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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagaccctttccaacaccaattttttttatggcatttaatatgtgagacacctgtgttcttcaattcattgtcctcccttactgtagGTCACAAGAGCAATTCTTGAAAACCCAAGTGACAATACGAAAGTGCACTTAATCTATGCCAATGTCACATATGATGACATTCTTCTAAAG

Basic information

species Oryza sativa
transcript LOC_Os05g40990.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os05g40990.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GLYMA20G05640.1 (Glycine max), 3'ss of exon 5
----------gtaaga----ccctttccaacaccaatttttt--ttatggcattt--aatatgtgagacacctgtgttcttcaattcat-tgtcctcccttactgtagGTCACAAGAGCAATTCTTGAAAACCCAAGTGACAATACGAAAGTGCACTTAATCTATGCCAATGTCACATATGATGACATTCTTCTAAAG
          ||||      || | ||   |    || |||   ||    |||||   |  | |||   | |  |  |  |  ||  || | |      || ||  |||| |||||||| ||  | ||||||| |   ||||| || ||  |  | || || |||||||||||||||| ||||||||||||| | |||
gtatgtgtaagtaaaggattccgtgtcttcctttgatctttcaatttctacatttttgaactttgaattagcaataattatatatatatatatttcttttttcttgagGTTACAAGAGCTATATTAGAAAACCAACAGGACAAAACCAACATAAATTTGATATATGCCAATGTCACATTTGATGACATTCTTTTGAAG

upper sequence: LOC_Os05g40990.1 (Oryza sativa), 3'ss of exon 5
lower sequence: Vv06s0009g01710.t01 (Vitis vinifera), 3'ss of exon 5
------------------------gtaagaccctttccaacaccaattttttttatggcatttaatatgtgagacacct-gtgttcttcaatt--cattgtcctcccttactg----tagGTCACAAGAGCAATTCTTGAAAACCCAAGTGACAATACGAAAGTGCACTTAATCTATGCCAATGTCACATATGATGACATTCTTCTAAAG
                        |   || ||||| | | |    |  ||| |||  ||  ||   |  |   ||  | | |||    ||||    |||   |  ||| ||     |||||||| ||||| ||  | |||||||||||||||||||| || |||||  | || |||||||||||||||||||| ||||||||| |||||
gtctgcattttacaagtggaaggagctggagccttttccatatagctcctttatatttcacatatcttcggcatcattttgggtttgataattgcttttgcttttacttgctccttttagGTCACTAGAGCCATATTAGAAAACCCAAGTGACAATACCAAGGTGCATCTTATTTATGCCAATGTCACATATGAGGACATTCTTTTAAAG
















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|29662070|gb|CB658345.1|CB658345
EST:     GAGCATTTGGAATGTTAGCTGGAGGATCAGGCATTACCCCAATGTTCCAA                         GTCACAAGAGCAATTCTTGAAAACCCAAGTGACAATACGAAAGTGCACTTA
genomic: GAGCATTTGGAATGTTAGCTGGAGGATCAGGCATTACCCCAATGTTCCAAgtaagaccct ... cttactgtagGTCACAAGAGCAATTCTTGAAAACCCAAGTGACAATACGAAAGTGCACTTA
EST: gi|3767986|gb|AU032013.1|AU032013
EST:     GAGCATTTGGAATGTTAGCTGGAGGATCAGGCATTACCCCAATGTTCCAA                         GTCACAAGAGGCAATTCTTGAAAACCCAAGTGACCAATCCGAAAGTGCACT
genomic: GAGCATTTGGAATGTTAGCTGGAGGATCAGGCATTACCCCAATGTTCCAAgtaagaccct ... cttactgtagGTCACAAGA-GCAATTCTTGAAAACCCAAGTGA-CAATACGAAAGTGCACT

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: 43 (upstream exon), 58 (downstream exon)
Score: 16

GGTCGCTTCAAATACCAACCTGGGCAAGTAAGAGCATTTGGAATGTTAGCTGGAGGATCAGGCATTACCCCAATGTTCCAAgtaagaccct ... cttactgtagGTCACAAGAGCAATTCTTGAAAACCCAAGTGACAATACGAAAGTGCACTTAATCTATGCCAATGTCACATATGATGACATTCTTCTAAAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

catttaatatgtgagacacctgtgttcttcaattcattgtcctcccttactgtagGTCACAAGAGCAATTCTTGAAAACCCAAGTGACAATACGAAAGTGCACTTAATCTATGCCAATGTCACATATGATGACATTCTTCTAAAG
                                           cccttac  putative branch site (score: 16)
                                ttcattgtcctccctt  CT-rich tract
                              aattcatt  TA-rich tract