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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagatatttttttaaaaaatatattcttgttgtctctttcttttcatattataatccttgtttggttaaccgtgccaattgaattatttccagGGCATTTCCATATTTTTGTTGGTGATTTAAGTTCTGAAGTGAATGATGCAACTCTTTATGCCTGTTTCTCAGCATATCCTTCTTGTTCGTAAGTCCTTTT

Basic information

species Zea mays
transcript GRMZM2G166355_T02
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G166355_T02 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os08g40880.1 (Oryza sativa), 3'ss of exon 5
gtgagatatttttttaaaaaatatattcttgttgtctctttcttttcatattataatccttgtttggttaaccgtgccaattgaattatttccagGGCATTTCCATATTTTTGTTGGTGATTTAAGTTCTGAAGTGAATGATGCAACTCTTTATGCCTGTTTCTCAGCATATCCTTCTTGTTCGTAAGTCCTTTT
|||||||||| ||  | ||||      | |||  |   ||| |||  | ||| |||| ||| |||||||||| ||||| | |||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||            
gtgagatattattaaagaaaaacctcacatgtctttcatttgtttcta-attttaattcttatttggttaactgtgcccactgaactatttccagGGCATTTCCATATTTTTGTTGGTGATTTAAGTTCTGAAGTGAATGATGCAACTCTTTATGCCTGTTTCTCAGCATATCCTTCTTGTTC------------
















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|32799959|gb|CD952195.1|CD952195
EST:     AATCAAGGTGAACTGGGCATATGCAAGTACGCAGAGGGAGGATACGTCAG                         GGCATTTCCATATTTTTGTTGGTGATTTA
genomic: AATCAAGGTGAACTGGGCATATGCAAGTACGCAGAGGGAGGATACGTCAGgtgagatatt ... ttatttccagGGCATTTCCATATTTTTGTTGGTGATTTA
EST: gi|32810117|gb|CD962351.1|CD962351
EST:     AATCAAGGTGAACTGGGCATATGCAAGTACGCAGAGGGAGGATACGTCAG                         GGCATTTCCATATTTTTGTTGGTGATTTA
genomic: AATCAAGGTGAACTGGGCATATGCAAGTACGCAGAGGGAGGATACGTCAGgtgagatatt ... ttatttccagGGCATTTCCATATTTTTGTTGGTGATTTA
EST: gi|61118503|gb|DN559464.1|DN559464
EST:     AATCAAGGTGAACTGGGCATATGCAAGTACGCAGAGGGAGGATACGTCAG                         GGCATTTCCATATTTTTGTTGGTGATTTAAG
genomic: AATCAAGGTGAACTGGGCATATGCAAGTACGCAGAGGGAGGATACGTCAGgtgagatatt ... ttatttccagGGCATTTCCATATTTTTGTTGGTGATTTAAG

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: 204

ATATGGACAAGCAATCAAGGTGAACTGGGCATATGCAAGTACGCAGAGGGAGGATACGTCAGgtgagatatt ... ttatttccagGGCATTTCCATATTTTTGTTGGTGATTTAAGTTCTGAAGTGAATGATGCAACTCTTTATGCCTGTTTCTCAGCATATCCTTCTTGTTCGTAAGTCCTTTT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 205

ATATGGACAAGCAATCAAGGTGAACTGGGCATATGCAAGTACGCAGAGGGAGGATACGTCAGgtgagatatt ... ttatttccagGGCATTTCCATATTTTTGTTGGTGATTTAAGTTCTGAAGTGAATGATGCAACTCTTTATGCCTGTTTCTCAGCATATCCTTCTTGTTCGTAAGTCCTTTT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 197

ATATGGACAAGCAATCAAGGTGAACTGGGCATATGCAAGTACGCAGAGGGAGGATACGTCAGgtgagatatt ... ttatttccagGGCATTTCCATATTTTTGTTGGTGATTTAAGTTCTGAAGTGAATGATGCAACTCTTTATGCCTGTTTCTCAGCATATCCTTCTTGTTCGTAAGTCCTTTT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 190

ATATGGACAAGCAATCAAGGTGAACTGGGCATATGCAAGTACGCAGAGGGAGGATACGTCAGgtgagatatt ... ttatttccagGGCATTTCCATATTTTTGTTGGTGATTTAAGTTCTGAAGTGAATGATGCAACTCTTTATGCCTGTTTCTCAGCATATCCTTCTTGTTCGTAAGTCCTTTT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcttttcatattataatccttgtttggttaaccgtgccaattgaattatttccagGGCATTTCCATATTTTTGTTGGTGATTTAAGTTCTGAAGTGAATGATGCAACTCTTTATGCCTGTTTCTCAGCATATCCTTCTTGTTCGTAAGTCCTTTT
                         ggttaac  putative branch site (score: 190)
                                             ttatttcc  putative PPT
                                      aattgaattattt  TA-rich tract