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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGCACAGGAAAGTAGGAAGGAAGAGCTGGAAAAGCTAATGCAAGACCAGGAAGCAATGAGGGCATCACTTCTGCAATGGTGCTATGCCAGCTACAGTGAGgtgcatgtctttttaggcttatttaataatcctgtcaacaatgacatttctttagagaagaacttttttattcttatgaatgtcatttttgtttcatgta...

Basic information

species Oryza sativa
transcript LOC_Os05g51530.2
intron # 8
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os05g51530.1 (Oryza sativa), 5'ss of exon 8
lower sequence: GRMZM2G128995_T01 (Zea mays), 5'ss of exon 8
AGCACAGGAAAGTAGGAAGGAAGAGCTGGAAAAGCTAATGCAAGACCAGGAAGCAATGAGGGCATCACTTCTGCAATGGTGCTATGCCAGCTACAGTGAGgtgcatgtctttttaggctta-tttaataatcctgtcaacaatgacatttctttagagaagaacttttttattcttatgaatgtcatttttgtttcatgta-------
||||||||||||| ||||| | ||| |||| |||||| |||||||||| ||||| |||||| |  | ||||| ||||||||||||||||||||||| ||||| | ||||||||    | || | || |  |     | ||||     |||  ||         | ||  |  ||||||  ||  ||| | || |  | ||        
AGCACAGGAAAGTCGGAAGCAGGAGATGGAGAAGCTACTGCAAGACCAAGAAGCCATGAGGACCACTCTTCTTCAATGGTGCTATGCCAGCTACAGCGAGgtacttgtcttttcctacataatctagtggtttgaacgacaactgtgttttcttt--------ccttaatgatcttattgattacatctctgctgtaagtgtcagtaa

upper sequence: LOC_Os05g51530.1 (Oryza sativa), 5'ss of exon 8
lower sequence: GRMZM2G144372_T01 (Zea mays), 5'ss of exon 8
AGCACAGGAAAGTAGGAAGGAAGAGCTGGAAAAGCTAATGCAAGACCAGGAAGCAATGAGGGCATCACTTCTGCAATGGTGCTATGCCAGCTACAGTGAGgtgcatgtctttttaggctta-tttaataatcctgtcaacaatgacatttctttagagaagaacttttttattcttatgaatgtcatttttgtttcatgta
||||||||||||  ||| | | ||| |||| |||||| ||| |||||| ||||| |||||| |  | ||||| || ||||| |||||||||||||| ||||| | ||||||||    | || | || |  ||||  | ||||   |||||||||    ||  | | | ||  |   ||    |   |   |||    | | 
AGCACAGGAAAGCCGGATGCAGGAGATGGAGAAGCTACTGCGAGACCAAGAAGCTATGAGGACCACTCTTCTTCAGTGGTGTTATGCCAGCTACAGCGAGgtacttgtcttttcctacataatctagtggtcctaacgacaactgcatttcttttcttaaagattctattgattacatttcagctgtaagtgtcagttat-

upper sequence: LOC_Os05g51530.1 (Oryza sativa), 5'ss of exon 8
lower sequence: GRMZM2G177912_T02 (Zea mays), 5'ss of exon 8
AGCACAGGAAAGTAGGAAGGAAGAGCTGGAAAAGCTAATGCAAGACCAGGAAGCAATGAGGGCATCACTTCTGCAATGGTGCTATGCCAGCTACAGTGAGgtgcat-gtctttttaggcttattt-aataatcctgtcaacaatgacatttctttagagaagaacttttttattcttatga-atgtcatttttgtt-tcatgta---
|||||| |||||||| ||| | ||| |||| ||| || ||| ||| |||||||  |||||| | || ||||||||||||||||||||||||||||||||||| | | |||||||    | ||||  | || ||||       ||||    |      | ||| | || |  | |  |  ||    ||||| ||||  | ||| |   
AGCACAAGAAAGTAGAAAGCAGGAGATGGAGAAGTTACTGCTAGAGCAGGAAGTTATGAGGACCTCGCTTCTGCAATGGTGCTATGCCAGCTACAGTGAGgtacttagtcttttccaacatattccagtagtcct-------atgatccctacccgcaaaagcatttctgcaatgatcagatgcttcattgttgtggttatgcagtt

upper sequence: LOC_Os05g51530.1 (Oryza sativa), 5'ss of exon 8
lower sequence: Vv14s0068g01280.t01 (Vitis vinifera), 5'ss of exon 8
AGCACAGGAAAGTAGGAAGGAAGAGCTGGAAAAGCTAATGCAAGACCAGGAAGCAATGAGGGCATCACTTCTGCAATGGTGCTATGCCAGCTACAGTGAGgtgcatgtctttttaggcttatttaataatcctgtcaacaatgacatttctttagaga---agaacttttttattcttatgaatgtcatttttgtttcatgta-
||||||||||||||||||||||||| |||||||  | |||| |||||||||| || | |||    | ||| |||||||||||||| |||| ||  | |||||       |||      || |||  |     ||  |  | ||| || || | | ||    |  |   ||| ||   |||   |  |||     |   |  || 
AGCACAGGAAAGTAGGAAGGAAGAGTTGGAAAAATTGATGCGAGACCAGGAAACATTTAGGAGCACTCTTTTGCAATGGTGCTATACCAGTTATGGGGAGgt----aattttcccaatttttttttttcctgtgaaataattgaaatatcatgaaagtttcaagaggctttgatatgtatttgttacatgaaaatagaaactaa

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|86841855|gb|CI337494.1|CI337494
EST:     TGCTATGCCAGCTACAGTGAG                         GTATTCAGTTCCTGGATGCACTTCTGTGCTGTGCGTGTCTTTGTAGAGAGC
genomic: TGCTATGCCAGCTACAGTGAGgtgcatgtct ... tattctgcagGTATTCAGTTCCTGGATGCACTTCTGTGCTGTGCGTGTCTTTGTAGAGAGC
EST: gi|29621004|gb|CB626015.1|CB626015
EST:     AAGCAATGAGGGCATCACTTCTGCAATGGTGCTATGCCAGCTACAGTGAG                         GTATTCAGTTCCTGGATGCACTTCTGTGCTGTGCGTGTCTTTGTAGAGAGC
genomic: AAGCAATGAGGGCATCACTTCTGCAATGGTGCTATGCCAGCTACAGTGAGgtgcatgtct ... tattctgcagGTATTCAGTTCCTGGATGCACTTCTGTGCTGTGCGTGTCTTTGTAGAGAGC
EST: gi|38476572|gb|CF960705.1|CF960705
EST:     AAGCAATGAGGGCATCACTTCTGCAATGGTGCTATGCCAGCTACAGTGAG                         GTATTCAGTTCCTGGATGCACTTCTGTGCTGTGCGTGTCTTTGTAGAGAGC
genomic: AAGCAATGAGGGCATCACTTCTGCAATGGTGCTATGCCAGCTACAGTGAGgtgcatgtct ... tattctgcagGTATTCAGTTCCTGGATGCACTTCTGTGCTGTGCGTGTCTTTGTAGAGAGC
EST: gi|44674895|gb|CR288329.1|CR288329
EST:     AAGCAATGA-GGCATCACTTCTGCAATGGTGCTATGCCAGCTACAGTGAG                         GTA-TCAG-TCCTGGATGCACTTCTGTGCTGTGCGTGTCTTTGTAGAGAGC
genomic: AAGCAATGAGGGCATCACTTCTGCAATGGTGCTATGCCAGCTACAGTGAGgtgcatgtct ... tattctgcagGTATTCAGTTCCTGGATGCACTTCTGTGCTGTGCGTGTCTTTGTAGAGAGC
EST: gi|29656670|gb|CB652945.1|CB652945
EST:     AAGCAATGAGGGCATCACTTCTGCAATGGTGCTATGCCAGCTACAGTGAG                         GTATTCAGTTCCT
genomic: AAGCAATGAGGGCATCACTTCTGCAATGGTGCTATGCCAGCTACAGTGAGgtgcatgtct ... tattctgcagGTATTCAGTTCCT
EST: gi|86412678|gb|CI067083.1|CI067083
EST:     AAGCAATGAGGGCATCACTTCTGTAATGGTGCTATGCCAGCTACAGTGAG                         GTATTCAGTTCCTGGATGCACTTCTGTGCTGTGCGTGTCTTTGTAGAGAGC
genomic: AAGCAATGAGGGCATCACTTCTGCAATGGTGCTATGCCAGCTACAGTGAGgtgcatgtct ... tattctgcagGTATTCAGTTCCTGGATGCACTTCTGTGCTGTGCGTGTCTTTGTAGAGAGC
EST: gi|88762888|gb|CI772444.1|CI772444
EST:     AAGCAATGAGGGCATCACTTCTGCAATGGTGCTATGCCAGCTACAGTGAG                         GTATTCAGTTCCTGGATGCACTTCTGTGCTGTGCGTGTCTTTGTAGAGAGC
genomic: AAGCAATGAGGGCATCACTTCTGCAATGGTGCTATGCCAGCTACAGTGAGgtgcatgtct ... tattctgcagGTATTCAGTTCCTGGATGCACTTCTGTGCTGTGCGTGTCTTTGTAGAGAGC
EST: gi|218479849|gb|FG959490.1|FG959490
EST:     AACCAATGAGGGCATCACTTCTGCAATGGTGCTATGCCAGCTACAGTGAG                         GTATTCAGTTCCTGGATGCACTTCTGTGCTGTGCGTGTCTTTGTAAAGAGC
genomic: AAGCAATGAGGGCATCACTTCTGCAATGGTGCTATGCCAGCTACAGTGAGgtgcatgtct ... tattctgcagGTATTCAGTTCCTGGATGCACTTCTGTGCTGTGCGTGTCTTTGTAGAGAGC
EST: gi|29674593|gb|CB670868.1|CB670868
EST:     AAGCAATGAGGGCATCACTTCTGCAATGGTGCTATGCCAGCTACAGTGAG                         GTATTCAGTTCCTGGATGCACTTCTGTGCTGTGCGTGTCTTTGTAGAGAGC
genomic: AAGCAATGAGGGCATCACTTCTGCAATGGTGCTATGCCAGCTACAGTGAGgtgcatgtct ... tattctgcagGTATTCAGTTCCTGGATGCACTTCTGTGCTGTGCGTGTCTTTGTAGAGAGC
EST: gi|25802832|gb|CA758793.1|CA758793
EST:     AAGCAATGAGGGCATCACTTCTGCAATGGTGCTATGCCAGCTACAGTGAG                         GTATTCAGTTCCTGGATGCACTTCTGTGCTGTGCGTGTCTTTGTAGAGAGC
genomic: AAGCAATGAGGGCATCACTTCTGCAATGGTGCTATGCCAGCTACAGTGAGgtgcatgtct ... tattctgcagGTATTCAGTTCCTGGATGCACTTCTGTGCTGTGCGTGTCTTTGTAGAGAGC
EST: gi|33381011|gb|CF196354.1|CF196354
EST:     AAGCAATGAGGGCATCACTTCTGCAATGGTGCTATGCCAGCTACAGTGAG                         GTATTCAGTTCCTGGATGCACTNNNGTGCTGTGCGTGTCTTTGT
genomic: AAGCAATGAGGGCATCACTTCTGCAATGGTGCTATGCCAGCTACAGTGAGgtgcatgtct ... tattctgcagGTATTCAGTTCCTGGATGCACTTCTGTGCTGTGCGTGTCTTTGT
EST: gi|29674594|gb|CB670869.1|CB670869
EST:     AAGCAATGAGGGCATCACTTCTGCAATGGTGCTATGCCAGCTACAGTGAG                         GTATTCAGTTCCTGGATGCACTTCTGTGCTGTGCGTGTCTTTGTAGAGAGC
genomic: AAGCAATGAGGGCATCACTTCTGCAATGGTGCTATGCCAGCTACAGTGAGgtgcatgtct ... tattctgcagGTATTCAGTTCCTGGATGCACTTCTGTGCTGTGCGTGTCTTTGTAGAGAGC
EST: gi|38565596|gb|CK085049.1|CK085049
EST:     AAGCAATGAGGGCATCACTTCTGCAATGGTGCTATGCCAGCTACAGTGAG                         GTATTCAGTTCCTGGATGCACTTCTGTGCTGTGCGTGTCTTTGTAGAGAGC
genomic: AAGCAATGAGGGCATCACTTCTGCAATGGTGCTATGCCAGCTACAGTGAGgtgcatgtct ... tattctgcagGTATTCAGTTCCTGGATGCACTTCTGTGCTGTGCGTGTCTTTGTAGAGAGC
EST: gi|29613963|gb|CB618976.1|CB618976
EST:     AAGCAATGAGGGCATCACTTCTGCAATGGTGCTATGCCAGCTACAGTGAG                         GTATTCAGTTCCTGGATGCACTTCTGTGCTGTGCGTGTCTTTGTAGAGAGC
genomic: AAGCAATGAGGGCATCACTTCTGCAATGGTGCTATGCCAGCTACAGTGAGgtgcatgtct ... tattctgcagGTATTCAGTTCCTGGATGCACTTCTGTGCTGTGCGTGTCTTTGTAGAGAGC
EST: gi|58654927|gb|CK043607.1|CK043607
EST:     AAGCAATGAGGGCATCACTTCTGCAATGGTGCTATGCCAGCTACAGTGAG                         GTATTCAGTTCCTGGATGCACTTCTGTGCTGTGCGTGTCTTTGTAGAGAGC
genomic: AAGCAATGAGGGCATCACTTCTGCAATGGTGCTATGCCAGCTACAGTGAGgtgcatgtct ... tattctgcagGTATTCAGTTCCTGGATGCACTTCTGTGCTGTGCGTGTCTTTGTAGAGAGC
EST: gi|58590593|gb|CF988901.1|CF988901
EST:     AAGCAATGAGGGCATCACTTCTGCAATGGTGCTATGCCAGCTACAGTGAG                         GTATTCAGTTCCTGGATGCACTTCTGTGCTGTGCGTGTCTTTGTAGAGAGC
genomic: AAGCAATGAGGGCATCACTTCTGCAATGGTGCTATGCCAGCTACAGTGAGgtgcatgtct ... tattctgcagGTATTCAGTTCCTGGATGCACTTCTGTGCTGTGCGTGTCTTTGTAGAGAGC
EST: gi|29612870|gb|CB617883.1|CB617883
EST:     AAGCAATGAGGGCATCACTTCTGCAATGGTGCTATGCCAGCTACAGTGAG                         GTATTCAGTTCCTGGATGCACTTCTGTGCTGTGCGTGTCTTTGTAGAGAGC
genomic: AAGCAATGAGGGCATCACTTCTGCAATGGTGCTATGCCAGCTACAGTGAGgtgcatgtct ... tattctgcagGTATTCAGTTCCTGGATGCACTTCTGTGCTGTGCGTGTCTTTGTAGAGAGC
EST: gi|88270309|gb|CI385567.1|CI385567
EST:     AGCAATGAGGGCATCACTTCTGCAATGGTGCTATGCCAGCTACAGTGAG                         GTATTCAGTTCCTGGATGCACTTCTGTGCTGTGCGTGTCTTTGTAGAGAGC
genomic: AGCAATGAGGGCATCACTTCTGCAATGGTGCTATGCCAGCTACAGTGAGgtgcatgtct ... tattctgcagGTATTCAGTTCCTGGATGCACTTCTGTGCTGTGCGTGTCTTTGTAGAGAGC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGCACAGGAAAGTAGGAAGGAAGAGCTGGAAAAGCTAATGCAAGACCAGGAAGCAATGAGGGCATCACTTCTGCAATGGTGCTATGCCAGCTACAGTGAGgtgcatgtctttttaggcttatttaataatcctgtcaacaatgacatttctttagagaagaacttttttattcttatgaatgtcatttttgtttcatgta

- - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA