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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGCCTACATGTTCGTCCACGACGGCCTGGTCCACCGCCGCTTCCCCGTCGGCCCCATCGCGAATGTGCCCTACTTCCGGCGAGTGGCCGCGGCCCACAAGgtacgagaccaccagctgctcactgacgtttactgcaccactactactagtccacgctgctactactactactggctagagagtgtacttttgctgattttctttgtgtggccacgagcag

Basic information

species Oryza sativa
transcript LOC_Os04g48880.1
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os04g48880.1 (Oryza sativa), 5'ss of exon 4
lower sequence: GRMZM2G398137_T01 (Zea mays), 5'ss of exon 4
GGCCTACATGTTCGTCCACGACGGCCTGGTCCACCGCCGCTTCCCCGTCGGCCCCATCGCGAATGTGCCCTACTTCCGGCGAGTGGCCGCGGCCCACAAGgtacg-----agaccaccagctgctcactgacgtttactgcaccactac-tactagtccacgctgctactactactactggctagagagtgtacttttgctgattttctttgtgtggccacgagcag
||||||||||||||||||||||||||||||||||||| |||| || |||||||||||||| || |||||||||||||| |||||||| || || |||||||||||      | | || ||  ||   ||  ||    ||    |||  | | ||  |||     |   || ||    |  ||     | |||||| |  ||                          
GGCCTACATGTTCGTCCACGACGGCCTGGTCCACCGCTGCTTTCCGGTCGGCCCCATCGCCAACGTGCCCTACTTCCGCCGAGTGGCTGCCGCTCACAAGgtacgcacgagggcgacgagaggccagctagcgacctctcgctcaccgcctcctcatccttctcgaagcttctgtagcatgcattctactgtactgt-act--------------------------

upper sequence: LOC_Os04g48880.1 (Oryza sativa), 5'ss of exon 4
lower sequence: GRMZM2G152135_T06 (Zea mays), 5'ss of exon 4
GGCCTACATGTTCGTCCACGACGGCCTGGTCCACCGCCGCTTCCCCGTCGGCCCCATCGCGAATGTGCCCTACTTCCGGCGAGTGGCCGCGGCCCACAAGgtacga---------gaccaccagctgctcactgacgtttactgcaccactactactagtccacgctgctacta--------ctactactggctagagagtgt--acttttgctgat---tttctttgtgtggccacgagcag------------------------------------------------------
|||||||||||||||||||||||||||||||||||||||||| || ||||||||||||||  | |||||||||||||| |||||||| ||  | ||||||||||           |||  | |   |  ||   || | |    ||||   ||| ||    |  ||  |||||         || | |||||  ||  |||    || |  |||||    ||| | | | |   |||   |                                                        
GGCCTACATGTTCGTCCACGACGGCCTGGTCCACCGCCGCTTTCCGGTCGGCCCCATCGCCGACGTGCCCTACTTCCGCCGAGTGGCTGCCTCGCACAAGgtacatagtacttacgacggcgacgaggccagccacctctcgctcaccgaaacttctgtagcgtgcatctactgtactgtgcctgcaactgggcaggcagtaccgacctgagctgacatgtttttctttcttttcaccgcccttttgcgcgctggctggtgtggcgtggctgggctcctcggcgatgtcgcgagcag

upper sequence: LOC_Os04g48880.1 (Oryza sativa), 5'ss of exon 4
lower sequence: GRMZM2G090051_T02 (Zea mays), 5'ss of exon 3
GGCCTACATGTTCGTCCACGACGGCCTGGTCCACCGCCGCTTCCCCGTCGGCCCCATCGCGAATGTGCCCTACTTCCGGCGAGTGGCCGCGGCCCACAAGgtacgagaccaccagctgctcactgacgtttactgcaccactactactagtccacgctgctactactactactggctagagagtgtact-tttgctgattttctttgtgtggccacgagcag
||||||||||||||| ||||||||||| ||||||||||||||||||||||| ||||||| ||| |||||||||||||| || || ||||| |||||  |||| ||   |  |   ||| ||  || | | ||     |  |  | |   | |  | |||    |   ||   || ||   |    | ||   ||| |                         
GGCCTACATGTTCGTGCACGACGGCCTCGTCCACCGCCGCTTCCCCGTCGGGCCCATCGAGAACGTGCCCTACTTCCGCCGCGTCGCCGCCGCCCATCAGgtccgctgctgctt-ctgttc--tgccttctatcatcctgcc-ccatctgcctgc-ctgtgtttgtaaccgttgcctgctgctgctgctgcctgcag-------------------------

upper sequence: LOC_Os04g48880.1 (Oryza sativa), 5'ss of exon 4
lower sequence: GRMZM2G164318_T01 (Zea mays), 5'ss of exon 4
GGCCTACATGTTCGTCCACGACGGCCTGGTCCACCGCCGCTTCCCCGTCGGCCCCATCGCGAATGTGCCCTACTTCCGGCGAGTGGCCGCGGCCCACAAGgtacgagaccaccagctgctcactgacgtttact-gcaccactactactagtccacgctgctactactactactggctagagagtgtacttttgctgattttctttgtgtggccacgagcag
|||||||||||||||||||||||||||||||||||||||||| || |||||||||||||| || |||||||||||||| |||||||| || || |||||||||||  ||   |  | ||     || |    || ||  | |  |    |   |   ||  | || ||   |    ||  || ||| | || | |||   |                     
GGCCTACATGTTCGTCCACGACGGCCTGGTCCACCGCCGCTTTCCGGTCGGCCCCATCGCCAACGTGCCCTACTTCCGCCGAGTGGCTGCCGCTCACAAGgtacgc-acggacgacggcgacgagaggccagctagcgacccctcgctcaccacctcctcatccttctcgaagcttctgtagcgtgca-ttctactgtgcta--------------------

upper sequence: LOC_Os04g48880.1 (Oryza sativa), 5'ss of exon 4
lower sequence: Vv02s0025g00240.t01 (Vitis vinifera), 5'ss of exon 5
GGCCTACATGTTCGTCCACGACGGCCTGGTCCACCGCCGCTTCCCCGTCGGCCCCATCGCGAATGTGCCCTACTTCCGGCGAGTGGCCGCGGCCCACAAGgtacgagaccaccagctgctcactgacgtttactgcaccactactactagtccacgctgctactactactactggctagagagtgtacttttgctgattttctttgtgtggccacgagcag
|||||||||||| |||||||||||||| |||||||| || ||||| ||||| |||||||| || || || ||  | ||   ||| ||  |||||||| | |||    | ||    |  | |    | | | |    ||||  | |   | |  |     ||| |  ||  | |    ||  | | | | | || | ||||  | | |||||     ||   
GGCCTACATGTTTGTCCACGACGGCCTTGTCCACCGTCGATTCCCTGTCGGACCCATCGCCAACGTCCCTTATCTACGAAAAGTAGCTTCGGCCCACCAAgta---aatcatacaccccacctacaagctgaa---accaaaattctcaatttatatcactatt--tatcaattatcaggaaatattcatatg-taatttcttgtatgtggattgcag---

upper sequence: LOC_Os04g48880.1 (Oryza sativa), 5'ss of exon 4
lower sequence: EDO99380 (Chlamydomonas reinhardtii), 5'ss of exon 5
------------------------------------GGCCTACATGTTCGTCCACGACGGCCTGGTCCACCGCCGCTTCCCCGTCGGCCCCATCGCGAATGTGCCCTACTTCCGGCGAGTGGCCGCGGCCCACAAGgtacgagaccaccagctgctcactgacgtttactgcaccactactactagtccacgctgctactactactactggctagagagtgtacttttgctgattttctttgtgtggccacgagcag
                                     |||||||||||| |||||||||||||||| ||||||||||||||||| || |||||||| || |||   |   |  | || | ||| | |     |  |||  |    |    ||||              ||||        | |||| |   ||||    | ||      |||| |   ||||    |||                            
CTTCGGCGCGGGTCTGGGCATCACGCTGTTCGGCATCGCCTACATGTTCTTCCACGACGGCCTGGTGCACCGCCGCTTCCCCGTGGGGCCCATCGCCAACgtgag-tgtgtgtgtcggg-ggctgggctgggctgggtgtg----cttgggctgg------------gctgcg-------tgctaggctgggctgtgtgtgct----tgggctgggcggtgtgtgcttg----------------------------

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|87021034|gb|CI271841.1|CI271841
EST:     GCCCCATCGCGAATGTGCCCTACTTCCGGCGAGTGGCCGCGGCCCACAAG                         ATACACCACACGGACAAGTTCGAGGGCGTACCGTATGGGCTGTTTCTTGGA
genomic: GCCCCATCGCGAATGTGCCCTACTTCCGGCGAGTGGCCGCGGCCCACAAGgtacgagacc ... ccacgagcagATACACCACACGGACAAGTTCGAGGGCGTACCGTATGGGCTGTTTCTTGGA
EST: gi|88721251|gb|CI744550.1|CI744550
EST:     GCCCCATCGCGAATGTGCCCTACTTCCGGCGAGTGGCCGCGGCCCACAAG                         ATACACCACACGGACAAGTTCGAGGGCGTACCGTATGGGCTGTTTCTTGGA
genomic: GCCCCATCGCGAATGTGCCCTACTTCCGGCGAGTGGCCGCGGCCCACAAGgtacgagacc ... ccacgagcagATACACCACACGGACAAGTTCGAGGGCGTACCGTATGGGCTGTTTCTTGGA
EST: gi|38468918|gb|CF953049.1|CF953049
EST:     GCCCCATCGCGAATGTGCCCTACTTCCGGCGAGTGGCCGCGGCCCACAAG                         ATACACCACACGGACAAGTTCGAGGGCGTACCGTATGGGCTGTTTCTTGGA
genomic: GCCCCATCGCGAATGTGCCCTACTTCCGGCGAGTGGCCGCGGCCCACAAGgtacgagacc ... ccacgagcagATACACCACACGGACAAGTTCGAGGGCGTACCGTATGGGCTGTTTCTTGGA
EST: gi|88245426|gb|CI245275.1|CI245275
EST:     GTGGCCGCGGCCCACAAG                         ATACACCACACGGACAAGTTCGAGGGCGTACCGTATGGGCTGTTTCTTGGA
genomic: GTGGCCGCGGCCCACAAGgtacgagacc ... ccacgagcagATACACCACACGGACAAGTTCGAGGGCGTACCGTATGGGCTGTTTCTTGGA
EST: gi|86478555|gb|CI121188.1|CI121188
EST:     GCCCCATCGCGAATGTGCCCTACTTCCGGCGAGTGGCCGCGGCCCACAAG                         ATACACCACACGGACAAGTTCGAGGGCGTACCGTATGGGCTGTTTCTTGGA
genomic: GCCCCATCGCGAATGTGCCCTACTTCCGGCGAGTGGCCGCGGCCCACAAGgtacgagacc ... ccacgagcagATACACCACACGGACAAGTTCGAGGGCGTACCGTATGGGCTGTTTCTTGGA
EST: gi|87022123|gb|CI259195.1|CI259195
EST:     CATCGCGAATGTGCCCTACTTCCGGCGAGTGGCCGCGGCCCACAAG                         ATACACCACACGGACAAGTTCGAGGGCGTACCGTATGGGCTGTTTCTTGGA
genomic: CATCGCGAATGTGCCCTACTTCCGGCGAGTGGCCGCGGCCCACAAGgtacgagacc ... ccacgagcagATACACCACACGGACAAGTTCGAGGGCGTACCGTATGGGCTGTTTCTTGGA
EST: gi|29684804|gb|CB681079.1|CB681079
EST:     GCCCCATCGCGAATGTGCCCTACTTCCGGCGAGTGGCCGCGGCCCACAAG                         ATACACCACACGGACAAGTTCGAGGGCGTACCGTATGGGCTGTTTCTTGGA
genomic: GCCCCATCGCGAATGTGCCCTACTTCCGGCGAGTGGCCGCGGCCCACAAGgtacgagacc ... ccacgagcagATACACCACACGGACAAGTTCGAGGGCGTACCGTATGGGCTGTTTCTTGGA

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: 54 (upstream exon), 57 (downstream exon)
Score: 9

GGCCTACATGTTCGTCCACGACGGCCTGGTCCACCGCCGCTTCCCCGTCGGCCCCATCGCGAATGTGCCCTACTTCCGGCGAGTGGCCGCGGCCCACAAGgtacgagacc ... ccacgagcagATACACCACACGGACAAGTTCGAGGGCGTACCGTATGGGCTGTTTCTTGGACCCAAG




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