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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGAAAATGCTCTTCGATTATTCTCACCAGCGCTTGCGATCGTTGATGAACATCTGACCAGACACTTGCCAAAGCAATGGTTAACTTCTTTAGCAATTGAGgtaccttaatttctctcttttctgtgagtgagtcttgtgcacattgaccagaatttgtttggcgcatctgagctctactttagtagtctctgtcatcttc...

Basic information

species Oryza sativa
transcript LOC_Os05g01470.2
intron # 8
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os05g01470.2 (Oryza sativa), 5'ss of exon 8
lower sequence: GRMZM2G098039_T01 (Zea mays), 5'ss of exon 8
AGAAAATGCTCTTCGATTATTCTCACCAGCGCTTGCGATCGTTGATGAACATCTGACCAGACACTTGCCAAAGCAATGGTTAACTTCTTTAGCAATTGAGgtaccttaatttctctcttttctgtgagtgagtcttgtgcacattgaccagaatttgtttggcgcatctgagctctactttagtagtctctgtcatcttc
||| |||||||||| ||| |||||||| |||||||| || |||||||||||| | |||||||||||||| |||||||||||||| ||||||||||||||||||||||  || |||  || | | || ||||||  |     ||| |  | | ||  |||  |   | |    |  |  |||   | | || |        
AGAGAATGCTCTTCAATTGTTCTCACCGGCGCTTGCAATTGTTGATGAACATTTAACCAGACACTTGCCCAAGCAATGGTTAACATCTTTAGCAATTGAGgtaccttggttactccattatatctgtgtgagttgt-----catgggtctggat--gttctgtagaac---acatttttttgtgaatttcag--------

upper sequence: LOC_Os05g01470.2 (Oryza sativa), 5'ss of exon 8
lower sequence: GLYMA12G28490.1 (Glycine max), 5'ss of exon 8
AGAAAATGCTCTTCGATTATTCTCACCAGCGCTTGCGATCGTTGATGAACATCTGACCAGACACTTGCCAAAGCAATGGTTAACTTCTTTAGCAATTGAGgtacctta-atttctctcttttctgtgagtgagtcttgtgcacattgaccagaatttgtttggcgcatctgagctctactttagtagtctctgtcatcttc--
 || ||||||||||| || || |||||    |||||  | |||||||||||||||||  ||||||| || | ||| |||||||| |||| |||| ||||||||    | |    |  |||     |   |||   |  |  | |||     | || ||| |     |||  |  | |  |  || | |  |  | || |    
TGAGAATGCTCTTCGCTTGTTTTCACCTCGCCTTGCAGTTGTTGATGAACATCTGACTCGACACTTACCTAGGCAGTGGTTAACATCTTCAGCACTTGAGgtatggaataggcatgccttggtcttttttgaacttgattaatattttgttgcatctgtattat-tatcccaa-tgtgttgaagaaatg-caattatgtgaac

upper sequence: LOC_Os05g01470.2 (Oryza sativa), 5'ss of exon 8
lower sequence: Vv12s0035g01920.t01 (Vitis vinifera), 5'ss of exon 9
AGAAAATGCTCTTCGATTATTCTCACCAGCGCTTGCGATCGTTGATGAACATCTGACCAGACACTTGCCAAAGCAATGGTTAACTTCTTTAGCAATTGAGgta--ccttaatttctctcttttctgtgagtgagtcttgtgcacattgaccagaatttgtttggcgcatctgagctctactttagtagtctctgtcatcttc-----
 || |||||||||||||||||||||||    ||||| || ||||||||| |||||||  ||||  | ||||  || |||||||| || ||   ||||||||||  || |||||| |     |  | |   |     || |  |  |   |||   ||        |  | |||  | |    ||  | |   |  ||  |||     
TGAGAATGCTCTTCGATTATTCTCACCCCGTCTTGCAATTGTTGATGAAGATCTGACTCGACATCTTCCAAGACAGTGGTTAACATCCTTGAAAATTGAGgtatgccctaatttgttatactcttatactttgtatttttatatgt---ccaagcttcacc--atgattttgatttttttacta--aattgattgcacattcacata

upper sequence: LOC_Os05g01470.2 (Oryza sativa), 5'ss of exon 8
lower sequence: Vv12s0035g02060.t01 (Vitis vinifera), 5'ss of exon 1
AGAAAATGCTCTTCGATTATTCTCACCAGCGCTTGCGATCGTTGATGAACATCTGACCAGACACTTGCCAAAGCAATGGTTAACTTCTTTAGCAATTGAGgtac--cttaatttctctcttttctgtgagtgagtcttgtgcacattgaccagaatttgtttggcgcatctgagctctactttagtagtctctgtcatcttc--
 || |||||||||| ||||||||||||    ||||| || |||||||||||||||||  ||||  | ||||  || |||||||| || ||   ||||||||||   | ||||||       |  | |   |     || |  |  |   |||   ||      |    |      | |  ||| ||| |   | |  |   |  
TGAGAATGCTCTTCAATTATTCTCACCCCGTCTTGCAATTGTTGATGAACATCTGACTTGACATCTTCCAAGACAGTGGTTAACATCCTTGAAAATTGAGgtatggcataatttgcaatgctcttatactttgtatttttatatgt---ccaagcttcaccatg-attttaatttttttttttggtactaaatttattgcacat

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|33675488|gb|CF303727.1|CF303727
EST:     ATCTGACCAGACACTTGCCAAAGCAATGGTTAACTTCTTTAGCAATTGAG                         GGAAAAGCCAAAGATACAGTTACTGTAATTGAGGCACCACGCCAATCTGAT
genomic: ATCTGACCAGACACTTGCCAAAGCAATGGTTAACTTCTTTAGCAATTGAGgtaccttaat ... tgaatttcagGGAAAAGCCAAAGATACAGTTACTGTAATTGAGGCACCACGCCAATCTGAT
EST: gi|33675097|gb|CF303336.1|CF303336
EST:     ATCTGACCAGACACTTGCCAAAGCAATGGTTAACTTCTTTAGCAATTGAG                         GGAAAAGCCAAAGATACAGTTACTGTAATTGAGGCACCACGCCAATCTGAT
genomic: ATCTGACCAGACACTTGCCAAAGCAATGGTTAACTTCTTTAGCAATTGAGgtaccttaat ... tgaatttcagGGAAAAGCCAAAGATACAGTTACTGTAATTGAGGCACCACGCCAATCTGAT
EST: gi|33675151|gb|CF303390.1|CF303390
EST:     ATCTGACCAGACACTTGCCAAAGCAATGGTTAACTTCTTTAGCAATTGAG                         GGAAAAGCCAAAGATACAGTTACTGTAATTGAGGCACCACGCCAATCTGAT
genomic: ATCTGACCAGACACTTGCCAAAGCAATGGTTAACTTCTTTAGCAATTGAGgtaccttaat ... tgaatttcagGGAAAAGCCAAAGATACAGTTACTGTAATTGAGGCACCACGCCAATCTGAT
EST: gi|33674758|gb|CF302997.1|CF302997
EST:     ATCTGACCAGACACTTGCCAAAGCAATGGTTAACTTCTTTAGCAATTGAG                         GGAAAAGCCAAAGATACAGTTACTGTAATTGAGGCACCACGCCAATCTGAT
genomic: ATCTGACCAGACACTTGCCAAAGCAATGGTTAACTTCTTTAGCAATTGAGgtaccttaat ... tgaatttcagGGAAAAGCCAAAGATACAGTTACTGTAATTGAGGCACCACGCCAATCTGAT
EST: gi|58609748|gb|CK037781.1|CK037781
EST:     GGTT-ACTTCTTTAGCAATTGAG                         GGAAAAGCCAAAGATACAGTTACTGTAATTGAGGCACCACGCCAATCTGAT
genomic: GGTTAACTTCTTTAGCAATTGAGgtaccttaat ... tgaatttcagGGAAAAGCCAAAGATACAGTTACTGTAATTGAGGCACCACGCCAATCTGAT
EST: gi|4715491|gb|AU056608.1|AU056608
EST:     ATCTGACCAGACACTTGCCAAAGCAATGGTTAACTTCTTTAGCAATTGAG                         GGAAAAGCCAAAGATACAGTTACTGTAATTGAGGCACCACGCCAATCTGAT
genomic: ATCTGACCAGACACTTGCCAAAGCAATGGTTAACTTCTTTAGCAATTGAGgtaccttaat ... tgaatttcagGGAAAAGCCAAAGATACAGTTACTGTAATTGAGGCACCACGCCAATCTGAT
EST: gi|11442586|gb|BF430489.1|BF430489
EST:     GGTTAACTTCTTTAGCAATTGAG                         GGAAAAGCCAAAGATACAGTTACTGTAATTGAGGCACCACGCCAATCTGAT
genomic: GGTTAACTTCTTTAGCAATTGAGgtaccttaat ... tgaatttcagGGAAAAGCCAAAGATACAGTTACTGTAATTGAGGCACCACGCCAATCTGAT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGAAAATGCTCTTCGATTATTCTCACCAGCGCTTGCGATCGTTGATGAACATCTGACCAGACACTTGCCAAAGCAATGGTTAACTTCTTTAGCAATTGAGgtaccttaatttctctcttttctgtgagtgagtcttgtgcacattgaccagaatttgtttggcgcatctgagctctactttagtagtctctgtcatcttc

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