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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacttttttcaaatgttaaaattgtaaatgatttctattctccttaatttttatttgttttgttatatatatttcagATGCCTAATCTTGCGGATGAATGGGGAACTTTCTGTGTTGGACATGGATGATGGACATGAACAATCACTTACTAATTCAGTTGAATTATTTTGGGTCACT

Basic information

species Oryza sativa
transcript LOC_Os02g54500.1
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g54500.1 (Oryza sativa), 3'ss of exon 8
lower sequence: GRMZM2G052750_T02 (Zea mays), 3'ss of exon 8
gtacttttttcaaatgttaaaattgtaaatgatttctattctccttaatttttatttgttttgttatatat-atttcagATGCCTAATCTTGCGGATGAATGGGGAACTTTCTGTGTTGGACATGGATGATGGACATGAACAATCACTTACTAATTCAGTTGAATTATTTTGGGTCACT
|||||||   |       | |||  || |  ||  || ||||||||  ||||||||  |||| |||| ||| || |||||||  | ||||||||||  |||||||| ||||||||| | |||||||| ||||||||||||||  | ||||| |||||| ||||| | ||||||||||| 
gtactttcgcc-----ccataatgttacacaatc-cttttctcctttgtttttattgttttttttatttatgatatcagATGTTTGATCTTGCGGACCAATGGGGAGCTTTCTGTGCTTGACATGGACGATGGACATGAACACGCTCTTACAAATTCAATTGAACTCTTTTGGGTCACC

upper sequence: LOC_Os02g54500.1 (Oryza sativa), 3'ss of exon 8
lower sequence: GRMZM2G475867_T01 (Zea mays), 3'ss of exon 8
gtacttttttcaaatgttaaaattgtaaatgatttctattctccttaatttttatttgttttgttatatat-atttcagATGCCTAATCTTGCGGATGAATGGGGAACTTTCTGTGTTGGACATGGATGATGGACATGAACAATCACTTACTAATTCAGTTGAATTATTTTGGGTCACT
||| ||  | |      ||| | ||| |   | | || || |||||  |||||||| ||||| | || ||| |  |||||||  | ||||||||||  |||||||| ||||||||| | |||||||| ||||||||||||||  | || || |||||| ||||| | ||||||||||| 
gtatttcctcc--cccctaataatgttacataatccttttatcctttgtttttatt-gttttttaatttatgaaatcagATGTTTGATCTTGCGGACCAATGGGGAGCTTTCTGTGCTTGACATGGACGATGGACATGAACACACTCTCACAAATTCAATTGAACTCTTTTGGGTCACC
















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|29627817|gb|CB632828.1|CB632828
EST:     CCGAAACATGATACTAATGGATCTTCTGACTTGTCCCAACAACCTTCAAG                         ATGCCTAATCTTGCGGATGAATGGGGAACTTTCTGTNGT-GGACATGGATG
genomic: CCGAAACATGATACTAATGGATCTTCTGACTTGTCCCAACAACCTTCAAGgtactttttt ... tatatttcagATGCCTAATCTTGCGGATGAATGGGGAACTTTCTGT-GTTGGACATGGATG
EST: gi|29686600|gb|CB682875.1|CB682875
EST:     CCGAAACATGATACTAATGGATCTTCTGACTTGTCCCAACAACCTTCAAG                         ATGCCTAATCTTGCGGATGAATGGGGAACTTTCTGTGTTGGACATGGATGA
genomic: CCGAAACATGATACTAATGGATCTTCTGACTTGTCCCAACAACCTTCAAGgtactttttt ... tatatttcagATGCCTAATCTTGCGGATGAATGGGGAACTTTCTGTGTTGGACATGGATGA
EST: gi|58607153|gb|CK035186.1|CK035186
EST:     CAACAACCTTCAAG                         ATGCCTAATCTTGCGGATGAATGGGGAACTTTCTGTGTTGGACATGGATGA
genomic: CAACAACCTTCAAGgtactttttt ... tatatttcagATGCCTAATCTTGCGGATGAATGGGGAACTTTCTGTGTTGGACATGGATGA
EST: gi|58674739|gb|CK063426.1|CK063426
EST:     CCGAAACATGATACTAATGGATCTTCTGACTTGTCCCAACAACCTTCAAG                         ATGCCTAATCTTGCGGATGAATGGGGAACTTTCTGTGTTGGACATGGATGA
genomic: CCGAAACATGATACTAATGGATCTTCTGACTTGTCCCAACAACCTTCAAGgtactttttt ... tatatttcagATGCCTAATCTTGCGGATGAATGGGGAACTTTCTGTGTTGGACATGGATGA
EST: gi|29673628|gb|CB669903.1|CB669903
EST:     CCGAAACATGATACTAATGGATCTTCTGACTTGTCCCAACAACCTTCAAG                         ATGCCTAATCTTGCGGATGAATGGGGAACTTTCTGTGTTGGACATGGATGA
genomic: CCGAAACATGATACTAATGGATCTTCTGACTTGTCCCAACAACCTTCAAGgtactttttt ... tatatttcagATGCCTAATCTTGCGGATGAATGGGGAACTTTCTGTGTTGGACATGGATGA
EST: gi|2310509|gb|C26664.1|C26664
EST:     CTGACTTGTCCCAACAACCTTCAAG                         ATGCCTAATCTTGCGGATGAATGGGGAACTTTCTGTGTTGGACATGGATGA
genomic: CTGACTTGTCCCAACAACCTTCAAGgtactttttt ... tatatttcagATGCCTAATCTTGCGGATGAATGGGGAACTTTCTGTGTTGGACATGGATGA
EST: gi|58612546|gb|CK040258.1|CK040258
EST:     CCGAAACATGATACTAATGGATCTTCTGACTTGTCCCAACAACCTTCAAG                         ATGCCTAATCTTGCGGATGAATGGGGAACTTTCTGTGTTGGACATGGATGA
genomic: CCGAAACATGATACTAATGGATCTTCTGACTTGTCCCAACAACCTTCAAGgtactttttt ... tatatttcagATGCCTAATCTTGCGGATGAATGGGGAACTTTCTGTGTTGGACATGGATGA

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: 61 (upstream exon), 58 (downstream exon)
Score: 13

GTCCACCTGTTTCGATGCGCTTCATTCCTGAACCAACTGATGAAGGAAAGCCGAAACATGATACTAATGGATCTTCTGACTTGTCCCAACAACCTTCAAGgtactttttt ... tatatttcagATGCCTAATCTTGCGGATGAATGGGGAACTTTCTGTGTTGGACATGGATGATGGACATGAACAATCACTTACTAATTCAGTTGAATTATTTTGGGTCACT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgtaaatgatttctattctccttaatttttatttgttttgttatatatatttcagATGCCTAATCTTGCGGATGAATGGGGAACTTTCTGTGTTGGACATGGATGATGGACATGAACAATCACTTACTAATTCAGTTGAATTATTTTGGGTCACT
                   ccttaat  putative branch site (score: 13)
             tattctccttaatttt  TA-rich tract