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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aagaaaataagttcatacttacaagcatctggtacatgtttttgaatgttctcaccttatttcaagtgagtgaccaagaaaatggtgtgagatgatgcagCTAGACACATTTTATGTGAAAAGCAGGGCAAGATTAATGAAGCGTACAAGAAGCTCAAGGAGGGATGGCTCGATAGTGGAGATAAAGTTCCACCAGCTGA

Basic information

species Physcomitrella patens
transcript PP1S217_91V6.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S217_91V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: Vv17s0000g06430.t01 (Vitis vinifera), 3'ss of exon 2
aagaaaataagttcatacttacaagcatctggtacatgtttttgaatgttctcaccttat-ttcaagtgagtgaccaagaaaatggtgtgagatgatgcagCTAGACACATTTTATGTGAAAAGCAGGGCAAGATTAATGAAGCGTACAAGAAGCTCAAGGAGGGATGGCTCGATAGTGGAGATAAAGTTCCACCAGCTGA
               | || |   |||| |         || | ||| |    |  | || |||| ||   |      |    |    |    |  | |||| ||||| || |||||||| ||||| ||||| ||||||||||| |||||||||||  | || || |||||   || |||||| || ||||||||||||||
------------gtctcctcatctgcattttagttggaattgttaatttaagtatttgatcttcatgttgattgttctggcctttcaattccct--tccagCAAGACATATCTTATGTGAGAAGCAAGGCAAAATTAATGAAGCATACAAGAAGCTACAAGATGGCTGGCTTAGTAATGGAGACAAGGTTCCACCAGCTGA
















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|162239202|gb|FC416484.1|FC416484
EST:     GAAGGGGAAGGCCGGCAAAGATGAGCTTGGGACTTGCACCTACGTGAAAG                         CTAGACACATTTTATGTGAAAAGCAGGGCAAGATTAATGAAGCGTACAAGA
genomic: GAAGGGGAAGGCCGGCAAAGATGAGCTTGGGACTTGCACCTACGTGAAAGgtattggggt ... gatgatgcagCTAGACACATTTTATGTGAAAAGCAGGGCAAGATTAATGAAGCGTACAAGA
EST: gi|18372342|gb|BJ203944.1|BJ203944
EST:     GAAGGGGAAGGCCGGCAAAGATGAGCTTGGGACTTGCACCTACGTGAAAG                         CTAGACACATTTTATGTGAAAAGCAGGGCAAGATTAATGAAGCGTACAAGA
genomic: GAAGGGGAAGGCCGGCAAAGATGAGCTTGGGACTTGCACCTACGTGAAAGgtattggggt ... gatgatgcagCTAGACACATTTTATGTGAAAAGCAGGGCAAGATTAATGAAGCGTACAAGA
EST: gi|37821957|gb|BJ580023.1|BJ580023
EST:     GAAGGGGAAGCCCGNCAAAGATGAGCTTGGGACTTGCACTTACGTGAAAG                         CTAGACACATTTTATGTGAAAAGCAGGNCAAGATTAATGAAGCGTACAAGA
genomic: GAAGGGGAAGGCCGGCAAAGATGAGCTTGGGACTTGCACCTACGTGAAAGgtattggggt ... gatgatgcagCTAGACACATTTTATGTGAAAAGCAGGGCAAGATTAATGAAGCGTACAAGA
EST: gi|18325545|gb|BJ157542.1|BJ157542
EST:     GAAGGGGAAGGCCGGCAAAGATGAGCTTGGGACTTGCACCTACGTGAAAG                         CTAGACACATTTTATGTGAAAAGCAGGGCAAGATTAATGAAGCGTACAAGA
genomic: GAAGGGGAAGGCCGGCAAAGATGAGCTTGGGACTTGCACCTACGTGAAAGgtattggggt ... gatgatgcagCTAGACACATTTTATGTGAAAAGCAGGGCAAGATTAATGAAGCGTACAAGA
EST: gi|162223114|gb|FC399693.1|FC399693
EST:     GAAGGGGAAGGCCGGCAAAGATGAGCTTGGGACTTGCACCTACGTGAAAG                         CTAGACACATTTTATGTGAAAAGCAGGGCAAGATTAATGAAGCGTACAAGA
genomic: GAAGGGGAAGGCCGGCAAAGATGAGCTTGGGACTTGCACCTACGTGAAAGgtattggggt ... gatgatgcagCTAGACACATTTTATGTGAAAAGCAGGGCAAGATTAATGAAGCGTACAAGA
EST: gi|37850127|gb|BJ608135.1|BJ608135
EST:     GAAGGGGAAGGCCGGCAAAGATGAGCTTGGGACTTGCACCTACGTGAAAG                         CTAGACACATTTTATGTGAAAAGCAGGGCAAGATTAATGAAGCGTACAAGA
genomic: GAAGGGGAAGGCCGGCAAAGATGAGCTTGGGACTTGCACCTACGTGAAAGgtattggggt ... gatgatgcagCTAGACACATTTTATGTGAAAAGCAGGGCAAGATTAATGAAGCGTACAAGA
EST: gi|162227771|gb|FC402387.1|FC402387
EST:     GAAGGGGAAGGCCGGCAAAGATGAGCTTGGGACTTGCACCTACGTGAAAG                         CTAGACACATTTTATGTGAAAAGCAGGGCAAGATTAATGAAGCGTACAAGA
genomic: GAAGGGGAAGGCCGGCAAAGATGAGCTTGGGACTTGCACCTACGTGAAAGgtattggggt ... gatgatgcagCTAGACACATTTTATGTGAAAAGCAGGGCAAGATTAATGAAGCGTACAAGA
EST: gi|18368840|gb|BJ200925.1|BJ200925
EST:     GAAGGGGAAGGCCGGCAAAGATGAGCTTGGGACTTGCACCTACGTGAAAG                         CTAGACACATTTTATGTGAAAAGCAGGGCAAGATTAATGAAGCGTACAAGA
genomic: GAAGGGGAAGGCCGGCAAAGATGAGCTTGGGACTTGCACCTACGTGAAAGgtattggggt ... gatgatgcagCTAGACACATTTTATGTGAAAAGCAGGGCAAGATTAATGAAGCGTACAAGA
EST: gi|37852029|gb|BJ610037.1|BJ610037
EST:     GAAGGGGAAGGCCGGCAAAGATGAGCTTGGGACTTGCACCTACGTGAAAG                         CTAGACACATTTTATGTGAAAAGCAGGGCAAGATTAATGAAGCGTACAAGA
genomic: GAAGGGGAAGGCCGGCAAAGATGAGCTTGGGACTTGCACCTACGTGAAAGgtattggggt ... gatgatgcagCTAGACACATTTTATGTGAAAAGCAGGGCAAGATTAATGAAGCGTACAAGA
EST: gi|162233101|gb|FC408508.1|FC408508
EST:     GAAGGGGAAGGCCGGCAAAGATGAGCTTGGGACTTGCACCTACGTGAAAG                         CTAGACACATTTTATGTGAAAAGCAGGGCAAGATTAATGAAGCGTACAAGA
genomic: GAAGGGGAAGGCCGGCAAAGATGAGCTTGGGACTTGCACCTACGTGAAAGgtattggggt ... gatgatgcagCTAGACACATTTTATGTGAAAAGCAGGGCAAGATTAATGAAGCGTACAAGA
EST: gi|18372510|gb|BJ204112.1|BJ204112
EST:     GAAGGGGAAGGCCGGCAAAGATGAGCTTGGGACTTGCACCTACGTGAAAG                         CTAGACACATTTTATGTGAAAAGCAGGGCAAGATTAATGAAGCGTACAAGA
genomic: GAAGGGGAAGGCCGGCAAAGATGAGCTTGGGACTTGCACCTACGTGAAAGgtattggggt ... gatgatgcagCTAGACACATTTTATGTGAAAAGCAGGGCAAGATTAATGAAGCGTACAAGA
EST: gi|162233100|gb|FC408507.1|FC408507
EST:     GAAGGGGAAGGCCGGCAAAGATGAGCTTGGGACTTGCACNTACGTGANAG                         CTAGACACATTTTATGTGAAAAGCAGGGCAAGATTAATGAAGCGTACAAGA
genomic: GAAGGGGAAGGCCGGCAAAGATGAGCTTGGGACTTGCACCTACGTGAAAGgtattggggt ... gatgatgcagCTAGACACATTTTATGTGAAAAGCAGGGCAAGATTAATGAAGCGTACAAGA
EST: gi|162227772|gb|FC402388.1|FC402388
EST:     GAAGGGGAAGGCCGGCAAAGATGAGCTTGGGACTTGCACCTACGTGAAAG                         CTAGACACATTTTATGTGAAAAGCAGGGCAAGATTAATGAAGCGTACAAGA
genomic: GAAGGGGAAGGCCGGCAAAGATGAGCTTGGGACTTGCACCTACGTGAAAGgtattggggt ... gatgatgcagCTAGACACATTTTATGTGAAAAGCAGGGCAAGATTAATGAAGCGTACAAGA
EST: gi|18342813|gb|BJ174849.1|BJ174849
EST:     GAAGGGGAAGGCCGGCAAAGATGAGCTTGGGACTTGCACCTACGTGAAAG                         CTAGACACATTTTATGTGAAAAGCAGGGCAAGATTAATGAAGCGTACAAGA
genomic: GAAGGGGAAGGCCGGCAAAGATGAGCTTGGGACTTGCACCTACGTGAAAGgtattggggt ... gatgatgcagCTAGACACATTTTATGTGAAAAGCAGGGCAAGATTAATGAAGCGTACAAGA

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: 47

GACGCCGGCAAGGGTAAGGCTGCAGCGAGTGAAGAGAAGGGAGGCAAGGGGAAGGGGAAGGCCGGCAAAGATGAGCTTGGGACTTGCACCTACGTGAAAGgtattggggt ... gatgatgcagCTAGACACATTTTATGTGAAAAGCAGGGCAAGATTAATGAAGCGTACAAGAAGCTCAAGGAGGGATGGCTCGATAGTGGAGATAAAGTTCCACCAGCTGA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atgttctcaccttatttcaagtgagtgaccaagaaaatggtgtgagatgatgcagCTAGACACATTTTATGTGAAAAGCAGGGCAAGATTAATGAAGCGTACAAGAAGCTCAAGGAGGGATGGCTCGATAGTGGAGATAAAGTTCCACCAGCTGA
   ttctcac  putative branch site (score: 47)
           ttatttcaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aagaaaataagttcatacttacaagcatctggtacatgtttttgaatgttctcaccttatttcaagtgagtgaccaagaaaatggtgtgagatgatgcagCTAGACACATTTTATGTGAAAAGCAGGGCAAGATTAATGAAGCGTACAAGAAGCTCAAGGAGGGATGGCTCGATAGTGGAGATAAAGTTCCACCAGCTGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA