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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTTGCTGTTAAGAAAATGAAGAAAAAGTATTATTCTTTTGAGGAATGTATGGGTTTGCGTGAAGTAAAGgtattttagaccagcgatgtttttttatcattccctgttatgttctttcaactgacatttcttgttattattttgttgaag

Basic information

species Zea mays
transcript GRMZM2G108829_T01
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G108829_T01 (Zea mays), 5'ss of exon 6
lower sequence: LOC_Os02g47220.3 (Oryza sativa), 5'ss of exon 1
-------------------------------GTTGCTGTTAAGAAAATGAAGAAAAAGTATTATTCTTTTGAGGAATGTATGGGTTTGCGTGAAGTAAAGgtattttagaccagcgatgtttttttatcattccctgttatgttctttcaactgacatttcttgttattattttgttgaag
                               || || ||||||||||||||||  || |||||||||||||||||||| ||| || | ||||||||||||||||||||    |  |||||    |     || |||| ||||  | ||||||||| ||||||         | | ||||||
GATTGTAAGCAAAATGTGCACTGATCTATAGGTGGCAGTTAAGAAAATGAAGAGGAAATATTATTCTTTTGAGGAATGCATGAGTCTACGTGAAGTAAAGgtattttaactgaaagatgtaccctc----tttcctgctatgaaccttcaactgatatttctc-------ctatattgaag

upper sequence: GRMZM2G108829_T01 (Zea mays), 5'ss of exon 6
lower sequence: LOC_Os02g47220.1 (Oryza sativa), 5'ss of exon 6
GTTGCTGTTAAGAAAATGAAGAAAAAGTATTATTCTTTTGAGGAATGTATGGGTTTGCGTGAAGTAAAGgtattttagaccagcgatgtttttttatcattccctgttatgttctttcaactgacatttcttgttattattttgttgaag
|| || ||||||||||||||||  || |||||||||||||||||||| ||| || | ||||||||||||||||||||    |  |||||    |     || |||| ||||  | ||||||||| ||||||         | | ||||||
GTGGCAGTTAAGAAAATGAAGAGGAAATATTATTCTTTTGAGGAATGCATGAGTCTACGTGAAGTAAAGgtattttaactgaaagatgtaccctc----tttcctgctatgaaccttcaactgatatttctc-------ctatattgaag
















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|47961778|gb|CN844487.1|CN844487
EST:     AGAAAAAGTATTATTCTTTTGAGGAATGTATGGGTTTGCGTGAAGTAAAG                         TCTTTGCGGCGCATGAATCATCCTAACATTGTGAAGCTCAAAGAGGTTATC
genomic: AGAAAAAGTATTATTCTTTTGAGGAATGTATGGGTTTGCGTGAAGTAAAGgtattttaga ... tttgttgaagTCTTTGCGGCGCATGAATCATCCTAACATTGTGAAGCTCAAAGAGGTTATC
EST: gi|67011156|gb|CO439905.1|CO439905
EST:     GGGTTTGCGTGAAGTAAAG                         TCTTTGCGGCGCATGAATCATCCTAACATTGTGAAGCTCAAAGAGGTTATC
genomic: GGGTTTGCGTGAAGTAAAGgtattttaga ... tttgttgaagTCTTTGCGGCGCATGAATCATCCTAACATTGTGAAGCTCAAAGAGGTTATC

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: 774

GTTGCTGTTAAGAAAATGAAGAAAAAGTATTATTCTTTTGAGGAATGTATGGGTTTGCGTGAAGTAAAGgtattttaga ... tttgttgaagTCTTTGCGGCGCATGAATCATCCTAACATTGTGAAGCTCAAAGAGGTTATCCGAGAAAATGATATATTATACTTCATAATGGAATACATG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 410

GTTGCTGTTAAGAAAATGAAGAAAAAGTATTATTCTTTTGAGGAATGTATGGGTTTGCGTGAAGTAAAGgtattttaga ... tttgttgaagTCTTTGCGGCGCATGAATCATCCTAACATTGTGAAGCTCAAAGAGGTTATCCGAGAAAATGATATATTATACTTCATAATGGAATACATG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 324

GTTGCTGTTAAGAAAATGAAGAAAAAGTATTATTCTTTTGAGGAATGTATGGGTTTGCGTGAAGTAAAGgtattttaga ... tttgttgaagTCTTTGCGGCGCATGAATCATCCTAACATTGTGAAGCTCAAAGAGGTTATCCGAGAAAATGATATATTATACTTCATAATGGAATACATG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 796

GTTGCTGTTAAGAAAATGAAGAAAAAGTATTATTCTTTTGAGGAATGTATGGGTTTGCGTGAAGTAAAGgtattttaga ... tttgttgaagTCTTTGCGGCGCATGAATCATCCTAACATTGTGAAGCTCAAAGAGGTTATCCGAGAAAATGATATATTATACTTCATAATGGAATACATG