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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aacggctatatgtaattggcttcctgtcgctacgaatcgattagatttattcttgacagtgggtaactgtgttggttggtgccgtgtattgtgtgcccagCAAGAGGACTTGAAGCAGTTTAGGCAGTGGGGAAGCAGAACCCCTGGGCACCCCGAGAATTTTGAGACCCCCGGTATTGAGGTGACCACCGGTCCTCTCG

Basic information

species Physcomitrella patens
transcript PP1S120_127V6.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S120_127V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: GRMZM2G033208_T01 (Zea mays), 3'ss of exon 1
aacggctatatgtaattggcttcc-tgtcgctacgaatcgatt-agatttattcttgacagtgggtaactgtgttggttggtgccgtgtattgtgtgcccagCAAGAGGACTTGAAGCAGTTTAGGCAGTGGGGAAGCAGAACCCCTGGGCACCCCGAGAATTTTGAGACCCCCGGTATTGAGGTGACCACCGGTCCTCTCG
|||   |    ||||||  | ||      ||| | |   | || | |   ||   | |   |  || ||||  || |||    | |||  | || ||   || | ||||||||||||||||| ||||| |||||||||||||| || || ||||| ||||| |||||||| || ||  |||| || |||||||         
aactattgagcgtaattcacctcagcagagctgccatgtgtttgataagcatctcttatgttatgtgactggatttgttctaactgtggttggtatgt--agGAGGAGGACTTGAAGCAGTTCAGGCAATGGGGAAGCAGAACACCGGGCCACCCTGAGAACTTTGAGACTCCAGGAGTTGAAGTTACCACCG---------
















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|100392587|gb|BY971784.1|BY971784
EST:     GCATGCTCCAGTATGCTCTCCTCCACCTCGCCGGGTACGACAGCGTTAAG                         CAAGAGGACTTGAAGCAGTTTAGG
genomic: GCATGCTCCAGTATGCTCTCCTCCACCTCGCCGGGTACGACAGCGTTAAGgtatgatgcc ... gtgtgcccagCAAGAGGACTTGAAGCAGTTTAGG
EST: gi|100443954|gb|BY982182.1|BY982182
EST:     CATGCTCCAGTATGCTCTCCTCCCAC-TCGCCGGGTACGACAGCGTTAAG                         CAAGAGGACTTGAA
genomic: CATGCTCCAGTATGCTCTCCTCC-ACCTCGCCGGGTACGACAGCGTTAAGgtatgatgcc ... gtgtgcccagCAAGAGGACTTGAA
EST: gi|100391075|gb|BY953085.1|BY953085
EST:     GCATGCTCCAGTATGCTCTCCTCCACCTCGCCGGGTACGACAGCGTTAAG                         CAAGAGGACTTGAAGCAGTTTAGGCAGTGGGGAAGCAGAACCCCTGGGCAC
genomic: GCATGCTCCAGTATGCTCTCCTCCACCTCGCCGGGTACGACAGCGTTAAGgtatgatgcc ... gtgtgcccagCAAGAGGACTTGAAGCAGTTTAGGCAGTGGGGAAGCAGAACCCCTGGGCAC
EST: gi|100361725|gb|BY947791.1|BY947791
EST:     GCATGCTCCAGTATGCTCTCCTCCACCTCGCCGGGTACGACAGCGTTAAG                         CAAGAGGACTTGAAGCAGTTTAGGCAGTGGGGAAGCAGAACCCCTGGGCAC
genomic: GCATGCTCCAGTATGCTCTCCTCCACCTCGCCGGGTACGACAGCGTTAAGgtatgatgcc ... gtgtgcccagCAAGAGGACTTGAAGCAGTTTAGGCAGTGGGGAAGCAGAACCCCTGGGCAC
EST: gi|100397735|gb|BY990374.1|BY990374
EST:     GCATGCTCCAGTATGCTCTCCTCCACCTCGCCGGGTACGACAGCGTTAAG                         CAAGAGGACTTGGAGCAGTTTAGGCAGTGGGGAAGCAGAACCCCTGGGCAC
genomic: GCATGCTCCAGTATGCTCTCCTCCACCTCGCCGGGTACGACAGCGTTAAGgtatgatgcc ... gtgtgcccagCAAGAGGACTTGAAGCAGTTTAGGCAGTGGGGAAGCAGAACCCCTGGGCAC

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: 56

GATGCATGCTCCAGTATGCTCTCCTCCACCTCGCCGGGTACGACAGCGTTAAGgtatgatgcc ... gtgtgcccagCAAGAGGACTTGAAGCAGTTTAGGCAGTGGGGAAGCAGAACCCCTGGGCACCCCGAGAATTTTGAGACCCCCGGTATTGAGGTGACCACCGGTCCTCTCG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttattcttgacagtgggtaactgtgttggttggtgccgtgtattgtgtgcccagCAAGAGGACTTGAAGCAGTTTAGGCAGTGGGGAAGCAGAACCCCTGGGCACCCCGAGAATTTTGAGACCCCCGGTATTGAGGTGACCACCGGTCCTCTCG
               gggtaac  putative branch site (score: 56)