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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atgaaaacatctgatgacaagaaataaaacgtgagtttcggagcttacactgctctgacaccgattaatatgttgcttacatgatgtgtttcgtttgcagCTTGATCATAGGAAGAAAGACTACAAGTTTGGGTTTGGTTTGACAGTGGGAGATTAA

Basic information

species Physcomitrella patens
transcript PP1S12_290V6.1
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S12_290V6.1 (Physcomitrella patens), 3'ss of exon 10
lower sequence: LOC_Os01g16910.1 (Oryza sativa), 3'ss of exon 10
atgaaaacatctgatgacaagaaataaaacgtgagtttcggagcttacactgctctg-acaccgattaatatgttg--cttacatgatgt-gtttcg-------tttgcagCTTGATCATAGGAAGAAAGACTACAAGTTTGGGTTTGGTTTGACAGTGGGAGATTAA-------------------------------------------
        ||||    |  | |  | ||   |     |||   | | || |    || |    || ||  || |||   | ||||||||| |||||        | |||||||||||||  |||||||||| ||||| |||||||||||| ||    | ||||| | |                                           
-------tatctagccatcataggtgaatttta----tcgtgccctgcatttagttgtatttggagtataattttgaattgacatgatgttgtttctacaatcctgtgcagCTTGATCACTGGAAGAAAGATTACAAATTTGGGTTTGGTATGGTTCTTGGAGAGTGAGGCAGTGTCGGCGGTTTCTTCGGAGACGCATGTACGATTATAG

upper sequence: PP1S12_290V6.1 (Physcomitrella patens), 3'ss of exon 10
lower sequence: GLYMA08G05280.1 (Glycine max), 3'ss of exon 10
-------------------------------------------atgaaaacatctgatgacaagaaataaaacgtgagtttcg----gagcttacactgctctgacaccgattaatatgtt---gcttacatg------atgtgtttcgtttgcagCTTGATCATAGGAAGAAAGACTACAAGTTTGGGTTTGGTTTGACAGTGGGAGATTAA-------------------------------------------
                                             | |   || ||   |  |   || |||    ||||| |    ||  ||  | |    |||      ||   || ||    || |||||      || ||| |   ||||||||||| || ||||| ||||||||||| ||||||||||||||||| || ||||| | |                                           
gtcaggcattttccttttatttttttccactgctatttttattgagtagggatgtgtgtagtatgcatgaaaatctagtttggtggggatgttgaattaggttgatcggcttttgcatttttgccctgacatggtttgcatatgtattcattgcagCTTGACCACAGGAAAAAAGACTACAAATTTGGGTTTGGTTTGACCGTTGGAGAATGAATAAGCCGGACTAGAGCTGTGTTTTCATTGCTGTAGCCAGCTT

upper sequence: PP1S12_290V6.1 (Physcomitrella patens), 3'ss of exon 10
lower sequence: GLYMA05G34360.3 (Glycine max), 3'ss of exon 10
---------------------------------------------------atgaaaacatctgatgacaagaaataaaacgtgagtttcggagcttacactgctctgacaccgattaatatgttgcttacatgatgtgtttcgtttgcagCTTGATCATAGGAAGAAAGACTACAAGTTTGGGTTTGGTTTGACAGTGGGAGATTAA-------------------------------------------
                                                   |||||||  |    ||    |  ||     || || ||  || |      |||  |    ||   | | ||| |  |   |||     | |   ||||||||||| || ||||| || |||||||| ||||||||||||||||| |||||||| | |                                           
gtcaggcatttttctttttgcttttccactgctctttttatttgagtagggatgaaaatctagtttggtgggggatgttgagttaggttttgatcggcttttgcatttttgcc--ctgacatggttttcgtatg-----tattaattgcagCTTGACCACAGGAAAAAGGACTACAAATTTGGGTTTGGTTTGACTGTGGGAGAATGAATAAACCGAACTGGAGCTGTGTTTTCATTGCTGTACCCAGCTT

upper sequence: PP1S12_290V6.1 (Physcomitrella patens), 3'ss of exon 10
lower sequence: Vv03s0097g00590.t01 (Vitis vinifera), 3'ss of exon 10
atgaaaacatctgatgacaagaaataaaacgtgagtttcggagcttacactgctctgacac--cgattaatatgttgcttacatgatgtgtttcgtttgcagCTTGATCATAGGAAGAAAGACTACAAGTTTGGGTTTGGTTTGACAGTGGGAGATTAA-------------------------------------------
 ||    || ||  |        ||         | ||   ||| | |   | |   ||    ||| |   ||  ||   | ||  ||  |||   |||||| | |||||  |||||||||||||||| |||||||||||  ||||||| ||||| ||                                            
-tgttttcagcttttcttttcctattgggttcatggttttcagcattcctggtttatactttacgactttgat-ctgacaaaattctgaatttgtcttgcagATAGATCACCGGAAGAAAGACTACAAATTTGGGTTTGGGCTGACAGTAGGAGAATAGAATAGATTAGAAGGCAATTTGTGCTGTTTTCTTCTCAGTTTTA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tacactgctctgacaccgattaatatgttgcttacatgatgtgtttcgtttgcagCTTGATCATAGGAAGAAAGACTACAAGTTTGGGTTTGGTTTGACAGTGGGAGATTAA
                            tgcttac  putative branch site (score: 2)
                                           tttcgttt  putative PPT
                  attaatatgtt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atgaaaacatctgatgacaagaaataaaacgtgagtttcggagcttacactgctctgacaccgattaatatgttgcttacatgatgtgtttcgtttgcagCTTGATCATAGGAAGAAAGACTACAAGTTTGGGTTTGGTTTGACAGTGGGAGATTAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT