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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AAGAAGCTGTTGAAAAGGACGCAACAAAGAATATTCATATTGATGGGACAGTGCATCCTTTGACGAGCTACGTGATTAACTATGTCAAATTTTTATTTGAgtaagtatatgatcatgtgcacttaatctttcctgtaatttgatagttgcattgctatactttcttgcatttcttcttcaatcctatccaccagtatgct...

Basic information

species Oryza sativa
transcript LOC_Os04g58880.1
intron # 7
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os04g58880.1 (Oryza sativa), 5'ss of exon 7
lower sequence: GRMZM2G074530_T01 (Zea mays), 5'ss of exon 1
AAGAAGCTGTTGAAAAGGACGCAACAAAGAATATTCATATTGATGGGACAGTGCATCCTTTGACGAGCTACGTGATTAACTATGTCAAATTTTTATTTGAgtaagtatatgatcatgtgcacttaatctttcctgtaatttgatagttgcattgctatacttt-cttgcatttcttcttcaatcctatccaccagtatgct
||||||||||||||||||| ||||||||||||||||||| |||||| ||||| |||||||| || ||||| ||||| |||||||| || ||||| ||||||||||||| | ||||  | | | |    |||  |||  | | |||  || || | | |||     |||   || | | |    | |  |       ||  |
AAGAAGCTGTTGAAAAGGATGCAACAAAGAATATTCATACTGATGGAACAGTTCATCCTTTAACAAGCTATGTGATCAACTATGTTAAGTTTTTGTTTGAgtaagtatctaatcaaatccgcatgcaattta-tgtgttgttataaatgaataggtgtacaagatttgtccttatccatgtgcctttccttttctaattat

upper sequence: LOC_Os04g58880.1 (Oryza sativa), 5'ss of exon 7
lower sequence: GLYMA10G34000.1 (Glycine max), 5'ss of exon 7
AAGAAGCTGTTGAAAAGGACGCAACAAAGAATATTCATATTGATGGGACAGTGCATCCTTTGACGAGCTACGTGATTAACTATGTCAAATTTTTATTTGAgtaagtatatgatcatgtgcacttaatctttcctgtaatttgatagttgcattgcta-tactttcttgcatttcttcttcaatcc--tatccaccagtatgct---
|||| || ||||| || || || || |||| |      |  ||||| || || |||||| | || ||||| || ||||||||||| || |||||||||||||||||  |      |   ||  | |||        |||||  |||    |     | |  ||||| |||||| ||  |   | |  |    || |  ||| |   
AAGAGGCAGTTGAGAAAGATGCTACGAAGACTGCAGTAACAGATGGAACTGTCCATCCTCTAACAAGCTATGTAATTAACTATGTGAAGTTTTTATTTGAgtaagttcagctatgttgtcatctgatccc------aattttgtagccataccatcaattatttctagcattttttgctgtgttcactgatgacaaaaatgttagt

upper sequence: LOC_Os04g58880.1 (Oryza sativa), 5'ss of exon 7
lower sequence: GLYMA20G33590.1 (Glycine max), 5'ss of exon 7
AAGAAGCTGTTGAAAAGGACGCAACAAAGAATATTCATATTGATGGGACAGTGCATCCTTTGACGAGCTACGTGATTAACTATGTCAAATTTTTATTTGAgtaagtatatgatcatgtgcacttaatctttcctgtaatttgatagttgcattgctatactttcttgcatttcttcttcaatcc--tatccaccagtatgct------
|||| || ||||| || || || ||||||| |      |  ||||| || || |||||| | || ||||| || ||||||||||| || |||||||||||||||||  |      |   ||  | |||        |||||  |||  ||||    ||  ||||| |||||| ||  |   | |  |    || |  ||| |      
AAGAGGCAGTTGAGAAAGATGCTACAAAGACTGCAGTAACAGATGGAACTGTCCATCCTCTAACAAGCTATGTAATTAACTATGTGAAGTTTTTATTTGAgtaagttcagctatgttgtcatctgatccc------aattttgtagccgcatca--attatttctagcattttttgctgtgttcactgatgacaaaaatgttagtcat

upper sequence: LOC_Os04g58880.1 (Oryza sativa), 5'ss of exon 7
lower sequence: GLYMA20G17500.1 (Glycine max), 5'ss of exon 4
AAGAAGCTGTTGAAAAGGACGCAACAAAGAATATTCATATTGATGGGACAGTGCATCCTTTGACGAGCTACGTGATTAACTATGTCAAATTTTTATTTGAgtaagtatatgatcatgtgcacttaatctttcctgtaattt--gatagttgcattgctatactttcttgcatttcttcttcaatcctatccaccagtatgct-----
||||||| ||||| || || || ||||||| |      | |||||| || || ||||||||||| ||||| |||||||||||||| || |||||||||||||||||      |||| ||  ||  ||  | | |  ||||    |      |  ||   |  | ||| |||||   | ||   |   ||     |  | |||     
AAGAAGCAGTTGAGAAAGATGCTACAAAGACTGCAGTAACTGATGGAACTGTCCATCCTTTGACAAGCTATGTGATTAACTATGTGAAGTTTTTATTTGAgtaagt------tcatatgtgctgtattctgcttcaaattctcaaccacacccatgaagttatctctagcattgtatatt-gttttcattggtgaaaaagctgcatc

upper sequence: LOC_Os04g58880.1 (Oryza sativa), 5'ss of exon 7
lower sequence: GLYMA10G23810.1 (Glycine max), 5'ss of exon 7
AAGAAGCTGTTGAAAAGGACGCAACAAAGAATATTCATATTGATGGGACAGTGCATCCTTTGACGAGCTACGTGATTAACTATGTCAAATTTTTATTTGAgtaagtatatgatcatgtgcacttaatctttcctgtaatttgatagttgcattgctatactt---tcttgcatttcttcttcaatcctatccaccagtatgct-----
||||||| ||||| || || || ||||||| |      | |||||| || || ||||||||||| ||||| |||||||||||||| || |||||||||||||||||      |||| |   ||  ||  | | |  ||||    ||  ||| |  |  | ||   ||| |||||   | ||   |   ||     || | |||     
AAGAAGCAGTTGAGAAAGATGCTACAAAGACTGCAGTAACTGATGGAACTGTCCATCCTTTGACAAGCTATGTGATTAACTATGTGAAGTTTTTATTTGAgtaagt------tcatttctgctgtattctgcttcaaattctcgagc-gcactcatgaagttatgtctagcattgtatatt-gttttaattggtgagaaagctgcgtc

upper sequence: LOC_Os04g58880.1 (Oryza sativa), 5'ss of exon 7
lower sequence: Vv13s0073g00170.t01 (Vitis vinifera), 5'ss of exon 7
AAGAAGCTGTTGAAAAGGACGCAACAAAGAATATTCATATTGATGGGACAGTGCATCCTTTGACGAGCTACGTGATTAACTATGTCAAATTTTTATTTGAgtaagta--tatgatcatgtgcacttaatctttcctgtaatttgatagttgcattg--ctatactttcttgcatttcttcttcaatcctatccaccagtatgct
||||||| |||||||| || |||||||| | |  |     |||||| || || ||||||||||| ||||| ||||| |||||||| || ||| | ||||||||||    | |||   |||   ||   |  |  ||  | | |  | |            | | |||| | |||      |       | || |  ||  |   
AAGAAGCAGTTGAAAAAGATGCAACAAAAACTGCTGTGTCTGATGGAACTGTTCATCCTTTGACAAGCTATGTGATCAACTATGTGAAGTTTCTTTTTGAgtaagcccctctgactgtgt-tgctatcttctagctccattcttttgggcaagacagataacagtttcatccatgctaattggtggtatttctattagggt---

upper sequence: LOC_Os04g58880.1 (Oryza sativa), 5'ss of exon 7
lower sequence: Vv08s0007g02340.t01 (Vitis vinifera), 5'ss of exon 7
AAGAAGCTGTTGAAAAGGACGCAACAAAGAATATTCATATTGATGGGACAGTGCATCCTTTGACGAGCTACGTGATTAACTATGTCAAATTTTTATTTGAgtaagtatatgatcatgtgcacttaatctttcctgtaatttgatagttgcattgctatactttcttgca--tttcttcttcaatcctatccaccagtatgct-
||||||| || ||||| || || ||||| | |  |  | ||||||| || |||||||||||||| ||||| || ||||| || || || ||||||||||||||||| |||     |||||  |  ||||  | ||   || |||  || ||| |  | | | |  |  |  | | |  | |  |  ||| |     |||| | 
AAGAAGCCGTAGAAAAAGATGCCACAAAAACTGCTGTTCTTGATGGAACTGTGCATCCTTTGACAAGCTATGTAATTAATTACGTGAAGTTTTTATTTGAgtaagtctatataactgtgctgtccatct--catgctgtt-gatcctttcatagacagaatctagtaaaagtatatgttgccctattattccttgatatgttc

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|29669620|gb|CB665895.1|CB665895
EST:     GTGCATCCTTTGACGAGCTACGTGATTAACTATGTCAAATTTTTATTTGA                         CTACCAGTCAACTCTAAAACAGCTCTTCCAGGAGTTCAAAAGGGAAGATGG
genomic: GTGCATCCTTTGACGAGCTACGTGATTAACTATGTCAAATTTTTATTTGAgtaagtatat ... tctttcgcagCTACCAGTCAACTCTAAAACAGCTCTTCCAGGAGTTCAAAGGGGAAGATGG
EST: gi|29677753|gb|CB674028.1|CB674028
EST:     GTGCATCCTTTGACGAGCTACGTGATTAACTATGTCAAATTTTTATTTGA                         CTACCAGTCAACTCTAAAACAGCTCTTCCAGGAGTTCAAAAGGGAAGATGG
genomic: GTGCATCCTTTGACGAGCTACGTGATTAACTATGTCAAATTTTTATTTGAgtaagtatat ... tctttcgcagCTACCAGTCAACTCTAAAACAGCTCTTCCAGGAGTTCAAAGGGGAAGATGG
EST: gi|29665182|gb|CB661457.1|CB661457
EST:     GTGCATCCTTTGACGAGCTACGTGATTAACTATGTCAAATTTTTATTTGA                         CTACCAGTCAACTCTAAAACAGCTCTTCCAGGAGTTCAAAAGGGAAGATGG
genomic: GTGCATCCTTTGACGAGCTACGTGATTAACTATGTCAAATTTTTATTTGAgtaagtatat ... tctttcgcagCTACCAGTCAACTCTAAAACAGCTCTTCCAGGAGTTCAAAGGGGAAGATGG

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: 66 (upstream exon), 64 (downstream exon)
Score: 44

AAGAAGCTGTTGAAAAGGACGCAACAAAGAATATTCATATTGATGGGACAGTGCATCCTTTGACGAGCTACGTGATTAACTATGTCAAATTTTTATTTGAgtaagtatat ... tctttcgcagCTACCAGTCAACTCTAAAACAGCTCTTCCAGGAGTTCAAAGGGGAAGATGGAACAGGTTCTGAGTTGGCCACTGTAACCATGAGTATCATGCAGGCTTTA




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