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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGCCAAGTCAAACTACATGTCAGCGGGTCAGATATCTGTCCCTATTGTTTTCAGAGGACCTAATGGAGCTGCTGCTGGAGTTGGCGCTCAACACTCGCAGgtttgtgatcagggaatggcttatgaattagtttatcatcctaggaccccattgaactttgtaaaagttcattgtttccttttgttgtgttgttctaccc...

Basic information

species Oryza sativa
transcript LOC_Os09g33500.1
intron # 7
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os09g33500.1 (Oryza sativa), 5'ss of exon 7
lower sequence: GRMZM2G128121_T01 (Zea mays), 5'ss of exon 1
TGCCAAGTCAAACTACATGTCAGCGGGTCAGATATCTGTCCCTATTGTTTTCAGAGGACCTAATGGAGCTGCTGCTGGAGTTGGCGCTCAACACTCGCAGgtttgtgatcagggaatggcttatgaattagtttatcatcctaggaccccattgaa--ctttgtaaaagttcattgtttccttttgttgtgttgtt-ctaccc-
                                   |||| ||||||||||| |||||||| ||||||||||||||||||||||| ||||||||||| ||||||||| |  | ||| | ||| |||   |||||    |     |   |  ||| |   | || ||     |  || |||||  || || |||| || | |||| 
-----------------------------------CTGTTCCTATTGTTTTTAGAGGACCAAATGGAGCTGCTGCTGGAGTTGGTGCTCAACACTCACAGgtttgtcag-atggagttgctcatg---tagttatgtacttacgtgtctgattaacatccttctacttcctatttttttccactttttatgttattgcgaccct

upper sequence: LOC_Os09g33500.1 (Oryza sativa), 5'ss of exon 7
lower sequence: GRMZM2G097226_T02 (Zea mays), 5'ss of exon 7
TGCCAAGTCAAACTACATGTCAGCGGGTCAGATATCTGTCCCTATTGTTTTCAGAGGACCTAATGGAGCTGCTGCTGGAGTTGGCGCTCAACACTCGCAGgtttgtgatcagggaatggcttatg-aattagtttatcatcctaggaccccattgaactttgtaaaagttcattgtttccttttgttgtgttgtt-ctaccc----
|||||||||||| || |||||||| |||||||||||||| ||||||||||| |||||||| || |||||||||||||||||||| ||||||||||| ||||||||| |  | ||||| ||| ||| | |||  | || ||    |   |  ||| | | |  |   | ||| |  |||    |  || |||| || | | ||    
TGCCAAGTCAAATTATATGTCAGCTGGTCAGATATCTGTTCCTATTGTTTTTAGAGGACCAAACGGAGCTGCTGCTGGAGTTGGTGCTCAACACTCACAGgtttgtcag-atggaattgctcatgtagttatgtaattat----gtgtctgatt-atcatccttctacttcctaatttttcatctttatgttattgccatcctttt

upper sequence: LOC_Os09g33500.1 (Oryza sativa), 5'ss of exon 7
lower sequence: GLYMA02G46380.2 (Glycine max), 5'ss of exon 7
TGCCAAGTCAAACTACATGTCAGCGGGTCAGATATCTGTCCCTATTGTTTTCAGAGGACCTAATGGAGCTGCTGCTGGAGTTGGCGCTCAACACTCGCAGgtttgtgatcagggaatggcttatgaattagtttatcatcctaggaccccattgaactttgtaaaagttcattgtttccttttgttgtgttgttctaccc-------------
 || || |||||||||||||| || || || |||||||| |||||||| || |||||||| ||||| || |||||||||||||| ||||| || || || || ||           ||  || |     ||   | | |  |   ||    |   |  |  ||||   |    ||||| | ||  | ||     | ||               
CGCAAAATCAAACTACATGTCTGCTGGGCAAATATCTGTGCCTATTGTCTTTAGAGGACCCAATGGTGCCGCTGCTGGAGTTGGTGCTCAGCATTCTCAAgtatggttctcctagctgctttcttttaaagacaaactttatttaactatttgagaactgataaataattcaggtttcgtctttgtatgcccaacaactttgcctttatgcag

upper sequence: LOC_Os09g33500.1 (Oryza sativa), 5'ss of exon 7
lower sequence: GLYMA14G36540.3 (Glycine max), 5'ss of exon 7
TGCCAAGTCAAACTACATGTCAGCGGGTCAGATATCTGTCCCTATTGTTTTCAGAGGACCTAATGGAGCTGCTGCTGGAGTTGGCGCTCAACACTCGCAGgtttgtgatcagggaatggcttatgaatta--gtttatcatcctaggaccccattgaactttgtaaa-agttca----ttgtttccttttgttgtgttgttctaccc--------
 || || |||||||||||||| || || || |||||||| |||||||| || |||||||| ||||| ||||||||||| ||||| ||||| || || || ||  | | ||        ||||     |||  |   | | |  |   ||    |   |  |  |||| | ||||    |||| |   | ||         | | ||         
CGCAAAATCAAACTACATGTCTGCTGGGCAAATATCTGTACCTATTGTCTTTAGAGGACCCAATGGTGCTGCTGCTGGGGTTGGTGCTCAGCATTCTCAAgtacg-gttctccttgctgctttctttttaaagacaaactttatttaactatttgagaactgataaataattcaggttttgtctttgtatgcccaacaactttgcctttatgcag

upper sequence: LOC_Os09g33500.1 (Oryza sativa), 5'ss of exon 7
lower sequence: GLYMA14G02380.2 (Glycine max), 5'ss of exon 7
TGCCAAGTCAAACTACATGTCAGCGGGTCAGATATCTGTCCCTATTGTTTTCAGAGGACCTAATGGAGCTGCTGCTGGAGTTGGCGCTCAACACTCGCAGgtttgtgatcagggaatggcttatgaattagtttatcatcctaggaccccattgaactttgtaaaagttcattgtttccttttgttgtgttgttctaccc-------------
 || || |||||||||||||| || || || ||||| || |||||||| || |||||||| ||||| ||||||||||| ||||| ||||| || || || ||  |           ||  || |     ||   | | |  |   |||   |   |  |  ||||   |    ||||| | ||  | ||     | ||               
CGCAAAATCAAACTACATGTCTGCTGGGCAAATATCGGTACCTATTGTCTTTAGAGGACCCAATGGTGCTGCTGCTGGGGTTGGTGCTCAGCATTCTCAAgtacggttctcctagctgctttcttttaaagacaaactttatttaaccatttgagaactgataaataattcaggtttcgtctttgtatgcccaacaacttttcctttatgcag

upper sequence: LOC_Os09g33500.1 (Oryza sativa), 5'ss of exon 7
lower sequence: AT5G50850.1 (Arabidopsis thaliana), 5'ss of exon 8
TGCCAAGTCAAACTACATGTCAGCGGGTCAGATATCTGTCCCTATTGTTTTCAGAGGACCTAATGGAGCTGCTGCTGGAGTTGGCGCTCAACACTCGCAGgtttgtgatcagggaatggcttatgaattagtttatcatcctaggaccccattgaactttgtaaaagttcattgtttccttttgttgtgttgttc-taccc-----
||| |||||||| |||||||| || || ||||||  ||| || || || || |||||||| ||||| ||||||||||| ||||| |||||||| || |||||    | |||   ||       ||||| | ||| | | | | | |  |  |  ||      | |  ||||     |    |  |   | | ||| ||        
TGCAAAGTCAAATTACATGTCTGCTGGACAGATAAATGTACCCATCGTCTTTAGAGGACCCAATGGTGCTGCTGCTGGTGTTGGAGCTCAACATTCTCAGgtaaacgctcacccaaaaaaaattgaat-aatttgtta-ctttgcattctttcaaa----agagaccttcagctactaaactgataaagatattcatataggatga

upper sequence: LOC_Os09g33500.1 (Oryza sativa), 5'ss of exon 7
lower sequence: Vv17s0000g00690.t01 (Vitis vinifera), 5'ss of exon 7
TGCCAAGTCAAACTACATGTCAGCGGGTCAGATATCTGTCCCTATTGTTTTCAGAGGACCTAATGGAGCTGCTGCTGGAGTTGGCGCTCAACACTCGCAGgtttgtgatcagggaatggcttatgaattagtttatcatcctaggaccccattgaactttgtaaaagttcattgtttccttt---tgttgtgttgttctaccc
||| ||||||||||| ||||| || |||||||||||||| || |||||||||||||| || ||||| |||||||| |||||||| || || || || ||||| |  |  ||     || || ||  | |  ||  | || | |     ||||   |  | || |   | | |     | | |   || | || |  | | |||
TGCAAAGTCAAACTATATGTCTGCTGGTCAGATATCTGTGCCAATTGTTTTCAGAGGGCCAAATGGGGCTGCTGCAGGAGTTGGTGCCCAGCATTCTCAGgtgta-gtccaaattctgtctgat--acttattgtttatgcgattttgccatcatatatggttagtctccttctaaccttctagatgctctgcttattttccc

upper sequence: LOC_Os09g33500.1 (Oryza sativa), 5'ss of exon 7
lower sequence: Vv01s0146g00310.t01 (Vitis vinifera), 5'ss of exon 8
TGCCAAGTCAAACTACATGTCAGCGGGTCAGATATCTGTCCCTATTGTTTTCAGAGGACCTAATGGAGCTGCTGCTGGAGTTGGCGCTCAACACTCGCAGgtttgtgatcagggaatggcttatgaattagtttatcatcctaggaccccattgaactttgtaaaa-gttcattgtttccttttgttgtgttgttctaccc
||| || |||||||||||||| || ||||||||||| || ||||||||||| |||||||| ||||| ||||| ||||||||||| || || ||||| |||||       | | |  |  ||  || |   | | |   |  | |   ||   |   || | ||  | |  | | ||     | ||     |      |   
TGCAAAATCAAACTACATGTCCGCTGGTCAGATATCCGTACCTATTGTTTTTAGAGGACCAAATGGTGCTGCCGCTGGAGTTGGTGCCCAGCACTCCCAGgtacactccctgaggttttctcttgcacctggtgact-tgtttgtcaccagcttttctctatatgatgcccgtggtgctgatctggatcataacataatga

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|88718362|gb|CI741451.1|CI741451
EST:     TCAGAGGACCTAATGGAGCTGCTGCTGGAGTTGGCGCCCAACACTCGCAG                         TGTTATGCGGCTTGGTATGCACATGTTCCGGGTCTTAAGGTTCTGGTTCCA
genomic: TCAGAGGACCTAATGGAGCTGCTGCTGGAGTTGGCGCTCAACACTCGCAGgtttgtgatc ... tggtttgcagTGTTATGCGGCTTGGTATGCACATGTTCCGGGTCTTAAGGTTCTGGTTCCA
EST: gi|87032949|gb|CI187573.1|CI187573
EST:     TCAGAGGACCTAATGGAGCTGCTGCTGGAGTTGGCGCTCAACACTCGCAG                         TGTTATGCGGCTTGGTATGCACATGTTCCGGGTCTTAAGGTTCTGGTTCCA
genomic: TCAGAGGACCTAATGGAGCTGCTGCTGGAGTTGGCGCTCAACACTCGCAGgtttgtgatc ... tggtttgcagTGTTATGCGGCTTGGTATGCACATGTTCCGGGTCTTAAGGTTCTGGTTCCA
EST: gi|58687862|gb|CK076549.1|CK076549
EST:     TCAGAGGACCTAATGGAGCTGCTGCTGGAGTGGGCGCTCAACACTCGCAG                         TGTTATGCGGCTTGGTATGCACATGTTCCGGGTCTTAAGGTTCTGGCTCCA
genomic: TCAGAGGACCTAATGGAGCTGCTGCTGGAGTTGGCGCTCAACACTCGCAGgtttgtgatc ... tggtttgcagTGTTATGCGGCTTGGTATGCACATGTTCCGGGTCTTAAGGTTCTGGTTCCA
EST: gi|29637529|gb|CB642538.1|CB642538
EST:     TCAGAGGACCTAATGGAGCTGCTGCTGGAGTTGGCGCTCAACACTCGCAG                         TGTTATGCGGCTTGGTATGCACATGTTCCGGGTCTTAAGGTTCTGGTTCCA
genomic: TCAGAGGACCTAATGGAGCTGCTGCTGGAGTTGGCGCTCAACACTCGCAGgtttgtgatc ... tggtttgcagTGTTATGCGGCTTGGTATGCACATGTTCCGGGTCTTAAGGTTCTGGTTCCA
EST: gi|33380822|gb|CF196165.1|CF196165
EST:     TCAGAGGACCTAATGGAGCTGCTGCTGGAGTTGGCGCTCAACACTCGCAG                         TGTTATGCGGCTTGGTATGCACATGTTCCGGGTCTTAAGGTTCTGGTTCCA
genomic: TCAGAGGACCTAATGGAGCTGCTGCTGGAGTTGGCGCTCAACACTCGCAGgtttgtgatc ... tggtttgcagTGTTATGCGGCTTGGTATGCACATGTTCCGGGTCTTAAGGTTCTGGTTCCA
EST: gi|157649975|gb|EX449609.1|EX449609
EST:     TGCTGGAGTTGGCGCTCAACACTCGCAG                         TGTTATGCGGCTTGGTATGCACATGTTCCGGGTCTTAAGGTTCTGGTTCCA
genomic: TGCTGGAGTTGGCGCTCAACACTCGCAGgtttgtgatc ... tggtttgcagTGTTATGCGGCTTGGTATGCACATGTTCCGGGTCTTAAGGTTCTGGTTCCA
EST: gi|29645720|gb|CB650727.1|CB650727
EST:     GTTGGCGCTCAACACTCGCAG                         TGTTATGCGGCTTGGTATGCACATGTTCCGGGTCTTAAGGTTCTGGTTCCA
genomic: GTTGGCGCTCAACACTCGCAGgtttgtgatc ... tggtttgcagTGTTATGCGGCTTGGTATGCACATGTTCCGGGTCTTAAGGTTCTGGTTCCA
EST: gi|58586864|gb|CF985172.1|CF985172
EST:     TCAGAGGACCTAATGGAGCTGCTGCTGGAGTTGGCGCTCAACACTCGCAG                         TGTTATGCGGCTTGGTATGCACATGTTCCGGGTCTTAAGGTTCTGGCTCCA
genomic: TCAGAGGACCTAATGGAGCTGCTGCTGGAGTTGGCGCTCAACACTCGCAGgtttgtgatc ... tggtttgcagTGTTATGCGGCTTGGTATGCACATGTTCCGGGTCTTAAGGTTCTGGTTCCA
EST: gi|29657623|gb|CB653898.1|CB653898
EST:     TCAGAGGACCTAATGGAGCTGCTGCTGGAGTTGGCGCTCAACACTCGCAG                         TGTTATGCGGCTTGGTATGCACATGTTCCGGGTCTTAAGGTTCTGGTTCCA
genomic: TCAGAGGACCTAATGGAGCTGCTGCTGGAGTTGGCGCTCAACACTCGCAGgtttgtgatc ... tggtttgcagTGTTATGCGGCTTGGTATGCACATGTTCCGGGTCTTAAGGTTCTGGTTCCA
EST: gi|27576086|gb|CA998780.1|CA998780
EST:     TCAGAGGACCTAATGGAGCTGCTGCTGGAGTTGGCGCTCAACACTCGCAG                         TGTTATGCGGCTTGGTATGCACATGTTCCGGGTCTTAAGGTTCTGGTTCCA
genomic: TCAGAGGACCTAATGGAGCTGCTGCTGGAGTTGGCGCTCAACACTCGCAGgtttgtgatc ... tggtttgcagTGTTATGCGGCTTGGTATGCACATGTTCCGGGTCTTAAGGTTCTGGTTCCA

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: 72 (upstream exon), 72 (downstream exon)
Score: 66

TGCCAAGTCAAACTACATGTCAGCGGGTCAGATATCTGTCCCTATTGTTTTCAGAGGACCTAATGGAGCTGCTGCTGGAGTTGGCGCTCAACACTCGCAGgtttgtgatc ... tggtttgcagTGTTATGCGGCTTGGTATGCACATGTTCCGGGTCTTAAGGTTCTGGTTCCATATTCTGCAGAAGATGCTCGTGGCTTGCTCAAAGCTGCGATTAGGGATC




<











<


<









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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGCCAAGTCAAACTACATGTCAGCGGGTCAGATATCTGTCCCTATTGTTTTCAGAGGACCTAATGGAGCTGCTGCTGGAGTTGGCGCTCAACACTCGCAGgtttgtgatcagggaatggcttatgaattagtttatcatcctaggaccccattgaactttgtaaaagttcattgtttccttttgttgtgttgttctaccc

- - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGGA