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

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaatacaaatattttttgtgtggataagatgctcccttgatcttgttgctgacttttttccctgccagGTTATGTATTGTGTTCCTTACCTTTAGTTGTATTGGGTATGCCATGCCTTTCATCCTCTGTGCAATGATATGCTGCTGCCTGCCCTGCATCATATCTGTT

Basic information

species Oryza sativa
transcript LOC_Os02g54624.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g54624.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G089466_T01 (Zea mays), 3'ss of exon 3
gtaaatacaaatattttttgtgtggataagatgctcc-----------cttgatcttgttgctgacttttt--tccctgccagGTTATGTATTGTGTTCCTTACCTTTAGTTGTATTGGGTATGCCATGCCTTTCATCCTCTGTGCAATGATATGCTGCTGCCTGCCCTGCATCATATCTGTT
||||||   ||    | ||   | ||| |||||   |           ||| ||| ||  ||||||||| |  | ||  ||||||| || ||||||||||| || |||||||| ||||||||||||||||| |||||||| ||||||||||||||||| ||||| |||||||| |||||| ||
gtaaatgtgaactgctcttcaattgatgagatgtcactatgtcagcttctttatcctgcagctgactttctacttcccaccagGTTGTGCATTGTGTTCCTCACTTTTAGTTGCATTGGGTATGCCATGCCATTCATCCTATGTGCAATGATATGCTGTTGCCTTCCCTGCATTATATCTATT

upper sequence: LOC_Os02g54624.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA13G43770.1 (Glycine max), 3'ss of exon 3
--gtaaatacaaatattttttgt--gtggataagatgctcccttga-tcttgttg----ctgacttttttccctgccagGTTATGTATTGTGTTCCTTACCTTTAGTTGTATTGGGTATGCCATGCCTTTCATCCTCTGTGCAATGATATGCTGCTGCCTGCCCTGCATCATATCTGTT
       ||| | | |||||  |       ||   | ||  || || ||||   |    |||   ||  |  |   |||||||||||||||||| ||||||||||| ||||| || ||||| ||||| || || || |||||||  || || ||||||||||| || || || ||||||
gtacctgtaccactgtttttgctcaaccagtattttactttctcgagtcttcgagtaatctgggcttcatgtcatgcagGTTATGTATTGTGTTTCTTACCTTTAGCTGTATCGGATATGCAATGCCATTTATACTTTGTGCAACTATTTGTTGCTGCCTGCCTTGTATAATTTCTGTT

upper sequence: LOC_Os02g54624.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA06G07690.1 (Glycine max), 3'ss of exon 2
---------------------------------gtaaatacaaatattttttgtgtggataagatgctcccttgatcttgttgctgacttttttccctgccagGTTATGTATTGTGTTCCTTACCTTTAGTTGTATTGGGTATGCCATGCCTTTCATCCTCTGTGCAATGATATGCTGCTGCCTGCCCTGCATCATATCTGTT
                                   | | ||||||| | ||    |   | ||| ||| ||    | |   ||||     |||| | || |||||||||| | ||||| ||||| ||||| |||||||| ||||| ||||| ||||| || |||||||  || |||||||||||||| ||||| || ||  | 
acaagcaattatttctccaaattaagttgaaccaaatacacaaataatcttctgatttcttaga-gcttccagattatatctgct--tccttttgcttggcagGTTATGTGTAGTGTTTCTTACTTTTAGCTGTATTGGTTATGCTATGCCCTTCATTCTATGTGCAACAATTTGCTGCTGCCTGCCTTGCATAATTTCCATC

upper sequence: LOC_Os02g54624.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA15G01570.1 (Glycine max), 3'ss of exon 3
----gtaaatacaaatattttttgt--gtggataagatgctcccttga-tctt-----gttgctgacttttttccctgccagGTTATGTATTGTGTTCCTTACCTTTAGTTGTATTGGGTATGCCATGCCTTTCATCCTCTGTGCAATGATATGCTGCTGCCTGCCCTGCATCATATCTGTT
     |  ||   | | |||||  |       ||   | ||  || || ||||       |   | |||  || | ||| |||||||||||||| || ||||||||||| ||||| || ||||| ||||| || || || |||||||  || || |||||||| || || || || ||||||
gtacttgtatctcattgtttttgctcaacctgtattttactttctcgagtcttcaaataatctgggcttcatttcatgc-agGTTATGTATTGTTTTTCTTACCTTTAGCTGTATCGGATATGCAATGCCATTTATACTTTGTGCAACTATTTGTTGCTGCCTACCTTGTATAATTTCTGTT

upper sequence: LOC_Os02g54624.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA17G30020.1 (Glycine max), 3'ss of exon 3
----------gtaaatacaaatattttttgtgtggataagatgctcccttgatcttgttgctgacttttttccct-gccagGTTATGTATTGTGTTCCTTACCTTTAGTTGTATTGGGTATGCCATGCCTTTCATCCTCTGTGCAATGATATGCTGCTGCCTGCCCTGCATCATATCTGTT
           |  || |    ||||  | |   |||   | | |    |||  || |  |||  |  | || || | |||||||||||| ||||| ||| | ||||| || ||||| ||||||||||| ||||| |||||| |||  || ||||| || || || || || || ||| | 
gtagcctttcattcattcttgcatttaatcttcagattttaagatattatgaaattatatctgcttcatatctcttggcagGTTATGTATAGTGTTTCTTGCATTTAGCTGCATTGGTTATGCCATGCCCTTCATTCTCTGTTCAACAATCTGCTGTTGTCTCCCTTGTATAATTTCTATC

upper sequence: LOC_Os02g54624.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA04G07570.1 (Glycine max), 3'ss of exon 3
-----------------------------------------------------------------------------------------------------------------------------------gtaaatacaaatattttttgtgtggataagatgctcccttgatcttgttgctgacttttttccctgccagGTTATGTATTGTGTTCCTTACCTTTAGTTGTATTGGGTATGCCATGCCTTTCATCCTCTGTGCAATGATATGCTGCTGCCTGCCCTGCATCATATCTGTT
                                                                                                                                     | | ||||||| | ||    |   | ||| ||| ||    | |   ||||     |||| | || |||||||||| | ||||| ||||| ||||| || || || ||||| ||||| ||||| ||||||||||  || |||||||||||||| || || || ||  | 
gtatagcctctcagcagctcttacatttagcatgtgtttggtaaaacatttttcaagagaaataatttttcaaaaattctctcatgaagctagcaaaaataaccaattgtttatccaaaccaagttgaacaaaatacacaaataatcttctgattttttaga-gcttccagattttatctgct--tccttttgcttggcagGTTATGTGTAGTGTTTCTTACTTTTAGCTGCATCGGTTATGCTATGCCCTTCATTCTCTGTGCAACAATTTGCTGCTGCCTGCCTTGTATAATTTCCATC

upper sequence: LOC_Os02g54624.1 (Oryza sativa), 3'ss of exon 3
lower sequence: AT4G32600.1 (Arabidopsis thaliana), 3'ss of exon 3
--------------------------gtaaatacaaatatttt-ttgtgtggat-aagatgctcccttgatcttgttgctgacttttttccctgccagGTTATGTATTGTGTTCCTTACCTTTAGTTGTATTGGGTATGCCATGCCTTTCATCCTCTGTGCAATGATATGCTGCTGCCTGCCCTGCATCATATCTGTT
                           || |  |||| ||     ||  |     ||||    ||| |  | |||||     || || |   | | ||||||||| | ||||| ||||||||||| |||||||| || || ||||| |||||||||||| |||  ||||| |||||| |||| ||||| || ||  ||
gtgatattcttttagatatacagcaattagactcaaacatcagactgcattttccaagactgacccatatttttgtt-----ctcttgtatgttctagGTTATGTTTAGTGTTTCTTACCTTTAGCTGTATTGGCTACGCGATGCCCTTCATCCTCTGTACAACAATATGTTGCTGCTTGCCTTGCATAATCTCAATT

upper sequence: LOC_Os02g54624.1 (Oryza sativa), 3'ss of exon 3
lower sequence: Vv04s0008g04280.t01 (Vitis vinifera), 3'ss of exon 3
-------------gtaaatacaaatattttttgtgtggataagatgctcccttgatcttgttgctgacttttt-----tccctgccagGTTATGTATTGTGTTCCTTACCTTTAGTTGTATTGGGTATGCCATGCCTTTCATCCTCTGTGCAATGATATGCTGCTGCCTGCCCTGCATCATATCTGTT
               |  ||  |   ||| |  | |  || |    || |  |||        |  | | |||     |||    |||||||||||| || || ||||||||||| ||||| || ||||||||||| ||||| || ||||| |  || ||||||||||| || || || || ||  | 
gtattgtttagtaccatttatcacattttgtcatttccattactcccttctgtgagaactcaacctattctttgcatttcctcatcagGTTATGTATAGTCTTTCTTACCTTTAGCTGTATCGGATATGCCATGCCGTTCATTCTATGTGCTACAATCTGCTGCTGCCTCCCTTGTATAATTTCCATC

upper sequence: LOC_Os02g54624.1 (Oryza sativa), 3'ss of exon 3
lower sequence: Vv11s0016g04450.t01 (Vitis vinifera), 3'ss of exon 3
------------------gtaaatacaaatattttttgtgtggataagatgctcccttgatcttgttgctgacttttttccctgccagGTTATGTATTGTGTTCCTTACCTTTAGTTGTATTGGGTATGCCATGCCTTTCATCCTCTGTGCAATGATATGCTGCTGCCTGCCCTGCATCATATCTGTT
                   || |||   |   ||| | |         |||        | ||  ||  ||   ||  |  |    ||||||||||||||||| ||||||||||| |||||||| || || ||||||||||| || ||||||||||||||||||||| |||| || || || ||  ||
gtattagtcaattcttgcttacatattgaccctttattttcactctgcatgaaaatccaacctgtttcttgggattgcttgc----agGTTATGTATTGTGTTTCTTACCTTTAGCTGTATTGGATACGCTATGCCTTTCATTCTATGTGCAATGATATGCTGCTGCTTGCCTTGTATAATTTCAATT

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|29658047|gb|CB654322.1|CB654322
EST:     TGGATATTTGGCGGGCGTTCTTCTGCTGCCGATGCTCCAAACTTGTACAG                         GTTATGTATTGTGTTCCTTACCTTTAGTTGTATTGGGTATGCCATGCCTTT
genomic: TGGATATTTGGCGGGCGTTCTTCTGCTGCCGATGCTCCAAACTTGTACAGgtaaatacaa ... tccctgccagGTTATGTATTGTGTTCCTTACCTTTAGTTGTATTGGGTATGCCATGCCTTT
EST: gi|33811814|gb|CF331794.1|CF331794
EST:     TGGATATTTGGCGGGCGTTCTTCTGCTGCCGATGCTCCAAACTTGTACAG                         GTTATGTATTGTGTTCCTTACCTTTAGTTGTATTGGGTATGCCATGCCTTT
genomic: TGGATATTTGGCGGGCGTTCTTCTGCTGCCGATGCTCCAAACTTGTACAGgtaaatacaa ... tccctgccagGTTATGTATTGTGTTCCTTACCTTTAGTTGTATTGGGTATGCCATGCCTTT
EST: gi|29629876|gb|CB634885.1|CB634885
EST:     TGGATATTTGGCGGGCGTTCTTCTGCTGCCGATGCTCCAAACTTGTACAG                         GTTATGTATTGTGTTCCTTACCTTTAGTTGTATTGGGTATGCCATGCCTTT
genomic: TGGATATTTGGCGGGCGTTCTTCTGCTGCCGATGCTCCAAACTTGTACAGgtaaatacaa ... tccctgccagGTTATGTATTGTGTTCCTTACCTTTAGTTGTATTGGGTATGCCATGCCTTT
EST: gi|218502640|gb|FG955084.1|FG955084
EST:     TGGATATTTGGCGGGCGTTCTTCTGCTGCCGATGCTCCAAACTTGTACAG                         GTTATGTATTGTGTTCCTTACCTTTAGTTGTATTGGGTATGCCATGCCTTT
genomic: TGGATATTTGGCGGGCGTTCTTCTGCTGCCGATGCTCCAAACTTGTACAGgtaaatacaa ... tccctgccagGTTATGTATTGTGTTCCTTACCTTTAGTTGTATTGGGTATGCCATGCCTTT

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: 59 (upstream exon), 69 (downstream exon)
Score: 13

AGATGGCCTTGGATTGTTTCTTTGCTGTGTGGTTTGTCGTAGGAAATGTGTGGATATTTGGCGGGCGTTCTTCTGCTGCCGATGCTCCAAACTTGTACAGgtaaatacaa ... tccctgccagGTTATGTATTGTGTTCCTTACCTTTAGTTGTATTGGGTATGCCATGCCTTTCATCCTCTGTGCAATGATATGCTGCTGCCTGCCCTGCATCATATCTGTT




<











<


<











 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttttgtgtggataagatgctcccttgatcttgttgctgacttttttccctgccagGTTATGTATTGTGTTCCTTACCTTTAGTTGTATTGGGTATGCCATGCCTTTCATCCTCTGTGCAATGATATGCTGCTGCCTGCCCTGCATCATATCTGTT
                                 tgctgac  putative branch site (score: 13)
                                       cttttttccctgcc  CT-rich tract
                                      actttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaatacaaatattttttgtgtggataagatgctcccttgatcttgttgctgacttttttccctgccagGTTATGTATTGTGTTCCTTACCTTTAGTTGTATTGGGTATGCCATGCCTTTCATCCTCTGTGCAATGATATGCTGCTGCCTGCCCTGCATCATATCTGTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC