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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGAAGAAAGGCGCATGTTTGATCATGTGACCTGCAACAGATCAGCATCTGTGGATGAAGTCACAGCACCTGGATCTCTTGCTCTAGATTTAATTGAACAAgtgggtcttagtaacaattttttggtgccatcacctggtatgaattattcctttgcctgcttgacatttacttttccatttattcag

Basic information

species Zea mays
transcript GRMZM2G465169_T02
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G465169_T02 (Zea mays), 5'ss of exon 6
lower sequence: LOC_Os06g20370.1 (Oryza sativa), 5'ss of exon 6
GGAAGAAAGGCGCATGTTTGATCATGTGACCTGCAACAGATCAGCATCTGTGGATGAAGTCACAGCACCTGGATCTCTTGCTCTAGATTTAATTGAACAAgtgggtcttagtaacaa---ttttttggtgccatcac---ctggtatgaattattcctttgcctgcttgacatttacttttccatttattcag
| |||||||| |||||||||||||||| ||||||||||||||||| ||||| || ||||||| ||||||||| ||||||| || ||| | ||||| |||||| | | | | || ||||||||||| || || ||| | ||| |||| ||| | ||||| || ||| | | || |||||
GCAAGAAAGGAGCATGTTTGATCATGTCACCTGCAACAGATCAGCCTCTGTAGACAAAGTCACTGCACCTGGAGCTCTTGCCCTGGATCTCATTGAGCAAgtgagattaaacagtaaatcttttttggtgcaattactgtctgacactaatccttccactgcat--ttgactttctgtttccaaattgttcag
















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|33095065|gb|CF055059.1|CF055059
EST:     TGGATGAAGTCACAGCACCTGGATCTCTTGCTCTAGATTTAATTGAACAA                         GCTGAGGTTGAGGTTCAAAGGTTAGACCAGCTGAAGTAC
genomic: TGGATGAAGTCACAGCACCTGGATCTCTTGCTCTAGATTTAATTGAACAAgtgggtctta ... atttattcagGCTGAGGTTGAGGTTCAAAGGTTAGACCAGCTGAAGTAC
EST: gi|32846311|gb|CD985992.1|CD985992
EST:     TGGATGAAGTCACAGCACCTGGATCTCTTGCTCTAGATTTAATTGAACAA                         GCTGAGGTTGAGGTTCAAAGGTTAGACCAGCTGAAGTA
genomic: TGGATGAAGTCACAGCACCTGGATCTCTTGCTCTAGATTTAATTGAACAAgtgggtctta ... atttattcagGCTGAGGTTGAGGTTCAAAGGTTAGACCAGCTGAAGTA
EST: gi|9731736|gb|BE510488.1|BE510488
EST:     TGGATGAAGTCACAGCACCTGGATCTCTTGCTCTAGATTTAATTGAACAA                         GCTGAGGTTGAGGTTCAAAGGTTAGACCAGCTGAAGTACAGCAAGATGAAA
genomic: TGGATGAAGTCACAGCACCTGGATCTCTTGCTCTAGATTTAATTGAACAAgtgggtctta ... atttattcagGCTGAGGTTGAGGTTCAAAGGTTAGACCAGCTGAAGTACAGCAAGATGAAA
EST: gi|32848300|gb|CD987981.1|CD987981
EST:     TGGATGAAGTCACAGCACCTGGATCTCTTGCTCTAGATTTAATTGAACAA                         GCTGAGGTTGAGGTTCAAAGGTTAGACCAGCTGAAGT
genomic: TGGATGAAGTCACAGCACCTGGATCTCTTGCTCTAGATTTAATTGAACAAgtgggtctta ... atttattcagGCTGAGGTTGAGGTTCAAAGGTTAGACCAGCTGAAGT
EST: gi|32944328|gb|CF049147.1|CF049147
EST:     TGGATGAAGTCACAGCACCTGGATCTCTTGCTCTAGATTTAATTGAACAA                         GCTGAGGTTGAGGTTCAAAGGTTAGACCAGCTGAAGT
genomic: TGGATGAAGTCACAGCACCTGGATCTCTTGCTCTAGATTTAATTGAACAAgtgggtctta ... atttattcagGCTGAGGTTGAGGTTCAAAGGTTAGACCAGCTGAAGT
EST: gi|32930378|gb|CF035190.1|CF035190
EST:     TGGATGAAGTCACAGCACCTGGATCTCTTGCTCTAGATTTAATTGAACAA                         GCTGAGGTTGAGGTTCAAAGGTTAGACCAGCTGAAGT
genomic: TGGATGAAGTCACAGCACCTGGATCTCTTGCTCTAGATTTAATTGAACAAgtgggtctta ... atttattcagGCTGAGGTTGAGGTTCAAAGGTTAGACCAGCTGAAGT

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: 48 (upstream exon), 48 (downstream exon)
Score: 299

GGAAGAAAGGCGCATGTTTGATCATGTGACCTGCAACAGATCAGCATCTGTGGATGAAGTCACAGCACCTGGATCTCTTGCTCTAGATTTAATTGAACAAgtgggtctta ... atttattcagGCTGAGGTTGAGGTTCAAAGGTTAGACCAGCTGAAGTACAGCAAGATGAAAGAAATAGCTTTCAAGAAGCAAAATGAGCTGGAAGATATCTACGCTGGTG


Block sizes: 49 (upstream exon), 45 (downstream exon)
Score: 42

GGAAGAAAGGCGCATGTTTGATCATGTGACCTGCAACAGATCAGCATCTGTGGATGAAGTCACAGCACCTGGATCTCTTGCTCTAGATTTAATTGAACAAgtgggtctta ... atttattcagGCTGAGGTTGAGGTTCAAAGGTTAGACCAGCTGAAGTACAGCAAGATGAAAGAAATAGCTTTCAAGAAGCAAAATGAGCTGGAAGATATCTACGCTGGTG


Block sizes: 46 (upstream exon), 48 (downstream exon)
Score: 44

GGAAGAAAGGCGCATGTTTGATCATGTGACCTGCAACAGATCAGCATCTGTGGATGAAGTCACAGCACCTGGATCTCTTGCTCTAGATTTAATTGAACAAgtgggtctta ... atttattcagGCTGAGGTTGAGGTTCAAAGGTTAGACCAGCTGAAGTACAGCAAGATGAAAGAAATAGCTTTCAAGAAGCAAAATGAGCTGGAAGATATCTACGCTGGTG


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 57

GGAAGAAAGGCGCATGTTTGATCATGTGACCTGCAACAGATCAGCATCTGTGGATGAAGTCACAGCACCTGGATCTCTTGCTCTAGATTTAATTGAACAAgtgggtctta ... atttattcagGCTGAGGTTGAGGTTCAAAGGTTAGACCAGCTGAAGTACAGCAAGATGAAAGAAATAGCTTTCAAGAAGCAAAATGAGCTGGAAGATATCTACGCTGGTG