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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttctgtgcagacgttcttgcgaagaaagctttcttgacagtgcttagtccagGTTTGCACGGCAAAGATGAATCTGAGCGATGAAGTGGATCTCGAGGACTATGTTTCTCGGCCTGATAAAATAAGCGCCGCCGAG

Basic information

species Selaginella moellendorffii
transcript EFJ38338
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ04233 (Selaginella moellendorffii), 3'ss of exon 4
lower sequence: GLYMA11G31470.1 (Glycine max), 3'ss of exon 4
---------------------------------------------------------------------------------------------------------gtttctgtgcagacgttcttgcgaagaaagctttcttgacagtgcttagtccagGTTTGCACGGCAAAGATGAATCTGAGCGATGAAGTGGATCTCGAGGACTATGTTTCTCGGCCTGATAAAATAAGCGCCGCCGAG
                                                                                                              | || ||    | ||     |  ||||  | |     || || |  ||||||||||| || ||||||||  |||| ||||| || ||||| ||||| ||||||||||| ||||| ||||| || || || |||
gcaagtcttatgggttttctatatgattcactggaaattttatattctgactttctgagtggcaaattttcgcttgttttgctgactcagtgccttttatattgaaaaaatttgtagtttattttcatctgctagctaacctcttgatggtttgatcagGTTTGCACAGCCAAGATGAACTTGAGTGATGAGGTAGATCTGGAGGATTATGTTTCTCGCCCTGACAAAATCAGTGCTGCTGAG

upper sequence: EFJ04233 (Selaginella moellendorffii), 3'ss of exon 4
lower sequence: Vv06s0004g08220.t01 (Vitis vinifera), 3'ss of exon 4
--------------------------------gtttctg---tgcagacgttcttgcgaagaaagctttcttgacagtg-----------cttagtccagGTTTGCACGGCAAAGATGAATCTGAGCGATGAAGTGGATCTCGAGGACTATGTTTCTCGGCCTGATAAAATAAGCGCCGCCGAG
                                ||||  |   | |||  |||  ||  ||  ||   |  ||   ||||           |||  |  |||||||||| || ||||||||  | |||||||| || ||  | |||||||||||||||||||| |||||||| || || || |||
acgtacttcttccttttctacaggttttcagtgttttggacttccagtagtttatggaaattaaatgtgttttgaagtggtctattttccctttttatagGTTTGCACTGCTAAGATGAACTTAAGCGATGAGGTTGACTTGGAGGACTATGTTTCTCGGCCAGATAAAATTAGTGCTGCTGAG

upper sequence: EFJ04233 (Selaginella moellendorffii), 3'ss of exon 4
lower sequence: PP1S147_100V6.1 (Physcomitrella patens), 3'ss of exon 4
--------------------------------------------------------------------------------gtttctgtgcagacgttcttgcgaagaaagctt-tcttgacagtgc-ttagtccagGTTTGCACGGCAAAGATGAATCTGAGCGATGAAGTGGATCTCGAGGACTATGTTTCTCGGCCTGATAAAATAAGCGCCGCCGAG
                                                                                 | ||| |   ||| |  | | |   || |  | | | ||| | |  || |  ||||| || || |||||||||||||| ||||| || || ||| | || |||||||||||| |||||||||||||||| || || |||
gtatgaatccttcttgctcaggcttgtgatttcgttcgtttcagaatcctacaggtgcgttttggaaatcgatgcgtggcatctcttt-tggacttcgtcgtggttaatgaatgtgtggactgagaattcgaacagGTATGTACTGCAAAGATGAATCTAAGCGAGGAGGTTGATTTAGAAGACTATGTTTCTAGGCCTGATAAAATAAGTGCTGCTGAG

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|169064807|gb|FE476127.1|FE476127
EST:     AGATTGAGTTCCCTCTGCCCGACAGGCGGCAAAAGCGGCTCGTTTTCCAG                         GTTTGCACGGCAAAGATGAATCTGAGCGATGAAGTGGATCTCGAGGACTAT
genomic: AGATTGAGTTCCCTCTGCCCGACAGGCGGCAAAAGCGGCTCGTTTTCCAGgtttctgtgc ... cttagtccagGTTTGCACGGCAAAGATGAATCTGAGCGATGAAGTGGATCTCGAGGACTAT
EST: gi|169109986|gb|FE511134.1|FE511134
EST:     AGATTGAGTTCCCTCTGCCCGACAGGCGGCAAAAGCGGCTCGTTTTCCAG                         GTTTGCACGGCAAAGATGAATCTGAGCGATGAAGTGGATCTCGAGGACTAT
genomic: AGATTGAGTTCCCTCTGCCCGACAGGCGGCAAAAGCGGCTCGTTTTCCAGgtttctgtgc ... cttagtccagGTTTGCACGGCAAAGATGAATCTGAGCGATGAAGTGGATCTCGAGGACTAT
EST: gi|169104525|gb|FE508125.1|FE508125
EST:     AGATTGAGTTCCCTCTGCCCGACAGGCGGCAAAAGCGGCTCGTTTTCCAG                         GTTTGCACGGCAAAGATGAATCTGAGCGATGAAGTGGATCTCGAGGACTAT
genomic: AGATTGAGTTCCCTCTGCCCGACAGGCGGCAAAAGCGGCTCGTTTTCCAGgtttctgtgc ... cttagtccagGTTTGCACGGCAAAGATGAATCTGAGCGATGAAGTGGATCTCGAGGACTAT
EST: gi|169100215|gb|FE502936.1|FE502936
EST:     AGATTGAGTTCCCTCTGCCCGACAGGCGGCAAAAGCGGCTCGTTTTCCAG                         GTTTGCACGGCAAAGATGAATCTGAGCGATGAAGTGGATCTCGAGGACTAT
genomic: AGATTGAGTTCCCTCTGCCCGACAGGCGGCAAAAGCGGCTCGTTTTCCAGgtttctgtgc ... cttagtccagGTTTGCACGGCAAAGATGAATCTGAGCGATGAAGTGGATCTCGAGGACTAT
EST: gi|169062254|gb|FE471068.1|FE471068
EST:     AGATTGAGTTCCCTCTGCCCGACAGGCGGCAAAAGCGGCTCGTTTTCCAG                         GTTTGCACGGCAAAGATGAATCTGAGCGATGAAGTGGATCTCGAGGACTAT
genomic: AGATTGAGTTCCCTCTGCCCGACAGGCGGCAAAAGCGGCTCGTTTTCCAGgtttctgtgc ... cttagtccagGTTTGCACGGCAAAGATGAATCTGAGCGATGAAGTGGATCTCGAGGACTAT
EST: gi|169100216|gb|FE502937.1|FE502937
EST:     AGATTGAGTTCCCTCTGCCCGACAGGCGGCAAAAGCGGCTCGTTTTCCAG                         GTTTGCACGGCAAAGATGAATCTGAGCGATGAAGTGGATCTCGAGGACTAT
genomic: AGATTGAGTTCCCTCTGCCCGACAGGCGGCAAAAGCGGCTCGTTTTCCAGgtttctgtgc ... cttagtccagGTTTGCACGGCAAAGATGAATCTGAGCGATGAAGTGGATCTCGAGGACTAT
EST: gi|169033190|gb|FE441210.1|FE441210
EST:     AGATTGAGTTCCCTCTGCCCGACAGGCGGCAAAAGCGGCTCGTTTTCCAG                         GTTTGCACGGCAAAGATGAATCTGAGCGATGAAGTGGATCTCGAGGACTAT
genomic: AGATTGAGTTCCCTCTGCCCGACAGGCGGCAAAAGCGGCTCGTTTTCCAGgtttctgtgc ... cttagtccagGTTTGCACGGCAAAGATGAATCTGAGCGATGAAGTGGATCTCGAGGACTAT
EST: gi|169067828|gb|FE473399.1|FE473399
EST:     AGATTGAGTTCCCTCTGCCCGACAGGCGGCAAAAGCGGCTCGTTTTCCAG                         GTTTGCACGGCAAAGATGAATCTGAGCGATGAAGTGGATCTCGAGGACTAT
genomic: AGATTGAGTTCCCTCTGCCCGACAGGCGGCAAAAGCGGCTCGTTTTCCAGgtttctgtgc ... cttagtccagGTTTGCACGGCAAAGATGAATCTGAGCGATGAAGTGGATCTCGAGGACTAT

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), 35 (downstream exon)
Score: 29

TGCGGACACTTTGGATCCCGCGCTCTTGCGTCCGGGAAGACTTGACAGGAAGATTGAGTTCCCTCTGCCCGACAGGCGGCAAAAGCGGCTCGTTTTCCAGgtttctgtgc ... cttagtccagGTTTGCACGGCAAAGATGAATCTGAGCGATGAAGTGGATCTCGAGGACTATGTTTCTCGGCCTGATAAAATAAGCGCCGCCGAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtttctgtgcagacgttcttgcgaagaaagctttcttgacagtgcttagtccagGTTTGCACGGCAAAGATGAATCTGAGCGATGAAGTGGATCTCGAGGACTATGTTTCTCGGCCTGATAAAATAAGCGCCGCCGAG
                                  tcttgac  putative branch site (score: 29)