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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgctaagcactacattatcttattttgtatatgaatggactatgatcgtgttcctaatgatggtattttgttccttagGAACATGGCGTGTTGGTGGTGTGCTTGCTGTTTCTCGCGCTTTTGGTGACAAACTCTTAAAGCAGTATGTAGTTGTGGATCCTGAGATTCGG

Basic information

species Oryza sativa
transcript LOC_Os04g56450.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os04g56450.2 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G056572_T05 (Zea mays), 3'ss of exon 5
--gtgctaagcactacattatcttattttgtatatgaatggactatgatcgtgttcctaatgatggtattttgttccttagGAACATGGCGTGTTGGTGGTGTGCTTGCTGTTTCTCGCGCTTTTGGTGACAAACTCTTAAAGCAGTATGTAGTTGTGGATCCTGAGATTCGG--------
   ||| || ||||   || |||||    || | |   |||| ||||||  |  | ||||||    |  |||||||  ||||||||||||| ||||||||||| ||||||||||| || |||||||||||||||||||||||||| ||||| ||||||||||| ||||| ||         
gtatgccaatcacttttttttcttaaaaagtttcttggtggaatatgattatccttctaatgcccatgctttgttctatagGAACATGGCGCGTTGGTGGTGTACTTGCTGTTTCGCGTGCTTTTGGTGACAAACTCTTAAAGCAATATGTGGTTGTGGATCCGGAGATCCGAGTACGTAA

upper sequence: LOC_Os04g56450.2 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G056572_T02 (Zea mays), 3'ss of exon 5
--gtgctaagcactacattatcttattttgtatatgaatggactatgatcgtgttcctaatgatggtattttgttccttagGAACATGGCGTGTTGGTGGTGTGCTTGCTGTTTCTCGCGCTTTTGGTGACAAACTCTTAAAGCAGTATGTAGTTGTGGATCCTGAGATTCGG
   ||| || ||||   || |||||    || | |   |||| ||||||  |  | ||||||    |  |||||||  ||||||||||||| ||||||||||| ||||||||||| || |||||||||||||||||||||||||| ||||| ||||||||||| ||||| || 
gtatgccaatcacttttttttcttaaaaagtttcttggtggaatatgattatccttctaatgcccatgctttgttctatagGAACATGGCGCGTTGGTGGTGTACTTGCTGTTTCGCGTGCTTTTGGTGACAAACTCTTAAAGCAATATGTGGTTGTGGATCCGGAGATCCGA

upper sequence: LOC_Os04g56450.2 (Oryza sativa), 3'ss of exon 5
lower sequence: GLYMA17G33690.2 (Glycine max), 3'ss of exon 6
-------gtgctaagcactacattatcttattttgtatatgaatggactatgatcgtgttcctaatgat----ggtattttgttccttagGAACATGGCGTGTTGGTGGTGTGCTTGCTGTTTCTCGCGCTTTTGGTGACAAACTCTTAAAGCAGTATGTAGTTGTGGATCCTGAGATTCGG
          || |    ||  || | ||||||  | |||  ||      || | || |   |    ||       | | ||||    |||||| ||| | |||||||| || ||||||||||| || || |||||||| | |||| | ||||||||||| ||||  ||||| || || | |
gtaaggtcatcttatagttagtttttgttatttgatttatagattcttgttgtttgtctctatggaaattttaaacactatgtttac-agGAACTTGGAGAGTTGGTGGAGTTCTTGCTGTTTCACGTGCATTTGGTGATAGACTCCTGAAGCAGTATGTTGTTGCTGATCCAGAAATCCAG

upper sequence: LOC_Os04g56450.2 (Oryza sativa), 3'ss of exon 5
lower sequence: GLYMA06G06310.1 (Glycine max), 3'ss of exon 5
--------------------------gtgctaagcactacattatcttattttgtatatgaa-tggac-tatgat-cgtgttcctaatgatggtattttgttccttagGAACATGGCGTGTTGGTGGTGTGCTTGCTGTTTCTCGCGCTTTTGGTGACAAACTCTTAAAGCAGTATGTAGTTGTGGATCCTGAGATTCGG
                           |  | |||  ||  ||   ||| ||  |  |  || |  |  ||| || | | |  ||| ||||   ||    |     |||||| ||| | ||||| ||||| |||||||||||||| || |||||||| | |||| | ||||||||||| ||||  ||||| || |||| |
gtaatgtcatcactcatcattaacatatagtcagctttagttttatttacttaattcaaaaaatatatatataatgcttatcactattgataacatcgcatatac-agGAACTTGGAGAGTTGGAGGTGTTCTTGCTGTTTCTCGTGCGTTTGGTGATAGACTCCTGAAGCAGTATGTTGTTGCTGATCCAGAAATTCAG

upper sequence: LOC_Os04g56450.2 (Oryza sativa), 3'ss of exon 5
lower sequence: GLYMA14G12220.1 (Glycine max), 3'ss of exon 5
-------------gtgctaagcactacattatcttattttgtatatgaatggactatgatcgtgttcct----aatgatggtattttgttccttagGAACATGGCGTGTTGGTGGTGTGCTTGCTGTTTCTCGCGCTTTTGGTGACAAACTCTTAAAGCAGTATGTAGTTGTGGATCCTGAGATTCGG
              |  | |||  |   |||| | ||||  |||| || |   || || | ||     |    |||      | | ||||    |||||| ||| | |||||||| || ||||||||||| || || |||||||| | |||| | ||||||||||| ||||  ||||| || || | |
gtaaggttatcttctagttagctttttgttatttgatttattataagattcatct-tgtttgtcactatggaaaatctaaacactatgtttac-agGAACTTGGAGAGTTGGTGGAGTTCTTGCTGTTTCACGTGCATTTGGTGATAGACTCCTGAAGCAGTATGTTGTTGCTGATCCAGAAATCCAG

upper sequence: LOC_Os04g56450.2 (Oryza sativa), 3'ss of exon 5
lower sequence: GLYMA04G06250.1 (Glycine max), 3'ss of exon 6
-------------------gtgctaagcactacattatcttattttgtatatgaatggactatgat-cgtgttcctaatgatggtattttgttccttagGAACATGGCGTGTTGGTGGTGTGCTTGCTGTTTCTCGCGCTTTTGGTGACAAACTCTTAAAGCAGTATGTAGTTGTGGATCCTGAGATTCGG
                    |  | |||  ||  ||   ||||||  | | | ||  || ||| ||   | |  ||  ||||   |||   |     |||||| ||| | ||||| ||||| |||||||||||||| || |||||||| | |||| | ||||||||||| ||||  ||||| || |||| |
gtaatgtcatcattaacatatagtcagctttagttttatttatttaat-tctaaaaaga-tataatgtttatctctgttgataacattacatatac-agGAACTTGGAGAGTTGGAGGTGTTCTTGCTGTTTCTCGTGCATTTGGTGATAGACTCCTGAAGCAGTATGTTGTTGCTGATCCAGAAATTCAG

upper sequence: LOC_Os04g56450.2 (Oryza sativa), 3'ss of exon 5
lower sequence: Vv04s0008g07320.t01 (Vitis vinifera), 3'ss of exon 6
-----------------------gtgctaagcacta--cattatcttattttgtatatgaatggactat-gatcgtgt-tcctaatgatggtattttgttccttagGAACATGGCGTGTTGGTGGTGTGCTTGCTGTTTCTCGCGCTTTTGGTGACAAACTCTTAAAGCAGTATGTAGTTGTGGATCCTGAGATTCGG
                        | | ||| | ||  |||      |  ||     ||| | |   || | | |  | | |||||||| | | || |||    |||||| ||| | ||||| ||||| |||||||||||||| || |||||||| | |||||| ||||||||||| ||||  ||||| || || | |
gtaaggacatcaatcgttaggtttttccaagtattaatcatagaacaaagtttccagtgatttggtaattgcttgcatcttctaatgattgaaattcgtttac-agGAACTTGGAGGGTTGGGGGTGTTCTTGCTGTTTCTCGTGCATTTGGTGATAGACTCTTGAAGCAGTATGTTGTTGCTGATCCAGAAATCCAG

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|14981649|gb|BI306327.1|BI306327
EST:     AGATGAGCGACAACGTATCGAAGATGCTGGAGGTTTTGTAATGTGGGCAG                         GAACATGGCGTGTTGGTGGTGTGCTTGCTGTTTCTCGCGCTTTTGGTGACA
genomic: AGATGAGCGACAACGTATCGAAGATGCTGGAGGTTTTGTAATGTGGGCAGgtgctaagca ... tgttccttagGAACATGGCGTGTTGGTGGTGTGCTTGCTGTTTCTCGCGCTTTTGGTGACA
EST: gi|5003298|gb|AU068447.1|AU068447
EST:     AGATGAGCGACAACGTATCGAAGATGCTGGAGGTTTTGTAATGTGGGCAG                         GAACATGGCGTGTTGGTGGTGTGCTTGCTGTTTCTCGCGCTTTTGGTGACA
genomic: AGATGAGCGACAACGTATCGAAGATGCTGGAGGTTTTGTAATGTGGGCAGgtgctaagca ... tgttccttagGAACATGGCGTGTTGGTGGTGTGCTTGCTGTTTCTCGCGCTTTTGGTGACA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttgtatatgaatggactatgatcgtgttcctaatgatggtattttgttccttagGAACATGGCGTGTTGGTGGTGTGCTTGCTGTTTCTCGCGCTTTTGGTGACAAACTCTTAAAGCAGTATGTAGTTGTGGATCCTGAGATTCGG
                            tcctaat  putative branch site (score: 2)
                                          ttttgttcctt  putative PPT
                                        tattttgtt  TA-rich tract