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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTGAGGATCGCTCGTATTTTCAACACATATGGTCCTAGAATGTGCCTGGACGATGGCCGAGTTGTCAGCAACTTCGTGGCCCAGgtacaaaagcatcccttgaaaagcttcttcccgttttcattcttttgctttctcgcag

Basic information

species Selaginella moellendorffii
transcript EFJ23020
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ23020 (Selaginella moellendorffii), 5'ss of exon 4
lower sequence: GRMZM2G359234_T03 (Zea mays), 5'ss of exon 4
GTGAGGATCGCTCGTATTTTCAACACATATGGTCCTAGAATGTGCCTGGACGATGGCCGAGTTGTCAGCAACTTCGTGGCCCAGgtaca---aaagcatcccttgaaaagcttcttcccgttttcattcttttgctttctcgcag--------------------
||| | || || ||||||||||| |||||||||||| | |||||||| |||||||| || || |||||||| || || || |||||          |||    |  |    || |    ||| | ||  || ||| ||    ||                     
GTGCGTATTGCCCGTATTTTCAATACATATGGTCCTCGTATGTGCCTCGACGATGGTCGTGTGGTCAGCAATTTTGTTGCACAGgtttgtttgctacatattatagactatttttcttagttgtgatatttatgcatttaaacatccatatgatcgtccttgcag

upper sequence: EFJ23020 (Selaginella moellendorffii), 5'ss of exon 4
lower sequence: GRMZM2G347717_T01 (Zea mays), 5'ss of exon 4
GTGAGGATCGCTCGTATTTTCAACACATATGGTCCTAGAATGTGCCTGGACGATGGCCGAGTTGTCAGCAACTTCGTGGCCCAGgtacaaaagcatcc-----cttgaaaagcttcttcccgttttcattcttttgctttctcgcag----------------------------
||||| || || || || || ||||||||||| ||| |||||||  | || |||||||||||||| |||||||| || || |||||         |         |||     |           | ||  |    |||   | | |                            
GTGAGAATTGCACGCATATTTAACACATATGGCCCTCGAATGTGTTTAGATGATGGCCGAGTTGTTAGCAACTTTGTTGCACAGgtttgtctcagtttgtgattctgatgcattggagaagaggattatcatagaacttcagcactgcttaaagttggcattgcttcatttctag

upper sequence: EFJ23020 (Selaginella moellendorffii), 5'ss of exon 4
lower sequence: AT3G53520.4 (Arabidopsis thaliana), 5'ss of exon 4
GTGAGGATCGCTCGTATTTTCAACACATATGGTCCTAGAATGTGCCTGGACGATGGCCGAGTTGTCAGCAACTTCGTGGCCCAGgtacaaaagcatc-----ccttgaaaagcttcttcccgttttcattcttttg----ctttctcgcag--------------------------
|| || || ||||||||||||||||||||||| || ||||||||||| || ||||| || ||||| || ||||| || ||||||||  |    | ||     | |  | |       |  ||| |  |  ||||||    |  |||  |||                          
GTTAGAATTGCTCGTATTTTCAACACATATGGGCCCAGAATGTGCCTTGATGATGGGCGTGTTGTTAGTAACTTTGTTGCCCAGgtttagctccttcatcaacataaagacaaccgctttcgtataaagccttttgaaaacactctgacagaactattgtggcttatatctatgcag

upper sequence: EFJ23020 (Selaginella moellendorffii), 5'ss of exon 4
lower sequence: PP1S60_124V6.1 (Physcomitrella patens), 5'ss of exon 5
GTGAGGATCGCTCGTATTTTCAACACATATGGTCCTAGAATGTGCCTGGACGATGGCCGAGTTGTCAGCAACTTCGTGGCCCAGgtacaaaagcatcccttgaaaa--gcttcttcccgttttcattcttttgctttctcgcag-------------------------------------------------------------------------------------------------------------
|||||||| ||||| || |||||||| ||||| |||||||||||| | |||||||| || ||||||||||||||||| || |||||         |  | |       | |  |  | |||||  | ||| || | | ||                                                                                                                 
GTGAGGATTGCTCGGATATTCAACACGTATGGACCTAGAATGTGCATTGACGATGGACGCGTTGTCAGCAACTTCGTTGCACAGgtttgctcttctttcctagtgcttggtattagcagtttttttccttctgttatatctatatctatatatttgttttgtttcgaggagtataattatttagatgtgttgcatgcttcagcctgttttcagtagctttggtaggatcggcttctaacactctttgtctcag

upper sequence: EFJ23020 (Selaginella moellendorffii), 5'ss of exon 4
lower sequence: PP1S209_52V6.1 (Physcomitrella patens), 5'ss of exon 4
GTGAGGATCGCTCGTATTTTCAACACATATGGTCCTAGAATGTGCCTGGACGATGGCCGAGTTGTCAGCAACTTCGTGGCCCAGgtacaaaagcatcccttgaaaagcttcttcccgttttcattcttttgctttctcgcag--------------------------------------------------------------------------------------------------------------
||  | || |||||||||||||| || ||||| || ||||||||  | || |||||  | ||||||||||||||||| || |||||   |     || | || | |   || |  | | |  | | |  |  | | |   ||                                                                                                              
GTTCGCATTGCTCGTATTTTCAATACGTATGGACCGAGAATGTGTATTGATGATGGTAGGGTTGTCAGCAACTTCGTCGCTCAGgtg--agtttttcgcatggacattatcgtgacatgtgtagtgtgattttatgtttgagtaattattcagtgttatgactaaattcggaagattgcgtcctatgcatgacctatttaatggcaattcagtgtttttctgacaaggttactgtttgccttcattatccag

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|169074523|gb|FE481156.1|FE481156
EST:     CTAGAATGTGCCTGGACGATGGCCGAGTTGTCAGCAACTTCGTGGCCCAG                         GCCCTCCGTAAAGAGCCTTTGACAGTCTATGGCGATGGAAAACAAACTCGG
genomic: CTAGAATGTGCCTGGACGATGGCCGAGTTGTCAGCAACTTCGTGGCCCAGgtacaaaagc ... tttctcgcagGCCCTCCGTAAAGAGCCTTTGACAGTCTATGGCGATGGAAAACAAACTCGG
EST: gi|169048386|gb|FE456308.1|FE456308
EST:     CTAGAATGTGCCTGGACGATGGCCGAGTTGTCAGCAACTTCGTGGCCCAG                         GCCCTCCGTAAAGAGCCTTTGACAGTCTATGGCGATGGAAAACAAACTCGG
genomic: CTAGAATGTGCCTGGACGATGGCCGAGTTGTCAGCAACTTCGTGGCCCAGgtacaaaagc ... tttctcgcagGCCCTCCGTAAAGAGCCTTTGACAGTCTATGGCGATGGAAAACAAACTCGG
EST: gi|169112170|gb|FE513513.1|FE513513
EST:     CTAGAATGTGCCTGGACGATGGCCGAGTTGTCAGCAACTTCGTGGCCCAG                         GCCCTCCGTAAAGAGCCTTTGACAGTCTATGGCGATGGAAAACAAACTCGG
genomic: CTAGAATGTGCCTGGACGATGGCCGAGTTGTCAGCAACTTCGTGGCCCAGgtacaaaagc ... tttctcgcagGCCCTCCGTAAAGAGCCTTTGACAGTCTATGGCGATGGAAAACAAACTCGG
EST: gi|169101487|gb|FE501460.1|FE501460
EST:     CTAGAATGTGCCTGGACGATGGCCGAGTTGTCAGCAACTTCGTGGCCCAG                         GCCCTCCGTAAAGAGCCTTTGACAGTCTATGGCGATGGAAAACAAACTCGG
genomic: CTAGAATGTGCCTGGACGATGGCCGAGTTGTCAGCAACTTCGTGGCCCAGgtacaaaagc ... tttctcgcagGCCCTCCGTAAAGAGCCTTTGACAGTCTATGGCGATGGAAAACAAACTCGG

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: 35 (upstream exon), 31 (downstream exon)
Score: 15

GTGAGGATCGCTCGTATTTTCAACACATATGGTCCTAGAATGTGCCTGGACGATGGCCGAGTTGTCAGCAACTTCGTGGCCCAGgtacaaaagc ... tttctcgcagGCCCTCCGTAAAGAGCCTTTGACAGTCTATGGCGATGGAAAACAAACTCGGAGCTTTCAGTTCGTCTCAGACTTG




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