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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacgatgaaccaaaaatctaccttgcttttctagatttctgttttggctgactgttttgattccttattagGCTGTTGGGAAAGTCCTCCCTGAGCTAAATGGAAAGCTCACTGGTATGGCCTTCCGAGTTCCAACACCAAATGTGTCTGTTGTCGACTTGACCTGCCGGA

Basic information

species Oryza sativa
transcript LOC_Os02g07490.1
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g07490.1 (Oryza sativa), 3'ss of exon 10
lower sequence: GRMZM2G051004_T01 (Zea mays), 3'ss of exon 10
gtacgatgaaccaaaaatctaccttgctt-ttctagatttctgttttg-gctgactgttttgattcc-ttattagGCTGTTGGGAAAGTCCTCCCTGAGCTAAATGGAAAGCTCACTGGTATGGCCTTCCGAGTTCCAACACCAAATGTGTCTGTTGTCGACTTGACCTGCCGGA
|||     | |||||     ||| ||| | || |||| |    |||||  ||||||| ||| | |   || | |||||||||| ||||| || |||||||| ||||||||||||||||| ||||||||||||||||||||||||||||| |||||||| |||||||| |||||||
gtagctgaagccaaaggcacaccatgcgtattttagactcaaattttgcactgactgatttcactttgttgtcagGCTGTTGGAAAAGTTCTGCCTGAGCTGAATGGAAAGCTCACTGGCATGGCCTTCCGAGTTCCAACACCAAATGTCTCTGTTGTGGACTTGACATGCCGGA

upper sequence: LOC_Os02g07490.1 (Oryza sativa), 3'ss of exon 10
lower sequence: GRMZM2G104632_T01 (Zea mays), 3'ss of exon 10
gtacgatgaaccaaaaatctaccttgcttt-tctagatttctgttttg-gctgactgttttgattcc-ttattagGCTGTTGGGAAAGTCCTCCCTGAGCTAAATGGAAAGCTCACTGGTATGGCCTTCCGAGTTCCAACACCAAATGTGTCTGTTGTCGACTTGACCTGCCGGA
|||     | |||||     ||| || ||  | |||| |    |||||  || |||| ||| | |   || | |||||||||| |||||||| |||||||| |||||||| |||||||||||||||||||||||||||||||||||||| |||||||| || ||||| |||||||
gtagctgaagccaaaggcacaccatgtttagtttagactcaaattttgcacttactggtttcactttattgtcagGCTGTTGGAAAAGTCCTGCCTGAGCTGAATGGAAAACTCACTGGTATGGCCTTCCGAGTTCCAACACCAAATGTCTCTGTTGTGGATTTGACATGCCGGA

upper sequence: LOC_Os02g07490.1 (Oryza sativa), 3'ss of exon 10
lower sequence: GLYMA16G09020.1 (Glycine max), 3'ss of exon 10
------gtacgatgaaccaaaaatctac-cttgcttttctagatttctgttttggctgactgttttgattccttat----tagGCTGTTGGGAAAGTCCTCCCTGAGCTAAATGGAAAGCTCACTGGTATGGCCTTCCGAGTTCCAACACCAAATGTGTCTGTTGTCGACTTGACCTGCCGGA
      |   |||| ||  | | | ||  ||| || || |   |    || || |      | |||| ||  | |      |||||||||||||||| || || |||||||||||||| |||||||| ||||| ||||| ||||| || || ||||| ||||| || |||||||| |||||| 
gtacaagatggatggacacagattttatgctttctattttcagtactggtatttgtgattaggtttgttttatgaaatcacagGCTGTTGGGAAAGTTCTTCCAGAGCTAAATGGAAAACTCACTGGGATGGCATTCCGTGTTCCGACTCCCAATGTTTCTGTGGTGGACTTGACTTGCCGGC

upper sequence: LOC_Os02g07490.1 (Oryza sativa), 3'ss of exon 10
lower sequence: GLYMA03G22790.1 (Glycine max), 3'ss of exon 10
------gtacgatgaaccaaaaatctaccttgcttttctagatttctgttttggctgactgttttgattccttat-----tagGCTGTTGGGAAAGTCCTCCCTGAGCTAAATGGAAAGCTCACTGGTATGGCCTTCCGAGTTCCAACACCAAATGTGTCTGTTGTCGACTTGACCTGCCGGA
      |   |||| ||  | | | ||   |   | | |  | | ||| | |    || ||  ||  ||   ||       |||| ||||||||||| || |||||||||||||| || |||||||| ||||| ||||| || || || || ||||| ||||| || |||||||| |||||| 
gtacaagatggatggacacagattttatgcttactattttcagtgctggtatatgagattgggtttgttttataaaatcacagGCCGTTGGGAAAGTTCTTCCTGAGCTAAATGGGAAACTCACTGGGATGGCATTCCGTGTACCGACTCCCAATGTTTCTGTGGTGGACTTGACTTGCCGGC

upper sequence: LOC_Os02g07490.1 (Oryza sativa), 3'ss of exon 10
lower sequence: AT1G16300.1 (Arabidopsis thaliana), 3'ss of exon 10
--------gtacgatgaaccaaaaatctaccttgcttttctagatttctgttttggc--tgactgttttgatt-ccttattagGCTGTTGGGAAAGTCCTCCCTGAGCTAAATGGAAAGCTCACTGGTATGGCCTTCCGAGTTCCAACACCAAATGTGTCTGTTGTCGACTTGACCTGCCGGA
         |  |   |   | | ||  || | || |  || || |  | |||  ||  ||||| ||||  ||  || | ||||||||||| || ||||| || || || |||||||| || || || ||||||||||| || |||||||||||||| |||||||| || || || || ||  
gtacccaaatttgtacagttatatataaacatagcat--ctggaatcatatttaagccatgacttttttacttgtctcaatagGCTGTTGGTAAGGTCCTTCCGGAACTCAATGGAAAACTAACAGGAATGGCCTTCCGTGTCCCAACACCAAATGTCTCTGTTGTGGATTTAACTTGTCGAC

upper sequence: LOC_Os02g07490.1 (Oryza sativa), 3'ss of exon 10
lower sequence: Vv19s0085g00600.t01 (Vitis vinifera), 3'ss of exon 10
--gtacgatgaaccaaaa----atctaccttgcttttc-tagatttctgttttggctgactgttttgattccttat--tagGCTGTTGGGAAAGTCCTCCCTGAGCTAAATGGAAAGCTCACTGGTATGGCCTTCCGAGTTCCAACACCAAATGTGTCTGTTGTCGACTTGACCTGCCGGA
   |  |||| |   ||     ||  |  | |  |  | || | || |     |  ||| | |     ||   |||  ||||||||||| |||||||| || || || || |||||||||||||| ||||||||||| || |||||||| ||||| |||||||| ||||| || || ||  
gtatgagatggatttaattcacatggaagtagaatcccataaagttgtacaaggtgtgattttgactgtttggtatcatagGCTGTTGGAAAAGTCCTTCCAGAACTCAACGGAAAGCTCACTGGAATGGCCTTCCGCGTCCCAACACCTAATGTCTCTGTTGTGGACTTAACTTGTCGAC

upper sequence: LOC_Os02g07490.1 (Oryza sativa), 3'ss of exon 10
lower sequence: PP1S309_73V6.3 (Physcomitrella patens), 3'ss of exon 7
----------------------------------------gtacgatgaaccaaaaatctaccttgcttt----tctagatttctgttttggctgactgttt-tgattccttatt-------agGCTGTTGGGAAAGTCCTCCCTGAGCTAAATGGAAAGCTCACTGGTATGGCCTTCCGAGTTCCAACACCAAATGTGTCTGTTGTCGACTTGACCTGCCGGA
                                         | |  | |      |||  |  |  || |    |||  |  |  |  |   |  | | ||  ||| ||   |||       ||||||| || || || || || ||  | ||||| ||||||||||||||||| ||||| || ||||| || ||||||||||| || ||| |||||   ||  
gtactgtgctcattatttggaccctggtggttagatgggactgctgtaagttgtgaatggagttgtctgtaaagtctgaacataggcctgatcccaattttcgtgactcgggattttcatgcagGCTGTGGGCAAGGTACTGCCAGAATTGAATGGGAAGCTCACTGGTATGGCTTTCCGTGTGCCAACTCCCAATGTGTCTGTGGTAGACCTGACCGTGCGAC

upper sequence: LOC_Os02g07490.1 (Oryza sativa), 3'ss of exon 10
lower sequence: EFJ15779 (Selaginella moellendorffii), 3'ss of exon 7
gtacgatgaaccaaaaatctaccttgcttttctagatttctgttttggctgactgttttgattccttattagGCTGTTGGGAAAGTCCTCCCTGAGCTAAATGGAAAGCTCACTGGTATGGCCTTCCGAGTTCCAACACCAAATGTGTCTGTTGTCGACTTGACCTGCCGGA
                 |||   ||  |   | |  | ||     |  || | ||||||  ||  || | ||||||| || || || || || ||||| ||||| |||||||| || ||||| ||||| || ||||| ||||| || || || ||||||||||| |||||  
----------------gtctcttttaatggacca--tgtccaaagtcactaaatgttttcgtt--ttctcagGCTGTCGGCAAGGTTCTTCCAGAGCTCAATGGCAAGCTCACAGGAATGGCGTTCCGTGTCCCAACTCCAAACGTCTCAGTCGTCGACTTGACGTGCCGAT

upper sequence: LOC_Os02g07490.1 (Oryza sativa), 3'ss of exon 10
lower sequence: EFJ32914 (Selaginella moellendorffii), 3'ss of exon 9
gtacgatgaaccaaaaatctaccttgcttttctagatttctgttttggctgactgttttgattccttattagGCTGTTGGGAAAGTCCTCCCTGAGCTAAATGGAAAGCTCACTGGTATGGCCTTCCGAGTTCCAACACCAAATGTGTCTGTTGTCGACTTGACCTGCCGGA
              |  |||   ||  |   | |  | ||     |  || | ||||||  ||  || | ||||||| || || || || || ||||| ||||| |||||||| || ||||| ||||| || ||||| ||||| || || || ||||||||||| |||||  
------------gcacgtctcttttaatggacca--tgtccaaagtcactaaatgttttcgtt--ttctcagGCTGTCGGCAAGGTTCTTCCAGAGCTTAATGGCAAGCTCACAGGAATGGCGTTCCGTGTCCCAACTCCAAACGTCTCAGTCGTCGACTTGACATGCCGAT

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|58675895|gb|CK064582.1|CK064582
EST:     GGCGTGGTGCTGCTCAAAACATAATTCCTAGCTCCACTGGTGCAGCCAAG                         GCTGTTGGGAAAGTCCTCCCTGAGCTAAATGGAAAGCTCACTGGTATGGCC
genomic: GGCGTGGTGCTGCTCAAAACATAATTCCTAGCTCCACTGGTGCAGCCAAGgtacgatgaa ... tccttattagGCTGTTGGGAAAGTCCTCCCTGAGCTAAATGGAAAGCTCACTGGTATGGCC
EST: gi|29677604|gb|CB673879.1|CB673879
EST:     GGCGTGGTGCTGCTCAAAACATAATTCCTAGCTCCACTGGTGCAGCCAAG                         GCTGTTGGGAAAGTCCTCCCTGAGCTAAATGGAAAGCTCACTGGTATGGCC
genomic: GGCGTGGTGCTGCTCAAAACATAATTCCTAGCTCCACTGGTGCAGCCAAGgtacgatgaa ... tccttattagGCTGTTGGGAAAGTCCTCCCTGAGCTAAATGGAAAGCTCACTGGTATGGCC
EST: gi|58680325|gb|CK069012.1|CK069012
EST:     GGCGTGGTGCTGCTCAAAACATAATTCCTAGCTCCACTGGTGCAGCCAAG                         GCTGTTGGGAAAGTCCTCCCTGAGCTAAATGGAAAGCTCACTGGTATGGCC
genomic: GGCGTGGTGCTGCTCAAAACATAATTCCTAGCTCCACTGGTGCAGCCAAGgtacgatgaa ... tccttattagGCTGTTGGGAAAGTCCTCCCTGAGCTAAATGGAAAGCTCACTGGTATGGCC
EST: gi|218505391|gb|FG946304.1|FG946304
EST:     GGCGTGGTGCTGCTCAAAACATAATTCCTANCTCCACTGGTGCAGCCAAG                         GCTGTTGGGAAAGTCCTCCCTGAGCTAAATGGAAAGCTCACTGGTATGGCC
genomic: GGCGTGGTGCTGCTCAAAACATAATTCCTAGCTCCACTGGTGCAGCCAAGgtacgatgaa ... tccttattagGCTGTTGGGAAAGTCCTCCCTGAGCTAAATGGAAAGCTCACTGGTATGGCC

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), 75 (downstream exon)
Score: 20

CCACCCAGAAGACTGTCGATGGCCCTTCAATGAAAGATTGGAGAGGAGGGCGTGGTGCTGCTCAAAACATAATTCCTAGCTCCACTGGTGCAGCCAAGgtacgatgaa ... tccttattagGCTGTTGGGAAAGTCCTCCCTGAGCTAAATGGAAAGCTCACTGGTATGGCCTTCCGAGTTCCAACACCAAATGTGTCTGTTGTCGACTTGACCTGCCGGA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tctaccttgcttttctagatttctgttttggctgactgttttgattccttattagGCTGTTGGGAAAGTCCTCCCTGAGCTAAATGGAAAGCTCACTGGTATGGCCTTCCGAGTTCCAACACCAAATGTGTCTGTTGTCGACTTGACCTGCCGGA
                                            ttccttatt  CT-rich tract
                                      ttttgatt  TA-rich tract