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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttgtcgacttcagttattttcagatatcttttttttaatgttttgcccattaacaacttccttggacagACACTTGTTGAGTTCTTTGGCACATTGTCAAGAGAGTGGGCTTTGGAATGCATGAAAGACCTTCTACTGGTTAATCTGAGGGGAAATCTTCAGATTGTTG

Basic information

species Zea mays
transcript GRMZM2G352837_T01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G352837_T01 (Zea mays), 3'ss of exon 5
lower sequence: Vv06s0004g06860.t01 (Vitis vinifera), 3'ss of exon 18
gtttgtcgacttcagttattttcagatatcttttttttaatgttttgcccattaacaacttccttgga-----cagACACTTGTTGAGTTCTTTGGCACATTGTCAAGAGAGTGGGCTTTGGAATGCATGAAAGACCTTCTACTGGTTAATCTGAGGGGAAATCTTCAGATTGTTG
||| |  |     |||  |    |  |   | | ||| |||||  |     ||   ||||   | | |     ||| | ||||||||||||||||| ||  | |||||||| |||||| | || || ||||||||||||||||| || |||||  | |  |||||||||||  |||
gttagatgctcaaagtgttacataacttgttctatttgaatgtagtatttttttctaactatatggtatatttcagGCTCTTGTTGAGTTCTTTGGAACTCTTTCAAGAGAATGGGCTCTTGAGTGTATGAAAGACCTTCTACTTGTCAATCTTCGTGCCAATCTTCAGATAATTG

upper sequence: GRMZM2G352837_T01 (Zea mays), 3'ss of exon 5
lower sequence: Vv13s0067g01290.t01 (Vitis vinifera), 3'ss of exon 18
gtttgtcgacttcagttat---tttcagatatcttttttttaatgttttgcccattaacaactt--ccttggacagACACTTGTTGAGTTCTTTGGCACATTGTCAAGAGAGTGGGCTTTGGAATGCATGAAAGACCTTCTACTGGTTAATCTGAGGGGAAATCTTCAGATTGTTG
|||| |  ||||||  | |   | |  | |  ||      |  |    |  | ||| |  || |     |   ||| ||||||| ||||||||||| ||  | ||| |||| ||||||||||| |||||||| |||||||| ||||| ||||| || || || ||||||||  |||
gtttttatacttcaactgtgtttcttggttcactaggaggttgtaaacttgctattgaatacgtggttctcttcagGCACTTGTAGAGTTCTTTGGTACGCTTTCACGAGAATGGGCTTTGGAGTGCATGAAGGACCTTCTTCTGGTCAATCTAAGAGGCAACCTTCAGATAATTG
















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: 45 (upstream exon), 47 (downstream exon)
Score: 222

CATTACTCAGAGTTGCCTGATATCAAGCGTGCCATTGTAAATACCCATGTCATTGAACCACAGgtttgtcgac ... ccttggacagACACTTGTTGAGTTCTTTGGCACATTGTCAAGAGAGTGGGCTTTGGAATGCATGAAAGACCTTCTACTGGTTAATCTGAGGGGAAATCTTCAGATTGTTG


Block sizes: 45 (upstream exon), 47 (downstream exon)
Score: 184

CATTACTCAGAGTTGCCTGATATCAAGCGTGCCATTGTAAATACCCATGTCATTGAACCACAGgtttgtcgac ... ccttggacagACACTTGTTGAGTTCTTTGGCACATTGTCAAGAGAGTGGGCTTTGGAATGCATGAAAGACCTTCTACTGGTTAATCTGAGGGGAAATCTTCAGATTGTTG


Block sizes: 45 (upstream exon), 47 (downstream exon)
Score: 166

CATTACTCAGAGTTGCCTGATATCAAGCGTGCCATTGTAAATACCCATGTCATTGAACCACAGgtttgtcgac ... ccttggacagACACTTGTTGAGTTCTTTGGCACATTGTCAAGAGAGTGGGCTTTGGAATGCATGAAAGACCTTCTACTGGTTAATCTGAGGGGAAATCTTCAGATTGTTG


Block sizes: 45 (upstream exon), 47 (downstream exon)
Score: 174

CATTACTCAGAGTTGCCTGATATCAAGCGTGCCATTGTAAATACCCATGTCATTGAACCACAGgtttgtcgac ... ccttggacagACACTTGTTGAGTTCTTTGGCACATTGTCAAGAGAGTGGGCTTTGGAATGCATGAAAGACCTTCTACTGGTTAATCTGAGGGGAAATCTTCAGATTGTTG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tattttcagatatcttttttttaatgttttgcccattaacaacttccttggacagACACTTGTTGAGTTCTTTGGCACATTGTCAAGAGAGTGGGCTTTGGAATGCATGAAAGACCTTCTACTGGTTAATCTGAGGGGAAATCTTCAGATTGTTG
                                 cattaac  putative branch site (score: 174)
                                          cttcctt  putative PPT
       agatatctttttttta  TA-rich tract