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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgaggatatgataaaaacgctccattattaaaaccattccgtttcttggggaaatcatcattctaatgataatgctttgctttgtgacattgcagCCTGGAGAAAACACTAAGAAAGTTGTCTTGTATAACCACCGGCGATAGTATCATGGTAGCTTACAACAACAAACAATACTACATTGACATTGTTGAAACA

Basic information

species Oryza sativa
transcript LOC_Os04g48770.1
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os04g48770.2 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G114220_T01 (Zea mays), 3'ss of exon 7
gtgaggatatgataaaaacgctccattatt--------aaaaccattccgtttcttggggaaatcatcattctaatgataatgctttgctttgtgacattgcagCCTGGAGAAAACACTAAGAAAGTTGTCTTGTATAACCACCGGCGATAGTATCATGGTAGCTTACAACAACAAACAATACTACATTGACATTGTTGAAACA
|| |||| |   | ||||   |||  || |        |||  |  | | |||||   || | |   | || | ||  | ||   ||||| |   |  || |||| |||| |||||  ||||||| || || ||  ||||||| || || || ||||||||||| ||||||||||||||||| || ||||| ||||||||||||
gtaaggaaacctttaaaattgtcctataatgatcttgaaaattctcttcatttctcttggcattaggcgttatcattctcattacttgctgttaaattttccagCTTGGAAAAAACTTTAAGAAATTTCTCCTGCTTAACCACGGGAGACAGCATCATGGTAGCCTACAACAACAAACAATATTATATTGATATTGTTGAAACA
















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|427856|gb|D23997.1|D23997
EST:     CACAACTGACTTTTTGGACATCTCAAATCCGAA-GCCAT                         CCTGGAGAAAACACTAAGAAACTTCTCTTGTTTAACCACCGGCGATAGTAT
genomic: CACAACTGACTTTTTGGACATCTCAAATCCGAAGGCCATgtgaggatat ... gacattgcagCCTGGAGAAAACACTAAGAAAGTTGTCTTGTATAACCACCGGCGATAGTAT
EST: gi|58687667|gb|CK076354.1|CK076354
EST:     TTGCAGCCTCACACAACTGACTTTTTGGACATCTCAAATCCGAAGGCCAT                         CCTGGAGAAAACACTAAGAAACTTCTCTTGTTTAACCACCGGCGATAGTAT
genomic: TTGCAGCCTCACACAACTGACTTTTTGGACATCTCAAATCCGAAGGCCATgtgaggatat ... gacattgcagCCTGGAGAAAACACTAAGAAAGTTGTCTTGTATAACCACCGGCGATAGTAT
EST: gi|58595974|gb|CK006502.1|CK006502
EST:     TTGCAGCCTCACACAACTGACTTTTTGGACATCTCAAATCCGAAGGCCAT                         CCTGGAGAAAACACTAAGAAACTTCTCTTGTTTAACCACCGGCGATAGTAT
genomic: TTGCAGCCTCACACAACTGACTTTTTGGACATCTCAAATCCGAAGGCCATgtgaggatat ... gacattgcagCCTGGAGAAAACACTAAGAAAGTTGTCTTGTATAACCACCGGCGATAGTAT

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), 25 (downstream exon)
Score: 9

ACACTGTCCGTGTAAAAAATACAACCCTTCCCAAGGGTACATATGTCAAGTTGCAGCCTCACACAACTGACTTTTTGGACATCTCAAATCCGAAGGCCATgtgaggatat ... gacattgcagCCTGGAGAAAACACTAAGAAAGTTGTCTTGTATAACCACCGGCGATAGTATCATGGTAGCTTACAACAACAAACAATACTACATTGACATTGTTGAAACA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtttcttggggaaatcatcattctaatgataatgctttgctttgtgacattgcagCCTGGAGAAAACACTAAGAAAGTTGTCTTGTATAACCACCGGCGATAGTATCATGGTAGCTTACAACAACAAACAATACTACATTGACATTGTTGAAACA
                    ttctaat  putative branch site (score: 9)
                   attctaatgataat  TA-rich tract