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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TCCAGCTCAGGCAGCATCTTTACTAGTACTGGGGCCTTTCGTGGACTTCTGGCTGACCAACAAAAGAGTTGATACTTTCAATTACACAGCAATAGTTACGgtatgcggtgattctctgtttatcttgttataaactgatcattagaaacccatatagctctactgataatttcaccaggtaaatattaattaccatgaaa...

Basic information

species Oryza sativa
transcript LOC_Os05g12490.1
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os05g12490.1 (Oryza sativa), 5'ss of exon 5
lower sequence: GRMZM5G823629_T03 (Zea mays), 5'ss of exon 5
TCCAGCTCAGGCAGCATCTTTACTAGTACTGGGGCCTTTCGTGGACTTCTGGCTGACCAACAAAAGAGTTGATACTTTCAATTACACAGCAATAGTTACGgtatgcggtgattctctgtttatcttgttataaactgatcattagaaacccatatagctctactgataatttcaccaggtaaatattaattaccatgaaa---
|||||| ||||||||||| ||  || || |||||||||| ||||||||||||||||| ||||||||||||||| |||| || |||||| |||||||||||||||| | |  || |         ||  | |  |    |  |   ||| ||  | |        ||  |   || | | |  |    | |||   |   |   
TCCAGCGCAGGCAGCATCATTGTTAATAGTGGGGCCTTTTGTGGACTTCTGGCTGACTAACAAAAGAGTTGATGCTTTTAACTACACATCAATAGTTACGgtatgtgatacttgttctcaatcatttatgtttatgtcttttgcaaaatcctcacaag---gaagaggaacccatctgtttcactcaagttagtttagcactg

upper sequence: LOC_Os05g12490.1 (Oryza sativa), 5'ss of exon 5
lower sequence: GRMZM2G089630_T01 (Zea mays), 5'ss of exon 6
TCCAGCTCAGGCAGCATCTTTACTAGTACTGGGGCCTTTCGTGGACTTCTGGCTGACCAACAAAAGAGTTGATACTTTCAATTACACAGCAATAGTTACGgtatgcggtgattctctg-----tttatcttgt----tataaactgatcattagaaacccatatagctctactgataatttcaccaggtaaatattaattaccatgaaa
|||||| ||||||||||| ||  ||||| |||| ||||| ||||||||||||||||||||||||||||| ||| |||| || |||||| ||||||||||||||||   |  |  ||||     |||||  |||    |  ||| |  |||  || ||     |    |||  |   | |    | || |    |||   ||        
TCCAGCCCAGGCAGCATCGTTGTTAGTATTGGGTCCTTTTGTGGACTTCTGGCTGACCAACAAAAGAGTCGATGCTTTTAACTACACATCAATAGTTACGgtatgtcatactattctgaatcatttatgctgtcttttgcaaaatcgtcacgaggaagaggaacctgtctgttt-cactcaagctagtttggcattgtcta--------
















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|86504197|gb|CI146830.1|CI146830
EST:     ACCAACAAAAGAGTTGATACTTTCAATTACACAGCAATAGTTACG                         TTCTTCATCATACTGTCGTGCATAATTGCTGTTGGGACCAACCTTANCCCA
genomic: ACCAACAAAAGAGTTGATACTTTCAATTACACAGCAATAGTTACGgtatgcggtg ... tgcattgtagTTCTTCATCATACTGTCGTGCATAATTGCTGTTGGGACCAACCTTAGCCAA
EST: gi|86419895|gb|CI054696.1|CI054696
EST:     GCCTGACCAACAAAAGAGGTGATACTTTCAATTACACAGCAATAGTTACG                         TTCTTCATCATACTGTCGTGCATAATTGCTGTTGGGACCAACCTTAGCCAA
genomic: GGCTGACCAACAAAAGAGTTGATACTTTCAATTACACAGCAATAGTTACGgtatgcggtg ... tgcattgtagTTCTTCATCATACTGTCGTGCATAATTGCTGTTGGGACCAACCTTAGCCAA
EST: gi|86496386|gb|CI139019.1|CI139019
EST:     GGCTGACCAACAAAAGAGTTGATACTTTCAATTACACAGCAATAGTTACG                         TTCTTCATCATACTGTCGTGCATAATTGCTGTTGGGACCAACCTTAGCCAA
genomic: GGCTGACCAACAAAAGAGTTGATACTTTCAATTACACAGCAATAGTTACGgtatgcggtg ... tgcattgtagTTCTTCATCATACTGTCGTGCATAATTGCTGTTGGGACCAACCTTAGCCAA
EST: gi|55431370|gb|CV728698.1|CV728698
EST:     GGCTGACCAACAAAAGAGTTGATACTTTCAATTACACAGCAATAGTTACG                         TTCTTCATCATACTGTCGTGCATAATTGCTGTTGGGACCAACCTTAGCCAA
genomic: GGCTGACCAACAAAAGAGTTGATACTTTCAATTACACAGCAATAGTTACGgtatgcggtg ... tgcattgtagTTCTTCATCATACTGTCGTGCATAATTGCTGTTGGGACCAACCTTAGCCAA
EST: gi|86500611|gb|CI143244.1|CI143244
EST:     GGCTGACCAACAAAAGAGTTGATACTTTCAATTACACAGCAATAGTTACG                         TTCTTCATCATACTGTCGTGCATAATTGCTGTTGGGACCAACCTTAGCCAA
genomic: GGCTGACCAACAAAAGAGTTGATACTTTCAATTACACAGCAATAGTTACGgtatgcggtg ... tgcattgtagTTCTTCATCATACTGTCGTGCATAATTGCTGTTGGGACCAACCTTAGCCAA

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: 71 (upstream exon), 39 (downstream exon)
Score: 4

TCCAGCTCAGGCAGCATCTTTACTAGTACTGGGGCCTTTCGTGGACTTCTGGCTGACCAACAAAAGAGTTGATACTTTCAATTACACAGCAATAGTTACGgtatgcggtg ... tgcattgtagTTCTTCATCATACTGTCGTGCATAATTGCTGTTGGGACCAACCTTAGCCAATTCATATGCATCGGAAGATTTACAGCAGTCTCGTTCCAAGTTCTAGGCC




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