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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttaatcaataatagttgcctaatcagttagacgctgtctctggtgctgtttaggaagttcttatatatctcaaatgtggaccaccatttgcttactacagGTGGCAAGGATAATTTTGTTCATCTACTTGTTTTACCACATATACTTTCACATTGATCAG

Basic information

species Oryza sativa
transcript LOC_Os01g56230.5
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g56230.5 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM5G825226_T03 (Zea mays), 3'ss of exon 7
ttaatcaataatagttgcctaatcagttagacgctgtctctggtgctgtttaggaagttcttatatatctc-----aaatgtggaccaccatttgcttactacagGTGGCAAGGATAATTTTGTTCATCTACTTGTTTTACCACATATACTTTCACATTGATCAG
 | ||   |  | ||  ||||||||||  | |  |   ||| || ||| ||||  | ||  | |   | ||     ||  |||||   ||| ||||||  | ||||||||| |||| ||||||||| ||||||||||||||||||| ||||| |||  |||||||
-tgatttttttttgt--cctaatcagt--gccaatccttcttgtactgcttagtgactttctgttattttctatctaatcgtggagagccaattgcttcatgcagGTGGCACGGATCATTTTGTTCGTCTACTTGTTTTACCACATTTACTTCCACTATGATCAG
















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|29660432|gb|CB656707.1|CB656707
EST:     GATCGAAAGCCTATCTTGTCAATGGTGTTACAATGTTTGTTGCATGGCTG                         GTGGCAAGGATAATTTTGTTCATCTACTTGTTTTACCACATATACTTTCAC
genomic: GATCGAAAGCCTATCTTGTCAATGGTGTTACAATGTTTGTTGCATGGCTGgtaagtgaaa ... cttactacagGTGGCAAGGATAATTTTGTTCATCTACTTGTTTTACCACATATACTTTCAC
EST: gi|24208073|gb|AU225100.1|AU225100
EST:     GATCGAAAGCCTATCTTGTCAATGGTGTTACAATGTTTGTTGCATGGCTG                         GTGGCAAGGATAATTTTGTTCATCTACTTGTTTTACCACATATACT
genomic: GATCGAAAGCCTATCTTGTCAATGGTGTTACAATGTTTGTTGCATGGCTGgtaagtgaaa ... cttactacagGTGGCAAGGATAATTTTGTTCATCTACTTGTTTTACCACATATACT
EST: gi|88260142|gb|CI361643.1|CI361643
EST:     GTTGCATGGCTG                         GTGGCAAGGATAATTTTGTTCATCTACTTGTTTTACCACATATACTTTCAC
genomic: GTTGCATGGCTGgtaagtgaaa ... cttactacagGTGGCAAGGATAATTTTGTTCATCTACTTGTTTTACCACATATACTTTCAC

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: 70 (upstream exon), 75 (downstream exon)
Score: 11

GTTTCTTGATACTGTTGGAATGAAAAGATCGAAAGCCTATCTTGTCAATGGTGTTACAATGTTTGTTGCATGGCTGgtaagtgaaa ... cttactacagGTGGCAAGGATAATTTTGTTCATCTACTTGTTTTACCACATATACTTTCACATTGATCAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctgtttaggaagttcttatatatctcaaatgtggaccaccatttgcttactacagGTGGCAAGGATAATTTTGTTCATCTACTTGTTTTACCACATATACTTTCACATTGATCAG
                                           tgcttac  putative branch site (score: 11)
                                         tttgctt  CT-rich tract
               ttatatatctcaaat  TA-rich tract