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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tatctaaccagtgtcacctacaactttgtcttactgtttatttactgatttgcattcagtgctgccatattttgatattttctgagtcaatgcttttcagGGTAATTTTGATCTTGTTGGGAACAATATGCCTGTCTTTTTTATCCGAGATGGGATGAAATTCCCTGACATGGTCCATGCTTTCAAGCCAAGTCCAAAGA

Basic information

species Oryza sativa
transcript LOC_Os06g51150.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os06g51150.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G088212_T02 (Zea mays), 3'ss of exon 2
tatctaaccagtgtcacctaca-actttgtcttactgtttatttactgatttgcattcagtgctgccatattttgatattttctgagtcaatgcttttcagGGTAATTTTGATCTTGTTGGGAACAATATGCCTGTCTTTTTTATCCGAGATGGGATGAAATTCCCTGACATGGTCCATGCTTTCAAGCCAAGTCCAAAGA
| |   |    |   |   ||  | ||| |   ||  |||||| ||   |||  || ||| |      ||| ||    ||||||   |   |  |||||||||||| ||||| || || || ||||| |||||||| ||||| || |||||||||||||||||||||||||||||||| ||||||||||| | ||||||||
tgttggatgccttcaagtgacccaatttttagaacactttattgacctttttatatccagagggatagtatcttatggttttcttcatgcgt-tttttcagGGTAACTTTGACCTCGTGGGTAACAACATGCCTGTGTTTTTCATACGAGATGGGATGAAATTCCCTGACATGGTCCACGCTTTCAAGCCGAATCCAAAGA

upper sequence: LOC_Os06g51150.1 (Oryza sativa), 3'ss of exon 3
lower sequence: EFJ36549 (Selaginella moellendorffii), 3'ss of exon 3
tatctaaccagtgtcacctacaactttgtcttactgtttatttactgatttgcattcagtgctgccatattttgatattttctgagtcaatgcttttcagGGTAATTTTGATCTTGTTGGGAACAATATGCCTGTCTTTTTTATCCGAGATGGGATGAAATTCCCTGACATGGTCCATGCTTTCAAGCCAAGTCCAAAGA
                        |||||  | || ||| |||  || ||| | |||  |  |  || |   || | | || ||  |          ||||| || |||||| | ||||| |||||| | || || || ||  |||| ||||| ||||| ||||||||||||||||||||  | ||||| |  |||| ||
-----------------------gtttgtagt-ctttttgttt--tgcttt-ctttcgtttttctcaaagaatgttgtgttgtggatg---------cagGGAAACTTTGATATGGTTGGAAACAATTTTCCCGTGTTCTTCGTCCGGGATGGAATGAAGTTCCCTGACATGGTCCATGCGCTGAAGCCCAACCCAAGGA

upper sequence: LOC_Os06g51150.1 (Oryza sativa), 3'ss of exon 3
lower sequence: EFJ18507 (Selaginella moellendorffii), 3'ss of exon 3
tatctaaccagtgtcacctacaactttgtcttactgtttatttact-gatttgcattcagtgctgccatattttgatattttctgagtcaatgcttttcagGGTAATTTTGATCTTGTTGGGAACAATATGCCTGTCTTTTTTATCCGAGATGGGATGAAATTCCCTGACATGGTCCATGCTTTCAAGCCAAGTCCAAAGA
                              ||   |||| |||  | |  || | |||  |  |  || |   ||   | || ||  |          ||||| || |||||| | ||||| |||||| | || || || ||  |||||||||| ||||| ||||||||||||||||||||  | ||||| |  |||| ||
----------------------------gtttgtagtttttttgtttggctttctttcgtttttctcaaagaatgtggtgttgtggatg---------cagGGAAACTTTGATATGGTTGGAAACAATTTTCCCGTGTTCTTCGTCCGAGATGGAATGAAGTTCCCTGACATGGTCCATGCGCTGAAGCCCAACCCAAGGA

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|427946|gb|D24091.1|D24091
EST:     AGACATTGAGGGATCCACGTGGTTTTGCTGTCAAGTTTTACACTAGAGAG                         GGTAATTTTGATCTTGTTGGGAACAATATGCCTGTNTTTTTTATCCGAGAT
genomic: AGACATTGAGGGATCCACGTGGTTTTGCTGTCAAGTTTTACACTAGAGAGgtacttgctc ... tgcttttcagGGTAATTTTGATCTTGTTGGGAACAATATGCCTGTCTTTTTTATCCGAGAT
EST: gi|29657922|gb|CB654197.1|CB654197
EST:     AGACATTGAGGGATCCACGTGGTTTTGCTGTCAAGTTTTACACTAGAGAG                         GGTAATTTTGATCTTGTTGGGAACAATATGCCTGTCTTTTTTATCCGAGAT
genomic: AGACATTGAGGGATCCACGTGGTTTTGCTGTCAAGTTTTACACTAGAGAGgtacttgctc ... tgcttttcagGGTAATTTTGATCTTGTTGGGAACAATATGCCTGTCTTTTTTATCCGAGAT
EST: gi|58692972|gb|CK081659.1|CK081659
EST:     AGACATTGAGGGATCCACGTGGTTTTGCTGTCAAGTTTTACACTAGAGAG                         GGTAATTTTGATCTTGTTGGGAACAATATGCCTGTCTTTTTTATCCGAGAT
genomic: AGACATTGAGGGATCCACGTGGTTTTGCTGTCAAGTTTTACACTAGAGAGgtacttgctc ... tgcttttcagGGTAATTTTGATCTTGTTGGGAACAATATGCCTGTCTTTTTTATCCGAGAT
EST: gi|29628364|gb|CB633375.1|CB633375
EST:     AGACATTGAGGGATCCACGTGGTTTTGCTGTCAAGTTTTACACTAGAGAG                         GGTAATTTTGATCTTGTTGGGAACAATATGCCTGTCTTTTTTATCCGAGAT
genomic: AGACATTGAGGGATCCACGTGGTTTTGCTGTCAAGTTTTACACTAGAGAGgtacttgctc ... tgcttttcagGGTAATTTTGATCTTGTTGGGAACAATATGCCTGTCTTTTTTATCCGAGAT
EST: gi|117240442|gb|CT842802.1|CT842802
EST:     AGACATTGAGGGATCCACGTGGTTTTGCTGTCAAGTTTTACACTAGAGAG                         GGTAATTTTGATCTTGTTGGGAACAATATGCCTGTCTTTTTTATCCGAGAT
genomic: AGACATTGAGGGATCCACGTGGTTTTGCTGTCAAGTTTTACACTAGAGAGgtacttgctc ... tgcttttcagGGTAATTTTGATCTTGTTGGGAACAATATGCCTGTCTTTTTTATCCGAGAT
EST: gi|58663995|gb|CK052681.1|CK052681
EST:     AGACATTGAGGGATCCACGTGGTTTTGCTGTCAAGTTTTACACTAGAGAG                         GGTAATTTTGATCTTGTTGGGAACAATATGCCTGTCTTTTTTATCCGAGAT
genomic: AGACATTGAGGGATCCACGTGGTTTTGCTGTCAAGTTTTACACTAGAGAGgtacttgctc ... tgcttttcagGGTAATTTTGATCTTGTTGGGAACAATATGCCTGTCTTTTTTATCCGAGAT
EST: gi|58678433|gb|CK067120.1|CK067120
EST:     GACACTTGAGGGATCCACGTGGTTTTGCTGTCAAGTTTTACACTAGAGAG                         GGTAATTTTGATCTTGTCCGGAACAATATGCCTGTCTTTTTTATCCGAGAT
genomic: GACA-TTGAGGGATCCACGTGGTTTTGCTGTCAAGTTTTACACTAGAGAGgtacttgctc ... tgcttttcagGGTAATTTTGATCTTGTTGGGAACAATATGCCTGTCTTTTTTATCCGAGAT
EST: gi|29623121|gb|CB628132.1|CB628132
EST:     AGACATTGAGGGATCCACGTGGTTTTGCTGTCAAGTTTTACACTAGAGAG                         GGTAATTTTGATCTTGTTGGGAACAATATGCCTGTCTTTTTTATCCGAGAT
genomic: AGACATTGAGGGATCCACGTGGTTTTGCTGTCAAGTTTTACACTAGAGAGgtacttgctc ... tgcttttcagGGTAATTTTGATCTTGTTGGGAACAATATGCCTGTCTTTTTTATCCGAGAT
EST: gi|29619347|gb|CB624359.1|CB624359
EST:     AGACATTGAGGGATCCACGTGGTTTTGCTGTCAAGTTTTACACTAGAGAG                         GGTAATTTTGATCTTGTTGGGAACAATATGCCTGTCTTTTTTATCCGAGAT
genomic: AGACATTGAGGGATCCACGTGGTTTTGCTGTCAAGTTTTACACTAGAGAGgtacttgctc ... tgcttttcagGGTAATTTTGATCTTGTTGGGAACAATATGCCTGTCTTTTTTATCCGAGAT
EST: gi|58669083|gb|CK057769.1|CK057769
EST:     AGACATTGAGGGATCCACGTGGTTTTGCTGTCAAGTTTTACACTAGAGAG                         GGTAATTTTGATCTTGTTGGGAACAATATGCCTGTCTTTTTTATCCGAGAA
genomic: AGACATTGAGGGATCCACGTGGTTTTGCTGTCAAGTTTTACACTAGAGAGgtacttgctc ... tgcttttcagGGTAATTTTGATCTTGTTGGGAACAATATGCCTGTCTTTTTTATCCGAGA-
EST: gi|29672050|gb|CB668325.1|CB668325
EST:     AGACATTGAGGGATCCACGTGGTTTTGCTGTCAAGTTTTACACTAGAGAG                         GGTAATTTTGATCTTGTTGGGAACAATATGCCTGTCTTTTTTATCCGAGAT
genomic: AGACATTGAGGGATCCACGTGGTTTTGCTGTCAAGTTTTACACTAGAGAGgtacttgctc ... tgcttttcagGGTAATTTTGATCTTGTTGGGAACAATATGCCTGTCTTTTTTATCCGAGAT
EST: gi|58694437|gb|CK083124.1|CK083124
EST:     AGACATTGAGGGATCCACGTGGTTTTGCTGTCAAGTTTTACACTAGAGAG                         GGTAATTTTGATCTTGTTGGGAACAATATGCCTGTCTTTTTTATCCGAGAT
genomic: AGACATTGAGGGATCCACGTGGTTTTGCTGTCAAGTTTTACACTAGAGAGgtacttgctc ... tgcttttcagGGTAATTTTGATCTTGTTGGGAACAATATGCCTGTCTTTTTTATCCGAGAT
EST: gi|38474000|gb|CF958132.1|CF958132
EST:     AGACATTGAGGGATCCACGTGGTTTTGCTGTCAAGTTTTACACTAGAGAG                         GGTAATTTTGATCTTGTTGGGAACAATATGCCTGTCTTTTTTATCCGAGAT
genomic: AGACATTGAGGGATCCACGTGGTTTTGCTGTCAAGTTTTACACTAGAGAGgtacttgctc ... tgcttttcagGGTAATTTTGATCTTGTTGGGAACAATATGCCTGTCTTTTTTATCCGAGAT
EST: gi|58608999|gb|CK037032.1|CK037032
EST:     AGACATTGAGGGATCCACGTGGTTTTGCTGTCAAGTTTTACACTAGAGAG                         GGTAATTTTGATCTTGTCGGGAACAATATGCCTGTCTTTTTTATCCGAGAT
genomic: AGACATTGAGGGATCCACGTGGTTTTGCTGTCAAGTTTTACACTAGAGAGgtacttgctc ... tgcttttcagGGTAATTTTGATCTTGTTGGGAACAATATGCCTGTCTTTTTTATCCGAGAT
EST: gi|58598738|gb|CK009266.1|CK009266
EST:     AGACATTGAGGGATCCACGTGGTTTTGCTGTCAAGTTTTACACTAGAGAG                         GGTAATTTTGATCTTGTTGGGAACAATATGCCTGTCTTTTTTATCCGAGAT
genomic: AGACATTGAGGGATCCACGTGGTTTTGCTGTCAAGTTTTACACTAGAGAGgtacttgctc ... tgcttttcagGGTAATTTTGATCTTGTTGGGAACAATATGCCTGTCTTTTTTATCCGAGAT
EST: gi|33678219|gb|CF306458.1|CF306458
EST:     AGACATTGAGGGATCCACGTGGTTTTGCTGTCAAGTTTTACACTAGAGAG                         GGTAATTTTGATCTTGTTGGGAACAATATGCCTGTCTTTTTTATCCGAGAT
genomic: AGACATTGAGGGATCCACGTGGTTTTGCTGTCAAGTTTTACACTAGAGAGgtacttgctc ... tgcttttcagGGTAATTTTGATCTTGTTGGGAACAATATGCCTGTCTTTTTTATCCGAGAT
EST: gi|58606081|gb|CK034114.1|CK034114
EST:     AGACATTGAGGGATCCACGTGGTTTTGCTGTCAAGTTTTACACTAGAGAG                         GGTAATTTTGATCTTGTTGGGAACAATATGCCTGTCTTTTTTATCCGAGAT
genomic: AGACATTGAGGGATCCACGTGGTTTTGCTGTCAAGTTTTACACTAGAGAGgtacttgctc ... tgcttttcagGGTAATTTTGATCTTGTTGGGAACAATATGCCTGTCTTTTTTATCCGAGAT
EST: gi|33678440|gb|CF306679.1|CF306679
EST:     AGACATTGAGGGATCCACGTGGTTTTGCTGTCAAGTTTTACACTAGAGAG                         GGTAATTTTGATCTTGTTGGGAACAATATGCCTGTCTTTTTTATCCGAGAT
genomic: AGACATTGAGGGATCCACGTGGTTTTGCTGTCAAGTTTTACACTAGAGAGgtacttgctc ... tgcttttcagGGTAATTTTGATCTTGTTGGGAACAATATGCCTGTCTTTTTTATCCGAGAT
EST: gi|58602279|gb|CK012807.1|CK012807
EST:     ACGTGGTTTTGCTGTCGAGTTTTACACTAGAGAG                         GGTAATTTTGATCTTGTTGGGAACAATATGCCTGTCTTTTTTATCCGAGAA
genomic: ACGTGGTTTTGCTGTCAAGTTTTACACTAGAGAGgtacttgctc ... tgcttttcagGGTAATTTTGATCTTGTTGGGAACAATATGCCTGTCTTTTTTATCCGAG-A
EST: gi|58690037|gb|CK078724.1|CK078724
EST:     AGACATTGAGGGATCCACGTGGTTTTGCTGTCAAGTTTTACACTAGAGAG                         GGTAATTTTGATCTTGTTGGGAACAATATGCCTGTCTTTTTTATCCGAGAT
genomic: AGACATTGAGGGATCCACGTGGTTTTGCTGTCAAGTTTTACACTAGAGAGgtacttgctc ... tgcttttcagGGTAATTTTGATCTTGTTGGGAACAATATGCCTGTCTTTTTTATCCGAGAT
EST: gi|58674207|gb|CK062893.1|CK062893
EST:     AGACATTGAGGGATCCACGTGGTTTTGCTGTCAAGTTTTACACTAGAGAG                         GGTAATTTTGATCTTGTTGGGAACAATATGCCTGTCTTTTTTATCCGAGAT
genomic: AGACATTGAGGGATCCACGTGGTTTTGCTGTCAAGTTTTACACTAGAGAGgtacttgctc ... tgcttttcagGGTAATTTTGATCTTGTTGGGAACAATATGCCTGTCTTTTTTATCCGAGAT
EST: gi|58695135|gb|CK083822.1|CK083822
EST:     AGACATTGAGGGATCCACGTGGTTTTGCTGTCAAGTTTTACACTAGAGAG                         GGTAATTTTGATCTTG
genomic: AGACATTGAGGGATCCACGTGGTTTTGCTGTCAAGTTTTACACTAGAGAGgtacttgctc ... tgcttttcagGGTAATTTTGATCTTG
EST: gi|33793425|gb|CF322592.1|CF322592
EST:     AGACATTGAGGGATCCACGTGGTTTTGCTGTCAAGTTTTACACTAGAGAG                         GGTAATTTTGATCTTGTTGGGAACAATATGCCTGTCTTTTTTATCCGAGAT
genomic: AGACATTGAGGGATCCACGTGGTTTTGCTGTCAAGTTTTACACTAGAGAGgtacttgctc ... tgcttttcagGGTAATTTTGATCTTGTTGGGAACAATATGCCTGTCTTTTTTATCCGAGAT
EST: gi|58613055|gb|CK040767.1|CK040767
EST:     AGACATTGAGGGATCCACGTGGTTTTGCTGTCAAGTTTTACACTAGAGAG                         GGTAATTTTGATCTTGTTGGGAACAATATGCCTGTCTTTTT-ATCCGAGAT
genomic: AGACATTGAGGGATCCACGTGGTTTTGCTGTCAAGTTTTACACTAGAGAGgtacttgctc ... tgcttttcagGGTAATTTTGATCTTGTTGGGAACAATATGCCTGTCTTTTTTATCCGAGAT
EST: gi|58666199|gb|CK054885.1|CK054885
EST:     AGACATTGAGGGATCCACGTGGTTTTGCTGTCAAGTTTTACACTAGAGAG                         GGTAATTTTGATCTTGTTGGGAACAATATGCCTGTCTTTTTTATCCGAGAT
genomic: AGACATTGAGGGATCCACGTGGTTTTGCTGTCAAGTTTTACACTAGAGAGgtacttgctc ... tgcttttcagGGTAATTTTGATCTTGTTGGGAACAATATGCCTGTCTTTTTTATCCGAGAT
EST: gi|58692263|gb|CK080950.1|CK080950
EST:     AGACATTGAGGGATCCACGTGGTTTTGCTGTCAAGTTTTACACTAGAGAG                         GGTAATTTTGATCTTGTTGGGAACAATATGCCTGTCTTTTTTATCCGAGAT
genomic: AGACATTGAGGGATCCACGTGGTTTTGCTGTCAAGTTTTACACTAGAGAGgtacttgctc ... tgcttttcagGGTAATTTTGATCTTGTTGGGAACAATATGCCTGTCTTTTTTATCCGAGAT
EST: gi|58601731|gb|CK012259.1|CK012259
EST:     AGACATTGAGGGATCCACGTGGTTTTGCTGTCAAGTTTTACACTAGAGAG                         GGTAATTTTGATCTTGTTGGGAACAATATGCCTGTCTTTTTTATCCGAGAT
genomic: AGACATTGAGGGATCCACGTGGTTTTGCTGTCAAGTTTTACACTAGAGAGgtacttgctc ... tgcttttcagGGTAATTTTGATCTTGTTGGGAACAATATGCCTGTCTTTTTTATCCGAGAT
EST: gi|33674814|gb|CF303053.1|CF303053
EST:     AGACATTGAGGGATCCACGTGGTTTTGCTGTCAAGTTTTACACTAGAGAG                         GGTAATTTTGATCTTGTTGGGAACAATATGCCTGTCTTTTTTATCCGAGAT
genomic: AGACATTGAGGGATCCACGTGGTTTTGCTGTCAAGTTTTACACTAGAGAGgtacttgctc ... tgcttttcagGGTAATTTTGATCTTGTTGGGAACAATATGCCTGTCTTTTTTATCCGAGAT
EST: gi|58674842|gb|CK063529.1|CK063529
EST:     AGACATTGAGGGATCCACGTGGTTTTGCTGTCAAGTTTTACACTAGAGAG                         GGTCCTTTTGATCTTGTTGGGAACAATATGCCTGTCTTTTTTATCCGAGAT
genomic: AGACATTGAGGGATCCACGTGGTTTTGCTGTCAAGTTTTACACTAGAGAGgtacttgctc ... tgcttttcagGGTAATTTTGATCTTGTTGGGAACAATATGCCTGTCTTTTTTATCCGAGAT
EST: gi|58671674|gb|CK060360.1|CK060360
EST:     AGACATTGAGGGATCCACGTGGTTTTGCTGTCAAGTTTTACACTAGAGAG                         GGTAATTTTGATCT
genomic: AGACATTGAGGGATCCACGTGGTTTTGCTGTCAAGTTTTACACTAGAGAGgtacttgctc ... tgcttttcagGGTAATTTTGATCT
EST: gi|29616047|gb|CB621059.1|CB621059
EST:     AGACATTGAGGGATCCACGTGGTTTTGCTGTCAAGTTTTACACTAGAGAG                         GGTAATTTTGATCTTGTTGGGAACAATATGCCTGTCTTTTTTATCCGAGAT
genomic: AGACATTGAGGGATCCACGTGGTTTTGCTGTCAAGTTTTACACTAGAGAGgtacttgctc ... tgcttttcagGGTAATTTTGATCTTGTTGGGAACAATATGCCTGTCTTTTTTATCCGAGAT

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: 75 (upstream exon), 66 (downstream exon)
Score: 45

CCCAGTTATTGTTCGGTTCTCCACAGTCGTGCATGAGCGTGGAAGCCCTGAGACATTGAGGGATCCACGTGGTTTTGCTGTCAAGTTTTACACTAGAGAGgtacttgctc ... tgcttttcagGGTAATTTTGATCTTGTTGGGAACAATATGCCTGTCTTTTTTATCCGAGATGGGATGAAATTCCCTGACATGGTCCATGCTTTCAAGCCAAGTCCAAAGA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgatttgcattcagtgctgccatattttgatattttctgagtcaatgcttttcagGGTAATTTTGATCTTGTTGGGAACAATATGCCTGTCTTTTTTATCCGAGATGGGATGAAATTCCCTGACATGGTCCATGCTTTCAAGCCAAGTCCAAAGA
                                             tgcttttc  CT-rich tract
                     atattttgatattttc  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tatctaaccagtgtcacctacaactttgtcttactgtttatttactgatttgcattcagtgctgccatattttgatattttctgagtcaatgcttttcagGGTAATTTTGATCTTGTTGGGAACAATATGCCTGTCTTTTTTATCCGAGATGGGATGAAATTCCCTGACATGGTCCATGCTTTCAAGCCAAGTCCAAAGA

- - - - - - - cacctac
- - - - - - - - - - - - - - -cttactg
- - - - - - - - - - - - - - - - - - - - -ttactga
- - - - - - - - - - - - - - - - - - - - - - - - - tgcattc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgctgcc