Skip to another splice site:
1  
 5'  3'   
2  
 5'  3'   
3  
 5'  3'   
4  
 5'  3'   
5  
 5'  3'   
6  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtactcttatatacttttgcctcccttatttttctgaaaaaaaatacttatgagacttgcattttagGGGGTCTCACATCTGAGTGGTTCAGTCTTGAAGCATCACTTCTAACTTTGGGCCTTACAATTGGAGCTCTATCATTTGTGCTGGAGCCAACCCCCAAAAC

Basic information

species Oryza sativa
transcript LOC_Os01g34390.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g34390.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G178859_T01 (Zea mays), 3'ss of exon 6
---------------gtaagtactcttatatacttttgcc--tcccttatttttctgaaaa---aaaatact-tatgagacttgcattt--tagGGGGTCTCACATCTGAGTGGTTCAGTCTTGAAGCATCACTTCTAACTTTGGGCCTTACAATTGGAGCTCTATCATTTGTGCTGGAGCCAACCCCCAAAAC
| | ||| | | ||| | | || ||||| || || || | |||| | | | || ||||||| |||||||| |||||||||||| ||||||| ||||| ||||| || |||||||| || |||||||||||||| || || || |||| ||| || ||
gtaagtactaaacatattggatttctactgtccttgtcttgatgtgttttttttttgtcaatttgggatcttatatggaattaacccttggtagGGGGGCTCACATCCGAGTGGTTCAGTTTTGAAGCTTCACTCCTAACATTAGGCCTTACCATCGGAGCTCTATCATTCGTCCTAGAACCAAGCCCGAAGAC

upper sequence: LOC_Os01g34390.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G162776_T03 (Zea mays), 3'ss of exon 6
----------------------------------------------------------------------gtaagtactcttatatacttttgcctccct-tatttttctgaaaaaaaatacttatgagacttgcattt-tagGGGGTCTCACATCTGAGTGGTTCAGTCTTGAAGCATCACTTCTAACTTTGGGCCTTACAATTGGAGCTCTATCATTTGTGCTGGAGCCAACCCCCAAAAC
|| || | | | | || | | | | | | |||| | |||||| | | | || ||||||| ||||||||||||||||| ||| ||||||| ||||| ||||| || |||||||| |||||| ||||||||||||||||| | |||| || || ||
gtaagtactaaccatattgaatttctagtttcatttttatgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgaatttgagatcttatggaattaacccttgtagGGGGCCTCACATCTGAGTGGTTTAGTTTTGAAGCTTCACTCCTAACATTAGGCCTTACCATTGGATCTCTATCATTTGTGCTGAAACCAAGTCCAAAGAC
















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|86828663|gb|CI278733.1|CI278733
EST:     GAAATTGTCTATACATGCTGCCCTTGGGATTTTTTGCATACAACT                         GGGGTCTCACATCTGAGTGGTTCAGTCTTGAAGCATCACTTCTAACTTTGG
genomic: GAAATTGTCTATACATGCTGCCCTTGGGATTTTTTGCATACAACTgtaagtactc ... tgcattttagGGGGTCTCACATCTGAGTGGTTCAGTCTTGAAGCATCACTTCTAACTTTGG
EST: gi|87015378|gb|CI275568.1|CI275568
EST:     ACTCAGAAATTGTCTATACATGCTGCCCTTGGGATTTGTTGCATACAACT                         GGGGTCTCACATCTGAGTGGTTCAGTCTTGAAGCATCACTTCTAACTTTGG
genomic: ACTCAGAAATTGTCTATACATGCTGCCCTTGGGATTTTTTGCATACAACTgtaagtactc ... tgcattttagGGGGTCTCACATCTGAGTGGTTCAGTCTTGAAGCATCACTTCTAACTTTGG
EST: gi|86495670|gb|CI138303.1|CI138303
EST:     GCCCTTGGGATTTTTTGCATACAACT                         GGGGTCTCACATCTGAGTGGTTCAGTCTTGAAGCATCACTTCTAACTTTGG
genomic: GCCCTTGGGATTTTTTGCATACAACTgtaagtactc ... tgcattttagGGGGTCTCACATCTGAGTGGTTCAGTCTTGAAGCATCACTTCTAACTTTGG
EST: gi|86492621|gb|CI135254.1|CI135254
EST:     TGCCCTTGGGATTTTTTGCATACAACT                         GGGGTCTCACATCTGAGTGGTTCAGTCTTGAAGCATCACTTCTAACTTTGG
genomic: TGCCCTTGGGATTTTTTGCATACAACTgtaagtactc ... tgcattttagGGGGTCTCACATCTGAGTGGTTCAGTCTTGAAGCATCACTTCTAACTTTGG
EST: gi|86505729|gb|CI148362.1|CI148362
EST:     GCCCTTGGGATTTTTTGCATACAACT                         GGGGTCTCACATCTGAGTGGTTCAGTCTTGAAGCATCACTTCTAACTTTGG
genomic: GCCCTTGGGATTTTTTGCATACAACTgtaagtactc ... tgcattttagGGGGTCTCACATCTGAGTGGTTCAGTCTTGAAGCATCACTTCTAACTTTGG
EST: gi|87021724|gb|CI276123.1|CI276123
EST:     ACTCAGAAATTGTCTATACATGCTGCCCTTGGGATTTTTTGCATACAACT                         GGGGTCTCACATCTGAGTGGTTCAGTCTTGAAGCATCACTTCTAACTTTGG
genomic: ACTCAGAAATTGTCTATACATGCTGCCCTTGGGATTTTTTGCATACAACTgtaagtactc ... tgcattttagGGGGTCTCACATCTGAGTGGTTCAGTCTTGAAGCATCACTTCTAACTTTGG
EST: gi|218501085|gb|FG955422.1|FG955422
EST:     ACTCAGAAATTGTCTATACATGCTGCCCTTGGGATTTTTTGCATACAACT                         GGGGTCTCACATCTGAGTGGTTCAGTCTTGAAGCATCACTTCTAACTTTGG
genomic: ACTCAGAAATTGTCTATACATGCTGCCCTTGGGATTTTTTGCATACAACTgtaagtactc ... tgcattttagGGGGTCTCACATCTGAGTGGTTCAGTCTTGAAGCATCACTTCTAACTTTGG
EST: gi|87021752|gb|CI276151.1|CI276151
EST:     AGAAATTGTCTATACATGCTGCCCTTGGGATTTTTTGCATACAACT                         GGGGTCTCACATCTGAGTGGTTCAGTCTTGAAGCATCACTTCTAACTTTGG
genomic: AGAAATTGTCTATACATGCTGCCCTTGGGATTTTTTGCATACAACTgtaagtactc ... tgcattttagGGGGTCTCACATCTGAGTGGTTCAGTCTTGAAGCATCACTTCTAACTTTGG
EST: gi|29662700|gb|CB658975.1|CB658975
EST:     ACTCAGAAATTGTCTATACATGCTGCCCTTGGGATTTTTTGCATACAACT                         GGGGTCTCACATCTGAGTGGTTCAGTCTTGAAGCATCACTTCTAACTTTGG
genomic: ACTCAGAAATTGTCTATACATGCTGCCCTTGGGATTTTTTGCATACAACTgtaagtactc ... tgcattttagGGGGTCTCACATCTGAGTGGTTCAGTCTTGAAGCATCACTTCTAACTTTGG
EST: gi|87015246|gb|CI275436.1|CI275436
EST:     ACTCAGAAATTGTCTATACATGCTGCCCTTGGGATTTTTTGCATACAACT                         GGGGTCTCACATCTGAGTGGTTCAGTCTTGAAGCATCACTTCTAACTTTGG
genomic: ACTCAGAAATTGTCTATACATGCTGCCCTTGGGATTTTTTGCATACAACTgtaagtactc ... tgcattttagGGGGTCTCACATCTGAGTGGTTCAGTCTTGAAGCATCACTTCTAACTTTGG
EST: gi|88829466|gb|CI074336.1|CI074336
EST:     CATGCTGCCCTTGGGATTTTTTGCATACAACT                         GGGGTCTCACATCTGAGTGGTTCAGTCTTGAAGCATCACTTCTAACTTTGG
genomic: CATGCTGCCCTTGGGATTTTTTGCATACAACTgtaagtactc ... tgcattttagGGGGTCTCACATCTGAGTGGTTCAGTCTTGAAGCATCACTTCTAACTTTGG

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: 73 (upstream exon), 57 (downstream exon)
Score: 8

CGAATGTTTTCTTTTGCTGATCCTACTGGTAAAAGAACTGCATGGGTATCACTCAGAAATTGTCTATACATGCTGCCCTTGGGATTTTTTGCATACAACTgtaagtactc ... tgcattttagGGGGTCTCACATCTGAGTGGTTCAGTCTTGAAGCATCACTTCTAACTTTGGGCCTTACAATTGGAGCTCTATCATTTGTGCTGGAGCCAACCCCCAAAAC




<











<


<











 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acttttgcctcccttatttttctgaaaaaaaatacttatgagacttgcattttagGGGGTCTCACATCTGAGTGGTTCAGTCTTGAAGCATCACTTCTAACTTTGGGCCTTACAATTGGAGCTCTATCATTTGTGCTGGAGCCAACCCCCAAAAC
             ttatttttctgaaaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagtactcttatatacttttgcctcccttatttttctgaaaaaaaatacttatgagacttgcattttagGGGGTCTCACATCTGAGTGGTTCAGTCTTGAAGCATCACTTCTAACTTTGGGCCTTACAATTGGAGCTCTATCATTTGTGCTGGAGCCAACCCCCAAAAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA