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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagaaacgtgtcgatcttgcctgtgatctttctcacaaaacccaatttgagtagtatgaagaaatctatctatagaaaagttgaatactaaatactcactagaatgtcgtggttggttccagTCTGCCAGCTCTGGAGCCACGAGGGCTGTCACTGAGGCTAAGATCAAGGTTGCCATCAATGGTTTCGGTCGTATCGGGCGTAATTTCATCCGTTGCTGGC

Basic information

species Physcomitrella patens
transcript PP1S11_397V6.2
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S11_397V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: GRMZM2G162845_T01 (Zea mays), 3'ss of exon 2
--------------------------------------gtaagaaa-cgtgtcg-atc-ttgcctgtgatctttctcacaaaacccaatttgagtagtatgaagaa--atctatctatagaaaagttgaat---actaaat-actcactagaatgt---cgtggttggttccagTCTGC-----CAGCTCTGGAGCCACGAGGGCTGTCACTGAGGCTAAGATCAAGGTTGCCATCAATGGTTTCGGTCGTATCGGGCGTAATTTCATCCGTTGCTGGC
                                      ||  |    |||| || ||| | || |  ||   | ||   |  | |    | || | |  ||  ||   |  | |||        | ||       ||   | |||| |  |  |||    |||  | | ||   || ||     | ||    |    | | ||||    || ||||| ||| ||||||| |||||||| || |||||||| ||||||||||| ||| | || |      
gtacgtgcctgcctgcccccgggccggccgatcgatccgtgcgcggtcgtgccgcatcgtagcgtaggaatgtgctagtagcaacacgatcgaatggcttggggattcacatgtctgcgccgctgctgcccctggctgcctgactcgcctgcttgtgcttgtgcatcgatcagATCGGCACCAGCGGCGGCAGGTTGAGGCGGGCGCCGACAGAGGCAAAGCTCAAGGTGGCCATCAACGGGTTCGGTCGCATCGGGCGTAACTTCCTGCGGT------
















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|162186359|gb|FC361667.1|FC361667
EST:     GCAAGCGCTCTGATGACCTCGCATCTATCGTGGCTGCTCAGTCTGCCGTG                         TCTGCCAGCTCTGGAGCCACGAGGGCTGTCACTGAGGCTAAGATCAAGGTT
genomic: GCAAGCGCTCTGATGACCTCGCATCTATCGTGGCTGCTCAGTCTGCCGTGgtaagaaacg ... ttggttccagTCTGCCAGCTCTGGAGCCACGAGGGCTGTCACTGAGGCTAAGATCAAGGTT
EST: gi|18331540|gb|BJ163551.1|BJ163551
EST:     GCAAGCGCTCTGATGACCTCGCATCTATCGTGGCTGCTCAGTCTGCCGTG                         TCTGCCAGCTCTGGAGCCACGAGGGCTGTCACTGAGGCTAAGATCAAGGTT
genomic: GCAAGCGCTCTGATGACCTCGCATCTATCGTGGCTGCTCAGTCTGCCGTGgtaagaaacg ... ttggttccagTCTGCCAGCTCTGGAGCCACGAGGGCTGTCACTGAGGCTAAGATCAAGGTT
EST: gi|100429021|gb|BY977900.1|BY977900
EST:     GCAAGCGCTCTGATGACCTCGCATCTATCGTGGCTGCTCAGTCTGCCGTG                         TCTGCCAGCTCTGGAGCCACGAGGGCTGTCACTGAGGCTAAGATCAAGGTT
genomic: GCAAGCGCTCTGATGACCTCGCATCTATCGTGGCTGCTCAGTCTGCCGTGgtaagaaacg ... ttggttccagTCTGCCAGCTCTGGAGCCACGAGGGCTGTCACTGAGGCTAAGATCAAGGTT
EST: gi|100409989|gb|BY974354.1|BY974354
EST:     GCAAGCGCTCTGATGACCTCGCATCTATCGTGGCTGCTCAGTCTGCCGTG                         TCTGCCAGCTCTGGAGCCACGAGGGCTGTCACTGAGGCTAAGATCAAGGTT
genomic: GCAAGCGCTCTGATGACCTCGCATCTATCGTGGCTGCTCAGTCTGCCGTGgtaagaaacg ... ttggttccagTCTGCCAGCTCTGGAGCCACGAGGGCTGTCACTGAGGCTAAGATCAAGGTT
EST: gi|100425657|gb|BY958705.1|BY958705
EST:     GCAAGCGCTCTGATGACCTCGCATCTATCGTGGCTGCTCAGTCTGCCGTG                         TCTGCCAGCTCTGGAGCCACGAGGGCTGTCACTGAGGCTAAGATCAAGGTT
genomic: GCAAGCGCTCTGATGACCTCGCATCTATCGTGGCTGCTCAGTCTGCCGTGgtaagaaacg ... ttggttccagTCTGCCAGCTCTGGAGCCACGAGGGCTGTCACTGAGGCTAAGATCAAGGTT
EST: gi|100353689|gb|BY983261.1|BY983261
EST:     GCAAGCGCTCTGATGACCTCGCATCTATCGTGGCTGCTCAGTCTGCCGTG                         TCTGCCAGCTCTGGAGCCACGAGGGCTGTCACTGANGCTAAGATCAAGGTT
genomic: GCAAGCGCTCTGATGACCTCGCATCTATCGTGGCTGCTCAGTCTGCCGTGgtaagaaacg ... ttggttccagTCTGCCAGCTCTGGAGCCACGAGGGCTGTCACTGAGGCTAAGATCAAGGTT
EST: gi|100431493|gb|BY960225.1|BY960225
EST:     GCAAGCGCTCTGATGACCTCGCATCTATCGTGGCTGCTCAGTCTGCCGTG                         TCTGCCAGCTCTGGAGCCACGAGGGCTGTCACTGAGGCTAAGATCAAGGTT
genomic: GCAAGCGCTCTGATGACCTCGCATCTATCGTGGCTGCTCAGTCTGCCGTGgtaagaaacg ... ttggttccagTCTGCCAGCTCTGGAGCCACGAGGGCTGTCACTGAGGCTAAGATCAAGGTT
EST: gi|100442976|gb|BY963471.1|BY963471
EST:     GCAAGCGCTCTGATGACCTCGCATCTATCGTGGCTGCTCAGTCTGCCGTG                         TCTGCCAGCTCTGGAGCCACGAGGGCTGTCACTGAGGCTAAGATCAAGGTT
genomic: GCAAGCGCTCTGATGACCTCGCATCTATCGTGGCTGCTCAGTCTGCCGTGgtaagaaacg ... ttggttccagTCTGCCAGCTCTGGAGCCACGAGGGCTGTCACTGAGGCTAAGATCAAGGTT
EST: gi|162195743|gb|FC371134.1|FC371134
EST:     GCAAGCGCTCTGATGACCTCGCATCTATCGTGGCTGCTCAGTCTGCCGTG                         TCTGCCAGCTCTGGAGCCACGAGGGCTGTCACTGAGGCTAAGATCAAGGTT
genomic: GCAAGCGCTCTGATGACCTCGCATCTATCGTGGCTGCTCAGTCTGCCGTGgtaagaaacg ... ttggttccagTCTGCCAGCTCTGGAGCCACGAGGGCTGTCACTGAGGCTAAGATCAAGGTT
EST: gi|100435524|gb|BY960955.1|BY960955
EST:     GCAAGCGCTCTGATGACCTCGCATCTATCGTGGCTGCTCAGTCTGCCGTG                         TCTGCCAGCTCTGGAGCCACGAGGGCTGTCACTGAGGCTAAGATCAAGGTT
genomic: GCAAGCGCTCTGATGACCTCGCATCTATCGTGGCTGCTCAGTCTGCCGTGgtaagaaacg ... ttggttccagTCTGCCAGCTCTGGAGCCACGAGGGCTGTCACTGAGGCTAAGATCAAGGTT
EST: gi|100452599|gb|CJ975350.1|CJ975350
EST:     GCAAGCGCTCTGATGACCTCGCATCTATCGTGGCTGCTCAGTCTGCCGTG                         TCTGCCAGCTCTGGAGCCACGAGGGCTGTCACTGAGGCTAAGATCAAGGTT
genomic: GCAAGCGCTCTGATGACCTCGCATCTATCGTGGCTGCTCAGTCTGCCGTGgtaagaaacg ... ttggttccagTCTGCCAGCTCTGGAGCCACGAGGGCTGTCACTGAGGCTAAGATCAAGGTT
EST: gi|18326329|gb|BJ158328.1|BJ158328
EST:     GCAAGCGCTCTGATGACCTCGCATCTATCGTGGCTGCTCAGTCTGCCGTG                         TCTGCCAGCTCTGGAGCCACGAGGGCTGTCACTGAGGCTAAGATCAAGGTT
genomic: GCAAGCGCTCTGATGACCTCGCATCTATCGTGGCTGCTCAGTCTGCCGTGgtaagaaacg ... ttggttccagTCTGCCAGCTCTGGAGCCACGAGGGCTGTCACTGAGGCTAAGATCAAGGTT
EST: gi|100385733|gb|BY987798.1|BY987798
EST:     GCAAGCGCTCTGATGACCTCGCATCTATCGTGGCTGCTCAGTCTGCCGTG                         TCTGCCAGCTCTGGAGCCACGAGGGCTGTCACTGAGGCTAAGATCAAGGTT
genomic: GCAAGCGCTCTGATGACCTCGCATCTATCGTGGCTGCTCAGTCTGCCGTGgtaagaaacg ... ttggttccagTCTGCCAGCTCTGGAGCCACGAGGGCTGTCACTGAGGCTAAGATCAAGGTT
EST: gi|100442351|gb|BY981375.1|BY981375
EST:     GCAAGCGCTCTGATGACCTCGCATCTATCGTGGCTGCTCAGTCTGCCGTG                         TCTGCCAGCTCTGGAGCCACGAGGGCTGTCACTGAGGCTAAGATCAAGGTT
genomic: GCAAGCGCTCTGATGACCTCGCATCTATCGTGGCTGCTCAGTCTGCCGTGgtaagaaacg ... ttggttccagTCTGCCAGCTCTGGAGCCACGAGGGCTGTCACTGAGGCTAAGATCAAGGTT
EST: gi|18346978|gb|BJ179024.1|BJ179024
EST:     GCAAGCGCTCTGATGACCTCGCATCTATCGTGGCTGCTCAGTCTGCCGTG                         TCTGCCAGCTCTGGAGCCACGAGGGCTGTCACTGAGGCTAAGATCAAGGTT
genomic: GCAAGCGCTCTGATGACCTCGCATCTATCGTGGCTGCTCAGTCTGCCGTGgtaagaaacg ... ttggttccagTCTGCCAGCTCTGGAGCCACGAGGGCTGTCACTGAGGCTAAGATCAAGGTT
EST: gi|100428306|gb|BY977737.1|BY977737
EST:     GCAAGCGCTCTGATGACCTCGCATCTATCGTGGCTGCTCAGTCTGCCGTG                         TCTGCCAGCTCTGGAGCCACGAGGGATGTCACTGAGGCTAAGATCAAGGTT
genomic: GCAAGCGCTCTGATGACCTCGCATCTATCGTGGCTGCTCAGTCTGCCGTGgtaagaaacg ... ttggttccagTCTGCCAGCTCTGGAGCCACGAGGGCTGTCACTGAGGCTAAGATCAAGGTT
EST: gi|18350798|gb|BJ182849.1|BJ182849
EST:     GCAAGCGCTCTGATGACCTCGCATCTATCGTGGCTGCTCAGTCTGCCGTG                         TCTGCCAGCTCTGGAGCCACGAGGGCTGTCACTGAGGCTAAGATCAAGGTT
genomic: GCAAGCGCTCTGATGACCTCGCATCTATCGTGGCTGCTCAGTCTGCCGTGgtaagaaacg ... ttggttccagTCTGCCAGCTCTGGAGCCACGAGGGCTGTCACTGAGGCTAAGATCAAGGTT
EST: gi|100444603|gb|BY964301.1|BY964301
EST:     GCAAGCGCTCTGATGACCTCGCATCTATCGTGGCTGCTCAGTCTGCCGTG                         TCTGCCAGCTCTGGAGCCACGAGGGCTGTCACTGAGGCTAAGATCAAGGTT
genomic: GCAAGCGCTCTGATGACCTCGCATCTATCGTGGCTGCTCAGTCTGCCGTGgtaagaaacg ... ttggttccagTCTGCCAGCTCTGGAGCCACGAGGGCTGTCACTGAGGCTAAGATCAAGGTT
EST: gi|100451144|gb|CJ974619.1|CJ974619
EST:     GCAAGCGCTCTGATGACCTCGCATCTATCGTGGCTGCTCAGTCTGCCGTG                         TCTGCCAGCTCTGGAGCCACGAGGGCTGTCACTGAGGCTAAGATCAAGGTT
genomic: GCAAGCGCTCTGATGACCTCGCATCTATCGTGGCTGCTCAGTCTGCCGTGgtaagaaacg ... ttggttccagTCTGCCAGCTCTGGAGCCACGAGGGCTGTCACTGAGGCTAAGATCAAGGTT
EST: gi|100365549|gb|BY966651.1|BY966651
EST:     GCAAGCGCTCTGATGACCTCGCATCTATCGTGGCTGCTCAGTCTGCCGTG                         TCTGCCAGCTCTGGAGCCACGAGGGCTGTCACTGAGGCTAAGATCAAGGTT
genomic: GCAAGCGCTCTGATGACCTCGCATCTATCGTGGCTGCTCAGTCTGCCGTGgtaagaaacg ... ttggttccagTCTGCCAGCTCTGGAGCCACGAGGGCTGTCACTGAGGCTAAGATCAAGGTT
EST: gi|18350585|gb|BJ182636.1|BJ182636
EST:     GCAAGCGCTCTGATGACCTCGCATCTATCGTGGCTGCTCAGTCTGCCGTG                         TCTGCCAGCTCTGGAGCCACGAGGGCTGTCACTGAGG
genomic: GCAAGCGCTCTGATGACCTCGCATCTATCGTGGCTGCTCAGTCTGCCGTGgtaagaaacg ... ttggttccagTCTGCCAGCTCTGGAGCCACGAGGGCTGTCACTGAGG

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: 46

GGGGCTTTCTGAATTCTCCGGCATGAAGAGCACTAATGCCGTCACTTTCGGCAAGCGCTCTGATGACCTCGCATCTATCGTGGCTGCTCAGTCTGCCGTGgtaagaaacg ... ttggttccagTCTGCCAGCTCTGGAGCCACGAGGGCTGTCACTGAGGCTAAGATCAAGGTTGCCATCAATGGTTTCGGTCGTATCGGGCGTAATTTCATCCGTTGCTGGC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atctatagaaaagttgaatactaaatactcactagaatgtcgtggttggttccagTCTGCCAGCTCTGGAGCCACGAGGGCTGTCACTGAGGCTAAGATCAAGGTTGCCATCAATGGTTTCGGTCGTATCGGGCGTAATTTCATCCGTTGCTGGC
                         tactcac  putative branch site (score: 46)
             ttgaatactaaata  TA-rich tract