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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CAAGGGAATGAAAGGCGCTGTTCAGAAGGCGGAAGAAATTGTGAAGAAAACTCCCAATTCGTACATGCTCCAACAATTTGAGAATCCAGCTAACCCGAAGgtatttcatccggcatgtggcggttgtaaatactgacttatgtgaagtcttgaaaaaatgatagttgagggtagttctcatgtttatcagaagatgttgtagttgctgatcgttgtttgtgtcatgtag

Basic information

species Physcomitrella patens
transcript PP1S71_187V6.1
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S71_187V6.1 (Physcomitrella patens), 5'ss of exon 4
lower sequence: EFJ24611 (Selaginella moellendorffii), 5'ss of exon 3
CAAGGGAATGAAAGGCGCTGTTCAGAAGGCGGAAGAAATTGTGAAGAAAACTCCCAATTCGTACATGCTCCAACAATTTGAGAATCCAGCTAACCCGAAGgtatttcatccggcatgtggcggttgtaaatactgacttatgtgaagtcttgaaaaaatgatagttgagggtagttctcatgtttatcagaagatgttgtagttgctgatcgttgtttgtgtcatgtag
 || || |||||||| || || ||||| || || || ||  ||||||| ||||| ||||| |||||||||||||||||||| || || || || || |||||   | |   | |   |     |   |  |    |||  | | | || |                                                                               
GAAAGGCATGAAAGGAGCAGTACAGAAAGCCGAGGAGATATTGAAGAAGACTCCAAATTCTTACATGCTCCAACAATTTGAAAACCCCGCAAATCCCAAGgtgcgttagttgtc---tctttatccgagtttaacactccttttacgtttcag----------------------------------------------------------------------------

upper sequence: PP1S71_187V6.1 (Physcomitrella patens), 5'ss of exon 4
lower sequence: EFJ17923 (Selaginella moellendorffii), 5'ss of exon 2
CAAGGGAATGAAAGGCGCTGTTCAGAAGGCGGAAGAAATTGTGAAGAAAACTCCCAATTCGTACATGCTCCAACAATTTGAGAATCCAGCTAACCCGAAGgtatttcatccggcatgtggcggttgtaaatactgacttatgtgaagtcttgaaaaaatgatagttgagggtagttctcatgtttatcagaagatgttgtagttgctgatcgttgtttgtgtcatgtag
||| || ||||| || |||||    ||||| ||||| |||||||  || || || ||| |||||||||| || ||||||||||| |||||||| ||||| |||    ||     ||       |   | |||     || | |    | |||  | |                                                                        
CAAAGGCATGAAGGGAGCTGTCTCAAAGGCTGAAGAGATTGTGAGCAAGACACCAAATGCGTACATGCTTCAGCAATTTGAGAACCCAGCTAATCCGAAAgtaagatattatcaattcttttctaccacata--actttctcttctcttttgctacag-----------------------------------------------------------------------
















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|67694755|gb|BJ954988.1|BJ954988
EST:     CTCCCAATTCGTACATGCTCCAACAATTTGAGAATCCAGCTAACCCGAAG                         GTGCATTTTGAGACCACCGGGCCAGAGATCTGGGAAGACACGGCTGGTAAG
genomic: CTCCCAATTCGTACATGCTCCAACAATTTGAGAATCCAGCTAACCCGAAGgtatttcatc ... tgtcatgtagGTGCATTTTGAGACCACCGGGCCAGAGATCTGGGAAGACACGGCTGGTAAG
EST: gi|162171775|gb|FC348951.1|FC348951
EST:     CTCCCAATTCGTACATGCTCCAACAATTTGAGAATCCAGCTAACCCGAAG                         GTGCATTTTGAGACCACCGGGCCAGAGATCTGGGAAGACACGGCTGGTAAG
genomic: CTCCCAATTCGTACATGCTCCAACAATTTGAGAATCCAGCTAACCCGAAGgtatttcatc ... tgtcatgtagGTGCATTTTGAGACCACCGGGCCAGAGATCTGGGAAGACACGGCTGGTAAG
EST: gi|162219672|gb|FC395876.1|FC395876
EST:     CAACAATTTGAGAATCCAGCTAACCCGAAG                         GTGCATTTTGAGACCACCGGGCCAGAGATCTGGGAAGACACGGCTGGTAAG
genomic: CAACAATTTGAGAATCCAGCTAACCCGAAGgtatttcatc ... tgtcatgtagGTGCATTTTGAGACCACCGGGCCAGAGATCTGGGAAGACACGGCTGGTAAG
EST: gi|162184261|gb|FC359683.1|FC359683
EST:     CTCCCAATTCGTACATGCTCCAACAATTTGAGAATCCAGCTAACCCGAAG                         GTGCATTTTGAGACCACCGGGCCAGAGATCTGGGAAGACACGGCTGGTAAG
genomic: CTCCCAATTCGTACATGCTCCAACAATTTGAGAATCCAGCTAACCCGAAGgtatttcatc ... tgtcatgtagGTGCATTTTGAGACCACCGGGCCAGAGATCTGGGAAGACACGGCTGGTAAG
EST: gi|208381504|gb|DC919506.1|DC919506
EST:     CTCCCAATTCGTACATGCTCCAACAATTTGAGAATCCAGCTAACCCGAAG                         GTGCATTTTGAGACCACCGGGCCAGAGATCTGGGAAGACACGGCTGGTAAG
genomic: CTCCCAATTCGTACATGCTCCAACAATTTGAGAATCCAGCTAACCCGAAGgtatttcatc ... tgtcatgtagGTGCATTTTGAGACCACCGGGCCAGAGATCTGGGAAGACACGGCTGGTAAG
EST: gi|162202798|gb|FC379780.1|FC379780
EST:     CTCCCAATTCGTACATGCTCCAACAATTTGAGAATCCAGCTAACCCGAAG                         GTGCATTTTGAGACCACCGGGCCAGAGATCTGGGAAGACACGGCTGGTAAG
genomic: CTCCCAATTCGTACATGCTCCAACAATTTGAGAATCCAGCTAACCCGAAGgtatttcatc ... tgtcatgtagGTGCATTTTGAGACCACCGGGCCAGAGATCTGGGAAGACACGGCTGGTAAG
EST: gi|16137490|gb|BI894354.1|BI894354
EST:     CTCCCAATTCGTACATGCTCCAACAATTTGAGAATCCAGCTAACCNGAAG                         GTGCATTTTGAGACCACCGGGCCAGAGATCTGGGAAGACACGGCTGGTAAG
genomic: CTCCCAATTCGTACATGCTCCAACAATTTGAGAATCCAGCTAACCCGAAGgtatttcatc ... tgtcatgtagGTGCATTTTGAGACCACCGGGCCAGAGATCTGGGAAGACACGGCTGGTAAG
EST: gi|208349485|gb|DC905623.1|DC905623
EST:     CTCCCAATTCGTACATGCTCCAACAATTTGAGANTCCAGCTANCC-GAAG                         GTGCATTTTGAG
genomic: CTCCCAATTCGTACATGCTCCAACAATTTGAGAATCCAGCTAACCCGAAGgtatttcatc ... tgtcatgtagGTGCATTTTGAG
EST: gi|18339257|gb|BJ171284.1|BJ171284
EST:     CTCCCAATTCGTACATGCTCCAACAATTTGAGAATCCAGCTAACCCGAAG                         GTGCATTTTGAGACCACCGGGCCAGAGATCTGGGAAGACACGGCTGGTAAG
genomic: CTCCCAATTCGTACATGCTCCAACAATTTGAGAATCCAGCTAACCCGAAGgtatttcatc ... tgtcatgtagGTGCATTTTGAGACCACCGGGCCAGAGATCTGGGAAGACACGGCTGGTAAG

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: 33 (upstream exon), 31 (downstream exon)
Score: 4

CAAGGGAATGAAAGGCGCTGTTCAGAAGGCGGAAGAAATTGTGAAGAAAACTCCCAATTCGTACATGCTCCAACAATTTGAGAATCCAGCTAACCCGAAGgtatttcatc ... tgtcatgtagGTGCATTTTGAGACCACCGGGCCAGAGATCTGGGAAGACACGGCTGGTAAGGTTGATATTCTCGTTGCTGGTATTGGTACTGGCGGAACTGTAACTGGAG




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