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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacagtctaaattgcagaagctatgttatgtatgaagctcttgaaatattctttgctattgctaaagcttgccccgttatacttatcagaattgtgtaactgatttatatttttttaatgaatactagGTCTTCTCACAATTGGCCCTCGTTTTGGTGGAGCTATTGATGATGCTGCTCGCTATTTTAGAGAAGCCCATGACAACGGATTATCGCCTTACGCATTTGT

Basic information

species Physcomitrella patens
transcript PP1S46_63V6.1
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S46_63V6.2 (Physcomitrella patens), 3'ss of exon 12
lower sequence: LOC_Os01g19450.1 (Oryza sativa), 3'ss of exon 13
gtacagtctaaattgcagaagctatgttatgtatgaagctcttgaaatattctttgctattgctaaagcttgccccgttatacttatcagaattgtgtaactgatttatatt-tttttaatgaatactagGTCTTCTCACAATTGGCCCTCGTTTTGGTGGAGCTATTGATGATGCTGCTCGCTATTTTAGAGAAGCCCATGACAACGGATTATCGCCTTACGCATTTGT
                   |||| | || |  ||| |  | |  ||| ||| |  | ||          |||      |||| |       |  |  ||  | ||  | |||  | || |   ||   |||| |  | ||||||||||| ||||||||||| || |||||||||||||| || || || | ||| ||  |||| |                         
----------------gtgagct-tcttctacatgtacatgt--aaacattgtccgtta--------agttgtttgaatatatt-------acagcataggttatgaagattgctattgaaatattgcagGTTTATTGACAATTGGCCCCCGTTTTGGTGGTGCAATTGATGATGCTGCCCGGTACTTCAAAGATGCATATGATAGA-----------------------

upper sequence: PP1S46_63V6.2 (Physcomitrella patens), 3'ss of exon 12
lower sequence: GRMZM2G045534_T01 (Zea mays), 3'ss of exon 1
gtacagtctaaattgcagaagctatgttatgtatgaagctcttgaaatattctttgctattgctaaagcttgccccgttatacttatcagaattgtgtaactgatttatatttttttaatgaatactagGTCTTCTCACAATTGGCCCTCGTTTTGGTGGAGCTATTGATGATGCTGCTCGCTATTTTAGAGAAGCCCATGACAACGGATTATCGCCTTACGCATTTGT
             ||    |  |   || |  ||| ||  |||    ||| |||||  ||||| | || || |     | ||||      ||   |  ||| | ||| | |||           |  |||  |  | ||||||||||| |||||||| ||||| ||||||||||| || || || || | ||| ||   ||| |                         
------------gtgagctatttgatttctacatgcagaacttc---tatcctttg--attgc-atagattactgatatgtact-gctgaaacattaaaacggctttctgttt-----------atcagGATTATTGACAATTGGCCCCCGTTTTGGCGGAGCAATTGATGATGCAGCCCGATACTTCAAAGATGCATGTGATAGG-----------------------

upper sequence: PP1S46_63V6.2 (Physcomitrella patens), 3'ss of exon 12
lower sequence: GLYMA17G03700.1 (Glycine max), 3'ss of exon 12
gtacagtctaaattgcagaagctatgttatgtatgaagctcttgaaatattctttgctattgctaaagcttgccccgttatac-ttatcagaattgtgtaactgatttatatttttttaatgaatactagGTCTTCTCACAATTGGCCCTCGTTTTGGTGGAGCTATTGATGATGCTGCTCGCTATTTTAGAGAAGCCCATGACAACGGATTATCGCCTTACGCATTTGT
        |||||    |   |||   | | ||     ||  |||| ||| ||| |    ||   |||    |     | |||  ||| |      | ||| ||||   || |    | |||||    |||| | || |||||||| ||||| ||||| || || ||||||||||||||||||||||| |  || ||| ||||||                         
-------gtaaatacaggcttctagtctttcta-----ctgctgaagtatgcttggtatctgactaagtccccgtgtctgtacactattatttccat-taaatgatcagtaatgagcttatgaaa--cagGTTTGCTTACAATTGGTCCTCGATTTGGGGGTGCCATTGATGATGCTGCTCGCTATTTCAAGGATGCCTATGACAGG-----------------------

upper sequence: PP1S46_63V6.2 (Physcomitrella patens), 3'ss of exon 12
lower sequence: GLYMA15G15010.1 (Glycine max), 3'ss of exon 12
gtacagtctaaattgcagaagctatgttatgtatgaagctcttg-aaatattctttgctattgctaaagcttgccccgttatacttatcagaattgtgtaactgatttatatttttttaatgaat------actagGTCTTCTCACAATTGGCCCTCGTTTTGGTGGAGCTATTGATGATGCTGCTCGCTATTTTAGAGAAGCCCATGACAACGGATTATCGCCTTACGCATTTGT
||| |  | |   |  |     |   ||||  ||| ||   | | |   ||    |    |  | ||| |||     | ||   | || | |||    |||   | |||    |   ||||||        |  |||| | || |||||||| ||||| ||||| || || |||||||||||||||||||| || |  || || |||||||                         
gtaaatacaagcctttaatctgtcaattattgatgtaggcatagtatgaatgtgataaggtgaccaaaactttgtatgctaa--taataataatgccataaaacagttagtaatgaataatgagcttctgaaacagGTATGCTTACAATTGGTCCTCGATTTGGGGGTGCCATTGATGATGCTGCTCGCTACTTCAAGGATGCTCATGACAGG-----------------------

upper sequence: PP1S46_63V6.2 (Physcomitrella patens), 3'ss of exon 12
lower sequence: GLYMA07G36840.1 (Glycine max), 3'ss of exon 14
gtacagtctaaattgcagaagctatgttatgtatgaagctcttgaaatattctttgctattgctaaagcttgccccgttatac-ttatcagaattgtgtaactgatttatatttttttaatgaatactagGTCTTCTCACAATTGGCCCTCGTTTTGGTGGAGCTATTGATGATGCTGCTCGCTATTTTAGAGAAGCCCATGACAACGGATTATCGCCTTACGCATTTGT
        |||||    |   |||   | | ||     ||  |||| ||| ||| |    ||   |||    |    || |||  ||| |      | ||| || |   || |    | |||||    |||| | || |||||||| ||||| ||||| || || ||||||||||||||||| ||||| |  || ||  ||||||                         
-------gtaaatacaggcttctagtctttcta-----ctgctgaagtatgcttggtatctgactaagtggccgtgtttgtacactattatttccat-taaatggtcagtaatgagcttatgaaa--cagGTTTGCTTACAATTGGTCCTCGATTTGGGGGTGCCATTGATGATGCTGCTCGTTATTTCAAGGATGCTTATGACAGG-----------------------

upper sequence: PP1S46_63V6.2 (Physcomitrella patens), 3'ss of exon 12
lower sequence: Vv05s0077g00950.t01 (Vitis vinifera), 3'ss of exon 13
gtacagtctaaattgcagaagctatgttatgtatgaagctcttgaaatattctttgctattgctaaagcttgccccgttatacttatcagaattgtgtaactgatttatatttttttaatgaatactagGTCTTCTCACAATTGGCCCTCGTTTTGGTGGAGCTATTGATGATGCTGCTCGCTATTTTAGAGAAGCCCATGACAACGGATTATCGCCTTACGCATTTGT
        ||||||| || |  ||||||   | |  |  |      |       |    |   |  |  |      | | || |        ||||| |||||||||       | ||||| | || |||  | || |||||||| || || ||||||||||||||||||||||||||||| || || |  || ||  |||| |                         
-------gtaaattgtagcaattatgtttcatttttatttagatggagggatcatatcttcattggaaat------gctgtagtgtgggcttttgtg-aactgattt-------tataatggaaac-agGCTTGCTTACAATTGGTCCCCGATTTGGTGGAGCTATTGATGATGCTGCTCGATACTTCAAGGACGCTTATGATAGG-----------------------

upper sequence: PP1S46_63V6.2 (Physcomitrella patens), 3'ss of exon 12
lower sequence: EFJ31368 (Selaginella moellendorffii), 3'ss of exon 12
gtacagtctaaattgcagaagctatgttatgtatgaagctcttgaaatattctttgctattgctaaagcttgccccgttatacttatcagaattgtgtaactgatttatatttttttaatgaatactagGTCTTCTCACAATTGGCCCTCGTTTTGGTGGAGCTATTGATGATGCTGCTCGCTATTTTAGAGAAGCCCATGACAACGGATTATCGCCTTACGCATTTGT
                                                                           |||   |||  |   | |||| |      |||| |  | |||  |   | | ||| ||||| ||||| || ||||||||||| ||||||||||||||||| || ||||| || | ||| ||  | |||||                        
------------------------------------------------------------------------gttcgtgtgactccttc-atttgtatt-----tttacaactatttgcttg-tgc-agGCCTTCTTACAATAGGACCTCGTTTTGGCGGAGCTATTGATGATGCAGCCCGCTACTTCAAAGATGCTTACGACAAG-----------------------

upper sequence: PP1S46_63V6.2 (Physcomitrella patens), 3'ss of exon 12
lower sequence: EFJ06573 (Selaginella moellendorffii), 3'ss of exon 12
gtacagtctaaattgcagaagctatgttatgtatgaagctcttgaaatattctttgctattgctaaagcttgccccgttatacttatcagaattgtgtaactg-atttatatttttttaatgaatact------agGTCTTCTCACAATTGGCCCTCGTTTTGGTGGAGCTATTGATGATGCTGCTCGCTATTTTAGAGAAGCCCATGACAACGGATTATCGCCTTACGCATTTGT
                                                                                            | |||| |||  ||   |||||||  ||  | |         ||| ||||| ||||| || ||||||||||| ||||||||||||||||| || ||||| || | ||| ||  | |||||                        
------------------------------------------------------------------------------------------gttcgtgtgactccatcggtatttttacaactattttcttgtgcagGCCTTCTTACAATAGGACCTCGTTTTGGCGGAGCTATTGATGATGCAGCCCGCTACTTCAAAGATGCTTACGACAAG-----------------------

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|67574889|gb|BJ947713.1|BJ947713
EST:     TATTGTCACTGCTCGTGCAGGAAAGGACTTGGTATCAAGTCTTGTGTCTG                         GTCTTCTCACAATTGGCCCTCGTTTTGGTGGAGCTATTGATGATGCTGCTC
genomic: TATTGTCACTGCTCGTGCAGGAAAGGACTTGGTATCAAGTCTTGTGTCTGgtacagtcta ... tgaatactagGTCTTCTCACAATTGGCCCTCGTTTTGGTGGAGCTATTGATGATGCTGCTC
EST: gi|208366526|gb|DC955602.1|DC955602
EST:     TATTGTCACTGCTCGTGCAGGAAAGGACTTGGTATCAAGTCTTGTGTCTG                         GTCTTCTCACAATTGGCCCTCGTTTTGGTGGAGCTATTGATGATGCTGCTC
genomic: TATTGTCACTGCTCGTGCAGGAAAGGACTTGGTATCAAGTCTTGTGTCTGgtacagtcta ... tgaatactagGTCTTCTCACAATTGGCCCTCGTTTTGGTGGAGCTATTGATGATGCTGCTC
EST: gi|162196012|gb|FC372183.1|FC372183
EST:     TATTGTCACTGCTCGTGCAGGAAAGGACTTGGTATCAAGTCTTGTGTCTG                         GTCTTCTCACAATTGGCCCTCGTTTTGGTGGAGCTATTGATGATGCTGCTC
genomic: TATTGTCACTGCTCGTGCAGGAAAGGACTTGGTATCAAGTCTTGTGTCTGgtacagtcta ... tgaatactagGTCTTCTCACAATTGGCCCTCGTTTTGGTGGAGCTATTGATGATGCTGCTC
EST: gi|100385297|gb|BY950889.1|BY950889
EST:     TATTGTCACTGCTCGTGCAGGANAGGACTTGGTATTAAGTCTTGTGTCTG                         GTCTTCTCACAATTGGCCCTCGTTTTGGTGGAGCTATTGATGATGCTGCTC
genomic: TATTGTCACTGCTCGTGCAGGAAAGGACTTGGTATCAAGTCTTGTGTCTGgtacagtcta ... tgaatactagGTCTTCTCACAATTGGCCCTCGTTTTGGTGGAGCTATTGATGATGCTGCTC

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: 21 (upstream exon), 19 (downstream exon)
Score: 3

ATAATGCTCTGTGCAGATCATGGCCCTGCTGTGTCTGGAGCACACAACACTATTGTCACTGCTCGTGCAGGAAAGGACTTGGTATCAAGTCTTGTGTCTGgtacagtcta ... tgaatactagGTCTTCTCACAATTGGCCCTCGTTTTGGTGGAGCTATTGATGATGCTGCTCGCTATTTTAGAGAAGCCCATGACAACGGATTATCGCCTTACGCATTTGT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ccgttatacttatcagaattgtgtaactgatttatatttttttaatgaatactagGTCTTCTCACAATTGGCCCTCGTTTTGGTGGAGCTATTGATGATGCTGCTCGCTATTTTAGAGAAGCCCATGACAACGGATTATCGCCTTACGCATTTGT
                                       ttttaat  putative branch site (score: 3)
                aattgtgtaactgatt  TA-rich tract
















Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacagtctaaattgcagaagctatgttatgtatgaagctcttgaaatattctttgctattgctaaagcttgccccgttatacttatcagaattgtgtaactgatttatatttttttaatgaatactagGTCTTCTCACAATTGGCCCTCGTTTTGGTGGAGCTATTGATGATGCTGCTCGCTATTTTAGAGAAGCCCATGACAACGGATTATCGCCTTACGCATTTGT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC