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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGGTGAAGTATTCTCCGGGAATCTGGATTGGTCTCCAATGCACAAAGATCCTGTGTTCTGGCGTGAGAACATCTCCAAGTTTGAAGAAAGCGACTTTCAGgttcttcttgacgtcttcaatgttgttctctttcttccatattcttctccttccttgtctctctggctcactccgtctcttgctaacaaaattgcaattg...

Basic information

species Physcomitrella patens
transcript PP1S21_158V6.1
intron # 10
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S21_158V6.1 (Physcomitrella patens), 5'ss of exon 10
lower sequence: GRMZM2G019999_T01 (Zea mays), 5'ss of exon 8
AGGTGAAGTATTCTCCGGGAATCTGGATTGGTCTCCAATGCACAAAGATCCTGTGTTCTGGCGTGAGAACATCTCCAAGTTTGAAGAAAGCGACTTTCAGgttcttcttgacgtct--tcaatgttgttctctttcttccatattcttctccttccttgtctctctggctcactccgtctcttgctaacaaaattgcaattg
|    ||||  |    ||  ||||||| |||||||||||||||||||||||    |||||||||||||||||   ||| ||||||||||  || || ||||| |  |||| | | |  ||    |||      ||     | | |  |  |     | | ||   | | | |   |     ||  || | ||  |   ||  
ACAGCAAGTTCTTCTTGGTCATCTGGACTGGTCTCCAATGCACAAAGATCCAAGTTTCTGGCGTGAGAACATTAACAATTTTGAAGAAAATGATTTCCAGgtacaccttgtcctttcatcttgattgaaaatatttaaataaacttgttgcacaattgggctaagtagtttaactctcaaattcatagctaagctattat--

upper sequence: PP1S21_158V6.1 (Physcomitrella patens), 5'ss of exon 10
lower sequence: GRMZM2G163233_T04 (Zea mays), 5'ss of exon 11
AGGTGAAGTATTCTCCGGGAATCTGGATTGGTCTCCAATGCACAAAGATCCTGTGTTCTGGCGTGAGAACATCTCCAAGTTTGAAGAAAGCGACTTTCAGgttcttcttgacgtcttcaatgttgttctctttcttccatattcttctccttccttgtctctctggctcactccgtctcttgctaacaaaattgcaattg-----------------------------------------------------------------------------------------------
|    ||||  |    ||  |||| || |||||||||||||||||||||||    |||||||||||||||||   ||| |||||||| |  || || |||||    |||| | | |    | | |  |  ||      |||  |||| |    ||||    | ||  |    ||  |  || | |||    |    || |                                                                                               
ACAGCAAGTTCTTCTTGGTCATCTTGACTGGTCTCCAATGCACAAAGATCCAAGTTTCTGGCGTGAGAACATTAACAATTTTGAAGAGAATGATTTCCAGgtatgccttgccctttcttctttgggacaattgtgattatacccttcgctggtcttgcaattgtgattttaccctccgttttccaactttgtgttcatagataagctattctggacaattcaatgttatagattagataggctcacaagcatttagctctgtggttgtgatgaaattgcacttataacttggcag

upper sequence: PP1S21_158V6.1 (Physcomitrella patens), 5'ss of exon 10
lower sequence: GLYMA02G06710.1 (Glycine max), 5'ss of exon 11
AGGTGAAGTATTCTCCGGGAATCTGGATTGGTCTCCAATGCACAAAGATCCTGTGTTCTGGCGTGAGAACATCTCCAAGTTTGAAGAAAGCGACTTTCAGgttcttcttgacgtcttcaatgttgttctctttcttccatattcttctccttccttgtctctctggctcactccgtctcttgctaacaaaa-ttgcaattg---
    |||||  ||   ||  |||||||||||||||| ||||||||||||||  | |||||||| || || ||   ||| ||||||||||  || || |||||   | |   | |  ||  |  | || |  |||  ||  ||||||    ||         |     |               ||||||   || || ||    
GCAAGAAGTTCTCCTTGGCCATCTGGATTGGTCTCCCATGCACAAAGATCCCATATTCTGGCGAGAAAATATAAACAACTTTGAAGAAAATGATTTCCAGgtatctat--gcattatcccttcttttatgcttcagccgaattcttga--ttaagcacacatgaaatttttggatgagaaaaataacaaggctttcagttactt

upper sequence: PP1S21_158V6.1 (Physcomitrella patens), 5'ss of exon 10
lower sequence: GLYMA16G25740.1 (Glycine max), 5'ss of exon 11
AGGTGAAGTATTCTCCGGGAATCTGGATTGGTCTCCAATGCACAAAGATCCTGTGTTCTGGCGTGAGAACATCTCCAAGTTTGAAGAAAGCGACTTTCAGgttctt---cttgacgtcttcaatgttgttctctttc---ttccatattcttctccttccttgtctctctggctcactccgtctcttgctaacaaaattgcaattg
    |||||  ||   ||  |||||||||||||||| ||||||||||||||  | |||||||| || || ||   ||| ||||||||||  || || |||||   |   | | |  |||||  |  | || |||||    || ||| |  |      |     |||||  || | |    |  | |  |   |   || | ||   
GCAAGAAGTTCTCCTTGGCCATCTGGATTGGTCTCCCATGCACAAAGATCCCATATTCTGGCGAGAAAATATAAACAACTTTGAAGAAAATGATTTCCAGgtatctgtgcattatctcttccttactcttttctttgttatttcatgtaatataaaattggcatctctggggatgatattgggtttcac---ctggatagaaa---

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|162193120|gb|FC371986.1|FC371986
EST:     CTGTGTTCTGGCGTGAGAACATCTCCAAGTTTGAAGAAAGCGACTTTCAG                         GTACTACGTATTTTGATTACGTTATTGGACAACTCCCGAGA
genomic: CTGTGTTCTGGCGTGAGAACATCTCCAAGTTTGAAGAAAGCGACTTTCAGgttcttcttg ... gtgcgtgaagGTACTACGTATTTTGATTACGTTATTGGACAACTCCCGAGA
EST: gi|37841730|gb|BJ599738.1|BJ599738
EST:     TGTGTTCTGGCGTGAGAACATCTCCAAGGTTTGAAGAAAGCGACTTTCAG                         GTACTACGTATTTTGATTACGTTATTGGACAACTCCCGAGATCCTAAAACC
genomic: TGTGTTCTGGCGTGAGAACATCTCCAA-GTTTGAAGAAAGCGACTTTCAGgttcttcttg ... gtgcgtgaagGTACTACGTATTTTGATTACGTTATTGGACAACTCCCGAGATCCTAAAACC
EST: gi|18334186|gb|BJ166202.1|BJ166202
EST:     GAAGAAAGCGACTTTCAG                         GTACTACGTATTTTGGTTACGTTATTGGACAACTCCCGAGATCCTAAAACC
genomic: GAAGAAAGCGACTTTCAGgttcttcttg ... gtgcgtgaagGTACTACGTATTTTGATTACGTTATTGGACAACTCCCGAGATCCTAAAACC
EST: gi|37847586|gb|BJ605594.1|BJ605594
EST:     CTGTGTTCTGGCGTGAGAACATCTCCAAGTTTGAAGAAAGCGACTTTCAG                         GTACTACGTATTTTGATTACGTTATTGGACAACTCCCGAGATCCTAAAACC
genomic: CTGTGTTCTGGCGTGAGAACATCTCCAAGTTTGAAGAAAGCGACTTTCAGgttcttcttg ... gtgcgtgaagGTACTACGTATTTTGATTACGTTATTGGACAACTCCCGAGATCCTAAAACC
EST: gi|162193119|gb|FC371985.1|FC371985
EST:     CTGTGTTCTGGCGTGAGAACATCTCCAAGTTTGAAGAAAGCGACTTTCAG                         GTTCTACGTATTTTGATTACGTTATTGGACAACTCCCGAGATCCTAAAACG
genomic: CTGTGTTCTGGCGTGAGAACATCTCCAAGTTTGAAGAAAGCGACTTTCAGgttcttcttg ... gtgcgtgaagGTACTACGTATTTTGATTACGTTATTGGACAACTCCCGAGATCCTAAAACC
EST: gi|162229967|gb|FC407329.1|FC407329
EST:     CTGTGTTCTGGCGTGAGAACATCTCCAAGTTTGAAGAAAGCGACTTTCAG                         GTACTACGTATTTTGATTACGTTATTGGACAACTCCCGAGATCCTAAAACG
genomic: CTGTGTTCTGGCGTGAGAACATCTCCAAGTTTGAAGAAAGCGACTTTCAGgttcttcttg ... gtgcgtgaagGTACTACGTATTTTGATTACGTTATTGGACAACTCCCGAGATCCTAAAACC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGGTGAAGTATTCTCCGGGAATCTGGATTGGTCTCCAATGCACAAAGATCCTGTGTTCTGGCGTGAGAACATCTCCAAGTTTGAAGAAAGCGACTTTCAGgttcttcttgacgtcttcaatgttgttctctttcttccatattcttctccttccttgtctctctggctcactccgtctcttgctaacaaaattgcaattg

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA