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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCTGGAGCTCGAGACCTGTCGTTTGATGCTCGTGGGTATGCTATTGTCTTTGTGGCCAACATTACAACAGCTGTTTACCTTGCTACTATAAACCGTATAGgtaacatttcattttcagttttgccacatacaatcccattctaaactacatagctttctaaccagcagttttgttttgttttag

Basic information

species Oryza sativa
transcript LOC_Os02g40030.1
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g40030.1 (Oryza sativa), 5'ss of exon 5
lower sequence: GRMZM2G133226_T04 (Zea mays), 5'ss of exon 5
GCTGGAGCTCGAGACCTGTCGTTTGATGCTCGTGGGTATGCTATTGTCTTTGTGGCCAACATTACAACAGCTGTTTACCTTGCTACTATAAACCGTATAGgtaacatttcattttcagttttgccacatacaatcccattctaaactacatag-ctttctaaccagcagttttgttttgttt-tag
||||||||||||||| |||| |||||||||||||||||||||||||||||||||||||||||||| |||||  |||||||||||||||| ||||||||||||||     || || |  |||| | ||||| | |    ||  |   |||| |  |||||| | |||  ||| | |||  |   |||
GCTGGAGCTCGAGACTTGTCATTTGATGCTCGTGGGTATGCTATTGTCTTTGTGGCCAACATTACGACAGCCATTTACCTTGCTACTATCAACCGTATAGgtaaag---cagttcct-ttttccaacatatagtgttctttcatcgtacaaaatctttctgatcagatgttctttttcttccatag

upper sequence: LOC_Os02g40030.1 (Oryza sativa), 5'ss of exon 5
lower sequence: GRMZM2G020976_T01 (Zea mays), 5'ss of exon 5
GCTGGAGCTCGAGACCTGTCGTTTGATGCTCGTGGGTATGCTATTGTCTTTGTGGCCAACATTACAACAGCTGTTTACCTTGCTACTATAAACCGTATAGgtaacatttcattttcagttttgccacatacaatcccattctaaactacatag-ctttctaaccagcagttttgttttgttttag--
||||||||||||||| |||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||| ||||||||||||||||| | |   || |   |||| | ||||| |||    ||| |   |||| |  |||||| |  ||  ||| | |||  |   |   
GCTGGAGCTCGAGACTTGTCATTTGATGCTCGTGGGTATGCTATTGTCTTTGTGGCCAACATTACAACAGCTGTTTATCTTGCTACCATAAACCGTATAGgtaaaagtagtttct---ttttccaacatataatgttcttccacgttacaaaatctttctgattagatgttctttttcttcccatag

upper sequence: LOC_Os02g40030.1 (Oryza sativa), 5'ss of exon 5
lower sequence: Vv11s0016g05710.t01 (Vitis vinifera), 5'ss of exon 5
GCTGGAGCTCGAGACCTGTCGTTTGATGCTCGTGGGTATGCTATTGTCTTTGTGGCCAACATTACAACAGCTGTTTACCTTGCTACTATAAACCGTATAGgtaacatttcattttca-gttttgccacatacaatccc--attctaaactacatag---ctttctaaccagcagttttgttttgttttag--------
||||||||||| |||||||| |||||  |   ||| ||||||||||| |||||||| ||||||   |||||||| || |||||| |||||   ||||| ||||  ||||  || | | || ||  ||  |   || |   ||  |||  | || ||   |||||||   |   ||  | ||||  |  |         
GCTGGAGCTCGGGACCTGTCATTTGACTCCTATGGCTATGCTATTGTTTTTGTGGCAAACATTTGTACAGCTGTATATCTTGCTTCTATATCTCGTATTGgtactattttgttcttatgtcttctcatgtttcattctctatggtaacgttcaaagtttctttctattgatatgtggtatttttctcaattgtctcag

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|29670135|gb|CB666410.1|CB666410
EST:     TGTGGCCAACATTACAACAGCTGTTTACCTTGCTACTATAAACCGTATAG                         GAAAATCTAGTGGTCTAAATAGCTTCGGCCTGATGTGGTGCAACG
genomic: TGTGGCCAACATTACAACAGCTGTTTACCTTGCTACTATAAACCGTATAGgtaacatttc ... tttgttttagGAAAATCTAGTGGTCTAAATAGCTTCGGCCTGATGTGGTGCAACG
EST: gi|29671157|gb|CB667432.1|CB667432
EST:     TGTGGCCAACATTACAACAGCTGTTTACCTTGCTACTATAAACCGTATAG                         GAAAATCTAGTGGTCTAAATAGCTTCGGCCTGATGTGGTGCAACG
genomic: TGTGGCCAACATTACAACAGCTGTTTACCTTGCTACTATAAACCGTATAGgtaacatttc ... tttgttttagGAAAATCTAGTGGTCTAAATAGCTTCGGCCTGATGTGGTGCAACG
EST: gi|29672145|gb|CB668420.1|CB668420
EST:     TGTGGCCAACATTACAACAGCTGTTTACCTTGCTACTATAAACCGTATAG                         GAAAATCTAGTGGTCTAAATAGCTTCGGCCTGATGTGGTGCAACG
genomic: TGTGGCCAACATTACAACAGCTGTTTACCTTGCTACTATAAACCGTATAGgtaacatttc ... tttgttttagGAAAATCTAGTGGTCTAAATAGCTTCGGCCTGATGTGGTGCAACG
EST: gi|25806370|gb|CA762331.1|CA762331
EST:     CAACATTACAACAGCTGTTTACCTTGCTACTATAAACNGTATAG                         GAAAATCTAGTGGTCTAAATAGCTTCGGCCTGATGTGGTGCAACG
genomic: CAACATTACAACAGCTGTTTACCTTGCTACTATAAACCGTATAGgtaacatttc ... tttgttttagGAAAATCTAGTGGTCTAAATAGCTTCGGCCTGATGTGGTGCAACG
EST: gi|29670136|gb|CB666411.1|CB666411
EST:     TGTGGCCAACATTACAACAGCTGTTTACCTTGCTACTATAAACCGTATAG                         GAAAATCTAGTGGTCTAAATAGCTTCGGCCTGATGTGGTGCAACG
genomic: TGTGGCCAACATTACAACAGCTGTTTACCTTGCTACTATAAACCGTATAGgtaacatttc ... tttgttttagGAAAATCTAGTGGTCTAAATAGCTTCGGCCTGATGTGGTGCAACG
EST: gi|29672495|gb|CB668770.1|CB668770
EST:     TGTGGCCAACATTACAACAGCTGTTTACCTTGCTACTATAAACCGTATAG                         GAAAATCTAGTGGTCTAAATAGCTTCGGCCTGATGTGGTGCAACG
genomic: TGTGGCCAACATTACAACAGCTGTTTACCTTGCTACTATAAACCGTATAGgtaacatttc ... tttgttttagGAAAATCTAGTGGTCTAAATAGCTTCGGCCTGATGTGGTGCAACG
EST: gi|2310116|gb|C26271.1|C26271
EST:     GCTACTATAAACCGTATAG                         GAAAATCTAGTGGTCTAAATAGCTTCGGCCTGATGTGGTGCAACG
genomic: GCTACTATAAACCGTATAGgtaacatttc ... tttgttttagGAAAATCTAGTGGTCTAAATAGCTTCGGCCTGATGTGGTGCAACG

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: 52 (upstream exon), 45 (downstream exon)
Score: 50

GCTGGAGCTCGAGACCTGTCGTTTGATGCTCGTGGGTATGCTATTGTCTTTGTGGCCAACATTACAACAGCTGTTTACCTTGCTACTATAAACCGTATAGgtaacatttc ... tttgttttagGAAAATCTAGTGGTCTAAATAGCTTCGGCCTGATGTGGTGCAACG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCTGGAGCTCGAGACCTGTCGTTTGATGCTCGTGGGTATGCTATTGTCTTTGTGGCCAACATTACAACAGCTGTTTACCTTGCTACTATAAACCGTATAGgtaacatttcattttcagttttgccacatacaatcccattctaaactacatagctttctaaccagcagttttgttttgttttag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGTT