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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatatcagcgtccaaatgtgaaagttagctttttggctgtaaaacaatttgagagagagagttgcgccataatgagtgtcttgttggagtgtttttgaagttttttgtgtctatttattgaatgataatattcatctggctcttacactcgctttttggttttccagACCATCAATGATTGGTACGACAGGGAGATTGATGCAATCAATGAGCCTTACAGACCCATCCCCTCTGGAGCCATCTCAGAGCCTGAA

Basic information

species Physcomitrella patens
transcript PP1S5_30V6.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S5_30V6.1 (Physcomitrella patens), 3'ss of exon 5
lower sequence: GLYMA18G43310.1 (Glycine max), 3'ss of exon 5
gtatatcagcgtccaaatgtgaaagttagctttttggctgtaaaacaatttgagagagagagttgcgccataatgagtgtcttgttggagtgtttttgaagttttttgtgtctatttattgaatgataatattcatctggc-----tcttacactcgctttttgg-----ttttccagACCATCAATGATTGGTACGACAGGGAGATTGATGCAATCAATGAGCCTTACAGACCCATCCCCTCTGGAGCCATCTCAGAGCCTGAA
                                                                                 || ||  | | | | | |||||||    |    | ||||| |||  | |||    ||| |     | | ||  |   || ||||     ||||  |||| || ||||||||||||||| | || ||||||||||| ||||| ||||| ||||| || || ||||| || || || |||  ||| 
------------------------------------------------------------------------------ccttttttttaatttatataaagttttgccagctgctatattggatgggagtatctcactgacacaagtataactttgaattattgggttaattttttagACTATGAATGATTGGTACGACCGAGAAATTGATGCAATAAATGAACCTTATAGACCAATTCCTTCTGGGGCAATATCTGAGAATGAG

upper sequence: PP1S5_30V6.1 (Physcomitrella patens), 3'ss of exon 5
lower sequence: EFJ13142 (Selaginella moellendorffii), 3'ss of exon 5
gtatatcagcgtccaaatgtgaaagttagctttttggctgtaaaacaatttgagagagagagttgcgccataatgagtgtcttgttggagtgtttttgaagttttttgtgtctatttattgaatgataatattcatctggctcttacactcgctttttggttttccagACCATCAATGATTGGTACGACAGGGAGATTGATGCAATCAATGAGCCTTACAGACCCATCCCCTCTGGAGCCATCTCAGAGCCTGAA
                                                                                                                       | | |     | |||   |   ||||   ||  | | ||  | || ||||||||||| |||||||| ||  | ||||| || || ||||| |||||||||||||| || || || |||||||| || || || |||
----------------------------------------------------------------------------------------------------------------------gttattttcctttttcgattctatcttcatcttccatatttctgtttcagACCATCAACGATTGGTATGATCGCGAGATAGACGCTATCAACGAGCCTTACAGACCAATTCCGTCAGGAGCCATATCCGAACCCGAA

upper sequence: PP1S5_30V6.1 (Physcomitrella patens), 3'ss of exon 5
lower sequence: EFJ14157 (Selaginella moellendorffii), 3'ss of exon 5
gtatatcagcgtccaaatgtgaaagttagctttttggctgtaaaacaatttgagagagagagttgcgccataatgagtgtcttgttggagtgtttttgaagttttttgtgtctatttattgaatgataatattcatctggctcttacactcgctttttggttttccagACCATCAATGATTGGTACGACAGGGAGATTGATGCAATCAATGAGCCTTACAGACCCATCCCCTCTGGAGCCATCTCAGAGCCTGAA
                                                                                                                       | | |     | |||   |   ||||   ||  | | ||  | || ||||||||||| |||||||| ||  | ||||| || || ||||| |||||||||||||| || || || |||||||| || || || |||
----------------------------------------------------------------------------------------------------------------------gttattttcctttttcgattctatcttcatcttccatatttctgtttcagACCATCAACGATTGGTATGATCGCGAGATAGACGCCATCAACGAGCCTTACAGACCAATTCCGTCAGGAGCCATATCCGAACCCGAA

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|208390670|gb|DC937826.1|DC937826
EST:     CGTTGACATGCATGTTGATGTCTGGACCTCTTCTTACAGGATACACTCAG                         ACCATCAATGATTGGTACGACAGGGAGATTGATGCAATCAATGAGCCTTAC
genomic: CGTTGACATGCATGTTGATGTCTGGACCTCTTCTTACAGGATACACTCAGgtatatcagc ... ggttttccagACCATCAATGATTGGTACGACAGGGAGATTGATGCAATCAATGAGCCTTAC
EST: gi|162163836|gb|FC340058.1|FC340058
EST:     CGTTGACATGCATGTTGATGTCTGGACCTCTTCTTACAGGATACACTCAG                         ACCATCAATGATTGGTACGACAGGGAGATTGATGCAATCAATGAGCCTTAC
genomic: CGTTGACATGCATGTTGATGTCTGGACCTCTTCTTACAGGATACACTCAGgtatatcagc ... ggttttccagACCATCAATGATTGGTACGACAGGGAGATTGATGCAATCAATGAGCCTTAC
EST: gi|208380750|gb|DC903270.1|DC903270
EST:     CGTTGACATGCATGTTGATGTCTGGACCTCTTCTTACAGGATACACTCAG                         ACCATCAATGATTGGTACGACAGGGAGATTGATGCAATCAATGAGCCTTAC
genomic: CGTTGACATGCATGTTGATGTCTGGACCTCTTCTTACAGGATACACTCAGgtatatcagc ... ggttttccagACCATCAATGATTGGTACGACAGGGAGATTGATGCAATCAATGAGCCTTAC
EST: gi|162165041|gb|FC342232.1|FC342232
EST:     CTTACAGGATACACTCAG                         ACCATCAATGATTGGTACGACAGGGAGATTGATGCAATCAATGAGCCTTAC
genomic: CTTACAGGATACACTCAGgtatatcagc ... ggttttccagACCATCAATGATTGGTACGACAGGGAGATTGATGCAATCAATGAGCCTTAC

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: 22 (upstream exon), 35 (downstream exon)
Score: 7

GCAATTTCCAGTGGACACTAGAGGATGTGGCCAAGTCGTTGACATGCATGTTGATGTCTGGACCTCTTCTTACAGGATACACTCAGgtatatcagc ... ggttttccagACCATCAATGATTGGTACGACAGGGAGATTGATGCAATCAATGAGCCTTACAGACCCATCCCCTCTGGAGCCATCTCAGAGCCTGAA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atttattgaatgataatattcatctggctcttacactcgctttttggttttccagACCATCAATGATTGGTACGACAGGGAGATTGATGCAATCAATGAGCCTTACAGACCCATCCCCTCTGGAGCCATCTCAGAGCCTGAA
                           ctcttac  putative branch site (score: 7)
                                       ctttttggttttcc  putative PPT
     ttgaatgataatatt  TA-rich tract