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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...taatacatagtagctccgtcatattagcattggtcgcaggttattcggtaacttggtgaccgcagtatgaaggtgatattttggtatgtttctcctgcagTGTGCCACTTTTGTAGGCACGGTGACGTACATGTCTCCTGAAAGGATCAACAACGAGTGTTATTCATATCCAGCGGACATATGGAGTCTTGGACTAGCAT

Basic information

species Physcomitrella patens
transcript PP1S92_27V6.2
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S92_27V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: EFJ31855 (Selaginella moellendorffii), 3'ss of exon 4
taatacatagtagctccgtcatattagcattggtcgcaggttattcggtaacttggtgaccgcagtatgaaggtgatattttggtatgtttctcctgcagTGTGCCACTTTTGTAGGCACGGTGACGTACATGTCTCCTGAAAGGATCAACAACGAGTGTTATTCATATCCAGCGGACATATGGAGTCTTGGACTAGCAT
                                   | | |   ||||  | ||| ||||||  ||    |   || |   ||   |  || ||   |||||||||||| ||||| ||||||||||| ||||||||||| || || |||||||||||||| || || || || ||||| || |||||||| ||||| || |
-----------------------------------gtatgc-gttcg-catcttagtgacca-agctcaagcctgcttaattttcactttgcttg-gcagTGTGCCACGTTTGTCGGCACGGTGACTTACATGTCTCCAGAGAGAATCAACAACGAGTGCTACTCGTACCCGGCGGATATCTGGAGTCTGGGACTTGCGT

upper sequence: PP1S92_27V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: EFJ38005 (Selaginella moellendorffii), 3'ss of exon 4
taatacatagtagctccgtcatattagcattggtcgcaggttattcggtaacttggtgaccgcagtatgaaggtgatattttggtatgtttctcctgcagTGTGCCACTTTTGTAGGCACGGTGACGTACATGTCTCCTGAAAGGATCAACAACGAGTGTTATTCATATCCAGCGGACATATGGAGTCTTGGACTAGCAT
                                   | | |   ||||  | ||| ||||||  ||    |   || |   || | |  || ||   |||||||||||| ||||| ||||||||||| ||||||||||| || || |||||||||||||| || || || || ||||| || |||||||| ||||| || |
-----------------------------------gtatgc-gttcg-catcttagtgacca-agctcaagcctgcttaatttgcactttgcttg-gcagTGTGCCACGTTTGTCGGCACGGTGACTTACATGTCTCCAGAGAGAATCAACAACGAGTGCTACTCGTACCCGGCGGATATCTGGAGTCTGGGACTTGCGT
















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|162172755|gb|FC348344.1|FC348344
EST:     AGTTTATACCTGAACCGATCCTCTCTGTTATTACTCGCAAAGTATTGCAG                         TGTGCCACTTTTGTAGGCACGGTGACGTACATGTCTCCTGAAAGGATCAAC
genomic: AGTTTATACCTGAACCGATCCTCTCTGTTATTACTCGCAAAGTATTGCAGgtaagtgttg ... tctcctgcagTGTGCCACTTTTGTAGGCACGGTGACGTACATGTCTCCTGAAAGGATCAAC




















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-Seq library.


Block sizes: 33 (upstream exon), 32 (downstream exon)
Score: 2

CCTTGAGTATATGGATGGTGGCTCCCTTGCTGATATTGTGCGCACGAAGAAGTTTATACCTGAACCGATCCTCTCTGTTATTACTCGCAAAGTATTGCAGgtaagtgttg ... tctcctgcagTGTGCCACTTTTGTAGGCACGGTGACGTACATGTCTCCTGAAAGGATCAACAACGAGTGTTATTCATATCCAGCGGACATATGGAGTCTTGGACTAGCAT































 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cggtaacttggtgaccgcagtatgaaggtgatattttggtatgtttctcctgcagTGTGCCACTTTTGTAGGCACGGTGACGTACATGTCTCCTGAAAGGATCAACAACGAGTGTTATTCATATCCAGCGGACATATGGAGTCTTGGACTAGCAT
 cggtaac  putative branch site (score: 2)
                                         tgtttctcct  putative PPT
                            tgatatttt  TA-rich tract