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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTGGTGTCGAGTGCTATCGTCGACAAGTACATTGGTGAGAGTGCTCGGCTAATCCGTGAAATGTTCGGCTATGCTCGTGATCACCAAgtatgtcgcgctagcttatcaaaacattgacatttttcttttcctttgcag

Basic information

species Selaginella moellendorffii
transcript EFJ28962
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ28962 (Selaginella moellendorffii), 5'ss of exon 6
lower sequence: LOC_Os02g10640.1 (Oryza sativa), 5'ss of exon 6
GTGGTGTCGAGTGCTATCGTCGACAAGTACATTGGTGAGAGTGCTCGGCTAATCCGTGAAATGTTCGGCTATGCTCGTGATCACCAAgtatgtcgcgctagct---tatcaaaacattgacatttttcttttcctttgcag----------------------------------------------
 | || || ||||||||  | |||||||||||||| |||||||| ||  | ||  | |||||||| |||||||| |||||||| |||||| |||    |  ||   ||        | || |  |   |   |||     |                                              
ATTGTTTCAAGTGCTATAATTGACAAGTACATTGGAGAGAGTGCCCGCTTGATTAGGGAAATGTTTGGCTATGCACGTGATCATCAAgtaagtcttaatctctctctacttttgtctggaaagctagttggacctaaattggcatcctcatttctgcaagacctactctgacatttacatgatctaa

upper sequence: EFJ28962 (Selaginella moellendorffii), 5'ss of exon 6
lower sequence: GRMZM2G171604_T01 (Zea mays), 5'ss of exon 6
GTGGTGTCGAGTGCTATCGTCGACAAGTACATTGGTGAGAGTGCTCGGCTAATCCGTGAAATGTTCGGCTATGCTCGTGATCACCAAgta--tgtcgcgctagcttatcaaaacattgacatttttcttttcctttgcag-----------------------------------------------
 | || || || |||||  | ||||| |||||||| || ||||||||  | ||  | |||||||| |||||||| |||||||||||||||  | ||    |   |  |  |  ||||   | ||        | |    |                                               
ATTGTTTCAAGCGCTATTATTGACAAATACATTGGAGAAAGTGCTCGTTTGATTAGAGAAATGTTTGGCTATGCACGTGATCACCAAgtaagtatcagaatttttatttcattcatttttaattcctgcaaacctaatgggtctgaactgatctttcatttatctgaaagacactaccatggtatgt

upper sequence: EFJ28962 (Selaginella moellendorffii), 5'ss of exon 6
lower sequence: GRMZM2G074037_T01 (Zea mays), 5'ss of exon 6
GTGGTGTCGAGTGCTATCGTCGACAAGTACATTGGTGAGAGTGCTCGGCTAATCCGTGAAATGTTCGGCTATGCTCGTGATCACCAAgta-----tgtcgcgctagcttatcaaaacattgacatttttcttttcctttgcag--------------------------------------------
|||||||| ||||||||| | || || ||||||||||| ||||| ||  |||| |||||||||||   |||||| ||||| || || |||     |||     |   |||||     ||  | |  |  || |||   |  |                                             
GTGGTGTCAAGTGCTATCATTGATAAATACATTGGTGAAAGTGCACGCTTAATTCGTGAAATGTTTAACTATGCACGTGAGCATCAGgtaagctttgttttattttgttatctgtgtatgtatacctagctattctgatttatttatttatttatataaagcactagttttcacggttttcactgtc

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|169035134|gb|FE444917.1|FE444917
EST:     AGAGTGCTCGGCTAATCCGTGAAATGTTCGGCTATGCTCGTGATCACCAA                         CCGTGCATCATTTTCATGGATGAAATCGACGCTATAGGCGGACGAAGGTTC
genomic: AGAGTGCTCGGCTAATCCGTGAAATGTTCGGCTATGCTCGTGATCACCAAgtatgtcgcg ... tcctttgcagCCGTGCATCATTTTCATGGATGAAATCGACGCTATAGGCGGACGGAGGTTC
EST: gi|169035135|gb|FE444918.1|FE444918
EST:     AGAGTGCTCGGCTAATCCGTGAAATGTTCGGCTATGCTCGTGATCACCAA                         CCGTGCATCATTTTCATGGATGAAATCGACGCTATAGGCGGACGAAGGTTC
genomic: AGAGTGCTCGGCTAATCCGTGAAATGTTCGGCTATGCTCGTGATCACCAAgtatgtcgcg ... tcctttgcagCCGTGCATCATTTTCATGGATGAAATCGACGCTATAGGCGGACGGAGGTTC
EST: gi|169071646|gb|FE477088.1|FE477088
EST:     AGAGTGCTCGGCTAATCCGTGAAATGTTCGGCTATGCTCGTGATCACCAA                         CCGTGCATCATTTTCATGGATGAAATCGACGCTATAGGCGGACGGAGGTTC
genomic: AGAGTGCTCGGCTAATCCGTGAAATGTTCGGCTATGCTCGTGATCACCAAgtatgtcgcg ... tcctttgcagCCGTGCATCATTTTCATGGATGAAATCGACGCTATAGGCGGACGGAGGTTC
EST: gi|169071647|gb|FE477089.1|FE477089
EST:     AGAGTGCTCGGCTAATCCGTGAAATGTTCGGCTATGCTCGTGATCACCAA                         CCGTGCATCATTTTCATGGATGANATCGACGCTATAGGCGGACGGAGGTTC
genomic: AGAGTGCTCGGCTAATCCGTGAAATGTTCGGCTATGCTCGTGATCACCAAgtatgtcgcg ... tcctttgcagCCGTGCATCATTTTCATGGATGAAATCGACGCTATAGGCGGACGGAGGTTC
EST: gi|169043515|gb|FE452635.1|FE452635
EST:     AGAGTGCTCGGCTAATCCGTGAAATGTTCGGCTATGCTCGTGATCACCAA                         CCGTGCATCATTTTCATGGATGAAATCGACGCTATAGGCGGACGAAGGTTC
genomic: AGAGTGCTCGGCTAATCCGTGAAATGTTCGGCTATGCTCGTGATCACCAAgtatgtcgcg ... tcctttgcagCCGTGCATCATTTTCATGGATGAAATCGACGCTATAGGCGGACGGAGGTTC
EST: gi|169040793|gb|FE447844.1|FE447844
EST:     AGAGTGCTCGGCTAATCCGTGAAATGTTCGGCTATGCTCGTGATCACCAA                         CCGTGCATCATTTTCATGGATGAAATCGACGCTNTAGGCGGACGAAGGTTC
genomic: AGAGTGCTCGGCTAATCCGTGAAATGTTCGGCTATGCTCGTGATCACCAAgtatgtcgcg ... tcctttgcagCCGTGCATCATTTTCATGGATGAAATCGACGCTATAGGCGGACGGAGGTTC
EST: gi|169027922|gb|FE434929.1|FE434929
EST:     AGAGTGCTCGGCTAATCCGTGAAATGTTCGGCTATGCTCGTGATCACCAA                         CCGTGCATCATTTTCATGGATGAAATCGACGCTATAGGCGGACGGAGGTTC
genomic: AGAGTGCTCGGCTAATCCGTGAAATGTTCGGCTATGCTCGTGATCACCAAgtatgtcgcg ... tcctttgcagCCGTGCATCATTTTCATGGATGAAATCGACGCTATAGGCGGACGGAGGTTC
EST: gi|169043514|gb|FE452634.1|FE452634
EST:     AGAGTGCTCGGCTAATCCGTGAAATGTTCGGCTATGCTCGTGATCACCAA                         CCGTGCATCATTTTCATGGATGAAATCGACGCTATAGGCGGACGAAGGTTC
genomic: AGAGTGCTCGGCTAATCCGTGAAATGTTCGGCTATGCTCGTGATCACCAAgtatgtcgcg ... tcctttgcagCCGTGCATCATTTTCATGGATGAAATCGACGCTATAGGCGGACGGAGGTTC
EST: gi|169027923|gb|FE434930.1|FE434930
EST:     AGAGTGCTCGGCTAATCCGTGAAATGTTCGGCTATGCTCGTGATCACCAA                         CCGTGCATCATTTTCATGGATGAAATCGACGCTATAGGCGGACGGAGGTTC
genomic: AGAGTGCTCGGCTAATCCGTGAAATGTTCGGCTATGCTCGTGATCACCAAgtatgtcgcg ... tcctttgcagCCGTGCATCATTTTCATGGATGAAATCGACGCTATAGGCGGACGGAGGTTC

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), 30 (downstream exon)
Score: 13

GTGGTGTCGAGTGCTATCGTCGACAAGTACATTGGTGAGAGTGCTCGGCTAATCCGTGAAATGTTCGGCTATGCTCGTGATCACCAAgtatgtcgcg ... tcctttgcagCCGTGCATCATTTTCATGGATGAAATCGACGCTATAGGCGGACGGAGGTTCAGTGAAGGTACCAGTGCTGACAGAGAAATCCAAAGAACACTTATGGAAC




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