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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagcattattgtgctacataattttgtgatcttctgagtttctgtctgaatcttacatcatttttatttcaaactgcagCTCACCAATGTTGCTAGTCTATGGTTCATGTCGCTTTTCATCTGTATTTTTGTCACTGGCATCCTTGAAATGAGATGGAGTGGTGTGGCCATCGATGACT

Basic information

species Oryza sativa
transcript LOC_Os07g14850.1
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os07g14850.1 (Oryza sativa), 3'ss of exon 12
lower sequence: GRMZM2G177631_T01 (Zea mays), 3'ss of exon 11
-------------gtaagcattattgtgctacataattttg---tgatcttctgagtttctgtctgaatcttacatcatttttatttcaaactgcagCTCACCAATGTTGCTAGTCTATGGTTCATGTCGCTTTTCATCTGTATTTTTGTCACTGGCATCCTTGAAATGAGATGGAGTGGTGTGGCCATCGATGACT
              |   |||||         | | || ||     || || |||||||  |||| |   | |  |  |||||  || ||| ||||||| |||||||| || ||| | ||||||||| | ||||||||||| || |  || || |||||||| |||||||| |||||||| ||||||||||| ||||
gtaaatatatggtatcgtcattaaaacaaagaagagttatggctctattttttgagttta-gtcttagcgtcaattttttttttgttgaaattgcagCTTACCAATGTCGCCAGTATCTGGTTCATGGCACTTTTCATCTGCATCTCCGTGACCGGCATCCTGGAAATGAGGTGGAGTGGCGTGGCCATCGACGACT

upper sequence: LOC_Os07g14850.1 (Oryza sativa), 3'ss of exon 12
lower sequence: Vv03s0038g04250.t01 (Vitis vinifera), 3'ss of exon 13
--------------gtaagcattattgtgctacataattttgtgatcttctga-gtttctgtctgaatcttacatcatttttatttcaaactgcagCTCACCAATGTTGCTAGTCTATGGTTCATGTCGCTTTTCATCTGTATTTTTGTCACTGGCATCCTTGAAATGAGATGGAGTGGTGTGGCCATCGATGACT
              | ||    | || | |   ||   |   | |  || |||      | ||   | |||     |  |||  |||  | ||||||| | ||||||||| ||| | |||||  | || ||||| |||||||||||||  ||| ||||||| |||||||||||||||||||| |  || ||||| |
gtatgagaatctaggcaactgatttttttcagaatgcctccttaactttatgatacacttatcctgaccttttccaaacttt--ttcctattgcagCTAAGCAATGTTGCGAGTTTGTGGTTTTTATCCCTTTTTATCTGTATTTTTGCGACTAGCATCCTGGAAATGAGATGGAGTGGTGTTGGAATTGATGATT

upper sequence: LOC_Os07g14850.1 (Oryza sativa), 3'ss of exon 12
lower sequence: Vv18s0122g00120.t01 (Vitis vinifera), 3'ss of exon 13
------gtaagcattattgtgctacataattttgtg------atcttctgagtttctgtctgaatctta-catcatttttatttcaaactgcagCTCACCAATGTTGCTAGTCTATGGTTCATGTCGCTTTTCATCTGTATTTTTGTCACTGGCATCCTTGAAATGAGATGGAGTGGTGTGGCCATCGATGACT
         ||| ||  |       ||||||||         ||| | |   |   | | ||| |   | |||   |||| |||  || ||||||| | ||| ||||||||  | |||||  |||| |||||||| ||||||||||  ||||| ||||| ||||||||||||||||| || |  || ||||| |
gtatgaaacagcgttgcttcttattataatttttctgaaagtatcctttagatgcatatttgattaaaatcatttattttgtttgtaa-tgcagCTTAGCAACGTTGCTAGCTTGTGGTTTCTGTCACTTTTCATTTGTATTTTTGCAACTGGTATCCTGGAAATGAGATGGAGTGGAGTTGGAATTGATGAAT

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|428808|gb|D24964.1|D24964
EST:     GTACCTTGCCTGCCATATGCTTGCTCACTGGGAAGTTTATCACTCCAGAG                         CTCACCAATGTTGCTAGTCTATGGTTCATGTCGCTTTTCATCTGTATTTTT
genomic: GTACCTTGCCTGCCATATGCTTGCTCACTGGGAAGTTTATCACTCCAGAGgtaagcatta ... caaactgcagCTCACCAATGTTGCTAGTCTATGGTTCATGTCGCTTTTCATCTGTATTTTT
EST: gi|58683077|gb|CK071764.1|CK071764
EST:     GTACCTTGCCTGCCATATGCTTGCTCACTGGGAAGTTTATCACTCCAGAG                         CTCACCAATGTTGCTAGTCTATGGTTCATGTCGCTTTTCATCTGTATTTTT
genomic: GTACCTTGCCTGCCATATGCTTGCTCACTGGGAAGTTTATCACTCCAGAGgtaagcatta ... caaactgcagCTCACCAATGTTGCTAGTCTATGGTTCATGTCGCTTTTCATCTGTATTTTT
EST: gi|396941331|gb|HO188540.1|HO188540
EST:     GTACCTTGCCTGCCATATGCTTGCTCACTGGGAAGTTTATCACTCCAGAG                         CTCACCAATGTTGCTAGTCTATGGTTCATGTCGCTTTTCATCTGTATTTTT
genomic: GTACCTTGCCTGCCATATGCTTGCTCACTGGGAAGTTTATCACTCCAGAGgtaagcatta ... caaactgcagCTCACCAATGTTGCTAGTCTATGGTTCATGTCGCTTTTCATCTGTATTTTT
EST: gi|29685626|gb|CB681901.1|CB681901
EST:     GTACCTTGCCTGCCATATGCTTGCTCACTGNGAAGTTTATCACTCCAGAG                         CTCACCAATGTTGCTAGTCTAT
genomic: GTACCTTGCCTGCCATATGCTTGCTCACTGGGAAGTTTATCACTCCAGAGgtaagcatta ... caaactgcagCTCACCAATGTTGCTAGTCTAT
EST: gi|58603732|gb|CK014260.1|CK014260
EST:     GTACCTTGCCTGCCATATGCTTGCTCACTGGGAAGTTTATGACGCCAGAG                         CTCACCAATG-TGCTAGTCTATGGTTCATGTCGCTTTTCATCTGTATTTTT
genomic: GTACCTTGCCTGCCATATGCTTGCTCACTGGGAAGTTTATCACTCCAGAGgtaagcatta ... caaactgcagCTCACCAATGTTGCTAGTCTATGGTTCATGTCGCTTTTCATCTGTATTTTT
EST: gi|33681294|gb|CF309533.1|CF309533
EST:     GTACCTTGCCTGCCATATGCTTGCTCACTGGGAAGTTTATCACTCCAGAG                         CTCACCAATGTTGCTAGTCTATGGTTCATGTCGCTTTTCATCTGTATTTTT
genomic: GTACCTTGCCTGCCATATGCTTGCTCACTGGGAAGTTTATCACTCCAGAGgtaagcatta ... caaactgcagCTCACCAATGTTGCTAGTCTATGGTTCATGTCGCTTTTCATCTGTATTTTT

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: 68 (upstream exon), 74 (downstream exon)
Score: 22

TATTAACTCTATCGTATATCCCTGGACATCCATTCCACTTCTGGCTTACTGTACCTTGCCTGCCATATGCTTGCTCACTGGGAAGTTTATCACTCCAGAGgtaagcatta ... caaactgcagCTCACCAATGTTGCTAGTCTATGGTTCATGTCGCTTTTCATCTGTATTTTTGTCACTGGCATCCTTGAAATGAGATGGAGTGGTGTGGCCATCGATGACT




<











<


<











 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgtgatcttctgagtttctgtctgaatcttacatcatttttatttcaaactgcagCTCACCAATGTTGCTAGTCTATGGTTCATGTCGCTTTTCATCTGTATTTTTGTCACTGGCATCCTTGAAATGAGATGGAGTGGTGTGGCCATCGATGACT
                         atcttac  putative branch site (score: 22)
                                    tttttatttc  putative PPT
                        aatcttacatcatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagcattattgtgctacataattttgtgatcttctgagtttctgtctgaatcttacatcatttttatttcaaactgcagCTCACCAATGTTGCTAGTCTATGGTTCATGTCGCTTTTCATCTGTATTTTTGTCACTGGCATCCTTGAAATGAGATGGAGTGGTGTGGCCATCGATGACT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA