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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CACAGGCCATGCTAACGAGAAGAACTTTGTAGGCTTGACAGTTAACAGCGAGTACATTGCGTGCGGTAGTGAAACGAACGAAGTCGTGGTGTATCACAAGgtaagtccatttgattgattttagagaaaaagagaatcaatctgaggcttttgtttgtttgttgcgagcag

Basic information

species Selaginella moellendorffii
transcript EFJ28584
intron # 12
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ28584 (Selaginella moellendorffii), 5'ss of exon 12
lower sequence: GLYMA14G05430.1 (Glycine max), 5'ss of exon 12
CACAGGCCATGCTAACGAGAAGAACTTTGTAGGCTTGACAGTTAACAGCGAGTACATTGCGTGCGGTAGTGAAACGAACGAAGTCGTGGTGTATCACAAGgtaagtccatttgattgat-tttagagaaaaagagaatcaatct--gaggcttttg----tttgtttgttgcgagcag
|| ||||||||| || ||||| |||||||| ||| | ||||| | ||| || ||||||||||| || |||||||| || |||||| | ||||| ||||||||  ||   ||| | | || | | |       | | ||    ||   | | |  ||    ||    ||       |||
CAAAGGCCATGCAAATGAGAAAAACTTTGTTGGCCTTACAGTAAGCAGTGAATACATTGCGTGTGGCAGTGAAACAAATGAAGTCTTTGTGTACCACAAGgtttgtggttttcaatcatgtgtcgttttcttgtgcatttgccttttatggtactgaggattcaactgcccttttcag

upper sequence: EFJ28584 (Selaginella moellendorffii), 5'ss of exon 12
lower sequence: Vv10s0523g00030.t01 (Vitis vinifera), 5'ss of exon 12
CACAGGCCATGCTAACGAGAAGAACTTTGTAGGCTTGACAGTTAACAGCGAGTACATTGCGTGCGGTAGTGAAACGAACGAAGTCGTGGTGTATCACAAGgtaag-------tccatttgattgattttagagaaaaaga---gaatcaatctgaggcttttgtttgtttgttgcgagcag
 | ||| ||| | || |||||||| ||||| ||  | ||||| |||||||| |||||||| || || |||||||| ||||||||  | | |||||||||||| |        | ||      |    ||||  |   ||     ||| ||| | |   || ||||   |||  |       
TAGAGGGCATTCAAATGAGAAGAATTTTGTGGGTCTCACAGTAAACAGCGAATACATTGCCTGTGGCAGTGAAACAAACGAAGTGTTCGCGTATCACAAGgttacaaaatacttcaagaagctagcattaggcatctagtcccaaattaatttaatttttgtgttcacttgcag-------

upper sequence: EFJ28584 (Selaginella moellendorffii), 5'ss of exon 12
lower sequence: PP1S135_17V6.1 (Physcomitrella patens), 5'ss of exon 12
CACAGGCCATGCTAACGAGAAGAACTTTGTAGGCTTGACAGTTAACAGCGAGTACATTGCGTGCGGTAGTGAAACGAACGAAGTCGTGGTGTATCACAAGgta--agtccatttgattgattttagagaaaaagagaatcaatctgaggcttt-tgtttgtttgttgcgagcag--------------------------
 | ||| ||  | || || ||||||||||| || ||||| || |||||||| ||||| || || || |||||||||||||| ||  | |||||||| ||||||     |   |||  || | |      ||   |||||  |  ||| | ||  ||||| || |      |                             
GAAAGGACACACCAATGAAAAGAACTTTGTTGGATTGACTGTCAACAGCGAATACATCGCCTGTGGCAGTGAAACGAACGAGGTGTTTGTGTATCATAAGgtattgtcctgattgtatgttctggttttaatttagaatttacatgacgtttcgtgttttttagaactcggttttgtatacatgaggcaaagtgaaattt

upper sequence: EFJ28584 (Selaginella moellendorffii), 5'ss of exon 12
lower sequence: PP1S81_234V6.1 (Physcomitrella patens), 5'ss of exon 11
CACAGGCCATGCTAACGAGAAGAACTTTGTAGGCTTGACAGTTAACAGCGAGTACATTGCGTGCGGTAGTGAAACGAACGAAGTCGTGGTGTATCACAAGgtaa-gtccatttgattgattttagagaaaaagagaatcaatctgaggcttttg--tttgtttgttgcgagcag---------------------------
 | ||| ||  | || |||||||||||||| ||  |||| || ||||| || ||  |||| |||||||||||| ||||||| ||| | |||||||| ||||||  | |         ||  |||    |        ||    | |  |||      || ||  |      |||                           
GAGAGGACACACGAATGAGAAGAACTTTGTGGGACTGACTGTCAACAGTGAATATGTTGCTTGCGGTAGTGAATCGAACGAGGTCTTTGTGTATCATAAGgtattggctggccctccgaacttatctcatgcatttgtctgcttaacacttccaacattattcatca-attcagtcacctgactctttcagggcttatgtg

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|169083268|gb|FE491884.1|FE491884
EST:     AGTACATTGCGTGCGGTAGTGAAACGAACGAAGTCGTGGTGTATCACAAG                         GAAGTTCCCAAGCCAGCAGCAAGGCACAGATTCACAAACCATGACTCGGAG
genomic: AGTACATTGCGTGCGGTAGTGAAACGAACGAAGTCGTGGTGTATCACAAGgtaagtccat ... ttgcgagcagGAAGTTCCCAAGCCAGCAGCAAGGCACAGATTCACAAACCATGACTCGGAG
EST: gi|169077264|gb|FE485150.1|FE485150
EST:     AGTACATTGCGTGCGGTAGTGAAACGAACGAAGTCGTGGTGTATCACAAG                         GAAGTTCCCAAGCCAGCAGCAAGGCACAGATTCACAAACCATGACTCGGAG
genomic: AGTACATTGCGTGCGGTAGTGAAACGAACGAAGTCGTGGTGTATCACAAGgtaagtccat ... ttgcgagcagGAAGTTCCCAAGCCAGCAGCAAGGCACAGATTCACAAACCATGACTCGGAG

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: 25 (upstream exon), 27 (downstream exon)
Score: 5

CACAGGCCATGCTAACGAGAAGAACTTTGTAGGCTTGACAGTTAACAGCGAGTACATTGCGTGCGGTAGTGAAACGAACGAAGTCGTGGTGTATCACAAGgtaagtccat ... ttgcgagcagGAAGTTCCCAAGCCAGCAGCAAGGCACAGATTCACAAACCATGACTCGGAGGAGAGCGACGACGATGTGTTCCACTTCATCAGTGCTGTGTGCTGGAAGA




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