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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CGAGAAGAAGCTCTACCTGGTCTTTGAGTACCTGGACTTGGATCTAAAGAAGCATATGGACAACAGCCCAGACTTCGCCAAGAGTCCACGAATGATTAAAgtatggtgagcccccaaaatctctccagcattcttgtgtggtgcttgtccttcactcacactttttttctttttttttggtttcctttctcgcag

Basic information

species Selaginella moellendorffii
transcript EFJ15022
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ37669 (Selaginella moellendorffii), 5'ss of exon 3
lower sequence: GLYMA15G14390.1 (Glycine max), 5'ss of exon 3
CGAGAAGAAGCTCTACCTGGTCTTTGAGTACCTGGACTTGGATCTAAAGAAGCATATGGACAACAGCCCAGACTTCGCCAAGAGTCCACGAATGATTAAAgtatggtgagcccccaaaatctctccagcattcttgtgtggtgcttgtc-cttcactcacactttttttctttttttttggtttcctttctcgcag-------
 ||||||    | || ||||| |||||||| |||||||||||||||||||| ||||||||       ||||| || |  ||   ||||||     | || ||   |||| |        ||| | |  |    || |    |  ||||  ||| | | | | || |     |   |       |   |   |  ||       
TGAGAAGCGATTGTATCTGGTTTTTGAGTATCTGGACTTGGATCTAAAGAAACATATGGATTCATCTCCAGAGTTTGTGAAAGATCCACGGCAAGTAAAGgtg-agtgacctgtggttttcttttcctcgga-ttataca-tatttgtaacttgagttatagttatgggagtgaataagaaacttaatctgccaagcaaatat

upper sequence: EFJ37669 (Selaginella moellendorffii), 5'ss of exon 3
lower sequence: GLYMA05G25320.1 (Glycine max), 5'ss of exon 2
CGAGAAGAAGCTCTACCTGGTCTTTGAGTACCTGGACTTGGATCTAAAGAAGCATATGGACAACAGCCCAGACTTCGCCAAGAGTCCACGAATGATTAAAgtatggtgagcccccaaaatctctccagcattcttgtgtggtgcttgtccttcactcacactttttttctttttttttggtttcctttctcgcag----------
 |||||||   | || ||||| ||||||||||| ||||| |||||||||||||| |||||       ||||| || || ||   |||||||    | ||||| || |||     |    | |||      |  ||||    |  |   | ||   | ||     || |  || |    |    |        |||          
TGAGAAGAGTTTGTATCTGGTTTTTGAGTACCTTGACTTAGATCTAAAGAAGCACATGGATTCATCTCCAGAATTTGCAAAAGATCCACGACAAGTAAAAgtgtg-tgacttatcttgttttcttt----tctttgtagatttttgagctttttgtaactgaagttatagttataagagagagcaagaaatacagcgtagccatc

upper sequence: EFJ37669 (Selaginella moellendorffii), 5'ss of exon 3
lower sequence: GLYMA08G08330.1 (Glycine max), 5'ss of exon 3
CGAGAAGAAGCTCTACCTGGTCTTTGAGTACCTGGACTTGGATCTAAAGAAGCATATGGACAACAGCCCAGACTTCGCCAAGAGTCCACGAATGATTAAAgtatggtgagcccccaaaatctctccagcattcttgtgtggtgcttgtccttcactcacactttttttctttttttttggtttcctttctcgcag----------
 |||||||   | || ||||| ||||||||||| ||||| |||||||||||||| |||||       ||||| || || ||   |||||||    | ||||| || |||     |    | ||| | | | | || || | |  ||||    || | | | || |             |   | || | | ||            
TGAGAAGAGTTTGTATCTGGTTTTTGAGTACCTTGACTTAGATCTAAAGAAGCACATGGATTCATCTCCAGAATTTGCAAAAGATCCACGACAACTAAAAgtgtg-tgacttatcttcttttcttc-gtagttttttgagctttttgtaa--cagttataattataagagagagcaa-gaaatactgtgtagccatcaaatgcct

upper sequence: EFJ37669 (Selaginella moellendorffii), 5'ss of exon 3
lower sequence: Vv15s0045g00310.t01 (Vitis vinifera), 5'ss of exon 4
CGAGAAGAAGCTCTACCTGGTCTTTGAGTACCTGGACTTGGATCTAAAGAAGCATATGGACAACAGCCCAGACTTCGCCAAGAGTCCACGAATGATTAAAgt-atggtgagcccccaaaatctctccagcattcttgtgtggtgcttgtccttcactcacactttttttctttttttt--tggtttcctttctcgcag-----
 ||||||  | | || || || |||||||| |||||||||||||| |||||||| |||||       || || || |||||   |  |||  |||| || || |   ||    |     |  | |  ||  ||| ||  |  |   | |  |      |   || || | ||  | |   || ||     | |          
TGAGAAGCGGTTATATCTAGTTTTTGAGTATCTGGACTTGGATCTGAAGAAGCACATGGATTCATCTCCGGATTTTGCCAAAGATTTACGTCTGATAAAGgtgactctgcaatcttctgacttttgaag-gttcctgcattata--tattttgggactatttttcttgttttaatatgaatgattaagactttaattatcctc

upper sequence: EFJ37669 (Selaginella moellendorffii), 5'ss of exon 3
lower sequence: PP1S25_198V6.3 (Physcomitrella patens), 5'ss of exon 5
CGAGAAGAAGCTCTACCTGGTCTTTGAGTACCTGGACTTGGATCTAAAGAAGCATATGGACAACAGCCCAGACTTCGCCAAGAGTCCACGAATGATTAAAgtatggtgagcccccaaaatctctccagcattcttgtgtggtgcttgtccttcactc-acactt----tttttctttttttttggtttcctttctcgcag--------------------------------------------------------------
 |||||     | ||| |||| ||||| ||||||||| | || ||||||||||||||||||| | |||| ||| | |||||    |||||  |||| || |||||   |  |         |   | |  |   ||| |   |||      |||  | | || |    || |  ||   | ||||  | ||  |||                                                                  
TGAGAAACGATTGTACTTGGTTTTTGAATACCTGGACCTCGACCTAAAGAAGCATATGGACACCTGCCCGGACCTTGCCAAAGACCCACGCTTGATCAAGgtatgtctaatcttttctgcattagc-gtgtatgtgttttaggctaaaagctcaaactatacgtcacattataattcggtattggaatactacctcaagatttatagcctctttgggttcatttgtgcctctggttaacagtgagtaaagctttgcgtgcag

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|70670191|gb|DN838768.1|DN838768
EST:     AGCATATGGACAACAGCCCAGACTTCGCCGAGAGTCCACGAATGATTAAA                         ACCTTTCTATATCAGATGATCCGAGGACTCGCGTACTGCCACTCGCACAGG
genomic: AGCATATGGACAACAGCCCAGACTTCGCCAAGAGTCCACGAATGATTAAAgtatggtgag ... tttctcgcagACCTTTCTATATCAGATGATCCGAGGACTCGCGTACTGCCACTCGCACAGG
EST: gi|169019993|gb|FE430850.1|FE430850
EST:     AGCATATGGACAACAGCCCAGACTTCGCCAAGAGTCCACGAATGATTAAA                         ACCTTTCTATATCAGATGATCCGAGGACTCGCGTACTGCCACTCGCACAGG
genomic: AGCATATGGACAACAGCCCAGACTTCGCCAAGAGTCCACGAATGATTAAAgtatggtgag ... tttctcgcagACCTTTCTATATCAGATGATCCGAGGACTCGCGTACTGCCACTCGCACAGG
EST: gi|169019992|gb|FE430849.1|FE430849
EST:     AGCATATGGACAACAGCCCAGACTTCGCCAAGAGTCCACGAATGATTAAA                         ACCTTTCTATATCAGATGATCCGAGGACTCGCGTACTGCCACTCGCACAGG
genomic: AGCATATGGACAACAGCCCAGACTTCGCCAAGAGTCCACGAATGATTAAAgtatggtgag ... tttctcgcagACCTTTCTATATCAGATGATCCGAGGACTCGCGTACTGCCACTCGCACAGG

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: 30 (upstream exon), 31 (downstream exon)
Score: 18

CGAGAAGAAGCTCTACCTGGTCTTTGAGTACCTGGACTTGGATCTAAAGAAGCATATGGACAACAGCCCAGACTTCGCCAAGAGTCCACGAATGATTAAAgtatggtgag ... tttctcgcagACCTTTCTATATCAGATGATCCGAGGACTCGCGTACTGCCACTCGCACAGGGTTCTTCACCGCGACTTGAAGCCACAAAATCTACTCATCGATCGTCGGA




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