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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgctgaatttatatgttgattcttctgtatagtttactctgcttgttgtgcaagggttaacctgagtatttaacaaaaatgcttctctgcatacacacagGGACATGGCTTTCGCACAGAACTTATATCCATGATTTTGGATTTAAAACCACGATTCTTGAGATTTCCTG

Basic information

species Zea mays
transcript GRMZM2G077299_T03
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G077299_T01 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os11g03730.2 (Oryza sativa), 3'ss of exon 6
------------------------------------------------tgctgaatttatatgttgattcttctgtatagtttactctg-----cttgttgtgcaagggttaacctgagtatttaacaaaaatgcttctctgcatacacacagGGACATGGCTTTCGCACAGAACTTATATCCATGATTTTGGATTTAAAACCACGATTCTTGAGATTTCCTG
                                                |||        | |  || |   | |||||||| ||   |       |   | | || ||| |      |||  ||  ||| | | ||| |    | ||| |||||||||||| |||||||||||||||||||| ||||| ||||| ||||||||||||||||||||||| ||||
gtacattatattttgttgtcaaacttcattactggaaaaggaaaacgatgccatgggctttttatgctatctatgtatagtgtatgataacactttaagtcttcatgggctttttcaagtgcttc-caacatttctttt----acacatacagGGACATGGTTTTCGCACAGAACTTATATCTATGATGTTGGACTTAAAACCACGATTCTTGAGATTCCCTG

upper sequence: GRMZM2G077299_T01 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os12g03470.5 (Oryza sativa), 3'ss of exon 6
--------------------------------------------------tgctgaatttatatgttgattcttctgtatagtttactctgcttgttgtgcaagggttaacctgagtatttaacaaaaatgcttctctgcatacacacagGGACATGGCTTTCGCACAGAACTTATATCCATGATTTTGGATTTAAAACCACGATTCTTGAGATTTCCTG
                                                  |  || | || |   | | |   ||| |||||| ||   | |   ||         |   | |       |      ||   |||| |  | |||  ||||||||||| |||||||||||||| ||||| ||||| ||||| ||||||||||||||||||||||| ||||
gtacattatattttgttatcaaacttcgttactggaaaaggaaaacgatatcatggactttttcat-gctatctctatatagtgtatgataccacttaaatcttcatgggctttttctactgcttccaacatttcttt-tacacattcagGGACATGGTTTTCGCACAGAACTAATATCTATGATGTTGGACTTAAAACCACGATTCTTGAGATTCCCTG
















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|71769433|gb|DR967370.1|DR967370
EST:     GAGTTGTCTGGTTTGATCAAGTATCACTCATGCCTGAAGACACATACAAG                         GGACATGGCTTTCGCACAGAACTTATATCCATGATTTTTGGATTTAAAAC
genomic: GAGTTGTCTGGTTTGATCAAGTATCACTCATGCCTGAAGACACATACAAGgtatattaca ... atacacacagGGACATGGCTTTCGCACAGAACTTATATCCATGATTTT-GGATTTAAAAC
EST: gi|71441725|gb|DR822775.1|DR822775
EST:     GAGTTGTCTGGTTTGATCAAGTATCACTCATGCCTGAAGACACATACAAG                         GGACATGGCTTTCGCACAGAACTTATATCCATGATTTTGGATTTAAAACCA
genomic: GAGTTGTCTGGTTTGATCAAGTATCACTCATGCCTGAAGACACATACAAGgtatattaca ... atacacacagGGACATGGCTTTCGCACAGAACTTATATCCATGATTTTGGATTTAAAACCA

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 4 RNA-Seq libraries.


Block sizes: 49 (upstream exon), 43 (downstream exon)
Score: 69

TAAAGGAACCAATAGAACCTCAAGGCTTCAAATAACAACTAACAAGAAAGGAGTTGTCTGGTTTGATCAAGTATCACTCATGCCTGAAGACACATACAAGgtatattaca ... atacacacagGGACATGGCTTTCGCACAGAACTTATATCCATGATTTTGGATTTAAAACCACGATTCTTGAGATTTCCTG


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 81

TAAAGGAACCAATAGAACCTCAAGGCTTCAAATAACAACTAACAAGAAAGGAGTTGTCTGGTTTGATCAAGTATCACTCATGCCTGAAGACACATACAAGgtatattaca ... atacacacagGGACATGGCTTTCGCACAGAACTTATATCCATGATTTTGGATTTAAAACCACGATTCTTGAGATTTCCTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 71

TAAAGGAACCAATAGAACCTCAAGGCTTCAAATAACAACTAACAAGAAAGGAGTTGTCTGGTTTGATCAAGTATCACTCATGCCTGAAGACACATACAAGgtatattaca ... atacacacagGGACATGGCTTTCGCACAGAACTTATATCCATGATTTTGGATTTAAAACCACGATTCTTGAGATTTCCTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 1316

TAAAGGAACCAATAGAACCTCAAGGCTTCAAATAACAACTAACAAGAAAGGAGTTGTCTGGTTTGATCAAGTATCACTCATGCCTGAAGACACATACAAGgtatattaca ... atacacacagGGACATGGCTTTCGCACAGAACTTATATCCATGATTTTGGATTTAAAACCACGATTCTTGAGATTTCCTG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgtgcaagggttaacctgagtatttaacaaaaatgcttctctgcatacacacagGGACATGGCTTTCGCACAGAACTTATATCCATGATTTTGGATTTAAAACCACGATTCTTGAGATTTCCTG
                      atttaac  putative branch site (score: 1316)
                   agtatttaacaaaaat  TA-rich tract