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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CATCATCTCTGCAATTGAGTTTGATAAATCTGGTGATCATCTTGCCACCGGAGACAGAGGAGGACGTGTTGTTTTATTTGAAAGGACAGATGCTCGGGATgtaagcaccattagttgaacttctcttgctcaatttcattattttatactcatgaaagtctatctgttagcag

Basic information

species Oryza sativa
transcript LOC_Os06g36770.1
intron # 2
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 2
lower sequence: GRMZM2G165418_T01 (Zea mays), 5'ss of exon 2
CATCATCTCTGCAATTGAGTTTGATAAATCTGGTGATCATCTTGCCACCGGAGACAGAGGAGGACGTGTTGTTTTATTTGAAAGGACAGATGCTCGGGATgtaagcaccattagt-tgaacttctcttg--ctcaatttcattattttatactcatgaaagtctatctgttagcag
|||||| ||||||||||| ||||| ||||||||||| ||||||||||| || || | |||||||||||| |||||||||||||||||||||| |||||||||||||||||   || ||||||| |||||   |  |||| | ||||||   || ||  ||||   | |   ||   
CATCATATCTGCAATTGAATTTGACAAATCTGGTGACCATCTTGCCACTGGGGATAAAGGAGGACGTGTGGTTTTATTTGAAAGGACAGATGTTCGGGATgtaagcaccacatgtatgaacttatcttggttttgattttaatatttttccctaat--aagttgttataccag---

upper sequence: LOC_Os06g36770.1 (Oryza sativa), 5'ss of exon 2
lower sequence: GRMZM2G165418_T02 (Zea mays), 5'ss of exon 3
CATCATCTCTGCAATTGAGTTTGATAAATCTGGTGATCATCTTGCCACCGGAGACAGAGGAGGACGTGTTGTTTTATTTGAAAGGACAGATGCTCGGGATgtaagcaccattagt-tgaacttctcttg--ctcaatttcattattttatactcatgaaagtctatctgttagcag
|||||| ||||||||||| ||||| ||||||||||| ||||||||||| || || | |||||||||||| |||||||||||||||||||||| |||||||||||||||||   || ||||||| |||||   |  |||| | ||||||   || ||  ||||   | |   |||||
CATCATATCTGCAATTGAATTTGACAAATCTGGTGACCATCTTGCCACTGGGGATAAAGGAGGACGTGTGGTTTTATTTGAAAGGACAGATGTTCGGGATgtaagcaccacatgtatgaacttatcttggttttgattttaatatttttccctaat--aagttgttataccagcag

upper sequence: LOC_Os06g36770.1 (Oryza sativa), 5'ss of exon 2
lower sequence: Vv11s0016g02550.t01 (Vitis vinifera), 5'ss of exon 2
CATCATCTCTGCAATTGAGTTTGATAAATCTGGTGATCATCTTGCCACCGGAGACAGAGGAGGACGTGTTGTTTTATTTGAAAGGACAGATGCTCGGGATgtaagc------accattagttgaacttctcttgctcaatttcat--tattttatactcatgaaagtctatctgttagcag----------------------------------------------------
|||||| ||||| ||||||||||| ||| |||| || |||||||| || || ||  | || ||||| || ||||||||||||||||||||     |||||||| |       | ||   | ||  | | | ||  |  ||||  |  |||||| |     |  |  |||  |  | |                                                        
CATCATTTCTGCTATTGAGTTTGACAAAACTGGAGACCATCTTGCGACTGGTGATCGTGGGGGACGGGTGGTTTTATTTGAAAGGACAGACAAGAGGGATgtatgttgttttatcacatgctgtgccttttttttttcattttctcttattttgtttcattttatttctggccttgatttacttctatatcacttcttgttgcaccattttaatgtaattgcataatgtatag

upper sequence: LOC_Os06g36770.1 (Oryza sativa), 5'ss of exon 2
lower sequence: Vv09s0002g02470.t01 (Vitis vinifera), 5'ss of exon 2
CATCATCTCTGCAATTGAGTTTGATAAATCTGGTGATCATCTTGCCACCGGAGACAGAGGAGGACGTGTTGTTTTATTTGAAAGGACAGATGCTCGGGATgtaagcaccattagttgaacttctcttgctcaatttcattattttatactcatgaaa-gtctatctgttagcag------------------------------------------
 || || ||||||||||||||||||||||||||||| || ||||| || || ||  | || || || || ||| ||||||| ||||| ||| |   ||||||  |   | ||  |   ||| ||  |  | | ||||  |||   |   | ||     | ||  |||||                                               
TATTATTTCTGCAATTGAGTTTGATAAATCTGGTGACCACCTTGCTACTGGTGATCGTGGGGGCCGGGTGGTTCTATTTGAGAGGACTGATACAAAGGATgtgcgt-tcttttttaacactactggtctttagtttctgtatccaaacttgataggttgccttactgttcttgtttctttcaatattatgatatctttatacactgtaatgtgtag

upper sequence: LOC_Os06g36770.1 (Oryza sativa), 5'ss of exon 2
lower sequence: PP1S138_11V6.1 (Physcomitrella patens), 5'ss of exon 2
CATCATCTCTGCAATTGAGTTTGATAAATCTGGTGATCATCTTGCCACCGGAGACAGAGGAGGACGTGTTGTTTTATTTGAAAGGACAGATGCTCGGGATgtaagcaccattagttg--aacttctcttgctcaatttcattattttatactcatgaaagtctatctgttagcag-----------------------------------------------------------------------------------------------------------------------
 |||||||| ||||||||||||||||||||||| || ||| | || || || ||  |||||||||||||||| || ||||| || || ||||     || || ||      |  |    |||||    || |  ||    |    ||||  |     | |||  ||| ||   |                                                                                                                        
TATCATCTCGGCAATTGAGTTTGATAAATCTGGGGAACATTTAGCAACTGGGGATCGAGGAGGACGTGTTGTGTTGTTTGACAGAACGGATGGCGTAGAGgtgagttttcgttttcacaaacttaggatgttggatgctgtagacttatctttcgctacgtcggtctctttaaacttgcgtctgagcagtacataaaattacagatcgtgctttgctagatgtttgaaaatgtccacatcctaagaaagaatataacacggtattcgtgctaatgcttatttttccttctgcag

upper sequence: LOC_Os06g36770.1 (Oryza sativa), 5'ss of exon 2
lower sequence: PP1S100_124V6.1 (Physcomitrella patens), 5'ss of exon 2
CATCATCTCTGCAATTGAGTTTGATAAATCTGGTGATCATCTTGCCACCGGAGACAGAGGAGGACGTGTTGTTTTATTTGAAAGGACAGATGCTCGGGATgtaagcaccattagttgaacttctcttgctcaatttcattattttatactcatgaaagtctatctgttagcag------------------------------
|||||||||||| ||||||||||||||| |||| || ||| | || || |||||| |||||||||| |||||  | ||||| ||||| ||||   | ||||||||  || ||   || | |||    |  |     | || || |      |      | |||   | |||                                
CATCATCTCTGCTATTGAGTTTGATAAAACTGGAGAGCATTTGGCGACTGGAGACCGAGGAGGACGAGTTGTGCTGTTTGAGAGGACGGATGGCAGAGATgtaaggcccgtt---tggatttcatccgtgccgaagcctttttgtgggtgtagagtgatatattgctgagcgtagatgtgtctgctgcaatcttcttgtgctg

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|58667099|gb|CK055785.1|CK055785
EST:     GAGACAGAGGAGGACGTGTTGTTTTATTTGAAAGGACAGATGCTCGGGAT                         AATGCCAGTCGGAGAGAAATGGAGAGACAAGATGCTCCGATTACTAGACAC
genomic: GAGACAGAGGAGGACGTGTTGTTTTATTTGAAAGGACAGATGCTCGGGATgtaagcacca ... ctgttagcagAATGCCAGTCGGAGAGAAATGGAGAGACAAGATGCTCCGATTACTAGACAC
EST: gi|88300529|gb|CI587333.1|CI587333
EST:     GAGACAGAGGAGGACGTGTTGTTTTATTTGAAAGGACAGATGCTCGGGAT                         AATGCCAGTCGGAGAGAAATGGAGAGAGAAGATGCTCCGATTACTAGACAC
genomic: GAGACAGAGGAGGACGTGTTGTTTTATTTGAAAGGACAGATGCTCGGGATgtaagcacca ... ctgttagcagAATGCCAGTCGGAGAGAAATGGAGAGACAAGATGCTCCGATTACTAGACAC
EST: gi|66912787|gb|CX099635.1|CX099635
EST:     GAGACAGAGGAGGACGTGTTGTTTTATTTGAAAGGACAGATGCTCGGGAT                         AATGCCAGTCGGAGAGAAATGGAGAGACAAGATGCTCCGATTACTAGACAC
genomic: GAGACAGAGGAGGACGTGTTGTTTTATTTGAAAGGACAGATGCTCGGGATgtaagcacca ... ctgttagcagAATGCCAGTCGGAGAGAAATGGAGAGACAAGATGCTCCGATTACTAGACAC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CATCATCTCTGCAATTGAGTTTGATAAATCTGGTGATCATCTTGCCACCGGAGACAGAGGAGGACGTGTTGTTTTATTTGAAAGGACAGATGCTCGGGATgtaagcaccattagttgaacttctcttgctcaatttcattattttatactcatgaaagtctatctgttagcag

- - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG