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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAATCTTCTTGGTGAAGATCTTGGGACACTTGGCATAAAAGAGCTAGAGCAGCTTGAGAAACAACTTGATTCATCCTTGAGGCACATTAGATCCACAAGGgtaatttgttaactgtttctcacatatgtttcagaaatgttgaaaaaaatttaactctaatcttgttgcag

Basic information

species Oryza sativa
transcript LOC_Os09g32948.1
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os09g32948.1 (Oryza sativa), 5'ss of exon 4
lower sequence: GRMZM2G097059_T01 (Zea mays), 5'ss of exon 4
GAATCTTCTTGGTGAAGATCTTGGGACACTTGGCATAAAAGAGCTAGAGCAGCTTGAGAAACAACTTGATTCATCCTTGAGGCACATTAGATCCACAAGGgtaatttgtt-----aactgtttctcacatatgtttcagaa--atgttgaaaaaaatttaactctaatcttgttgcag-----------------------
|||| | |||||||||||||| ||  |||||||  | |||||||| || ||||||||||| ||| ||||||||||||| || ||||| |||||||||||||| | | |||     |||| ||||  | ||  |||  |  |   | ||   |  ||  ||    | |      |||                         
GAATTTGCTTGGTGAAGATCTGGGTTCACTTGGTGTCAAAGAGCTTGATCAGCTTGAGAAGCAAATTGATTCATCCTTAAGTCACATAAGATCCACAAGGgtgactcgttgaacaaactatttccta-atgcgttaaaatatagtttttggacgaagctagtgttgacaacactgccctccatatttataattaatgaacc

upper sequence: LOC_Os09g32948.1 (Oryza sativa), 5'ss of exon 4
lower sequence: GRMZM2G129034_T02 (Zea mays), 5'ss of exon 4
GAATCTTCTTGGTGAAGATCTTGGGACACTTGGCATAAAAGAGCTAGAGCAGCTTGAGAAACAACTTGATTCATCCTTGAGGCACATTAGATCCACAAGGgtaatttgttaactgtttctcacatatgtttcagaaatgttgaaaaaaatttaactctaatcttgttgcag
|||| | |||||||||||||| ||| |||||||  | |||||||| |||||||||||||| ||||||||                                                                                                      
GAATTTGCTTGGTGAAGATCTGGGGTCACTTGGTGTCAAAGAGCTTGAGCAGCTTGAGAAGCAACTTga------------------------------------------------------------------------------------------------------

upper sequence: LOC_Os09g32948.1 (Oryza sativa), 5'ss of exon 4
lower sequence: GRMZM2G129034_T01 (Zea mays), 5'ss of exon 4
GAATCTTCTTGGTGAAGATCTTGGGACACTTGGCATAAAAGAGCTAGAGCAGCTTGAGAAACAACTTGATTCATCCTTGAGGCACATTAGATCCACAAGGgtaatttgtt-----aactgtttctca------catatgtttcaga-------aatgttgaaaaaa--att--taactctaatcttgttgcag-------
|||| | |||||||||||||| ||| |||||||  | |||||||| |||||||||||||| ||||||||||||||||| |||||||| ||||||||||||||||||  ||     |||  |||   |       || | |||  ||       | |||||| || |   ||  ||  ||||||      ||         
GAATTTGCTTGGTGAAGATCTGGGGTCACTTGGTGTCAAAGAGCTTGAGCAGCTTGAGAAGCAACTTGATTCATCCTTAAGGCACATAAGATCCACAAGGgtaattcattgaagaaaccattttctaatgcgttatttcttttggatgaagctagtgttgataacacagttcatatttctaattaacaagccattttgaa

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|55408991|gb|CV721367.1|CV721367
EST:     AGCTTGAGAAACAACTTGATTCATCCTTGAGGCACATTAGATCCACAAGG                         ACACAGCATATGCTTGATCAGCTCACTGATCTCCAGAGGAGG
genomic: AGCTTGAGAAACAACTTGATTCATCCTTGAGGCACATTAGATCCACAAGGgtaatttgtt ... cttgttgcagACACAGCATATGCTTGATCAGCTCACTGATCTCCAGAGGAGG
EST: gi|66915572|gb|CX102420.1|CX102420
EST:     CTTGATTCATCCTTGAGGCACATTAGATCCACAAGG                         ACACAGCATATGCTTGATCAGCTCACTGATCTCCAGAGGAGG
genomic: CTTGATTCATCCTTGAGGCACATTAGATCCACAAGGgtaatttgtt ... cttgttgcagACACAGCATATGCTTGATCAGCTCACTGATCTCCAGAGGAGG
EST: gi|55408198|gb|CV720574.1|CV720574
EST:     AGCTTGAGAAACAACTTGATTCATCCTTGAGGCACATTAGATCCACAAGG                         ACACAGCATATGCTTGATCAGCTCACTGATCTCCAGAGGAGG
genomic: AGCTTGAGAAACAACTTGATTCATCCTTGAGGCACATTAGATCCACAAGGgtaatttgtt ... cttgttgcagACACAGCATATGCTTGATCAGCTCACTGATCTCCAGAGGAGG

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: 64 (upstream exon), 42 (downstream exon)
Score: 141

GAATCTTCTTGGTGAAGATCTTGGGACACTTGGCATAAAAGAGCTAGAGCAGCTTGAGAAACAACTTGATTCATCCTTGAGGCACATTAGATCCACAAGGgtaatttgtt ... cttgttgcagACACAGCATATGCTTGATCAGCTCACTGATCTCCAGAGGAGG




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