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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtctattatatttgcaaagtcattgtttaccttttatatttcctctggttgattgccccatccatatttagttacccttttatctaaattgtttgctttccacagGCCATTAAGATTTTGAACATGATCAAACTATATGGGAAGCCCATAAGAGTAAACAAG

Basic information

species Zea mays
transcript GRMZM2G170699_T01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G170699_T01 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os10g31900.1 (Oryza sativa), 3'ss of exon 3
gtaagtctattatatttgcaaagtcattgtttaccttttatatttcctctggttgattgccccatccatatttagttacccttttatctaaattgtttgctttccacagGCCATTAAGATTTTGAACATGATCAAACTATATGGGAAGCCCATAAGAGTAAACAAG
||||||||||  |   || |     || ||     | |  | |   || |   |       |||| || || ||| |   || || ||| |  | |||  |||    |||| |||||||||||||| |||||||| |||||||| || || |||||||||||||||
gtaagtctatcttgggtgaaggcaaatagtacttttctactgtacactttcaata-----tccattca-atatagcttttctgtt-tcttatctatttatttttt-tagGCTATTAAGATTTTGAATATGATCAAGCTATATGGAAAACCAATAAGAGTAAACAAG
















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|74240862|gb|DT648776.1|DT648776
EST:     ACCAGGGATATGGATTTGTAGAATTCAGGAGTGAGGAAGATGCAGATTAT                         GCCATTAAGATTTTGAACATGATCAAACTATATGGGAAGCCCATAAGAGTA
genomic: ACCAGGGATATGGATTTGTAGAATTCAGGAGTGAGGAAGATGCAGATTATgtaagtctat ... ctttccacagGCCATTAAGATTTTGAACATGATCAAACTATATGGGAAGCCCATAAGAGTA
EST: gi|89248214|gb|DY620000.1|DY620000
EST:     ACCAGGGATATGGATTTGTAGAATTCAGGAGCGAGGAAGATGCAGATTAT                         GCCATTAAGATTTTGAACATGATCAAACTATATGGGAAGCCCATAAGAGTA
genomic: ACCAGGGATATGGATTTGTAGAATTCAGGAGTGAGGAAGATGCAGATTATgtaagtctat ... ctttccacagGCCATTAAGATTTTGAACATGATCAAACTATATGGGAAGCCCATAAGAGTA
EST: gi|88746230|gb|DY530371.1|DY530371
EST:     ACCAGGGATATGGATTTGTAGAATTCAGGAGTGAGGAAGATGCAGATTAT                         GCCATTAAGATTTTGAACATGATCAAACTATATGGGAAGCCCATAAGAGTA
genomic: ACCAGGGATATGGATTTGTAGAATTCAGGAGTGAGGAAGATGCAGATTATgtaagtctat ... ctttccacagGCCATTAAGATTTTGAACATGATCAAACTATATGGGAAGCCCATAAGAGTA
EST: gi|78124096|gb|DV542480.1|DV542480
EST:     ACCAGGGATATGGATTTGTAAAATTCAGGAGTGAGGAAGATGCAGATTAT                         GCCATTAAGATTTTGAACATGATCAAACTATATGGGAAGCCCATAAGAGTA
genomic: ACCAGGGATATGGATTTGTAGAATTCAGGAGTGAGGAAGATGCAGATTATgtaagtctat ... ctttccacagGCCATTAAGATTTTGAACATGATCAAACTATATGGGAAGCCCATAAGAGTA
EST: gi|21843149|gb|BQ703730.1|BQ703730
EST:     ACCAGGGATATGGATTTGTAGAATTCAGGAGTGAGGAAGATGCAGATTAT                         GCCATTAAGATTTTGAACATGATCAAACTATATGGGAAGCCCATAAGAGTA
genomic: ACCAGGGATATGGATTTGTAGAATTCAGGAGTGAGGAAGATGCAGATTATgtaagtctat ... ctttccacagGCCATTAAGATTTTGAACATGATCAAACTATATGGGAAGCCCATAAGAGTA
EST: gi|101395862|gb|EB819858.1|EB819858
EST:     ACCAGGGATATGGATTTGTAGAATTCAGGAGTGAGGAAGATGCAGATTAT                         GCCATTAAGATTTTGAACATGATCAAACTATATGGGAAGCCCATAAGAGTA
genomic: ACCAGGGATATGGATTTGTAGAATTCAGGAGTGAGGAAGATGCAGATTATgtaagtctat ... ctttccacagGCCATTAAGATTTTGAACATGATCAAACTATATGGGAAGCCCATAAGAGTA

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: 85

TTAATGTGTATGTCCCAAAAGACAGAGTTACAAATTTACACCAGGGATATGGATTTGTAGAATTCAGGAGTGAGGAAGATGCAGATTATgtaagtctat ... ctttccacagGCCATTAAGATTTTGAACATGATCAAACTATATGGGAAGCCCATAAGAGTAAACAAG


Block sizes: 45 (upstream exon), 48 (downstream exon)
Score: 45

TTAATGTGTATGTCCCAAAAGACAGAGTTACAAATTTACACCAGGGATATGGATTTGTAGAATTCAGGAGTGAGGAAGATGCAGATTATgtaagtctat ... ctttccacagGCCATTAAGATTTTGAACATGATCAAACTATATGGGAAGCCCATAAGAGTAAACAAG


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 67

TTAATGTGTATGTCCCAAAAGACAGAGTTACAAATTTACACCAGGGATATGGATTTGTAGAATTCAGGAGTGAGGAAGATGCAGATTATgtaagtctat ... ctttccacagGCCATTAAGATTTTGAACATGATCAAACTATATGGGAAGCCCATAAGAGTAAACAAG


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 51

TTAATGTGTATGTCCCAAAAGACAGAGTTACAAATTTACACCAGGGATATGGATTTGTAGAATTCAGGAGTGAGGAAGATGCAGATTATgtaagtctat ... ctttccacagGCCATTAAGATTTTGAACATGATCAAACTATATGGGAAGCCCATAAGAGTAAACAAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gattgccccatccatatttagttacccttttatctaaattgtttgctttccacagGCCATTAAGATTTTGAACATGATCAAACTATATGGGAAGCCCATAAGAGTAAACAAG
                               atctaaa  putative branch site (score: 51)
                                         tttgctttcc  putative PPT
                           ttttatctaaattgtt  TA-rich tract