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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gttgctggcctgaattctgtcaattcttcaatttaatgacccttttctcctactgagcttctctaatttcttgatttcgacaatgtctgttcttgtgcagAATGGCCGTGGAGAAGTTCCCAGACAACAGAATGCTTGGTCACCGTGAGATTGTTGACGGGAAG

Basic information

species Oryza sativa
transcript LOC_Os01g46750.3
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g46750.3 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G002614_T01 (Zea mays), 3'ss of exon 1
gttgctggcctga--attctgtcaattcttcaatttaatgacccttttctcctactgagcttctctaatttcttgatttcgacaatgtctg--ttcttgtgcagAATGGCCGTGGAGAAGTTCCCAGACAACAGAATGCTTGGTCACCGTGAGATTGTTGACGGGAAG
 |        ||   |     |   ||||| | || ||| |   |  | | ||  ||    ||||  | | ||  |||||   | | | ||  | |||   ||| ||||||||||||||||  ||| |||||||||||||||| || |||||||||||||| ||||||
ctcttaaatttggtgacatatttttttctttatttcaataaatatagtgttctcttg----tctcccaatactgaatttctttagtctgtggatccttacacagCATGGCCGTGGAGAAGTATCCAAACAACAGAATGCTTGGCCATCGTGAGATTGTTGATGGGAAG
















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|88741007|gb|CI764515.1|CI764515
EST:     GGCTTCCCGCCGCCCGTCGCCGGCCTGGACTGCTGCTACGACATCTTCCG                         AATGGCCGTGGAGAAGTTCCCAGACAACAGAATGCTTGGTCACCGTGAGAT
genomic: GGCTTCCCGCCGCCCGTCGCCGGCCTGGACTGCTGCTACGACATCTTCCGgtgagtggct ... tcttgtgcagAATGGCCGTGGAGAAGTTCCCAGACAACAGAATGCTTGGTCACCGTGAGAT
EST: gi|88739149|gb|CI762657.1|CI762657
EST:     GGCTTCCCGCCGCCCGTCGCCGGCCTGGACTGCTGCTACGACATCTTCCG                         AATGGCCGTGGAGAAGTTCCCAGACAACAGAATGCTTGGTCACCGTGAGAT
genomic: GGCTTCCCGCCGCCCGTCGCCGGCCTGGACTGCTGCTACGACATCTTCCGgtgagtggct ... tcttgtgcagAATGGCCGTGGAGAAGTTCCCAGACAACAGAATGCTTGGTCACCGTGAGAT
EST: gi|58691021|gb|CK079708.1|CK079708
EST:     CTGGACTGCTGCTACGACATCTTCCG                         AATGGCCGTGGAGAAGTTCCCAGACAACAGAATGCTTGGTCACCGTGAGAT
genomic: CTGGACTGCTGCTACGACATCTTCCGgtgagtggct ... tcttgtgcagAATGGCCGTGGAGAAGTTCCCAGACAACAGAATGCTTGGTCACCGTGAGAT

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: 21 (upstream exon), 64 (downstream exon)
Score: 6

ACGGCCGGCCCTCCGTGGGCCCCGCCTACCGGAGCGCCTTCGCCCGCGGCGGCTTCCCGCCGCCCGTCGCCGGCCTGGACTGCTGCTACGACATCTTCCGgtgagtggct ... tcttgtgcagAATGGCCGTGGAGAAGTTCCCAGACAACAGAATGCTTGGTCACCGTGAGATTGTTGACGGGAAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tctcctactgagcttctctaatttcttgatttcgacaatgtctgttcttgtgcagAATGGCCGTGGAGAAGTTCCCAGACAACAGAATGCTTGGTCACCGTGAGATTGTTGACGGGAAG
                                        tctgttctt  CT-rich tract
                  taatttcttgattt  TA-rich tract