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

TGCTAGATTTGAGCGGCATTCTCACCGTATTCTTCTGTGGTATTGTAATGTCACATTACACTTGGCATAACGTCACAGAGAGTTCAAGAGTTACAACAAAgtaaattataattctcattccatattctactgtttaatgattagcttcagttcgtagaaaaactaaacaaaacttactggtttgttttgtcctttcacctcag

Basic information

species Oryza sativa
transcript LOC_Os07g47100.2
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os07g47100.2 (Oryza sativa), 5'ss of exon 9
lower sequence: GRMZM2G027851_T03 (Zea mays), 5'ss of exon 7
TGCTAGATTTGAGCGGCATTCTCACCGTATTCTTCTGTGGTATTGTAATGTCACATTACACTTGGCATAACGTCACAGAGAGTTCAAGAGTTACAACAAAgtaaattataattctcattccatattctactgtttaatgattagcttcagttcgtagaaaaactaaacaaaacttactggtttgttttgtcctttcacctcag
|||||||| |||| |||||||| |||||||||||||| || || || ||||| |||||||| ||||| || || |||||||| |||||||| ||||| |||||| |  |  || |||||     ||   ||  | |    |  | |    ||  || |  ||         | || ||  |  |  || | | ||||| |   
TGCTAGATCTGAGTGGCATTCTTACCGTATTCTTCTGCGGCATCGTGATGTCGCATTACACCTGGCACAATGTGACAGAGAGCTCAAGAGTCACAACCAAgtaattattccttgtcattt----tttcgctagtaatgtttctgttctgcttaataaacgaatgctgactgaattccttttgggcctttttcattcacttag-

upper sequence: LOC_Os07g47100.2 (Oryza sativa), 5'ss of exon 9
lower sequence: GLYMA07G38160.1 (Glycine max), 5'ss of exon 9
TGCTAGATTTGAGCGGCATTCTCACCGTATTCTTCTGTGGTATTGTAATGTCACATTACACTTGGCATAACGTCACAGAGAGTTCAAGAGTTACAACAAAgtaaattataattctcattccatattctactgtttaatgattagcttcagttcgtagaaaaactaaacaaaacttactggtttgttttgtcctttcacctcag
|  |   ||| || | |||||| || || |||||||| || ||||| ||||| || ||||| |||||||| || ||||||||||||||||| ||||| |||||  | | | |  |||   || |||| | |    |   |  || |  || |  ||   | ||||   ||      ||| |||   ||  |||  | |     
TATTTTCTTTAAGTGCCATTCTGACTGTTTTCTTCTGCGGCATTGTTATGTCTCACTACACGTGGCATAATGTGACAGAGAGTTCAAGAGTGACAACCAAgtacgtgaaattcttca--acacattc-attaggcatgtacaagat--agctactaatgatactacttaa------ctgattttaatttccctgccgcag---

upper sequence: LOC_Os07g47100.2 (Oryza sativa), 5'ss of exon 9
lower sequence: GLYMA10G30020.1 (Glycine max), 5'ss of exon 10
TGCTAGATTTGAGCGGCATTCTCACCGTATTCTTCTGTGGTATTGTAATGTCACATTACACTTGGCATAACGTCACAGAGAGTTCAAGAGTTACAACAAAgtaaattataattctcattccatattctactgtttaatgattagcttcagttcgtagaaaaactaaacaaaactt-actggtttgttttgtcctttcacctcag
|     || |||| ||||||||||| |||||||| ||||||||||| ||||| ||||| || ||||||||||| || |||||||||||| | || || |||||  |     |||| |    || | ||   |||   |     |    |||   | | | | ||||||| |  || ||     | ||                 
TATGTTATCTGAGTGGCATTCTCACTGTATTCTTTTGTGGTATTGTTATGTCTCATTATACCTGGCATAACGTGACCGAGAGTTCAAGAATCACTACCAAgtatgtc----ttctaaacagatttcctcaagttatgtacactgtccaagtctat-gcatacctaaacatattttcacccaactcttgcag-------------

upper sequence: LOC_Os07g47100.2 (Oryza sativa), 5'ss of exon 9
lower sequence: GLYMA03G40290.1 (Glycine max), 5'ss of exon 9
TGCTAGATTTGAGCGGCATTCTCACCGTATTCTTCTGTGGTATTGTAATGTCACATTACACTTGGCATAACGTCACAGAGAGTTCAAGAGTTACAACAAAgtaaat----tataattctcattccatattctactgtttaatgattagcttcagttcgtagaaaaactaaacaaaacttactggtttgttttgtcctttcacctcag
|     || |||| ||||||||||| |||||||||||||| ||||| ||||| ||||| ||||||||||| || || ||||| || ||| | || || ||||| ||    || |    |   | ||   |   || | ||  |||    ||  | | |||  |      ||    |  || |    |  || |   || ||      
TATGGTATCTGAGTGGCATTCTCACTGTATTCTTCTGTGGGATTGTTATGTCTCATTATACTTGGCATAATGTGACTGAGAGCTCGAGAATAACTACCAAgtatatcctctaaacaaatttcttcaagctaagctatatatggatctatttggggtagtaacactgtctaatttgatatattaaactactt-gctgttacag-----

upper sequence: LOC_Os07g47100.2 (Oryza sativa), 5'ss of exon 9
lower sequence: GLYMA19G42900.1 (Glycine max), 5'ss of exon 9
TGCTAGATTTGAGCGGCATTCTCACCGTATTCTTCTGTGGTATTGTAATGTCACATTACACTTGGCATAACGTCACAGAGAGTTCAAGAGTTACAACAAAgtaaattata-attctcattccatattctactgtttaatgattagcttcagttcgtagaaaaactaaacaaaacttactggtttgttttgtcctttcacctcag
|     || |||| |||||||| || |||||||||||||| ||||| ||||| ||||| ||||||||||| || || ||||| || ||| | || || ||||| ||  |  |  |    | ||   |    | | ||  |||    ||  ||| |  |   |   | ||         || ||| ||    | | |     |||
TATGGTATCTGAGTGGCATTCTTACTGTATTCTTCTGTGGGATTGTTATGTCTCATTATACTTGGCATAATGTGACTGAGAGCTCGAGAATAACTACCAAgtatatcctctagacattcttcaagctaagttatatatggatctatttgggttgg--gggtagtaacactgtctaatttgatttattaaaacttgttgttacag

upper sequence: LOC_Os07g47100.2 (Oryza sativa), 5'ss of exon 9
lower sequence: GLYMA17G02560.1 (Glycine max), 5'ss of exon 8
TGCTAGATTTGAGCGGCATTCTCACCGTATTCTTCTGTGGTATTGTAATGTCACATTACACTTGGCATAACGTCACAGAGAGTTCAAGAGTTACAACAAAgtaaattataattctcattccatattctactgtttaatgattagcttcagttcgtagaaaaactaaacaaaacttactggtttgttttgtcctttcacctcag
|  |   ||| || | |||||| || || |||||||| || ||||| ||||| || ||||| |||||||| || ||||||||||||||||| ||||| |||||  | | | |  |||   || |||| |      |   |  || ||  | |  ||   | ||||  |  |||| | |  |||   |  | |           
TATTTTCTTTAAGTGCCATTCTGACTGTTTTCTTCTGCGGCATTGTTATGTCTCACTACACGTGGCATAATGTGACAGAGAGTTCAAGAGTGACAACCAAgtacgtgaaattcttca--acacattc-atgagacatgtacaagatt--gctactaatgatacta--cttaactgattaatttccctgctgcag---------

upper sequence: LOC_Os07g47100.2 (Oryza sativa), 5'ss of exon 9
lower sequence: GLYMA20G37370.1 (Glycine max), 5'ss of exon 10
TGCTAGATTTGAGCGGCATTCTCACCGTATTCTTCTGTGGTATTGTAATGTCACATTACACTTGGCATAACGTCACAGAGAGTTCAAGAGTTACAACAAAgtaaattataattctcattccatattctactgtttaatgattagc-ttcagttcgtagaaaaactaaacaaaacttactggtttgttttgtcctttcacctcag
||    || |||| ||||||||||| |||||||| ||||| ||||| ||||| ||||| || |||||||| || || |||||||||||| | || || |||||  |     |||| | |  || | ||   | |  | |   |   | ||  ||   | | | ||||||| |  ||      |  |      ||| ||      
TGTCCTATCTGAGTGGCATTCTCACTGTATTCTTTTGTGGGATTGTCATGTCTCATTATACCTGGCATAATGTGACTGAGAGTTCAAGAATCACTACCAAgtatgtc----ttctaaatagatttcctcaagatatacgcacactgtccaagtctatgcatacctaaacatatttt------tcatccaactcttgcag-----

upper sequence: LOC_Os07g47100.2 (Oryza sativa), 5'ss of exon 9
lower sequence: AT3G05030.2 (Arabidopsis thaliana), 5'ss of exon 6
TGCTAGATTTGAGCGGCATTCTCACCGTATTCTTCTGTGGTATTGTAATGTCACATTACACTTGGCATAACGTCACAGAGAGTTCAAGAGTTACAACAAAgtaaattataattctcattccatattctactgtttaatgattagcttcagttcgtagaaaaactaaacaaaacttactggtttgttttgtcctttcacctcag---
|  | |  ||||| || || || || ||||| |||||||| ||||| ||||| |||||||||||||| || ||||| ||||| |||||| |||| || ||||||  ||| |    ||||     ||||     || |  |  |  |  | |   |   |    |   ||| |||||||   ||  | ||   || |          
TATTCGCCTTGAGTGGTATCCTAACTGTATTTTTCTGTGGGATTGTGATGTCCCATTACACTTGGCACAATGTCACCGAGAGCTCAAGAATTACTACCAAgtaa--tatgacctccatt-----ttct----cttgaaaacaaattcaaatgttttcca----tcttcaatacttacttactttctatgcatttacgatgagacag

upper sequence: LOC_Os07g47100.2 (Oryza sativa), 5'ss of exon 9
lower sequence: AT5G27150.1 (Arabidopsis thaliana), 5'ss of exon 10
TGCTAGATTTGAGCGGCATTCTCACCGTATTCTTCTGTGGTATTGTAATGTCACATTACACTTGGCATAACGTCACAGAGAGTTCAAGAGTTACAACAAAgtaaattataattctcattccatattctactgtttaatgattagcttcagttcgtagaaaaactaaacaaaacttactggtttgttttgtcctttcacctcag
|  | || |||||||| || ||||| || || |||||||||||||| ||||| |||||||| ||||| || || || ||||| |||||| | |||||||||||    |  | | |  || |     ||  || | |  ||||| |   | ||  ||      | ||  |  |  |  || ||| ||| |      ||      
TTTTCGACTTGAGCGGTATCCTCACTGTGTTTTTCTGTGGTATTGTGATGTCCCATTACACATGGCACAATGTAACGGAGAGCTCAAGAATAACAACAAAgtatgcaa--actttagtttctccgccttttgctga--gattaac---actttctacct--cccaatgattatcttatgatttttttcgatgaaacag-----

upper sequence: LOC_Os07g47100.2 (Oryza sativa), 5'ss of exon 9
lower sequence: Vv07s0104g01280.t01 (Vitis vinifera), 5'ss of exon 9
TGCTAGATTTGAGCGGCATTCTCACCGTATTCTTCTGTGGTATTGTAATGTCACATTACACTTGGCATAACGTCACAGAGAGTTCAAGAGTTACAACAAAgtaaattata-----------attctc----attccatattctactgtttaatgattagcttcagttcgtagaaaaactaaacaaaacttactggtttgttttgtcctttcacctcag---
|| |  |||| || ||||||||||| |||||||| || || ||||| |||||||| ||||| ||||||||||| || || ||||||||||| || |||||||||  || |           ||| ||    | ||   |  | | | | | || |||   ||   | |  | ||||| ||      |  || |  | |||||     | | |  |  |   
TGTTCTATTTAAGTGGCATTCTCACTGTATTCTTTTGCGGGATTGTCATGTCACACTACACCTGGCATAACGTGACTGAAAGTTCAAGAGTCACCACAAAgtaagctaaatcttcagaaatattttctcaaaatctggaacccattttcttattattttattttttcccaaaaaaaattatgttgcatgtattt-tctgtttctgtttatgatttttgcag

upper sequence: LOC_Os07g47100.2 (Oryza sativa), 5'ss of exon 9
lower sequence: Vv14s0030g00710.t01 (Vitis vinifera), 5'ss of exon 9
TGCTAGATTTGAGCGGCATTCTCACCGTATTCTTCTGTGGTATTGTAATGTCACATTACACTTGGCATAACGTCACAGAGAGTTCAAGAGTTACAACAAAgtaaattataattctcattccatattctactgtttaatgattag--cttcagttcgta----gaaaaactaaacaaaacttactg---gtttgttttgtcctttcacctcag-----------
|  |  ||||||| ||||||||||| ||||| |||||||| ||||||||||| |||||||| ||||| || || ||||||||||||||||| || || |||||  | ||  | || |   || |||  |   |||  || | ||   ||   ||  ||     |||||     ||  |||  |||   |  ||||||    | |  |   |            
TATTCTATTTGAGTGGCATTCTCACGGTATTTTTCTGTGGGATTGTAATGTCCCATTACACGTGGCACAATGTTACAGAGAGTTCAAGAGTCACTACCAAgtatgt-attttcctgaaagca-attggaacattttttggtcaggatttatatttttatttcaaaaaataggtcattactggctgtatgcctgttttaatttctgtctataaaatttccacag

upper sequence: LOC_Os07g47100.2 (Oryza sativa), 5'ss of exon 9
lower sequence: PP1S113_117V6.1 (Physcomitrella patens), 5'ss of exon 8
TGCTAGATTTGAGCGGCATTCTCACCGTATTCTTCTGTGGTATTGTAATGTCACATTACACTTGGCATAACGTCACAGAGAGTTCAAGAGTTACAACAAAgtaaatt-----ataattctca--ttccatattcta--ctgtttaatgattagct---tcagttcgtagaaaaactaa-acaaaacttactggtttgttttgtcctttcacctcag------------------------------------------
|  |  | ||||| || || ||| | || ||||| ||||| ||||||||||| ||||||||||||||||| ||||| || | |||  ||   ||||| | |||  ||     ||   ||| |  ||| || |||||  ||    || || | ||    |||  |  |    | ||| |  |  || ||  |||    |   ||  |   ||    |                                          
TTTTCTACTTGAGTGGAATACTCTCAGTGTTCTTTTGTGGCATTGTAATGTCTCATTACACTTGGCATAATGTCACGGAAAATTCTCGAACCACAACCAGgtacgttccttcatgcctcttagcttcgatgttctatactagcgaacgaatggcaacatcaaatattcttgagactgatgcgtaatttcttggaggttggagttatgatactgatgcttgtcatcaacgtgacattaatgcactttggtgattcacag

upper sequence: LOC_Os07g47100.2 (Oryza sativa), 5'ss of exon 9
lower sequence: PP1S169_48V6.1 (Physcomitrella patens), 5'ss of exon 9
TGCTAGATTTGAGCGGCATTCTCACCGTATTCTTCTGTGGTATTGTAATGTCACATTACACTTGGCATAACGTCACAGAGAGTTCAAGAGTTACAACAAAgtaaattataattctcattccatattctactgtt--taatgattagcttcagttcgta--gaaaaactaaacaaaacttactggtttgttttgtcctttcacctcag--------------------------------------------------------
|  |  | ||||| || |||||| | || ||||| || || ||||||||||| ||||||||||||||||||||||| |||| |||  || | ||||  |||||  || ||      |   ||  |||||  | |  |    |||||  |  |||  |   ||| |  |    || |  |   |  ||   | |    |  |||                                                            
TTTTCTACTTGAGTGGAATTCTCTCAGTGTTCTTTTGCGGCATTGTAATGTCTCATTACACTTGGCATAACGTCACGGAGAATTCTCGAATCACAAGCAAgtacgttttataatgtacctcagtttctatgggtgttgcaaattagtatttgtttatgtcgaatatttttggaacagatgtagaatttcctcggaactagacccattattcaatgctgatactaagcgtcaatgttatgttgatacgttttggttaattgcag

upper sequence: LOC_Os07g47100.2 (Oryza sativa), 5'ss of exon 9
lower sequence: PP1S31_203V6.1 (Physcomitrella patens), 5'ss of exon 10
TGCTAGATTTGAGCGGCATTCTCACCGTATTCTTCTGTGGTATTGTAATGTCACATTACACTTGGCATAACGTCACAGAGAGTTCAAGAGTTACAACAAAgtaa--attataattctcattcc--atattctactgtttaatgattagcttcagttcgtagaaaaactaaacaaaacttactggtttgttttgtcctttcacctcag
|  |  |  |||| || ||||| ||||| ||||| ||||| |||||||||||||| ||||| |||||||||||||| || || ||| |||| || || |||||   ||      | ||| |    || | ||  |  |  |  |  |  || |  |  |  | |  | |   | ||    ||      ||| |||  ||        
TTTTCTACCTGAGTGGAATTCTTACCGTCTTCTTTTGTGGCATTGTAATGTCACACTACACCTGGCATAACGTCACTGAAAGCTCACGAGTAACTACCAAgtaggcatctcttctttcagttgggatgtccttttcatctaacagaatttttatctgttgaataggccacgtacaagcagctcaag-atttagtctatttg------

upper sequence: LOC_Os07g47100.2 (Oryza sativa), 5'ss of exon 9
lower sequence: EFJ05720 (Selaginella moellendorffii), 5'ss of exon 8
TGCTAGATTTGAGCGGCATTCTCACCGTATTCTTCTGTGGTATTGTAATGTCACATTACACTTGGCATAACGTCACAGAGAGTTCAAGAGTTACAACAAAgtaaattataattctcattccatattctactgtttaatgattagcttcagttcgtagaaaaactaaacaaaacttactggtttgttttgtcctttcacctcag
|| |  |  |||| || || ||||| || ||||| ||||| ||||| ||||||||||| || ||||| |||||||| ||||| |||||| | ||||| ||||     | | |    | ||  |||  ||   |||||    |  || |||                                                     
TGTTCTACCTGAGTGGGATCCTCACAGTCTTCTTTTGTGGCATTGTTATGTCACATTATACATGGCACAACGTCACGGAGAGCTCAAGAATCACAACCAAgt-----acagtgacaaatctgtatcttatgttttaacttattcctgcag-----------------------------------------------------

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|88577662|gb|CI674260.1|CI674260
EST:     TCACATTACACTTGGCATAACGTCACAGAGAGTTCAAGAGTTACAACAAA                         GCACGCATTTGCAACTCTGTCCTTCATTGCTGAGACTTTTCTCTTCCTGTA
genomic: TCACATTACACTTGGCATAACGTCACAGAGAGTTCAAGAGTTACAACAAAgtaaattata ... ttcacctcagGCACGCATTTGCAACTCTGTCCTTCATTGCTGAGACTTTTCTCTTCCTGTA
EST: gi|27549114|gb|CA767092.2|CA767092
EST:     TCACATTACACTTGGCATAACGTCACAGAGAGTTCAAGAGTTACAACAAA                         GCACGCATTTGCAACTCTGTCCTTCATTGCTGAGACTTTTCTCTTCCTGTA
genomic: TCACATTACACTTGGCATAACGTCACAGAGAGTTCAAGAGTTACAACAAAgtaaattata ... ttcacctcagGCACGCATTTGCAACTCTGTCCTTCATTGCTGAGACTTTTCTCTTCCTGTA