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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTTCCAGGCGGAGATCAATCAATTGTTGAGTTTGATCATTAACACCTTCTATAGCAACAAGGAGATTTTCTTGCGAGAACTCATCAGTAATTCCTCGGATgtaagtgttttttcacccttgcttgtgtactgtttgtgtctcatcgtgtctctatttgtcatttgcggtggagttggcgaggccggcgtttcccgtagag...

Basic information

species Physcomitrella patens
transcript PP1S291_62V6.1
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S291_62V6.1 (Physcomitrella patens), 5'ss of exon 1
lower sequence: GLYMA02G47210.1 (Glycine max), 5'ss of exon 1
TTTCCAGGCGGAGATCAATCAATTGTTGAGTTTGATCATTAACACCTTCTATAGCAACAAGGAGATTTTCTTGCGAGAACTCATCAGTAATTCCTCGGATgtaagtgttttttcac-------ccttgcttgtgtactgtttgt---gtctcatcgtgtctctatttgtcatttgcggtggagttggcgaggccggcgtttcccgtagag
||| ||||| |||||||| ||  |  | ||| | ||||| ||||||||||| |||||||||||||| ||  | || || |||||||| ||| |||| ||||||||  ||| |||          |||| |  |    |  ||||   ||||  | || | || ||||||   || ||      ||   | |  ||   |||         
TTTTCAGGCCGAGATCAACCAGCTCCTCAGTCTAATCATCAACACCTTCTACAGCAACAAGGAGATCTTTCTTCGTGAGCTCATCAGCAATGCCTCTGATgtaagattttcttcctgcttctttcttgttcttacgatccttgttaggtcttttggtatttccatttgttcattacgtcct--ttactgcgatcgttcttta--------

upper sequence: PP1S291_62V6.1 (Physcomitrella patens), 5'ss of exon 1
lower sequence: GLYMA08G03690.1 (Glycine max), 5'ss of exon 1
-----------------TTTCCAGGCGGAGATCAATCAATTGTTGAGTTTGATCATTAACACCTTCTATAGCAACAAGGAGATTTTCTTGCGAGAACTCATCAGTAATTCCTCGGATgtaagtgttttttcacccttgcttgtgtactgtttgtgtctcatcgtgtctctatttgtcatttgcggtggagttggcgaggccggcgtttcccgtagag--
                 ||||||| | |||||||| ||  |  | ||| | ||||| ||||||||||| |||||||||||||||||| |  | || |||||||| ||| |||| ||| ||||  || ||  |   | |  |   |  |  |  |      |  |  |  | ||  ||  |  |  |   ||    |      | |  |   || |    
GAAACTGAGACGTTTGCTTTCCAGTCCGAGATCAACCAGCTCCTTAGTCTTATCATCAACACCTTCTACAGCAACAAGGAGATTTTCCTTAgtgagctcatcagcaatgcctctgatttaag-attcttatattatagggttcatgtttatcatactctgtttttccattgttgctccgtaaca-taacgtccctgtattgtgagaattatgtgggtag

upper sequence: PP1S291_62V6.1 (Physcomitrella patens), 5'ss of exon 1
lower sequence: GLYMA08G44590.1 (Glycine max), 5'ss of exon 1
TTTCCAGGCGGAGATCAATCAATTGTTGAGTTTGATCATTAACACCTTCTATAGCAACAAGGAGATTTTCTTGCGAGAACTCATCAGTAATTCCTCGGATgtaagtgttttttcacccttgcttgtgtactgtttgtgtctcatcgtgtc----tctatttgtcatttgcggtggagttggcgaggccggcgtttcccgtagag
||||||||| |||||||| ||  |  | ||| | ||||| |||||||||||   |||||||||||||||| | || ||||||||||| ||  |||| |||||| || || ||      | |||  |  |||  |||| |||  | || ||    | | ||| |  | | |    || ||       |   | |      |    
TTTCCAGGCTGAGATCAACCAGCTCCTCAGTCTCATCATCAACACCTTCTACTCCAACAAGGAGATTTTCCTTCGTGAACTCATCAGCAACGCCTCCGATgtacgt-ttcttcgtttttcgctccttgacttgttgtttctgcttgtttcgtgatgtgtttatgttcttcatccgattttattcaactaacatgctttatt---

upper sequence: PP1S291_62V6.1 (Physcomitrella patens), 5'ss of exon 1
lower sequence: Vv19s0015g01090.t01 (Vitis vinifera), 5'ss of exon 1
TTTCCAGGCGGAGATCAATCAATTGTTGAGTTTGATCATTAACACCTTCTATAGCAACAAGGAGATTTTCTTGCGAGAACTCATCAGTAATTCCTCGGATgtaagtgttttttcacccttgcttgtgtactgtttgtgtctcatcgtgtctctatttgtcatttgcggtggagttggcgaggccggcgtttcccgtagag-----
||||||||| |||||||| ||| | |||||||||||||| ||||||||||| |||||||||||||||||  | || || |||||||| |||||||| |||||||||  | |   ||  ||  |  | |  | |     | | |||   | | | || |  ||   | ||    || |||        |||  | || |       
TTTCCAGGCTGAGATCAACCAACTCTTGAGTTTGATCATCAACACCTTCTACAGCAACAAGGAGATTTTTCTCCGTGAGCTCATCAGCAATTCCTCTGATgtaagtcctat---actttttatctttttttttcctcatttaatcagtttttttttcgcgatc--ctgttttatttgcggctgatctgttctctgttggtttatt

upper sequence: PP1S291_62V6.1 (Physcomitrella patens), 5'ss of exon 1
lower sequence: Vv00s0194g00030.t01 (Vitis vinifera), 5'ss of exon 1
TTTCCAGGCGGAGATCAATCAATTGTTGAGTTTGATCATTAACACCTTCTATAGCAACAAGGAGATTTTCTTGCGAGAACTCATCAGTAATTCCTCGGATgtaagtgttt-------tttcacccttgcttgtgtactgtttgtgtctcatcg--tgtctctatttgtcatttgcggtggagttggcgaggccg-gcgtttcccgtagag
 ||||||||||||||||| ||  || | ||| | ||||| ||||| |||||||||||||||||||||||| | || ||  ||||||| |||||||| ||||| ||| ||        |||| || |  ||| |    | |  |  ||| ||||  ||  | | ||   | | |    ||    |   || ||   ||| ||         
ATTCCAGGCGGAGATCAACCAGCTGCTCAGTCTCATCATCAACACTTTCTATAGCAACAAGGAGATTTTCCTTCGTGAGATCATCAGCAATTCCTCCGATgtgagttttcagaacagtttctccttcacttctccttt-taaggatctgatcgactgcgtgtgttgcgcgtatttcatgttcgtaatgatgcaatgcgatt---------

upper sequence: PP1S291_62V6.1 (Physcomitrella patens), 5'ss of exon 1
lower sequence: EFJ25533 (Selaginella moellendorffii), 5'ss of exon 1
TTTCCAGGCGGAGATCAATCAATTGTTGAGTTTGATCATTAACACCTTCTATAGCAACAAGGAGATTTTCTTGCGAGAACTCATCAGTAATTCCTCGGATgtaagtgtttttt-cacccttgcttgtgtactgtttgtgt-ctcatcgtgtctctatttgtcatttgcggtggagttggcgaggccggcgtttcccgtagag-------
 ||||||||||||||||| ||  |  | ||| | ||||| ||||||||||| |||||||||||||| |||||||| || |||||||| ||| |||||||||| ||||||   | | |  | |    | |  |  |  | | |||||||  ||| |   |    | |||| |    |   |||     || ||     |           
CTTCCAGGCGGAGATCAACCAGCTTCTCAGTCTCATCATCAACACCTTCTACAGCAACAAGGAGATCTTCTTGCGGGAGCTCATCAGCAATGCCTCGGATgtgagtgttagatgctcgttcggcgatattttactgctattctcatcg-atctttgccttctttctgcgatttc-tcaccgatctttgcattctttctgcgatttccag

upper sequence: PP1S291_62V6.1 (Physcomitrella patens), 5'ss of exon 1
lower sequence: EFJ29061 (Selaginella moellendorffii), 5'ss of exon 1
TTTCCAGGCGGAGATCAATCAATTGTTGAGTTTGATCATTAACACCTTCTATAGCAACAAGGAGATTTTCTTGCGAGAACTCATCAGTAATTCCTCGGATgtaagtgttttttcacccttgcttgtgtactgtttgtgtctcatcgtgtctctatttgtcatttgcggtggagttggcgaggccggcgtttcccgtagag
 |||||||| |||||||| ||  |  | ||| | ||||| ||||| ||||| ||||||||||||||||||||||| || |||||||| ||| |||||||||| ||| |||   |  ||||| |  |  |  |||  ||||  |     ||| | ||  ||   ||| | |  | ||  ||  || |              
GTTCCAGGCTGAGATCAACCAGCTTCTCAGTCTCATCATCAACACTTTCTACAGCAACAAGGAGATTTTCTTGCGGGAGCTCATCAGCAATGCCTCGGATgtgagtatttcgcc-tccttgttcttcca--gttcttgtcaaac----tctttcttcttctcatgctgcgccgctg-tgactccag--------------

upper sequence: PP1S291_62V6.1 (Physcomitrella patens), 5'ss of exon 1
lower sequence: EFJ22362 (Selaginella moellendorffii), 5'ss of exon 1
TTTCCAGGCGGAGATCAATCAATTGTTGAGTTTGATCATTAACACCTTCTATAGCAACAAGGAGATTTTCTTGCGAGAACTCATCAGTAATTCCTCGGATgtaagtgtttttt-cacccttgcttgtgtactgtt-tgtgtctcatcgtgtctctatttgtcatttgcggtggagttggcgaggccggcgtttcccgtagag-------
 ||||||||||||||||| ||  |  | ||| | ||||| ||||||||||| |||||||||||||| |||||||| || |||||||| ||| |||||||||| ||||||   | | |  | |    | |     |  |  ||||||||  ||| |   |    | |||| |    |   |||     |||||     |           
CTTCCAGGCGGAGATCAACCAGCTTCTCAGTCTCATCATCAACACCTTCTACAGCAACAAGGAGATCTTCTTGCGGGAGCTCATCAGCAATGCCTCGGATgtgagtgttagatgctcgttcggcgatatttcactgcgattctcatcg-atctttgccttctttctgcgatttc-tcaccgatctttgcgttctttctgcgatttccag

upper sequence: PP1S291_62V6.1 (Physcomitrella patens), 5'ss of exon 1
lower sequence: EFJ17594 (Selaginella moellendorffii), 5'ss of exon 1
TTTCCAGGCGGAGATCAATCAATTGTTGAGTTTGATCATTAACACCTTCTATAGCAACAAGGAGATTTTCTTGCGAGAACTCATCAGTAATTCCTCGGATgtaagtgttttttcacccttgcttgtgtactgtttgtgtctcatcgtgtctctatttgtcatttgcggtggagttggcgaggccggcgtttcccgtagag
 |||||||| |||||||| ||  |  | ||| | ||||| ||||| ||||| ||||||||||||||||||||||| || |||||||| ||| |||||||||| ||| |||      ||| | |  |  |  |||  ||||  |     ||| | ||  ||   ||| | |  | ||  ||  || |              
GTTCCAGGCTGAGATCAACCAGCTTCTCAGTCTCATCATCAACACTTTCTACAGCAACAAGGAGATTTTCTTGCGGGAGCTCATCAGCAATGCCTCGGATgtgagtatttcg----cctcgttcttcca--gttcttgtcaaac----tctttcttcttctcatgctgcgctgctg-tgactccag--------------

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|162220894|gb|FC395871.1|FC395871
EST:     ATAGCAACAAGGAGATTTTCTTGCGAGAACTCATCAGTAATTCCTCGGAT                         GCTTTGGACAAGATTCGCTTCGAGTCCTTGACAGATAAGAGCAAACTAGAT
genomic: ATAGCAACAAGGAGATTTTCTTGCGAGAACTCATCAGTAATTCCTCGGATgtaagtgttt ... gcatttgcagGCTTTGGACAAGATTCGCTTCGAGTCCTTGACAGATAAGAGCAAACTAGAT
EST: gi|67716690|gb|BJ966950.1|BJ966950
EST:     ATAGCAACAAGGAGATTTTCTTGCGAGAACTCATCAGTAATTCCTCGGAT                         GCTTTGGACAAGATTCGCTTCGAGTCCTTGACAGATAAGAGCAAACTAGAT
genomic: ATAGCAACAAGGAGATTTTCTTGCGAGAACTCATCAGTAATTCCTCGGATgtaagtgttt ... gcatttgcagGCTTTGGACAAGATTCGCTTCGAGTCCTTGACAGATAAGAGCAAACTAGAT
EST: gi|18325603|gb|BJ157600.1|BJ157600
EST:     ATAGCAACAAGGAGATTTTCTTGCGAGAACTCATCAGTAATTCCTCGGAT                         GCTTTGGACAAGATTCGCTTCGAGTCCTTGACAGATAAGAGCAAACTAGAT
genomic: ATAGCAACAAGGAGATTTTCTTGCGAGAACTCATCAGTAATTCCTCGGATgtaagtgttt ... gcatttgcagGCTTTGGACAAGATTCGCTTCGAGTCCTTGACAGATAAGAGCAAACTAGAT
EST: gi|67575232|gb|BJ948056.1|BJ948056
EST:     ATAGCAACAAGGAGATTTTCTTGCGAGAACTCATCAGTAATTCCTCGGAT                         GCTTTGGACAAGATTCGCTTCGAGTCCTTGACAGATAANAGCAAACTAGAT
genomic: ATAGCAACAAGGAGATTTTCTTGCGAGAACTCATCAGTAATTCCTCGGATgtaagtgttt ... gcatttgcagGCTTTGGACAAGATTCGCTTCGAGTCCTTGACAGATAAGAGCAAACTAGAT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TTTCCAGGCGGAGATCAATCAATTGTTGAGTTTGATCATTAACACCTTCTATAGCAACAAGGAGATTTTCTTGCGAGAACTCATCAGTAATTCCTCGGATgtaagtgttttttcacccttgcttgtgtactgtttgtgtctcatcgtgtctctatttgtcatttgcggtggagttggcgaggccggcgtttcccgtagag

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