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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttatgttaaacttagcccgtaattttacctagtccactcttgattcttccatcgtactaatctcttactgtggtatttacacaacgaaaccaattactctgtgttatctaagaaatgtctgtgttcgttgggcagGGAGTGCACGACATTTTCCAGGGATCTCCCGAGAGAATGTGGGAACCAAATGAGCCACGCATCAACAAGATTGTATTCATAGGCAAGAATCTCAATGGGG

Basic information

species Oryza sativa
transcript LOC_Os02g55630.1
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g55630.1 (Oryza sativa), 3'ss of exon 9
lower sequence: GRMZM2G180418_T01 (Zea mays), 3'ss of exon 14
gtttatgttaaacttagcccgtaattttacctag-tccactcttgattcttccatcgtactaatctcttactgtggtatttacacaacgaaaccaattactctgtgttatctaagaaatgtctgtgttcgt-tgggcagGGAGTGCACGACATTTTCCAGGGATCTCCCGAGAGAATGTGGGAACCAAATGAGCCACGCATCAACAAGATTGTATTCATAGGCAAGAATCTCAATGGGG
                        ||| || | | |  ||  || |   || || |     ||  ||| |   ||  ||| | |   || |     | |  |||  ||   |       |  ||| || |  ||| |||||||| || |||||||||||||||||||| |||||||||||||| ||||||||||| ||||||||||||||||| ||||| |||| ||| ||||||   |
------------------------tttgacttggatagacattttaacattacacca---aaaattctcagactgacattgataagccgta-----tgaacctgacttgctt-------gcttgtttttgcatggccagGGAGTCCATGACATTTTCCAGGGATCTCCTGAGAGAATGTGGGAGCCAAATGAGCCGCGCATCAACAAGATTGTCTTCATCGGCAGGAACCTCAATAAAG

upper sequence: LOC_Os02g55630.1 (Oryza sativa), 3'ss of exon 9
lower sequence: GRMZM2G180418_T02 (Zea mays), 3'ss of exon 14
gtttatgttaaacttagcccgtaattttacctagtccactcttgattcttccatcgtactaatctcttactgtggtatttacacaacgaaaccaattactctgtgttatctaagaaatgtctgtgttcgttgggcagGGAGTGCACGACATTTTCCAGGGATCTCCCGAGAGAATGTGGGAACCAAATGAGCCACGCATCAACAAGATTGTATTCATAGGCAAGAATCTCAATGGGG--------------------------------------------------------------------------------------
                                                                                                                           | ||   ||| |||||||| || |||||||||||||||||||| |||||||||||||| ||||||||||| ||||||||||||||||| ||||| |||| ||| ||||||   |                                                                                      
---------------------------------------------------------------------------------------------------------------------------ttttgcatggccagggagtccatgacattttccagggatctcctgagagaatgtgggagccaaatgagccgcgcatcaacaagattgtcttcatcggcagGAACCTCAATAAAGAAGAGCTGGATAAGGGGTTCAAGGATTGCCTACTGAAGAAATAGAGTGATTTCAGAATAGTCGGGATATAGATCTCCAGTTTTGGC
















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|88996744|gb|CI389410.1|CI389410
EST:     GTGGAATGCCTCAGCGCTTTGTCTGTCAG                         GGAGTGCACGACATTTTGCAGGGATCTCCCGAGAAAATGTGGGAACCAAAT
genomic: GTGGAATGCCTCAGCGCTTTGTCTTTCAGgtttatgtta ... cgttgggcagGGAGTGCACGACATTTTCCAGGGATCTCCCGAGAGAATGTGGGAACCAAAT
EST: gi|86872960|gb|CI326957.1|CI326957
EST:     AGTGGAATGCCTCAGCGCTTTGTCTTTCAG                         GGAGTGCACCACATTTTCCAGGGATCTCCCGAGAGAATGTGGGAACCAAAT
genomic: AGTGGAATGCCTCAGCGCTTTGTCTTTCAGgtttatgtta ... cgttgggcagGGAGTGCACGACATTTTCCAGGGATCTCCCGAGAGAATGTGGGAACCAAAT
EST: gi|86865251|gb|CI330819.1|CI330819
EST:     TGAAGGGGCTACTTTCTGTCAGTGGAATGCCTCAGCGCTTTGTCTTTCAG                         GGAGTGCACGACATTTTCCAGGGATCTCCCGAGAGAATGTGGGAACCAAAT
genomic: TGAAGGGGCTACTTTCTGTCAGTGGAATGCCTCAGCGCTTTGTCTTTCAGgtttatgtta ... cgttgggcagGGAGTGCACGACATTTTCCAGGGATCTCCCGAGAGAATGTGGGAACCAAAT
EST: gi|86842188|gb|CI338516.1|CI338516
EST:     TGAA-GGGCTACTTTCTGTCAGTGGAATGCCTCAGCGCTTTGTCTTTCAG                         GGAGTGCACGACATTTTCCAGGGATCTCCCGAGAGAATGTGGGAACCAAAT
genomic: TGAAGGGGCTACTTTCTGTCAGTGGAATGCCTCAGCGCTTTGTCTTTCAGgtttatgtta ... cgttgggcagGGAGTGCACGACATTTTCCAGGGATCTCCCGAGAGAATGTGGGAACCAAAT
EST: gi|88249704|gb|CI249553.1|CI249553
EST:     GCTACTTTCTGTCAGTGGAATGCCTCAGCGCTTTGTCTTTCAG                         GGAGTGCACGACATTTTCCAGGGATCTCCCGAGAGAATGTGGGAACCAAAT
genomic: GCTACTTTCTGTCAGTGGAATGCCTCAGCGCTTTGTCTTTCAGgtttatgtta ... cgttgggcagGGAGTGCACGACATTTTCCAGGGATCTCCCGAGAGAATGTGGGAACCAAAT
EST: gi|88989013|gb|CI040740.1|CI040740
EST:     TGAAGGGGCTACTTTCTGTCAGTGGAATGCCTCAGCGCTTTGTCTTTCAG                         GGAGTGCACGACATTTTCCAGGGATCTCCCGAGAGAATGTGGGAACCAAAT
genomic: TGAAGGGGCTACTTTCTGTCAGTGGAATGCCTCAGCGCTTTGTCTTTCAGgtttatgtta ... cgttgggcagGGAGTGCACGACATTTTCCAGGGATCTCCCGAGAGAATGTGGGAACCAAAT
EST: gi|86871807|gb|CI331184.1|CI331184
EST:     GGAATGCCTCAGCGCTTTGTCTTTCAG                         GGAGTGCACGACATTTTCCAGGGATCTCCCGAGAGAATGT-GGAACCAAAT
genomic: GGAATGCCTCAGCGCTTTGTCTTTCAGgtttatgtta ... cgttgggcagGGAGTGCACGACATTTTCCAGGGATCTCCCGAGAGAATGTGGGAACCAAAT

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: 72 (upstream exon), 61 (downstream exon)
Score: 36

CATGTGGTTGGGAAACCTACTGCTAGAACGCAGCGATGACATATACCGGATGAAGGGGCTACTTTCTGTCAGTGGAATGCCTCAGCGCTTTGTCTTTCAGgtttatgtta ... cgttgggcagGGAGTGCACGACATTTTCCAGGGATCTCCCGAGAGAATGTGGGAACCAAATGAGCCACGCATCAACAAGATTGTATTCATAGGCAAGAATCTCAATGGGG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acaacgaaaccaattactctgtgttatctaagaaatgtctgtgttcgttgggcagGGAGTGCACGACATTTTCCAGGGATCTCCCGAGAGAATGTGGGAACCAAATGAGCCACGCATCAACAAGATTGTATTCATAGGCAAGAATCTCAATGGGG
                       ttatctaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtttatgttaaacttagcccgtaattttacctagtccactcttgattcttccatcgtactaatctcttactgtggtatttacacaacgaaaccaattactctgtgttatctaagaaatgtctgtgttcgttgggcagGGAGTGCACGACATTTTCCAGGGATCTCCCGAGAGAATGTGGGAACCAAATGAGCCACGCATCAACAAGATTGTATTCATAGGCAAGAATCTCAATGGGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAGA