCAGATAAGCCTGTTCCGAATGCCACTCTACAAGTTACTGGTGCTGTTGGTTGGAGAAGAGAGGGTCTTATGTACAAGAAGAACGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAC