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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagactacaaaatacttgtatatttttctgtacttatctttctaccagcattttctaatagctcatcctcaataattgctaattgcagATTATTGGTGAGATTTCTGTATCTGGCGCAACATACAAATCCATGGAGTTTGTTGGATCAACTGTGGAAAGTCTAAAT

Basic information

species Oryza sativa
transcript LOC_Os02g03260.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g03260.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G370852_T03 (Zea mays), 3'ss of exon 7
gtaagactacaaaatac-ttgtatatttttctgtacttatctttctaccagcattttctaatagctcatcctcaataattgctaattgcagATTATTGGTGAGATTTCTGTATCTGGCGCAACATACAAATCCATGGAGTTTGTTGGATCAACTGTGGAAAGTCTAAAT
|||||  |||||  |   || | | | || ||   ||||   | ||||| | |     | |   || || ||   |||| | || || |||||||||||||||||||| |||||||| ||||| |||||||| ||||||||||||||||||||||| ||||||||||  
gtaagcttacaagctgtgttatgtttgttccttcccttaggat-ctacctgtaacca-tgacttcttattcttgttaatcggtacttacagATTATTGGTGAGATTTCAGTATCTGGTGCAACCTACAAATCGATGGAGTTTGTTGGATCAACTGTAGAAAGTCTAACC

upper sequence: LOC_Os02g03260.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G010044_T02 (Zea mays), 3'ss of exon 6
gtaagactacaaaatacttgtatattt-ttctgtacttatctttctaccagcattttctaatagctcatcctcaataattgctaattgcagATTATTGGTGAGATTTCTGTATCTGGCGCAACATACAAATCCATGGAGTTTGTTGGATCAACTGTGGAAAGTCTAAAT
|||||  || ||  |  |  || |||| |||  | ||||   |    || | | |    | |   | || ||   ||||||||  || ||||||||||| |||||||| |||||||| || || |||||||| ||||||||||||||||||||||| ||||||||||  
gtaagcttataagctg-tgctacatttgttcctttcttaggatctaccctgtaatcgggacttatt-attcttgttaattgctgcttacagATTATTGGAGAGATTTCAGTATCTGGTGCGACCTACAAATCAATGGAGTTTGTTGGATCAACTGTAGAAAGTCTAACC

upper sequence: LOC_Os02g03260.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GLYMA20G34160.1 (Glycine max), 3'ss of exon 8
---------------------------------------------------gtaagactacaaaatacttgtatatttttctgtacttatctttctaccagcattttctaatagctcatcctcaataattgctaattgcagATTATTGGTGAGATTTCTGTATCTGGCGCAACATACAAATCCATGGAGTTTGTTGGATCAACTGTGGAAAGTCTAAAT
                                                     ||   ||    | |   ||||||| |       || ||| | | |     |||  |  |    |    | || ||     | |  ||||| |||||||| || ||||| ||||| |||||||| ||| | ||||||||||||||  ||||  | |||||| ||| |
gtgggtaatgggttcctctcatgtttttccatttgaatgaaatgctgttaatcaaagttatgtgacatgagtatattataacactgttgtctgttttct----tttcgtggtgttgccatttgaaaaaccatcatt--cagATCATTGGTGAAATATCTGTGTCTGGTGCAACATATAAAACGATGGAGTTTGTTGGGACAACAATTGAAAGTTTAAGT

upper sequence: LOC_Os02g03260.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GLYMA17G37540.1 (Glycine max), 3'ss of exon 7
------------------------------------gtaagactacaa--aatacttgtatatttttctgtacttatctttctaccagcattttctaatagctcatcct--caataattgctaatt------gcagATTATTGGTGAGATTTCTGTATCTGGCGCAACATACAAATCCATGGAGTTTGTTGGATCAACTGTGGAAAGTCTAAAT
                                    |  | |  | |   |  |  ||  |||  || | | || || ||  | | ||||  |   || |   ||||||  ||  ||| | |  ||       |||||||||||||| ||  ||||  |||| |||||||| ||||| ||||||||||| ||  ||||||| |||||| |||  
agtaagtgccttgattctgtacttttgtttctgttggacatagcatagccatcaggtgactatgattgtttgctcattttcatgc-agcaaatataaaaattacatccttacatgaatggatggtttaccttacaGATTATTGGTGAAATAACTGTGGCTGGTGCAACATATAAATCGATGGAGTTTGTCGGTACAACTGTTGAAAGTTTAAC-

upper sequence: LOC_Os02g03260.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GLYMA14G40570.1 (Glycine max), 3'ss of exon 7
-----------------------------------gtaagactacaa--aatacttgtatatttttctgtacttatctttctaccagcattttctaatagctcatcctca-at-----aattgctaa--ttgcagATTATTGGTGAGATTTCTGTATCTGGCGCAACATACAAATCCATGGAGTTTGTTGGATCAACTGTGGAAAGTCTAAAT
                                   |  | |  | |   | ||  ||    |  ||   | || || ||  | | ||||  |   || |   |||||| | ||     ||| | | |  || |||||||||||||| ||  ||||  |||| |||||||| ||||| ||||||||||||||  |||| || |||||| ||| |
gtaagttccttgattctgaacttttgtttctgttggacatatcataggcattaggtgaccgtgattgcttgctcattttcatgc-agcaaatataaaaattacatccttacatgaatgaatggtttaccttacagATTATTGGTGAAATAACTGTGGCTGGGGCAACATATAAATCGATGGAGTTTGTTGGTACAACCGTTGAAAGTTTAACT

upper sequence: LOC_Os02g03260.1 (Oryza sativa), 3'ss of exon 6
lower sequence: Vv08s0056g01640.t01 (Vitis vinifera), 3'ss of exon 7
---------gtaagactacaaaatacttgtatatttttctgtacttatctttctaccagc-attttctaatagctcatcctcaataattgctaa--ttgcagATTATTGGTGAGATTTCTGTATCTGGCGCAACATACAAATCCATGGAGTTTGTTGGATCAACTGTGGAAAGTCTAAAT
         ||  |  |      ||    || |||| |  ||  ||  |||      |   || || || | | |  |    |||  ||  | |  ||||||||||||||||| || || || ||||| |||||||| ||||||||||| ||||||||    ||||| |||||||| | |
tatgtgtgtgtgtgtgtgtgtgttaaacttaaatttgttggtgttttacttaaatttattgatgttttattggttggtaa--aatggtttttcaccttgcagATTATTGGTGAAATATCAGTTTCTGGGGCAACATATAAATCCATGGAATTTGTTGGCAGTACTGTTGAAAGTCTGACT

upper sequence: LOC_Os02g03260.1 (Oryza sativa), 3'ss of exon 6
lower sequence: Vv05s0049g01980.t01 (Vitis vinifera), 3'ss of exon 7
---------------------------------------------------------------------------------gtaagactacaaaatacttgtatatttttctg-tactt------atctttcta-ccagcattttctaatagctcatcctcaataattg------ctaattgcagATTATTGGTGAGATTTCTGTATCTGGCGCAACATACAAATCCATGGAGTTTGTTGGATCAACTGTGGAAAGTCTAAAT
                                                                                  || ||   || |    |||| || ||  ||| |  ||      ||   | |  ||  | |||| | || |     | |||  || ||      |   ||||||||||||||||| || ||||| |||||||| ||||| ||||| ||||| ||||||||  | ||||| |||||| ||| |
gtaagtcttactagcactagtggcgttctttcatttttaaagggcataatctttccacccatggaatatgttgtgtttttaatatgagcccatatcggttgtttacttcgctgatgttttaatggattggtatggccttcctttttttatggtcttgcttcacaaaatggcctttcactttgcagATTATTGGTGAAATATCTGTTTCTGGCGCGACATATAAATCTATGGAATTTGTTGGCACTACTGTTGAAAGTTTAACT

upper sequence: LOC_Os02g03260.1 (Oryza sativa), 3'ss of exon 6
lower sequence: EFJ16666 (Selaginella moellendorffii), 3'ss of exon 6
gtaagactacaaaatacttgtatatttttctgtacttatctttctaccagcattttctaatagctcatcctcaataattgctaattgcagATTATTGGTGAGATTTCTGTATCTGGCGCAACATACAAATCCATGGAGTTTGTTGGATCAACTGTGGAAAGTCTAAAT
                  ||| |   ||| |      | ||  || || | | ||   ||   || ||   |     |||       ||||| ||||| |||||  |||| || || |||||||||||||| ||||||||||||||| || |||| ||| || | |  
---------------gtgtgtttcgatttttagcaagagctggctccctgtactt--gaagtacttatatgcg--cgttgaggcacacagATCATTGGAGAGATCACTGTTTCCGGTGCAACATACAAATCAATGGAGTTTGTTGGAACAGCTGTAGAACGTATGACG

upper sequence: LOC_Os02g03260.1 (Oryza sativa), 3'ss of exon 6
lower sequence: EFJ32611 (Selaginella moellendorffii), 3'ss of exon 6
gtaagactacaaaatacttgtatatttttctgtacttatctttctaccagcattttctaatagctcatcctcaataattgctaattgcagATTATTGGTGAGATTTCTGTATCTGGCGCAACATACAAATCCATGGAGTTTGTTGGATCAACTGTGGAAAGTCTAAAT----------------------
              |  ||| || |||  |   |  |  ||  ||       |  |  ||   || ||   |     |||       ||||| ||||| |||||  |||| || || |||||||||||||| ||||||||||||||  || |||| ||| || | |                        
-----------gtgtgtttggatctttagcgagagctggctccctg------tacttgaagtacttatatgcg--cgttgaggcacacagATCATTGGAGAGATCACTGTTTCCGGTGCAACATACAAATCAATGGAGTTTGTTGGGACAGCTGTAGAACGTATGACGGTCAGTTCTTTTTCCCCTTACC

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|88340371|gb|CI659577.1|CI659577
EST:     TAGATGGAGAAATGCCACCTTATTTACTTGCAAAGGATCTGATTTTACAA                         ATTATTGGTGAGATTTCTGTATCTGGCGCAACATACAAATCCATGGAGTTT
genomic: TAGATGGAGAAATGCCACCTTATTTACTTGCAAAGGATCTGATTTTACAAgtaagactac ... ctaattgcagATTATTGGTGAGATTTCTGTATCTGGCGCAACATACAAATCCATGGAGTTT
EST: gi|218494441|gb|FG968569.1|FG968569
EST:     TAGATGGAGAAATGCCACCTTATTTACTTGCAAAGGATCTGATTTTACAA                         ATTATTGGTGAGATTTCTGTATCTGGCGCAACATACAAATCCATGGAGTTT
genomic: TAGATGGAGAAATGCCACCTTATTTACTTGCAAAGGATCTGATTTTACAAgtaagactac ... ctaattgcagATTATTGGTGAGATTTCTGTATCTGGCGCAACATACAAATCCATGGAGTTT
EST: gi|88336267|gb|CI648854.1|CI648854
EST:     TAGATGGAGAAATGCCACCTTATTTACTTGCAAAGGATCTGATTTTACAA                         ATTATTGGTGAGATTTCTGTATCTGGCGCAACATACAAATCCATGGAGTTT
genomic: TAGATGGAGAAATGCCACCTTATTTACTTGCAAAGGATCTGATTTTACAAgtaagactac ... ctaattgcagATTATTGGTGAGATTTCTGTATCTGGCGCAACATACAAATCCATGGAGTTT
EST: gi|88307301|gb|CI641939.1|CI641939
EST:     TAGATGGAGAAATGCCACCTTATTTACTTGCAAAGGATCTGATTTTACAA                         ATTATTGGTGAGATTTCTGTATCTGGCGCAACATACAAATCCATGGAGTTT
genomic: TAGATGGAGAAATGCCACCTTATTTACTTGCAAAGGATCTGATTTTACAAgtaagactac ... ctaattgcagATTATTGGTGAGATTTCTGTATCTGGCGCAACATACAAATCCATGGAGTTT
EST: gi|2312204|gb|C28359.1|C28359
EST:     TAGATGGAGAAATGCCACCTTATTTACTTGCAAAGGATCTGATTTTACAA                         ATTATTGGTGAGATTTCTGTATCTGGCGCAACATACAAATCCATGGAGTTT
genomic: TAGATGGAGAAATGCCACCTTATTTACTTGCAAAGGATCTGATTTTACAAgtaagactac ... ctaattgcagATTATTGGTGAGATTTCTGTATCTGGCGCAACATACAAATCCATGGAGTTT
EST: gi|88329810|gb|CI651478.1|CI651478
EST:     TAGATGGAGAAATGCCACCTTATTTACTTGCAAAGGATCTGATTTTACAA                         ATTATTGGTGAGATTTCTGTATCTGGCGCAACATACAAATCCATGGAGTTT
genomic: TAGATGGAGAAATGCCACCTTATTTACTTGCAAAGGATCTGATTTTACAAgtaagactac ... ctaattgcagATTATTGGTGAGATTTCTGTATCTGGCGCAACATACAAATCCATGGAGTTT
EST: gi|88571723|gb|CI663096.1|CI663096
EST:     TAGATGGAGAAATGCCACCTTATTTACTTGCAAAGGATCTGATTTTACAA                         ATTATTGGTGAGATTTCTGTATCTGGCGCAACATACAAATCCATGGAGTTT
genomic: TAGATGGAGAAATGCCACCTTATTTACTTGCAAAGGATCTGATTTTACAAgtaagactac ... ctaattgcagATTATTGGTGAGATTTCTGTATCTGGCGCAACATACAAATCCATGGAGTTT
EST: gi|88326072|gb|CI651125.1|CI651125
EST:     TAGATGGAGAAATGCCACCTTATTTACTTGCAAAGGATCTGATTTTACAA                         ATTATTGGTGAGATTTCTGTATCTGGCGCAACATACAAATCCATGGAGTTT
genomic: TAGATGGAGAAATGCCACCTTATTTACTTGCAAAGGATCTGATTTTACAAgtaagactac ... ctaattgcagATTATTGGTGAGATTTCTGTATCTGGCGCAACATACAAATCCATGGAGTTT
EST: gi|29628818|gb|CB633829.1|CB633829
EST:     TAGATGGAGAAATGCCACCTTATTTACTTGCAAAGGATCTGATTTTACAA                         ATTATTGGTGAGATTTCTGTATCTGGCGCAACATACAAATCCATGGAGTTT
genomic: TAGATGGAGAAATGCCACCTTATTTACTTGCAAAGGATCTGATTTTACAAgtaagactac ... ctaattgcagATTATTGGTGAGATTTCTGTATCTGGCGCAACATACAAATCCATGGAGTTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttatctttctaccagcattttctaatagctcatcctcaataattgctaattgcagATTATTGGTGAGATTTCTGTATCTGGCGCAACATACAAATCCATGGAGTTTGTTGGATCAACTGTGGAAAGTCTAAAT
                                           tgctaat  putative branch site (score: 2)
                                     aataattgctaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagactacaaaatacttgtatatttttctgtacttatctttctaccagcattttctaatagctcatcctcaataattgctaattgcagATTATTGGTGAGATTTCTGTATCTGGCGCAACATACAAATCCATGGAGTTTGTTGGATCAACTGTGGAAAGTCTAAAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CATGGA