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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgaggccgggttcctgagctctctttcttttttttttcttaattcatgtcgcttcgtccttccgataacccacgggccacggccattcccagGCCCGTCGAAGAAGGTGAAGCTGGACTGGGACACGAGGCTGAGGATCGCAGTGGGCGCCGCGCAGGGGCTGGCGTACCTCCACCACGACTGCAACCCGCG

Basic information

species Zea mays
transcript GRMZM2G082855_T03
intron # 24
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G082855_T02 (Zea mays), 3'ss of exon 23
lower sequence: LOC_Os06g03970.1 (Oryza sativa), 3'ss of exon 24
gtgaggccgggttcctgagctctctttcttttttttttcttaattcatgtcgcttcgtccttccgataacccacgggccacggccattcccagGCCCGTCGAAGAAGGTGAAGCTGGACTGGGACACGAGGCTGAGGATCGCAGTGGGCGCCGCGCAGGGGCTGGCGTACCTCCACCACGACTGCAACCCGCG
    |   ||| |    | || |   || |   |  ||  | || |||   || ||  ||||   || | | |      | |  | ||  |||| || || ||||| ||||||||  |||||||||| || ||||||||||| || || || || || |||||||| || |||||||| ||||||||||| ||
----gttagggcttgaaacctttggctcatggataatttgttat-cattatgcatctccctt---atgatctata---tatgatccttttcagGTCCATCAAAGAAAGTGAAGCTCAACTGGGACACAAGACTGAGGATCGCGGTCGGAGCTGCACAAGGGCTGGCCTATCTCCACCATGACTGCAACCCTCG

upper sequence: GRMZM2G082855_T02 (Zea mays), 3'ss of exon 23
lower sequence: EFJ16326 (Selaginella moellendorffii), 3'ss of exon 24
gtgaggccgggttcctgagctctctttcttttttttttcttaattcatgtcgcttcgtccttccgataacccacgggccacggccattcccagGCCCGTCGAAGAAGGTGAAGCTGGACTGGGACACGAGGCTGAGGATCGCAGTGGGCGCCGCGCAGGGGCTGGCGTACCTCCACCACGACTGCAACCCGCG
                         |     || |  ||||  ||      |||    | ||   || | |    ||  ||     || ||||| ||   ||  ||||||| ||| ||||||||| || || |||  |||||  ||||||| ||||||||||||| |||||| |||||| |||||| ||| ||
------------------------gtatgacttctcatcttcctttgcaaagctctaacgttttcatgatcttttggaaac-----tttccagGACCAGTGAGAAAGGTGACGCTCGACTGGGACGCGCGGTTGATCATCGCGCTGGGCGCTGCGCAGGGGCTGGAGTACCTGCACCACAACTGCAGCCCCCG

upper sequence: GRMZM2G082855_T02 (Zea mays), 3'ss of exon 23
lower sequence: EFJ17800 (Selaginella moellendorffii), 3'ss of exon 24
gtgaggccgggttcctgagctctctttcttttttttttcttaattcatgtcgcttcgtccttccgataacccacgggccacggcca-ttcccagGCCCGTCGAAGAAGGTGAAGCTGGACTGGGACACGAGGCTGAGGATCGCAGTGGGCGCCGCGCAGGGGCTGGCGTACCTCCACCACGACTGCAACCCGCG
                                            |    || |||| || || | |    | |        ||  | || ||||| ||   ||  ||||||| ||| ||||||||| || || |||  |||||  ||||||| ||||||||||||| ||||||||||||| |||||| ||| ||
-----------------------------------------gtatagcttctcttcttctttgcaaagctctaaatcttgtggaaactttccagGACCAGTGAGAAAGGTGACGCTCGACTGGGACGCGCGGTTGATCATCGCGCTGGGCGCTGCGCAGGGGCTGGAGTACCTCCACCACAACTGCAGCCCCCG

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|148957564|gb|EC903660.2|EC903660
EST:     GCTGTTCTACGACTACATGGAGAACGGCTCCCTGTGGGATCTTCTCCATG                         GCCCGTCGAAGAAGGTGAAGCTGGACTGGGACACGAGGCTGAGGATCGCAG
genomic: GCTGTTCTACGACTACATGGAGAACGGCTCCCTGTGGGATCTTCTCCATGgtgaggccgg ... ccattcccagGCCCGTCGAAGAAGGTGAAGCTGGACTGGGACACGAGGCTGAGGATCGCAG
EST: gi|78117622|gb|DV536009.1|DV536009
EST:     GCTGTTCTACGACTACATGGAGAACGGCTCCCTGTGGGATCTTCTCCATG                         GCCCGTCGAAGAAGGTGAAGCTGGACTGGGACACGAGGCTGAGGATCGCAG
genomic: GCTGTTCTACGACTACATGGAGAACGGCTCCCTGTGGGATCTTCTCCATGgtgaggccgg ... ccattcccagGCCCGTCGAAGAAGGTGAAGCTGGACTGGGACACGAGGCTGAGGATCGCAG
EST: gi|149088301|gb|EE177395.2|EE177395
EST:     GCTGTTCTACGACTACATGGAGAACGGCTCCCTGTGGGATCTTCTCCATG                         GCCCCGTCGA-GAAGGTGAAGCTGGACTGGGACACGAGGCTGAGGATCGCA
genomic: GCTGTTCTACGACTACATGGAGAACGGCTCCCTGTGGGATCTTCTCCATGgtgaggccgg ... ccattcccagGCCC-GTCGAAGAAGGTGAAGCTGGACTGGGACACGAGGCTGAGGATCGCA

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: 909

AGGAACCTCGTCAGCCTCCACGGCTTCTCGCTCTCCCCTCACGGGAACCTGCTGTTCTACGACTACATGGAGAACGGCTCCCTGTGGGATCTTCTCCATGgtgaggccgg ... ccattcccagGCCCGTCGAAGAAGGTGAAGCTGGACTGGGACACGAGGCTGAGGATCGCAGTGGGCGCCGCGCAGGGGCTGGCGTACCTCCACCACGACTGCAACCCGCG


Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 108

AGGAACCTCGTCAGCCTCCACGGCTTCTCGCTCTCCCCTCACGGGAACCTGCTGTTCTACGACTACATGGAGAACGGCTCCCTGTGGGATCTTCTCCATGgtgaggccgg ... ccattcccagGCCCGTCGAAGAAGGTGAAGCTGGACTGGGACACGAGGCTGAGGATCGCAGTGGGCGCCGCGCAGGGGCTGGCGTACCTCCACCACGACTGCAACCCGCG


Block sizes: 48 (upstream exon), 34 (downstream exon)
Score: 2

AGGAACCTCGTCAGCCTCCACGGCTTCTCGCTCTCCCCTCACGGGAACCTGCTGTTCTACGACTACATGGAGAACGGCTCCCTGTGGGATCTTCTCCATGgtgaggccgg ... ccattcccagGCCCGTCGAAGAAGGTGAAGCTGGACTGGGACACGAGGCTGAGGATCGCAGTGGGCGCCGCGCAGGGGCTGGCGTACCTCCACCACGACTGCAACCCGCG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 721

AGGAACCTCGTCAGCCTCCACGGCTTCTCGCTCTCCCCTCACGGGAACCTGCTGTTCTACGACTACATGGAGAACGGCTCCCTGTGGGATCTTCTCCATGgtgaggccgg ... ccattcccagGCCCGTCGAAGAAGGTGAAGCTGGACTGGGACACGAGGCTGAGGATCGCAGTGGGCGCCGCGCAGGGGCTGGCGTACCTCCACCACGACTGCAACCCGCG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttaattcatgtcgcttcgtccttccgataacccacgggccacggccattcccagGCCCGTCGAAGAAGGTGAAGCTGGACTGGGACACGAGGCTGAGGATCGCAGTGGGCGCCGCGCAGGGGCTGGCGTACCTCCACCACGACTGCAACCCGCG
                         cgataac  putative branch site (score: 721)
                                             ccattccc  putative PPT