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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gtttctgaaagccaaaacaactagcactatgatatttgtaatgcctttccatccttatttttggtgaatggtgataaagcatgtttactactgtcaatagGTCCTTGCTTTCAATGGTCAGCCTGTGAAGAATTTGAAGAACTTAGTGTCAATGGTTGAAAATTGCAAGGATGAATTCTTGAAGTTTGATCTGGAGTATG

Basic information

species Oryza sativa
transcript LOC_Os02g50880.1
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g50880.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G144501_T02 (Zea mays), 3'ss of exon 7
-------------------------------------------------------gtttctgaaagccaaaacaactagcactatgatatttgtaatgcctttccatccttatttttggtgaatggtgataaagcatgtttactactgtcaatagGTCCTTGCTTTCAATGGTCAGCCTGTGAAGAATTTGAAGAACTTAGTGTCAATGGTTGAAAATTGCAAGGATGAATTCTTGAAGTTTGATCTGGAGTATG
                                                        ||  || |    |  |   || |      ||   | | |||| || | |  |  || | | ||||| ||   |     ||| |||  || |||  | |||| |||||||||||||| |||||||| || ||||| |||||||||| | | ||||| |||||||||||||||||||| ||||||||||||||||||||||
gtaataaaagcttctagtatctagttctgtgatcactagcatgtcttttaagccacttcttgcagtatattattgctggagactcga--atggcaatgtctgttctgcactactgt-ggtgactga-aacttttcatttttg-tattgttcacagGTTCTTGCTTTCAATGGCCAGCCTGTAAAAAATTTAAAGAACTTAGCGACCATGGTGGAAAATTGCAAGGATGAATTTTTGAAGTTTGATCTGGAGTATG

upper sequence: LOC_Os02g50880.1 (Oryza sativa), 3'ss of exon 7
lower sequence: AC212112.4_FGT002 (Zea mays), 3'ss of exon 7
------------------------gtttctgaaa-gcca---aaacaa---ctagcactatgatatttgtaatgccttt-----ccatccttatttttggtga--atggtga-taaagcatgt----ttactactgtcaatagGTCCTTGCTTTCAATGGTCAGCCTGTGAAGAATTTGAAGAACTTAGTGTCAATGGTTGAAAATTGCAAGGATGAATTCTTGAAGTTTGATCTGGAGTATG
                        ||  ||   | |||    || | |   || ||| |||  | ||  |   | ||       | ||   | || |     |   |||| | | || | | |    ||  || |||    |||| |||||||||||||| |||||||| || ||||| |||||||| | | | ||||| |||||||||||||||||||| ||||||||||||||||||||||
gtaataacagcttctagttctgtggtcactagcatgccttttaagccatttcttgcagtatattgttcctggaggctcgaatgacaatgtctgttctgcactactgtggtcactgaaacttttcatttttttattgttcgcagGTACTTGCTTTCAATGGCCAGCCTGTTAAAAATTTAAAGAACTTGGCGACCATGGTGGAAAATTGCAAGGATGAATTTTTGAAGTTTGATCTGGAGTATG

upper sequence: LOC_Os02g50880.1 (Oryza sativa), 3'ss of exon 7
lower sequence: Vv17s0000g07900.t01 (Vitis vinifera), 3'ss of exon 7
gtttctgaaagccaaaacaactagcact-atgatatttgtaatgcctttccatccttatttttggtgaatggtgataaagcatgtttactactgtcaatagGTCCTTGCTTTCAATGGTCAGCCTGTGAAGAATTTGAAGAACTTAGTGTCAATGGTTGAAAATTGCAAGGATGAATTCTTGAAGTTTGATCTGGAGTATG
   || ||| | ||      | |   || |||||    | |      ||  | | | | || |  |||||| |     |   ||||| |||||| |   |||| |||||| |||||||| |||||||||||||| |||||| ||| |     ||||| || |  ||  | || ||||| ||||| |||||||| || ||  
--gtcagaatggcagtcttgcaaatgcttatgatgcaagaagctggcttttaccttcagttgt--tgaatgct---ttattttgttt-ctactggc--cagGTTCTTGCTCTCAATGGTAAGCCTGTGAAGAATCTGAAGAGCTTGGCCAACATGGTAGAGAGCTGTGATGACGAATTTTTGAAATTTGATCTAGAATACC

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|163929409|gb|EG713834.1|EG713834
EST:     TGCTTGTAGCAGATATCAATATCGGTTATGAAGAGATTGTCAATACTCAG                         GTCCTTGCTTTCAATGGTCAGCCTGTGAAGAATTTGAAGAACTTAGTGTCA
genomic: TGCTTGTAGCAGATATCAATATCGGTTATGAAGAGATTGTCAATACTCAGgtaatacaaa ... ctgtcaatagGTCCTTGCTTTCAATGGTCAGCCTGTGAAGAATTTGAAGAACTTAGTGTCA
EST: gi|58677029|gb|CK065716.1|CK065716
EST:     TGCTTGTAGCAGATATCAATATCGGTTATGAAGAGATTGTCAATACTCAG                         GTCCTTGCTTTCAATGGTCAGCCTGTGAAGAATTTGAAGAACTTAGTGTCA
genomic: TGCTTGTAGCAGATATCAATATCGGTTATGAAGAGATTGTCAATACTCAGgtaatacaaa ... ctgtcaatagGTCCTTGCTTTCAATGGTCAGCCTGTGAAGAATTTGAAGAACTTAGTGTCA
EST: gi|29642428|gb|CB647435.1|CB647435
EST:     TGCTTGTAGCAGATATCAATATCGGTTATGAAGAGATTGTCAATACTCAG                         GTCCTTGCTTTCAATGGTCAGCCTGTGAAGAATTTGAAGAACTTAGTGTCA
genomic: TGCTTGTAGCAGATATCAATATCGGTTATGAAGAGATTGTCAATACTCAGgtaatacaaa ... ctgtcaatagGTCCTTGCTTTCAATGGTCAGCCTGTGAAGAATTTGAAGAACTTAGTGTCA
EST: gi|66914360|gb|CX101208.1|CX101208
EST:     CAGATATCAATATCGGTTATGAAGAGATTGTCAATACTCAG                         GTCCTTGCTTTCAATGGTCAGCCTGTGAAGAATTTGAAGAACTTAGTGTCA
genomic: CAGATATCAATATCGGTTATGAAGAGATTGTCAATACTCAGgtaatacaaa ... ctgtcaatagGTCCTTGCTTTCAATGGTCAGCCTGTGAAGAATTTGAAGAACTTAGTGTCA
EST: gi|88688423|gb|CI731999.1|CI731999
EST:     GGTTATGAAGAGATTGTCAATACTCAG                         GTCCTTGCTTTCAATGGTCAGCCTGTGAAGAATTTGAAGAACTTAGTGTCA
genomic: GGTTATGAAGAGATTGTCAATACTCAGgtaatacaaa ... ctgtcaatagGTCCTTGCTTTCAATGGTCAGCCTGTGAAGAATTTGAAGAACTTAGTGTCA
EST: gi|29622435|gb|CB627446.1|CB627446
EST:     TGCTTGTAGCAGATATCAATATCGGTTATGAAGAGATTGTCAATACTCAG                         GTCCTTGCTTTCAATGGTCAGCCTGTGAAGAATTTGAAGAACTTAGTGTCA
genomic: TGCTTGTAGCAGATATCAATATCGGTTATGAAGAGATTGTCAATACTCAGgtaatacaaa ... ctgtcaatagGTCCTTGCTTTCAATGGTCAGCCTGTGAAGAATTTGAAGAACTTAGTGTCA
EST: gi|396941237|gb|HO188446.1|HO188446
EST:     TGCTTGTAGCAGATATCAATATCGGTTATGAAGAGATTGTCAATACTCAG                         GTCCTTGCTTTCAATGGTCAGCCTGTGAAGAATTTGAAGAACTTAGTGTCA
genomic: TGCTTGTAGCAGATATCAATATCGGTTATGAAGAGATTGTCAATACTCAGgtaatacaaa ... ctgtcaatagGTCCTTGCTTTCAATGGTCAGCCTGTGAAGAATTTGAAGAACTTAGTGTCA
EST: gi|58668496|gb|CK057182.1|CK057182
EST:     TGCTTGTAGCAGATATCAATATCGGTTATGAAGAGATTGTCAATACTCAG                         GTCCTTGCTTTCAATGGTCAGCCTGTGAAGAATTTGAAGAACTTAGTGTCA
genomic: TGCTTGTAGCAGATATCAATATCGGTTATGAAGAGATTGTCAATACTCAGgtaatacaaa ... ctgtcaatagGTCCTTGCTTTCAATGGTCAGCCTGTGAAGAATTTGAAGAACTTAGTGTCA
EST: gi|218496236|gb|FG947883.1|FG947883
EST:     TGCTTGTAGCAGATATCAATATCGGTTATGAAGAGATTGTCAATACTCAG                         GTCCTTGCTTTCAATGGTCAGCCTGTGAAGAATTTGAAGAACTTAGTGTCA
genomic: TGCTTGTAGCAGATATCAATATCGGTTATGAAGAGATTGTCAATACTCAGgtaatacaaa ... ctgtcaatagGTCCTTGCTTTCAATGGTCAGCCTGTGAAGAATTTGAAGAACTTAGTGTCA
EST: gi|58681016|gb|CK069703.1|CK069703
EST:     TGCTTGTAGCAGATATCAATATCGGTTATGAAGAGATTGTCAATACTCAG                         GTCCTTGCTTTCAATGGTCAGCCTGTGAAGAATTTGAAGAACTTAGTGTCA
genomic: TGCTTGTAGCAGATATCAATATCGGTTATGAAGAGATTGTCAATACTCAGgtaatacaaa ... ctgtcaatagGTCCTTGCTTTCAATGGTCAGCCTGTGAAGAATTTGAAGAACTTAGTGTCA
EST: gi|29632216|gb|CB637225.1|CB637225
EST:     ATCGGTTATGAAGAGATTGTCAATACTCAG                         GTCCTTGCTTTCAATGGTCAGCCTGTGAAGAATTTGAAGAACTTAGTGTCA
genomic: ATCGGTTATGAAGAGATTGTCAATACTCAGgtaatacaaa ... ctgtcaatagGTCCTTGCTTTCAATGGTCAGCCTGTGAAGAATTTGAAGAACTTAGTGTCA

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: 61 (upstream exon), 75 (downstream exon)
Score: 48

GTGCTTGTAGCAGATATCAATATCGGTTATGAAGAGATTGTCAATACTCAGgtaatacaaa ... ctgtcaatagGTCCTTGCTTTCAATGGTCAGCCTGTGAAGAATTTGAAGAACTTAGTGTCAATGGTTGAAAATTGCAAGGATGAATTCTTGAAGTTTGATCTGGAGTATG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttccatccttatttttggtgaatggtgataaagcatgtttactactgtcaatagGTCCTTGCTTTCAATGGTCAGCCTGTGAAGAATTTGAAGAACTTAGTGTCAATGGTTGAAAATTGCAAGGATGAATTCTTGAAGTTTGATCTGGAGTATG
         ttattttt  TA-rich tract
















Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtttctgaaagccaaaacaactagcactatgatatttgtaatgcctttccatccttatttttggtgaatggtgataaagcatgtttactactgtcaatagGTCCTTGCTTTCAATGGTCAGCCTGTGAAGAATTTGAAGAACTTAGTGTCAATGGTTGAAAATTGCAAGGATGAATTCTTGAAGTTTGATCTGGAGTATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
-tttctga
- - - - - - -aaaacaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gtgaatg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aagcatg