Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   		7  
 5'  3'   		8  
 5'  3'   		9  
 5'  3'   		10  
 5'  3'   		11  
 5'  3'   		12  
 5'  3'   		13  
 5'  3'   		14  
 5'  3'   		15  
 5'  3'   		16  
 5'  3'   		17  
 5'  3'   		18  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aaattagaacgatgtgatggaaaagttagaagtttgaagaaaaagtttggaactaaactcggcttgagctatgcatctaatctagtgatttctgacgcagCCTTGCGTCATACATCACAGACGATGAAATTCGAAAAGGCATCCTCTTTCCATCAATCTCAAG

Basic information

species Oryza sativa
transcript LOC_Os10g35960.1
intron # 16
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os10g35960.1 (Oryza sativa), 3'ss of exon 16
lower sequence: GRMZM2G085747_T01 (Zea mays), 3'ss of exon 16
aaattagaacgatgtgatggaaaagttagaagtttgaagaaaaagtttggaactaaactcggcttgagctatgcatctaatctagtgatttctg--acgcagCCTTGCGTCATACATCACAGACGATGAAATTCGAAAAGGCATCCTCTTTCCATCAATCTCAAG
 || || |   |  |  |    |  | ||   ||           | | |     |      |   |  |||  |   | ||||   |||| ||  | ||||||| || ||||||||||||||||| |||||||||||||| |||||||| || ||  |||| ||
-aactacactaaaattgtttccacttgagtcattctgtttgctgttcttgcggagaggatcacagaatttatataagca-tctatctatttttgcaatgcagCCTGGCATCATACATCACAGACGACGAAATTCGAAAAGGAATCCTCTTCCCTTCGGTCTCCAG
















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|88228130|gb|CI227610.1|CI227610
EST:     GTGCTCGGCATATTACAGATGGCATGCTCCAATCAGCAGCTGAGGTG                         CCTTGCGTCATACATCACAGACGATGAAATTCGAAAAGGCATCCTCTTTC
genomic: GTGCTCGGCATATTACAGATGGCATGCTCCAATCAGCAGCTGA-GTGgtaagtttta ... tctgacgcagCCTTGCGTCATACATCACAGACGATGAAATTCGAAAAGGCATCCTCTTTC
EST: gi|58610908|gb|CK038620.1|CK038620
EST:     TCAGGTGCTCGGCATATTACAGATGGCATGCTTCAATCAGCAGCTGAGTG                         CCTTGCGTCATACATCACAGACGATGAAATTCGAAAAGGCATCCTCTTTCC
genomic: TCAGGTGCTCGGCATATTACAGATGGCATGCTCCAATCAGCAGCTGAGTGgtaagtttta ... tctgacgcagCCTTGCGTCATACATCACAGACGATGAAATTCGAAAAGGCATCCTCTTTCC
EST: gi|29664102|gb|CB660377.1|CB660377
EST:     TCAGGTGCTCGGCATATTACAGATGGCATGCTCCAATCAGCAGCTGAGTG                         CCTTGCGTCATACATCACAGACGATGAAATTCGAAAAGGCATCCTCTTTCC
genomic: TCAGGTGCTCGGCATATTACAGATGGCATGCTCCAATCAGCAGCTGAGTGgtaagtttta ... tctgacgcagCCTTGCGTCATACATCACAGACGATGAAATTCGAAAAGGCATCCTCTTTCC
EST: gi|29615205|gb|CB620218.1|CB620218
EST:     TCAGGTGCTCGGCATATTACAGATGGCATGCTCCAATCAGCAGCTGAGTG                         CCTTGCGTCATACATCACAGACGATGAAATTCGAAAAGGCATCCTCTTTCC
genomic: TCAGGTGCTCGGCATATTACAGATGGCATGCTCCAATCAGCAGCTGAGTGgtaagtttta ... tctgacgcagCCTTGCGTCATACATCACAGACGATGAAATTCGAAAAGGCATCCTCTTTCC
EST: gi|29671881|gb|CB668156.1|CB668156
EST:     TCAGGTGCTCGGCATATTACAGATGGCATGCTCCAATCAGCAGCTGAGTG                         CCTTGCGTCATACATCACAGACGATGAAATTCGAAAAGGCATCCTCTTTCC
genomic: TCAGGTGCTCGGCATATTACAGATGGCATGCTCCAATCAGCAGCTGAGTGgtaagtttta ... tctgacgcagCCTTGCGTCATACATCACAGACGATGAAATTCGAAAAGGCATCCTCTTTCC
EST: gi|88225783|gb|CI225699.1|CI225699
EST:     ATGCTCCAATCAGCAGCTGAGTG                         CCTTGCGTCATACATCACAGACGATGAAATTCGAAAAGGCATCCTCTTTCC
genomic: ATGCTCCAATCAGCAGCTGAGTGgtaagtttta ... tctgacgcagCCTTGCGTCATACATCACAGACGATGAAATTCGAAAAGGCATCCTCTTTCC
EST: gi|29662805|gb|CB659080.1|CB659080
EST:     TCAGGTGCTCGGCATATTACAGATGGCATGCTCCAATCAGCAGCTGAGTG                         CCTTGCGTCATACATCACAGACGATGAAATTCGAAAAGGCATCCTCTTTCC
genomic: TCAGGTGCTCGGCATATTACAGATGGCATGCTCCAATCAGCAGCTGAGTGgtaagtttta ... tctgacgcagCCTTGCGTCATACATCACAGACGATGAAATTCGAAAAGGCATCCTCTTTCC
EST: gi|88271063|gb|CI386918.1|CI386918
EST:     CATATTACAGATGGCATGCTCCAATCAGCAGCT-AGTG                         CCTTGCGTCATACATCACAGACGAT-AAATTCGAAAAGGCATCCTCTTTCC
genomic: CATATTACAGATGGCATGCTCCAATCAGCAGCTGAGTGgtaagtttta ... tctgacgcagCCTTGCGTCATACATCACAGACGATGAAATTCGAAAAGGCATCCTCTTTCC

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), 63 (downstream exon)
Score: 35

TATCGGTTTAGGAGCCCTTCTTTCAGGTGCTCGGCATATTACAGATGGCATGCTCCAATCAGCAGCTGAGTGgtaagtttta ... tctgacgcagCCTTGCGTCATACATCACAGACGATGAAATTCGAAAAGGCATCCTCTTTCCATCAATCTCAAG




<











<


<











 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttggaactaaactcggcttgagctatgcatctaatctagtgatttctgacgcagCCTTGCGTCATACATCACAGACGATGAAATTCGAAAAGGCATCCTCTTTCCATCAATCTCAAG
                                            ttctgac  putative branch site (score: 35)
                                           tttct  CT-rich tract
     aactaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aaattagaacgatgtgatggaaaagttagaagtttgaagaaaaagtttggaactaaactcggcttgagctatgcatctaatctagtgatttctgacgcagCCTTGCGTCATACATCACAGACGATGAAATTCGAAAAGGCATCCTCTTTCCATCAATCTCAAG

- - - - - - tgtgatg
- - - - - - - - - - - - - - - - - -gaagaaa
- - - - - - - - - - - - - - - - - - - - - - - - -gaactaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cggcttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ctatgca