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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgtgcttcagaatttattttagtttttgtttctctttattttaggaggatattctacccagttttgcaaatatgggtttctgatgttcttttattctcccaatcagGAAAATGGATATCAACTATTATTCCTCAGTGCTAGAGCTATAGTTCAGGCATACCTGACCAAAAACTTTCTATTCAACCTAAAACAG

Basic information

species Oryza sativa
transcript LOC_Os05g38710.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os05g38710.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G099481_T01 (Zea mays), 3'ss of exon 5
gtgtgcttcagaatttattttagtttttgtttctctttattttaggaggatattctacccagttttgcaaatatgg--gtttctgatgttcttttattctcccaatcagGAAAATGGATATCAACTATTATTCCTCAGTGCTAGAGCTATAGTTCAGGCATACCTGACCAAAAACTTTCTATTCAACCTAAAACAG
             |||  |  | ||| ||     |||   ||| |  |  | ||     |  || ||    | ||    | |||   || ||| |||| || ||| |||||||| || ||||||||| ||||||| ||||||||||| || || |||||||| || || || ||||| || || || || ||||||
------------gtttgatg-attttctgaaagacttccattttgatgcttctttcttgcctttgtggggttgtgcttatgtctagggtacttctatt-tctcaaccagGAAAACGGTTATCAACTACTATTCCTTAGTGCTAGAGCAATTGTCCAGGCATATCTCACGAAGAACTTCCTCTTTAATCTCAAACAG
















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|58663295|gb|CK051981.1|CK051981
EST:     GACGAGATTGGAGTCAGTCTGGTGTTGCTCGTCTTTTTTCTGCAATAAAG                         GAAAATGGATATCAACTATTATTCCTCAGTGCTAGAGCTATAGTTCAGGCA
genomic: GACGAGATTGGAGTCAGTCTGGTGTTGCTCGTCTTTTTTCTGCAATAAAGgtgtgcttca ... tcccaatcagGAAAATGGATATCAACTATTATTCCTCAGTGCTAGAGCTATAGTTCAGGCA
EST: gi|33657019|gb|CF279633.1|CF279633
EST:     GACGAGATTGGAGTCAGTCTGGTGTTGCTCGTCTTTTTTCTGCAATAAAG                         GAAAATGGATATCAACTATTATTCCTCAGTGCTAGAGC
genomic: GACGAGATTGGAGTCAGTCTGGTGTTGCTCGTCTTTTTTCTGCAATAAAGgtgtgcttca ... tcccaatcagGAAAATGGATATCAACTATTATTCCTCAGTGCTAGAGC
EST: gi|29646339|gb|CB651346.1|CB651346
EST:     GACGAGATTGGAGTCAGTCTGGTGTTGCTCGTCTTTTTTCTGCAATAAAG                         GAAAATGGATATCAACTATTATTCCTCAGTGCTA
genomic: GACGAGATTGGAGTCAGTCTGGTGTTGCTCGTCTTTTTTCTGCAATAAAGgtgtgcttca ... tcccaatcagGAAAATGGATATCAACTATTATTCCTCAGTGCTA

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: 67 (upstream exon), 70 (downstream exon)
Score: 24

GTCTGATGTGTTGGGCCAGGTCATGCCTTTAGTTGGACGAGATTGGAGTCAGTCTGGTGTTGCTCGTCTTTTTTCTGCAATAAAGgtgtgcttca ... tcccaatcagGAAAATGGATATCAACTATTATTCCTCAGTGCTAGAGCTATAGTTCAGGCATACCTGACCAAAAACTTTCTATTCAACCTAAAACAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttctacccagttttgcaaatatgggtttctgatgttcttttattctcccaatcagGAAAATGGATATCAACTATTATTCCTCAGTGCTAGAGCTATAGTTCAGGCATACCTGACCAAAAACTTTCTATTCAACCTAAAACAG
                          ttctgat  putative branch site (score: 24)
                                tgttcttttattctcc  CT-rich tract
                                  ttcttttatt  TA-rich tract