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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGTATCGACATCGAAGCCGGCGGGCGCAACAAGAAGACCAAGCGGACAGCCCCCAAGAGTGACAATGTCTACCTCAAGCTGCTCGTCAAGgtgagtgcgtgggatttggcattggatctatagcggttgcccgatttctcacgcattttcttttccattccctctctgtcag

Basic information

species Selaginella moellendorffii
transcript EFJ22685
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ22685 (Selaginella moellendorffii), 5'ss of exon 2
lower sequence: PP1S536_8V6.1 (Physcomitrella patens), 5'ss of exon 2
GGTATCGACATCGAAGCCGGCGGGCGCAACAAGAAGACCAAGCGGACAGCCCCCAAGAGTGACAATGTCTACCTCAAGCTGCTCGTCAAGgtgagtgcgtgggatttggcattggatctatagcggt-tgcccgatttctcac----gcattttcttttccattccctctctgtcag----------------------------------------------------------------------------------------------
||||| ||  |  | ||||| || |||||||||||||||||||| ||||| |||||||| |||||||| ||||| ||||| || || |||||     |   | |       |||  |  ||||  || |  |||| ||  | |      |  |   |||| |||     | | ||                                                                                                
GGTATAGATTTGAAGGCCGGGGGTCGCAACAAGAAGACCAAGCGTACAGCGCCCAAGAGCGACAATGTGTACCTGAAGCTTCTTGTGAAGgtactccccaagaagcattgcttgttttaatagttgtctatccgaatttactcttcgaaacctgagtttcaattagggttttctcgtggattgtttgactacactattgggcagtcaagttattttttcttttagttactttcatttcttttttgttgaatggtgtgattatttttcgcag

upper sequence: EFJ22685 (Selaginella moellendorffii), 5'ss of exon 2
lower sequence: PP1S536_8V6.2 (Physcomitrella patens), 5'ss of exon 1
----------GGTATCGACATCGAAGCCGGCGGGCGCAACAAGAAGACCAAGCGGACAGCCCCCAAGAGTGACAATGTCTACCTCAAGCTGCTCGTCAAGgtgagtgcgtgggatttggcattggatctatagcggt-tgcccgattt----ctcacgcattttcttttccattccctctctgtcag----------------------------------------------------------------------------------------------
          ||||| ||  |  | ||||| || |||||||||||||||||||| ||||| |||||||| |||||||| ||||| ||||| || || |||||     |   | |       |||  |  ||||  || |  |||| ||    ||     |  |   |||| |||     | | ||                                                                                                
CGGCGTGTAGGGTATAGATTTGAAGGCCGGGGGTCGCAACAAGAAGACCAAGCGTACAGCGCCCAAGAGCGACAATGTGTACCTGAAGCTTCTTGTGAAGgtactccccaagaagcattgcttgttttaatagttgtctatccgaatttactcttcgaaacctgagtttcaattagggttttctcgtggattgtttgactacactattgggcagtcaagttattttttcttttagttactttcatttcttttttgttgaatggtgtgattatttttcgcag

upper sequence: EFJ22685 (Selaginella moellendorffii), 5'ss of exon 2
lower sequence: PP1S45_191V6.1 (Physcomitrella patens), 5'ss of exon 2
GGTATCGACATCGAAGCCGGCGGGCGCAACAAGAAGACCAAGCGGACAGCCCCCAAGAGTGACAATGTCTACCTCAAGCTGCTCGTCAAGgtgagtgcgtgggatttggcattggatctatagcggttgcccgatttctcacgcattttcttttccattccctctctgtcag------------------------------------------------------------------------------------------
||||||||| |  | ||||| || |||||||||||||||||||| || || |||||||||| |||||| || || ||||| || || ||||||| |     | |    ||| |     | || | ||||           |||    ||  |     |    | |  |  |                                                                                           
GGTATCGACTTGAAGGCCGGGGGCCGCAACAAGAAGACCAAGCGCACCGCGCCCAAGAGTGGCAATGTTTATCTAAAGCTCCTTGTGAAGgtgattttaaagaa----gcacttcccatttatctgttgttttgcagaggacgtggatttctcggagtctgatttgagataagggtttccaacgtggtttggggtgatcgtgttactgattgggccagtgtttttcccctaaattttctaacgttataatgtctcctttcag

upper sequence: EFJ22685 (Selaginella moellendorffii), 5'ss of exon 2
lower sequence: PP1S304_9V6.1 (Physcomitrella patens), 5'ss of exon 2
GGTATCGACATCGAAGCCGGCGGGCGCAACAAGAAGACCAAGCGGACAGCCCCCAAGAGTGACAATGTCTACCTCAAGCTGCTCGTCAAGgtg--------agtgcgtgggatttggcattggatctatagcggttgcccgatttctcacgcattttcttttccat-tccctctctgtcag---------
||||||||  |  | ||||| || ||||||||||| |||||||| || || ||||||||  | ||||||||||| ||||| ||||| ||||||        | ||  |        || || | |||        |  |  ||||   | | |  ||    |  || |||   |||   |          
GGTATCGATTTGAAGGCCGGTGGCCGCAACAAGAAAACCAAGCGTACCGCTCCCAAGAGCCAGAATGTCTACCTGAAGCTTCTCGTTAAGgtgcacctcttaatgtttacagccgcgcctttgctcttcgtttcctctctcatttaagatgaaacttagggtatatatccacttctaggatgactgattg

upper sequence: EFJ22685 (Selaginella moellendorffii), 5'ss of exon 2
lower sequence: PP1S2_233V6.1 (Physcomitrella patens), 5'ss of exon 2
GGTATCGACATCGAAGCCGGCGGGCGCAACAAGAAGACCAAGCGGACAGCCCCCAAGAGTGACAATGTCTACCTCAAGCTGCTCGTCAAGgtgagtgcgtgggatttggcatt-----ggatctatag--cggttgcccgatttctcacgcatt------------ttcttttccattccctctctgtcag
||||||||  |  | ||||| || ||||||||||||||||| || ||||| |||||||| |  || || ||||| ||||| ||||| ||||||| |   |  | |   |||||     |  |||||      ||| |  |   |||     |                 ||  |    | ||| |||  | 
GGTATCGATTTGAAGGCCGGTGGTCGCAACAAGAAGACCAAACGTACAGCTCCCAAGAGCGGTAACGTATACCTTAAGCTTCTCGTGAAGgtgatttgatatgctcctgcattctcgcgtgtctatgttttagtttcttgtcatctggtaaaaagaaaggaagaaagagttcactggacactcgctggga-

upper sequence: EFJ22685 (Selaginella moellendorffii), 5'ss of exon 2
lower sequence: PP1S45_11V6.1 (Physcomitrella patens), 5'ss of exon 2
GGTATCGACATCGAAGCCGGCGGGCGCAACAAGAAGACCAAGCGGACAGCCCCCAAGAGTGACAATGTCTACCTCAAGCTGCTCGTCAAGgtgagtgcgtgggatttggcattggatctat---agcggttgcccgatttctcacgcattttcttttccatt--ccctctctgtcag--------------
||||||||| |  | ||||| || ||||||||||| |||||||| || || ||||||||  | ||||||||||| ||||| || || |||||  |    ||  |||  | ||||  |       ||   |  |  || |   |  |  ||    ||  |||    | |    | ||               
GGTATCGACTTGAAGGCCGGTGGTCGCAACAAGAAAACCAAGCGTACTGCTCCCAAGAGCCAGAATGTCTACCTTAAGCTTCTTGTGAAGgtatgcttctgt-attctgtattgacttcgcttgagatatatcttgagtcgacgtgtgttgctgttctcatgagtcgtgaaaggcaaactccagtgcgtaa

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|169052996|gb|FE460711.1|FE460711
EST:     AGCGGACAGCCCCCAAGAGTGACAATGTCTACCTCAAGCTGCTCGTCAAG                         CTCTACCGCTTCTTGGTCAGAAGGACCAACAGCAAATTCAACGCTGTGATC
genomic: AGCGGACAGCCCCCAAGAGTGACAATGTCTACCTCAAGCTGCTCGTCAAGgtgagtgcgt ... tctctgtcagCTCTACCGCTTCTTGGTCAGAAGGACCAACAGCAAATTCAACGCTGTGATC
EST: gi|169099479|gb|FE500510.1|FE500510
EST:     AGCGGACAGCCCCCAAGAGTGACAATGTCTACCTCAAGCTGCTCGTCAAG                         CTCTACCGCTTCTTGGTCAGAAGGACCAACAGCAAATTCAACGCTGTGATC
genomic: AGCGGACAGCCCCCAAGAGTGACAATGTCTACCTCAAGCTGCTCGTCAAGgtgagtgcgt ... tctctgtcagCTCTACCGCTTCTTGGTCAGAAGGACCAACAGCAAATTCAACGCTGTGATC
EST: gi|70671039|gb|DN839616.1|DN839616
EST:     AGCGGACAGCCCCCAAGAGTGACAATGTCTACCTCAAGCTGCTCGTCAAG                         CTCTACCGCTTCTTGGTCAGAAGGACCAACAGCAAATTCAACGCTGTGATC
genomic: AGCGGACAGCCCCCAAGAGTGACAATGTCTACCTCAAGCTGCTCGTCAAGgtgagtgcgt ... tctctgtcagCTCTACCGCTTCTTGGTCAGAAGGACCAACAGCAAATTCAACGCTGTGATC
EST: gi|169076248|gb|FE485694.1|FE485694
EST:     AGCGGACAGCCCCCAAGAGTGACAATGTCTACCTCAAGCTGCTCGTCAAG                         CTCTACCGGTTCTTGGTCAGAAGGACCAACAGCAAATTCAACGCTGTGATC
genomic: AGCGGACAGCCCCCAAGAGTGACAATGTCTACCTCAAGCTGCTCGTCAAGgtgagtgcgt ... tctctgtcagCTCTACCGCTTCTTGGTCAGAAGGACCAACAGCAAATTCAACGCTGTGATC
EST: gi|169099478|gb|FE500509.1|FE500509
EST:     AGCGGACAGCCCCCAAGAGTGACAATGTCTACCTCAAGCTGCTCGTCAAG                         CTCTACCGCTTCTTGGTCAGAAGGACCAACAGCAAATTCAACGCTGTGATC
genomic: AGCGGACAGCCCCCAAGAGTGACAATGTCTACCTCAAGCTGCTCGTCAAGgtgagtgcgt ... tctctgtcagCTCTACCGCTTCTTGGTCAGAAGGACCAACAGCAAATTCAACGCTGTGATC
EST: gi|169035084|gb|FE445920.1|FE445920
EST:     AGCGGACAGCCCCCAAGAGTGACAATGTCTACCTCAAGCTGCTCGTCAAG                         CTCTACCGGTTCTTGGTCAGAAGGACCAACAGCAAATTCAACGCTGTGATC
genomic: AGCGGACAGCCCCCAAGAGTGACAATGTCTACCTCAAGCTGCTCGTCAAGgtgagtgcgt ... tctctgtcagCTCTACCGCTTCTTGGTCAGAAGGACCAACAGCAAATTCAACGCTGTGATC

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 1 RNA-Seqlibrary.


Block sizes: 35 (upstream exon), 35 (downstream exon)
Score: 53

GGTATCGACATCGAAGCCGGCGGGCGCAACAAGAAGACCAAGCGGACAGCCCCCAAGAGTGACAATGTCTACCTCAAGCTGCTCGTCAAGgtgagtgcgt ... tctctgtcagCTCTACCGCTTCTTGGTCAGAAGGACCAACAGCAAATTCAACGCTGTGATCCTCAAGCGGCTCTTCATGAGCAAAACCAACCAGCCGCCAGTGTCCCTCT




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGTATCGACATCGAAGCCGGCGGGCGCAACAAGAAGACCAAGCGGACAGCCCCCAAGAGTGACAATGTCTACCTCAAGCTGCTCGTCAAGgtgagtgcgtgggatttggcattggatctatagcggttgcccgatttctcacgcattttcttttccattccctctctgtcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGCT