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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttggctatttgcagcctacatttcatgcaattaagcatttaattcttgtagttgcagcttcgaaagcattttaatgattcaattatgttttcatttgcagTTTCCAATCACTGCCATTCGAGAAATCAAGATTCTGAAGAAGTTGCAACATGCGAATGTCATTAAATTGAAGGAGATTGTGACCTCTAAAG

Basic information

species Physcomitrella patens
transcript PP1S3_535V6.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S3_535V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: GLYMA20G10960.1 (Glycine max), 3'ss of exon 2
---ttggctatttgcagcctacatttcatgcaattaagcatt-taattcttgtagttgcagcttcgaaagcattttaatgattcaattatgttttcatttgcagTTTCCAATCACTGCCATTCGAGAAATCAAGATTCTGAAGAAGTTGCAACATGCGAATGTCATTAAATTGAAGGAGATTGTGACCTCTAAAG
   |  | |  ||  |  ||  | ||   | |  ||    ||    |   |||  |   ||  ||     | | | |||  | |  | |  |||    ||||||||||| || ||||| || || |||||||| ||||||||||| ||||| ||||  ||||| || || ||||| || |||||||| |||  ||
atttcagtttattaaaatctgaagttgcagtagctatatgttgctgtgtctgtgatatgagtctcc----cttctgaatcgtactgtaaattttgtcattgcagTTTCCTATAACTGCTATACGTGAAATCAAAATTCTGAAGAAATTGCACCATGAAAATGTAATCAACTTGAAAGAAATTGTGACTTCTCCAG

upper sequence: PP1S3_535V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: GLYMA14G04410.1 (Glycine max), 3'ss of exon 2
ttggctatttgcagcctacatttcatgcaattaagcatttaattcttgtagttgcagcttcgaaagca--ttttaatgattcaattatgttttcatttgcagTTTCCAATCACTGCCATTCGAGAAATCAAGATTCTGAAGAAGTTGCAACATGCGAATGTCATTAAATTGAAGGAGATTGTGACCTCTAAAG
     | |        | || |  |   || |  | | |||    |   |  ||  ||| |    ||   | | ||  ||   || |  ||| |  ||||||||||| || |||||||| ||||||||||| ||||| |||||  | || ||||  ||||| || ||  ||||||| ||||||||   || ||
--cattgtacatgctattcaatgaacctaaatcggaagttacagttaaaatctgttgctacagttgctcctctgaactatattataaattttgccattgcagTTTCCTATAACTGCCATACGAGAAATCAAAATTCTAAAGAAACTACACCATGAAAATGTGATCAAGCTGAAGGAAATTGTGACTGATACAG
















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|67704726|gb|BJ964959.1|BJ964959
EST:     GTGAAGTTGTTGCGCTGAAGAAAGTTCGTATGGACAATGAGAAGGAAGGG                         TTTCCAATCACTGCCATTCGAGAAATCAAGATTCTGAAGAAGTTGCAACAT
genomic: GTGAAGTTGTTGCGCTGAAGAAAGTTCGTATGGACAATGAGAAAGAAGGGgtatgacgat ... tcatttgcagTTTCCAATCACTGCCATTCGAGAAATCAAGATTCTGAAGAAGTTGCAACAT
EST: gi|67718151|gb|BJ968410.1|BJ968410
EST:     GTGAAGTTGTTGCGCTGAAGAAAGTTCGTATGGACAATGAGAAAGAAGGG                         TTTCCAATCACTGCCATTCGAGAAATCAAGATTCTGAAGAAGTTGCAACAT
genomic: GTGAAGTTGTTGCGCTGAAGAAAGTTCGTATGGACAATGAGAAAGAAGGGgtatgacgat ... tcatttgcagTTTCCAATCACTGCCATTCGAGAAATCAAGATTCTGAAGAAGTTGCAACAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgtagttgcagcttcgaaagcattttaatgattcaattatgttttcatttgcagTTTCCAATCACTGCCATTCGAGAAATCAAGATTCTGAAGAAGTTGCAACATGCGAATGTCATTAAATTGAAGGAGATTGTGACCTCTAAAG
                       ttttaat  putative branch site (score: 3)
                                          ttttcattt  putative PPT
                      attttaatgattcaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttggctatttgcagcctacatttcatgcaattaagcatttaattcttgtagttgcagcttcgaaagcattttaatgattcaattatgttttcatttgcagTTTCCAATCACTGCCATTCGAGAAATCAAGATTCTGAAGAAGTTGCAACATGCGAATGTCATTAAATTGAAGGAGATTGTGACCTCTAAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAT