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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagattggttttcaacttgcacctcctatatattagttctattgtcaacgaccccccccccccagcaatcgaagtgaatctctaaactactagacatataaaatatgctagaccaaagttctgttttgcatttggatatttcctattgatggatgaacttgcatttttttatgcagGTATCTTCAGATTTGAGCATTGTTGATCTTGATGTTCCATTTGGATTGATGCTTGCTCTTGGTGCCAGCATAAATGCATATAGCAATCTGGGGGTGTTGG

Basic information

species Zea mays
transcript AC234203.1_FGT004
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AC234203.1_FGT004 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os11g05700.1 (Oryza sativa), 3'ss of exon 3
gtgagattggttttcaacttgcacctcctatatattagttctattgtcaacgaccccccccccccagcaatcgaagtgaatctctaaactactagacatataaaatatgctagaccaaagttctgttttgcatttggatatttcctattgatggatgaacttgc-atttttttatgcagGTATCTTCAGATTTGAGCATTGTTGATCTTGATGTTCCATTTGGATTGATGCTTGCTCTTGGTGCCAGCATAAATGCATATAGCAATCTGGGGGTGTTGG
                                                                                                    ||| | ||  || | || |    |||    |||||||||| || | |||  ||||| || |||    ||  | |||||||| |||||||||||||| |||| ||| ||||||||||||||    || ||| ||    |    |||||| ||||||||||||||||||||||||| ||||
---------------------------------------------------------------------------------------------------gtaagaaatcttaaagcata----tgtgaaacatttggatactttcgattagtggattaaattgttgattcctcatgcagGTCTCTTCAGATTTGAGTATTGCTGACCTTGATGTTCCATTCTTCTTCATGTTTAGCATGAACGCCAGCTTAAATGCATATAGCAATCTGGGGGTATTGG

upper sequence: AC234203.1_FGT004 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os11g05700.1 (Oryza sativa), 3'ss of exon 3
gtgagattggttttcaacttgcacctcctatatattagttctattgtcaacgaccccccccccccagcaatcgaagtgaatctctaaactactagacatataaaatatgctagaccaaagttctgttttgcatttggatatttcctattgatggatgaacttgc-atttttttatgcagGTATCTTCAGATTTGAGCATTGTTGATCTTGATGTTCCATTTGGATTGATGCTTGCTCTTGGTGCCAGCATAAATGCATATAGCAATCTGGGGGTGTTGG
                                                                                                    ||| | ||  || | || |    |||    |||||||||| || | |||  ||||| || |||    ||  | |||||||| |||||||||||||| |||| ||| ||||||||||||||    || ||| ||    |    |||||| ||||||||||||||||||||||||| ||||
---------------------------------------------------------------------------------------------------gtaagaaatcttaaagcata----tgtgaaacatttggatactttcgattagtggattaaattgttgattcctcatgcagGTCTCTTCAGATTTGAGTATTGCTGACCTTGATGTTCCATTCTTCTTCATGTTTAGCATGAACGCCAGCTTAAATGCATATAGCAATCTGGGGGTATTGG

upper sequence: AC234203.1_FGT004 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os06g06440.1 (Oryza sativa), 3'ss of exon 4
gtgagattggttttcaacttgcacctcctatatattagttctattgtcaacgaccccccccccccagcaatcgaagtgaatctctaaac-tactagacatataaaatatgctagaccaaagttctgttttgcatttggatatttcctattgatggatgaacttgcatttttttatgcagGTATCTTCAGATTTGAGCATTGTTGATCTTGATGTTCCATTTGGATTGATGCTTGCTCTTGGTGCCAGCATAAATGCATATAGCAATCTGGGGGTGTTGG
                                                                             |||   |||||| ||   || |    |||  || || |  | |||||  |||  |||||| | | || | |||| ||             ||| | ||| |||| ||||||||| |||| |||||||| ||||| ||||||||    || ||| ||    || | |||||| |||||||||| |||||||||||||| ||||
-------------------------------------------------------------------------gtaagaactcctaaacatatgtgaaagtggaaagctgatatattacagttccattt-acatttgaacaatttcgattggtg------------ctttctcatgtagGTTTCTTCAGATCTGAGTATTGTTGACCTTGACGTTCCATTCTTCTTCATGTTTAGCATTAGCGCCAGCTTAAATGCATACAGCAATCTGGGGGTATTGG

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: 102

TGCGCCAATGTCCTTTTTTGATTCTACCCCTCTTGGAAGGATACTTAGCCGGGTAAGGATACTTAAACAAATTGTTCATATCCCTGAGATATATTGGGTGgtgagattgg ... ttttatgcagGTATCTTCAGATTTGAGCATTGTTGATCTTGATGTTCCATTTGGATTGATGCTTGCTCTTGGTGCCAGCATAAATGCATATAGCAATCTGGGGGTGTTGG


Block sizes: 45 (upstream exon), 48 (downstream exon)
Score: 450

TGCGCCAATGTCCTTTTTTGATTCTACCCCTCTTGGAAGGATACTTAGCCGGGTAAGGATACTTAAACAAATTGTTCATATCCCTGAGATATATTGGGTGgtgagattgg ... ttttatgcagGTATCTTCAGATTTGAGCATTGTTGATCTTGATGTTCCATTTGGATTGATGCTTGCTCTTGGTGCCAGCATAAATGCATATAGCAATCTGGGGGTGTTGG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 551

TGCGCCAATGTCCTTTTTTGATTCTACCCCTCTTGGAAGGATACTTAGCCGGGTAAGGATACTTAAACAAATTGTTCATATCCCTGAGATATATTGGGTGgtgagattgg ... ttttatgcagGTATCTTCAGATTTGAGCATTGTTGATCTTGATGTTCCATTTGGATTGATGCTTGCTCTTGGTGCCAGCATAAATGCATATAGCAATCTGGGGGTGTTGG


Block sizes: 48 (upstream exon), 47 (downstream exon)
Score: 165

TGCGCCAATGTCCTTTTTTGATTCTACCCCTCTTGGAAGGATACTTAGCCGGGTAAGGATACTTAAACAAATTGTTCATATCCCTGAGATATATTGGGTGgtgagattgg ... ttttatgcagGTATCTTCAGATTTGAGCATTGTTGATCTTGATGTTCCATTTGGATTGATGCTTGCTCTTGGTGCCAGCATAAATGCATATAGCAATCTGGGGGTGTTGG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgttttgcatttggatatttcctattgatggatgaacttgcatttttttatgcagGTATCTTCAGATTTGAGCATTGTTGATCTTGATGTTCCATTTGGATTGATGCTTGCTCTTGGTGCCAGCATAAATGCATATAGCAATCTGGGGGTGTTGG
                      tattgat  putative branch site (score: 165)
                                        cattttttt  putative PPT
                                     ttgcatttttttat  TA-rich tract