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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cgcatgatttctgtctgtactgaacgacgagagtttagcattaggttgtggtctgtttgtatgtttgaattaattttcctggttgtctgtatttttacagACTGTGGAGCAGACAATACCTTGAAACCTGGGGATGTGATCCAGTGTCGGGAGTGTGGTTATCGCATCCTTTACAAGAAGAGGACAAGGC

Basic information

species Physcomitrella patens
transcript PP1S403_37V6.2
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S403_37V6.2 (Physcomitrella patens), 3'ss of exon 1
lower sequence: LOC_Os01g34614.1 (Oryza sativa), 3'ss of exon 1
cgcatgatttctgtctgtactgaacg-acgagagtttagc-attaggttgtggtctgtttgtatgtttgaattaattttcctggttgtctgtatttttacagACTGTGGAGCAGACAATACCTTGAAACCTGGGGATGTGATCCAGTGTCGGGAGTGTGGTTATCGCATCCTTTACAAGAAGAGGACAAGGC---
   ||| ||||| |||  |  |   | |   || | | || | | |  |  |||    ||||    ||    ||       || || ||| | | ||  |||| || ||||| || || ||  |||| || || |||||||||||||| || || ||||| ||||||||||| ||||||||| | ||  | |   
gtgatggtttctctctccatcggttggattggattatggctagttgaattcggttcagttgtcaaattttgatatcaaatgtgattttctttgtctt--cagATTGCGGAGCTGAGAACACACTGAAGCCAGGAGATGTGATCCAGTGCCGTGAATGTGGCTATCGCATCCTCTACAAGAAGCGTACCCGCCGGA

upper sequence: PP1S403_37V6.2 (Physcomitrella patens), 3'ss of exon 1
lower sequence: LOC_Os05g05980.1 (Oryza sativa), 3'ss of exon 1
cgcatgatttctgtctgtactgaacgacgagagtttagc--attaggttgtggtctgtttgt---atgtttgaattaattttcctggttgtctgtatttttacagACTGTGGAGCAGACAATACCTTGAAACCTGGGGATGTGATCCAGTGTCGGGAGTGTGGTTATCGCATCCTTTACAAGAAGAGGACAAGGC---
     | | ||  |  ||       ||   || | | ||   ||  |||  | | |   |||   || |||||  | ||       ||  | | | | | | |||| |||||||| || || ||  |||| || || |||||||||||||| || || ||||| ||||||||||| ||||||||| | ||  | |   
---tcgctctccattggttggattggattggattatggctagttgagttcagttttagctgtcaaatttttgatatgatgaaat--gtgatttttctctcttcagATTGTGGAGCTGAGAACACACTGAAGCCAGGAGATGTGATCCAGTGCCGTGAATGTGGCTATCGCATCCTCTACAAGAAGCGCACCCGCCGGA

upper sequence: PP1S403_37V6.2 (Physcomitrella patens), 3'ss of exon 1
lower sequence: GRMZM2G540834_T01 (Zea mays), 3'ss of exon 1
---cgcatgatt-tctgtctgtactgaacgacgagagtttagcattaggttgtggtctgtttgtatgtttgaattaattttcctggttgtctgtatttttacagACTGTGGAGCAGACAATACCTTGAAACCTGGGGATGTGATCCAGTGTCGGGAGTGTGGTTATCGCATCCTTTACAAGAAGAGGACAAGGC--
   | ||| ||| |  |  |||   |    |    | |  || |      ||   ||    |  || ||     | || |    |   |    | || || |||| |||||||| || || ||  |||| ||    |||||||||||||| || ||||| || || |||||||| ||||||||| ||||    |  
attcccataattgtgggaatgtttggtttcatcttaatcaagtaaagtactgaattcctcgtccatattc----tgatgtgaacgaaagctgcttttgtttcagATTGTGGAGCTGAGAACACGCTGAAGCCGACAGATGTGATCCAGTGCCGTGAGTGGGGCTACCGCATCCTCTACAAGAAGCGGACCCATCGA

upper sequence: PP1S403_37V6.2 (Physcomitrella patens), 3'ss of exon 1
lower sequence: EFJ25254 (Selaginella moellendorffii), 3'ss of exon 1
cgcatgatttctgtctgtactgaacgacgagagtttagcattaggttgtggtctgtttgtatgtttgaattaattttcctggttgtctgtatttttacagACTGTGGAGCAGACAATACCTTGAAACCTGGGGATGTGATCCAGTGTCGGGAGTGTGGTTATCGCATCCTTTACAAGAAGAGGACAAGGC---
                              | |    ||   | ||| |  |  | |||   || ||  ||  |    ||  |||| ||         ||| |||||| | |||||| |  | || |||||||||||||| ||||| ||||| || || ||||||||||| ||||||||||| ||  |     
------------------------------gtgagcggcgccatgttttacttcgcttg---gtgtgggtttttagatctttttgtttgc-------tagATTGTGGAACCGACAATTCGCTCAAGCCTGGGGATGTGATACAGTGCCGGGAATGCGGCTATCGCATCCTCTACAAGAAGAGAACTCGAAGGA

upper sequence: PP1S403_37V6.2 (Physcomitrella patens), 3'ss of exon 1
lower sequence: EFJ23246 (Selaginella moellendorffii), 3'ss of exon 1
cgcatgatttctgtctgtactgaacgacgagagtttagcattaggttgtggtctgtttgtatgtttgaattaattttcctggttgtctgtatttttacagACTGTGGAGCAGACAATACCTTGAAACCTGGGGATGTGATCCAGTGTCGGGAGTGTGGTTATCGCATCCTTTACAAGAAGAGGACAAGGC----------
                              | |    ||   | | | |  |  | |||   || ||  ||  |    ||  |||| ||         ||| |||||| | |||||| |  | || |||||||||||||| ||||| ||||| || || ||||||||||| ||||||||||| ||  |            
------------------------------gtgagcggcgccatgcttttcttcgcttg---gtgtgggtttttacatctttttgtttgc-------tagATTGTGGAACCGACAATTCGCTCAAGCCTGGGGATGTGATACAGTGCCGGGAATGCGGCTATCGCATCCTCTACAAGAAGAGAACTCGAAGAAGTAAGCG

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|67570685|gb|BJ943509.1|BJ943509
EST:     CGGTAGCATGTCTGCTCCCCCTCCCGAGCCTGTCACCTACCTTTGTGGTG                         ACTGTGGAGCAGACAATACCTTGAAACCTGGGGATGTGATCCAGTGTCGGG
genomic: CGGTAGCATGTCTGCTCCCCCTCCCGAGCCTGTCACCTACCTTTGTGGTGgttagtgctt ... atttttacagACTGTGGAGCAGACAATACCTTGAAACCTGGGGATGTGATCCAGTGTCGGG
EST: gi|67699164|gb|BJ959397.1|BJ959397
EST:     CGGTAGCATGTCTGCTCCCCCTCCCGAGCCTGTCACCTACCTTTGTGGTG                         ACTGTGGAGCAGACAATACCTTGAAACCTGGGGATGTGATCCAGTGTCGGG
genomic: CGGTAGCATGTCTGCTCCCCCTCCCGAGCCTGTCACCTACCTTTGTGGTGgttagtgctt ... atttttacagACTGTGGAGCAGACAATACCTTGAAACCTGGGGATGTGATCCAGTGTCGGG
EST: gi|67693976|gb|BJ954209.1|BJ954209
EST:     CGGTAGCATGTCTGCTCCCCCTCCCGAGCCTGTCACCTACCTTTGTGGTG                         ACTGTGGAGCAGACAATACCTTGAAACCTGGGGATGTGATCCAGTGTCGGG
genomic: CGGTAGCATGTCTGCTCCCCCTCCCGAGCCTGTCACCTACCTTTGTGGTGgttagtgctt ... atttttacagACTGTGGAGCAGACAATACCTTGAAACCTGGGGATGTGATCCAGTGTCGGG
EST: gi|162215439|gb|FC391935.1|FC391935
EST:     CGGTAGCATGTCTGCTCCCCCTCCCGAGCCTGTCACCTACCTTTGTGGTG                         ACTGTGGAGCAGACAATACCTTGAAACCTGGGGATGTGATCCAGTGTCGGG
genomic: CGGTAGCATGTCTGCTCCCCCTCCCGAGCCTGTCACCTACCTTTGTGGTGgttagtgctt ... atttttacagACTGTGGAGCAGACAATACCTTGAAACCTGGGGATGTGATCCAGTGTCGGG
EST: gi|162205253|gb|FC380935.1|FC380935
EST:     CGGTAGCATGTCTGCTCCCCCTCCCGAGCCTGTCACCTACCTTTGTGGTG                         ACTGTGGAGCAGACAATACCTTGAAACCTGGGGATGTGATCCAGTGTCGGG
genomic: CGGTAGCATGTCTGCTCCCCCTCCCGAGCCTGTCACCTACCTTTGTGGTGgttagtgctt ... atttttacagACTGTGGAGCAGACAATACCTTGAAACCTGGGGATGTGATCCAGTGTCGGG
EST: gi|67576831|gb|BJ949655.1|BJ949655
EST:     CGGTAGCATGTCTGCTCCCCCTCCCGAGCCTGTCACCTACCTTTGTGGTG                         ACTGTGGAGCAGACAATACCTTGAAACCTGGGGATGTGATCCAGTGTCGGG
genomic: CGGTAGCATGTCTGCTCCCCCTCCCGAGCCTGTCACCTACCTTTGTGGTGgttagtgctt ... atttttacagACTGTGGAGCAGACAATACCTTGAAACCTGGGGATGTGATCCAGTGTCGGG
EST: gi|67575684|gb|BJ948508.1|BJ948508
EST:     CGGTAGCATGTCTGCTCCCCCTCCCGAGCCTGTCACCTACCTTTGTGGTG                         ACTGTGGAGCAGACAATACCTTGAAACCTGGGGATGTGATCCAGTGTCGGG
genomic: CGGTAGCATGTCTGCTCCCCCTCCCGAGCCTGTCACCTACCTTTGTGGTGgttagtgctt ... atttttacagACTGTGGAGCAGACAATACCTTGAAACCTGGGGATGTGATCCAGTGTCGGG
EST: gi|37835035|gb|BJ593047.1|BJ593047
EST:     CGGTAGCATGTCTGCTCCCCCTCCCGAGCCTGTCACCTACCTTTGTGGTG                         ACTGTGGAGCAGACAATACCTTGAAACCTGGGGATGTGATCCAGTGTCGGG
genomic: CGGTAGCATGTCTGCTCCCCCTCCCGAGCCTGTCACCTACCTTTGTGGTGgttagtgctt ... atttttacagACTGTGGAGCAGACAATACCTTGAAACCTGGGGATGTGATCCAGTGTCGGG
EST: gi|18353565|gb|BJ185620.1|BJ185620
EST:     CGGTAGCATGTCTGCTCCCCCTCCCGAGCCTGTCACCTACCTTTGTGGTG                         ACTGTGGAGCAGACAATACCTTGAAACCTGGGGATGTGATCCAGTGTCGGG
genomic: CGGTAGCATGTCTGCTCCCCCTCCCGAGCCTGTCACCTACCTTTGTGGTGgttagtgctt ... atttttacagACTGTGGAGCAGACAATACCTTGAAACCTGGGGATGTGATCCAGTGTCGGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgtggtctgtttgtatgtttgaattaattttcctggttgtctgtatttttacagACTGTGGAGCAGACAATACCTTGAAACCTGGGGATGTGATCCAGTGTCGGGAGTGTGGTTATCGCATCCTTTACAAGAAGAGGACAAGGC
                      aattaat  putative branch site (score: 3)
                                            tattttt  putative PPT
          tttgtatgtttgaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cgcatgatttctgtctgtactgaacgacgagagtttagcattaggttgtggtctgtttgtatgtttgaattaattttcctggttgtctgtatttttacagACTGTGGAGCAGACAATACCTTGAAACCTGGGGATGTGATCCAGTGTCGGGAGTGTGGTTATCGCATCCTTTACAAGAAGAGGACAAGGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA