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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtaattactttctagttctctctgtgatctactagacaaattagcaatggattttaatgcatgtctttgcactcttcagGTTTCATCATGATGTGCCCACAACTATTCATCAACTACAAGCTGAAGTCTGTTGCTCATATGCCATGGAGGCAAATGACCTACAAGTTCCTCAACACCAT

Basic information

species Oryza sativa
transcript LOC_Os04g36050.1
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os04g36050.1 (Oryza sativa), 3'ss of exon 10
lower sequence: GRMZM2G437119_T02 (Zea mays), 3'ss of exon 10
gtaagtaattactttctagttctctctgt------gatctactagacaa-attagcaatggatttta-atgcatgtctttgcactcttcagGTTTCATCATGATGTGCCCACAACTATTCATCAACTACAAGCTGAAGTCTGTTGCTCATATGCCATGGAGGCAAATGACCTACAAGTTCCTCAACACCAT
||||| || || |     || |   | ||      ||| |  ||  | | || |||   | |  ||  ||   |  |||| || |||||||||||||||||||||||||| ||| |||| ||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||| ||
gtaagcaactattccactgtccctccagtttatttgatgtgataatctacataagcttagaagcttgtataattaactttccattcttcagGTTTCATCATGATGTGCCCCCAATTATTTATCAACTACAAGCTGAAGTCTGTTGCTCATATGCCATGGAGACAAATGACCTACAAGTTCCTCAACACTAT

upper sequence: LOC_Os04g36050.1 (Oryza sativa), 3'ss of exon 10
lower sequence: GRMZM2G016894_T01 (Zea mays), 3'ss of exon 9
gtaagtaattacttt-ctagttc-----tctctgtgatctactagacaa-attagcaatggatttta-atgcatgtctttgc-actcttcagGTTTCATCATGATGTGCCCACAACTATTCATCAACTACAAGCTGAAGTCTGTTGCTCATATGCCATGGAGGCAAATGACCTACAAGTTCCTCAACACCAT
||||| || || |   ||   ||     | | | |||| |  ||  |   ||||||  ||||  ||| ||   |  |||| | | |||||||||||||| ||||||||||| ||| | || ||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||| ||
gtaagcaactattccactccctcaccagtttgtttgatatgataacctgcattagctgtggagcttatatatgtaacttttccattcttcagGTTTCATTATGATGTGCCCCCAATTGTTTATCAACTACAAGCTGAAGTCTGTTGCTCATATGCCATGGAGACAAATGACCTACAAGTTCCTCAACACTAT

upper sequence: LOC_Os04g36050.1 (Oryza sativa), 3'ss of exon 10
lower sequence: AT5G08500.1 (Arabidopsis thaliana), 3'ss of exon 10
---------gtaagtaattacttt---ctagttctct-ctgtgatctactagacaaattagcaatggattttaatgcatgtctttgcactctt-cagGTTTCATCATGATGTGCCCACAACTATTCATCAACTACAAGCTGAAGTCTGTTGCTCATATGCCATGGAGGCAAATGACCTACAAGTTCCTCAACACCAT
          |    |||||| ||   | |||||    || |  | |  | ||   | | | | | ||  | ||||  |   ||||   | || |||||||||| |||||||| || ||| | ||||||||||| ||||||||||| || || ||| | ||||||||||||||||| || |||||||||||||| ||
gtaaaaatccttcaaaattaccttagaccagttcaaaactctcgtgtggttgattcaattg-agtcgaaatcaatgtgt---tttgtgtttttacagGTTTCATAATGATGTGTCCTCAATTGTTCATCAACTATAAGCTGAAGTCAGTAGCACATTTACCATGGAGGCAAATGACATATAAGTTCCTCAACACAAT

upper sequence: LOC_Os04g36050.1 (Oryza sativa), 3'ss of exon 10
lower sequence: AT5G23575.1 (Arabidopsis thaliana), 3'ss of exon 10
gtaagtaattactttctagttctctctgtgatctactagacaaattagcaatgga----ttttaatgcatgtctttgcactcttcagGTTTCATCATGATGTGCCCACAACTATTCATCAACTACAAGCTGAAGTCTGTTGCTCATATGCCATGGAGGCAAATGACCTACAAGTTCCTCAACACCAT
    |||||  | |||    ||  |     | ||  |    |  |      || |    |||| |     |  ||||   | | ||||||||||||||||||| || || |||||||||||||||||||| || || || || ||| | |||||||| || ||||| ||||||||||||||||||||
----gtaatagccttcaccatccttaaaataactgttgagaatctctcttgtgaagctgttttgagtttggggtttgttttgtgcagGTTTCATCATGATGTGTCCTCAGCTATTCATCAACTACAAGCTTAAATCAGTGGCACATTTACCATGGAGACAGATGACTTACAAGTTCCTCAACACCAT

upper sequence: LOC_Os04g36050.1 (Oryza sativa), 3'ss of exon 10
lower sequence: Vv07s0130g00170.t01 (Vitis vinifera), 3'ss of exon 10
--------------------------------------------------------------------------------------gtaagtaattactttctagttctctctgtgatctactagacaaattagcaatggattttaatgcatgtctttgcactcttcagGTTTCATCATGATGTGCCCACAACTATTCATCAACTACAAGCTGAAGTCTGTTGCTCATATGCCATGGAGGCAAATGACCTACAAGTTCCTCAACACCAT
                                                                                           | |  |  |  |  ||| |    |  | | |   | |||| | |     | || ||   |   |||||     | |||||||||| ||||||||||| ||  | ||||| ||||| |||||||| ||||| |||||| | || |||||||| ||||| |||||||||||||| |||||
gtaagcccttgaattccttttattgttttctgctgctgctgctgctgttgttcccgagttcacatcagcccagttgggccatcaattcgcctcagcatctgttctttcacatctttgttttcgttataaat-atctgacaacttgaacaaaaaactttgt----tgcagGTTTCATTATGATGTGCCCTCAGTTGTTCATAAACTATAAGCTGAAATCTGTGGCTCATCTACCCTGGAGGCAGATGACGTACAAGTTCCTCAATACCAT

upper sequence: LOC_Os04g36050.1 (Oryza sativa), 3'ss of exon 10
lower sequence: PP1S64_201V6.1 (Physcomitrella patens), 3'ss of exon 10
---------------------------------------------gtaagtaattactt-tctagttctctct----gtgatc---tactagacaa---------attagcaatggat---tttaatgc--atgtctttgcactcttcagGTTTCATCATGATGTGCCCACAACTATTCATCAACTACAAGCTGAAGTCTGTTGCTCATATGCCATGGAGGCAAATGACCTACAAGTTCCTCAACACCAT
                                             | |  |  |  ||| ||| | | ||  |    || ||    || ||||||           |||    ||| |   |  | | |  |  | ||   |     ||||||| ||||||||||| ||||| || || |||||||||||| |||||||||| ||||| ||||| ||| | || |||||||||||||||||||| || ||
gtaagttcaaggccatcattggtgattattcatgtttttctgggtgcacttgttggcttctctggatatcaattcaagtaattggttattagacagtcacacgtcgttaatggtggttatgtcgagtactaacctgttcatatgtaccagGTTTTATCATGATGTGTCCACAGCTTTTTATCAACTACAAGTTGAAGTCTGTAGCTCACATGCCTTGGCGACAGATGACCTACAAGTTCCTCAATACTAT

upper sequence: LOC_Os04g36050.1 (Oryza sativa), 3'ss of exon 10
lower sequence: EFJ29253 (Selaginella moellendorffii), 3'ss of exon 10
gtaagtaattactttctagttctctctgtga-tctactag-acaaattagcaatggattttaatgcatgtctttgcactcttc----agGTTTCATCATGATGTGCCCACAACTATTCATCAACTACAAGCTGAAGTCTGTTGCTCATATGCCATGGAGGCAAATGACCTACAAGTTCCTCAACACCAT
                           |||| || |||   ||   ||  |  ||  | | |   ||||| | ||   | |      ||||||||||||||||||||| || || ||||||||||||||||| ||||| || || ||  | || ||| | |||||||| ||||||||||||||||| ||
---------------------------gtgagtccactgtcaccgcttttccttgtctgtaagatcatgtgtgtgtgttgtgtgaaaagGTTTCATCATGATGTGCCCCCAGCTCTTCATCAACTACAAGCTCAAGTCCGTGGCGCACCTCCCCTGGCGCCAAATGACTTACAAGTTCCTCAACACAAT

upper sequence: LOC_Os04g36050.1 (Oryza sativa), 3'ss of exon 10
lower sequence: EFJ13811 (Selaginella moellendorffii), 3'ss of exon 10
gtaagtaattactttctagttctctctgtga-tctactag-acaaattagcaatggattttaatgcatgtctttgcactcttc----agGTTTCATCATGATGTGCCCACAACTATTCATCAACTACAAGCTGAAGTCTGTTGCTCATATGCCATGGAGGCAAATGACCTACAAGTTCCTCAACACCAT
                           |||| || |||   ||   ||  |  ||  | | |   ||||| | ||   | |      ||||||||||||||||||||| || || ||||||||||||||||| ||||| || |||||  | || ||| | |||||||| ||||||||||||||||| ||
---------------------------gtgagtccactgtcaccgcttttccttgtctgtaagatcatgtgtgtgtgttgtgtgaaaagGTTTCATCATGATGTGCCCCCAGCTCTTCATCAACTACAAGCTCAAGTCCGTGGCTCACCTCCCCTGGCGCCAAATGACTTACAAGTTCCTCAACACAAT

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|163928407|gb|EG711331.1|EG711331
EST:     CTGGTACTCATGGATACTCTCTTCTCTCACAAGTTGTGTGTACATGTTTG                         GTTTCATCATGATGTGCCCACAACTATTCATCAACTACAAGCTGAAGTCTG
genomic: CTGGTACTCATGGATACTCTCTTCTCTCACAAGTTGTGTGTACATGTTTGgtaagtaatt ... cactcttcagGTTTCATCATGATGTGCCCACAACTATTCATCAACTACAAGCTGAAGTCTG
EST: gi|38478536|gb|CF962669.1|CF962669
EST:     CTCTTCTCTCACAAGTTGTGTGTACATGTTTG                         GTTTCATCATGATGTGCCCACGACTATTCATCAACTACAAGCTGAAGTCTG
genomic: CTCTTCTCTCACAAGTTGTGTGTACATGTTTGgtaagtaatt ... cactcttcagGTTTCATCATGATGTGCCCACAACTATTCATCAACTACAAGCTGAAGTCTG
EST: gi|9788969|gb|BE530979.1|BE530979
EST:     CTGGTACTCATGGATACTCTCTTCTCTCACAAGTTGTGTGTACATGTTTG                         GTTTCATCATGATGTGCCCACAACTATTCATCAACTACAAGCTGAAGTCTG
genomic: CTGGTACTCATGGATACTCTCTTCTCTCACAAGTTGTGTGTACATGTTTGgtaagtaatt ... cactcttcagGTTTCATCATGATGTGCCCACAACTATTCATCAACTACAAGCTGAAGTCTG
EST: gi|88288451|gb|CI661656.1|CI661656
EST:     CTGGTACTCATGGATACTCTCTTCTCTCACAAGTTGTGTGTACATGTTTG                         GTTTCATCATGATGTGCCCACAACTATTCATC
genomic: CTGGTACTCATGGATACTCTCTTCTCTCACAAGTTGTGTGTACATGTTTGgtaagtaatt ... cactcttcagGTTTCATCATGATGTGCCCACAACTATTCATC
EST: gi|218503668|gb|FG954354.1|FG954354
EST:     CTGGTACTCATGGATACTCTCTTCTCTCACAAGTTGTGTGTACATGTTTG                         GTTTCATCATGATGTGCCCACAACTATTCATCAACTACAAGCTGAAGTCTG
genomic: CTGGTACTCATGGATACTCTCTTCTCTCACAAGTTGTGTGTACATGTTTGgtaagtaatt ... cactcttcagGTTTCATCATGATGTGCCCACAACTATTCATCAACTACAAGCTGAAGTCTG
EST: gi|218504968|gb|FG957275.1|FG957275
EST:     CTGGTACTCATGGATACTCTCTTCTCTCACAAGTTGTGTGTACATGTTTG                         GTTTCATCATGATGTGCCCACAACTATTCATCAACTACAAGCTGAAGTCTG
genomic: CTGGTACTCATGGATACTCTCTTCTCTCACAAGTTGTGTGTACATGTTTGgtaagtaatt ... cactcttcagGTTTCATCATGATGTGCCCACAACTATTCATCAACTACAAGCTGAAGTCTG
EST: gi|38475772|gb|CF959905.1|CF959905
EST:     CTGGTACTCATGGATACTCTCTTCTCTCACAAGTTGGGTGTACATGTTTG                         GTTTCATCATGATGTGCCCACAACTATTCAT-ATATATACAAGCTGAAGTC
genomic: CTGGTACTCATGGATACTCTCTTCTCTCACAAGTTGTGTGTACATGTTTGgtaagtaatt ... cactcttcagGTTTCATCATGATGTGCCCACAACTATTCATCA-AC-TACAAGCTGAAGTC
EST: gi|25802973|gb|CA758934.1|CA758934
EST:     CTGGTACTCATGGATACTCTCTTCTCTCACAAGTTGTGTGTACATGTTTG                         GTTTCATCATGATGTGCCCACAACTATTCATCAACTACAAGCTGAAGTCTG
genomic: CTGGTACTCATGGATACTCTCTTCTCTCACAAGTTGTGTGTACATGTTTGgtaagtaatt ... cactcttcagGTTTCATCATGATGTGCCCACAACTATTCATCAACTACAAGCTGAAGTCTG
EST: gi|218488433|gb|FG948916.1|FG948916
EST:     CTGGTACTCATGGATACTCTCTTCTCTCACAAGTTGTGTGTACATGTTTG                         GTTTCATCATGATGTGCCCACAACTATTCATCAACTACAAGCTGAAGTCTG
genomic: CTGGTACTCATGGATACTCTCTTCTCTCACAAGTTGTGTGTACATGTTTGgtaagtaatt ... cactcttcagGTTTCATCATGATGTGCCCACAACTATTCATCAACTACAAGCTGAAGTCTG
EST: gi|218488312|gb|FG953545.1|FG953545
EST:     CTCTCTTCTCTCACAAGTTGTGTGTACATGTTTG                         GTTTCATCATGATGTGCCCACAACTATTCATCAACTACAAGCTGAAGTCTG
genomic: CTCTCTTCTCTCACAAGTTGTGTGTACATGTTTGgtaagtaatt ... cactcttcagGTTTCATCATGATGTGCCCACAACTATTCATCAACTACAAGCTGAAGTCTG
EST: gi|218488425|gb|FG948908.1|FG948908
EST:     CTGGTACTCATGGATACTCTCTTCTCTCACAAGTTGTGTGTACATGTTTG                         GTTTCATCATGATGTGCCCACAACTATTCATCAACTACAAGCTGAAGTCTG
genomic: CTGGTACTCATGGATACTCTCTTCTCTCACAAGTTGTGTGTACATGTTTGgtaagtaatt ... cactcttcagGTTTCATCATGATGTGCCCACAACTATTCATCAACTACAAGCTGAAGTCTG
EST: gi|38476812|gb|CF960945.1|CF960945
EST:     TGGATACTC-CTTCTCTCACAAGTTGTGTGTACATGTTTG                         GTTTCATCATGATGTGCCCACAACTATTCAGTCGACTACAAGCTGAAGTCT
genomic: TGGATACTCTCTTCTCTCACAAGTTGTGTGTACATGTTTGgtaagtaatt ... cactcttcagGTTTCATCATGATGTGCCCACAACTATTCA-TCAACTACAAGCTGAAGTCT
EST: gi|58677997|gb|CK066684.1|CK066684
EST:     CTGGTACTCATGGATACTCTCTTCTCTCACAAGTTGTGTGTACATGTTTG                         GTTTCATCATGATGTGCCCACAACTATTCATCAACTACAAGCTGAAGTCTG
genomic: CTGGTACTCATGGATACTCTCTTCTCTCACAAGTTGTGTGTACATGTTTGgtaagtaatt ... cactcttcagGTTTCATCATGATGTGCCCACAACTATTCATCAACTACAAGCTGAAGTCTG
EST: gi|86898793|gb|CI296087.1|CI296087
EST:     CTGGTACTCATGGATACTCTCTTCTCTCACAAGTTGTGTGTACATGTTTG                         GTTTCATCATGATGTGCCCACAACTATTCATCAACTACAAGCTGAAGTCTG
genomic: CTGGTACTCATGGATACTCTCTTCTCTCACAAGTTGTGTGTACATGTTTGgtaagtaatt ... cactcttcagGTTTCATCATGATGTGCCCACAACTATTCATCAACTACAAGCTGAAGTCTG
EST: gi|58688332|gb|CK077019.1|CK077019
EST:     CTGGTACTCATGGATACTCTCTTCTCTCACAAGTTGTGTGTACATGTTTG                         G-TTCATCATGATGTG-CCACAACTATTCATCAACTACAAGCTGAAGTCTG
genomic: CTGGTACTCATGGATACTCTCTTCTCTCACAAGTTGTGTGTACATGTTTGgtaagtaatt ... cactcttcagGTTTCATCATGATGTGCCCACAACTATTCATCAACTACAAGCTGAAGTCTG
EST: gi|218481009|gb|FG969194.1|FG969194
EST:     CTGGTACTCATGGATACTCTCTTCTCTCACAAGTTGTGTGTACATGTTTG                         GTTTCATCATGATGTGCCCACAACTATTCATCAACTACAAGCTGAAGTCTG
genomic: CTGGTACTCATGGATACTCTCTTCTCTCACAAGTTGTGTGTACATGTTTGgtaagtaatt ... cactcttcagGTTTCATCATGATGTGCCCACAACTATTCATCAACTACAAGCTGAAGTCTG
EST: gi|58598976|gb|CK009504.1|CK009504
EST:     CTCTTCTCTCACAAGTTGTGTGTACATGTTTG                         GTTTCATCATGATGTGCCCACAAGTATTCATCAACTACAAGCTGAAGTCTG
genomic: CTCTTCTCTCACAAGTTGTGTGTACATGTTTGgtaagtaatt ... cactcttcagGTTTCATCATGATGTGCCCACAACTATTCATCAACTACAAGCTGAAGTCTG
EST: gi|66923041|gb|CX109889.1|CX109889
EST:     CTGGTACTCATGGATACTCTCTTCTCTCACAAGTTGTGTGTACATGTTTG                         GTTTCATCATGATGTGCCCACAACTATTCATCAACTACAAGCTGAAGTCTG
genomic: CTGGTACTCATGGATACTCTCTTCTCTCACAAGTTGTGTGTACATGTTTGgtaagtaatt ... cactcttcagGTTTCATCATGATGTGCCCACAACTATTCATCAACTACAAGCTGAAGTCTG

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: 64 (upstream exon), 52 (downstream exon)
Score: 28

CTTGTGTTCTGTTTCTCCATCTATTCCCTTAAGTATGAGAAACACAAGAGCTGGTACTCATGGATACTCTCTTCTCTCACAAGTTGTGTGTACATGTTTGgtaagtaatt ... cactcttcagGTTTCATCATGATGTGCCCACAACTATTCATCAACTACAAGCTGAAGTCTGTTGCTCATATGCCATGGAGGCAAATGACCTACAAGTTCCTCAACACCAT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgatctactagacaaattagcaatggattttaatgcatgtctttgcactcttcagGTTTCATCATGATGTGCCCACAACTATTCATCAACTACAAGCTGAAGTCTGTTGCTCATATGCCATGGAGGCAAATGACCTACAAGTTCCTCAACACCAT
                           ttttaat  putative branch site (score: 28)
                                       tctttgcactcttc  putative PPT
                          attttaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagtaattactttctagttctctctgtgatctactagacaaattagcaatggattttaatgcatgtctttgcactcttcagGTTTCATCATGATGTGCCCACAACTATTCATCAACTACAAGCTGAAGTCTGTTGCTCATATGCCATGGAGGCAAATGACCTACAAGTTCCTCAACACCAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG