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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ccgaaaagcaacgtcttacagttagacactgtctgccggaaaggactgattgtgcggttcgtgaaagtgtgttgattggcgctgtgtgttgtgttctcagGAAGAAGACTTAAAGCAGTTTAGGCAGTGGGGAAGCAGAACCCCTGGGCACCCCGAGAATTTTGAGACCCCCGGTATTGAGGTGACCACCGGTCCTCTCG

Basic information

species Physcomitrella patens
transcript PP1S120_164V6.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S120_164V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: GRMZM2G033208_T01 (Zea mays), 3'ss of exon 1
----ccgaaaagcaacgtcttacagtt-agacactgtctgccgga-aaggactgattgtgcggttcgtgaaagtgtgttgattggcgctgtgtgttgtgttctcagGAAGAAGACTTAAAGCAGTTTAGGCAGTGGGGAAGCAGAACCCCTGGGCACCCCGAGAATTTTGAGACCCCCGGTATTGAGGTGACCACCGGTCCTCTCG
        |  | ||       |||   ||   |  | ||   || ||| |    || ||    |  ||  | ||  ||  ||    ||||| |||| ||    |||| || ||||| |||||||| ||||| |||||||||||||| || || ||||| ||||| |||||||| || ||  |||| || |||||||         
aactattgagcgtaattcacctcagcagagctgccatgtgtttgataagcatctcttatg----ttatgtgactggatttgttctaactgtg-gttg-gtatgtagGAGGAGGACTTGAAGCAGTTCAGGCAATGGGGAAGCAGAACACCGGGCCACCCTGAGAACTTTGAGACTCCAGGAGTTGAAGTTACCACCG---------
















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|100433314|gb|BY960543.1|BY960543
EST:     GCATGCTCCAGTACGCTCTCCTCCACCTCGCTGGGTACGACAGTGTTCAG                         GAAGAAGACTTAAAGCAGTTTAGGC
genomic: GCATGCTCCAGTACGCTCTCCTCCACCTCGCTGGGTACGACAGTGTTCAGgtatgtttac ... gtgttctcagGAAGAAGACTTAAAGCAGTTTAGGC
EST: gi|100446557|gb|CJ970856.1|CJ970856
EST:     GCATGCTCCAGTACGCTCTCCTCCACCTCGCTGGGTACGACAGTGTTCAG                         GAANAANACTTAAAGCAGTTTAGGCAGTGGGGAAGCANAACCCCTGGGCAC
genomic: GCATGCTCCAGTACGCTCTCCTCCACCTCGCTGGGTACGACAGTGTTCAGgtatgtttac ... gtgttctcagGAAGAAGACTTAAAGCAGTTTAGGCAGTGGGGAAGCAGAACCCCTGGGCAC
EST: gi|100442191|gb|BY963084.1|BY963084
EST:     GCATGCTCCAGTACGCTCTCCTCCACCTCGCTGGGTACGACAGTGTTCAG                         GAAGAAGACTTAAAGCAGTTTAGGCAGTGGGGAAGCAGAACCCCTGGGCAC
genomic: GCATGCTCCAGTACGCTCTCCTCCACCTCGCTGGGTACGACAGTGTTCAGgtatgtttac ... gtgttctcagGAAGAAGACTTAAAGCAGTTTAGGCAGTGGGGAAGCAGAACCCCTGGGCAC
EST: gi|18368720|gb|BJ200805.1|BJ200805
EST:     GCATGCTCCAGTACGCTCTCCTCCACCTCGCTGGGTACGACAGTGTTCAG                         GAAGAAGACTTAAAGCAGTTTAGGCAGTGGGGAAGCAGAACCCCTGGGCAC
genomic: GCATGCTCCAGTACGCTCTCCTCCACCTCGCTGGGTACGACAGTGTTCAGgtatgtttac ... gtgttctcagGAAGAAGACTTAAAGCAGTTTAGGCAGTGGGGAAGCAGAACCCCTGGGCAC
EST: gi|100404862|gb|BY991318.1|BY991318
EST:     GCATGCTCCAGTACGCTCTCCTCCACCTCGCTGGGTACGACAGTGTTCAG                         GAAGAAGACTTAAAGCAGTTTAGGCAGTGGGGAAGCAGAACCCCTGGGCAC
genomic: GCATGCTCCAGTACGCTCTCCTCCACCTCGCTGGGTACGACAGTGTTCAGgtatgtttac ... gtgttctcagGAAGAAGACTTAAAGCAGTTTAGGCAGTGGGGAAGCAGAACCCCTGGGCAC
EST: gi|100443241|gb|BY963537.1|BY963537
EST:     GCATGCTCCAGTACGCTCTCCTCCACCTCGCTGGGTACGACAGTGTTCAG                         GAAGAAGACTTAAAGCAGTTTAGGCAGTGGGGAAGCAGGACCCCTGGGCAC
genomic: GCATGCTCCAGTACGCTCTCCTCCACCTCGCTGGGTACGACAGTGTTCAGgtatgtttac ... gtgttctcagGAAGAAGACTTAAAGCAGTTTAGGCAGTGGGGAAGCAGAACCCCTGGGCAC

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: 35 (upstream exon), 35 (downstream exon)
Score: 94

GATGCATGCTCCAGTACGCTCTCCTCCACCTCGCTGGGTACGACAGTGTTCAGgtatgtttac ... gtgttctcagGAAGAAGACTTAAAGCAGTTTAGGCAGTGGGGAAGCAGAACCCCTGGGCACCCCGAGAATTTTGAGACCCCCGGTATTGAGGTGACCACCGGTCCTCTCG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctgattgtgcggttcgtgaaagtgtgttgattggcgctgtgtgttgtgttctcagGAAGAAGACTTAAAGCAGTTTAGGCAGTGGGGAAGCAGAACCCCTGGGCACCCCGAGAATTTTGAGACCCCCGGTATTGAGGTGACCACCGGTCCTCTCG
                                              tgttctc  CT-rich tract