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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgctttatataactatgttatgtccatttttaataacgagaataatagtctccttctgatcagactatttttttgttaatatgtttctattagCTACTCTGAGTCTGATTATTTCAAGCAAGCACTTCGCCAAGGTGCACCAGCAAAACCTAGGGAACCGAGAATTCCTCGAATGCCACACTT

Basic information

species Oryza sativa
transcript LOC_Os05g05780.1
intron # 16
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os05g05780.1 (Oryza sativa), 3'ss of exon 16
lower sequence: AC235535.1_FGT001 (Zea mays), 3'ss of exon 16
gtatgctttatataactatgttatgtccatttttaataacgagaataatagtctccttctgatcagactatttttttgttaatatgtttctattagCTACTCTGAGTCTGATTATTTCAAGCAAGCACTTCGCCAAGGTGCACCAGCAAAACCTAGGGAACCGAGAATTCCTCGAATGCCACACTT
                ||||        |||||| |   |  ||      ||||  | || ||  |||  | |||||    |  |||   |  ||||||||||||||||||||| || |||||||| |||||||||||||||||||| || |||||||| || || |||||  ||||||| |||||
---------------gtatgcacctcttattttttaggtcatgacacgctgtctaatacttatttgaccttattttt----aactgtcatttgtagCTACTCTGAGTCTGATTACTTTAAGCAAGCGCTTCGCCAAGGTGCACCAGCGAAGCCTAGGGAGCCAAGGATTCCAAGAATGCCGCACTT

upper sequence: LOC_Os05g05780.1 (Oryza sativa), 3'ss of exon 16
lower sequence: GRMZM2G010085_T01 (Zea mays), 3'ss of exon 13
gtatgctttatataactatgttatgtccatttttaataacgaga--ataatagtctccttctgatcagactatttttttgttaatatgtttctattagCTACTCTGAGTCTGATTATTTCAAGCAAGCACTTCGCCAAGGTGCACCAGCAAAACCTAGGGAACCGAGAATTCCTCGAATGCCACACTT
                     ||||  | | ||  ||    ||   ||  || | |  | || ||  |||  | ||||     |  |||   |  |||||||||||||||||| || || |||||||||||||||||||||||||||||||| ||||||||||| || |||||  ||||||| |||||
--------------------gtatgctcctcttctatttttaggccatggtactgtagtacttatttgaccttatttt-----aactgtcatttgtagCTACTCTGAGTCTGACTACTTTAAGCAAGCACTTCGCCAAGGTGCACCAGCAAAGCCTAGGGAACCAAGGATTCCAAGAATGCCGCACTT

upper sequence: LOC_Os05g05780.1 (Oryza sativa), 3'ss of exon 16
lower sequence: EFJ06565 (Selaginella moellendorffii), 3'ss of exon 16
gtatgctttatataactatgttatgtccatttttaataacgagaataatagtctccttctgatcagactatttttttgttaatatgttt--ctatt--agCTACTCTGAGTCTGATTATTTCAAGCAAGCACTTCGCCAAGGTGCACCAGCAAAACCTAGGGAACCGAGAATTCCTCGAATGCCACACTT
                                                 |||||   |  ||  | || |  ||||   ||||    ||  |||||  ||||||||||| || |||||||||||||||||| |  |    |||| | |    ||| |||  || ||  |||||||||||||||| ||  |
----------------------------------------------gtgagtctttcttcgaataaacaaccttttctctaatgctcttgactattgtagCTACTCTGAATCCGATTATTTCAAGCAAGCAATGAGAACCGGTGGATCGAGCAAATCTAAAGAGCCACGAATTCCTCGAATGCCTCAACT

upper sequence: LOC_Os05g05780.1 (Oryza sativa), 3'ss of exon 16
lower sequence: EFJ31365 (Selaginella moellendorffii), 3'ss of exon 16
gtatgctttatataactatgttatgtccatttttaataacgagaataatagtctccttctgatcagactatttttttgttaata----tgtttctattagCTACTCTGAGTCTGATTATTTCAAGCAAGCACTTCGCCAAGGTGCACCAGCAAAACCTAGGGAACCGAGAATTCCTCGAATGCCACACTT
                                                 |||||   |  ||  | || |  |||||  ||||     || || |  |||||||||||| || |||||||||||||||||| |  |    |||| | |    ||| |||  || ||  |||||||||||||||| || ||
----------------------------------------------gtgagtctttcttcgaataaacaaccttttt-ctaatgctcttgattattgtagCTACTCTGAATCCGATTATTTCAAGCAAGCAATGAGAACCGGTGGATCGAGTAAATCTAAAGAGCCACGAATTCCTCGAATGCCTCAATT

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|58692379|gb|CK081066.1|CK081066
EST:     GTCACTGACAACTGGATAGAGCCAACCAGCAGAAGAGAAAGGAAGCGAAA                         CTACTCTGAGTCTGATTATTTCAAGCAAGCACTTCGCC
genomic: GTCACTGACAACTGGATAGAGCCAACCAGCAGAAGAGAAAGGAAGCGAAAgtatgcttta ... tttctattagCTACTCTGAGTCTGATTATTTCAAGCAAGCACTTCGCC




















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: 74 (upstream exon), 71 (downstream exon)
Score: 34

GATGAAAACAAACTTGATTTTAAGAAGTTGGTCACTGACAACTGGATAGAGCCAACCAGCAGAAGAGAAAGGAAGCGAAAgtatgcttta ... tttctattagCTACTCTGAGTCTGATTATTTCAAGCAAGCACTTCGCCAAGGTGCACCAGCAAAACCTAGGGAACCGAGAATTCCTCGAATGCCACACTT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agaataatagtctccttctgatcagactatttttttgttaatatgtttctattagCTACTCTGAGTCTGATTATTTCAAGCAAGCACTTCGCCAAGGTGCACCAGCAAAACCTAGGGAACCGAGAATTCCTCGAATGCCACACTT
                                   tgttaat  putative branch site (score: 34)
                                             tttctatt  putative PPT
                         actatttttttgttaa  TA-rich tract