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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCCAGAAATGGTGGTAGGTTGGTACCATTCCCATCCTGGATTTGGTTGCTGGCTTTCAGGAGTTGACATCAATACTCAACAGgtttggtgcatatttcagacattttttcttcagtatgaaaggaatcctgtaacttggtttaacaagagatgattcctgtatttgtcattacattttttat...

Basic information

species Oryza sativa
transcript LOC_Os05g30800.1
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os05g30800.1 (Oryza sativa), 5'ss of exon 3
lower sequence: GRMZM2G467059_T03 (Zea mays), 5'ss of exon 3
GCCAGAAATGGTGGTAGGTTGGTACCATTCCCATCCTGGATTTGGTTGCTGGCTTTCAGGAGTTGACATCAATACTCAACAGgttt-----ggtgcatatttcagacattttttcttcagtatgaaaggaatcctgtaacttggtttaacaagagatgattcctgtatttgtcattacattttttat
|||||||||||| ||||| ||||| || || |||||||| || ||||||||||| ||||| ||||| ||||||||||| ||||| |       | ||  | |   | |        ||  |   ||  | ||    |   ||| |  |       ||   || |||  || | | |||   |     
GCCAGAAATGGTTGTAGGCTGGTATCACTCACATCCTGGCTTCGGTTGCTGGCTATCAGGCGTTGATATCAATACTCAGCAGgtctttacaaatccacttgtttaaaagggaccggtctatgaaaataggatagcttctgttgttgcactgtactatatgtcatgtcattataaatactgat-----

upper sequence: LOC_Os05g30800.1 (Oryza sativa), 5'ss of exon 3
lower sequence: GRMZM2G033626_T01 (Zea mays), 5'ss of exon 3
GCCAGAAATGGTGGTAGGTTGGTACCATTCCCATCCTGGATTTGGTTGCTGGCTTTCAGGAGTTGACATCAATACTCAACAGgtttggtgcatatttcagacattttttcttcagtatgaaaggaatcctgtaacttggtttaacaagagatgattcctgtatttgt--cattacattttttat---------
|||||||||||| ||||||||||| || || |||||||| || || |||||||| ||||| || || ||||||||||| ||||| |  |||| ||      || || ||||  |     ||||| ||| | |    |||| || ||| | | |||  |||   |  |  || |  | | | | |         
GCCAGAAATGGTTGTAGGTTGGTATCACTCACATCCTGGCTTCGGATGCTGGCTATCAGGCGTCGATATCAATACTCAGCAGgtcta-tgcaaatc-----cacttgttctcta-----aaagggatcttttggaatggtctatcaaaacaggatagctgctgtcattgcactgtactatatgtcatgtcaac

upper sequence: LOC_Os05g30800.1 (Oryza sativa), 5'ss of exon 3
lower sequence: PP1S181_105V6.1 (Physcomitrella patens), 5'ss of exon 4
GCCAGAAATGGTGGTAGGTTGGTACCATTCCCATCCTGGATTTGGTTGCTGGCTTTCAGGAGTTGACATCAATACTCAACAGgtttggtgcatatttcagacattttttcttcagtatgaaaggaatcctgtaacttggtttaacaagagatgattcctgtatttgtcattacattttttat---------------------------------------------------------------------
|||||||||||| || || ||||| ||||| ||||| || |||||||||||| | || || || || || ||||||||||||||  | |     || ||   | |||   |   |  |    ||  ||| | ||  ||         || |  || ||   || |  |      ||   ||                                                                      
GCCAGAAATGGTTGTGGGCTGGTATCATTCACATCCAGGTTTTGGTTGCTGGTTATCTGGTGTGGATATAAATACTCAACAGgtaagttaggc-ttgcactaactttcgttcttgcgttttggg--tcccg-aatgtgcaacggtg-gaaacaataccatgatctaacgcagtcttccatagttgggagaccggtatccccctccagaatcactgccagtgttctaaagcagtatccttgtgtatttgcag

upper sequence: LOC_Os05g30800.1 (Oryza sativa), 5'ss of exon 3
lower sequence: PP1S46_324V6.1 (Physcomitrella patens), 5'ss of exon 3
GCCAGAAATGGTGGTAGGTTGGTACCATTCCCATCCTGGATTTGGTTGCTGGCTTTCAGGAGTTGACATCAATACTCAACAGgt----ttggtgcatatttcagacattttttcttcagtatgaaaggaatcctgtaacttggtttaacaagagatgattcctgtatttgtcattacattttttat
 ||||| |||||||| || ||||||||||| ||||| || |||||||||||| | || || || || ||||||||||| |||||    | |||  ||| || ||   |    ||||     | ||  |  |  | | |       ||  ||||  || |      ||| ||    || ||  || |
ACCAGAGATGGTGGTGGGCTGGTACCATTCTCATCCAGGTTTTGGTTGCTGGTTGTCTGGCGTGGATATCAATACTCAGCAGgtaatttaggtttataatt-aggtttggcatctttttgttaaagtggttgttatgaac--acatacaaagatgtggtgaacaaattggtgga-acgttggtttt

upper sequence: LOC_Os05g30800.1 (Oryza sativa), 5'ss of exon 3
lower sequence: EFJ33925 (Selaginella moellendorffii), 5'ss of exon 3
GCCAGAAATGGTGGTAGGTTGGTACCATTCCCATCCTGGATTTGGTTGCTGGCTTTCAGGAGTTGACATCAATACTCAACAGgtttgg---tgcatatttcagacattttttcttcagtatgaaaggaatcctgtaacttggtttaacaagagatgattcctgtatttgtcattacattttttat
|   |||||||| ||||| ||||||||||| |||||||| ||||| |||||||| || ||||| |||||||| || || || ||  |    |  | |  | |    |    | |||  | |        || | |   |  |                                           
GAGTGAAATGGTTGTAGGATGGTACCATTCTCATCCTGGTTTTGGCTGCTGGCTATCCGGAGTAGACATCAACACCCAGCAAgtaagaatctatagaacttaagtttcacgttttctttgtttgctttttcttttttgtcag-------------------------------------------

upper sequence: LOC_Os05g30800.1 (Oryza sativa), 5'ss of exon 3
lower sequence: EFJ16494 (Selaginella moellendorffii), 5'ss of exon 3
GCCAGAAATGGTGGTAGGTTGGTACCATTCCCATCCTGGATTTGGTTGCTGGCTTTCAGGAGTTGACATCAATACTCAACAGgtttggtgcatatttcagacattttttcttcagtatgaaaggaatcctgtaacttggtttaacaagagatgattcctgtatttgtcattacattttttat
  | |||||||| ||||| ||||| ||||| ||||||||||| || ||||||||||| |||||||| ||||||||||||||||   || | | |      |  | |||  |||| | || | ||| | |    |  || |||      |  ||| |  || |                    
ATCGGAAATGGTTGTAGGATGGTATCATTCACATCCTGGATTCGGGTGCTGGCTTTCTGGAGTTGATATCAATACTCAACAGgcaaggagaaaaaagtcta-gtctttgtttcactttggatggagttcacagatatgttttgg---aacttgacttgtgcag-------------------

upper sequence: LOC_Os05g30800.1 (Oryza sativa), 5'ss of exon 3
lower sequence: EFJ37436 (Selaginella moellendorffii), 5'ss of exon 3
GCCAGAAATGGTGGTAGGTTGGTACCATTCCCATCCTGGATTTGGTTGCTGGCTTTCAGGAGTTGACATCAATACTCAACAGgtttgg-tgcatatttcagacattttttcttcagtatgaaaggaatcctgtaacttggtttaacaagagatgattcctgtatttgtcattacattttttat
|   |||||||| ||||| ||||||||||| |||||||| ||||| |||||||| || ||||| |||||||| || || || ||  |  |  |||   |  |  |||    ||   | ||   |    | | |   || ||                                          
GAGTGAAATGGTTGTAGGATGGTACCATTCTCATCCTGGTTTTGGCTGCTGGCTATCCGGAGTAGACATCAACACCCAGCAAgtaagaatctatagaacttaagtttcacgttttctttgtttg---ccttttctttttgtcag---------------------------------------

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|29615551|gb|CB620563.1|CB620563
EST:     ATCCTGGATTTGGTTGCTGGCTTTCAGGAGTTGACATCAATACTCAACAG                         AGTTTTGAAGCTTTAAACCCCAGGGCAGTTGCCGTCGTGATAGATCCCATC
genomic: ATCCTGGATTTGGTTGCTGGCTTTCAGGAGTTGACATCAATACTCAACAGgtttggtgca ... gaacatgcagAGTTTTGAAGCTTTAAACCCCAGGGCAGTTGCCGTCGTGATAGATCCCATC
EST: gi|58599931|gb|CK010459.1|CK010459
EST:     ATCCTGGATTTGGTTGCTGGCTTTCAGGAGTTGACATCAATACTCAACAG                         AGTTTTGAAGCTTTAAACCCCAGGGCAGTTGCCGTCGTGATAGATCCCATC
genomic: ATCCTGGATTTGGTTGCTGGCTTTCAGGAGTTGACATCAATACTCAACAGgtttggtgca ... gaacatgcagAGTTTTGAAGCTTTAAACCCCAGGGCAGTTGCCGTCGTGATAGATCCCATC
EST: gi|58681730|gb|CK070417.1|CK070417
EST:     ATCCTGGATTTGGTTGCTGGCTTTCAGGAGTTGACATCAATACTCAACAG                         AGTTTTGAAGCTTTAAACCCCAGGGCAGTTGCCGTCGTGATAGATCCCATC
genomic: ATCCTGGATTTGGTTGCTGGCTTTCAGGAGTTGACATCAATACTCAACAGgtttggtgca ... gaacatgcagAGTTTTGAAGCTTTAAACCCCAGGGCAGTTGCCGTCGTGATAGATCCCATC
EST: gi|33682841|gb|CF311080.1|CF311080
EST:     ATCCTGGATTTGGTTGCTGGCTTTCAGGAGTTGACATCAATACTCAACAG                         AGTTTTGAAGCTTTAAACCCCAGGGCAGTTGCCGTCGTGATAGATCCCATC
genomic: ATCCTGGATTTGGTTGCTGGCTTTCAGGAGTTGACATCAATACTCAACAGgtttggtgca ... gaacatgcagAGTTTTGAAGCTTTAAACCCCAGGGCAGTTGCCGTCGTGATAGATCCCATC
EST: gi|58686484|gb|CK075171.1|CK075171
EST:     ATCCTGGATTTGGTTGCTGGCTTTCAGGAGTTGACATCAATACTCAACAG                         AGTTTTGAAGCTTTAAACCCCAGGGCAGTTGCCGTCGTGATAGATCCCATC
genomic: ATCCTGGATTTGGTTGCTGGCTTTCAGGAGTTGACATCAATACTCAACAGgtttggtgca ... gaacatgcagAGTTTTGAAGCTTTAAACCCCAGGGCAGTTGCCGTCGTGATAGATCCCATC
EST: gi|29620645|gb|CB625656.1|CB625656
EST:     ATCCTGGATTTGGTTGCTGGCTTTCAGGAGTTGACATCAATACTCAACAG                         AGTTTTGAAGCTTTAAACCCCAGGGCAGTTGCCGTCGTGATAGATCCCATC
genomic: ATCCTGGATTTGGTTGCTGGCTTTCAGGAGTTGACATCAATACTCAACAGgtttggtgca ... gaacatgcagAGTTTTGAAGCTTTAAACCCCAGGGCAGTTGCCGTCGTGATAGATCCCATC
EST: gi|218498489|gb|FG961937.1|FG961937
EST:     ATCCTGGATTTGGTTGCTGGCTTTCAGGAGTTGACATCAATACTCAACAG                         AGTTTTGAAGCTTTAAACCCCAGGGCAGTTGCCGTCGTGATAGATCCCATC
genomic: ATCCTGGATTTGGTTGCTGGCTTTCAGGAGTTGACATCAATACTCAACAGgtttggtgca ... gaacatgcagAGTTTTGAAGCTTTAAACCCCAGGGCAGTTGCCGTCGTGATAGATCCCATC
EST: gi|86495846|gb|CI138479.1|CI138479
EST:     ATCCTGGATTTGGTTGCTGGCTTTCAGGAGTTGACATCAATACTCAACAG                         AGTTTTGAAGCTTTAAACCCCAGGGCAGTTGCCGTCGTGATAGATCCCATC
genomic: ATCCTGGATTTGGTTGCTGGCTTTCAGGAGTTGACATCAATACTCAACAGgtttggtgca ... gaacatgcagAGTTTTGAAGCTTTAAACCCCAGGGCAGTTGCCGTCGTGATAGATCCCATC
EST: gi|117227458|gb|CT846600.1|CT846600
EST:     ATCCTGGATTTGGTTGCTGGCTTTCAGGAGTTGACATCAATACTCAACAG                         AGTTTTGAAGCTTTAAACCCCAGGGCAGTTGCCGTCGTGATAGATCCCATC
genomic: ATCCTGGATTTGGTTGCTGGCTTTCAGGAGTTGACATCAATACTCAACAGgtttggtgca ... gaacatgcagAGTTTTGAAGCTTTAAACCCCAGGGCAGTTGCCGTCGTGATAGATCCCATC

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: 69 (upstream exon), 73 (downstream exon)
Score: 42

GCCAGAAATGGTGGTAGGTTGGTACCATTCCCATCCTGGATTTGGTTGCTGGCTTTCAGGAGTTGACATCAATACTCAACAGgtttggtgca ... gaacatgcagAGTTTTGAAGCTTTAAACCCCAGGGCAGTTGCCGTCGTGATAGATCCCATCCAAAGTGTCAAGGGGAAAGTTGTCATTGATGCATTTCGCCTTATTAACC




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