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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TAATAACTACATCTCTGTTGGAGCCTCTGGAGCTTTATTTGGACTGCTTGGATCAATGCTTTCTGAGCTTATTATGAACTGGACTATTTATTCCAACAAGgttagtaaatgagatagatgcacatacattttcactattcagttgcttgatgtttgttttgatcaagctaatccactcttgcag

Basic information

species Oryza sativa
transcript LOC_Os09g35730.1
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os09g35730.1 (Oryza sativa), 5'ss of exon 3
lower sequence: GRMZM2G033937_T01 (Zea mays), 5'ss of exon 3
TAATAACTACATCTCTGTTGGAGCCTCTGGAGCTTTATTTGGACTGCTTGGATCAATGCTTTCTGAGCTTATTATGAACTGGACTATTTATTCCAACAAGgttagtaaatgagatagatgcacatacatttt-cactattcagttgcttgatgtttgttttgatca---agctaatccactcttgcag
 |||||||||||||||||||| || ||||||||||||||||| ||||||||||| ||||||||||||||  | |||||||||||||| || ||||||||||  |||| |    | ||||  | ||| | |||    ||| ||| ||||||||  |  ||| | ||    |  ||||   |||||||||
GAATAACTACATCTCTGTTGGTGCTTCTGGAGCTTTATTTGGCCTGCTTGGATCCATGCTTTCTGAGCTACTCATGAACTGGACTATATACTCCAACAAGgccagtacaattaacagataaatatatactttattttatccagctgcttgatagtcatttagctcgtatacttaatttgctcttgcag

upper sequence: LOC_Os09g35730.1 (Oryza sativa), 5'ss of exon 3
lower sequence: GRMZM2G116514_T01 (Zea mays), 5'ss of exon 3
TAATAACTACATCTCTGTTGGAGCCTCTGGAGCTTTATTTGGACTGCTTGGATCAATGCTTTCTGAGCTTATTATGAACTGGACTATTTATTCCAACAAGgttagtaaatgagatagatgcacatacatttt-cactattcagttgcttgatgtttgttttgatca---agctaatccactcttgcag
 || | ||||||||| ||||| || ||||||||| ||||||| ||||| ||||| ||||||||||| ||  | |||||||||||||| || ||||||||||  |||| | |  ||| ||| | | |||||||    ||| |||||| |||||  | | || | |||   |  ||||   |||||||||
GAACAGCTACATCTCCGTTGGTGCTTCTGGAGCTCTATTTGGCCTGCTGGGATCCATGCTTTCTGAACTACTCATGAACTGGACTATATACTCCAACAAGgccagtacaagcaataaatgaata-acattttattttatccagttgattgataatcgcttagctcatctacttaatttgctcttgcag

upper sequence: LOC_Os09g35730.1 (Oryza sativa), 5'ss of exon 3
lower sequence: GRMZM2G012167_T01 (Zea mays), 5'ss of exon 1
TAATAACTACATCTCTGTTGGAGCCTCTGGAGCTTTATTTGGACTGCTTGGATCAATGCTTTCTGAGCTTATTATGAACTGGACTATTTATTCCAACAAGgttagtaaatgagatagatgcacatacattttcactattc-agttgcttgatgtttgttttgatca---agctaatccactcttgcag
                            |||||| ||||||| ||||| ||||| ||||||||||| ||  | |||||||||||||| || ||||||||||  |||| | |  ||| ||| | | |||||||   | ||| ||||| |||||  | | || | |||   |  ||||   |||||||||
----------------------------GGAGCTCTATTTGGCCTGCTGGGATCCATGCTTTCTGAACTACTCATGAACTGGACTATATACTCCAACAAGgccagtataagtaataaatgaata-acattttattttttccagttgattgataatcgcttagctcatctacttaatttgctcttgcag

upper sequence: LOC_Os09g35730.1 (Oryza sativa), 5'ss of exon 3
lower sequence: GLYMA20G29570.1 (Glycine max), 5'ss of exon 3
TAATAACTACATCTCTGTTGGAGCCTCTGGAGCTTTATTTGGACTGCTTGGATCAATGCTTTCTGAGCTTATTATGAACTGGACTATTTATTCCAACAAGgttagtaaatgagat-----agatgcacatacattttcactattcagttgcttgatgtttgttttgatcaagctaatccactcttgcag------------------------------------------------------------------------------------------------
 |   || ||||||||||||| || ||||| ||  | |||||||| |||||  ||||||| ||||| ||||| |  ||||||||||| |||||||| || || |||  |    ||     || |   | || ||||| |    |   |   | | | ||  ||||  ||||  |||   || | |  |                                                                                                 
CAGAGACCACATCTCTGTTGGTGCTTCTGGTGCCCTTTTTGGACTTCTTGGCGCAATGCTGTCTGAACTTATCACAAACTGGACTATATATTCCAATAAAgtgagtgtacctaattctttaggtcagccta-atttttatggctttctgcatggttattaatttttttcaatataagagacacctcaaatcttctacactttggctcattgtaatcaattagtttcatatctttaaattatattaacatggcacaagttaacttttttttttactcttgttgtag

upper sequence: LOC_Os09g35730.1 (Oryza sativa), 5'ss of exon 3
lower sequence: GLYMA09G26610.2 (Glycine max), 5'ss of exon 3
TAATAACTACATCTCTGTTGGAGCCTCTGGAGCTTTATTTGGACTGCTTGGATCAATGCTTTCTGAGCTTATTATGAACTGGACTATTTATTCCAACAAGgttagta-aatgagatagatgcacatac-attttcactattcagttgcttgatgtttgttttgatcaagctaat--ccactcttgcag------------
||  ||| | ||||||||||| || ||||| ||| |||||||||| |||||  |||||||||| || ||||| |  ||||||| ||||||| |||| ||||| |||| || |  || | | | ||| | |||||   | |     || ||| |  || ||||||  | |  |||    | | ||                
TAGAAACAATATCTCTGTTGGTGCTTCTGGTGCTCTATTTGGACTTCTTGGTGCAATGCTTTCAGAACTTATCACAAACTGGAGTATTTATACCAATAAGgtgagtataaagtcattggttcccatcctatttttgttttctgtgtgtttgttagttcttttgaaaaggaaaatgattaatgttatgaaaagattgacaa

upper sequence: LOC_Os09g35730.1 (Oryza sativa), 5'ss of exon 3
lower sequence: AT5G07250.2 (Arabidopsis thaliana), 5'ss of exon 3
TAATAACTACATCTCTGTTGGAGCCTCTGGAGCTTTATTTGGACTGCTTGGATCAATGCTTTCTGAGCTTATTATGAACTGGACTATTTATTCCAACAAGgttagta--aatgagatagatgc-----acatacatttt-cactattcagttgcttgatgtttgt--tttgatcaagctaatcc-actcttgcag-----
 |  |||   |||||||||||||| ||||| ||| | ||||| || ||||| |||||||| ||||| ||| | |  |||||||| || || || |||||||||| ||  |||  | |           |||||||  |  | | ||   ||||  | |||||| |  | ||| ||     | |  | |  ||||      
CAGAAACAGTATCTCTGTTGGAGCTTCTGGTGCTCTTTTTGGCCTCCTTGGCTCAATGCTCTCTGAACTTTTCACCAACTGGACAATCTACTCTAACAAGgttaataccaatctgcttttcatttcaaacatacaaatcactccatcatgttggctcatgtttctgatctgagcatatgtaccagattgctgcactcctg

upper sequence: LOC_Os09g35730.1 (Oryza sativa), 5'ss of exon 3
lower sequence: AT5G07250.1 (Arabidopsis thaliana), 5'ss of exon 3
TAATAACTACATCTCTGTTGGAGCCTCTGGAGCTTTATTTGGACTGCTTGGATCAATGCTTTCTGAGCTTATTATGAACTGGACTATTTATTCCAACAAGgttagta--aatgagatagatgca-catacattttcactattcagttgc-ttgatgtttgttt-tgatc-aagctaatccactcttgcag
 |  |||   |||||||||||||| ||||| ||| | ||||| || ||||| |||||||| ||||| ||| | |  |||||||| || || || |||||||||| ||  |||  | |        || ||||    |  | ||  |    |||     ||||| |||||  |||  ||  ||        
CAGAAACAGTATCTCTGTTGGAGCTTCTGGTGCTCTTTTTGGCCTCCTTGGCTCAATGCTCTCTGAACTTTTCACCAACTGGACAATCTACTCTAACAAGgttaataccaatctgcttttcatttcaaacatacaaatcactccatcatgttggctcatgtttctgatctgagcatatgtaccag-----

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|33687784|gb|CF316023.1|CF316023
EST:     GATCAATGCTTTCTGAGCTTATTATGAACTGGACTATTTATTCCAACAAG                         GCGGCAGCCATAATAACTCTTCTATTTATAATCGCAATCAACTTGGCTATT
genomic: GATCAATGCTTTCTGAGCTTATTATGAACTGGACTATTTATTCCAACAAGgttagtaaat ... actcttgcagGCAGCAGCCATAATAACTCTTCTATTTATAATCGCAATCAACTTGGCTATT
EST: gi|38478939|gb|CF963072.1|CF963072
EST:     GATCAATGCTTTCTGAGCTTATTATGAACTGGACTATTTATTCCAACAAG                         GCAGCAGCCATAATAACTCTTCTATTTATAATCGCAATCAACTTGGCTATT
genomic: GATCAATGCTTTCTGAGCTTATTATGAACTGGACTATTTATTCCAACAAGgttagtaaat ... actcttgcagGCAGCAGCCATAATAACTCTTCTATTTATAATCGCAATCAACTTGGCTATT
EST: gi|88546842|gb|CI477093.1|CI477093
EST:     GAACTGGACTATTTACTCCAACAAG                         GCAGCAGCCATAATAACTCTTCTATTTATAATCGCAATCAACTTGGCTATT
genomic: GAACTGGACTATTTATTCCAACAAGgttagtaaat ... actcttgcagGCAGCAGCCATAATAACTCTTCTATTTATAATCGCAATCAACTTGGCTATT
EST: gi|27578050|gb|CB000745.1|CB000745
EST:     GATCAATGCTTTCTGAGCTTATTATGAACTGGACTATTTATTCCAACAAG                         GCAGCAGCCATAATAACTCTTCTATTTATAATCGCAATCAACTTGGCTATT
genomic: GATCAATGCTTTCTGAGCTTATTATGAACTGGACTATTTATTCCAACAAGgttagtaaat ... actcttgcagGCAGCAGCCATAATAACTCTTCTATTTATAATCGCAATCAACTTGGCTATT
EST: gi|11442952|gb|BF430849.1|BF430849
EST:     GATCAATGCTTTCTGAGCTTATTATGAACTGGACTATTTATTCCAACAAG                         GCAGCAGCCATAATAACTCTTCTATTTATAATCGCAATCAACTTGGCTATT
genomic: GATCAATGCTTTCTGAGCTTATTATGAACTGGACTATTTATTCCAACAAGgttagtaaat ... actcttgcagGCAGCAGCCATAATAACTCTTCTATTTATAATCGCAATCAACTTGGCTATT
EST: gi|9866306|gb|AU102056.1|AU102056
EST:     GGACTATTTATTCCAACAAG                         GCAGCAGCCATAATAACTCTTCTATTTATAATCGCAATCAACTTGGCTATT
genomic: GGACTATTTATTCCAACAAGgttagtaaat ... actcttgcagGCAGCAGCCATAATAACTCTTCTATTTATAATCGCAATCAACTTGGCTATT
EST: gi|218497364|gb|FG953028.1|FG953028
EST:     GATCAATGCTTTCTGAGCTTATTATGAACTGGACTATTTATTCCAACAAG                         GCAGCAGCCATAATAACTCTTCTATTTATAATCGCAATCAACTTGGCTATT
genomic: GATCAATGCTTTCTGAGCTTATTATGAACTGGACTATTTATTCCAACAAGgttagtaaat ... actcttgcagGCAGCAGCCATAATAACTCTTCTATTTATAATCGCAATCAACTTGGCTATT
EST: gi|218497582|gb|FG955137.1|FG955137
EST:     GATCAATGCTTTCTGAGCTTATTATGAACTGGACTATTTATTCCAACAAG                         GCAGCAGCCATAATAACTCTTCTATTTATAATCGCAATCAACTTGGCTATT
genomic: GATCAATGCTTTCTGAGCTTATTATGAACTGGACTATTTATTCCAACAAGgttagtaaat ... actcttgcagGCAGCAGCCATAATAACTCTTCTATTTATAATCGCAATCAACTTGGCTATT
EST: gi|218485738|gb|FG958746.1|FG958746
EST:     GATCAATGCTTTCTGAGCTTATTATGAACTGGACTATTTATTCCAACAAG                         GCAGCAGCCATAATAACTCTTCTATTTATAATCGCAATCAACTTGGCTATT
genomic: GATCAATGCTTTCTGAGCTTATTATGAACTGGACTATTTATTCCAACAAGgttagtaaat ... actcttgcagGCAGCAGCCATAATAACTCTTCTATTTATAATCGCAATCAACTTGGCTATT
EST: gi|29659848|gb|CB656123.1|CB656123
EST:     GATCAATGCTTTCTGAGCTTATTATGAACTGGACTATTTATTCCAACAAG                         GCAGCAGCCATAATAACTCTTCTATTTATAATCGCAATCAACTTGGCTATT
genomic: GATCAATGCTTTCTGAGCTTATTATGAACTGGACTATTTATTCCAACAAGgttagtaaat ... actcttgcagGCAGCAGCCATAATAACTCTTCTATTTATAATCGCAATCAACTTGGCTATT
EST: gi|38479876|gb|CF963965.1|CF963965
EST:     TCCATGCTTTCTGAGCTTATTATAGAACCTGGACTATTTATTCCAAGAGG                         GCAGCAGCCATAATAACTCTTCTATTTATAATCGCAATCAACTTGGCTATT
genomic: TCAATGCTTTCTGAGCTTATTAT-GAA-CTGGACTATTTATTCCAACAAGgttagtaaat ... actcttgcagGCAGCAGCCATAATAACTCTTCTATTTATAATCGCAATCAACTTGGCTATT
EST: gi|88546060|gb|CI475668.1|CI475668
EST:     GCTTATTATGAACTGGACTATTTACTCCAACAAG                         GCAGCAGCCATAATAACTCTTCTATTTATAATCGCAATCAACTTGGCTATT
genomic: GCTTATTATGAACTGGACTATTTATTCCAACAAGgttagtaaat ... actcttgcagGCAGCAGCCATAATAACTCTTCTATTTATAATCGCAATCAACTTGGCTATT
EST: gi|163928838|gb|EG711925.1|EG711925
EST:     GATCAATGCTTTCTGAGCTTATTATGAACTGGACTATTTATTCCAACAAG                         GCAGCAGCCATAATAACTCTTCTATTTATAATCGCAATCAACTTGGCTATT
genomic: GATCAATGCTTTCTGAGCTTATTATGAACTGGACTATTTATTCCAACAAGgttagtaaat ... actcttgcagGCAGCAGCCATAATAACTCTTCTATTTATAATCGCAATCAACTTGGCTATT

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 1 RNA-Seqlibrary.


Block sizes: 67 (upstream exon), 75 (downstream exon)
Score: 60

TAATAACTACATCTCTGTTGGAGCCTCTGGAGCTTTATTTGGACTGCTTGGATCAATGCTTTCTGAGCTTATTATGAACTGGACTATTTATTCCAACAAGgttagtaaat ... actcttgcagGCAGCAGCCATAATAACTCTTCTATTTATAATCGCAATCAACTTGGCTATTGGGATACTACCTCATGCCGATAACTTTGCTCATATCGGTGGATTTGTGA




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TAATAACTACATCTCTGTTGGAGCCTCTGGAGCTTTATTTGGACTGCTTGGATCAATGCTTTCTGAGCTTATTATGAACTGGACTATTTATTCCAACAAGgttagtaaatgagatagatgcacatacattttcactattcagttgcttgatgtttgttttgatcaagctaatccactcttgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT