Skip to another splice site:
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 5'  3'   		2  
 5'  3'   		3  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGGGCTTTCTGAATTCTCCGGCATGAAGAGCACTAATGCCGTCACTTTCGGCAAGCGCTCTGATGACCTCGCATCTATCGTGGCTGCTCAGTCTGCCGTGgtaagaaacgtgtcgatcttgcctgtgatctttctcacaaaacccaatttgagtagtatgaagaaatctatctatagaaaagttgaatactaaatactcactagaatgtcgtggttggttccag

Basic information

species Physcomitrella patens
transcript PP1S11_397V6.2
intron # 2
splice site 5'
intron type U2

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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Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGGGCTTTCTGAATTCTCCGGCATGAAGAGCACTAATGCCGTCACTTTCGGCAAGCGCTCTGATGACCTCGCATCTATCGTGGCTGCTCAGTCTGCCGTGgtaagaaacgtgtcgatcttgcctgtgatctttctcacaaaacccaatttgagtagtatgaagaaatctatctatagaaaagttgaatactaaatactcactagaatgtcgtggttggttccag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT