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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TCAGCAGATGATCTGCGTATAAATCTATGGAATTTGGAGATAAATAACCAGAGCTTCAATATTGTTGACGTGAAGCCTCCAAACATGGAAGACCTAACGGgtaactccatttagtaccttatttcttacatgatttgtgctcaactttgaattaatgtactgcagcatggataaaattgattgatggaagctttcttaat...

Basic information

species Oryza sativa
transcript LOC_Os06g36770.1
intron # 7
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os06g36770.1 (Oryza sativa), 5'ss of exon 7
lower sequence: GRMZM2G165418_T02 (Zea mays), 5'ss of exon 8
TCAGCAGATGATCTGCGTATAAATCTATGGAATTTGGAGATAAATAACCAGAGCTTCAATATTGTTGACGTGAAGCCTCCAAACATGGAAGACCTAACGGgtaactccatttagtaccttatttcttacatgatttgtgctcaactttg--aattaatgtactgcagcatgga--taaaattgattgatggaagctttcttaat
|||||||||||||| || |||||| ||||||| ||||| ||||| | ||||||||| || |||||||| ||||||||| ||||||||||||| ||||| ||||| |||| |||||  | || || ||  |  |||| | || |   |||  |||| |  |  || ||  | |   |   ||| |   |   |    ||   |  
TCAGCAGATGATCTCCGAATAAATTTATGGAACTTGGAAATAAACAGCCAGAGCTTTAACATTGTTGATGTGAAGCCTACAAACATGGAAGATCTAACAGgtaattccacttagt--cataatttttttaacatttatcctaagtgttgcaaatttacttgatgaagttttgccttcccatttaacaaaaaagagattgcaa--

upper sequence: LOC_Os06g36770.1 (Oryza sativa), 5'ss of exon 7
lower sequence: AT1G17720.2 (Arabidopsis thaliana), 5'ss of exon 7
TCAGCAGATGATCTGCGTATAAATCTATGGAATTTGGAGATAAATAACCAGAGCTTCAATATTGTTGACGTGAAGCCTCCAAACATGGAAGACCTAACGGgta----actccatttagtaccttatttcttacatgatttgtgctcaactttgaatta-atgt-----actgcagcatggataaaattgattgatggaagctttcttaat--------------------------------------
|| || |||||||||||  ||||||| ||||||||||| || |  |||||||| |||||||||||||| || |||||  |||||||||| ||| |||| ||||    ||| |   || |   |||  | |||| |  | ||  || | | |||| | | ||||     ||  |   |    ||  ||  |||  |   |  |||  |  |                                      
TCGGCTGATGATCTGCGAGTAAATCTCTGGAATTTGGAAATTAGCAACCAGAGTTTCAATATTGTTGATGTTAAGCCCACAAACATGGAGGACTTAACTGgtatgctacttctcctattttgttagatgttactttgtatggtcttaccattgattcatatgtcaacaacctccttacttttattatctatttttttcacgtttactgcttgtcgagcatgcttctaaatgctacatggtctgtgcag

upper sequence: LOC_Os06g36770.1 (Oryza sativa), 5'ss of exon 7
lower sequence: Vv09s0002g02470.t01 (Vitis vinifera), 5'ss of exon 7
TCAGCAGATGATCTGCGTATAAATCTATGGAATTTGGAGATAAATAACCAGAGCTTCAATATTGTTGACGTGAAGCCTCCAAACATGGAAGACCTAACGGgtaactccatttagtaccttatttcttacatg-atttgtgctcaactttgaattaatgtactgcagcatggataaaattgattgatggaagctttcttaat--
||||| ||||||||||| ||||| || ||||| ||||| || |  ||||| ||||||||||||||||| ||||||||| |||| ||||| || ||||| |||||    ||| | ||  |   |||| | ||  | || | |||    |  | ||  |||       |   |  |   || ||  ||    |||   || |   
TCAGCTGATGATCTGCGAATAAACCTTTGGAACTTGGAAATTAGCAACCAAAGCTTCAATATTGTTGATGTGAAGCCTGCAAATATGGAGGATCTAACTGgtaaaattatt-actaattatcttctgatattcagttatactctgtgtgtattttgtgtgtcttttccaaggcacttttaat--atatttgctaaattgacct

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|58675521|gb|CK064208.1|CK064208
EST:     GAAGCCTCCAAACATGGAAGACCTAACGG                         AGGTCATTACATGTGCGGAGTTCCACCCAACTCATTGTAATACACTGGCCT
genomic: GAAGCCTCCAAACATGGAAGACCTAACGGgtaactccat ... gatatttcagAGGTCATTACATGTGCGGAGTTCCACCCAACTCATTGTAATACACTGGCCT
EST: gi|2310581|gb|C26736.1|C26736
EST:     GAGCTTCAATATTGTTGACGTGAAGCCTCCAAACATGGAAGACCTAACGG                         AGGTCATTACATGTGCGGAGTTCCACCCAACTCATTGTAATACACTGGCCT
genomic: GAGCTTCAATATTGTTGACGTGAAGCCTCCAAACATGGAAGACCTAACGGgtaactccat ... gatatttcagAGGTCATTACATGTGCGGAGTTCCACCCAACTCATTGTAATACACTGGCCT
EST: gi|58687462|gb|CK076149.1|CK076149
EST:     GAGCTTCAATATTGTTGACGTGAAGCCTCCAAACATGGAAGACCTAACGG                         AGGTCATTACATGTGCGGAGTTCCACCCAACTCATTGTAATACACTGGCCT
genomic: GAGCTTCAATATTGTTGACGTGAAGCCTCCAAACATGGAAGACCTAACGGgtaactccat ... gatatttcagAGGTCATTACATGTGCGGAGTTCCACCCAACTCATTGTAATACACTGGCCT
EST: gi|218499339|gb|FG949286.1|FG949286
EST:     GAGCTTC-ATATTGTTGACGTGAAGCCTCCAAACATGGAAGACCTAACGG                         AGGTCACTTACATGTGCGGAGTTCCACCCAACTCATTGTAATACACTGGCC
genomic: GAGCTTCAATATTGTTGACGTGAAGCCTCCAAACATGGAAGACCTAACGGgtaactccat ... gatatttcagAGGTCA-TTACATGTGCGGAGTTCCACCCAACTCATTGTAATACACTGGCC
EST: gi|58660482|gb|CK049162.1|CK049162
EST:     GAGCTTCAATATTGTTGACGTGAAGCCTCCAAACATGGAAGACCTAACGG                         AGGTCATTACATGTGCGGAGTTCCACCCAACTCATTGTAATACACTGGCCT
genomic: GAGCTTCAATATTGTTGACGTGAAGCCTCCAAACATGGAAGACCTAACGGgtaactccat ... gatatttcagAGGTCATTACATGTGCGGAGTTCCACCCAACTCATTGTAATACACTGGCCT
EST: gi|66912957|gb|CX099805.1|CX099805
EST:     GAGCTTCAATATTGTTGACGTGAAGCCTCCAAACATGGAAGACCTAACGG                         AGGTCATTACATGTGCGGAGTTCCACCCAACTCATTGTAATACACTGGCCT
genomic: GAGCTTCAATATTGTTGACGTGAAGCCTCCAAACATGGAAGACCTAACGGgtaactccat ... gatatttcagAGGTCATTACATGTGCGGAGTTCCACCCAACTCATTGTAATACACTGGCCT
EST: gi|58593657|gb|CF991965.1|CF991965
EST:     GAAGCCTCCAAACATGGAAGACCTAACGG                         AGGTCATTACATGTGCGGAGTTCCACCCAGCTCATTGTAATACACTGGCCT
genomic: GAAGCCTCCAAACATGGAAGACCTAACGGgtaactccat ... gatatttcagAGGTCATTACATGTGCGGAGTTCCACCCAACTCATTGTAATACACTGGCCT
EST: gi|58588909|gb|CF987217.1|CF987217
EST:     GAGCTTCAATATTGTTGACGTGAAGCCTCCAAACATGGAAGACCTAACGG                         AGGTCATTACAT
genomic: GAGCTTCAATATTGTTGACGTGAAGCCTCCAAACATGGAAGACCTAACGGgtaactccat ... gatatttcagAGGTCATTACAT
EST: gi|58674786|gb|CK063473.1|CK063473
EST:     GAAGCCTCCAAACATGGAAGA-CTAACGG                         AGGTCATTACATGTGCGGAGTTCCACCCAGCTCATTGTAATACACTGGCCT
genomic: GAAGCCTCCAAACATGGAAGACCTAACGGgtaactccat ... gatatttcagAGGTCATTACATGTGCGGAGTTCCACCCAACTCATTGTAATACACTGGCCT
EST: gi|58688813|gb|CK077500.1|CK077500
EST:     GAGCTTCAATATTGTTGACGTGAAGCCTCCAAACATGGAAGACCTAACGG                         AGGTCATTACATGTGCGGAGTTCCACCCAACTCATTGTAATACACTGGCCT
genomic: GAGCTTCAATATTGTTGACGTGAAGCCTCCAAACATGGAAGACCTAACGGgtaactccat ... gatatttcagAGGTCATTACATGTGCGGAGTTCCACCCAACTCATTGTAATACACTGGCCT
EST: gi|33796287|gb|CF324010.1|CF324010
EST:     GAGCTTCAATATTGTTGACGTGAAGCCTCCAAACATGGAAGACCTAACGG                         AGGTCATTACATGTNGCGGAGTTCCACCCAACTCATTGTAATACACTGGCC
genomic: GAGCTTCAATATTGTTGACGTGAAGCCTCCAAACATGGAAGACCTAACGGgtaactccat ... gatatttcagAGGTCATTACATGT-GCGGAGTTCCACCCAACTCATTGTAATACACTGGCC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TCAGCAGATGATCTGCGTATAAATCTATGGAATTTGGAGATAAATAACCAGAGCTTCAATATTGTTGACGTGAAGCCTCCAAACATGGAAGACCTAACGGgtaactccatttagtaccttatttcttacatgatttgtgctcaactttgaattaatgtactgcagcatggataaaattgattgatggaagctttcttaat

- - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA