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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtcagtctcaatagctgcaaacccatctgtgttgcttcgtgttatgtgatttcgccgaagcctaacccgtcttcttcttgtcgcagatcattgctgatgccatcttttggtcttgtgcagTTTTTCTTAACCCTGACTCGGAGTACCACACCGTCAGCCTCCTCGACTCCCTCGATGCTTACCAAAGGTGTACCTTGGGAGGAATACAACCTAATGCTAC

Basic information

species Physcomitrella patens
transcript PP1S49_6V6.1
intron # 1
splice site 3'
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|100409426|gb|BY992005.1|BY992005
EST:     TGCCTGGGCTGCAAGCCAGAATTTTCGACCACGAGTTGGGGATTCTCTCG                         TTTTTCTTAACCCTGACTCGGAGTACCACACCGTCAGCCTCCTCGACTCCC
genomic: TGCCTGGGCTGCAAGCCAGAATTTTCGACCACGAGTTGGGGATTCTCTCGgtcagtctca ... tcttgtgcagTTTTTCTTAACCCTGACTCGGAGTACCACACCGTCAGCCTCCTCGACTCCC
EST: gi|100429025|gb|BY977902.1|BY977902
EST:     TGCCTGGGCTGCAAGCCAGAATTTTCGACCACGAGTTGGGGATTCTCTCG                         TTTTTCTTAACCCTGACTCGGAGTACCACACCGTCAGCCTCCTCGACTCCC
genomic: TGCCTGGGCTGCAAGCCAGAATTTTCGACCACGAGTTGGGGATTCTCTCGgtcagtctca ... tcttgtgcagTTTTTCTTAACCCTGACTCGGAGTACCACACCGTCAGCCTCCTCGACTCCC
EST: gi|208357544|gb|DC913986.1|DC913986
EST:     TGCCTGGGCTGCAAGCCAGAATTTTCGACCACGAGTTGGGGATTCTCTCG                         TTTTTCTTAACCCTGACTCGGAGTACCACACCGTCAGCCTCCTCGACTCCC
genomic: TGCCTGGGCTGCAAGCCAGAATTTTCGACCACGAGTTGGGGATTCTCTCGgtcagtctca ... tcttgtgcagTTTTTCTTAACCCTGACTCGGAGTACCACACCGTCAGCCTCCTCGACTCCC
EST: gi|100418792|gb|BY975742.1|BY975742
EST:     GCCTGGGCTGCTAGCCAGAATTTTCGACCACGAGTTGGGGATTCTCTCNG                         TTTT-CTTAACCCTGACTCGGAGTAC-ACACCGTCAGCCTCCTCGACTCC
genomic: GCCTGGGCTGCAAGCCAGAATTTTCGACCACGAGTTGGGGATTCTCTC-Ggtcagtctca ... tcttgtgcagTTTTTCTTAACCCTGACTCGGAGTACCACACCGTCAGCCTCCTCGACTCC
EST: gi|208370691|gb|DC936841.1|DC936841
EST:     TGCCTGGGCTGCAAGCCAGAATTTTCGACCACGAGTTGGGGATTCTCTCG                         TTTTTCTTAACCCTGACTCGGAGTACCACACCGTCAGCCTCCTCGACTCCC
genomic: TGCCTGGGCTGCAAGCCAGAATTTTCGACCACGAGTTGGGGATTCTCTCGgtcagtctca ... tcttgtgcagTTTTTCTTAACCCTGACTCGGAGTACCACACCGTCAGCCTCCTCGACTCCC
EST: gi|100442476|gb|BY963170.1|BY963170
EST:     TGCCTGGGCTGCAAGCCAGAATTTTCGACCACGAGTTGGGGATTCTCTCG                         TTTTTCTTAACCCTGACTCGGAGTACCACACCGTCAGCCTCCTCGACTCCC
genomic: TGCCTGGGCTGCAAGCCAGAATTTTCGACCACGAGTTGGGGATTCTCTCGgtcagtctca ... tcttgtgcagTTTTTCTTAACCCTGACTCGGAGTACCACACCGTCAGCCTCCTCGACTCCC
EST: gi|208379681|gb|DC903736.1|DC903736
EST:     TGCCTGGGCTGCAAGCCAGAATTTTCGACCACGAGTTGGGGATTCTCTCG                         TTTTTCTTAACCCTGACTCGGAGTACCACACCGTCAGCCTCCTCGACTCCC
genomic: TGCCTGGGCTGCAAGCCAGAATTTTCGACCACGAGTTGGGGATTCTCTCGgtcagtctca ... tcttgtgcagTTTTTCTTAACCCTGACTCGGAGTACCACACCGTCAGCCTCCTCGACTCCC
EST: gi|208344593|gb|DC909152.1|DC909152
EST:     TGCCTGGGCTGCAAGCCAGAATTTTCGACCACGAGTTGGGGATTCTCTCG                         TTTTTCTTAACCCTGACTCGGAGTACCACACCGTCAGCCTCCTCGACTCCC
genomic: TGCCTGGGCTGCAAGCCAGAATTTTCGACCACGAGTTGGGGATTCTCTCGgtcagtctca ... tcttgtgcagTTTTTCTTAACCCTGACTCGGAGTACCACACCGTCAGCCTCCTCGACTCCC
EST: gi|208394038|gb|DC957119.1|DC957119
EST:     TGCCTGGGCTGCAAGCCAGAATTTTCGACCACGAGTTGGGGATTCTCTCG                         TTTTTCTTAACCCTGACTCGGAGTACCACACCGTCAGCCTCCTCGACTCCC
genomic: TGCCTGGGCTGCAAGCCAGAATTTTCGACCACGAGTTGGGGATTCTCTCGgtcagtctca ... tcttgtgcagTTTTTCTTAACCCTGACTCGGAGTACCACACCGTCAGCCTCCTCGACTCCC
EST: gi|100440272|gb|BY962150.1|BY962150
EST:     TGCCTGGGCTGCAAGCCAGAATTTTCGACCACGAGTTGGGGATTCTCTCG                         TTTTTCTTAACCCTGACTCGGAGTACCACACCGTCAGCCTCCTCGACTCCC
genomic: TGCCTGGGCTGCAAGCCAGAATTTTCGACCACGAGTTGGGGATTCTCTCGgtcagtctca ... tcttgtgcagTTTTTCTTAACCCTGACTCGGAGTACCACACCGTCAGCCTCCTCGACTCCC
EST: gi|208400765|gb|DC904943.1|DC904943
EST:     TGCCTGGGCTGCAAGCCAGAATTTTCGACCACGAGTTGGGGATTCTCTCG                         TTTTTCTTAACCCTGACTCGGAGTACCACACCGTCAGCCTCCTCGACTCCC
genomic: TGCCTGGGCTGCAAGCCAGAATTTTCGACCACGAGTTGGGGATTCTCTCGgtcagtctca ... tcttgtgcagTTTTTCTTAACCCTGACTCGGAGTACCACACCGTCAGCCTCCTCGACTCCC
EST: gi|100409444|gb|BY992014.1|BY992014
EST:     TGCCTGGGCTGCAAGCCAGAATTTTCGACCACGAGTTGGGGATTCTCTCG                         TTTTTCTTAACCCTGACTCGGAGTACCACACCGTCAGCCTCCTCGACTCCC
genomic: TGCCTGGGCTGCAAGCCAGAATTTTCGACCACGAGTTGGGGATTCTCTCGgtcagtctca ... tcttgtgcagTTTTTCTTAACCCTGACTCGGAGTACCACACCGTCAGCCTCCTCGACTCCC
EST: gi|18372912|gb|BJ204514.1|BJ204514
EST:     TGCCTGGGCTGCAAGCCAGAATTTTCGACCACGAGTTGGGGATTCTCTCG                         TTTTTCTTAACCCTGACTCGGAGTACCACACCGTCAGCCTCCTCGACTCCC
genomic: TGCCTGGGCTGCAAGCCAGAATTTTCGACCACGAGTTGGGGATTCTCTCGgtcagtctca ... tcttgtgcagTTTTTCTTAACCCTGACTCGGAGTACCACACCGTCAGCCTCCTCGACTCCC

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: 30 (upstream exon), 33 (downstream exon)
Score: 9

GAGATAGTTGTGGGCGGCACAAAGGGGTGGACCACTGGGTTTGATTACGATGCCTGGGCTGCAAGCCAGAATTTTCGACCACGAGTTGGGGATTCTCTCGgtcagtctca ... tcttgtgcagTTTTTCTTAACCCTGACTCGGAGTACCACACCGTCAGCCTCCTCGACTCCCTCGATGCTTACCAAAGGTGTACCTTGGGAGGAATACAACCTAATGCTAC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cccgtcttcttcttgtcgcagatcattgctgatgccatcttttggtcttgtgcagTTTTTCTTAACCCTGACTCGGAGTACCACACCGTCAGCCTCCTCGACTCCCTCGATGCTTACCAAAGGTGTACCTTGGGAGGAATACAACCTAATGCTAC
                          tgctgat  putative branch site (score: 9)
                                    atctttt  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtcagtctcaatagctgcaaacccatctgtgttgcttcgtgttatgtgatttcgccgaagcctaacccgtcttcttcttgtcgcagatcattgctgatgccatcttttggtcttgtgcagTTTTTCTTAACCCTGACTCGGAGTACCACACCGTCAGCCTCCTCGACTCCCTCGATGCTTACCAAAGGTGTACCTTGGGAGGAATACAACCTAATGCTAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGGA