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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagcacctaatataatgatgtttctttttctttattggctttattttttactaagattttaacctgttttttcaatagCTGGCTTGGCAAGATCACACTAGAGACATACATTTCCCAGATTCACATTTGGCTCAG

Basic information

species Oryza sativa
transcript LOC_Os05g50510.1
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os05g50510.1 (Oryza sativa), 3'ss of exon 12
lower sequence: GRMZM2G458538_T01 (Zea mays), 3'ss of exon 7
gtaagcacctaa---tataatg-----atgtttctttttctttattggctttattttttactaaga--ttttaacctgttttttcaatagCTGGCTTGGCAAGATCACACTAGAGACATACATTTCCCAGATTCACATTTGGCTCAG
|||||||   ||   | || |      ||  ||| | |  ||| |||||||  |     ||||||   ||||||  |    ||   | || |||||||||||||| ||||| ||||| || ||||| ||||| || |||||||| ||
gtaagcattaaaatttttactacctacattgttcatgtgttttcttggcttactccaccactaagtatttttaatgtacacttgtgacagATGGCTTGGCAAGATTACACTCGAGACTTATATTTCTCAGATCCATATTTGGCTTAG

upper sequence: LOC_Os05g50510.1 (Oryza sativa), 3'ss of exon 12
lower sequence: GLYMA05G25780.1 (Glycine max), 3'ss of exon 13
------------------------------------------------------gtaagcacctaatataatgatgtttctttttctttattggctttattttttactaagattttaacctgttttttcaatagCTGGCTTGGCAAGATCACACTAGAGACATACATTTCCCAGATTCACATTTGGCTCAG
                                                       |  |    | || |  |||    | | ||| ||| ||   ||| |||| |  |  || |||  ||  |||||  |  || |||||||||||||| ||  | |||||||||||||||||| |||| |||||| | ||
gtatgtgttctttaccctaattattgaaattctatgttgattggttttggattattttgttttttatttggtgactgctatctttttttctt---ttttttttcttttctgaattttccccatttttgtatcagGTGGCTTGGCAAGATTACTTTGGAGACATACATTTCCCAGTTTCATATTTGGTTAAG

upper sequence: LOC_Os05g50510.1 (Oryza sativa), 3'ss of exon 12
lower sequence: GLYMA08G08730.1 (Glycine max), 3'ss of exon 13
-----------------------------------gtaagc--acctaatataatgatgtttctttttctttattggctttattttttactaagattttaacctgttttttcaatagCTGGCTTGGCAAGATCACACTAGAGACATACATTTCCCAGATTCACATTTGGCTCAG
                                   || |       |   || ||  ||||| | |||  | ||  |  |  ||||||  |  || |||  ||   ||||  |  || |||||||||||||| ||  | |||||||||||||||||| |||| |||||| | ||
gtacgtgttctttaccttaattattgaaattccatgttaattggttttggatcattttgtttttatttggtgataagtatcttttttt-ttctgaatttcccccacttttgtatcagGTGGCTTGGCAAGATTACTTTGGAGACATACATTTCCCAGTTTCATATTTGGTTAAG

upper sequence: LOC_Os05g50510.1 (Oryza sativa), 3'ss of exon 12
lower sequence: AT5G46340.1 (Arabidopsis thaliana), 3'ss of exon 13
--------gtaagcaccta-atataa--tgatgtttctttttctttattggctttattttttactaagattttaacctgttttttcaatagCTGGCTTGGCAAGATCACACTAGAGACATACATTTCCCAGATTCACATTTGGCTCAG
            | || || || |||  | |    |  |||  | |  | || | ||||     ||| | | |   |  || | |    || |||||||||||||||||  ||||||| |||||||||||| |||| || ||||| ||
gtgagtcaactcgtacttacatttaaactaaaacctggtttgatatgcttgcctcatttccatgtaaaactctttacatttctctgcgcagGTGGCTTGGCAAGATCACTTTAGAGACTTACATTTCCCAGTTTCATATATGGCTAAG

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|117217788|gb|CT845133.1|CT845133
EST:     CTACGCAACTGCACCCAGCAGTTGAGGAGTGCCTCCTTGGCTCTTTTCGC                         CTGGCTTGGCAAGATCACACTAGAGACATACATTTCCCAGATTCACATTTG
genomic: CTACGCAACTGCACCCAGCAGTTGAGGAGTGCCTCCTTGGCTCTTTTCGCgtaagcacct ... ttttcaatagCTGGCTTGGCAAGATCACACTAGAGACATACATTTCCCAGATTCACATTTG
EST: gi|27576336|gb|CA999030.1|CA999030
EST:     CTACGCAACTGCACCCAGCAGTTGAGGAGTGCCTCCTTGGCTCTTTTCGC                         CTGGCTTGGCAAGATCACACTAGAGACATACATTTCCCAGATTCACATTTG
genomic: CTACGCAACTGCACCCAGCAGTTGAGGAGTGCCTCCTTGGCTCTTTTCGCgtaagcacct ... ttttcaatagCTGGCTTGGCAAGATCACACTAGAGACATACATTTCCCAGATTCACATTTG

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: 49 (upstream exon), 57 (downstream exon)
Score: 15

TGTTTATATCTGCCTACGCAACTGCACCCAGCAGTTGAGGAGTGCCTCCTTGGCTCTTTTCGCgtaagcacct ... ttttcaatagCTGGCTTGGCAAGATCACACTAGAGACATACATTTCCCAGATTCACATTTGGCTCAG




<











<


<











 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctttttctttattggctttattttttactaagattttaacctgttttttcaatagCTGGCTTGGCAAGATCACACTAGAGACATACATTTCCCAGATTCACATTTGGCTCAG
                                 ttttaac  putative branch site (score: 15)
                                       cctgttttttc  CT-rich tract
                tttattttttactaag  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagcacctaatataatgatgtttctttttctttattggctttattttttactaagattttaacctgttttttcaatagCTGGCTTGGCAAGATCACACTAGAGACATACATTTCCCAGATTCACATTTGGCTCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGATCA