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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...taatttaagttgttaacgggtaatgggagggtggttgattgatctaaagctcctatctctctctctctctcggctaaagaatggtttttttcacttgcagTTGGAGGTCTTCTGAATGCGACTTTTGGCAATGCAACGGAAATGATTATATGCATCATTGCTTTACGGAAGAAAATGATACGAGTTGTACAGTTATCACT

Basic information

species Physcomitrella patens
transcript PP1S336_18V6.2
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S336_18V6.2 (Physcomitrella patens), 3'ss of exon 5
lower sequence: GRMZM2G046480_T01 (Zea mays), 3'ss of exon 4
----------taatttaa-gttgt-taacgggtaatgggagggtggttgattgatctaaagctcctatctctctctctctctcg----gctaaagaatggtttttttcact------tgcagTTGGAGGTCTTCTGAATGCGACTTTTGGCAATGCAACGGAAATGATTATATGCATCATTGCTTTACGGAAGAAAATGATACGAGTTGTACAGTTATCACT
          |  |   | | |||   ||   |  |       |  | | || |  |||        |    ||  || | | |    | |  | ||   ||| |||  ||      ||||||||| || || |||||||| || ||||| ||||||||||||||||||||||  ||    ||  |    ||    ||||| ||||| || |||   |||||
gtgtgttctttgctcccatgctgtgctacatttcctaaacaaatattagctttaattaacatctgcttagtacttactatttagtaaagatgtaaaaccttttcttttccttctaattgcagTTGGGGGGCTACTGAATGCTACATTTGGAAATGCAACGGAAATGATTATATCAATATACGCACTGAAAAATGGGATGATTCGAGTCGTCCAGCAGTCACT

upper sequence: PP1S336_18V6.2 (Physcomitrella patens), 3'ss of exon 5
lower sequence: GRMZM2G053004_T01 (Zea mays), 3'ss of exon 3
-----taatttaagttgttaacgggtaatggga---gggtggttgattgatctaaagctcctatctctctctctctctcggctaaagaatggtttttttc-----------acttgcagTTGGAGGTCTTCTGAATGCGACTTTTGGCAATGCAACGGAAATGATTATATGCATCATTGCTTTACGGAAGAAAATGATACGAGTTGTACAGTTATCACT
     |  |||       |  || |  ||         | || | |   |     | ||       ||   |     |  |  ||    |    ||||||           | ||| |||||| || || |||||||| || ||||| ||||||||||||||||||||||  ||    ||  |    ||    ||||| || || || |||   |||||
gtatgttctttggtcccatgccgtgctatctttcctaagcggctaagcaaatcttaactttagcagctgcttagtattttgtaaagatgtaacctttttccttttccatctaattgaagTTGGGGGGCTACTGAATGCTACATTTGGAAATGCAACGGAAATGATTATATCAATATACGCACTGAAAAATGGGATGATTCGGGTCGTCCAGCAGTCACT

upper sequence: PP1S336_18V6.2 (Physcomitrella patens), 3'ss of exon 5
lower sequence: GRMZM2G040017_T02 (Zea mays), 3'ss of exon 4
taatttaagttgttaacgggtaatgggagggtggttgattgatctaaagctcc-tatctctctctctctctcggctaaagaatggtttttttcacttgcagTTGGAGGTCTTCTGAATGCGACTTTTGGCAATGCAACGGAAATGATTATATGCATCAT-TGCTTTACGGAAGAAAATGATACGAGTTGTACAGTTATCACT
     || |    |  |   | ||||      |     ||||  |||  ||   |     ||      |  || || |        |||  | |  ||||||||| || ||||||||||| || ||||| |||||||| |||||||| || ||||  || ||||||    ||   |||||| ||||| || |||   |||||
----gtatgcctctttctctttatggctaatagccaatttgaaataatactagatgagggtcctcgaatggcgactgattt-caactttcctgaactgcagTTGGTGGCCTTCTGAATGCTACATTTGGAAATGCAACCGAAATGATCAT-TGCAGTATATGCTTTGAAAAATGGAATGATCCGAGTAGTGCAGCAGTCACT

upper sequence: PP1S336_18V6.2 (Physcomitrella patens), 3'ss of exon 5
lower sequence: GRMZM2G143356_T02 (Zea mays), 3'ss of exon 5
taatttaagttgttaacgggtaatgggagggtggttgattgatctaaagctcctatctctctctctctctcggctaaagaatggtttttttcacttgcagTTGGAGGTCTTCTGAATGCGACTTTTGGCAATGCAACGGAAATGATTATATGCATCAT-TGCTTTACGGAAGAAAATGATACGAGTTGTACAGTTATCACT
     || |    |  |     ||||      |     ||||  |||  ||   |       |||          |||   ||  ||  |  ||| |||||||| || ||||||||||| || ||||| |||||||| |||||||| || ||||  || ||||||    ||   |||||| ||||| || |||   |||||
----gtatgcctctttctctgtatggctaatagtcaacttgaaataagactataagagagtcctc----------aaatggtgacttactgaact-gcagTTGGTGGCCTTCTGAATGCTACATTTGGAAATGCAACTGAAATGATCAT-TGCAATATATGCTTTGAAAAATGGAATGATCCGAGTAGTGCAGCAGTCACT

upper sequence: PP1S336_18V6.2 (Physcomitrella patens), 3'ss of exon 5
lower sequence: GLYMA15G00380.2 (Glycine max), 3'ss of exon 3
taatttaagttgttaacgggtaatgggagggtggttgattgatctaaagctcctatctctctctctctctcggctaaagaatggtttttttcacttgcagTTGGAGGTCTTCTGAATGCGACTTTTGGCAATGCAACGGAAATGATTATATGCATCATTGCTTTACGGAAGAAAATGATACGAGTTGTACAGTTATCACT
                        |      |  || |||   ||    ||| ||   | |     ||||   | |   | | || ||  |  || |||||||| ||||| || ||||| || |||||||||||||| |||||||||||||  ||   ||| ||    |  || |||||| | ||||| |||  ||| ||
------------------------gtatccctcttttatttccctttttctcttaaggcccgtatcctcttttcaactcactcgtgttgctttct-gcagTTGGGGGTCTGCTTAATGCCACCTTTGGCAATGCAACTGAAATGATTATATCAATTTATGCATTGAAAAGCAATATGATAAGGGTTGTTCAGCAATCCCT

upper sequence: PP1S336_18V6.2 (Physcomitrella patens), 3'ss of exon 5
lower sequence: GLYMA13G44960.1 (Glycine max), 3'ss of exon 3
-taatttaagttgttaacgggtaatgggagggtggttgattgatctaaagctcctatctctctctctctctcggctaaagaatggtttttttcacttgcagTTGGAGGTCTTCTGAATGCGACTTTTGGCAATGCAACGGAAATGATTATATGCATCATTGCTTTACGGAAGAAAATGATACGAGTTGTACAGTTATCACT
 ||   | | || ||  |   |  |       |     ||| |||     ||||  | | |||   ||        ||   |    | ||   | |||||||||| ||||| || ||||| || || ||||||||||| |||||||||||||  ||   ||| ||    |  || |||||| | ||||| |||  |||  |
gtatcctcatttattttctttttct-------tttcctatttatcattctctccc-tttgtctgcttcgtcaattcaactcacttctgttcatatttgcagTTGGGGGTCTGCTTAATGCCACATTCGGCAATGCAACTGAAATGATTATATCAATTTATGCATTGGAAAGCAATATGATAAGGGTTGTTCAGCAATCTTT

upper sequence: PP1S336_18V6.2 (Physcomitrella patens), 3'ss of exon 5
lower sequence: Vv09s0018g01840.t01 (Vitis vinifera), 3'ss of exon 4
taatttaagttgttaacgggtaatgggagggtggttgattgatctaaagct---cctatctctctctctctctcggctaaagaatggtttttttcacttg------cagTTGGAGGTCTTCTGAATGCGACTTTTGGCAATGCAACGGAAATGATTATATGCATCATTGCTTTACGGAAGAAAATGATACGAGTTGTACAGTTATCACT
          | |  |    |  ||    | |   | ||  |||     ||    || |||     | |     |  ||     |  |||||||| ||||      ||||||| |||||||| ||||| || ||||||||||| || |||||||| || |  ||   ||| ||   | |    |||||| ||||||| |||  |||| |
---------ctatccaaaatttttgtattgtttccttatctatcctttcctggatctgtcttctaatatgaggtgtttattttttattttttttcccttggatctgcagTTGGGGGTCTTCTAAATGCTACCTTTGGCAATGCGACAGAAATGATAATTTCAATGTATGCATTGAAGCATGGGATGATAAGAGTTGTTCAGCAATCATT

upper sequence: PP1S336_18V6.2 (Physcomitrella patens), 3'ss of exon 5
lower sequence: EFJ12361 (Selaginella moellendorffii), 3'ss of exon 1
taatttaagttgttaacgggtaatgggagggtggttgattgatctaaagctcctatctctctctctctctcggctaaagaatggtttt-tttcacttgcagTTGGAGGTCTTCTGAATGCGACTTTTGGCAATGCAACGGAAATGATTATATGCATCATTGCTTTACGGAAGAAAATGATACGAGTTGTACAGTTATCACT
                                   | ||  ||   |  | | | ||||  || |       |  || |     |||| |||| |||||||| || || |||||||||||||| ||||| ||||| || || |||||||| |  ||| | ||| | |||||    ||||| || || || ||| | || ||
----------------------------------gtaataaatt--atacccttttctcgatcacaaagagagtgaatggtcctttttgtttctcttgcagTCGGTGGCCTTCTGAATGCGACGTTTGGAAATGCCACCGAGATGATTATCTCTATCTTCGCTCTGCGGAATGGCATGATCCGCGTGGTTCAGCTGTCGCT

upper sequence: PP1S336_18V6.2 (Physcomitrella patens), 3'ss of exon 5
lower sequence: EFJ33760 (Selaginella moellendorffii), 3'ss of exon 1
taatttaagttgttaacgggtaatgggagggtggttgattgatctaaagctcctatctctctctctctctcggctaaagaatggtttttttca-----cttgcagTTGGAGGTCTTCTGAATGCGACTTTTGGCAATGCAACGGAAATGATTATATGCATCATTGCTTTACGGAAGAAAATGATACGAGTTGTACAGTTATCACT
                                        |   ||||         | ||||  || |   |  |  ||||||| |||||       |||||||| || || |||||||||||||| ||||| ||||| || || |||||||| |  ||| | ||| | |||||    ||||| || || || ||| | || ||
----------------------------------------gtaataaattatacccttttctcgatcacaaagagagtgaatggtcttttttgtttctcttgcagTCGGTGGCCTTCTGAATGCGACGTTTGGAAATGCCACCGAGATGATTATCTCTATCTTCGCTCTGCGGAATGGCATGATCCGCGTGGTTCAGCTGTCGCT

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|162267367|gb|FC443910.1|FC443910
EST:     ACAACTGTCTTTTTTCACTGGTTCGACAG                         TTGGAGGTCTTCTGAATGCGACTTTTGGCAATGCAACGGAAATGATTATAT
genomic: ACAACTGTCTTTTTTCACTGGTTCGACAGgtaattctcg ... tcacttgcagTTGGAGGTCTTCTGAATGCGACTTTTGGCAATGCAACGGAAATGATTATAT
EST: gi|100431991|gb|BY978610.1|BY978610
EST:     ACAACTGTCTTTTTTCACTGGTTCGACAG                         TTGGAGGTCTTCTGAATGCGACTTTTGGCAATGCAACGGAAATGATTATAT
genomic: ACAACTGTCTTTTTTCACTGGTTCGACAGgtaattctcg ... tcacttgcagTTGGAGGTCTTCTGAATGCGACTTTTGGCAATGCAACGGAAATGATTATAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaagctcctatctctctctctctctcggctaaagaatggtttttttcacttgcagTTGGAGGTCTTCTGAATGCGACTTTTGGCAATGCAACGGAAATGATTATATGCATCATTGCTTTACGGAAGAAAATGATACGAGTTGTACAGTTATCACT
                          ggctaaa  putative branch site (score: 3)
                                       tttttttcacttgc  putative PPT
                                       tttttttca  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
taatttaagttgttaacgggtaatgggagggtggttgattgatctaaagctcctatctctctctctctctcggctaaagaatggtttttttcacttgcagTTGGAGGTCTTCTGAATGCGACTTTTGGCAATGCAACGGAAATGATTATATGCATCATTGCTTTACGGAAGAAAATGATACGAGTTGTACAGTTATCACT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA