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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtagataatcctattggactagcttggataatttgcattggtagttggcagcagttatgaaatactatggatctaaattcaaaaaattgcagGAATTACCTCTGCTTCAGGAATTGCAGCAGAACTAGGCATTCCGCTAACCCATCGAGGTGTTGCTACCAG

Basic information

species Zea mays
transcript GRMZM2G000739_T01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G000739_T01 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os01g44050.1 (Oryza sativa), 3'ss of exon 3
gta-gataatcctattggactagcttggataatttgcattggtagttggcagcagttatgaaatactatggatctaaattcaaaaaattgcagGAATTACCTCTGCTTCAGGAATTGCAGCAGAACTAGGCATTCCGCTAACCCATCGAGGTGTTGCTACCAG
|||  | ||||    |    ||||||| ||| | |||| |     |||  |       ||| ||   |    | | |||     ||| |||||||||||| || ||||||||||||||||||||||| |||||||| ||||||||| ||||||||||||||||
gtataacaatcactatatggtagcttgaatactctgcacttccttttgtgac------tgagatgtgaattgtgtgaat----gaaaatgcagGAATTACATCAGCTTCAGGAATTGCAGCAGAACTTGGCATTCCACTAACCCATAGAGGTGTTGCTACCAG
















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|87298768|gb|DY470771.1|DY470771
EST:     AGAGATGGATTTCTTACAGCAACAGGGAATCAAAGTTGAAATTATCCCAG                         GAATTACCTCTGCTTCAGGAATTGCAGCAGAACTAGGCATTCCGCTAACCC
genomic: AGAGATGGATTTCTTACAGCAACAGGGAATCAAAGTTGAAATTATCCCAGgtagataatc ... aaaattgcagGAATTACCTCTGCTTCAGGAATTGCAGCAGAACTAGGCATTCCGCTAACCC
EST: gi|22489197|gb|BU049133.1|BU049133
EST:     AGAGATGGATTTCTTACAGCAACAGGGAATCAAAGTTGAAATTATCCCAG                         GAATTACCTCTGCTTCAGGAATTGCAGCAGAACTAGGCATTCCGCTAACCC
genomic: AGAGATGGATTTCTTACAGCAACAGGGAATCAAAGTTGAAATTATCCCAGgtagataatc ... aaaattgcagGAATTACCTCTGCTTCAGGAATTGCAGCAGAACTAGGCATTCCGCTAACCC
EST: gi|18384084|gb|BM417284.1|BM417284
EST:     AGAGATGGATTTCTTACAGCAACAGGGAATCAAAGTTGAAATTATCCCAG                         GAATTACCTCTGCTTCAGGAATT
genomic: AGAGATGGATTTCTTACAGCAACAGGGAATCAAAGTTGAAATTATCCCAGgtagataatc ... aaaattgcagGAATTACCTCTGCTTCAGGAATT

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), 47 (downstream exon)
Score: 63

GTTTTTGGAAGGGGTGGAGAAGAGATGGATTTCTTACAGCAACAGGGAATCAAAGTTGAAATTATCCCAGgtagataatc ... aaaattgcagGAATTACCTCTGCTTCAGGAATTGCAGCAGAACTAGGCATTCCGCTAACCCATCGAGGTGTTGCTACCAG


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 100

GTTTTTGGAAGGGGTGGAGAAGAGATGGATTTCTTACAGCAACAGGGAATCAAAGTTGAAATTATCCCAGgtagataatc ... aaaattgcagGAATTACCTCTGCTTCAGGAATTGCAGCAGAACTAGGCATTCCGCTAACCCATCGAGGTGTTGCTACCAG


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 137

GTTTTTGGAAGGGGTGGAGAAGAGATGGATTTCTTACAGCAACAGGGAATCAAAGTTGAAATTATCCCAGgtagataatc ... aaaattgcagGAATTACCTCTGCTTCAGGAATTGCAGCAGAACTAGGCATTCCGCTAACCCATCGAGGTGTTGCTACCAG


Block sizes: 47 (upstream exon), 47 (downstream exon)
Score: 47

GTTTTTGGAAGGGGTGGAGAAGAGATGGATTTCTTACAGCAACAGGGAATCAAAGTTGAAATTATCCCAGgtagataatc ... aaaattgcagGAATTACCTCTGCTTCAGGAATTGCAGCAGAACTAGGCATTCCGCTAACCCATCGAGGTGTTGCTACCAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttggtagttggcagcagttatgaaatactatggatctaaattcaaaaaattgcagGAATTACCTCTGCTTCAGGAATTGCAGCAGAACTAGGCATTCCGCTAACCCATCGAGGTGTTGCTACCAG
                                 atctaaa  putative branch site (score: 47)
                                 atctaaattcaaaaaa  TA-rich tract