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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTTCGCATTGCTCGTATTTTCAATACGTATGGACCGAGAATGTGTATTGATGATGGTAGGGTTGTCAGCAACTTCGTCGCTCAGgtgagtttttcgcatggacattatcgtgacatgtgtagtgtgattttatgtttgagtaattattcagtgttatgactaaattcggaagattgcgtcctatgcatgacctatttaatggcaattcagtgtttttctgacaaggttactgtttgccttcattatccag

Basic information

species Physcomitrella patens
transcript PP1S209_52V6.1
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S209_52V6.1 (Physcomitrella patens), 5'ss of exon 4
lower sequence: LOC_Os01g62020.1 (Oryza sativa), 5'ss of exon 4
GTTCGCATTGCTCGTATTTTCAATACGTATGGACCGAGAATGTGTATTGATGATGGTAGGGTTGTCAGCAACTTCGTCGCTCAGgtgagtttttcgcatggacattatcgtgacatgtgtagtgtgattttatgtttgagtaattattcagtgttatgactaaattcggaagattgcgtcctatgcatgacctatttaatggcaattcagtgtttttctgacaaggttactgtttgccttcattatccag
|| ||||||||||| ||||||||||| ||||| ||  |||||||| | ||||||||  | || || ||||| || || || |||||  ||||  | | |   |  |||  |   |  | |    || ||  |  |||| |           ||| |  |  |||||| ||           ||| |||||      |  | |                                                
GTGCGCATTGCTCGCATTTTCAATACATATGGCCCTCGAATGTGTCTAGATGATGGCCGTGTGGTTAGCAATTTTGTTGCCCAGgttcgtttaacacgtac-cgctattttattaacttt----tggttacacatttgcgc----------tgtcaatatgaaattctgag--------tttatacatgattatcattgtag------------------------------------------------

upper sequence: PP1S209_52V6.1 (Physcomitrella patens), 5'ss of exon 4
lower sequence: AT3G53520.4 (Arabidopsis thaliana), 5'ss of exon 4
GTTCGCATTGCTCGTATTTTCAATACGTATGGACCGAGAATGTGTATTGATGATGGTAGGGTTGTCAGCAACTTCGTCGCTCAGgtgagtttttcgcatggacattatcgtgacatgtgtagtgtgattttatgtttgagtaattattcagtgttatgactaaattcggaagattgcgtcctatgcatgacctatttaatggcaattcagtgtttttctgacaaggttactgtttgccttcattatccag
||| | ||||||||||||||||| || ||||| || ||||||||  ||||||||||  | ||||| || ||||| || || |||||     |    |||  |||| |     ||   | | || | |    |   ||  | ||  | ||  ||  |  ||||      |  | ||   || ||||||                                                               
GTTAGAATTGCTCGTATTTTCAACACATATGGGCCCAGAATGTGCCTTGATGATGGGCGTGTTGTTAGTAACTTTGTTGCCCAGgtttagctccttcatcaacataaagacaaccgctttcgtataa----agccttttgaaaacactc--tgacagaacta----ttgtggcttatatc-tatgcag--------------------------------------------------------------

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

upper sequence: PP1S209_52V6.1 (Physcomitrella patens), 5'ss of exon 4
lower sequence: EFJ30517 (Selaginella moellendorffii), 5'ss of exon 5
GTTCGCATTGCTCGTATTTTCAATACGTATGGACCGAGAATGTGTATTGATGATGGTAGGGTTGTCAGCAACTTCGTCGCTCAGgtg--agtttttcgcatggacattatcgtgacatgtgtagtgtgattttatgtttgagtaattattcagtgttatgactaaattcggaagattgcgtcctatgcatgacctatttaatggcaattcagtgtttttctgacaaggttactgtttgccttcattatccag
||  | || |||||||||||||| || ||||| || ||||||||  | || |||||  | ||||||||||||||||| || |||||   |     ||   || | |   || |  | | |  | | |   ||||  ||   | |                                                                                                            
GTGAGGATCGCTCGTATTTTCAACACATATGGTCCTAGAATGTGCCTGGACGATGGCCGAGTTGTCAGCAACTTCGTGGCCCAGgtacaaaagcatccgttgaaaagcttcttcccgttttcattct---tttactttctcgcag-----------------------------------------------------------------------------------------------------------

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|162196627|gb|FC374917.1|FC374917
EST:     CGAGAATGTGTATTGATGATGGTAGGGTTGTCAGCAACTTCGTCGCTCAG                         GCCCTGAGGAAAGAGCCCATGACAGTTTATGGTGATGGAAAGCAGACGAGA
genomic: CGAGAATGTGTATTGATGATGGTAGGGTTGTCAGCAACTTCGTCGCTCAGgtgagttttt ... cattatccagGCCCTGAGGAAAGAGCCCATGACAGTTTATGGTGATGGAAAGCAGACGAGA
EST: gi|162207029|gb|FC383038.1|FC383038
EST:     CGAGAATGTGTATTGATGATGGTAGGGTTGTCAGCAACTTCGTCGCTCAG                         GCCCTGAGGAAAGAGCCCATGACAGTTTATGGTGATGGAAAGCAGACGAGA
genomic: CGAGAATGTGTATTGATGATGGTAGGGTTGTCAGCAACTTCGTCGCTCAGgtgagttttt ... cattatccagGCCCTGAGGAAAGAGCCCATGACAGTTTATGGTGATGGAAAGCAGACGAGA
EST: gi|162261552|gb|FC437569.1|FC437569
EST:     CGAGAATGTGTATTGATGATGGTAGGGTTGTCAGCAACTTCGTCGCTCAG                         GCCCTGAGGAAAGAGCCCATGACAGTTTATGGTGATGGAAAGCAGACGAGA
genomic: CGAGAATGTGTATTGATGATGGTAGGGTTGTCAGCAACTTCGTCGCTCAGgtgagttttt ... cattatccagGCCCTGAGGAAAGAGCCCATGACAGTTTATGGTGATGGAAAGCAGACGAGA
EST: gi|67699664|gb|BJ959897.1|BJ959897
EST:     CGAGAATGTGTATTGATGATGGTAGGGTTGTCAGCAACTTCGTCGCTCAG                         GCCCTGAGGAAAGAGCCCATGACAGTTTATGGTGATGGAAAGCAGACGAGA
genomic: CGAGAATGTGTATTGATGATGGTAGGGTTGTCAGCAACTTCGTCGCTCAGgtgagttttt ... cattatccagGCCCTGAGGAAAGAGCCCATGACAGTTTATGGTGATGGAAAGCAGACGAGA
EST: gi|37852244|gb|BJ610252.1|BJ610252
EST:     CGAGAATGTGTATTGATGATGGTAGGGTTGTCAGCAACTTCGTCGCTCAG                         GCCCTGAGGAAAGAGCCCATGACAGTTTATGGTGATGGAAAGCAGACGAGA
genomic: CGAGAATGTGTATTGATGATGGTAGGGTTGTCAGCAACTTCGTCGCTCAGgtgagttttt ... cattatccagGCCCTGAGGAAAGAGCCCATGACAGTTTATGGTGATGGAAAGCAGACGAGA
EST: gi|162194370|gb|FC371088.1|FC371088
EST:     CGAGAATGTGTATTGATGATGGTAGGGTTGTCAGCAACTTCGTCGCTCAG                         GCCCTGAGGAAAGAGCCCATGACAGTTTATGGTGATGGAAAGCAGACGAGA
genomic: CGAGAATGTGTATTGATGATGGTAGGGTTGTCAGCAACTTCGTCGCTCAGgtgagttttt ... cattatccagGCCCTGAGGAAAGAGCCCATGACAGTTTATGGTGATGGAAAGCAGACGAGA
EST: gi|162193738|gb|FC371265.1|FC371265
EST:     CGAGAATGTGTATTGATGATGGTAGGGTTGTCAGCAACTTCGTCGCTCAG                         GCCCTGAGGAAAGAGCCCATGACAGTTTATGGTGATGGAAAGCAGACGAGA
genomic: CGAGAATGTGTATTGATGATGGTAGGGTTGTCAGCAACTTCGTCGCTCAGgtgagttttt ... cattatccagGCCCTGAGGAAAGAGCCCATGACAGTTTATGGTGATGGAAAGCAGACGAGA
EST: gi|162155079|gb|FC330873.1|FC330873
EST:     CGAGAATGTGTATTGATGATGGTAGGGTTGTCAGCAACTTCGTCGCTCAG                         GCCCTGAGGAAAGAGCCCATGACAGTTTATGGTGATGGAAAGC
genomic: CGAGAATGTGTATTGATGATGGTAGGGTTGTCAGCAACTTCGTCGCTCAGgtgagttttt ... cattatccagGCCCTGAGGAAAGAGCCCATGACAGTTTATGGTGATGGAAAGC
EST: gi|67695896|gb|BJ956129.1|BJ956129
EST:     CGAGAATGTGTATTGATGATGGTAGGGTTGTCAGCAACTTCGTCGCTCAG                         GCCCTGAGGAAAGAGCCCATGACAGTTTATGGTGATGGAAAGCAGACGAGA
genomic: CGAGAATGTGTATTGATGATGGTAGGGTTGTCAGCAACTTCGTCGCTCAGgtgagttttt ... cattatccagGCCCTGAGGAAAGAGCCCATGACAGTTTATGGTGATGGAAAGCAGACGAGA
EST: gi|162155078|gb|FC330872.1|FC330872
EST:     CGAGAATGTGTATTGATGATGGTAGGGTTGTCAGCAACTTCGTCGCTCAG                         GCCCTGAGGAAAGAGCCCATGACAGTTTATGGTGATGGAAAGCAGACGAGA
genomic: CGAGAATGTGTATTGATGATGGTAGGGTTGTCAGCAACTTCGTCGCTCAGgtgagttttt ... cattatccagGCCCTGAGGAAAGAGCCCATGACAGTTTATGGTGATGGAAAGCAGACGAGA
EST: gi|162245552|gb|FC424106.1|FC424106
EST:     CGAGAATGTGTATTGATGATGGTAGGGTTGTCAGCAACTTCGTCGCTCAG                         GCCNTGAGGAAAGAGCCCATGACAGTTTATGGTGATGGAAAGCAGACGAGA
genomic: CGAGAATGTGTATTGATGATGGTAGGGTTGTCAGCAACTTCGTCGCTCAGgtgagttttt ... cattatccagGCCCTGAGGAAAGAGCCCATGACAGTTTATGGTGATGGAAAGCAGACGAGA
EST: gi|37825569|gb|BJ583635.1|BJ583635
EST:     GAGAATGTGTATTGATGATGGTAGGGTTGTCAGCAACTTCGTCGCTCCAG                         GCCCTGAGGAAAGAGCCCATGACAGTTTATGGTGATGGAAAGCAGACGAG
genomic: GAGAATGTGTATTGATGATGGTAGGGTTGTCAGCAACTTCGTCGCT-CAGgtgagttttt ... cattatccagGCCCTGAGGAAAGAGCCCATGACAGTTTATGGTGATGGAAAGCAGACGAG
EST: gi|162193739|gb|FC371266.1|FC371266
EST:     CGAGAATGTGTATTGATGATGGTAGGGTTGTCAGCAACTTCGTCGCTCAG                         GCCCTGAGGAAAGAGCCCATGACAGTTTATGGTGATGGAAAGCAGACGAGA
genomic: CGAGAATGTGTATTGATGATGGTAGGGTTGTCAGCAACTTCGTCGCTCAGgtgagttttt ... cattatccagGCCCTGAGGAAAGAGCCCATGACAGTTTATGGTGATGGAAAGCAGACGAGA
EST: gi|18338390|gb|BJ170414.1|BJ170414
EST:     TCGTCGCTCAG                         GCCNTGAGGAAAGAGCCCATGACAGTTTATGGTGATGGAAAGCAGACGAGA
genomic: TCGTCGCTCAGgtgagttttt ... cattatccagGCCCTGAGGAAAGAGCCCATGACAGTTTATGGTGATGGAAAGCAGACGAGA

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), 25 (downstream exon)
Score: 15

GTTCGCATTGCTCGTATTTTCAATACGTATGGACCGAGAATGTGTATTGATGATGGTAGGGTTGTCAGCAACTTCGTCGCTCAGgtgagttttt ... cattatccagGCCCTGAGGAAAGAGCCCATGACAGTTTATGGTGATGGAAAGCAGACGAGAAGTTTCCAGTATGTTTCAGATCTG




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