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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatccttacaatatatgctatgacagacacaatattgtttcctcaaagccaacactcttgttttcagcattaactaaaataccctcagATATGATATAGTTGTTGATGCAACTGACAACCTTCCTACTAGGTATATGATCAGCGATTGCTGTGTTTTGCTGAACAAG

Basic information

species Zea mays
transcript GRMZM2G160842_T02
intron # 5
splice site 3'
intron type U12 (go to U12 genes for details)

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G160842_T02 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os02g32460.1 (Oryza sativa), 3'ss of exon 5
gtatccttacaatatatgctatgac---agacacaatattgtttcctc-aaagccaacactcttgttttcagcattaactaaaataccctcagATATGATATAGTTGTTGATGCAACTGACAACCTTCCTACTAGGTATATGATCAGCGATTGCTGTGTTTTGCTGAACAAG
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gtatgctatcgaaacattaagtgtcttgagacaatatattgtgccttttagagtttactgaatttttttttccactga-tggatcaatcacagATATGATATAGTTGTAGATGCCACGGACAATCTTCCTACTCGATACATGATCAGTGACTGTTGTGTGTTGCTGAATAAG
















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|211086842|gb|FL241958.1|FL241958
EST:     GAGTATCACCATACTCTGAAGCCATGCAATGCTTTGGAGGTTGCACGGAA                         ATATGATATASTTGTTGATGCAACTGACAACCTTCCTACTAGGTATATGAT
genomic: GAGTATCACCATACTCTGAAGCCATGCAATGCTTTGGAGGTTGCACGGAAgtatccttac ... ataccctcagATATGATATAGTTGTTGATGCAACTGACAACCTTCCTACTAGGTATATGAT
EST: gi|148954835|gb|EC900308.2|EC900308
EST:     GAGTATCACCATACTCTGAAGCCATGCAATGCTTTGGAGGTTGCACGGAA                         ATATGATATAGTTGTTGATGCAACTGACAACCTTCCTACTAGGTATATGAT
genomic: GAGTATCACCATACTCTGAAGCCATGCAATGCTTTGGAGGTTGCACGGAAgtatccttac ... ataccctcagATATGATATAGTTGTTGATGCAACTGACAACCTTCCTACTAGGTATATGAT

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: 39 (upstream exon), 49 (downstream exon)
Score: 159

GATTAATTCCTCTATCAAAGTAGTAGAGTATCACCATACTCTGAAGCCATGCAATGCTTTGGAGGTTGCACGGAAgtatccttac ... ataccctcagATATGATATAGTTGTTGATGCAACTGACAACCTTCCTACTAGGTATATGATCAGCGATTGCTGTGTTTTGCTGAACAAG


Block sizes: 39 (upstream exon), 49 (downstream exon)
Score: 100

GATTAATTCCTCTATCAAAGTAGTAGAGTATCACCATACTCTGAAGCCATGCAATGCTTTGGAGGTTGCACGGAAgtatccttac ... ataccctcagATATGATATAGTTGTTGATGCAACTGACAACCTTCCTACTAGGTATATGATCAGCGATTGCTGTGTTTTGCTGAACAAG


Block sizes: 39 (upstream exon), 49 (downstream exon)
Score: 114

GATTAATTCCTCTATCAAAGTAGTAGAGTATCACCATACTCTGAAGCCATGCAATGCTTTGGAGGTTGCACGGAAgtatccttac ... ataccctcagATATGATATAGTTGTTGATGCAACTGACAACCTTCCTACTAGGTATATGATCAGCGATTGCTGTGTTTTGCTGAACAAG


Block sizes: 39 (upstream exon), 49 (downstream exon)
Score: 75

GATTAATTCCTCTATCAAAGTAGTAGAGTATCACCATACTCTGAAGCCATGCAATGCTTTGGAGGTTGCACGGAAgtatccttac ... ataccctcagATATGATATAGTTGTTGATGCAACTGACAACCTTCCTACTAGGTATATGATCAGCGATTGCTGTGTTTTGCTGAACAAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attgtttcctcaaagccaacactcttgttttcagcattaactaaaataccctcagATATGATATAGTTGTTGATGCAACTGACAACCTTCCTACTAGGTATATGATCAGCGATTGCTGTGTTTTGCTGAACAAG
 agcattaac  putative branch site 
                                              taccctc  putative PPT
                                   attaactaaaata  TA-rich tract