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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttgtgtttcagcgaaatcttgatccttgtatattttgaatttttgtagagaatacttcctagtcgtgggcaacttggaagtattttactgaattctggaacaaaagtatcttcagataatttggaaccttaacatctcataatttttttcataaatagAGCATCCTTGTGGAGCCGACCAGTGGCAACACCGGCATTGGCTTGGCTTTCATCGCTGCTGCCAAAGGGTACAAGCTCATCCTCACTATGCCTGCATCAA

Basic information

species Physcomitrella patens
transcript PP1S71_187V6.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S71_187V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: EFJ16446 (Selaginella moellendorffii), 3'ss of exon 1
gtttgtgtttcagcgaaatcttgatccttgtatattttgaatttttgtagagaatacttcctagtcgtgggcaacttggaagtattttactgaattctggaacaaaagtatcttcagataatttggaaccttaacatctcataatttttttcataaatagAGCATCCTTGTGGAGCCGACCAGTGGCAACACCGGCATTGGCTTGGCTTTCATCGCTGCTGCCAAAGGGTACAAGCTCATCCTCACTATGCCTGCATCAA
                                                                           | | ||  |    ||  ||||           || |  ||    ||  | |    ||  | |||| |  || ||| |     |||||| | || |||||||| || ||||| ||||| || |||||  |||| ||||||||||| ||||| || |||||||||||||| || ||||| || || |
--------------------------------------------------------------------------gtagaaaaaaacaaacaaaatttct------tggtcttctcgtccaaacttgg---ttggc-tctcctgtttgtttcct---gtagAGCGTTCTCGTGGAGCCTACGAGTGGAAACACTGGAATTGGTCTGGCGTTCATCGCTGCGGCCAAGGGCTACAAGCTCATCCTGACCATGCCCGCGTCGA

upper sequence: PP1S71_187V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: EFJ17923 (Selaginella moellendorffii), 3'ss of exon 1
gtttgtgtttcagcgaaatcttgatccttgtatattttgaatttttgtagagaatacttcctagtcgtgggcaacttggaagtattttactgaattctggaacaaaagtatcttcagataatttggaaccttaacatctcataatttttttcataaatagAGCATCCTTGTGGAGCCGACCAGTGGCAACACCGGCATTGGCTTGGCTTTCATCGCTGCTGCCAAAGGGTACAAGCTCATCCTCACTATGCCTGCATCAA
                                                                                           |||  |   ||||||| |   |     |    |  || |||         |  | ||| |      |||||| | || |||||||| || ||||| ||||| || |||||  |||| ||||||||||| ||||| || ||||||||||||||||| ||||| ||||| |
----------------------------------------------------------------------------------------gtagaaaac--aaacaaaatttcttggtcttctcgtccaaacttggttggctctcctgtttgtttcctgtagAGCGTTCTCGTGGAGCCTACGAGTGGAAACACTGGGATTGGTCTGGCGTTCATCGCTGCGGCCAAGGGCTACAAGCTCATCCTCACCATGCCCGCATCGA
















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|208390856|gb|DC942202.1|DC942202
EST:     TCAGCATGATCACTGACGCAGAGAGCAAGGGTGCGATTACTCCAGGAAAG                         AGCATCCTTGTGGAGCCGACCAGTGGCAACACCGGCATTGGCTTGGCTTTC
genomic: TCAGCATGATCACTGACGCAGAGAGCAAGGGTGCGATTACTCCAGGAAAGgtttgtgttt ... tcataaatagAGCATCCTTGTGGAGCCGACCAGTGGCAACACCGGCATTGGCTTGGCTTTC
EST: gi|100385278|gb|BY950870.1|BY950870
EST:     TCAGCATGATCACTGACGCAGAGAGCAAGGGTGCGATTACTCCAGGAAAG                         AGCATCCTTGTGGAGCCGACCAGTGGCAACACCGGCATTGGCTTGGCTTTC
genomic: TCAGCATGATCACTGACGCAGAGAGCAAGGGTGCGATTACTCCAGGAAAGgtttgtgttt ... tcataaatagAGCATCCTTGTGGAGCCGACCAGTGGCAACACCGGCATTGGCTTGGCTTTC
EST: gi|100409032|gb|BY991846.1|BY991846
EST:     TCAGCATGATCACTGACGCAGAGAGCAAGGGTGCGATTACTCCAGGAAAG                         AGCATCCTTGTGGAGCCGACCAGTGGCAACACCGGCATTGGCTTGGCTTTC
genomic: TCAGCATGATCACTGACGCAGAGAGCAAGGGTGCGATTACTCCAGGAAAGgtttgtgttt ... tcataaatagAGCATCCTTGTGGAGCCGACCAGTGGCAACACCGGCATTGGCTTGGCTTTC
EST: gi|162171775|gb|FC348951.1|FC348951
EST:     TCAGCATGATCACTGACGCAGAGAGCAAGGGTGCGATTACTCCAGGAAAG                         AGCATCCTTGTGGAGCCGACCAGTGGCAACACCGGCATTGGCTTGGCTTTC
genomic: TCAGCATGATCACTGACGCAGAGAGCAAGGGTGCGATTACTCCAGGAAAGgtttgtgttt ... tcataaatagAGCATCCTTGTGGAGCCGACCAGTGGCAACACCGGCATTGGCTTGGCTTTC
EST: gi|162184261|gb|FC359683.1|FC359683
EST:     TCAGCATGATCACTGACGCAGAGAGCAAGGGTGCGATTACTCCAGGAAAG                         AGCATCCTTGTGGAGCCGACCAGTGGCAACACCGGCATTGGCTTGGCTTTC
genomic: TCAGCATGATCACTGACGCAGAGAGCAAGGGTGCGATTACTCCAGGAAAGgtttgtgttt ... tcataaatagAGCATCCTTGTGGAGCCGACCAGTGGCAACACCGGCATTGGCTTGGCTTTC
EST: gi|100363590|gb|BY966464.1|BY966464
EST:     TCAGCATGATCACTGACGCAGAGAGCAAGGGTGCGATTACTCCAGGAAAG                         AGCATCCTTGTGGAGCCGACCAGTGGCAACACCGGCATTGGCTTGGCTTTC
genomic: TCAGCATGATCACTGACGCAGAGAGCAAGGGTGCGATTACTCCAGGAAAGgtttgtgttt ... tcataaatagAGCATCCTTGTGGAGCCGACCAGTGGCAACACCGGCATTGGCTTGGCTTTC
EST: gi|208349485|gb|DC905623.1|DC905623
EST:     TCAGCATGATCACTGACGCAGAGAGCAAGGGTGCGATTACTCCAGGAAAG                         AGCATCCTTGTGGAGCCGACCAGTGGCAACACCGGCATTGGCTTGGCTTTC
genomic: TCAGCATGATCACTGACGCAGAGAGCAAGGGTGCGATTACTCCAGGAAAGgtttgtgttt ... tcataaatagAGCATCCTTGTGGAGCCGACCAGTGGCAACACCGGCATTGGCTTGGCTTTC

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: 34 (upstream exon), 35 (downstream exon)
Score: 8

GATTGGATTCAGCATGATCACTGACGCAGAGAGCAAGGGTGCGATTACTCCAGGAAAGgtttgtgttt ... tcataaatagAGCATCCTTGTGGAGCCGACCAGTGGCAACACCGGCATTGGCTTGGCTTTCATCGCTGCTGCCAAAGGGTACAAGCTCATCCTCACTATGCCTGCATCAA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aagtatcttcagataatttggaaccttaacatctcataatttttttcataaatagAGCATCCTTGTGGAGCCGACCAGTGGCAACACCGGCATTGGCTTGGCTTTCATCGCTGCTGCCAAAGGGTACAAGCTCATCCTCACTATGCCTGCATCAA
                       ccttaac  putative branch site (score: 8)
                                       tttttttcat  putative PPT
                         ttaacatctcataatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtttgtgtttcagcgaaatcttgatccttgtatattttgaatttttgtagagaatacttcctagtcgtgggcaacttggaagtattttactgaattctggaacaaaagtatcttcagataatttggaaccttaacatctcataatttttttcataaatagAGCATCCTTGTGGAGCCGACCAGTGGCAACACCGGCATTGGCTTGGCTTTCATCGCTGCTGCCAAAGGGTACAAGCTCATCCTCACTATGCCTGCATCAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTCA