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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtataacttcacaagtttttcgcaaatccgcgctttcccatttagagaatatgtgctaggttatgtgcgacacattacttttaagtaatgcttgataactccatttttccctgcatagaataacatatatgtttttggaacttgcagAGATTGCATCTAAACAGGGTCATGATGATGTATCGAAGCTAACACCAACTGACATTGCTATTGAG

Basic information

species Oryza sativa
transcript LOC_Os02g51410.1
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g51410.1 (Oryza sativa), 3'ss of exon 8
lower sequence: GRMZM2G070218_T01 (Zea mays), 3'ss of exon 8
gtataacttcacaagtttttcgcaaatccgcgctttcccatttagagaatatgtgctaggttat-gtgcgacacattacttttaagtaatgcttgataactccatttttccctgcatagaataacatatatgtttttggaacttgcagAGATTGCATCTAAACAGGGTCATGATGATGTATCGAAGCTAACACCAACTGACATTGCTATTGAG
                                                      |  || ||    | ||    ||     | |  | ||| |       ||||  || |  || ||  |   ||| |  |||   ||| | ||||||||||||||| |||||| |||||||||||||| || ||||| ||||| ||||| ||||| ||||||
------------------------------------------------------gtaagattcccatccggataatctggctgactttatggtcagatgttccaagttccagtggattaa---acacacctgtgcctggcatttgcagAGATTGCATGTAAACAAGGTCATGATGATGTCTCTAAGCTGACACCTACTGATATTGCAATTGAG

upper sequence: LOC_Os02g51410.1 (Oryza sativa), 3'ss of exon 8
lower sequence: GRMZM2G070218_T02 (Zea mays), 3'ss of exon 8
gtataacttcacaagtttttcgcaaatccgcgctttcccatttagagaatatgtgctaggttatgtgcgacacattacttttaagtaatgcttgataactccatttttccctgcatagaataacatatatgtttttggaacttgcagAGATTGCATCTAAACAGGGTCATGATGATGTATCGAAGCTAACACCAACTGACATTGCTATTGAG
                          |  | | ||  |    | ||   || |       |    | ||    ||     | |  | ||| |       ||||  || |  || ||  |   ||| |  |||   ||| | ||||||||||||||| |||||| |||||||||||||| || ||||| ||||| ||||| ||||| ||||||
-------------------------gtaagggtttctc----tggaaggtaag-----attcccatccggataatctggctgactttatggtcagatgttccaagttccagtggattaa---acacacctgtgcctggcatttgcagAGATTGCATGTAAACAAGGTCATGATGATGTCTCTAAGCTGACACCTACTGATATTGCAATTGAG

upper sequence: LOC_Os02g51410.1 (Oryza sativa), 3'ss of exon 8
lower sequence: GRMZM2G161566_T03 (Zea mays), 3'ss of exon 6
gtataacttcacaagtttttcgcaaatccgcgctttcccatttagagaatatgt--gctagg---ttatgtgcgacacattacttttaagtaatgcttgataactccatttttccctgca-tagaataacatatatgtttttggaacttgcagAGATTGCATCTAAACAGGGTCATGATGATGTATCGAAGCTAACACCAACTGACATTGCTATTGAG
                                  ||||||| | || ||||     ||||     |||||  |      |   |  | ||   |||||   |  |   ||      | || | || ||||| |   ||   ||| | |||||||||||||||||||||| |||||||  ||||| || ||||| |  || ||||| || || ||||||
----------------------------gtaagattcccatctggataataatctggctaaaactttatgatcagatggtccttcatgagacttgcttag-agttatgttccgagttccagtggattaacacacccgtgcctggcatttgcagAGATTGCATCTAAACAAGGTCATGGCGATGTCTCTAAGCTGATGCCGACTGATATCGCAATTGAG

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|117246028|gb|CT862500.1|CT862500
EST:     GCAAAGGGGCGATGCTTATGCAAATGCTGATGTGAGGGTTTCTCTTGAAG                         AGATTGCATCTAAACAGGGTCATGATGATGTATCGAAGCTAACACCAACTG
genomic: GCAAAGGGGCGATGCTTATGCAAATGCTGATGTGAGGGTTTCTCTTGAAGgtataacttc ... gaacttgcagAGATTGCATCTAAACAGGGTCATGATGATGTATCGAAGCTAACACCAACTG
EST: gi|29661028|gb|CB657303.1|CB657303
EST:     GCAAAGGGGCGATGCTTATGCAAATGCTGATGTGAGGGTTTCTCTTGAAG                         AGATTGCATCTAAACAGGGTCATGATGATGTATCGAAGCTAACACCAACTG
genomic: GCAAAGGGGCGATGCTTATGCAAATGCTGATGTGAGGGTTTCTCTTGAAGgtataacttc ... gaacttgcagAGATTGCATCTAAACAGGGTCATGATGATGTATCGAAGCTAACACCAACTG
EST: gi|13421097|gb|AU175176.1|AU175176
EST:     G-AAAGGGGCGATGCTTATGCAAATGCTGATGTGAGGGTTTCTCTTGAAG                         AGATTGCATCTAAACAGGGTCATGATGATGTATCGAAGCTAACACCAACTG
genomic: GCAAAGGGGCGATGCTTATGCAAATGCTGATGTGAGGGTTTCTCTTGAAGgtataacttc ... gaacttgcagAGATTGCATCTAAACAGGGTCATGATGATGTATCGAAGCTAACACCAACTG
EST: gi|88662165|gb|CI465740.1|CI465740
EST:     GCAAAGGGGCGATGCTTATGCAAATGCTGATNTGAGGGTTTTTCTTGAAG                         AGATTGCATCTAAACAGGGTCATGATGATGTATCGAAGCTAACACCAACTG
genomic: GCAAAGGGGCGATGCTTATGCAAATGCTGATGTGAGGGTTTCTCTTGAAGgtataacttc ... gaacttgcagAGATTGCATCTAAACAGGGTCATGATGATGTATCGAAGCTAACACCAACTG
EST: gi|29687751|gb|CB684026.1|CB684026
EST:     GCAAAGGGGCGATGCTTATGCAAATGCTGATGTGAGGGTTTCTCTTGAAG                         AGATTGCATCTAAACAGGGTCATGATGATGTATCGAAGCTAACACCAACTG
genomic: GCAAAGGGGCGATGCTTATGCAAATGCTGATGTGAGGGTTTCTCTTGAAGgtataacttc ... gaacttgcagAGATTGCATCTAAACAGGGTCATGATGATGTATCGAAGCTAACACCAACTG
EST: gi|38479517|gb|CF963624.1|CF963624
EST:     GCAAAGGGGCGATGCTTATGCAAATGCTGATGTGAGGGTTTCTCTTGAAG                         AGATTGCATCTAAACAGGGTCATGATGATGTATCGAAGCTAACACCAACTG
genomic: GCAAAGGGGCGATGCTTATGCAAATGCTGATGTGAGGGTTTCTCTTGAAGgtataacttc ... gaacttgcagAGATTGCATCTAAACAGGGTCATGATGATGTATCGAAGCTAACACCAACTG
EST: gi|29660345|gb|CB656620.1|CB656620
EST:     GCAAAGGGGCGATGCTTATGCAAATGCTGATGTGAGGGTTTCTCTTGAAG                         AGATTGCATCTAAACAGGGTCATGATGATGTATCGAAGCTAACACCAACTG
genomic: GCAAAGGGGCGATGCTTATGCAAATGCTGATGTGAGGGTTTCTCTTGAAGgtataacttc ... gaacttgcagAGATTGCATCTAAACAGGGTCATGATGATGTATCGAAGCTAACACCAACTG
EST: gi|88994897|gb|CI036478.1|CI036478
EST:     GGGGCGATGCTTATGCAAATGCTGATGTGAGGGTTTCTCTTGAAG                         AGATTGCATCTAAACAGGGTCATGATGATGTATCGAAGCTAACACCAACTG
genomic: GGGGCGATGCTTATGCAAATGCTGATGTGAGGGTTTCTCTTGAAGgtataacttc ... gaacttgcagAGATTGCATCTAAACAGGGTCATGATGATGTATCGAAGCTAACACCAACTG
EST: gi|29687750|gb|CB684025.1|CB684025
EST:     GCAAAGGGGCGATGCTTATGCAAATGCTGATGTGAGGGTTTCTCTTGAAG                         AGATTGCATCTAAACAGGGTCATGATGATGTA
genomic: GCAAAGGGGCGATGCTTATGCAAATGCTGATGTGAGGGTTTCTCTTGAAGgtataacttc ... gaacttgcagAGATTGCATCTAAACAGGGTCATGATGATGTA
EST: gi|29660284|gb|CB656559.1|CB656559
EST:     GCAAAGGGGCGATGCTTATGCAAATGCTGATGTGAGGGTTTCTCTTGAAG                         AGATTGCATCTAAACAGGGTCATGATGATGTATCGAAGCTAACACCAACTG
genomic: GCAAAGGGGCGATGCTTATGCAAATGCTGATGTGAGGGTTTCTCTTGAAGgtataacttc ... gaacttgcagAGATTGCATCTAAACAGGGTCATGATGATGTATCGAAGCTAACACCAACTG
EST: gi|87019864|gb|CI299262.1|CI299262
EST:     GCAAAGGGGCGATGCTTATGCAAATGCTGATGTGAGGGTTTCTCTTGAAG                         AGATTGCATCTAAACAGGGTCATGATGATGTATCGAAGCTAACACCAACTG
genomic: GCAAAGGGGCGATGCTTATGCAAATGCTGATGTGAGGGTTTCTCTTGAAGgtataacttc ... gaacttgcagAGATTGCATCTAAACAGGGTCATGATGATGTATCGAAGCTAACACCAACTG
EST: gi|38475540|gb|CF959673.1|CF959673
EST:     GCAAAGGGGCGATGCTTATGCAAATGCTGATGTGAGGGTTTCTCTTGAAG                         AGATTGCATCTAAACAGGGTCATGATGATGTATCGAAGCTAACACCAACTG
genomic: GCAAAGGGGCGATGCTTATGCAAATGCTGATGTGAGGGTTTCTCTTGAAGgtataacttc ... gaacttgcagAGATTGCATCTAAACAGGGTCATGATGATGTATCGAAGCTAACACCAACTG

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: 72 (upstream exon), 65 (downstream exon)
Score: 65

GCTTTTTCTAAACTCAGCATGCTCGCGGAGCAAAGGGGCGATGCTTATGCAAATGCTGATGTGAGGGTTTCTCTTGAAGgtataacttc ... gaacttgcagAGATTGCATCTAAACAGGGTCATGATGATGTATCGAAGCTAACACCAACTGACATTGCTATTGAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgataactccatttttccctgcatagaataacatatatgtttttggaacttgcagAGATTGCATCTAAACAGGGTCATGATGATGTATCGAAGCTAACACCAACTGACATTGCTATTGAG
                         gaataac  putative branch site (score: 65)
                      atagaataacatatat  TA-rich tract