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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGCTAGATTTGAGCGGCATTCTCACCGTATTCTTCTGTGGTATTGTAATGTCACATTACACTTGGCATAACGTCACAGAGAGTTCAAGAGTTACAACAAAgtaaattataattctcattccatattctactgtttaatgattagcttcagttcgtagaaaaactaaacaaaacttactggtttgttttgtcctttcacctcag

Basic information

species Oryza sativa
transcript LOC_Os07g47100.1
intron # 10
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

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: 75 (upstream exon), 72 (downstream exon)
Score: 18

TGCTAGATTTGAGCGGCATTCTCACCGTATTCTTCTGTGGTATTGTAATGTCACATTACACTTGGCATAACGTCACAGAGAGTTCAAGAGTTACAACAAAgtaaattata ... ttcacctcagGCACGCATTTGCAACTCTGTCCTTCATTGCTGAGACTTTTCTCTTCCTGTATGTTGGGATGGATGCATTGGATATTGAAAAATGGGAGTTTGCCAGTGAC




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