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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CACAGGCCATGCTAACGAGAAGAACTTTGTAGGCTTGACAGTTAACAGCGAGTACATTGCGTGCGGTAGTGAAACGAACGAAGTCGTGGTGTATCACAAAgtaagtccatttgattgattctagagaaaaagagaatcaatctgaggcttttgtttgtttgttgcgagcag

Basic information

species Selaginella moellendorffii
transcript EFJ20512
intron # 12
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ20512 (Selaginella moellendorffii), 5'ss of exon 12
lower sequence: GLYMA14G05430.1 (Glycine max), 5'ss of exon 12
CACAGGCCATGCTAACGAGAAGAACTTTGTAGGCTTGACAGTTAACAGCGAGTACATTGCGTGCGGTAGTGAAACGAACGAAGTCGTGGTGTATCACAAAgtaagtccatttgattgat-tctagagaaaaagagaatcaatct--gaggcttttg----tttgtttgttgcgagcag
|| ||||||||| || ||||| |||||||| ||| | ||||| | ||| || ||||||||||| || |||||||| || |||||| | ||||| ||||| ||  ||   ||| | | || | | |       | | ||    ||   | | |  ||    ||    ||       |||
CAAAGGCCATGCAAATGAGAAAAACTTTGTTGGCCTTACAGTAAGCAGTGAATACATTGCGTGTGGCAGTGAAACAAATGAAGTCTTTGTGTACCACAAGgtttgtggttttcaatcatgtgtcgttttcttgtgcatttgccttttatggtactgaggattcaactgcccttttcag

upper sequence: EFJ20512 (Selaginella moellendorffii), 5'ss of exon 12
lower sequence: PP1S135_17V6.1 (Physcomitrella patens), 5'ss of exon 12
CACAGGCCATGCTAACGAGAAGAACTTTGTAGGCTTGACAGTTAACAGCGAGTACATTGCGTGCGGTAGTGAAACGAACGAAGTCGTGGTGTATCACAAAgtaa-gtccatttgattgattctagagaaaaag-agaatcaatctgaggcttt-tgtttgtttgttgcgagcag--------------------------
 | ||| ||  | || || ||||||||||| || ||||| || |||||||| ||||| || || || |||||||||||||| ||  | |||||||| || |||  ||||   |  |   |||| |    ||   |||||  |  ||| | ||  ||||| || |      |                             
GAAAGGACACACCAATGAAAAGAACTTTGTTGGATTGACTGTCAACAGCGAATACATCGCCTGTGGCAGTGAAACGAACGAGGTGTTTGTGTATCATAAGgtattgtcctgattgtatgttctggttttaatttagaatttacatgacgtttcgtgttttttagaactcggttttgtatacatgaggcaaagtgaaattt
















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|169111049|gb|FE512470.1|FE512470
EST:     AGTACATTGCGTGCGGTAGTGAAACGAACGAAGTCGTGGTGTATCACAAA                         GAAGTTCCCAAGCCAGCAGCAAGGCACAGATTCACAAACCATGACTCGGAG
genomic: AGTACATTGCGTGCGGTAGTGAAACGAACGAAGTCGTGGTGTATCACAAAgtaagtccat ... ttgcgagcagGAAGTTCCCAAGCCAGCAGCAAGGCACAGATTCACAAACCATGACTCGGAG
EST: gi|169076926|gb|FE485306.1|FE485306
EST:     AGTACATTGCGTGCGGTAGTGAAACGAACGAAGTCGTGGTGTATCACAAA                         GAAGTTCCCAAGCCAGCAGCAAGGCACAGATTCACAAACCATGACTCGGAG
genomic: AGTACATTGCGTGCGGTAGTGAAACGAACGAAGTCGTGGTGTATCACAAAgtaagtccat ... ttgcgagcagGAAGTTCCCAAGCCAGCAGCAAGGCACAGATTCACAAACCATGACTCGGAG
EST: gi|70669297|gb|DN837874.1|DN837874
EST:     AGTACATTGCGTGCGGTAGTGAAACGAACGAAGTCGTGGTGTATCACAAA                         GAAGTTCCCAAGCCAGCAGCAAGGCACAGATTCACAAACCATGACTCGGAG
genomic: AGTACATTGCGTGCGGTAGTGAAACGAACGAAGTCGTGGTGTATCACAAAgtaagtccat ... ttgcgagcagGAAGTTCCCAAGCCAGCAGCAAGGCACAGATTCACAAACCATGACTCGGAG
EST: gi|169064441|gb|FE472108.1|FE472108
EST:     AGTACATTGCGTGCGGTAGTGAAACGAACGAAGTCGTGGTGTATCACAAA                         GAAGTTCCCAAGCCAGCAGCAAGGCACAGATTCACAAACCATGACTCGGAG
genomic: AGTACATTGCGTGCGGTAGTGAAACGAACGAAGTCGTGGTGTATCACAAAgtaagtccat ... ttgcgagcagGAAGTTCCCAAGCCAGCAGCAAGGCACAGATTCACAAACCATGACTCGGAG
EST: gi|169076925|gb|FE485305.1|FE485305
EST:     AGTACATTGCGTGCGGTAGTGAAACGAACGAAGTCGTGGTGTATCACAAA                         GAAGTTCCCAAGCCAGCAGCAAGGCACAGATTCACAAACCATGACTCGGAG
genomic: AGTACATTGCGTGCGGTAGTGAAACGAACGAAGTCGTGGTGTATCACAAAgtaagtccat ... 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

CACAGGCCATGCTAACGAGAAGAACTTTGTAGGCTTGACAGTTAACAGCGAGTACATTGCGTGCGGTAGTGAAACGAACGAAGTCGTGGTGTATCACAAAgtaagtccat ... ttgcgagcagGAAGTTCCCAAGCCAGCAGCAAGGCACAGATTCACAAACCATGACTCGGAGGAGAGCGACGACGATGTGTTCCACTTCATCAGTGCTGTGTGCTGGAAGA




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