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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TCTATCAAAGCCTCCAGTATGGGCTCTAATAGTATCACATTTTTGCCATAATTGGGGAACCTTCATTCTTCTAACATGGATGCCTACATACTACAACCAGgttcttacaatttaatacccactgcccatatcagacaatggtagcatatcctgttcttggtggttgtactcaccaggtgctcttatccag

Basic information

species Oryza sativa
transcript LOC_Os09g39680.1
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os09g39680.1 (Oryza sativa), 5'ss of exon 6
lower sequence: GRMZM2G088196_T01 (Zea mays), 5'ss of exon 6
TCTATCAAAGCCTCCAGTATGGGCTCTAATAGTATCACATTTTTGCCATAATTGGGGAACCTTCATTCTTCTAACATGGATGCCTACATACTACAACCAGgttcttacaatttaataccc----actgcccatatcagacaatggtagcatatcctgttcttggt--------ggttgtactcaccaggtgctcttatccag
|||||||||| ||||||| |||||||| ||| ||||||||||||||||||| |||||||| || |||||  ||||||||||||| ||||||||||| ||||||  |||||| | || |      ||        |    || || ||   |   || ||  ||          | ||||  || |||  | || ||| ||||
TCTATCAAAGGCTCCAGTGTGGGCTCTCATAATATCACATTTTTGCCATAACTGGGGAACATTTATTCTGTTAACATGGATGCCCACATACTACAATCAGgtttctacaatgttatgctgtgaaacgtttggctttgctcattgttaaagttatctattggtgtcatgccatcgcttgttgtccccaaatccttttacccag

upper sequence: LOC_Os09g39680.1 (Oryza sativa), 5'ss of exon 6
lower sequence: GRMZM2G046681_T01 (Zea mays), 5'ss of exon 6
TCTATCAAAGCCTCCAGTATGGGCTCTAATAGTATCACATTTTTGCCATAATTGGGGAACCTTCATTCTTCTAACATGGATGCCTACATACTACAACCAGgttcttacaatttaatac--------------------ccactgcccatatcagacaatggtagcatatcctgttcttggtggttgtactcaccaggtgctcttatccag
|||||||||| ||||||| |||||||| ||| ||||||||||||||||||| |||||||| ||||||||||||||||||||||| ||||||||||| ||||||  ||| || | || |                    ||| |    | || | | |||| ||||||||| ||   ||||   |||| ||| |||  | || ||||||||
TCTATCAAAGGCTCCAGTGTGGGCTCTCATAATATCACATTTTTGCCATAACTGGGGAACATTCATTCTTCTAACATGGATGCCCACATACTACAATCAGgttgctaccatgttatgctgtgaaacgtttgactttccccattatttaaattatataatgatagcatatcatgccattgg---ttgtgctccccaaatccttttatccag

upper sequence: LOC_Os09g39680.1 (Oryza sativa), 5'ss of exon 6
lower sequence: GLYMA18G46790.1 (Glycine max), 5'ss of exon 4
--------------------------------------------------------TCTATCAAAGCCTCCAGTATGGGCTCTAATAGTATCACATTTTTGCCATAATTGGGGAACCTTCATTCTTCTAACATGGATGCCTACATACTACAACCAGgttcttacaatttaatacccactgcccatatcagacaatggtagcatatcctgttcttggtggttgtactcaccaggtgctcttatccag
                                                        | |||||||| | || || | |||||| ||| | || || || || || |||||  | || || ||||||||||| ||||||||||| |||||||| |||||  | ||  |||              ||||   | | |      | ||                                         
ATACTGGAAGGCAATTTATCAAATGCACATGTTTCTTCCATTCCTTGGAAATTGATTTTATCAAAGGCACCTGTTTTGGCTCTTATAATCTCCCACTTCTgtcacaattgaaggacatttattcttctaacctggatgcctacttactacaatcaggtattaacccttt-----ttttgataaatatttaatagtatacataaat-----------------------------------------

upper sequence: LOC_Os09g39680.1 (Oryza sativa), 5'ss of exon 6
lower sequence: GLYMA07G07570.1 (Glycine max), 5'ss of exon 6
TCTATCAAAGCCTCCAGTATGGGCTCTAATAGTATCACATTTTTGCCATAATTGGGGAACCTTCATTCTTCTAACATGGATGCCTACATACTACAACCAGgttcttacaattta-atacccactgcccatatcagacaatggtagcatat----cctgttcttggtggttgtactcaccaggtgctct-tatccag----
| |||||||  | || || |||||| ||||| | || || || |||||||||||||| || || |||||  |||| ||||||||||| |||||||| ||||| ||| |  |||| |   |  ||     | |    ||    |   | ||     ||   |||   |  | |||    |     |  | |||| |     
TTTATCAAAAGCACCTGTTTGGGCTTTAATAATCTCTCACTTCTGCCATAATTGGGGGACATTTATTCTATTAACCTGGATGCCTACCTACTACAATCAGgtgcttgctgtttataagtcttcttttttttttttgcagaattcataaatgatttctaaccttttagaatatacatgtccttgacaatgtatctataata

upper sequence: LOC_Os09g39680.1 (Oryza sativa), 5'ss of exon 6
lower sequence: GLYMA03G01060.1 (Glycine max), 5'ss of exon 6
TCTATCAAAGCCTCCAGTATGGGCTCTAATAGTATCACATTTTTGCCATAATTGGGGAACCTTCATTCTTCTAACATGGATGCCTACATACTACAACCAGgttcttacaatttaatacccactgcc------catatcagacaatggtagcatatcctgttcttggtggttgtactcacca--ggtgctcttatccag--
| |||||||  | || || |||||| ||||| | || || || ||||| |||||||| || || |||||  |||| ||||||||||| |||||||| ||||| |||||  ||||  |    ||  |      | | |||||       |     | ||   |||   |  | |||    |   |    |  |||| |   
TTTATCAAAAGCACCTGTTTGGGCTTTAATAATCTCTCACTTCTGCCACAATTGGGGGACATTTATTCTATTAACCTGGATGCCTACCTACTACAATCAGgtgcttactgtttatgagtttctttcttttttcttctcagaattcataaatgacttctaaccttttagaatatacatgtccttgacaatgctatctataa

upper sequence: LOC_Os09g39680.1 (Oryza sativa), 5'ss of exon 6
lower sequence: AT4G00370.1 (Arabidopsis thaliana), 5'ss of exon 7
TCTATCAAAGCCTCCAGTATGGGCTCTAATAGTATCACATTTTTGCCATAATTGGGGAACCTTCATTCTTCTAACATGGATGCCTACATACTACAACCAGgttc---------ttacaatttaatacccactgccca----tatcagacaatggtagcatatcctgttcttggtggttgtactcaccaggtgctcttatccag
 || || || || ||||| |||||||| ||| | || || || ||||||||||||||||| ||||| ||  | ||||||||||| ||||| ||||| ||||  |          | || ||  || |  ||||   |    | |  |  ||       | |  ||  |||   | ||||  ||        |||         
ACTGTCTAAACCCCCAGTCTGGGCTCTCATAATTTCCCACTTCTGCCATAATTGGGGAACTTTCATACTATTGACATGGATGCCCACATATTACAATCAGgcacggagttcagcttcagttatatccttactgtttaatattttttgtgaacaagtaaagagactcctctctattgttggtctttgatcacgctgcag-----

upper sequence: LOC_Os09g39680.1 (Oryza sativa), 5'ss of exon 6
lower sequence: Vv15s0046g02390.t01 (Vitis vinifera), 5'ss of exon 6
TCTATCAAAGCCTCCAGTATGGGCTCTAATAGTATCACATTTTTGCCATAATTGGGGAACCTTCATTCTTCTAACATGGATGCCTACATACTACAACCAGgttcttacaattt-----aatacccactgcccatatcagacaatggtagc-atatcctgttcttggtgg--ttgtactcaccaggtgctcttatccag--
| | || ||| | ||||| |||||||| ||| | || ||||| |||||||| |||||||| || ||||||||||||||||||||||| ||||| || |||||  |||  | ||      |      || |     ||| | | |  |  | ||||    ||| |||     || ||   |||||    |  | ||||   
TTTGTCGAAGGCACCAGTTTGGGCTCTCATAATCTCCCATTTCTGCCATAACTGGGGAACTTTTATTCTTCTAACATGGATGCCTACGTACTATAATCAGgtatttaagacttttcgggactggtcctactttggtcaaatattcatttccatatttctttcctggaaagtttatagataccagtattttgtctccaaaa

upper sequence: LOC_Os09g39680.1 (Oryza sativa), 5'ss of exon 6
lower sequence: PP1S31_182V6.1 (Physcomitrella patens), 5'ss of exon 6
TCTATCAAAGCCTCCAGTATGGGCTCTAATAGTATCACATTTTTGCCATAATTGGGGAACCTTCATTCTTCTAACATGGATGCCTACATACTACAACCAGgttct---tacaatttaatacccactgcccatatcagacaatggtagcatatcctgttcttggtggt-tgtactcaccaggtgctcttatccag---------------------------------------------------------------------------------------------------
  | || ||  |||| || ||||| || ||  |||  || || || |||||||||||||| || || || || || |||||||| ||||||||||||||||| |    | |  | ||  |   ||  |    |  | | |||    |  ||| || || ||| |  | | |  | |   |  |||   |||                                                                                                      
ATTGTCCAAAGCTCCTGTGTGGGCGCTTATTATATGCCACTTCTGTCATAATTGGGGAACATTTATCCTCCTTACTTGGATGCCCACATACTACAACCAGgtacaatatgcgttgtatgatttacgtcgagaagtacataattaatgtttattctctttttgatactattttattatttgtagcttacatcattttattttttgattattcaatatatggttactgctctaggggtctgtgattcattacgaggaactgcttaatttagtttgaaaagtgcatactattacag

upper sequence: LOC_Os09g39680.1 (Oryza sativa), 5'ss of exon 6
lower sequence: EFJ10498 (Selaginella moellendorffii), 5'ss of exon 5
TCTATCAAAGCCTCCAGTATGGGCTCTAATAGTATCACATTTTTGCCATAATTGGGGAACCTTCATTCTTCTAACATGGATGCCTACATACTACAACCAGgttcttacaatttaatacccactgcccatatca-gacaatggtagcatatcctgttcttggtggttgtactcaccaggtgctcttatccag
||||||  | ||  | || ||||| |||||||| |  || |||||||| || ||||| || ||||||||  | ||||||||||| || |||||||||||||||   ||  | |  |     ||      || | || | |  | | ||                                           
TCTATCTGAACCATCTGTGTGGGCGCTAATAGTTTGTCACTTTTGCCACAACTGGGGGACTTTCATTCTCTTGACATGGATGCCGACGTACTACAACCAGgttgacact-tctcttgatttctaagttcattatgaaagtatttgtatgcag---------------------------------------

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|29678655|gb|CB674930.1|CB674930
EST:     ATTGGGGAACCTTCATTCTTCTAACATGGATGCCTACATACTACAACCAG                         GTTCTTAAGTTCAATCTTACTGAATCTGGGCTTTTGTGTGTCTTGCCGTGG
genomic: ATTGGGGAACCTTCATTCTTCTAACATGGATGCCTACATACTACAACCAGgttcttacaa ... tcttatccagGTTCTTAAGTTCAATCTTACTGAATCTGGGCTTTTGTGTGTCTTGCCGTGG
EST: gi|33654152|gb|CF276766.1|CF276766
EST:     ATTGGGGAACCTTCATTCTTCTAACATGGATGCCTACATACTACAACCAG                         GTTCTTAAGTTCAATCTTACTGAATCTGGGCTTTTGTGTGTCTTGCCGTGG
genomic: ATTGGGGAACCTTCATTCTTCTAACATGGATGCCTACATACTACAACCAGgttcttacaa ... tcttatccagGTTCTTAAGTTCAATCTTACTGAATCTGGGCTTTTGTGTGTCTTGCCGTGG
EST: gi|66923741|gb|CX110589.1|CX110589
EST:     ATTGGGGAACCTTCATTCTTCTAACATGGATGCCTACATACTACAACCAG                         GTTCTTAAGTTCAATCTTACTGAATCTGGGCTTTTGTGTGTCTTGCCGTGG
genomic: ATTGGGGAACCTTCATTCTTCTAACATGGATGCCTACATACTACAACCAGgttcttacaa ... tcttatccagGTTCTTAAGTTCAATCTTACTGAATCTGGGCTTTTGTGTGTCTTGCCGTGG
EST: gi|58687295|gb|CK075982.1|CK075982
EST:     ATTGGGGAACCTTCATTCTTCTAACATGGATGCCTACATACTACAACCAG                         GTTCTTAAGTTCAATCTTACTGAATCTGGGCTTTTGTGTGTCTTGCCGTGG
genomic: ATTGGGGAACCTTCATTCTTCTAACATGGATGCCTACATACTACAACCAGgttcttacaa ... tcttatccagGTTCTTAAGTTCAATCTTACTGAATCTGGGCTTTTGTGTGTCTTGCCGTGG
EST: gi|29615966|gb|CB620978.1|CB620978
EST:     ATTGGGGAACCTTCATTCTTCTAACATGGATGCCTACATACTACAACCAG                         GTTCTTAAGTTCAATCTTACTGAATCTGGGCTTTTGTGTGTCTTGCCGGGG
genomic: ATTGGGGAACCTTCATTCTTCTAACATGGATGCCTACATACTACAACCAGgttcttacaa ... tcttatccagGTTCTTAAGTTCAATCTTACTGAATCTGGGCTTTTGTGTGTCTTGCCGTGG

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: 65 (upstream exon), 75 (downstream exon)
Score: 31

TCTATCAAAGCCTCCAGTATGGGCTCTAATAGTATCACATTTTTGCCATAATTGGGGAACCTTCATTCTTCTAACATGGATGCCTACATACTACAACCAGgttcttacaa ... tcttatccagGTTCTTAAGTTCAATCTTACTGAATCTGGGCTTTTGTGTGTCTTGCCGTGGCTGACAATGGCTATATTTGCGAATATTGGTGGCTGGATTGCTGACACTC




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TCTATCAAAGCCTCCAGTATGGGCTCTAATAGTATCACATTTTTGCCATAATTGGGGAACCTTCATTCTTCTAACATGGATGCCTACATACTACAACCAGgttcttacaatttaatacccactgcccatatcagacaatggtagcatatcctgttcttggtggttgtactcaccaggtgctcttatccag

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