Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aaattctggagtgatcggtgaagtgtttaatatggttgacttcagtttcaactgatttgttcatcgagcttgctgtaactatggccgcatattgctgcagGAGGAGGACTTGAAGCAATTCAGGCAATGGGGAAGCAAGACTCCAGGCCATCCCGAGAACTTCGAGACGCCCGGAGTTGAAGTTACCACTG

Basic information

species Oryza sativa
transcript LOC_Os06g04270.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os06g04270.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G033208_T01 (Zea mays), 3'ss of exon 1
aaattctggagtg------atcggtgaagtgtt-taatatggttgacttcagtttcaactgatttgttcatcgagcttgctgtaactatggccgcatattgctgcagGAGGAGGACTTGAAGCAATTCAGGCAATGGGGAAGCAAGACTCCAGGCCATCCCGAGAACTTCGAGACGCCCGGAGTTGAAGTTACCACTG
 || | | ||| |      | |   | || | |   || || ||||      | ||   || | |||  |  |   ||| | ||||| |||  |  ||    || ||||||||||||||||||| |||||||||||||||||||  || || ||||| || |||||||| ||||| || ||||||||||||||||| |
-aactattgagcgtaattcacctcagcagagctgccatgtgtttgataagcatctcttatgttatgtg-actggatttgttctaactgtggttg-gta----tgtagGAGGAGGACTTGAAGCAGTTCAGGCAATGGGGAAGCAGAACACCGGGCCACCCTGAGAACTTTGAGACTCCAGGAGTTGAAGTTACCACCG

upper sequence: LOC_Os06g04270.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GLYMA10G43990.1 (Glycine max), 3'ss of exon 1
aaatt--ctggagtgatcggtgaagtgtttaatatggttgacttcagtttcaactgatttgttcatcga-gcttgctgtaactatggccgcatattgctgcagGAGGAGGACTTGAAGCAATTCAGGCAATGGGGAAGCAAGACTCCAGGCCATCCCGAGAACTTCGAGACGCCCGGAGTTGAAGTTACCACTG
|  ||  |  |  ||| |  ||| |     |||||  |||       ||| || |  |  | || ||    | ||   |   | |  | |  |        ||||  | ||| | ||| ||||| | |||||||||||||  ||||| || ||||| |||||||| ||||| |  ||||||||||| ||||| |
aggttgacatggatgacctttgatgga---aatataattgtgaagcttttaaagttgtgggatcttcattacctgaatttgttgtttcggggttacatgatagGAACAAGACCTTAAGGAATTCCGACAATGGGGAAGCAGAACTCCTGGACATCCTGAGAACTTTGAGACCCTTGGAGTTGAAGTGACCACAG

upper sequence: LOC_Os06g04270.1 (Oryza sativa), 3'ss of exon 1
lower sequence: AT2G45290.1 (Arabidopsis thaliana), 3'ss of exon 1
--------------------------------------------------------------------aaattc-tggagtgatcggtgaagtgtttaatatggttgacttc--agtttcaa----ctgatttgttcatcgagctt-------gctgtaactatggccgcatattgctgcagGAGGAGGACTTGAAGCAATTCAGGCAATGGGGAAGCAAGACTCCAGGCCATCCCGAGAACTTCGAGACGCCCGGAGTTGAAGTTACCACTG
                                                                    |||| |   || || || ||        | || ||||    ||   ||| |  |      || ||||  | | | |||       |||| | |  ||      | ||     ||||||| || ||||||   ||| | ||||||||||| ||||||||||| ||||| ||||| || ||||| || || |||||||  || ||||
gtttgtgttctcttactctgcttattaagtttgtatccttttagtttacattattgagattacatagtaaatacacagattgttccgtttccctgctcatttggtgatttttggagtcttgagatttagaattgtagaaccaacttaagatttgctgaagcagtgttgaagttttttattagGAGGAAGATTTGAAGAGCTTCCGTCAATGGGGAAGTAAGACTCCAGGACATCCTGAGAATTTTGAGACTCCTGGTGTTGAAGCCACTACTG

upper sequence: LOC_Os06g04270.1 (Oryza sativa), 3'ss of exon 1
lower sequence: AT3G60750.1 (Arabidopsis thaliana), 3'ss of exon 1
-------------------------------------------aaattctgga-gtgatcggtgaagtgtttaatatgg--ttgacttcagtttcaactgat--ttgttc--atcgagcttgctgtaactatggccgcatattgctgc-agGAGGAGGACTTGAAGCAATTCAGGCAATGGGGAAGCAAGACTCCAGGCCATCCCGAGAACTTCGAGACGCCCGGAGTTGAAGTTACCACTG
                                           || |  || | ||  |   |  ||||  ||   ||    ||  || |  |||| |||||   || |   |      |  ||| ||   ||   | || |   |   ||||||| || |||||||| ||| | ||||||||||||||||| ||||| ||||| ||||| |||||||| || ||| ||||||| || ||||
gtctgtgatctcttctctgtttaattgctttcgatctgatcgtaattgatgaatgtagtaactttagtggatagattgaatctgttttgatattcatctgatggctgcttgaagtagattcactgaaaaggtgtttggatttgtttattagGAGGAAGATTTGAAGCAGTTCCGTCAATGGGGAAGCAAGACACCAGGACATCCTGAGAATTTCGAGACTCCTGGAATTGAAGTCACTACTG

upper sequence: LOC_Os06g04270.1 (Oryza sativa), 3'ss of exon 1
lower sequence: EFJ07676 (Selaginella moellendorffii), 3'ss of exon 1
aaattctggagtgatcggtgaagtgtttaatatggttgacttcagtttcaactgatttgttcatcgagcttgctgtaactatgg---ccgcatattgctgcagGAGGAGGACTTGAAGCAATTCAGGCAATGGGGAAGCAAGACTCCAGGCCATCCCGAGAACTTCGAGACGCCCGGAGTTGAAGTTACCACTG
                        ||    | |   |   |  |||||| |    ||   |||  |  ||| || | |  ||||    |     |   | ||||| ||||| |||||||||||| | |||||||| ||||  ||||| |||||||| |||||||||||||| ||||| || ||||| || ||||
------------------------gtaggctctccattgatctagtttcgagcttttctatcaaagttcttcctttcaacatggatttcttgcttgtttccagGAAGAGGATTTGAAGCAATTCCGTCAATGGGGCAGCAGAACTCCTGGCCATCCAGAGAACTTCGAGACTCCCGGCGTGGAAGTCACGACTG

upper sequence: LOC_Os06g04270.1 (Oryza sativa), 3'ss of exon 1
lower sequence: EFJ07729 (Selaginella moellendorffii), 3'ss of exon 1
aaattctggagtgatcggtgaagtgtttaatatggttgacttcagtttcaactgatttgttcatcgagcttgctgtaactatgg---ccgcatattgctgcagGAGGAGGACTTGAAGCAATTCAGGCAATGGGGAAGCAAGACTCCAGGCCATCCCGAGAACTTCGAGACGCCCGGAGTTGAAGTTACCACTG
                        ||    | |   |   |  |||||| |    ||   |||  |  ||| || | |  ||||    |   | |   | ||||| ||||| |||||||||||| | |||||| | ||||  ||||| || ||||| |||||||||||||| ||||| || ||||| || ||||
------------------------gtaggctctccattgatctagtttcgagcttttctatcaaagttcttcctttcaacatggatttcttgtttgtttccagGAAGAGGATTTGAAGCAATTCCGTCAATGGAGCAGCAGAACTCCTGGTCATCCAGAGAACTTCGAGACTCCCGGCGTGGAAGTCACGACTG

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|29628849|gb|CB633860.1|CB633860
EST:     GCATGCTCCAGTACGCCCTGCTCCACCTCGCCGGCTACGACGCCGTCTTG                         GAGGAGGACTTGAAGCAATTCAGGCAATGGGGAAGCAAGACTCCAGGCCAT
genomic: GCATGCTCCAGTACGCCCTGCTCCACCTCGCCGGCTACGACGCCGTCTTGgtaagcgctt ... attgctgcagGAGGAGGACTTGAAGCAATTCAGGCAATGGGGAAGCAAGACTCCAGGCCAT
EST: gi|29616150|gb|CB621162.1|CB621162
EST:     GCATGCTCCAGTACGCCCTGCTCCACCTCGCCGGCTACGACGCCGTCTTG                         GAGGAGGACTTGAAGCAATTCAGGCAATGGGGAAGCAAGACTCCAGGCCAT
genomic: GCATGCTCCAGTACGCCCTGCTCCACCTCGCCGGCTACGACGCCGTCTTGgtaagcgctt ... attgctgcagGAGGAGGACTTGAAGCAATTCAGGCAATGGGGAAGCAAGACTCCAGGCCAT
EST: gi|58665775|gb|CK054461.1|CK054461
EST:     GCCGGCTACGACGCCGTCTTG                         GAGGAGGACTTGAAGCAATTCAGGCAATGGGGAAGCAAGACTCCAGGCCAT
genomic: GCCGGCTACGACGCCGTCTTGgtaagcgctt ... attgctgcagGAGGAGGACTTGAAGCAATTCAGGCAATGGGGAAGCAAGACTCCAGGCCAT
EST: gi|58605211|gb|CK033244.1|CK033244
EST:     CGACG-CGTCTTG                         GAGGAGGACTTGAAGCAATTCAGGCAATGGGGAAGCAAGACTCCAGGCCAT
genomic: CGACGCCGTCTTGgtaagcgctt ... attgctgcagGAGGAGGACTTGAAGCAATTCAGGCAATGGGGAAGCAAGACTCCAGGCCAT
EST: gi|58694852|gb|CK083539.1|CK083539
EST:     GCATGCTCCAGTACGCCCTGCTCCACCTCGCCGGCTACGACGCCGTCTTG                         GAGGAGGACTTGAAGCAATTCAGGCAATGGGGAAGCAAGACTCCAGGCCAT
genomic: GCATGCTCCAGTACGCCCTGCTCCACCTCGCCGGCTACGACGCCGTCTTGgtaagcgctt ... attgctgcagGAGGAGGACTTGAAGCAATTCAGGCAATGGGGAAGCAAGACTCCAGGCCAT
EST: gi|38471630|gb|CF955761.1|CF955761
EST:     TGCTCCAGTACGCCCTGCTCCACCTCGCCGGCTACGACGCCGTCTTG                         GAGGAGGACTTGAAGCAATTCAGGCAATGGGGAAGCAAGACTCCAGGCCAT
genomic: TGCTCCAGTACGCCCTGCTCCACCTCGCCGGCTACGACGCCGTCTTGgtaagcgctt ... attgctgcagGAGGAGGACTTGAAGCAATTCAGGCAATGGGGAAGCAAGACTCCAGGCCAT
EST: gi|58605667|gb|CK033700.1|CK033700
EST:     GCATGCTCCAGTACGCCCTGCTCCACCTCGCCGGCTACGAC-CCGTCTTG                         GAGGAGGACTTGA
genomic: GCATGCTCCAGTACGCCCTGCTCCACCTCGCCGGCTACGACGCCGTCTTGgtaagcgctt ... attgctgcagGAGGAGGACTTGA
EST: gi|13420644|gb|AU174734.1|AU174734
EST:     GCATGCTCCAGTACGCCCTGCTCCACCTCGCCGGCTACGACGCCGTCTTG                         GAGGAGGACTTGAAGCAATTCAGGCAATGGGGAAGCAAGACTCCAGGCCAT
genomic: GCATGCTCCAGTACGCCCTGCTCCACCTCGCCGGCTACGACGCCGTCTTGgtaagcgctt ... attgctgcagGAGGAGGACTTGAAGCAATTCAGGCAATGGGGAAGCAAGACTCCAGGCCAT
EST: gi|29658985|gb|CB655260.1|CB655260
EST:     GCATGCTCCAGTACGCCCTGCTCCACCTCGCCGGCTACGACGCCGTCTTG                         GAGGAGGACTTGAAGCAATTCAGGCAATGGGGAAGCAAGACTCCAGGCCAT
genomic: GCATGCTCCAGTACGCCCTGCTCCACCTCGCCGGCTACGACGCCGTCTTGgtaagcgctt ... attgctgcagGAGGAGGACTTGAAGCAATTCAGGCAATGGGGAAGCAAGACTCCAGGCCAT
EST: gi|58693155|gb|CK081842.1|CK081842
EST:     GCATGCTCCAGTACGCCCTGCTCCACCTCGCCGGCTACGACGCCGTCTTG                         GAGGAGGACTTGAAGCAATTCAGGCAATGGGGAAGCAAGACTCCAGGCCAT
genomic: GCATGCTCCAGTACGCCCTGCTCCACCTCGCCGGCTACGACGCCGTCTTGgtaagcgctt ... attgctgcagGAGGAGGACTTGAAGCAATTCAGGCAATGGGGAAGCAAGACTCCAGGCCAT
EST: gi|58611195|gb|CK038907.1|CK038907
EST:     CCATGCTCCAGTACGCC-TGCTCCACCTCGCCGGCTACGACGCCGTCTTG                         GAGGAGGACTTGAAGCAATTCAGGCAATGGGGAAGCAAGACTCCAGGCCAT
genomic: GCATGCTCCAGTACGCCCTGCTCCACCTCGCCGGCTACGACGCCGTCTTGgtaagcgctt ... attgctgcagGAGGAGGACTTGAAGCAATTCAGGCAATGGGGAAGCAAGACTCCAGGCCAT
EST: gi|29624781|gb|CB629792.1|CB629792
EST:     GCATGCTCCAGTACGCCCTGCTCCACCTCGCCGGCTACGACGCCGTCTTG                         GAGGAGGACTTGAAGCAATTCAGGCAATGGGGAAGCAAGACTCCAGGCCAT
genomic: GCATGCTCCAGTACGCCCTGCTCCACCTCGCCGGCTACGACGCCGTCTTGgtaagcgctt ... attgctgcagGAGGAGGACTTGAAGCAATTCAGGCAATGGGGAAGCAAGACTCCAGGCCAT
EST: gi|44679342|gb|CR292776.1|CR292776
EST:     GGCTA-GACGCCGTCTTG                         GAGGAGGACTTGAAGCAATTCAGGCAATGGGGAAGCAAGACTCCAGGCCAT
genomic: GGCTACGACGCCGTCTTGgtaagcgctt ... attgctgcagGAGGAGGACTTGAAGCAATTCAGGCAATGGGGAAGCAAGACTCCAGGCCAT
EST: gi|29627380|gb|CB632391.1|CB632391
EST:     GCATGCTCCAGTACGCCCTGCTCCACCTCGCCGGCTACGACGCCGTCTTG                         GAGGAGGACTTGAAGCAATTCAGGCAATGGGGAAGCAAGACTCCAGGCCAT
genomic: GCATGCTCCAGTACGCCCTGCTCCACCTCGCCGGCTACGACGCCGTCTTGgtaagcgctt ... attgctgcagGAGGAGGACTTGAAGCAATTCAGGCAATGGGGAAGCAAGACTCCAGGCCAT
EST: gi|58610004|gb|CK038037.1|CK038037
EST:     GCATGCTCCAGTACGCCCTGCTCCACCTCGCCGGCTACGACGCCGTCTTG                         GAGGAGGACTTGAAGCAATTCAGGCAATGGGGAAGCAAGACTCCAGGCCAT
genomic: GCATGCTCCAGTACGCCCTGCTCCACCTCGCCGGCTACGACGCCGTCTTGgtaagcgctt ... attgctgcagGAGGAGGACTTGAAGCAATTCAGGCAATGGGGAAGCAAGACTCCAGGCCAT
EST: gi|58612824|gb|CK040536.1|CK040536
EST:     CATGCTCCAGTACTGCCCTGCTCCACCTCGCCGGCTACGACGCCGTCTTG                         GAGGAGGACTTGAAGCAATTCAGGCAATGGGGAAGCAAGACTCCAGGCCAT
genomic: CATGCTCCAGTAC-GCCCTGCTCCACCTCGCCGGCTACGACGCCGTCTTGgtaagcgctt ... attgctgcagGAGGAGGACTTGAAGCAATTCAGGCAATGGGGAAGCAAGACTCCAGGCCAT
EST: gi|29616061|gb|CB621073.1|CB621073
EST:     GCATGCTCCAGTACGCCCTGCTCCACCTCGCCGGCTACGACGCCGTCTTG                         GAGGAGGACTTGAAGCAATTCAGGCAATGGGGAAGCAAGACTCCAGGCCAT
genomic: GCATGCTCCAGTACGCCCTGCTCCACCTCGCCGGCTACGACGCCGTCTTGgtaagcgctt ... attgctgcagGAGGAGGACTTGAAGCAATTCAGGCAATGGGGAAGCAAGACTCCAGGCCAT
EST: gi|300215739|gb|HO088365.1|HO088365
EST:     GCATGCTCCAGTACGCCCTGCTCCACCTCGCCGGCTACGACGCCGTCTTG                         GAGGAGGACTTGAAGCAATTCAGGCAATGGGGAAGCAAGACTCCAGGCCAT
genomic: GCATGCTCCAGTACGCCCTGCTCCACCTCGCCGGCTACGACGCCGTCTTGgtaagcgctt ... attgctgcagGAGGAGGACTTGAAGCAATTCAGGCAATGGGGAAGCAAGACTCCAGGCCAT
EST: gi|29658871|gb|CB655146.1|CB655146
EST:     GCATGCTCCAGTACGCCCTGCTCCACCTCGCCGGCTACGACGCCGTCTTG                         GAGGAGGACTTGAAGCAATTCAGGCAATGGGGAAGCAAGACTCCAGGCCAT
genomic: GCATGCTCCAGTACGCCCTGCTCCACCTCGCCGGCTACGACGCCGTCTTGgtaagcgctt ... attgctgcagGAGGAGGACTTGAAGCAATTCAGGCAATGGGGAAGCAAGACTCCAGGCCAT
EST: gi|29658330|gb|CB654605.1|CB654605
EST:     GCATGCTCCAGTACGCCCTGCTCCACCTCGCCGGCTACGACGCCGTCTTG                         GAGGAGGACTTGAAGCAATTCAGGCAATGGGGAAGCAAGACTCCAGGCCAT
genomic: GCATGCTCCAGTACGCCCTGCTCCACCTCGCCGGCTACGACGCCGTCTTGgtaagcgctt ... attgctgcagGAGGAGGACTTGAAGCAATTCAGGCAATGGGGAAGCAAGACTCCAGGCCAT
EST: gi|58674058|gb|CK062744.1|CK062744
EST:     GCATGCTCCAGTACGCCCTGCTCCACCTCGCCGGCTACGACGCCGTCTTG                         GAGGAGGACTTGAAGCAATTCAGGCAATGGGGAAGCAAGACTCCAGGCCAT
genomic: GCATGCTCCAGTACGCCCTGCTCCACCTCGCCGGCTACGACGCCGTCTTGgtaagcgctt ... attgctgcagGAGGAGGACTTGAAGCAATTCAGGCAATGGGGAAGCAAGACTCCAGGCCAT
EST: gi|58670081|gb|CK058767.1|CK058767
EST:     GCATGCTCCAGTACGCCCTGCTCCACCTCGCCGGCTACGACGCCGTCTTG                         GAGGAGGACTTGAAGCAATTCAGGCAATGGGGAAGCAAGACTCCAGGCCAT
genomic: GCATGCTCCAGTACGCCCTGCTCCACCTCGCCGGCTACGACGCCGTCTTGgtaagcgctt ... attgctgcagGAGGAGGACTTGAAGCAATTCAGGCAATGGGGAAGCAAGACTCCAGGCCAT
EST: gi|88299800|gb|CI577302.1|CI577302
EST:     GCATGCTCCAGTACGCCCTGCTCCACCTCGCCGGCTACGACGCCGTCTTG                         GAGGAGGACTTGAAGCAATTCAGGCAATGGGGAAGCAAGACTCCAGGCCAT
genomic: GCATGCTCCAGTACGCCCTGCTCCACCTCGCCGGCTACGACGCCGTCTTGgtaagcgctt ... attgctgcagGAGGAGGACTTGAAGCAATTCAGGCAATGGGGAAGCAAGACTCCAGGCCAT

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), 73 (downstream exon)
Score: 155

CCCCTACTGGTTCAACCGCGACCGCTTCATCCTCTCCGCCGGCCACGGCTGCATGCTCCAGTACGCCCTGCTCCACCTCGCCGGCTACGACGCCGTCTTGgtaagcgctt ... attgctgcagGAGGAGGACTTGAAGCAATTCAGGCAATGGGGAAGCAAGACTCCAGGCCATCCCGAGAACTTCGAGACGCCCGGAGTTGAAGTTACCACTG




<











<


<











 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttcaactgatttgttcatcgagcttgctgtaactatggccgcatattgctgcagGAGGAGGACTTGAAGCAATTCAGGCAATGGGGAAGCAAGACTCCAGGCCATCCCGAGAACTTCGAGACGCCCGGAGTTGAAGTTACCACTG
                           ctgtaac  putative branch site (score: 155)
         atttgtt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aaattctggagtgatcggtgaagtgtttaatatggttgacttcagtttcaactgatttgttcatcgagcttgctgtaactatggccgcatattgctgcagGAGGAGGACTTGAAGCAATTCAGGCAATGGGGAAGCAAGACTCCAGGCCATCCCGAGAACTTCGAGACGCCCGGAGTTGAAGTTACCACTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - -atggttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ttgctgt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gccgcat