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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGACGCATGTGCACATTCCTTCTTTGATGAGCTACGAGAGCCCAATGCACGCCTGCCAAATGGTCGTCCATTCCCTCCTCTGTTCAACTTCAAGCATGAAgtaagtaaacgagaacattttcaaacagtcgctttttatggtacatttatatttacctgtcatggatgcttatcaatgctcatttctggtatgcag

Basic information

species Oryza sativa
transcript LOC_Os01g10840.1
intron # 11
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g10840.1 (Oryza sativa), 5'ss of exon 11
lower sequence: GRMZM2G045330_T01 (Zea mays), 5'ss of exon 10
TGACGCATGTGCACATTCCTTCTTTGATGAGCTACGAGAGCCCAATGCACGCCTGCCAAATGGTCGTCCATTCCCTCCTCTGTTCAACTTCAAGCATGAAgtaagtaaacgaga-acatt------ttcaaacagtcgctttttatggtacatttatattt---acctgtcatggatgcttatca----------atgctcatttctg--gtatgcag
|||||||||||| ||| ||||||| |||||||| ||    || || |||||||| ||||| || || || |||||||| || || ||||||||||| |||||||| | || | | ||| |      ||||| ||||   ||            ||   ||    | |||   |    ||||||||          || | | ||||||  ||  ||||
TGACGCATGTGCTCATCCCTTCTTCGATGAGCTGCGGACACCGAACGCACGCCTACCAAACGGCCGCCCGTTCCCTCCGCTCTTTAACTTCAAGCACGAAgtaagcagactaaacacagtgcgaagttcaagcagttaattcaagccacgtgcttcagttcttgatctgctgttt-cgcttatcactcttcgaccatccccttttctgccgtgcgcag

upper sequence: LOC_Os01g10840.1 (Oryza sativa), 5'ss of exon 11
lower sequence: GRMZM2G472625_T01 (Zea mays), 5'ss of exon 11
TGACGCATGTGCACATTCCTTCTTTGATGAGCTACGAGAGCCCAATGCACGCCTGCCAAATGGTCGTCCATTCCCTCCTCTGTTCAACTTCAAGCATGAAgtaagtaaacgagaacattttcaaacagtcgctttttatggtacatttatatttacctgtcatggatgcttatcaat---gctcatttctggtatgcag---------------------------------------------
||| ||||| || ||| |||||||||||||||| || | ||| |||||||| || ||||| || |||||||||||||| || || |||||||| ||||| ||||| |||| | ||||   |  ||   |||  |||      ||  ||   ||      | |  ||     |   ||   | |      || | | | |                                             
TGATGCATGCGCTCATCCCTTCTTTGATGAGCTCCGGGCGCCGAATGCACGTCTACCAAACGGCCGTCCATTCCCTCCGCTCTTTAACTTCAAACATGAGgtaagcaaacta-aacacagtgcaaagttcg--tttagccagacgcttcagttcggtcattaaagacctgaaaggatccagtttgcacttgctctactgttttgctcatcagttaccccccccccctttttttttgctatgcag

upper sequence: LOC_Os01g10840.1 (Oryza sativa), 5'ss of exon 11
lower sequence: GLYMA12G15470.2 (Glycine max), 5'ss of exon 10
TGACGCATGTGCACATTCCTTCTTTGATGAGCTACGAGAGCCCAATGCACGCCTGCCAAATGGTCGTCCATTCCCTCCTCTGTTCAACTTCAAGCATGAAgtaagtaaacgag----aacattttca--aacagtcgctttttatgg-tacatttatatttacctgtcatggatgcttatcaatgctcatttctggtatgcag
 || |||||||||||| | |||||||||||||| || || || ||||| || || || ||||| |||||| | || || || ||||||||||| || || |||  ||    ||    |   |||| |  ||  ||  | | | | || |     | | |  ||   ||||  |||  ||||  |     |   |  | | |  
GGAAGCATGTGCACATCCTTTCTTTGATGAGCTTCGCGAACCAAATGCCCGGCTACCTAATGGCCGTCCACTGCCCCCACTTTTCAACTTCAAACAGGAGgtatatatcttagtcgtattttttttattaaatgtgacgtgtcaaggctgttgctttgtccactgttcatt-atgtatatctgtatgactacttactttac--

upper sequence: LOC_Os01g10840.1 (Oryza sativa), 5'ss of exon 11
lower sequence: GLYMA06G06850.1 (Glycine max), 5'ss of exon 11
TGACGCATGTGCACATTCCTTCTTTGATGAGCTACGAGAGCCCAATGCACGCCTGCCAAATGGTCGTCCATTCCCTCCTCTGTTCAACTTCAAGCATGAAgtaagtaaacgagaacattt-----tcaaacagtcgcttt--ttatggtacatttatatttacctgtcatggatgcttatca-atgctcatttctggtatgcag
||| |||||||||||| | ||||||||||| || || || || ||||| ||| ||||||||||||||||||| || ||||| || |||||||| || |||||||||     | |   |||     ||| || |  |||||     |     |||| || | ||   || |  | |||    | |   |   ||||  | |    
TGAAGCATGTGCACATCCTTTCTTTGATGAACTTCGTGAACCTAATGCTCGCTTGCCAAATGGTCGTCCATTTCCCCCTCTATTTAACTTCAAACAGGAAgtaagtccttaaaactctttcttggtcatactggtgctttggcagtaaattatttgtactgaca-atcttaaaggctaggaataaaattgattctattttt---

upper sequence: LOC_Os01g10840.1 (Oryza sativa), 5'ss of exon 11
lower sequence: GLYMA04G06760.1 (Glycine max), 5'ss of exon 11
TGACGCATGTGCACATTCCTTCTTTGATGAGCTACGAGAGCCCAATGCACGCCTGCCAAATGGTCGTCCATTCCCTCCTCTGTTCAACTTCAAGCATGAAgtaagtaaacgagaacattttcaaacagtcgctttt----tatggtacatttatatttac-ctgtcatggatgcttatcaatgctcatttctggtatgcag
||| |||||||||||| | ||||||||||| || || || ||||| || ||||||||||||||||| ||||| || ||||| || |||||||| || |||||||||     | || | | |      | |    ||    | ||| |      |||||   ||  ||   |      || | |   |    || ||     
TGAAGCATGTGCACATCCTTTCTTTGATGAACTTCGTGAACCCAACGCTCGCCTGCCAAATGGTCGCCCATTTCCCCCTCTATTTAACTTCAAACAGGAAgtaagtccttaataaaactctttcttggccttacttgtgctctggcagtaaattatttgtactaacacaaacttaactctaggaataaaattgatactat-

upper sequence: LOC_Os01g10840.1 (Oryza sativa), 5'ss of exon 11
lower sequence: GLYMA13G30060.1 (Glycine max), 5'ss of exon 11
TGACGCATGTGCACATTCCTTCTTTGATGAGCTACGAGAGCCCAATGCACGCCTGCCAAATGGTCGTCCATTCCCTCCTCTGTTCAACTTCAAGCATGAAgtaagtaaacgag--aacattttcaaacagtcgctttttatggtacatttatatttacctgtcatgg-atgcttatcaatgc--tcatttctggtatgcag
||| |||||||||||| | ||||||||||| || ||||| |||||||| ||||||||||||||||||||||| |||||| | || ||||||||||| |||||||||     |   | | || |  | ||      |  | ||| |      |||||       ||   |   |||  |||    |   | ||| | |  | 
TGAAGCATGTGCACATCCTTTCTTTGATGAACTTCGAGAACCCAATGCTCGCCTGCCAAATGGTCGTCCATTTCCTCCTTTATTTAACTTCAAGCAGGAAgtaagtccttaaattatctttcttcatcaaatttgtgctttggcagtaaactatttgtacagaatttcaaaattaggaataaaattgatactgtttttaa-

upper sequence: LOC_Os01g10840.1 (Oryza sativa), 5'ss of exon 11
lower sequence: GLYMA06G42840.1 (Glycine max), 5'ss of exon 11
TGACGCATGTGCACATTCCTTCTTTGATGAGCTACGAGAGCCCAATGCACGCCTGCCAAATGGTCGTCCATTCCCTCCTCTGTTCAACTTCAAGCATGAAgtaagtaaacgaga-acattttcaaaca---gtcgctttttatgg-tacatttatatttacctgtcatggatgcttatcaatgctcatttctggtatgcag--
 || |||||||||||| | |||||||||||||| || ||||| ||||| || || || ||||| | |||| | || || || ||||||||||| || || |||  ||    ||    |||||  |  |   ||  | | | | || |     | | ||||||  ||||  |    ||||  |     |  ||  ||| ||   
GGAAGCATGTGCACATCCTTTCTTTGATGAGCTTCGCGAGCCAAATGCCCGTCTTCCTAATGGCCATCCACTGCCCCCACTTTTCAACTTCAAACAGGAGgtatatatcttagtcgtattttttattaaatgtgacatgtcaaggctgttgctttgtttaccattcataaag---tatctgtatgactacctactatacatct

upper sequence: LOC_Os01g10840.1 (Oryza sativa), 5'ss of exon 11
lower sequence: GLYMA05G29200.1 (Glycine max), 5'ss of exon 10
TGACGCATGTGCACATTCCTTCTTTGATGAGCTACGAGAGCCCAATGCACGCCTGCCAAATGGTCGTCCATTCCCTCCTCTGTTCAACTTCAAGCATGAAgtaagta-aacgagaacattttcaaacagtcgctttttatggtacatttatatttacctgtcatg-gatgcttatcaatgctcat--ttctggtatgcag------------------------------------------------------------------------------------
 || |||||||||||  | ||||||||||| || || || |||||||| | | ||||| ||||||||||||| || ||||| |||||||| || || || || |||    |   | ||| |||    ||       | | |||  |   | || ||  || | |   || |   |  ||| |||   |||| | || |||                                                                                    
AGAAGCATGTGCACACCCATTCTTTGATGAACTCCGTGAACCCAATGCTCACTTGCCAGATGGTCGTCCATTTCCCCCTCTATTCAACTTTAAACAAGAGgtgagtgtggctgcatcatcttct--tagctatgaatgaaggt-tacaaaaatctaaatgccctacaatacgattttatgatcaagattcttg-atacagcttcattatgaatatatccatgatctgatattcagtaagtaccttgtttagggtctattacatgtttatgttctatgtttacag

upper sequence: LOC_Os01g10840.1 (Oryza sativa), 5'ss of exon 11
lower sequence: GLYMA08G12370.1 (Glycine max), 5'ss of exon 11
TGACGCATGTGCACATTCCTTCTTTGATGAGCTACGAGAGCCCAATGCACGCCTGCCAAATGGTCGTCCATTCCCTCCTCTGTTCAACTTCAAGCATGAAgtaagta-aacgagaacattttca-aacagtcgctttttatggtacatttatatttacc-tgtcatggatgcttatcaatgctcatttctggtatgcag------------------------------------------------------------------------------------
 || |||||||| ||  | ||||||||||| || || || |||||||| | | ||||| ||||||||||||| || ||||| |||||||| || || || || |||    |   | | | |||  | |  |   |     |   | |  | ||  | || |   ||  |   |||| ||     |||  || ||  |||                                                                                    
AGAAGCATGTGCTCACCCATTCTTTGATGAACTCCGTGAACCCAATGCTCACTTGCCAGATGGTCGTCCATTTCCCCCTCTATTCAACTTAAAACAAGAGgtgagtgtggctgcatcgtcttcttagctatgaatgaaggttacaaaaatctaaatgccctacaatacaattttatgaacaag-attcttgatagacagcttcattatgaatatatccatgatctgatattcactaagtaccttgtttagggtctattacatgtttatgttctatgtttacag

upper sequence: LOC_Os01g10840.1 (Oryza sativa), 5'ss of exon 11
lower sequence: GLYMA15G09090.1 (Glycine max), 5'ss of exon 11
TGACGCATGTGCACATTCCTTCTTTGATGAGCTACGAGAGCCCAATGCACGCCTGCCAAATGGTCGTCCATTCCCTCCTCTGTTCAACTTCAAGCATGAAgtaagtaaacgag--aacattttcaaacagtcgctttttatggt------acatttatatttacctgtcatggatgcttatcaatgctcatttctggtatgcag
||| |||||||||||| | ||||||||||| || ||||| ||| |||| ||||||||||||||||||||||| |||||||| || |||||||| || |||||||||     |   | | || |  | ||  |   |  | |||       | |||| ||   |||  |    |||    |  ||   | ||  ||| | |    
TGAAGCATGTGCACATCCTTTCTTTGATGAACTTCGAGAACCCCATGCTCGCCTGCCAAATGGTCGTCCATTTCCTCCTCTATTTAACTTCAAACAGGAAgtaagtccttaaattacctttcttcatcatacttgtgctctggcggtaaaatatttgtacagaccatttcaagattaggaataaaattgata-ctgttttt---

upper sequence: LOC_Os01g10840.1 (Oryza sativa), 5'ss of exon 11
lower sequence: GLYMA12G33950.1 (Glycine max), 5'ss of exon 11
TGACGCATGTGCACATTCCTTCTTTGATGAGCTACGAGAGCCCAATGCACGCCTGCCAAATGGTCGTCCATTCCCTCCTCTGTTCAACTTCAAGCATGAAgtaagtaaacgagaacattttcaaacagtcgctttt-tatggtaca---tttatatttacctgtcatggatgcttatcaatgctcatttctggtatgcag------------------------------------------------------------------------------------------------------
 || |||   |||||| | |||||||| ||||| || ||||||||||| || || || |||||||||||| | ||||| || |||||||| || || |||||| |||      |    ||||    | | | | |   ||   |||      | |||   ||||  || ||| || |   | | ||||| ||   |                                                                                                          
GGAAGCAATGGCACATCCTTTCTTTGACGAGCTTCGCGAGCCCAATGCCCGGCTACCTAATGGTCGTCCACTGCCTCCACTTTTCAACTTTAAACAGGAAgtatgtatctctaattggtttctcctattagatctgacataacacaaaacggaaattgcactgt--tgaatgtttgtttttacacatttgtgtggtctgaatatcagttaatcataacagcattgtgctgctgaaaggattatgtactttttattttctcatgatatccatataattttgtaatgaaaacatttgattgcag

upper sequence: LOC_Os01g10840.1 (Oryza sativa), 5'ss of exon 11
lower sequence: Vv10s0003g01480.t01 (Vitis vinifera), 5'ss of exon 11
TGACGCATGTGCACATTCCTTCTTTGATGAGCTACGAGAGCCCAATGCACGCCTGCCAAATGGTCGTCCATTCCCTCCTCTGTTCAACTTCAAGCATGAAgtaagtaaacg-agaacattttcaaacagtcgctttttatggtacatttatatttacctgtcatggat-gcttatcaatgctcatttctggtatgcag---
 || |||||||||||| | |||||||||||||| ||||| |||||||| ||||||||||||||||||||||| || ||||| ||||| || ||||| ||||||||       |    ||||| | |   |    || |||   |  | || | | |  | |  |     || |    |||    |   |  | |       
AGAAGCATGTGCACATCCTTTCTTTGATGAGCTCCGAGAACCCAATGCCCGCCTGCCAAATGGTCGTCCATTACCACCTCTCTTCAATTTTAAGCAGGAAgtaagggtttttattttatttttatatt-ttttattctatataatttctaaactaatttcttgtctccagcctgaacatgtctgtccataatttcttcatg

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|87035894|gb|CI190516.1|CI190516
EST:     GCCTGCCAAATGGTCGTCCATTCCCTCCTCTGTTCAACTTCAAGCATGAA                         CTAGCCAGCGCCTCTCCAGAACTCATCCACAGGCTCATACCGGATCATATC
genomic: GCCTGCCAAATGGTCGTCCATTCCCTCCTCTGTTCAACTTCAAGCATGAAgtaagtaaac ... tggtatgcagCTAGCCAGCGCCTCTCCAGAACTCATCCACAGGCTCATACCGGATCATATC
EST: gi|38478755|gb|CF962888.1|CF962888
EST:     GCCTGCCAAATGGTCGTCCATTCCCTCCTCTGTTCAACTTCAAGCATGAA                         CTAGCCAGCGCCTCTCCAGAACTCATCCACAGGCTCATACCGGATCATATC
genomic: GCCTGCCAAATGGTCGTCCATTCCCTCCTCTGTTCAACTTCAAGCATGAAgtaagtaaac ... tggtatgcagCTAGCCAGCGCCTCTCCAGAACTCATCCACAGGCTCATACCGGATCATATC
EST: gi|112786757|gb|EE591387.1|EE591387
EST:     GCCTGCCAAATGGTCGTCCATTCCCTCCTCTGTTCAACTTCAAGCATGAA                         CTAGCCAGCGCCTCTCCAGAACTCATCCACAGGCTCATACCGGATCATATC
genomic: GCCTGCCAAATGGTCGTCCATTCCCTCCTCTGTTCAACTTCAAGCATGAAgtaagtaaac ... tggtatgcagCTAGCCAGCGCCTCTCCAGAACTCATCCACAGGCTCATACCGGATCATATC
EST: gi|58604473|gb|CK015001.1|CK015001
EST:     GCCTGCCAAATGGTCGTCCATTCCCTCCTCTGTTCAACTTCAAGCATGAA                         CTAGCCAGCGCCTCTCCAGAACTCATCCACAGGCTCATACCGGATCATATC
genomic: GCCTGCCAAATGGTCGTCCATTCCCTCCTCTGTTCAACTTCAAGCATGAAgtaagtaaac ... tggtatgcagCTAGCCAGCGCCTCTCCAGAACTCATCCACAGGCTCATACCGGATCATATC
EST: gi|29616356|gb|CB621368.1|CB621368
EST:     GCCTGCCAAATGGTCGTCCATTCCCTCCTCTGTTCAACTTCAAGCATGAA                         CTAGCCGGCGCCTCTCCAGAACTCATCCACAGGCTCATACCGGATCATATC
genomic: GCCTGCCAAATGGTCGTCCATTCCCTCCTCTGTTCAACTTCAAGCATGAAgtaagtaaac ... tggtatgcagCTAGCCAGCGCCTCTCCAGAACTCATCCACAGGCTCATACCGGATCATATC
EST: gi|58667409|gb|CK056095.1|CK056095
EST:     GCCTGCCAAATGGTCGTCCATTCCCTCCTCTGTTCAACTTCAAGCATGAA                         CTAGCCAGCGCCTCTCCAGAACTCATCCACAGGCTCATACCGGATCATATC
genomic: GCCTGCCAAATGGTCGTCCATTCCCTCCTCTGTTCAACTTCAAGCATGAAgtaagtaaac ... tggtatgcagCTAGCCAGCGCCTCTCCAGAACTCATCCACAGGCTCATACCGGATCATATC
EST: gi|58604067|gb|CK014595.1|CK014595
EST:     GCCTGCCAAATGGTCGTCCATTCCCTCCTCTGTTCAACTTCAAGCATGAA                         CTAGCCAGCGCCTCTCCAGAACTCATCCACAGGCTCATACCGGATCATATC
genomic: GCCTGCCAAATGGTCGTCCATTCCCTCCTCTGTTCAACTTCAAGCATGAAgtaagtaaac ... tggtatgcagCTAGCCAGCGCCTCTCCAGAACTCATCCACAGGCTCATACCGGATCATATC
EST: gi|218485319|gb|FG946192.1|FG946192
EST:     GCCTGCCAAATGGTCGTCCATTCCCTCCTCTGTTCAACTTCAAGCATGAA                         CTAGCCAGCGCCTCTCCAGAACTCATCCACAGGCTCATACCGGATCATATC
genomic: GCCTGCCAAATGGTCGTCCATTCCCTCCTCTGTTCAACTTCAAGCATGAAgtaagtaaac ... tggtatgcagCTAGCCAGCGCCTCTCCAGAACTCATCCACAGGCTCATACCGGATCATATC
EST: gi|58601487|gb|CK012015.1|CK012015
EST:     GCCTGCCAAATGGTCGTCCATTCCCTCCTCTGTTCAACTTCAAGCATGAA                         CTAGCCAGCGCCTCTCCAGAACTCATCCACAGGCTCATACCGGATCATATC
genomic: GCCTGCCAAATGGTCGTCCATTCCCTCCTCTGTTCAACTTCAAGCATGAAgtaagtaaac ... tggtatgcagCTAGCCAGCGCCTCTCCAGAACTCATCCACAGGCTCATACCGGATCATATC
EST: gi|218482065|gb|FG957114.1|FG957114
EST:     CCTGCCAAATGGTCGTCCATTCCCTCCTCTGTTCAACTTCAAGCAATGAA                         CTAGCCAGCGCCTCTCCAGAACTCATCCACAGGCTCATACCGGATCATAT
genomic: CCTGCCAAATGGTCGTCCATTCCCTCCTCTGTTCAACTTCAAGCA-TGAAgtaagtaaac ... tggtatgcagCTAGCCAGCGCCTCTCCAGAACTCATCCACAGGCTCATACCGGATCATAT
EST: gi|58676242|gb|CK064929.1|CK064929
EST:     GCCTGCCAAATGGTCGTCCATTCCCTCCTCTGTTCAACTTCAAGCATGAA                         CTAGCCAGCGCCTCTCCAGAACTCATCCACAGGCTCATACCGGATCATATC
genomic: GCCTGCCAAATGGTCGTCCATTCCCTCCTCTGTTCAACTTCAAGCATGAAgtaagtaaac ... tggtatgcagCTAGCCAGCGCCTCTCCAGAACTCATCCACAGGCTCATACCGGATCATATC
EST: gi|218485963|gb|FG956967.1|FG956967
EST:     GCCTGCCAAATGGTCGTCCATTCCCTCCTCTGTTCAACTTCAAGCATGAA                         CTAGCCAGCGCCTCTCCAGAACTCATCCACAGGCTCATACCGGATCATATC
genomic: GCCTGCCAAATGGTCGTCCATTCCCTCCTCTGTTCAACTTCAAGCATGAAgtaagtaaac ... tggtatgcagCTAGCCAGCGCCTCTCCAGAACTCATCCACAGGCTCATACCGGATCATATC
EST: gi|218490655|gb|FG954523.1|FG954523
EST:     GCCTGCCAAATGGTCGTCCATTCCCTCCTCTGTTCAACTTCAAGCATGAA                         CTAGCCAGCGCCTCTCCAGAACTCATCCACAGGCTCATACCGGATCATATC
genomic: GCCTGCCAAATGGTCGTCCATTCCCTCCTCTGTTCAACTTCAAGCATGAAgtaagtaaac ... tggtatgcagCTAGCCAGCGCCTCTCCAGAACTCATCCACAGGCTCATACCGGATCATATC
EST: gi|58591644|gb|CF989952.1|CF989952
EST:     GCCTGCCAAATGGTCGTCCATTCCCTCCTCTGTTCAACTTCAAGCATGAA                         CTAGCCAGCGCCTCTCCAGAACTCATCCACAGGCTCATACCGGATCATATC
genomic: GCCTGCCAAATGGTCGTCCATTCCCTCCTCTGTTCAACTTCAAGCATGAAgtaagtaaac ... tggtatgcagCTAGCCAGCGCCTCTCCAGAACTCATCCACAGGCTCATACCGGATCATATC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGACGCATGTGCACATTCCTTCTTTGATGAGCTACGAGAGCCCAATGCACGCCTGCCAAATGGTCGTCCATTCCCTCCTCTGTTCAACTTCAAGCATGAAgtaagtaaacgagaacattttcaaacagtcgctttttatggtacatttatatttacctgtcatggatgcttatcaatgctcatttctggtatgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTCCTC