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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatggcggttgatttttaaataaaaacgtattacaaatacttaaataactcttaatgccgtcaatagtctgatgggtggcatgtaagtgtcgcagttctagtcttcttgaagtactagttgacgccctatgttttcatttatttatttatttacttttctcgttgttgcagTGTTACTCATCAGATCCTTCCATAGCAGACGGGTATTTTACTGTCCTGGCTGAAGTGTACATGCGTCAAGAAGTACCCAAATGTGATATACCACGTCTAC

Basic information

species Physcomitrella patens
transcript PP1S1_377V6.1
intron # 16
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S1_377V6.1 (Physcomitrella patens), 3'ss of exon 16
lower sequence: LOC_Os02g58410.1 (Oryza sativa), 3'ss of exon 16
gtatggcggttgatttttaaataaaaacgtattacaaatacttaaataactcttaatgccgtcaatagtctgatgggtggcatgtaagtgtcgcagttctagtcttcttgaagtactagttgacgcccta--tgttttcatttatttatttatttacttttctcgttgtt-gcagTGTTACTCATCAGATCCTTCCATAGCAGACGGGTATTTTACTGTCCTGGCTGAAGTGTACATGCGTCAAGAAGTACCCAAATGTGATATACCACGTCTAC
                                                                           | |  || |    | || |   || ||  | |||    |   |||| |     |   ||   |||  | || | || |  ||| | |   |  || ||||||||||||  ||||| || | ||| |||| |||||||| | |||||| |||||||| ||||||||||| ||| | || || ||||| || |   |  |  
-------------------------------------------------------------------------aagttctcaagctcttctcacttctc-agcatccttatgttgacagtttaatttgtgcttgccatcacctgttaaatt-tcgactatacctatcatttgcagTGTTACTCTCCAGATTCTCCAATATCAGATGGGTATTTCAGTGTCCTTGCTGAAGTATACATGCGTCAGGAAATTCCAAAGTGTGAGATCCAGAGAATTT

upper sequence: PP1S1_377V6.1 (Physcomitrella patens), 3'ss of exon 16
lower sequence: EFJ32912 (Selaginella moellendorffii), 3'ss of exon 16
gtatggcggttgatttttaaataaaaacgtattacaaatacttaaataactcttaatgccgtcaatagtctgatgggtggcatgtaagtgtcgcagttctagtcttcttgaagtactagttgacgccctatgttttcatttatttatttatttacttttctcgttgttgcagTGTTACTCATCAGATCCTTCCATAGCAGACGGGTATTTTACTGTCCTGGCTGAAGTGTACATGCGTCAAGAAGTACCCAAATGTGATATACCACGTCTAC
                                                                                                                      |||   |   ||  |  | | || ||  |    ||||| ||  ||| ||||||||| ||||| || |||||||| || || || || |||||| |||| || || ||||||||||||||  | ||  |||| |  || || |  | | | ||  
----------------------------------------------------------------------------------------------------------------------gtttgtgatttac-tcatgagtttttggtggcattactatttacgt-gttgcagTGCTACTCTTCTGATCCTTCTATCGCGGATGGATATTTTTCTGTTCTTGCCGAAGTGTACATGCGGTACGAGATACCAAGGTGCGACACCCAAAGACTGT

upper sequence: PP1S1_377V6.1 (Physcomitrella patens), 3'ss of exon 16
lower sequence: EFJ15776 (Selaginella moellendorffii), 3'ss of exon 16
gtatggcggttgatttttaaataaaaacgtattacaaatacttaaataactcttaatgccgtcaatagtctgatgggtggcatgtaagtgtcgcagttctagtcttcttgaagtactagttgacgccctatgttttcatttatttatttatttacttttctcgttgttgcagTGTTACTCATCAGATCCTTCCATAGCAGACGGGTATTTTACTGTCCTGGCTGAAGTGTACATGCGTCAAGAAGTACCCAAATGTGATATACCACGTCTAC
                                                                                                                 |  |  || ||  | |  |||||   |    |   ||||||| |||     |||||||||| ||||| || |||||||| || || || ||||||||| |||| || || ||||||||||||||  | ||  |||| |  || || |  | | | ||  
---------------------------------------------------------------------------------------------------------------gtttgtgatttac-tcatgagtttttggtggcattactatttacgttt-----tgttgcagTGCTACTCTTCTGATCCTTCTATCGCGGATGGGTATTTTTCTGTTCTTGCCGAAGTGTACATGCGGTACGAGATACCAAGGTGCGACACCCAAAGACTGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agttgacgccctatgttttcatttatttatttatttacttttctcgttgttgcagTGTTACTCATCAGATCCTTCCATAGCAGACGGGTATTTTACTGTCCTGGCTGAAGTGTACATGCGTCAAGAAGTACCCAAATGTGATATACCACGTCTAC
 agttgac  putative branch site (score: 4)
                                 tttacttttctcgtt  putative PPT
           tatgttttcatttatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatggcggttgatttttaaataaaaacgtattacaaatacttaaataactcttaatgccgtcaatagtctgatgggtggcatgtaagtgtcgcagttctagtcttcttgaagtactagttgacgccctatgttttcatttatttatttatttacttttctcgttgttgcagTGTTACTCATCAGATCCTTCCATAGCAGACGGGTATTTTACTGTCCTGGCTGAAGTGTACATGCGTCAAGAAGTACCCAAATGTGATATACCACGTCTAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT