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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatgttgaccttcctggccgcatcttgttttcgttgtttgaccgagttccatgcagctgctgacgacttcccatatctgcagGCGGAGTTGCATAATGTGAGAAGCCAACTGCTAAGTGATTTCACTCCCGATGACATGTGTCCTACAAGCACTCAGTTCTTTGAAATGCATGTTGATAATC

Basic information

species Zea mays
transcript GRMZM2G168449_T03
intron # 15
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G168449_T01 (Zea mays), 3'ss of exon 15
lower sequence: LOC_Os07g10550.1 (Oryza sativa), 3'ss of exon 16
gtaatgttgaccttcctggccgcatcttgttttcgttgtttgacc--gagttccatg-------------------------cagctgctgacgacttc-ccatatctgcagGCGGAGTTGCATAATGTGAGAAGCCAACTGCTAAGTGATTTCACTCCCGATGACATGTGTCCTACAAGCACTCAGTTCTTTGAAATGCATGTTGATAATC
|||||||| | ||||      |  || |   ||| |||||||| |  ||| || |||                         || | ||||| |||||| |  | |||||||||||||||| ||| |||||  |  ||||||||||| |||||| ||||||||||||||||||| ||||||||||| || ||||||     || ||||||  
gtaatgttcatcttctcaatggtctcctaaattcattgtttgaacatgagctcaatgaaactgctgtattcgctaaaaagtgcaaccgctgatgacttctctgtttctgcagGCGGAGTTGAATAGTGTGAAGAATCAACTGCTAAGCGATTTCTCTCCCGATGACATGTGTCCAACAAGCACTCATTTTTTTGAAGCAACTGGTGATAACT
















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|87154189|gb|DY398978.1|DY398978
EST:     GAGAATGCATAGTCTCCACAATCATGAACAACATTGCAAATATGATGGAT                         GCGGAGTTGCATAATGTGAGAAGCCAACTGCTAAGTGATTTCACTCCCGAT
genomic: GAGAATGCATAGTCTCCACAATCATGAACAACATTGCAAATATGATGGATgtaatgttga ... atatctgcagGCGGAGTTGCATAATGTGAGAAGCCAACTGCTAAGTGATTTCACTCCCGAT
EST: gi|22545084|gb|BU097443.1|BU097443
EST:     GAGAATGCATAGTCTCCACAATCATGAACAACATTGCAAATATGATGGAT                         GCGGAGTTGCATAATGTGAGAAGCCAACTGCTAAGTGATTTCACTCCCGAT
genomic: GAGAATGCATAGTCTCCACAATCATGAACAACATTGCAAATATGATGGATgtaatgttga ... atatctgcagGCGGAGTTGCATAATGTGAGAAGCCAACTGCTAAGTGATTTCACTCCCGAT
EST: gi|26455539|gb|CA827122.1|CA827122
EST:     GAGAATGCATAGTCTCCACAATCATGAACAACATTGCAAATATGATGGAT                         GCGGAGTTGCATAATGTGAGAAGCCAACTGCTAAGTGATTTCACTCCCGAT
genomic: GAGAATGCATAGTCTCCACAATCATGAACAACATTGCAAATATGATGGATgtaatgttga ... atatctgcagGCGGAGTTGCATAATGTGAGAAGCCAACTGCTAAGTGATTTCACTCCCGAT
EST: gi|78085280|gb|DV513673.1|DV513673
EST:     GAGAATGCATAGTCTCCACAATCATGAACAACATTGCAAATATGATGGAT                         GCGGAGTTGCATAATGTGAGAAGCCAACTGCTAAGTGATTTCACTCCCGAT
genomic: GAGAATGCATAGTCTCCACAATCATGAACAACATTGCAAATATGATGGATgtaatgttga ... atatctgcagGCGGAGTTGCATAATGTGAGAAGCCAACTGCTAAGTGATTTCACTCCCGAT

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: 25

TAATGCACTGAAGTCCCTCTCAGAAATAGAACTGTCAGAAAGTCAATCTCGAGAATGCATAGTCTCCACAATCATGAACAACATTGCAAATATGATGGATgtaatgttga ... atatctgcagGCGGAGTTGCATAATGTGAGAAGCCAACTGCTAAGTGATTTCACTCCCGATGACATGTGTCCTACAAGCACTCAGTTCTTTGAAATGCATGTTGATAATC


Block sizes: 44 (upstream exon), 49 (downstream exon)
Score: 14

TAATGCACTGAAGTCCCTCTCAGAAATAGAACTGTCAGAAAGTCAATCTCGAGAATGCATAGTCTCCACAATCATGAACAACATTGCAAATATGATGGATgtaatgttga ... atatctgcagGCGGAGTTGCATAATGTGAGAAGCCAACTGCTAAGTGATTTCACTCCCGATGACATGTGTCCTACAAGCACTCAGTTCTTTGAAATGCATGTTGATAATC


Block sizes: 35 (upstream exon), 49 (downstream exon)
Score: 12

TAATGCACTGAAGTCCCTCTCAGAAATAGAACTGTCAGAAAGTCAATCTCGAGAATGCATAGTCTCCACAATCATGAACAACATTGCAAATATGATGGATgtaatgttga ... atatctgcagGCGGAGTTGCATAATGTGAGAAGCCAACTGCTAAGTGATTTCACTCCCGATGACATGTGTCCTACAAGCACTCAGTTCTTTGAAATGCATGTTGATAATC


Block sizes: 45 (upstream exon), 43 (downstream exon)
Score: 36

TAATGCACTGAAGTCCCTCTCAGAAATAGAACTGTCAGAAAGTCAATCTCGAGAATGCATAGTCTCCACAATCATGAACAACATTGCAAATATGATGGATgtaatgttga ... atatctgcagGCGGAGTTGCATAATGTGAGAAGCCAACTGCTAAGTGATTTCACTCCCGATGACATGTGTCCTACAAGCACTCAGTTCTTTGAAATGCATGTTGATAATC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttttcgttgtttgaccgagttccatgcagctgctgacgacttcccatatctgcagGCGGAGTTGCATAATGTGAGAAGCCAACTGCTAAGTGATTTCACTCCCGATGACATGTGTCCTACAAGCACTCAGTTCTTTGAAATGCATGTTGATAATC
                              tgctgac  putative branch site (score: 36)
                                       cttcccat  putative PPT