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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CATCATCTCTGCAATTGAGTTTGACAAATCCGGTGACCATCTTGCCACTGGAGATAGAGGTGGTCGTGTAGTTTTATTTGAAAGGACTGACTCCAGGGATgtaagtaccacacactatctaagttatgtaggtttcttgtttaaatctcttgttctcatagaagtcaatttatatgcag

Basic information

species Oryza sativa
transcript LOC_Os02g13110.2
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g13110.2 (Oryza sativa), 5'ss of exon 2
lower sequence: GRMZM2G069631_T02 (Zea mays), 5'ss of exon 2
CATCATCTCTGCAATTGAGTTTGACAAATCCGGTGACCATCTTGCCACTGGAGATAGAGGTGGTCGTGTAGTTTTATTTGAAAGGACTGACTCCAGGGATgtaagtaccacacactatctaagttatgtagg-tttcttgtttaaatctcttgttctcatagaagtcaatttatatgcag
||| || ||||||||||||||||||||||| ||  | |||||||| ||||||||||||||||| ||||| ||||| || ||||| || |||      ||||||||| | ||||  ||| |||||| | ||   ||||||| ||||||||| ||| | |||||  |  ||| ||| |||||
CATAATATCTGCAATTGAGTTTGACAAATCTGGGAATCATCTTGCTACTGGAGATAGAGGTGGACGTGTGGTTTTGTTCGAAAGAACAGACATTGCTGATgtaagtgctacac--tatataagttctataatctttcttgcttaaatctcgtgtgcccatagt-gctaatgtatgtgcag

upper sequence: LOC_Os02g13110.2 (Oryza sativa), 5'ss of exon 2
lower sequence: Vv11s0016g02550.t01 (Vitis vinifera), 5'ss of exon 2
CATCATCTCTGCAATTGAGTTTGACAAATCCGGTGACCATCTTGCCACTGGAGATAGAGGTGGTCGTGTAGTTTTATTTGAAAGGACTGACTCCAGGGATgtaagt------accacacactat--ctaagttatgtaggtttcttgt-ttaaatctcttgttctcatagaagtcaatttatatgcag---------------------------------------------
|||||| ||||| ||||||||||||||| | || ||||||||||| ||||| ||| | || || || || ||||||||||||||||| |||   ||||||||| ||      | ||||  || |  ||   || | |   |||||  | ||   | || | || |    |   |  |||||  |  |                                              
CATCATTTCTGCTATTGAGTTTGACAAAACTGGAGACCATCTTGCGACTGGTGATCGTGGGGGACGGGTGGTTTTATTTGAAAGGACAGACAAGAGGGATgtatgttgttttatcacatgctgtgccttttttttttcattttctcttattttgtttcattttatttctggccttgatttacttctatatcacttcttgttgcaccattttaatgtaattgcataatgtatag

upper sequence: LOC_Os02g13110.2 (Oryza sativa), 5'ss of exon 2
lower sequence: Vv04s0008g00840.t01 (Vitis vinifera), 5'ss of exon 2
CATCATCTCTGCAATTGAGTTTGACAAATCCGGTGACCATCTTGCCACTGGAGATAGAGGTGGTCGTGTAGTTTTATTTGAAAGGACTGACTCCAGGGATgtaagt-accacacactat-ctaagttatgtaggtttcttgtttaaatctcttgttctcatagaagtcaatttatatgcag-------
 ||||| || || ||||||||||| ||| | || ||||||||||| ||||||||| | || ||||| || ||||||||| | || |||||  | ||||||||| ||  | | ||  | | ||   |||| | | | ||   | ||  | | ||| | || |         ||| | | ||        
TATCATATCAGCTATTGAGTTTGATAAAACTGGGGACCATCTTGCTACTGGAGATCGTGGGGGTCGGGTGGTTTTATTTAACAGAACTGATACGAGGGATgtatgttgctagactgtttgcttgtttattttgttgtcagatgtatttgtgttggtttctttatgtgttgtttgt-ttcactttgtag

upper sequence: LOC_Os02g13110.2 (Oryza sativa), 5'ss of exon 2
lower sequence: Vv09s0002g02470.t01 (Vitis vinifera), 5'ss of exon 2
CATCATCTCTGCAATTGAGTTTGACAAATCCGGTGACCATCTTGCCACTGGAGATAGAGGTGGTCGTGTAGTTTTATTTGAAAGGACTGACTCCAGGGATgtaagtaccacac-actatctaagttatgtaggtttcttgtttaaatctctt--gttctcatagaagtcaatttatatgcag---------------------------------
 || || ||||||||||||||||| ||||| |||||||| ||||| ||||| ||| | || || || || ||| ||||||| ||||||||  | | ||||||  || |      |  |     | | | ||| ||   | |  |||  |  |  |||  | ||    ||   ||   | ||                                  
TATTATTTCTGCAATTGAGTTTGATAAATCTGGTGACCACCTTGCTACTGGTGATCGTGGGGGCCGGGTGGTTCTATTTGAGAGGACTGATACAAAGGATgtgcgttcttttttaacactactggtctttagtttctgtatccaaacttgataggttgccttactgttcttgtttctttcaatattatgatatctttatacactgtaatgtgtag

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|33675300|gb|CF303539.1|CF303539
EST:     GAGATAGAGGTGGTCGTGTAGTTTTATTTGAAAGGACTGACTCCAGGGAT                         AGCGCCAGTCGGAGTGAACTTGAGAGACAAGATTACCCGATTGCCAGGCAT
genomic: GAGATAGAGGTGGTCGTGTAGTTTTATTTGAAAGGACTGACTCCAGGGATgtaagtacca ... ttatatgcagAGCGCCAGTCGGAGTGAACTTGAGAGACAAGATTACCCGATTGCCAGGCAT
EST: gi|33675340|gb|CF303579.1|CF303579
EST:     GAGATAGAGGTGGTCGTGTAGTTTTATTTGAAAGGACTGACTCCAGGGAT                         AGCGCCAGTCGGAGTGAACTTGAGAGACAAGATTACCCGATTGCCAGGCAT
genomic: GAGATAGAGGTGGTCGTGTAGTTTTATTTGAAAGGACTGACTCCAGGGATgtaagtacca ... ttatatgcagAGCGCCAGTCGGAGTGAACTTGAGAGACAAGATTACCCGATTGCCAGGCAT
EST: gi|13165086|gb|AU173883.1|AU173883
EST:     GAGATAGAGGTGGTCGTGTAGTTTTATTTGAAAGGACTGACTCCAGGGAT                         AGCGCCAGTCGGAGTGAACTTGAGAGACAAGATTACCCGATTGCCAGGCAT
genomic: GAGATAGAGGTGGTCGTGTAGTTTTATTTGAAAGGACTGACTCCAGGGATgtaagtacca ... ttatatgcagAGCGCCAGTCGGAGTGAACTTGAGAGACAAGATTACCCGATTGCCAGGCAT
EST: gi|9864945|gb|AU100695.1|AU100695
EST:     GAGATAGAGGTGGTCGTGTAGTTTTATTTGAAAGGACTGACTCCAGGGAT                         AGCGCCAGTCGGAGTGAACTTGAGAGACAAGATTACCCGATTGCCAGGCAT
genomic: GAGATAGAGGTGGTCGTGTAGTTTTATTTGAAAGGACTGACTCCAGGGATgtaagtacca ... ttatatgcagAGCGCCAGTCGGAGTGAACTTGAGAGACAAGATTACCCGATTGCCAGGCAT

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: 70 (upstream exon), 68 (downstream exon)
Score: 15

CATCATCTCTGCAATTGAGTTTGACAAATCCGGTGACCATCTTGCCACTGGAGATAGAGGTGGTCGTGTAGTTTTATTTGAAAGGACTGACTCCAGGGATgtaagtacca ... ttatatgcagAGCGCCAGTCGGAGTGAACTTGAGAGACAAGATTACCCGATTGCCAGGCATCCTGAATTCCGTTACAAGACTGAATTTCAGAGTCATGAACCTGAG




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