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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagcccagcgccctgcagggagcacgtaacgctctctctggtcggccgggcccacctgtcagagccatccaattgggatctgacctgccacgtgtccgtttcttacagGGCCTCGGGATTACGCTGTTCGGCATGGCCTACATGTTCGTCCACGACGGCCTGGTCCACCGCCGCTTCCCCGTCGGCCCCATCGCGAATGTGCCCTACT

Basic information

species Oryza sativa
transcript LOC_Os04g48880.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os04g48880.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G164318_T01 (Zea mays), 3'ss of exon 3
-------------------------------------gtaagcccagc-gccctgcagggagcacgtaacgctctctctggtcggccgggcc-cacctgtcag--agccatccaattgggatctgacctgccacgtgtccgtttcttacagGGCCTCGGGATTACGCTGTTCGGCATGGCCTACATGTTCGTCCACGACGGCCTGGTCCACCGCCGCTTCCCCGTCGGCCCCATCGCGAATGTGCCCTACT
                                     ||  |   ||  |    || ||  | ||  | |  | |  ||||| ||| |||   |    |||||  |   |||| | || ||||| |||  |||||||||    ||  |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| || |||||||||||||| || ||||||||||
gtaagctagccacgtacagtatctcggtgtgttgtgtgtctggttagttggttggctggctggacccagctgt-tgcctggtaggcagggtggctggcgtcagccacgtatccgactgtgatctcaccctccacgtgtcttcctcccacagGGCCTCGGGATTACGCTGTTCGGCATGGCCTACATGTTCGTCCACGACGGCCTGGTCCACCGCCGCTTTCCGGTCGGCCCCATCGCCAACGTGCCCTACT

upper sequence: LOC_Os04g48880.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G090051_T02 (Zea mays), 3'ss of exon 2
--gtaagcccagcgccctgcagggagcacgtaacgctctctctggtcggccgggcccacctgtcagagccatccaattgggatctgacctgccacgtgtccgtttcttacagGGCCTCGGGATTACGCTGTTCGGCATGGCCTACATGTTCGTCCACGACGGCCTGGTCCACCGCCGCTTCCCCGTCGGCCCCATCGCGAATGTGCCCTACT
    | |  |  |  |  |   || |  |    | |   | | | ||||||||  |  |    |       ||  | | || |||| || ||  ||    | |      ||||| || ||||| ||| ||||||| ||||||||||||||||| ||||||||||| ||||||||||||||||||||||| ||||||| ||| ||||||||||
gtacacggtcttcctctggtgtggtggccaaggcacgtgcac-gctcggccggctctgctctgc-------tctgacttggctctggccggcgtcgctcgcat----cgcagGGGCTGGGGATCACGTTGTTCGGGATGGCCTACATGTTCGTGCACGACGGCCTCGTCCACCGCCGCTTCCCCGTCGGGCCCATCGAGAACGTGCCCTACT

upper sequence: LOC_Os04g48880.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G152135_T06 (Zea mays), 3'ss of exon 3
-------------------------------------gtaagcccagcgccctgcagggagcacgtaacgctctctctggtcggccgggcccacctgtcag-----agccatccaattgggatctgacctgccacgtgtccgtttcttacagGGCCTCGGGATTACGCTGTTCGGCATGGCCTACATGTTCGTCCACGACGGCCTGGTCCACCGCCGCTTCCCCGTCGGCCCCATCGCGAATGTGCCCTACT
                                     ||      ||     ||   |||  ||  | | |||||   ||| |  |  |||  ||||||||      |  |||| | || ||||| |||  |||||||||    | | ||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| || ||||||||||||||  | ||||||||||
gtaagctagctagctagccacggactgtgcctggttagtttagttagttggttggtcggatgacccacctctctcagcggtggtgcctgcctgcctgtcagccacgggggatccgactgtgatctcaccctccacgtgtcttcatgtcacagGGCCTGGGGATTACGCTGTTCGGCATGGCCTACATGTTCGTCCACGACGGCCTGGTCCACCGCCGCTTTCCGGTCGGCCCCATCGCCGACGTGCCCTACT

upper sequence: LOC_Os04g48880.1 (Oryza sativa), 3'ss of exon 3
lower sequence: Vv02s0025g00240.t01 (Vitis vinifera), 3'ss of exon 4
gtaagcccagcgccctgcagggagcacgtaacgctctctctggtcggccgggcccacctgtcagagccatccaattgggatctgacctgccacgtgtccgtttcttacagGGCCTCGGGATTACGCTGTTCGGCATGGCCTACATGTTCGTCCACGACGGCCTGGTCCACCGCCGCTTCCCCGTCGGCCCCATCGCGAATGTGCCCTACT
 || |    | |   |  | ||||     || | ||    |||    | |     || | |  |     | | | |    | |    |   |  | |   ||| |  ||||| || || || ||  |||| ||||||||||||||||| |||||||||||||| |||||||| || ||||| ||||| |||||||| || || || ||  
ttacgtggcgtggtgttgatggagagaagaaagatc---gtgggaatctgtttttacattttggcatgtttctaat----tttagttt--tatttatttattt-tcgcagGGACTAGGAATAACAGTGTTTGGCATGGCCTACATGTTTGTCCACGACGGCCTTGTCCACCGTCGATTCCCTGTCGGACCCATCGCCAACGTCCCTTATC

upper sequence: LOC_Os04g48880.1 (Oryza sativa), 3'ss of exon 3
lower sequence: EDO99380 (Chlamydomonas reinhardtii), 3'ss of exon 4
---------gtaagcccagcgccctgcagggagcacgtaacgctctct-ctggtcggccgggcccacctgtcagag--ccatccaa----ttgggatctgacctgccacgtgtccgtttcttacagGGCCTCGGGATTACGCTGTTCGGCATGGCCTACATGTTCGTCCACGACGGCCTGGTCCACCGCCGCTTCCCCGTCGGCCCCATCGCGAATGTGCCCTACT
         |   || |     |  || ||| |   | | | |  ||| |   |   ||    | ||||| |      |||||| |           | || | ||  |||||  | |||     ||| || || || |||||||||||||| |||||||||||| |||||||||||||||| ||||||||||||||||| |                        
tcatactacgcgtgctccatctcgggcggggcggtggcatcccattcttcccatttcccaccactacctgcctacctcccatcccaaacccccaacccagATCGGCGGCGTGT--GCTTCGGCGCGGGTCTGGGCATCACGCTGTTCGGCATCGCCTACATGTTCTTCCACGACGGCCTGGTGCACCGCCGCTTCCCCGTGG------------------------

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|86478555|gb|CI121188.1|CI121188
EST:     CTGCTTCGGCGCG                         GGCCTCGGGATTACGCTGTTCGGCATGGCCTACATGTTCGTCCACGACGGC
genomic: CTGCTTCGGCGCGgtaagcccag ... tttcttacagGGCCTCGGGATTACGCTGTTCGGCATGGCCTACATGTTCGTCCACGACGGC




















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: 20 (upstream exon), 31 (downstream exon)
Score: 1

CAACGACGTGTTCGCCATCACCAACGCCGTGCCGGCCATCTCCCTCCTCGCCTACGGCTTCTTCCACCGGGGCATCGTCCCCGGCCTCTGCTTCGGCGCGgtaagcccag ... tttcttacagGGCCTCGGGATTACGCTGTTCGGCATGGCCTACATGTTCGTCCACGACGGCCTGGTCCACCGCCGCTTCCCCGTCGGCCCCATCGCGAATGTGCCCTACT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acctgtcagagccatccaattgggatctgacctgccacgtgtccgtttcttacagGGCCTCGGGATTACGCTGTTCGGCATGGCCTACATGTTCGTCCACGACGGCCTGGTCCACCGCCGCTTCCCCGTCGGCCCCATCGCGAATGTGCCCTACT
                        atctgac  putative branch site (score: 1)
                                         tccgtttctt  putative PPT
                                             tttctta  TA-rich tract