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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagcagttgttcttctaaggctgactacaacttggatgctttcagGTTGACATTGCAATCCCAGAAGTTTTTGTAGGTGGCCTGCTAGGAGCAATGTTGATATTTGTATTTAGTGCATGGTCGTGTGCGGCAGTAGGCAAAACAG

Basic information

species Selaginella moellendorffii
transcript EFJ13082
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ14101 (Selaginella moellendorffii), 3'ss of exon 10
lower sequence: LOC_Os02g33490.1 (Oryza sativa), 3'ss of exon 11
----------------------------gtaagcagttgttcttctaaggctgactacaa-cttggat----gctttcagGTTGACATTGCAATCCCAGAAGTTTTTGTAGGTGGCCTGCTAGGAGCAATGTTGATATTTGTATTTAGTGCATGGTCGTGTGCGGCAGTAGGCAAAACAG
                             | |     ||| ||| |||     |  |    ||||  |    | || ||||||||||| ||||||||||| |||||||| |||||  | || ||  ||||| | |||||  | |||||||||||| | ||| | || || |||| ||| |
gtattttattacttagacacgcaaaatacttactttctgtgcttataacatatataatggtcttgtgtaatggattgcagGTTGACATAGCAATCCCAGAGGTTTTTGTTGGTGGTTTACTTGGTTCAATGCTTATATTCCTGTTTAGTGCATGGGCTTGTTCTGCTGTTGGCAGAACTG

upper sequence: EFJ14101 (Selaginella moellendorffii), 3'ss of exon 10
lower sequence: PP1S105_42V6.2 (Physcomitrella patens), 3'ss of exon 12
-----------------------------------------------------------------------------------------------------------gtaagcagttgttcttctaaggctgactacaacttggatgctttcagGTTGACATTGCAATCCCAGAAGTTTTTGTAGGTGGCCTGCTAGGAGCAATGTTGATATTTGTATTTAGTGCATGGTCGTGTGCGGCAGTAGGCAAAACAG
                                                                                                           ||  |    |||  |  |     |    |    |||  ||  ||||||| || ||||||||||||||||| |||||||| ||| || | ||  | ||| | || | | | || ||||| ||| | ||||| || || |||  |||||
gtatgacaaatttatgctcctgcaaccagggttcaatcactgcattagctgggaagcaaaggttttcaagattggatttatgcataagtatgtaggaattgcaaccggtgggggcctgtggtaatcgaaatcctcattgtttg--tgaattcagGTGGATATTGCAATCCCAGAAGTATTTGTAGGAGGCTTGTTGGGGTCTATGCTTATTTATCTGTTCAGTGCCTGGGCATGTGCTGCTGTGGGCCGAACAG
















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 1 RNA-Seqlibrary.


Block sizes: 32 (upstream exon), 25 (downstream exon)
Score: 11

CAAGGGATTTGCTATAGGCTCCGCTGCGTTAGCGTCTTTTCTTCTGTTCAGCGCTTACATGGACGAAGTATCGTCTTTTACTCAGATTAGCTTTACTGAGgtaagcagtt ... atgctttcagGTTGACATTGCAATCCCAGAAGTTTTTGTAGGTGGCCTGCTAGGAGCAATGTTGATATTTGTATTTAGTGCATGGTCGTGTGCGGCAGTAGGCAAAACAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtaagcagttgttcttctaaggctgactacaacttggatgctttcagGTTGACATTGCAATCCCAGAAGTTTTTGTAGGTGGCCTGCTAGGAGCAATGTTGATATTTGTATTTAGTGCATGGTCGTGTGCGGCAGTAGGCAAAACAG
                            ggctgac  putative branch site (score: 11)
                                              tgctttc  putative PPT