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 5'  3'   		2  
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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tcggcttctcagcggctagcacacaatgattttaatttggcagttgtatgattgcaactgaccctaagcttgaaatctgagaaatttctgtcttccgcagTTGCTCGAAAAGGACCCAGCTCTCAGCAAGTATCACTCAGTGAAGGACACTGTTTCGGCTATCAAACGATTTGGAGACGTTCTCGTCATCCTCGTTGCAG

Basic information

species Physcomitrella patens
transcript PP1S42_209V6.1
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|162226904|gb|FC403092.1|FC403092
EST:     TAGGCCAGAGCCGTGGCATGGCCACCCGCTCCGGAGCTCGCGAGGATTTG                         TTGCTCGAAAAGGACCCAGCTCTCAGCAAGTATCACTCAGTGAAGGACACT
genomic: TAGGCCAGAGCCGTGGCATGGCCACCCGCTCCGGAGCTCGCGAGGATTTGgtttgttgca ... tcttccgcagTTGCTCGAAAAGGACCCAGCTCTCAGCAAGTATCACTCAGTGAAGGACACT
EST: gi|67691721|gb|BJ951954.1|BJ951954
EST:     TAGGCCAGAGCCGTGGCATGGCCACCCGCTCCGGAGCTCGCGAGGATTTG                         TTGCTCGAAAAGGACCCAGCTCTCAGCAAGTATCACTCAGTGAAGGACACT
genomic: TAGGCCAGAGCCGTGGCATGGCCACCCGCTCCGGAGCTCGCGAGGATTTGgtttgttgca ... tcttccgcagTTGCTCGAAAAGGACCCAGCTCTCAGCAAGTATCACTCAGTGAAGGACACT
EST: gi|18329651|gb|BJ161657.1|BJ161657
EST:     TAGGCCAGAGCCGTGGCATGGCCACCCGCTCCGGAGCTCGCGAGGATTTG                         TTGCTCGAAAAGGACCCAGCTCTCAGCAAGTATCACTCAGTGAAGGACACT
genomic: TAGGCCAGAGCCGTGGCATGGCCACCCGCTCCGGAGCTCGCGAGGATTTGgtttgttgca ... tcttccgcagTTGCTCGAAAAGGACCCAGCTCTCAGCAAGTATCACTCAGTGAAGGACACT
EST: gi|162243721|gb|FC421842.1|FC421842
EST:     AGGCCAGAGCCGTGGCATGGCCACCCGCTCACGGAGCTCGCGAGGATTTG                         TTGCTCGAAAAGGACACCAGCTCTCAGCAAGTATCACTCAGTGAAGGACAC
genomic: AGGCCAGAGCCGTGGCATGGCCACCCGCTC-CGGAGCTCGCGAGGATTTGgtttgttgca ... tcttccgcagTTGCTCGAAAAGGAC-CCAGCTCTCAGCAAGTATCACTCAGTGAAGGACAC
EST: gi|67696121|gb|BJ956354.1|BJ956354
EST:     GAGCCGTGGCATGGCCACCCGCTTCNGAGCTCGCGAGGATTTG                         TTGCTCGAAAAGGACCCAGCTCTCAGCAAGTATCACTCAGTGAAGGACACT
genomic: GAGCCGTGGCATGGCCACCCGCTCCGGAGCTCGCGAGGATTTGgtttgttgca ... tcttccgcagTTGCTCGAAAAGGACCCAGCTCTCAGCAAGTATCACTCAGTGAAGGACACT
EST: gi|67578900|gb|BJ951067.1|BJ951067
EST:     TAGGCCAGAGCCGTGGCATGGCCACCCGCTCCGGAGCTCGCGAGGATTTG                         TTGCTCGAAAAGGACCCAGCTCTCAGCAAGTATCACTCAGTGAAGGACACT
genomic: TAGGCCAGAGCCGTGGCATGGCCACCCGCTCCGGAGCTCGCGAGGATTTGgtttgttgca ... tcttccgcagTTGCTCGAAAAGGACCCAGCTCTCAGCAAGTATCACTCAGTGAAGGACACT
EST: gi|6167660|gb|AW145924.1|AW145924
EST:     TAGGCCAGAGCCGTGGCATGGCCACCCGCTCCGGAGCTCGCGAGGATTTG                         TTGCTCGAAAAGGACCCAGCTCTCAGCAAGTATCACTCAGTGAAGGACACT
genomic: TAGGCCAGAGCCGTGGCATGGCCACCCGCTCCGGAGCTCGCGAGGATTTGgtttgttgca ... tcttccgcagTTGCTCGAAAAGGACCCAGCTCTCAGCAAGTATCACTCAGTGAAGGACACT
EST: gi|67508501|gb|BJ941366.1|BJ941366
EST:     TAGGCCAGAGCCGTGGCATGGCCACCCGCTCCGGAGCTCGCGAGGATTTG                         TTGCTCGAAAAGGACCCAGCTCTCAGCAAGTATCACTCAGTGAAGGACACT
genomic: TAGGCCAGAGCCGTGGCATGGCCACCCGCTCCGGAGCTCGCGAGGATTTGgtttgttgca ... tcttccgcagTTGCTCGAAAAGGACCCAGCTCTCAGCAAGTATCACTCAGTGAAGGACACT
EST: gi|162205089|gb|FC381798.1|FC381798
EST:     TAGGCCAGAGCCGTGGCATGGCCACCCGCTCCGGAGCTCGCGAGGATTTG                         TTGCTCGAAAAGGACCCAGCTCTCAGCAAGTATCACTCAGTGAAGGACACT
genomic: TAGGCCAGAGCCGTGGCATGGCCACCCGCTCCGGAGCTCGCGAGGATTTGgtttgttgca ... tcttccgcagTTGCTCGAAAAGGACCCAGCTCTCAGCAAGTATCACTCAGTGAAGGACACT
EST: gi|67507635|gb|BJ940515.1|BJ940515
EST:     TAGGCCAGAGCCGTGGCATGGCCACCCGCTCCGGAGCTCGCGAGGATTTG                         TTGCTCGAAAAGGACCCAGCTCTCAGCAAGTATCACTCAGTGAAGGACACT
genomic: TAGGCCAGAGCCGTGGCATGGCCACCCGCTCCGGAGCTCGCGAGGATTTGgtttgttgca ... tcttccgcagTTGCTCGAAAAGGACCCAGCTCTCAGCAAGTATCACTCAGTGAAGGACACT
EST: gi|162243720|gb|FC421841.1|FC421841
EST:     TAGGCCAGAGCCGTGGCATGGCCACCCGCTCCGGAGCTCGCGAGGATTTG                         TTGCTCGAAAAGGACCCAGCTCTCAGCAAGTATCACTCAGTGAAGGACACT
genomic: TAGGCCAGAGCCGTGGCATGGCCACCCGCTCCGGAGCTCGCGAGGATTTGgtttgttgca ... tcttccgcagTTGCTCGAAAAGGACCCAGCTCTCAGCAAGTATCACTCAGTGAAGGACACT
EST: gi|67572747|gb|BJ945571.1|BJ945571
EST:     TAGGCCAGAGCCGTGGCATGGCCACCCGCTCCGGAGCTCGCGAGGATTTG                         TTGCTCGAAAAGGACCCAGCTCTCAGCAAGTATCACTCAGTGAAGGACACT
genomic: TAGGCCAGAGCCGTGGCATGGCCACCCGCTCCGGAGCTCGCGAGGATTTGgtttgttgca ... tcttccgcagTTGCTCGAAAAGGACCCAGCTCTCAGCAAGTATCACTCAGTGAAGGACACT
EST: gi|162226905|gb|FC403093.1|FC403093
EST:     TAGGCCAGAGCCGTGGCATGGCCACCCGCTCCGGAGCTCGCGAGGATTTG                         TTGCTCGAAAAGGACCCAGCTCTCAGCAAGTATCACTCAGTGAAGGACACT
genomic: TAGGCCAGAGCCGTGGCATGGCCACCCGCTCCGGAGCTCGCGAGGATTTGgtttgttgca ... tcttccgcagTTGCTCGAAAAGGACCCAGCTCTCAGCAAGTATCACTCAGTGAAGGACACT

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), 30 (downstream exon)
Score: 18

TGTAGCAGTCATGCAGGCTGTACGGAGCTCGATCGCTAGGCGTCTGGTCGTAGGCCAGAGCCGTGGCATGGCCACCCGCTCCGGAGCTCGCGAGGATTTGgtttgttgca ... tcttccgcagTTGCTCGAAAAGGACCCAGCTCTCAGCAAGTATCACTCAGTGAAGGACACTGTTTCGGCTATCAAACGATTTGGAGACGTTCTCGTCATCCTCGTTGCAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtatgattgcaactgaccctaagcttgaaatctgagaaatttctgtcttccgcagTTGCTCGAAAAGGACCCAGCTCTCAGCAAGTATCACTCAGTGAAGGACACTGTTTCGGCTATCAAACGATTTGGAGACGTTCTCGTCATCCTCGTTGCAG
          aactgac  putative branch site (score: 18)
                                       tttctgtcttccgc  putative PPT
                                  agaaattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tcggcttctcagcggctagcacacaatgattttaatttggcagttgtatgattgcaactgaccctaagcttgaaatctgagaaatttctgtcttccgcagTTGCTCGAAAAGGACCCAGCTCTCAGCAAGTATCACTCAGTGAAGGACACTGTTTCGGCTATCAAACGATTTGGAGACGTTCTCGTCATCCTCGTTGCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA