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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gagaaaggatagttgagtgctccagctgctctcgcagttctgtgcaaccaacggcttgttcttaacccccttctctgccaccaaaaccgatctatttcagGCAGGAGATTCGCTCTGCCACGAGCTCGATGACTTCGGTTCCAAAGCCACTGAAATTCCTCCGCCCACACTTTGGAACTCTCAAGTCCTATTTCGAAACA

Basic information

species Zea mays
transcript GRMZM2G155384_T01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G155384_T01 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os02g05340.1 (Oryza sativa), 3'ss of exon 2
gagaaaggatagttgagtgctccagctgctctcgcagttctgtgcaaccaacggct--tgttcttaacccccttctctgccaccaaaa--ccgatctatttc--agGCAGGAGATTCGCTCTGCCACGAGCTCGATGACTTCGGTTCCAAAGCCACTGAAATTCCTCCGCCCACACTTTGGAACTCTCAAGTCCTATTTCGAAACA
      |  || ||   | | |||           | ||   |   |||||    |  || | | |   || |  |||| ||| ||||   |   ||   |   |||||||||||||| || ||||| ||||| ||||| || || ||||||||||||||||||||||| ||||||| |||||| |||||||| || || ||||| 
------gtttattttgatccaccatagttagatttacttggttaagaccaaattttgttgctttgatttccatcttctgtcactaaaatatcatcctccctaaaagGCAGGAGATTCGTTCCGCCACAAGCTCAATGACATCTGTACCAAAGCCACTGAAATTCCTCCGGCCACACTATGGAACACTCAAGTCTTACTTTGAAACC

upper sequence: GRMZM2G155384_T01 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA06G44340.1 (Glycine max), 3'ss of exon 2
gagaaaggatagttgagtgctccagctgctctcgc----agttctgtgcaa----ccaacggcttgttcttaacccc----cttctctgccaccaaaaccgatc------tatttcagGCAGGAGATTCGCTCTGCCACGAGCTCGATGACTTCGGTTCCAAAGCCACTGAAATTCCTCCGCCCACACTTTGGAACTCTCAAGTCCTATTTCGAAACA
  | ||   |||||   ||||| | |||  | |      | ||   ||  |        |   || ||||           | | | ||  |    ||    |       | || |||||| || |||||  || |||||||||| |||||||||||||| |||||| |||| ||||| || || || | ||| ||||| ||| ||||||  ||||| 
--gtaaacctagttttatgctcgaactgaacacattttgatttgaatgggaatttttggctatttattctagttttgaatgcatgtttgaaattggaatttgtggttgtgtgttgcagGCAAGAAATTCGAACTTCCACGAGCTCTATGACTTCGGTTCCTAAGCCATTGAAGTTCCTTCGTCCGCATTATGGCACTCTTAAGACCTATTATGAAACT

upper sequence: GRMZM2G155384_T01 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA12G13410.1 (Glycine max), 3'ss of exon 2
gagaaaggatagttgagtgctccagctgctc----tcgcagttctgtgcaaccaacggcttgttcttaacccccttctctgccaccaaaaccga----------tctatttcagGCAGGAGATTCGCTCTGCCACGAGCTCGATGACTTCGGTTCCAAAGCCACTGAAATTCCTCCGCCCACACTTTGGAACTCTCAAGTCCTATTTCGAAACA
  | ||   |||||   ||||| |   |  |    |   | ||   || |          | || ||       || | ||      |||  |           | | ||  ||||| || |||||  || |||||||||| |||||||||||||| |||||  |||| ||||| ||||| || | ||| ||||| ||  | ||||  ||||| 
--gtaaacctagttttatgctcgaaaggaacaaattttgatttgaatggacatttttaactattttttttagttttatttgtgtttgaaattggaatgtgtggttgtgttctagGCAAGAAATTCGAACTTCCACGAGCTCTATGACTTCGGTTCCTAAGCCGTTGAAGTTCCTTCGCCCTCATTATGGCACTCTTAAAACGTATTATGAAACT

upper sequence: GRMZM2G155384_T01 (Zea mays), 3'ss of exon 2
lower sequence: EFJ26022 (Selaginella moellendorffii), 3'ss of exon 2
gagaaaggatagttgagtgctccagctgctctcgcagttctgtgcaaccaacggcttgttcttaacccccttctctgccaccaaaaccgatctattt---cagGCAGGAGATTCGCTCTGCCACGAGCTCGATGACTTCGGTTCCAAAGCCACTGAAATTCCTCCGCCCACACTTTGGAACTCTCAAGTCCTATTTCGAAACA
                                        |  || |  |   | ||  || |            ||     |  | |  | | | |   |||||| ||||||||   ||| || ||||| |||||||| || || ||||| ||||||||||||||||| || | ||| ||| | ||| | |  ||| | | |
---------------------------------------gtacgcgagtaggagtttaatcgt---------tcgtgttgtgaggagctgtgtgtatgcgcagGCAAGAGATTCGGAGTGCTACAAGCTCCATGACTTCCGTGCCCAAGCCGCTGAAATTCCTCCGCCCGCATTATGGGACTTTGAAGGCGTTCTTCCAGAAA

upper sequence: GRMZM2G155384_T01 (Zea mays), 3'ss of exon 2
lower sequence: EFJ14427 (Selaginella moellendorffii), 3'ss of exon 2
gagaaaggatagttgagtgctccagctgctctcgcagttctgtgcaaccaacggcttgttcttaacccccttctctgccaccaaaaccgatctattt---cagGCAGGAGATTCGCTCTGCCACGAGCTCGATGACTTCGGTTCCAAAGCCACTGAAATTCCTCCGCCCACACTTTGGAACTCTCAAGTCCTATTTCGAAACA
                                        |  || |  |   | ||  || |          | ||     |  | |  | | | |   |||||| ||||||||   ||| || ||||| |||||||| || || ||||| ||||||||||||||||| || | ||||||| | ||| | |  ||| | | |
---------------------------------------gtacgcgagtaggagtttaatcgt---------ttgtgttgtgaggagctgtgtgtatgcgcagGCAAGAGATTCGGAGTGCTACAAGCTCCATGACTTCCGTGCCCAAGCCGCTGAAATTCCTCCGCCCGCATTATGGAACTTTGAAGGCGTTCTTCCAGAAA

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|18649994|gb|BM498813.1|BM498813
EST:     GCGCAGGACGCGGATCCCGGCGTGCAGTAGCTCGCGCTCGAGAGCATGAG                         GCAGGAGATTC
genomic: GCGCAGGACGCGGATCCCGGCGTGCAGAAGCTCGCGCTCGAGAGCATGAGgtaccgctcg ... tctatttcagGCAGGAGATTC
EST: gi|19822561|gb|BQ048585.1|BQ048585
EST:     GCGCAGGACGCGGATCCCGGCGTGCAGAAGCTCGCGCTCGAGAGCATGAG                         GCAGGAGATTC
genomic: GCGCAGGACGCGGATCCCGGCGTGCAGAAGCTCGCGCTCGAGAGCATGAGgtaccgctcg ... tctatttcagGCAGGAGATTC
EST: gi|86468329|gb|DY234699.1|DY234699
EST:     GCGCAGGACGCGGATCCCGGCGTGCAGAAGCTCGCGCTCGAGAGCATGAG                         GCAGGAGATTCGCTCT
genomic: GCGCAGGACGCGGATCCCGGCGTGCAGAAGCTCGCGCTCGAGAGCATGAGgtaccgctcg ... tctatttcagGCAGGAGATTCGCTCT

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), 49 (downstream exon)
Score: 342

CGGAGGAGGATCTGGCGCTCAAGGAGCAGCTGGAGCTCTACGTCGTGCGGGCGCAGGACGCGGATCCCGGCGTGCAGAAGCTCGCGCTCGAGAGCATGAGgtaccgctcg ... tctatttcagGCAGGAGATTCGCTCTGCCACGAGCTCGATGACTTCGGTTCCAAAGCCACTGAAATTCCTCCGCCCACACTTTGGAACTCTCAAGTCCTATTTCGAAACA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 195

CGGAGGAGGATCTGGCGCTCAAGGAGCAGCTGGAGCTCTACGTCGTGCGGGCGCAGGACGCGGATCCCGGCGTGCAGAAGCTCGCGCTCGAGAGCATGAGgtaccgctcg ... tctatttcagGCAGGAGATTCGCTCTGCCACGAGCTCGATGACTTCGGTTCCAAAGCCACTGAAATTCCTCCGCCCACACTTTGGAACTCTCAAGTCCTATTTCGAAACA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 301

CGGAGGAGGATCTGGCGCTCAAGGAGCAGCTGGAGCTCTACGTCGTGCGGGCGCAGGACGCGGATCCCGGCGTGCAGAAGCTCGCGCTCGAGAGCATGAGgtaccgctcg ... tctatttcagGCAGGAGATTCGCTCTGCCACGAGCTCGATGACTTCGGTTCCAAAGCCACTGAAATTCCTCCGCCCACACTTTGGAACTCTCAAGTCCTATTTCGAAACA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 219

CGGAGGAGGATCTGGCGCTCAAGGAGCAGCTGGAGCTCTACGTCGTGCGGGCGCAGGACGCGGATCCCGGCGTGCAGAAGCTCGCGCTCGAGAGCATGAGgtaccgctcg ... tctatttcagGCAGGAGATTCGCTCTGCCACGAGCTCGATGACTTCGGTTCCAAAGCCACTGAAATTCCTCCGCCCACACTTTGGAACTCTCAAGTCCTATTTCGAAACA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaccaacggcttgttcttaacccccttctctgccaccaaaaccgatctatttcagGCAGGAGATTCGCTCTGCCACGAGCTCGATGACTTCGGTTCCAAAGCCACTGAAATTCCTCCGCCCACACTTTGGAACTCTCAAGTCCTATTTCGAAACA
              tcttaac  putative branch site (score: 219)
                                             tctatttc  putative PPT
                                            atctattt  TA-rich tract