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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tttgccgctacatatgcaattgtttacgttacagaataaaatatgcttgtaacgactgaatcgagaggttatccaatgattgtctctattttgtgtatagGTACCGTGAATTGGCACACCGGGTGGATGAGGCACTTGGCTTCATGACTGCAGCAGGGCTAACAGTCGACCATCCGATAATGACAACAACTGACTTCTGG

Basic information

species Oryza sativa
transcript LOC_Os07g42960.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os07g42960.2 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G365160_T02 (Zea mays), 3'ss of exon 2
tttgccgctacatatgcaattgtttacgttacagaataaaatatgcttgtaacgactgaatcgagag-gttatccaatgattg---tctctatt----ttgtgtatagGTACCGTGAATTGGCACACCGGGTGGATGAGGCACTTGGCTTCATGACTGCAGCAGGGCTAACAGTCGACCATCCGATAATGACAACAACTGACTTCTGG
|| ||| |||| | | | ||| | | || || | || ||| | | | ||| ||| ||| | | ||| | | |||||||||||||||||||| || |||||||||| || ||||| |||||||||||| | ||||| ||||||||||| ||||||||||| || ||||||||||||
-------atatttatctaattttggttgaattaaaattgtgtgt-ctgcaaatggctaaatatatatcataatctgatgtttgatattttcattggaatgatatatagGTACCGTGAATTGGCCCATAGGGTGGATGATGCTCTTGGGTTCATGACTGCATCGGGGCTTACAGTCGACCACCCGATAATGACGACTACTGACTTCTGG

upper sequence: LOC_Os07g42960.2 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G359822_T01 (Zea mays), 3'ss of exon 2
tttgccgctacatatgcaattgtttacgt-tacagaataaaatatgcttgtaacgactgaatcgagaggttatccaatgattgtctctattttgtgtatagGTACCGTGAATTGGCACACCGGGTGGATGAGGCACTTGGCTTCATGACTGCAGCAGGGCTAACAGTCGACCATCCGATAATGACAACAACTGACTTCTGG---------------------
| |||||| | | | | | |||||| | | | | || | | || || | | |||| ||||||||||||||| || ||||||||||||| ||||| |||||||||||||||||||| ||||||||||| ||||||||||| || ||||||||||||
-------------ttaaaattgtgtgtctgcaaatggttaaatatatatatcataatctgat---------gttcgatattttcattggcatgccatatacgtaccgtgaattggcccatagGGTGGATGAGGCTCTTGGGTTCATGACTGCAGCAGGGCTTACAGTCGACCACCCGATAATGACGACTACTGACTTCTGGACCTCGCATGAGTGCCTTCTC

upper sequence: LOC_Os07g42960.2 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G117707_T02 (Zea mays), 3'ss of exon 2
tttgccgctacatatgcaattg-tttacgttacagaataaaatatgcttgtaa-cgactgaatcgagag-gttatccaatgatt-----gtctctatt----ttgtgtatagGTACCGTGAATTGGCACACCGGGTGGATGAGGCACTTGGCTTCATGACTGCAGCAGGGCTAACAGTCGACCATCCGATAATGACAACAACTGACTTCTGG
| | || | ||| ||| | | || | || ||| || | ||| | | | ||| ||| || | | ||| | | |||||||||||||||||| || ||||||||||||| ||||| |||||||||||||||||||| ||||| ||||| ||||||||||| || ||||||||||||
------------tgttcatctaattttggttgaaataaaatttgtgtttgcaaatggtcaaataaatatcataatctgatggtttgagtattttcattggaatgacatctagGTACCGTGAATTGGCCCATAGGGTGGATGAGGCTCTTGGGTTCATGACTGCAGCAGGGCTTACAGTTGACCACCCGATAATGACGACTACTGACTTCTGG

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|29616018|gb|CB621030.1|CB621030
EST:     GTCACGCAGTGGAACCTCGATTTCATGGATCACAGCGAACAAGGAGACAG                         GTACCGTGAATTGGCACACCGGGTGGATGAGGCACTTGGCTTCATGACTGC
genomic: GTCACGCAGTGGAACCTCGATTTCATGGATCACAGCGAACAAGGAGACAGgtgagaaatt ... ttgtgtatagGTACCGTGAATTGGCACACCGGGTGGATGAGGCACTTGGCTTCATGACTGC
EST: gi|13165446|gb|AU174243.1|AU174243
EST:     GTCACGCAGTGGAACCTCGATTTCATGGATCACAGCGAACAAGGAGACAG                         GTACCGTGAATTGGCACACCGGGTGGATGAGGCACTTGGCTTCATGACTGC
genomic: GTCACGCAGTGGAACCTCGATTTCATGGATCACAGCGAACAAGGAGACAGgtgagaaatt ... ttgtgtatagGTACCGTGAATTGGCACACCGGGTGGATGAGGCACTTGGCTTCATGACTGC
EST: gi|428990|gb|D25146.1|D25146
EST:     CTCGATTTCATGGATCACAGCGAACAAGGAGACAG                         GTACCGTGAATTGGCACACCGGGTGGATGAGGCACTTGGCTTCATGACTGC
genomic: CTCGATTTCATGGATCACAGCGAACAAGGAGACAGgtgagaaatt ... ttgtgtatagGTACCGTGAATTGGCACACCGGGTGGATGAGGCACTTGGCTTCATGACTGC

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: 73 (upstream exon), 75 (downstream exon)
Score: 141

TCAACCTGCTCCGCGCCTTCGCCACGGGAGGGTACGCCGCCATGCAGCGCGTCACGCAGTGGAACCTCGATTTCATGGATCACAGCGAACAAGGAGACAGgtgagaaatt ... ttgtgtatagGTACCGTGAATTGGCACACCGGGTGGATGAGGCACTTGGCTTCATGACTGCAGCAGGGCTAACAGTCGACCATCCGATAATGACAACAACTGACTTCTGG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttgtaacgactgaatcgagaggttatccaatgattgtctctattttgtgtatagGTACCGTGAATTGGCACACCGGGTGGATGAGGCACTTGGCTTCATGACTGCAGCAGGGCTAACAGTCGACCATCCGATAATGACAACAACTGACTTCTGG
 ttgtaac  putative branch site (score: 141)
 tctctatttt  putative PPT
 tctatttt  TA-rich tract