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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGATACTGCTGGCCAGGAGCGCTTCCGGAGTTTGATTCCCAGCTACATACGGGATTCGTCCGTGGCAGTCGTCGTGTACGATGTAGCGAgtaagttgttgcttcttgcgtttctcgatcatacaaaacttcgcttccag

Basic information

species Selaginella moellendorffii
transcript EFJ30542
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ30542 (Selaginella moellendorffii), 5'ss of exon 3
lower sequence: PP1S39_147V6.1 (Physcomitrella patens), 5'ss of exon 5
GGATACTGCTGGCCAGGAGCGCTTCCGGAGTTTGATTCCCAGCTACATACGGGATTCGTCCGTGGCAGTCGTCGTGTACGATGTAGCGAgtaagttgttgcttc-ttgcgtttctcgatcatacaa-aacttcgcttccag------------------------------------------------
||| |||||||| |||||| | ||  |||||||||||||||||||||| |||||||||||||||||||| || || || |||||  | |||||||  ||| ||  ||   || | | |    ||     |||  |                                                      
GGACACTGCTGGACAGGAGAGGTTTAGGAGTTTGATTCCCAGCTACATCCGGGATTCGTCCGTGGCAGTGGTTGTCTATGATGTTTCCAgtaagtatttgtttgattttcttacccaagagcactgtgtctttacacttgagttgttgcgtaagatttgttagaaggatggcctctactggtgtatcaa

upper sequence: EFJ30542 (Selaginella moellendorffii), 5'ss of exon 3
lower sequence: PP1S346_29V6.1 (Physcomitrella patens), 5'ss of exon 4
GGATACTGCTGGCCAGGAGCGCTTCCGGAGTTTGATTCCCAGCTACATACGGGATTCGTCCGTGGCAGTCGTCGTGTACGATGTAGCGAgtaagttgttgcttcttgcg----------tttctcgatcatacaaaacttcgctt---ccag-------------------------------------
|||||| ||||| |||||| | ||| ||||||| ||||| || ||||| |||||||||||||||||||| || |||||||||||  | |||||||   |  || |  |           ||| |   ||| |||    | || ||    |||                                     
GGATACCGCTGGACAGGAGAGGTTCAGGAGTTTAATTCCTAGTTACATTCGGGATTCGTCCGTGGCAGTGGTTGTGTACGATGTTTCAAgtaagtacatttttgtgacaaaagaggaattttgttcctcacacagttgtacggttggctcagtattagtacattaattgtttcactgatgtaacacggg

upper sequence: EFJ30542 (Selaginella moellendorffii), 5'ss of exon 3
lower sequence: PP1S2_143V6.1 (Physcomitrella patens), 5'ss of exon 5
GGATACTGCTGGCCAGGAGCGCTTCCGGAGTTTGATTCCCAGCTACATACGGGATTCGTCCGTGGCAGTCGTCGTGTACGATGTAGCGAgtaagttgttgct----tcttgcgtttctcgatcatacaaaacttcgcttccag---------------------------------------
||| || ||||| || ||||| ||| ||||||||||||| |||||||| ||||| |||||||||||||| || ||||| |||||  ||||| |||  ||| |      || |  |    || |||  | | || | |    ||                                       
GGACACAGCTGGACAAGAGCGGTTCAGGAGTTTGATTCCTAGCTACATTCGGGACTCGTCCGTGGCAGTGGTTGTGTATGATgtttcgagtgagtatttgttgaatcttttcaatgaaagagcattaacacctgcacaaaaagttgtcaaggtttgcatctgtaaaaatttttccatcattg

upper sequence: EFJ30542 (Selaginella moellendorffii), 5'ss of exon 3
lower sequence: PP1S456_9V6.1 (Physcomitrella patens), 5'ss of exon 4
GGATACTGCTGGCCAGGAGCGCTTCCGGAGTTTGATTCCCAGCTACATACGGGATTCGTCCGTGGCAGTCGTCGTGTACGATGTAGCGAgtaagttgttgcttcttgcgtt--------tctcgatcat-acaaaacttcgcttccag-----------------------------------------
||| || ||||| || ||| | ||| ||||||| |||||||||||||| || || ||||| |||||||| || || ||||||||  |||||||||   |   |   || ||        | ||| || | ||  | ||  |||                                              
GGACACAGCTGGACAAGAGAGGTTCAGGAGTTTAATTCCCAGCTACATTCGAGACTCGTCTGTGGCAGTAGTTGTTTACGATGTTTCGAgtaagtatatatataaggcattgtaaggagtttcgttcttcacctagctgtgctgtggtcactgtattcgcgtgttaatagttgcattgacataacaaga

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|169047767|gb|FE454623.1|FE454623
EST:     CAGCTACATACGGGATTCGTCCGTGGCAGTCGTCGTGTACGATGTAGCGA                         ATCGCCAGTCGTTTCTAAACACGGCCAGATGGGTGGAAGAAGTCCGCACGG
genomic: CAGCTACATACGGGATTCGTCCGTGGCAGTCGTCGTGTACGATGTAGCGAgtaagttgtt ... tcgcttccagATCGCCAGTCGTTTCTAAACACGGCCAGATGGGTGGAAGAAGTCCGCACGG
EST: gi|169042136|gb|FE454179.1|FE454179
EST:     CAGCTACATACGGGATTCGTCCGTGGCAGTCGTCGTGTACGATGTAGCGA                         ATCGCCAGTCGTTTCTAAACACGGCCAGATGGGTGGAAGAAGTCCGCACGG
genomic: CAGCTACATACGGGATTCGTCCGTGGCAGTCGTCGTGTACGATGTAGCGAgtaagttgtt ... tcgcttccagATCGCCAGTCGTTTCTAAACACGGCCAGATGGGTGGAAGAAGTCCGCACGG
EST: gi|70669602|gb|DN838179.1|DN838179
EST:     CAGCTACATACGGGATTCGTCCGTGGCAGTCGTCGTGTACGATGTAGCGA                         ATCGCCAGTCGTTTCTAAACACGGCCAGATGGGTGGAAGAAGTCCGCACGG
genomic: CAGCTACATACGGGATTCGTCCGTGGCAGTCGTCGTGTACGATGTAGCGAgtaagttgtt ... tcgcttccagATCGCCAGTCGTTTCTAAACACGGCCAGATGGGTGGAAGAAGTCCGCACGG
EST: gi|169074100|gb|FE481747.1|FE481747
EST:     CAGCTACATACGGGATTCGTCCGTGGCAGTCGTCGTGTACGATGTAGCGA                         ATCGCCAGTCGTTTCTAAACACGGCCAGATGGGTGGAAGAAGTCCGCACGG
genomic: CAGCTACATACGGGATTCGTCCGTGGCAGTCGTCGTGTACGATGTAGCGAgtaagttgtt ... tcgcttccagATCGCCAGTCGTTTCTAAACACGGCCAGATGGGTGGAAGAAGTCCGCACGG
EST: gi|169074099|gb|FE481746.1|FE481746
EST:     CAGCTACATACGGGATTCGTCCGTGGCAGTCGTCGTGTACGATGTAGCGA                         ATCGCCAGTCGTTTCTAAACACGGCCAGATGGGTGGAAGAAGTCCGCACGG
genomic: CAGCTACATACGGGATTCGTCCGTGGCAGTCGTCGTGTACGATGTAGCGAgtaagttgtt ... tcgcttccagATCGCCAGTCGTTTCTAAACACGGCCAGATGGGTGGAAGAAGTCCGCACGG
EST: gi|169054140|gb|FE462375.1|FE462375
EST:     CAGCTACATACGGGATTCGTCCGTGGCAGTCGTCGTGTACGATGTAGCGA                         ATCGCCAGTCGTTTCTAAACACGGCCAGATGGGTGGAAGAAGTCCGCACGG
genomic: CAGCTACATACGGGATTCGTCCGTGGCAGTCGTCGTGTACGATGTAGCGAgtaagttgtt ... tcgcttccagATCGCCAGTCGTTTCTAAACACGGCCAGATGGGTGGAAGAAGTCCGCACGG
EST: gi|169036632|gb|FE446556.1|FE446556
EST:     CAGCTACATACGGGATTCGTCCGTGGCAGTCGTCGTGTACGATGTAGCGA                         ATCGCCAGTCGTTTCTAAACACGGCCAGATGGGTGGAAGAAGTCCGCACGG
genomic: CAGCTACATACGGGATTCGTCCGTGGCAGTCGTCGTGTACGATGTAGCGAgtaagttgtt ... tcgcttccagATCGCCAGTCGTTTCTAAACACGGCCAGATGGGTGGAAGAAGTCCGCACGG

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: 34 (upstream exon), 35 (downstream exon)
Score: 49

GGATACTGCTGGCCAGGAGCGCTTCCGGAGTTTGATTCCCAGCTACATACGGGATTCGTCCGTGGCAGTCGTCGTGTACGATGTAGCGAgtaagttgtt ... tcgcttccagATCGCCAGTCGTTTCTAAACACGGCCAGATGGGTGGAAGAAGTCCGCACGGAGCGGGGTAGCGATGTCATCATCGTTCTCGTCGGGAACAAGACGGATTT




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