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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TAGTGTTGATTTCAAGCAAAGGTCAAGGTTCTCATATTCTGGAGTTTGATGAAGAGCTTTTCTTCATATACCTTCTTCCACCTATAATCTTCAATGCTGGgtatgttaacgttatccacttgacatctattgctgaagaaactgaagtagagcaggatagcttcagattctctattattgtcgatcttgtgttggtgacc...

Basic information

species Physcomitrella patens
transcript PP1S169_48V6.1
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S169_48V6.1 (Physcomitrella patens), 5'ss of exon 2
lower sequence: GLYMA07G38160.1 (Glycine max), 5'ss of exon 2
TAGTGTTGATTTCAAGCAAAGGTCAAGGTTCTCATATTCTGGAGTTTGATGAAGAGCTTTTCTTCATATACCTTCTTCCACCTATAATCTTCAATGCTGGgtatgttaacgttatccacttgacatctattgctgaagaaactgaagtagagcaggatagcttcagattctctattat-tgtcgatcttgtgttggtgacc
|  | ||| || | |    |||  || | ||||||||  | |  ||   |||||| ||||||||||| |||||||||||||| || ||||||||||| ||||  ||| || |     | ||      | ||  |    |   |  | |      |  || || || | | |   ||   |   ||| |||  ||| |    
TTATATTGTTTACCACGGGAGGAAAAAGCTCTCATATATTAGTTTTCAGTGAAGATCTTTTCTTCATTTACCTTCTTCCACCCATCATCTTCAATGCCGGgttagttcacttctcttaattttttatttttcttattcagctttcaattacat-gcttaactgcataatttaagttgcattatgattttgatttgttagaa

upper sequence: PP1S169_48V6.1 (Physcomitrella patens), 5'ss of exon 2
lower sequence: GLYMA10G30020.1 (Glycine max), 5'ss of exon 3
TAGTGTTGATTTCAAGCAAAGGTCAAGGTTCTCATATTCTGGAGTTTGATGAAGAGCTTTTCTTCATATACCTTCTTCCACCTATAATCTTCAATGCTGGgtatgttaacgttatccacttgacatc-tattgctgaagaaactgaagtagagcaggatagcttcagattctctattattgtcgatcttgtgttggtgacc-----------
|  | ||| | |  ||    ||  || | || |||||||| |  ||   |||||| |||||||| ||||| ||||| ||||||||||| |||||||| |||||     |  || |    ||| || | | |  |||   |    | | | ||        |||| | | | | ||| |||||| |  |   |  |  ||             
TCATTTTGCTGTTTAGTGGTGGCAAAAGCTCACATATTCTTGTTTTCAGTGAAGATCTTTTCTTTATATATCTTCTACCACCTATAATATTCAATGCCGGgta-----attttctttttttggcagcatttcactgtgtagttaggaatcgat-------gcttgatactatttatcattgtctaattaaagaagaggaggtattttgtttt

upper sequence: PP1S169_48V6.1 (Physcomitrella patens), 5'ss of exon 2
lower sequence: GLYMA17G02560.1 (Glycine max), 5'ss of exon 2
TAGTGTTGATTTCAAGCAAAGGTCAAGGTTCTCATATTCTGGAGTTTGATGAAGAGCTTTTCTTCATATACCTTCTTCCACCTATAATCTTCAATGCTGGgtatgttaacgttatccacttgacatctattgctgaagaaactgaagtagagcaggatagcttcagattctctattattgtcgatcttgtg--ttggtgacc
|  | ||| || | |    |||  || | |||||||| || |  ||   |||||| ||||||||||| || ||||||||||| || ||||||||||| ||||  ||| ||        |||    | ||||  |      | | |  |           |||  | | |   || |||        || ||  ||| ||   
TTATATTGTTTACTACTGGAGGAAAAAGCTCTCATATACTTGTCTTCAGTGAAGATCTTTTCTTCATTTATCTTCTTCCACCCATCATCTTCAATGCCGGgttagttcactactcttgcttcttttttattatttttcttatttagctttcatttacatgct--aaactgcataatataagttgcattatgatttgttggaa

upper sequence: PP1S169_48V6.1 (Physcomitrella patens), 5'ss of exon 2
lower sequence: GLYMA20G37370.1 (Glycine max), 5'ss of exon 3
TAGTGTTGATTTCAAGCAAAGGTCAAGGTTCTCATATTCTGGAGTTTGATGAAGAGCTTTTCTTCATATACCTTCTTCCACCTATAATCTTCAATGCTGGgtatgttaacgttatccacttgacatctattgctgaagaaactgaagtagagcaggatagcttcagattctctattattgtcgatcttgtgttggtgacc------------
|  | ||| | |  ||    ||  || | || |||||||| |  ||   |||||| |||||||| ||||||||||| || |||||||| || ||||| |||||  || |  ||      ||| || |  ||  |        || |||   | |     |||| | | | | ||| |||||| |  |   |  || ||              
TCATTTTGCTGTTTAGTGGTGGCAAAAGCTCGCATATTCTTGTTTTCAGTGAAGATCTTTTCTTTATATACCTTCTGCCGCCTATAATATTTAATGCCGGgtaattttatttt------ttggcagcatttctttg------tgtagtgaggaatcgatgcttgatactatttatcattgtctaattaaagaaggggaggtgttttgttttg

upper sequence: PP1S169_48V6.1 (Physcomitrella patens), 5'ss of exon 2
lower sequence: GLYMA03G40290.1 (Glycine max), 5'ss of exon 2
TAGTGTTGATTTCAAGCAAAGGTCAAGGTTCTCATATTCTGGAGTTTGATGAAGAGCTTTTCTTCATATACCTTCTTCCACCTATAATCTTCAATGCTGGgtat-gttaacgttatccacttgacatctattgctgaagaaactgaagtagagcaggatagcttcag-attctcta-ttattgtcgatcttgtgttggtgacc-------------------------------------------------
|  | ||| | |  ||    ||| || | || ||| |||| |  ||   |||||| |||||||| ||||||||||| |||||||| || || ||||| |||||  |||      | | ||| |   |||| || | | ||   | || |     | | |   || |  ||| |||| ||| |  | | |   ||   || |                                                   
TCATTTTGTTGTTGAGTCGCGGTAAAAGCTCGCATCTTCTAGTTTTCAGTGAAGATCTTTTCTTTATATACCTTCTGCCACCTATCATATTTAATGCCGGgtaaagtttttagcaccaactagttgtctaatgataatgaggataaaatgtttgacgctgtatttatcattgtctaattagttgcaacccaatgaaagttattttgtacttagagcaaggtatacataagtgatgttacataattattgcag

upper sequence: PP1S169_48V6.1 (Physcomitrella patens), 5'ss of exon 2
lower sequence: GLYMA19G42900.1 (Glycine max), 5'ss of exon 2
TAGTGTTGATTTCAAGCAAAGGTCAAGGTTCTCATATTCTGGAGTTTGATGAAGAGCTTTTCTTCATATACCTTCTTCCACCTATAATCTTCAATGCTGGgta----tgttaacgttatccacttgac-----atctattgctgaagaaactgaagt---agagcaggatagcttcagattctcta--ttattgtcgatcttgtgttggtgacc---------------------
|  | ||| | |  ||    ||| || | || ||| |||| |  ||    ||||| |||||||| ||||||||||| |||||||| || || ||||| |||||    | | | |   | | |  || |     |   ||||   ||  || ||       |  | |   ||  ||  | ||  ||    | | || | ||||||  |     |                      
TCATTTTGTTGTTGAGTCGCGGTAAAAGCTCGCATCTTCTAGTTTTCAGCGAAGATCTTTTCTTTATATACCTTCTGCCACCTATCATATTTAATGCCGGgtaaagttttcagcaccaactagctgtctaatgaatcattgtctaattaattggcaccccaatgaaaattattttgtgttttcctgatctctagttgttcttgtacttagagcaaggtatacatgattattccag

upper sequence: PP1S169_48V6.1 (Physcomitrella patens), 5'ss of exon 2
lower sequence: Vv07s0104g01280.t01 (Vitis vinifera), 5'ss of exon 2
---TAGTGTTGATTTCAAGCAAAGGTCAAGGTTCTCATATTCTGGAGTTTGATGAAGAGCTTTTCTTCATATACCTTCTTCCACCTATAATCTTCAATGCTGGgtatgttaacgttatccacttgacatctattgctgaagaaactgaagtagagcaggatagcttcagattctctattattgtcgatcttgtgttggtgacc-
   |  | || | | || |   |||  |    || |  ||| |    ||  |||| || |||||||||||||| |||||||| ||||| || |||||||||||||| |||    || | || ||  ||    ||  |     || |||| || |     ||   |        | || | |     ||   | ||   |     
TTCTCCTATTAACTACAGG---AGGAAAGATCTCACTCATTTTACTATTCAATGAGGAACTTTTCTTCATATATCTTCTTCCTCCTATCATATTCAATGCTGGgtaagtttgtttt-ttcatttttcacgattttatatctgaagtgaaatacaatctaattcttgtgatcgttttaatttgacttatgaagggtgcttttttc

upper sequence: PP1S169_48V6.1 (Physcomitrella patens), 5'ss of exon 2
lower sequence: Vv05s0020g01960.t01 (Vitis vinifera), 5'ss of exon 3
TAGTGTTGATTTCAAGCAAAGGTCAAGGTTCTCATATTCTGGAGTTTGATGAAGAGCTTTTCTTCATATACCTTCTTCCACCTATAATCTTCAATGCTGGgtatgttaacgttatccacttgacatctattgctgaagaaactgaagtagagca----ggatagcttcagattctctattattgtcgatcttgtgttggtgacc
|  |  |  |  | | |  |||  || | || |||||| | |  ||   |||||| |||||||| || || |||||||||||||| || || ||||||||||| |||    || |  |    |  || |||  |||| |   ||      |  |      || | ||||  || | |||      |  |    || |  |    
TTATTCTACTAACCACCCGAGGAAAAAGCTCACATATTTTAGTATTCAGTGAAGATCTTTTCTTTATTTATCTTCTTCCACCTATCATTTTTAATGCTGGgtaagttggatttcttaatgcaaactcgatt--tgaatattttgttcgtcattatcatcaatggattcat-ttatttatccagagcagttagatgcttattct-

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|162195589|gb|FC371890.1|FC371890
EST:     GAAGAGCTTTTCTTCATATACCTTCTTCCACCTATAATCTTCAATGCTGG                         GTTCCAGGTTAAGAAGAAGGAATTCTTTCGGAATTTCATAACAATCATGTT
genomic: GAAGAGCTTTTCTTCATATACCTTCTTCCACCTATAATCTTCAATGCTGGgtatgttaac ... tgattctcagGTTCCAGGTTAAGAAGAAGGAATTCTTTCGGAATTTCATAACAATCATGTT
EST: gi|162255349|gb|FC432075.1|FC432075
EST:     TTTCTTCATATACCTTCTTCCACCTATAATCTTCAATGCTGG                         GTTCCAGGTTAAGAAGAAGGAATTCTTTCGGAATTTCATAACAATCATGTT
genomic: TTTCTTCATATACCTTCTTCCACCTATAATCTTCAATGCTGGgtatgttaac ... tgattctcagGTTCCAGGTTAAGAAGAAGGAATTCTTTCGGAATTTCATAACAATCATGTT
EST: gi|18366347|gb|BJ198426.1|BJ198426
EST:     AAAGAGCTTTTCTTCATATACCTTCTTCCACCTATAATCTTCAATGCTGG                         GTTCCAGGTTAAGAAGAAGGAATTCTTTCGGAATTTCATAACAATCATGTT
genomic: GAAGAGCTTTTCTTCATATACCTTCTTCCACCTATAATCTTCAATGCTGGgtatgttaac ... tgattctcagGTTCCAGGTTAAGAAGAAGGAATTCTTTCGGAATTTCATAACAATCATGTT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TAGTGTTGATTTCAAGCAAAGGTCAAGGTTCTCATATTCTGGAGTTTGATGAAGAGCTTTTCTTCATATACCTTCTTCCACCTATAATCTTCAATGCTGGgtatgttaacgttatccacttgacatctattgctgaagaaactgaagtagagcaggatagcttcagattctctattattgtcgatcttgtgttggtgacc

- - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG