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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtgacgagcattttattgtttatgaatggattgcatttgctcaacgctgtttacatcccccagGACATCAAGTTTGCTGTTCATGCACACCCAACTTTGTCTGAGGTTCTGGATGAGCTCTTCAAAGCTGCCAAG

Basic information

species Oryza sativa
transcript LOC_Os01g23610.1
intron # 13
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g23610.1 (Oryza sativa), 3'ss of exon 13
lower sequence: GRMZM2G145595_T01 (Zea mays), 3'ss of exon 13
-----------------------------gtaagtgacgagcatttt-attgtttatg-aatg------gattgcatttgctcaacgctgtttacatcccccagGACATCAAGTTTGCTGTTCATGCACACCCAACTTTGTCTGAGGTTCTGGATGAGCTCTTCAAAGCTGCCAAG
                             |||        |||||||  || | |    ||||      | ||  |||||| ||   |  |||  | ||  ||||||||||||||||||||||||||||||||||| |||||||| ||||||||||| |||||||| |||||||||
gtgagtttgtcatgcattctgttagctgtgtagcatttctgcatttttgttctctgcataatgctaaacgcttaaatttgcacataaccttttgtaccctgcagGACATCAAGTTTGCTGTTCATGCACACCCAACGTTGTCTGAAGTTCTGGATGAACTCTTCAAGGCTGCCAAG

upper sequence: LOC_Os01g23610.1 (Oryza sativa), 3'ss of exon 13
lower sequence: GLYMA17G03560.1 (Glycine max), 3'ss of exon 13
---------------------------------------------------gtaagtgacgagcattttattgtttatgaatggattgcatttgctcaa---cgctgttt----acatcccccagGACATCAAGTTTGCTGTTCATGCACACCCAACTTTGTCTGAGGTTCTGGATGAGCTCTTCAAAGCTGCCAAG
                                                    |        ||  ||| | |||| ||  ||        |||| | ||   | | ||||      |     |||||||| || ||||| ||||||||||| ||||||||||| |||||||| ||||| || |||||| | || |||
gtaagtttttctaccacatttatgtgtgcacctggcatttagttattaataatggtctcaaagtctttcactgtt-atttatcctgcctgtttggtaaatttcaccgttttgtggtacaatgcagGACATAAAATTTGCCGTTCATGCACATCCAACTTTGTCCGAGGTTCTTGATGAACTATTCAAATCAGCAAAG

upper sequence: LOC_Os01g23610.1 (Oryza sativa), 3'ss of exon 13
lower sequence: GLYMA07G37050.1 (Glycine max), 3'ss of exon 13
-----------------------------------------------gtaagtgacgagcattttattgtttatgaatggattgcatttgctcaa---cgctgttt----acatcccccagGACATCAAGTTTGCTGTTCATGCACACCCAACTTTGTCTGAGGTTCTGGATGAGCTCTTCAAAGCTGCCAAG
                                                  ||| || |    || | |  ||||  ||        |||| | ||   | | ||||      |     |||||||| || ||||| ||||||||||| ||||||||||| |||||||| ||||| || |||||| | || |||
gtaaatttttctaccacatttatgtgtattggcatttagttactaataatagtcacaaagtcttcact-cttatttatcctgcttgtttggtaaatttcaccgttttgtggtacaatgcagGACATAAAATTTGCAGTTCATGCACATCCAACTTTGTCCGAGGTTCTTGATGAACTATTCAAATCAGCAAAG

upper sequence: LOC_Os01g23610.1 (Oryza sativa), 3'ss of exon 13
lower sequence: Vv14s0060g01330.t01 (Vitis vinifera), 3'ss of exon 13
-----------------------------------------------------------------------------------------------gtaagtgacgagcattttattgtttatgaatggattgcatttgc-----tcaacgctgtttacatcccccagGACATCAAGTTTGCTGTTCATGCACACCCAACTTTGTCTGAGGTTCTGGATGAGCTCTTCAAAGCTGCCAAG
                                                                                                  |      |  || | || |||  |   |   || |||| |      |  ||      | || ||  |||||||| |||||||||||||||||||| ||||| ||||| ||||| || || || ||||||||| |||| |||
gttttttttttttttctccatttgcccatacaatttgcaagacagtaataccaaatcctctttacatctatggcatgattcattatgttttgactcataccattcaaaatataatggttgctattttccttccattcgtcatctttcacaacccgtgcaccctgcagGACATAAAGTTTGCTGTTCATGCACATCCAACCTTGTCCGAGGTGCTTGACGAACTCTTCAAATCTGCTAAG

upper sequence: LOC_Os01g23610.1 (Oryza sativa), 3'ss of exon 13
lower sequence: Vv05s0077g01210.t01 (Vitis vinifera), 3'ss of exon 13
------------------------------gtaagtgacga-gcattttattgtttatgaatggattgcatttgctcaacgctgttt---acatcccccagGACATCAAGTTTGCTGTTCATGCACACCCAACTTTGTCTGAGGTTCTGGATGAGCTCTTCAAAGCTGCCAAG
                              | |||||| |  | |     | | || | | ||    | ||||   ||   || |||   ||| |   |||||||| || |||||||||||||| || ||||| ||||| || || |||||||| ||||| ||| | || |||
tcaaactcaatcatctcttggtttcttcttgaaagtgagggtggaaccggtagcttgtta-tgatgagtattttgacatttcttttttggacaccttacagGACATAAAATTTGCTGTTCATGCGCATCCAACCTTGTCAGAAGTGCTGGATGAACTCTTTAAATCAGCTAAG

upper sequence: LOC_Os01g23610.1 (Oryza sativa), 3'ss of exon 13
lower sequence: Vv14s0060g01410.t01 (Vitis vinifera), 3'ss of exon 5
-----------------------------gtaagtgacgagcattttattgtttatgaatggattgcatttgct-----caacgctgtttacatcccccagGACATCAAGTTTGCTGTTCATGCACACCCAACTTTGTCTGAGGTTCTGGATGAGCTCTTCAAAGCTGCCAAG
                             |||       |  || | || |||  |   |   || |||| |         ||  | | | || ||  ||||||||  ||||||||||||||||||| ||||| ||||| ||||| || ||  | ||||||||| |||| |||
ttatggcatgattcattatgttttgactcgtac-cattcaaaatataatggttgctattttccttccattcgtcatctctcacaatctgtgcaccctgcagGACATAGAGTTTGCTGTTCATGCACATCCAACCTTGTCCGAGGTGCTTGACAAACTCTTCAAATCTGCTAAG

upper sequence: LOC_Os01g23610.1 (Oryza sativa), 3'ss of exon 13
lower sequence: PP1S112_186V6.1 (Physcomitrella patens), 3'ss of exon 13
------------------------------------------------------------------gtaagtgacgagcattttattgtttatgaatg-gattgcatttgctcaacgctgtttacatcccc--cagGACATCAAGTTTGCTGTTCATGCACACCCAACTTTGTCTGAGGTTCTGGATGAGCTCTTCAAAGCTGCCAAG
                                                                  |||  || | ||  | |   | |  |    || |||| | | |    | |  |   |   ||     ||||||||||| |||||||| ||||| || || || |||||||| ||  |||| |||||||||||  | || |||
gtgagtgccaagtttcattttactagaattgtctgccgaaccttgacgtctaatggatgtgatgatgtagttgtcaag--tctcgctatcgaatgctgcgatttcttctaacaacccattgctctgtctttgacagGACATCAAATTTGCTGTGCATGCCCATCCGACCTTGTCTGAAGTGTTGGACGAGCTCTTCAAGTCAGCGAAG

upper sequence: LOC_Os01g23610.1 (Oryza sativa), 3'ss of exon 13
lower sequence: PP1S35_94V6.1 (Physcomitrella patens), 3'ss of exon 13
---------------------------------------------------------------------------gtaagtgacgagca--ttttattgtttatgaatggattgcatttgctcaac--gctgtttacatcccccagGACATCAAGTTTGCTGTTCATGCACACCCAACTTTGTCTGAGGTTCTGGATGAGCTCTTCAAAGCTGCCAAG
                                                                            | | |      ||  | ||  | |  ||   ||  |     |    ||||  | ||||    |     ||||||||||||||||||||||||| || || || || ||||| ||| |||| ||||| ||||| || || |||
gtgagtccatgaactcatttgattcacagttgctgctgaaccttttaattcccagctaggatccttgatttaccaatcaatattcgtcacgtcttgctatcgattgctgtgtattcctaaaacaactggttgttcttcttgaatagGACATCAAGTTTGCTGTTCATGCCCATCCCACCTTATCTGAAGTTTTGGACGAGCTGTTCAAGGCAGCTAAG

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|88851216|gb|CI373974.1|CI373974
EST:     AACGCCACTGCCCTCGGAACTCGTGTACAA                         GACATCAAGTTTGCTGTTCATGCACACCCAACTTTGTCTGAGGGTCTGGAT
genomic: AACGCCATTGCCCTCGGAACTCGTGTACAAgtaagtgacg ... catcccccagGACATCAAGTTTGCTGTTCATGCACACCCAACTTTGTCTGAGGTTCTGGAT
EST: gi|29637258|gb|CB642267.1|CB642267
EST:     ACCTCATCCACGAGGCATCAAACGCCATTGCCCTCGGAACTCGTGTACAA                         GACATCAAGTTTGCTGTTCATGCACACCCAACTTTGTCTGAGGTTCTGGAT
genomic: ACCTCATCCACGAGGCATCAAACGCCATTGCCCTCGGAACTCGTGTACAAgtaagtgacg ... catcccccagGACATCAAGTTTGCTGTTCATGCACACCCAACTTTGTCTGAGGTTCTGGAT
EST: gi|86887058|gb|CI325873.1|CI325873
EST:     ACCTCATCCACGAGGCATCAAACGCCATTGCCCTCGGAACTCGTGTACAA                         GACATCAAGTTTGCTGTTCATGCACACCCAACTTTGTCTGAGGTTCTGGAT
genomic: ACCTCATCCACGAGGCATCAAACGCCATTGCCCTCGGAACTCGTGTACAAgtaagtgacg ... catcccccagGACATCAAGTTTGCTGTTCATGCACACCCAACTTTGTCTGAGGTTCTGGAT
EST: gi|22304992|gb|BQ906214.1|BQ906214
EST:     GCCCTCGGAACTCGTGTACAA                         GACATCAAGTTTGCTGTTCATGCACACCC-ACTTTGTCTGAGGTTCTGGAT
genomic: GCCCTCGGAACTCGTGTACAAgtaagtgacg ... catcccccagGACATCAAGTTTGCTGTTCATGCACACCCAACTTTGTCTGAGGTTCTGGAT
EST: gi|88518587|gb|CI446241.1|CI446241
EST:     TTGCCCTCGGAAGTCGTGTACAA                         GACATCAAGTTTGCTGTTCATGCACACCCAACTTTGTCTGAGGTTCTGGAT
genomic: TTGCCCTCGGAACTCGTGTACAAgtaagtgacg ... catcccccagGACATCAAGTTTGCTGTTCATGCACACCCAACTTTGTCTGAGGTTCTGGAT

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: 60 (upstream exon), 72 (downstream exon)
Score: 31

TGACACTGGAGAAATTCTTGGAGTTCACATATTAGGTTTGCATGCTGCTGACCTCATCCACGAGGCATCAAACGCCATTGCCCTCGGAACTCGTGTACAAgtaagtgacg ... catcccccagGACATCAAGTTTGCTGTTCATGCACACCCAACTTTGTCTGAGGTTCTGGATGAGCTCTTCAAAGCTGCCAAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cattttattgtttatgaatggattgcatttgctcaacgctgtttacatcccccagGACATCAAGTTTGCTGTTCATGCACACCCAACTTTGTCTGAGGTTCTGGATGAGCTCTTCAAAGCTGCCAAG
                                             catccccc  CT-rich tract
     tattgtttatgaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagtgacgagcattttattgtttatgaatggattgcatttgctcaacgctgtttacatcccccagGACATCAAGTTTGCTGTTCATGCACACCCAACTTTGTCTGAGGTTCTGGATGAGCTCTTCAAAGCTGCCAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGC