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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGTTGAGGAGTATCACATAGATGGATTTCGATTTGACCTTGCAAGTGTTCTTTGTCGTGGACCAGATGGTTGTCCTCTTGATGCACCTCCACTCATCAAGgtataatgtagatgcagactttaggtttgaacactaaatatgtatggctgcttaccaagcctgtgcagaccgaattttgtttgtctaaataagtgaattt...

Basic information

species Oryza sativa
transcript LOC_Os09g29404.1
intron # 12
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os09g29404.1 (Oryza sativa), 5'ss of exon 12
lower sequence: GRMZM2G150796_T03 (Zea mays), 5'ss of exon 12
GGTTGAGGAGTATCACATAGATGGATTTCGATTTGACCTTGCAAGTGTTCTTTGTCGTGGACCAGATGGTTGTCCTCTTGATGCACCTCCACTCATCAAGgtataatgtagatgcagactttaggtttgaacactaaatatgtatggctgcttaccaagcctgtgcagaccgaattttgtttgtctaaataagtgaattt---------
|||| ||||||||||||||||||||||||| ||||||||||| ||||||||||||||||||||||||||  |||||||||||||||||||||| || ||||||     |   |||| |  | | |  ||  || |   | | |     |   |  ||    |||||      | |      |   | ||  | |  ||||         
GGTTAAGGAGTATCACATAGATGGATTTCGGTTTGACCTTGCGAGTGTTCTTTGTCGTGGACCAGATGGCAGTCCTCTTGATGCACCTCCACTTATTAAGgtac----ttcttgca-atatcaagcctg--caatggtttttttcctttagctgtcatttttgtgcttttttagtc--agataaatgaagtactatatttgctgcaaac

upper sequence: LOC_Os09g29404.1 (Oryza sativa), 5'ss of exon 12
lower sequence: GLYMA06G10540.1 (Glycine max), 5'ss of exon 10
GGTTGAGGAGTATCACATAGATGGATTTCGATTTGACCTTGCAAGTGTTCTTTGTCGTGGACCAGATGGTTGTCCTCTTGATGCACCTCCACTCATCAAGgta--taatgtagatgcagactttaggtttgaacactaaatatgtatggctgcttaccaagcctgtgcagaccgaattttgtttgtctaaataagtgaattt---
|||    || || ||  | ||||||||||||||||| ||||||||||| || ||||| |||   ||||| |  || ||  ||||||| ||||| || | ||||  ||||  | ||||| |   ||  ||| |  | |    |  | |   |   ||  |  | | |   |   |   |  ||| || ||  | ||  | ||    
GGTCACCGAATACCATGTGGATGGATTTCGATTTGATCTTGCAAGTGTCCTGTGTCGAGGAATTGATGGCTCCCCCCTCAATGCACCCCCACTTATTAGGgtaaataattaatatgcacaagctatatttaatgagt--tcagttgttattttctaggacacttattgtgcttg---tcagttagtttagttcagccatttgaga

upper sequence: LOC_Os09g29404.1 (Oryza sativa), 5'ss of exon 12
lower sequence: Vv18s0001g06520.t01 (Vitis vinifera), 5'ss of exon 13
GGTTGAGGAGTATCACATAGATGGATTTCGATTTGACCTTGCAAGTGTTCTTTGTCGTGGACCAGATGGTTGTCCTCTTGATGCACCTCCACTCATCAAGgtataatgtagatgcagactttaggtttgaacactaaatatgtatggctgcttaccaagcctgtgcagaccgaattttgtttgtctaaataagtgaattt--
|||    ||||||||  | ||||||||||||||||| || || || ||||||||||| ||| ||||||||| ||| ||| |||| || ||| | || | ||||     |  ||  | | ||||  |     |  |  | |   ||| ||||  ||  ||| | |        |  | ||   || | || |||  |   |  
GGTCATTGAGTATCATGTGGATGGATTTCGATTTGATCTGGCTAGCGTTCTTTGTCGAGGAACAGATGGTTCTCCACTTAATGCTCCCCCAATTATTAGGgtaagccatgtatataca-tttaaatacattctatccaaacagatgactgca-acatagcatctttttttaaatatatggaagtttgaagaagaaacaatga

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|218500325|gb|FG953825.1|FG953825
EST:     TTGTCGTGGACCAGATGGTTGTCCTCTTGATGCACCTCCACTCATCAAG                         GAAATTGCCAAAGATGCTGTATTATCTAGATGTAAGATCATTGCTGAACCT
genomic: TTGTCGTGGACCAGATGGTTGTCCTCTTGATGCACCTCCACTCATCAAGgtataatgta ... ttggttgtagGAAATTGCCAAAGATGCTGTATTATCTAGATGTAAGATCATTGCTGAACCT
EST: gi|58587143|gb|CF985451.1|CF985451
EST:     GGGTGCGTGGACCAGATGGTTGTCCTCTTGATGCACCTCCACTCATCAAG                         GAAATTGCCAAAGATGCTGTATTATCTAGATGTAAGATCATTGCTGAACCT
genomic: TTGT-CGTGGACCAGATGGTTGTCCTCTTGATGCACCTCCACTCATCAAGgtataatgta ... ttggttgtagGAAATTGCCAAAGATGCTGTATTATCTAGATGTAAGATCATTGCTGAACCT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGTTGAGGAGTATCACATAGATGGATTTCGATTTGACCTTGCAAGTGTTCTTTGTCGTGGACCAGATGGTTGTCCTCTTGATGCACCTCCACTCATCAAGgtataatgtagatgcagactttaggtttgaacactaaatatgtatggctgcttaccaagcctgtgcagaccgaattttgtttgtctaaataagtgaattt

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG