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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtcagaaattcagaatgctcaattgatttgtactttctactttacctttatttatgagttatatgtatcgctaagttgcacatttttctcctatacatggagcatagatttttagatattctttatgcgctctgccctgcttctgattatctctcttggtctgctgtcatcatgcagGTGTTATTGCCATGGCAAATTCTGGACCTGATTCCAATGGATCGCAGTTTTACATTACCACAATCAAGACAAGCTG

Basic information

species Oryza sativa
transcript LOC_Os09g36670.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os09g36670.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G158237_T05 (Zea mays), 3'ss of exon 4
gtcagaaattcagaatgctcaattgatttgtactttctactttacctttatttatgagttatatgtatcgctaagttgcacatttttctcctatacatgga-gcatagatttttagatattctttatgcgctctgccctgcttctgattatctctcttggtctgctgtcatcatgcagGTGTTATTGCCATGGCAAATTCTGGACCTGATTCCAATGGATCGCAGTTTTACATTACCACAATCAAGACAAGCTG
                                                                         | |     ||   | |   ||     ||    ||  | | |  || || || |       ||  |   |||  | |    | | || | ||||||| |   ||||| ||| |||| ||||| |||||||||| |||||| |||||||| ||||||||||| || || ||||||||||||||
-------------------------------------------------------------------------aatcatgaatgggtgtttgatcttctgacaggtatctatctgaatttttttaaattaggatggtc-atttccaact-ctacccctgctttgctgtctt---gcagGGGTTGTTGCTATGGCGAATTCTGGACTTGATTCTAATGGATCTCAGTTTTACATAACTACTATCAAGACAAGCTG

upper sequence: LOC_Os09g36670.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G371271_T01 (Zea mays), 3'ss of exon 10
gtcagaaattcagaatgctcaattgatttgtactttctactttacctttatttatgagttatatgtatcgctaagttgcacatttttctcctatacatggagcatagatttttagatattctttatgcgctctgccctgcttctgattatctctcttggtctgctgtcatcatgcagGTGTTATTGCCATGGCAAATTCTGGACCTGATTCCAATGGATCGCAGTTTTACATTACCACAATCAAGACAAGCTG
                                                                         | |     ||   | |   ||     ||        | |  || ||| ||||               |||  | |    | | || | ||||||| |   ||||| ||| |||| ||||| |||||||||| |||||| |||||||| ||||||||||| || || ||||||||||||||
-------------------------------------------------------------------------aatcatgaatgggtgtttgatcttctgacaggtatctatctgaaattttttaaattaggatggtcatttccaact-ctacccctgctttgctgtctt---gcagGGGTTGTTGCTATGGCGAATTCTGGACTTGATTCTAATGGATCTCAGTTTTACATAACTACTATCAAGACAAGCTG

upper sequence: LOC_Os09g36670.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G086243_T01 (Zea mays), 3'ss of exon 9
gtcagaaattcagaatgctcaa-ttgatttgtactt--tctactttacctttatttatgagttatatgtatcgctaagttgcacatttttctcctatacatgga-gcatagatttttagatattctttatgcgctctgccctgcttctgattatctctcttggtctgctgtcatcatgcagGTGTTATTGCCATGGCAAATTCTGGACCTGATTCCAATGGATCGCAGTTTTACATTACCACAATCAAGACAAGCTG
||      |||    || |  | ||  ||| || ||  |  |   |  |||  ||    |    |   | | || || |     ||   | |   ||   | ||    ||  | | |  | ||| || |       ||  |   |||  | |    | | || | ||||||| |   ||||| ||| ||||  |||| |||||||||| |||||| |||||||| |||||| |||| || || ||||||||||||||
gtatttttttccttttgttttactttgtttatatttatttcatcctgacttggttagcaaccggtcaatgtggccaaatcatgaatgggtgtttgatcttttgacaggtatctatctgaaaatttttaaattagaatggtc-atttccaact-ctacccctgctttgctgtctt---gcagGGGTTGTTGCTGTGGCGAATTCTGGACTTGATTCTAATGGATCTCAGTTT-ACATAACTACTATCAAGACAAGCTG

upper sequence: LOC_Os09g36670.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GLYMA11G11370.1 (Glycine max), 3'ss of exon 5
gtcagaaattcagaatgctcaattgatttgtactttctactttacctttatttatgagttatatgtatcgctaagttgcacatttttctcc-tatacatggagcatagatttttagatattctttatgcgctctgccctgcttctgattatctctcttgg--tctgctgtcatcat-gcagGTGTTATTGCCATGGCAAATTCTGGACCTGATTCCAATGGATCGCAGTTTTACATTACCACAATCAAGACAAGCTG
                                               | | | |  | ||   || ||       || ||  || || |   |||   |  | | | ||| |||   | |  ||| |  | | ||      ||    || | ||| |       | ||  ||| || ||||| ||| || | ||||||||||| ||||||||||||||||| || ||||||| | |||||||| | ||| | || ||
----------------------------------------------gtgagtaacaatttgcttggatgaaagcatttcattttattattaatatttttataac-ttgatgtttttctgtcatttctaagatatgtg----tttGAGTTGTTTCTATGAAATCTTACTCCCATGATTGCAGGAGTTGTTTCTATGGCAAATTCAGGACCTGATTCCAATGGCTCACAGTTTTTCCTTACCACAGTGAAGGCCAGATG

upper sequence: LOC_Os09g36670.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GLYMA12G03540.1 (Glycine max), 3'ss of exon 5
gtcagaaattcagaatgctcaattgatttgtactttctactttacctttatttatgagttatatgtatcgctaagttgcacatttttctcctatacatgga-gcatagatttttagatattctt-tatgcgctctgccctgcttctga-ttatctctcttgg--tctgctgtcatcat-gcagGTGTTATTGCCATGGCAAATTCTGGACCTGATTCCAATGGATCGCAGTTTTACATTACCACAATCAAGACAAGCTG
                                                      ||||| | |  |   |||  | || |    |||| | |    ||  |    |  ||   | ||| || || | |    |||    ||  | ||| || | ||| |       | ||  ||| || ||||||||| || | ||||||||||| ||||||||||||||||| || ||||||| | |||||||| | ||| | || ||
-----------------------------------------------------gtgagtaacaatt--tgcttggatgaaagcatttcgctttattattaatatttttataacttgatgtttttctgtcatttctaagatgtgtttgagttgtttctataaaatcttactcccatgattgcagGTGTTGTTTCTATGGCAAATTCAGGACCTGATTCCAATGGCTCACAGTTTTTCTTTACCACAGTGAAGGCCAGATG

upper sequence: LOC_Os09g36670.1 (Oryza sativa), 3'ss of exon 5
lower sequence: Vv03s0038g02200.t01 (Vitis vinifera), 3'ss of exon 5
gtcagaaattcagaatgctcaattgatttgtactttctactttacctttatttatgagttat-atgtatcgctaagttgcacatttttctcc--tatacatggagcat-agatttttagatattctttatgcgctctgccctgcttctgattatctctcttggtctgctgtcatcatgcagGTGTTATTGCCATGGCAAATTCTGGACCTGATTCCAATGGATCGCAGTTTTACATTACCACAATCAAGACAAGCTG
               | ||| |||   |     | | |  || |  |||  || ||  || |  | ||   |  ||    |   | ||      | | ||| | |  | | | ||||  | |||   | ||  |  | | |   | ||  || |    |    | |  ||      || ||||||| || ||||||  ||||| ||||||||||| ||||| || ||||||| ||| |||||| ||||| | |||||
--------------gttctctattacatctctttatttggttgattttttcttctggtttcttgtatactccctagacaaattctctttaaaagttttcatagggattcaaaattttcaagattgagtttgttcctttctcccttcctctttgtgaaacc--atatattgcttggttgtagGTGTTGTTTCCATGGTGAATTCAGGACCTGATTCTAATGGCTCTCAGTTTTTCATCACCACAGTCAAGGCTAGCTG

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|58601241|gb|CK011769.1|CK011769
EST:     TGGGGGCACCTTCCCAGATGAGAATTTCATAGTAAAACATACACATCCAG                         GTGTTATTGCCATGGCAAATTCTGGACCTGATTCCAATGGATCGCAGTTTT
genomic: TGGGGGCACCTTCCCAGATGAGAATTTCATAGTAAAACATACACATCCAGgtcagaaatt ... catcatgcagGTGTTATTGCCATGGCAAATTCTGGACCTGATTCCAATGGATCGCAGTTTT
EST: gi|88830470|gb|CI010670.1|CI010670
EST:     TGGGGGCACCTTCCCAGATGAGAATTTCATAGTAAAACATACACATCCAG                         GTGTTATTGCCATGGCAAATTCTGGACCTGATTCCAATGGATCGCAGTTTT
genomic: TGGGGGCACCTTCCCAGATGAGAATTTCATAGTAAAACATACACATCCAGgtcagaaatt ... catcatgcagGTGTTATTGCCATGGCAAATTCTGGACCTGATTCCAATGGATCGCAGTTTT
EST: gi|58691487|gb|CK080174.1|CK080174
EST:     TGGGGGCACCTTCCCAGATGAGAATTTCATAGTAAAACATACACATCCAG                         GTGTTATTGCCATGGCAAATTCTGGACCTGATTCCAATGGATCGCAGTTTT
genomic: TGGGGGCACCTTCCCAGATGAGAATTTCATAGTAAAACATACACATCCAGgtcagaaatt ... catcatgcagGTGTTATTGCCATGGCAAATTCTGGACCTGATTCCAATGGATCGCAGTTTT

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), 60 (downstream exon)
Score: 12

CAGGGTGGGGACATAGTTAGAGGTGATGGAAAAGGAAGTGAGTCTATATATGGGGGCACCTTCCCAGATGAGAATTTCATAGTAAAACATACACATCCAGgtcagaaatt ... catcatgcagGTGTTATTGCCATGGCAAATTCTGGACCTGATTCCAATGGATCGCAGTTTTACATTACCACAATCAAGACAAGCTG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttatgcgctctgccctgcttctgattatctctcttggtctgctgtcatcatgcagGTGTTATTGCCATGGCAAATTCTGGACCTGATTCCAATGGATCGCAGTTTTACATTACCACAATCAAGACAAGCTG
                  ttctgat  putative branch site (score: 12)
                     tgattat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtcagaaattcagaatgctcaattgatttgtactttctactttacctttatttatgagttatatgtatcgctaagttgcacatttttctcctatacatggagcatagatttttagatattctttatgcgctctgccctgcttctgattatctctcttggtctgctgtcatcatgcagGTGTTATTGCCATGGCAAATTCTGGACCTGATTCCAATGGATCGCAGTTTTACATTACCACAATCAAGACAAGCTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCTG