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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gaaagggtcgatgtcggttctgatgtacgaaatattatgtgtggtaggtgctttcaggttgtgcgaaatggactaacacattcttatccgtttgcttcagATTGGGCAGAGCCATCCAACTGGTTTGACTACTAATCTTTTGAAGCTTTTCGAGCCTAGGCCTCCTTTGGAATTCAAGCCCCCTCCTGAAAAGCGAAAGT

Basic information

species Physcomitrella patens
transcript PP1S332_45V6.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S332_45V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: GLYMA11G07200.2 (Glycine max), 3'ss of exon 1
----------------------------------gaaagggtcgatgtcggttctgatgtacgaaatattatgtgtggtaggtgctttca----ggttgtgcgaaatggactaacacattcttatccgtttgctt--cagATTGGGCAGAGCCATCCAACTGGTTTGACTACTAATCTTTTGAAGCTTTTCGAGCCTAGGCCTCCTTTGGAATTCAAGCCCCCTCCTGAAAAGCGAAAGT
                                         ||  |   || ||| |  |  | | | |       | ||||   | ||     | ||||    | || |  |  | ||||   |  ||||| |   |||||||| ||||| || ||||| ||| | ||  | || || |||||||| ||||||||||||||||| ||||| | |||||| ||||| || || ||||| |
gtccctctccaatcccttcttcccttacaatttttttcttttcttttctggatcttaattttggattctcgacctagctagggtttatcgctgcgcttgttgagattgtaacacta-attcgcgtttgtttgttatgcagATTGGACAGAGTCACCCAACCGGTCTCACAGCGAACCTGTTGAAGCTCTTCGAGCCTAGGCCTCCGTTGGAGTACAAGCCACCTCCGGAGAAACGAAAAT

upper sequence: PP1S332_45V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: GLYMA01G38120.1 (Glycine max), 3'ss of exon 1
------------------------------------------------------------gaaagggtcgatgtcggttctgatgtacgaaatattatgtgtggtaggtgctttcaggttgtgcgaaatggactaacacatt-cttatccgtt---------tgcttcagATTGGGCAGAGCCATCCAACTGGTTTGACTACTAATCTTTTGAAGCTTTTCGAGCCTAGGCCTCCTTTGGAATTCAAGCCCCCTCCTGAAAAGCGAAAGT
                                                               |   |  || | || |     |  | |  ||   | | | | ||    | |   ||| ||  | |  || |  |   ||  || |  |||          | | |||||||| ||||| || ||||| ||| | ||  | || || |||||||| ||||||||||||||||| ||||| | |||||| ||||| || || || || |
gtccctctccaaccttctctcaccccttcttcccttacaattgttttcttcttttcttttctgaatcttaattttggattct-cgacctagctagggtttatcgcagcgcgtgttgagtt-tgtaacactgattcgcgttttgtttgtttgttgtgtatcggcgatgcagATTGGACAGAGTCACCCAACCGGTCTAACAGCGAACCTGTTGAAGCTCTTCGAGCCTAGGCCTCCGTTGGAGTACAAGCCGCCTCCGGAGAAACGGAAAT

upper sequence: PP1S332_45V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: EFJ17734 (Selaginella moellendorffii), 3'ss of exon 1
gaaagggtcgatgtcggttctgatgtacgaaatattatgtgtggtaggtgctttcaggttgtgcgaaatggactaacacattcttatccgtttgctt-cagATTGGGCAGAGCCATCCAACTGGTTTGACTACTAATCTTTTGAAGCTTTTCGAGCCTAGGCCTCCTTTGGAATTCAAGCCCCCTCCTGAAAAGCGAAAGT
                                           ||| ||    ||  |          | ||    |   |||| | || ||| ||| ||||| || ||||||||||| || || |||||| | |||||||||||||| ||||||||  |||||||| | || | |||||| || || || ||||| ||  
-------------------------------------------gtaagtctcgtctcgcctcttctctttgatcggc---ttctcagcccttttctttcagATCGGCCAGAGCCATCCCACCGGATTGACTGCGAATCTTTTGAAGCTCTTCGAGCCGCGGCCTCCTCTCGAGTACAAGCCGCCGCCGGAGAAGCGGAATC

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|18355039|gb|BJ187098.1|BJ187098
EST:     CCGGTCGCACCAAGACGCAGAACCGTGCCACTGTGCAGCAGCTTAAACTG                         ATTGGGCAGAGCCATCCAACTGGTTTGACTACTAATCTTTTGAAGCTTTTC
genomic: CCGGTCGCACCAAGACGCAGAACCGTGCCACTGTGCAGCAGCTTAAACTGgtgagtcttt ... tttgcttcagATTGGGCAGAGCCATCCAACTGGTTTGACTACTAATCTTTTGAAGCTTTTC
EST: gi|18342127|gb|BJ174162.1|BJ174162
EST:     CCGGTCGCACCAAGACGCAGAACCGTGCCACTGTGCAGCAGCTTAAACTG                         ATTGGGCAGAGCCATCCAACTGGTTTGACTACTAATCTTTTGAAGCTTTTC
genomic: CCGGTCGCACCAAGACGCAGAACCGTGCCACTGTGCAGCAGCTTAAACTGgtgagtcttt ... tttgcttcagATTGGGCAGAGCCATCCAACTGGTTTGACTACTAATCTTTTGAAGCTTTTC
EST: gi|67718772|gb|BJ969031.1|BJ969031
EST:     CCGGTCGCACCAAGACGCAGAACCGTGCCACTGTGCAGCAGCTTAAACTG                         ATTGGGCAGAGCCATCCAACTGGTTTGACTACTAATCTTTTGAAGCTTTTC
genomic: CCGGTCGCACCAAGACGCAGAACCGTGCCACTGTGCAGCAGCTTAAACTGgtgagtcttt ... tttgcttcagATTGGGCAGAGCCATCCAACTGGTTTGACTACTAATCTTTTGAAGCTTTTC
EST: gi|100452661|gb|CJ975381.1|CJ975381
EST:     CCGGTCGCACCAAGACGCAGAACCGTGCCACTGTGCAGCAGCTTAAACTG                         ATTGGGCAGAGCCATCCAACTGGTTTGACTACTAATCTTTTGAAGCTTTTC
genomic: CCGGTCGCACCAAGACGCAGAACCGTGCCACTGTGCAGCAGCTTAAACTGgtgagtcttt ... tttgcttcagATTGGGCAGAGCCATCCAACTGGTTTGACTACTAATCTTTTGAAGCTTTTC
EST: gi|67712849|gb|BJ966298.1|BJ966298
EST:     CCGGTCGCACCAAGACGCAGAACCGTGCCACTGTGCAGCAGCTTAAACTG                         ATTGGGCAGAGCCATCCAACTGGTTTGACTACTAATCTTTTGAAGCTTTTC
genomic: CCGGTCGCACCAAGACGCAGAACCGTGCCACTGTGCAGCAGCTTAAACTGgtgagtcttt ... tttgcttcagATTGGGCAGAGCCATCCAACTGGTTTGACTACTAATCTTTTGAAGCTTTTC
EST: gi|162156991|gb|FC333353.1|FC333353
EST:     CCGGTCGCACCAAGACGCAGAACCGTGCCACTGTGCAGCAGCTTAAACTG                         ATTGGGCAGAGCCATCCAACTGGTTTGACTACTAATCTTTTGAAGCTTTTC
genomic: CCGGTCGCACCAAGACGCAGAACCGTGCCACTGTGCAGCAGCTTAAACTGgtgagtcttt ... tttgcttcagATTGGGCAGAGCCATCCAACTGGTTTGACTACTAATCTTTTGAAGCTTTTC
EST: gi|67704075|gb|BJ964308.1|BJ964308
EST:     CCGGTCGCACCAAGACGCAGAACCGTGCCACTGTGCAGCAGCTTAAACTG                         ATTGGGCAGAGCCATCCAACTGGTTTGACTACTAATCTTTTGAAGCTTTTC
genomic: CCGGTCGCACCAAGACGCAGAACCGTGCCACTGTGCAGCAGCTTAAACTGgtgagtcttt ... tttgcttcagATTGGGCAGAGCCATCCAACTGGTTTGACTACTAATCTTTTGAAGCTTTTC
EST: gi|100391079|gb|BY953089.1|BY953089
EST:     CCGGTCGCACCAAGACGCAGAACCGTGCCACTGTGCAGCAGCTTAAACTG                         ATTGGGCAGAGCCATCCAACTGGTTTGACTACTAATCTTTTGAAGCTTTTC
genomic: CCGGTCGCACCAAGACGCAGAACCGTGCCACTGTGCAGCAGCTTAAACTGgtgagtcttt ... tttgcttcagATTGGGCAGAGCCATCCAACTGGTTTGACTACTAATCTTTTGAAGCTTTTC
EST: gi|100388050|gb|BY988523.1|BY988523
EST:     CCGGTCGCACCAAGACACAGAACCGTGCCACTGTGCAGCAGCTTAAACTG                         ATTGGGCAGAGCCATCCAACTGGTTTGACTACTAATCTTTTGAAGCTTTTC
genomic: CCGGTCGCACCAAGACGCAGAACCGTGCCACTGTGCAGCAGCTTAAACTGgtgagtcttt ... tttgcttcagATTGGGCAGAGCCATCCAACTGGTTTGACTACTAATCTTTTGAAGCTTTTC
EST: gi|18373032|gb|BJ204634.1|BJ204634
EST:     CCGGTCGCACCAAGACGCAGAACCGTGCCACTGTGCAGCAGCTTAAACTG                         ATTGGGCAGAGCCATCCAACTGGTTTGACTACTAATCTTTTGAAGCTTTTC
genomic: CCGGTCGCACCAAGACGCAGAACCGTGCCACTGTGCAGCAGCTTAAACTGgtgagtcttt ... tttgcttcagATTGGGCAGAGCCATCCAACTGGTTTGACTACTAATCTTTTGAAGCTTTTC

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), 32 (downstream exon)
Score: 9

CATGGGCGATTATGGCGACGCCTACATGCGCAAGGATGCTTCGGGTCCGCCCGGTCGCACCAAGACGCAGAACCGTGCCACTGTGCAGCAGCTTAAACTGgtgagtcttt ... tttgcttcagATTGGGCAGAGCCATCCAACTGGTTTGACTACTAATCTTTTGAAGCTTTTCGAGCCTAGGCCTCCTTTGGAATTCAAGCCCCCTCCTGAAAAGCGAAAGT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aggtgctttcaggttgtgcgaaatggactaacacattcttatccgtttgcttcagATTGGGCAGAGCCATCCAACTGGTTTGACTACTAATCTTTTGAAGCTTTTCGAGCCTAGGCCTCCTTTGGAATTCAAGCCCCCTCCTGAAAAGCGAAAGT
                         gactaac  putative branch site (score: 9)
                                             tttgcttc  putative PPT
                                  attcttat  TA-rich tract