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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGTATGCCAAAAGATTCTTACACCCTGATATCGTGGCATCTTATGAGTACATATTTATCTGGGACGAGGATCTTGGAGTTGAGCATTTTAACGCAGAGGAgtatgctttcgatcttcattgaacaatttctcaattgcagatttctggtgattctgctgacaggatttacaatgcag

Basic information

species Oryza sativa
transcript LOC_Os01g73970.1
intron # 8
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g73970.1 (Oryza sativa), 5'ss of exon 8
lower sequence: GLYMA13G39990.1 (Glycine max), 5'ss of exon 8
GGTATGCCAAAAGATTCTTACACCCTGATATCGTGGCATCTTATGAGTACATATTTATCTGGGACGAGGATCTTGGAGTTGAGCATTTTAACGCAGAGGAgtatgctttcgatcttcat----tgaacaatttctcaatt---gcagatttctggtgattctgctgacaggatt-tacaatgcag
||||||| |||||||| || ||||||||||| ||  || ||||||| || || ||||| ||||| || ||||||||||| || || || || |||||  |||||  |||  ||||   |    ||  ||| ||    |||   |||  |||  | | | |    |||| | ||| ||     |||
GGTATGCTAAAAGATTTTTGCACCCTGATATAGTATCAGCTTATGAATATATTTTTATTTGGGATGAAGATCTTGGAGTAGAACACTTCAATGCAGACAAgtattattttcatctgtctaatctgctcaaatttgatatttatgcaacttttagtttaattaattgactgtattctattccccag

upper sequence: LOC_Os01g73970.1 (Oryza sativa), 5'ss of exon 8
lower sequence: GLYMA12G29800.1 (Glycine max), 5'ss of exon 8
GGTATGCCAAAAGATTCTTACACCCTGATATCGTGGCATCTTATGAGTACATATTTATCTGGGACGAGGATCTTGGAGTTGAGCATTTTAACGCAGAGGAgtatgctttcgatcttcat----tgaacaatttctcaatt---gcagatttctggtgattctgctgacaggatt-tacaatgcag
||||||| |||||||| || ||||||||||| ||  || ||||||| || || ||||| ||||| || ||||||||||| || || || || |||||  |||||  |||  ||||   |    ||  ||| ||    |||   |||  |||  | | | |    | || | ||| ||     |||
GGTATGCTAAAAGATTTTTGCACCCTGATATAGTATCAGCTTATGAATATATTTTTATTTGGGATGAAGATCTTGGAGTAGAACACTTCAATGCAGACAAgtattattttcatctgtctagtctgctcaaatttgatatttatgcaacttttagtttaattaattaactgtattctattcaccag

upper sequence: LOC_Os01g73970.1 (Oryza sativa), 5'ss of exon 8
lower sequence: AT1G08040.1 (Arabidopsis thaliana), 5'ss of exon 8
GGTATGCCAAAAGATTCTTACACCCTGATATCGTGGCATCTTATGAGTACATATTTATCTGGGACGAGGATCTTGGAGTTGAGCATTTTAACGCAGAGGAgtatgctttcgatcttca-ttg-aacaatttctcaattgcagatttctggtgattctgctgacaggatttacaatgcag
||||||| || ||||| || || |||||| | ||  || |||||||||| |||||||| ||||| || ||||||||||| ||||| || || |||||   ||    |     |||  | ||| |        ||| |  || || | |     || |  |      |||| ||      
GGTATGCAAAGAGATTTTTGCATCCTGATGTTGTCTCAGCTTATGAGTATATATTTATATGGGATGAAGATCTTGGAGTCGAGCACTTCAATGCAGATAGgtgaattacttgtctgaaattgtagttgcagatcagtgaca-atctttacaatttttatt--ttaaattttcag-----

upper sequence: LOC_Os01g73970.1 (Oryza sativa), 5'ss of exon 8
lower sequence: AT2G28310.1 (Arabidopsis thaliana), 5'ss of exon 8
GGTATGCCAAAAGATTCTTACACCCTGATATCGTGGCATCTTATGAGTACATATTTATCTGGGACGAGGATCTTGGAGTTGAGCATTTTAACGCAGAGGAgtatgctttcgatcttcattgaacaatttctcaattgcagatttctggtgattctgctgacagg--atttacaatgcag
|||| || || || || || || |||||| | ||| || ||||||||||||||||||| ||||| || ||||||||||| |||||||| || || ||  |||| | | |   |  || |  |  |      ||||   | ||||    |  || || ||  |    ||| | | | |||
GGTACGCGAAGAGGTTTTTGCATCCTGATGTTGTGTCAGCTTATGAGTACATATTTATATGGGATGAAGATCTTGGAGTGGAGCATTTCAATGCGGATAAgtaagttattacttgtc-tgaagtagcagaacaatcttatattttacatt-ttgtgatggaattctattaaaacttcag

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|58595145|gb|CF993453.1|CF993453
EST:     TGAGCATTTTAACGCAGAGGA                         GTACATTAAACTTGTCAAGAAATATCAGCTAGAAGTCTCACAACCTGGTTT
genomic: TGAGCATTTTAACGCAGAGGAgtatgctttc ... tacaatgcagGTACATTAAACTTGTCAAGAAATATCAGCTAGAAATCTCACAACCTGGTTT
EST: gi|58694661|gb|CK083348.1|CK083348
EST:     ATATTTATCTGGGACGAGGATCTTGGAGTTGAGCATTTTAACGCAGAGGA                         GTACATTAAACTTGTCAAGAAATATCAGCTAGAAATCTCACAACCTGGTTT
genomic: ATATTTATCTGGGACGAGGATCTTGGAGTTGAGCATTTTAACGCAGAGGAgtatgctttc ... tacaatgcagGTACATTAAACTTGTCAAGAAATATCAGCTAGAAATCTCACAACCTGGTTT
EST: gi|29641984|gb|CB646991.1|CB646991
EST:     ATATTTATCTGGGACGAGGATCTTGGAGTTGAGCATTTTAACGCAGAGGA                         GTACATTAGACTTGTCAAGAAATATCAGCTAGAAATCTCACAAC
genomic: ATATTTATCTGGGACGAGGATCTTGGAGTTGAGCATTTTAACGCAGAGGAgtatgctttc ... tacaatgcagGTACATTAAACTTGTCAAGAAATATCAGCTAGAAATCTCACAAC
EST: gi|29663566|gb|CB659841.1|CB659841
EST:     ATATTTATCTGGGACGAGGATCTTGGAGTTGAGCATTTTAACGCAGAGGA                         GTACATTAAACTTGTCAAGAAATATCAGCTAGAAATCTCACAACCTGGTTT
genomic: ATATTTATCTGGGACGAGGATCTTGGAGTTGAGCATTTTAACGCAGAGGAgtatgctttc ... tacaatgcagGTACATTAAACTTGTCAAGAAATATCAGCTAGAAATCTCACAACCTGGTTT
EST: gi|29641985|gb|CB646992.1|CB646992
EST:     ATATTTATCTGGGACGAGGATCTTGGAGTTGAGCATTTTAACGCAGAGGA                         GTACATTAAACTTGTCAAGAAATATCAGCTAGAAATCTCACAACCTGGTGT
genomic: ATATTTATCTGGGACGAGGATCTTGGAGTTGAGCATTTTAACGCAGAGGAgtatgctttc ... tacaatgcagGTACATTAAACTTGTCAAGAAATATCAGCTAGAAATCTCACAACCTGGTTT

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: 51 (upstream exon), 59 (downstream exon)
Score: 22

GGTATGCCAAAAGATTCTTACACCCTGATATCGTGGCATCTTATGAGTACATATTTATCTGGGACGAGGATCTTGGAGTTGAGCATTTTAACGCAGAGGAgtatgctttc ... tacaatgcagGTACATTAAACTTGTCAAGAAATATCAGCTAGAAATCTCACAACCTGGTTTAGAGCCAGATCGGGGATTGACATGGCAGATGACCAAAAGAAGAGGGGAT




<











<


<









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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGTATGCCAAAAGATTCTTACACCCTGATATCGTGGCATCTTATGAGTACATATTTATCTGGGACGAGGATCTTGGAGTTGAGCATTTTAACGCAGAGGAgtatgctttcgatcttcattgaacaatttctcaattgcagatttctggtgattctgctgacaggatttacaatgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA