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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_Os04g56450.2
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

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: 69 (upstream exon), 64 (downstream exon)
Score: 61

CTATAGCTGTTTCAAAAGATCACAAGCCTGATCAGACAGATGAGCGACAACGTATCGAAGATGCTGGAGGTTTTGTAATGTGGGCAGgtgctaagca ... tgttccttagGAACATGGCGTGTTGGTGGTGTGCTTGCTGTTTCTCGCGCTTTTGGTGACAAACTCTTAAAGCAGTATGTAGTTGTGGATCCTGAGATTCGG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttgtatatgaatggactatgatcgtgttcctaatgatggtattttgttccttagGAACATGGCGTGTTGGTGGTGTGCTTGCTGTTTCTCGCGCTTTTGGTGACAAACTCTTAAAGCAGTATGTAGTTGTGGATCCTGAGATTCGG
                            tcctaat  putative branch site (score: 61)
                                          ttttgttcctt  putative PPT
                                        tattttgtt  TA-rich tract