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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGGTAGGGCGGGCCCTGCCCACTGCCACCAATGAGACCCCGAAGGCTTACCGCATGAAGCTATGGGCCACTAACGAAGTGCGCGCCAAGTCGAAGTTCTGgtaagtcactcttcaaaaaatatttgtgatcttcagaaattatatggtaacctggcttggtatttatgtctgagagagcaagaattgcctcctggccagt...

Basic information

species Physcomitrella patens
transcript PP1S56_243V6.1
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S56_243V6.3 (Physcomitrella patens), 5'ss of exon 2
lower sequence: LOC_Os05g49030.1 (Oryza sativa), 5'ss of exon 2
TGGTAGGGCGGGCCCTGCCCACTGCCACCAATGAGACCCCGAAGGCTTACCGCATGAAGCTATGGGCCACTAACGAAGTGCGCGCCAAGTCGAAGTTCTGgtaagtcactcttcaaaaaatatttgtgatcttcagaaattatatggtaacctggcttggtatttatgtctgagagagcaagaattgcctcctggccagt
|||| || || || || || ||  ||  | |||||  ||| |||   |||||||||||||| |||||||| ||||| || ||||||||||| ||||||||||  ||  | |   ||    ||| | ||||     ||   |   || |||  | | |    ||||     ||   |     |    |             
TGGTGGGTCGCGCGCTCCCGACCCCCGGCGATGAGCACCCCAAGATCTACCGCATGAAGCTCTGGGCCACCAACGAGGTCCGCGCCAAGTCCAAGTTCTGgttggtgtcgcaagaactcttatctatgatgccttgatccttcgtg-taatttcgttgatgatttcgtgttgtttgtttgcgcgcag-------------

upper sequence: PP1S56_243V6.3 (Physcomitrella patens), 5'ss of exon 2
lower sequence: LOC_Os01g54870.1 (Oryza sativa), 5'ss of exon 2
TGGTAGGGCGGGCCCTGCCCACTGCCACCAATGAGACCCCGAAGGCTTACCGCATGAAGCTATGGGCCACTAACGAAGTGCGCGCCAAGTCGAAGTTCTGgtaagtcactcttcaaaaaatatttgtgatcttcagaaattatatggtaacctggcttggtatttatgtctgagagagcaagaattgcctcctggccagt--
|||| ||| ||| |||||| ||  | ||| | |||  ||| |||   |||||||||||||| ||||| || ||||| || ||||||||||| |||||||||| ||      |||  |      | | ||      |  ||| | | |      |  | ||| |||   | |     ||  |   |    |    ||  |   
TGGTGGGGAGGGGCCTGCCGACGCCGACCGACGAGCACCCCAAGATCTACCGCATGAAGCTCTGGGCTACCAACGAGGTCCGCGCCAAGTCCAAGTTCTGgtgaggg----ttcggatccccctcgcgaatgc--gccattgtttcgcgcttggtttaggtgtttggatgtcgttcagtgacgttactttgtctgcgtgcag

upper sequence: PP1S56_243V6.3 (Physcomitrella patens), 5'ss of exon 2
lower sequence: GRMZM2G022619_T02 (Zea mays), 5'ss of exon 2
TGGTAGGGCGGGCCCTGCCCACTGCCACCAATGAGACCCCGAAGGCTTACCGCATGAAGCTATGGGCCACTAACGAAGTGCGCGCCAAGTCGAAGTTCTGgtaagtcactcttcaaaaaatatttgtgatcttcagaaattatatggtaacctggcttggt-atttatgtctgagagagcaagaattgcctcctggccagt--
|||| || || || ||||| ||  | ||| |||||  ||| |||   |||||||||||||| |||||||||||||| || |||||||||||||||||||||| |||  |              || || |        ||| | || |    |   |  ||    ||| |||||  | |   |  |||| | || ||  |   
TGGTGGGTCGCGCGCTGCCGACCCCGACCGATGAGCACCCCAAGATCTACCGCATGAAGCTCTGGGCCACTAACGAGGTTCGCGCCAAGTCGAAGTTCTGgtcagtgccgtacaccctggggcttatgct-----aggattctctgattgtttttttccgttgcgtatttctgacggtg-gcgtcttgcttgcttgcgtgcag

upper sequence: PP1S56_243V6.3 (Physcomitrella patens), 5'ss of exon 2
lower sequence: GRMZM2G113720_T01 (Zea mays), 5'ss of exon 2
TGGTAGGGCGGGCCCTGCCCACTGCCACCAATGAGACCCCGAAGGCTTACCGCATGAAGCTATGGGCCACTAACGAAGTGCGCGCCAAGTCGAAGTTCTGgtaagtcactcttcaaaaaatatttgtgatcttcagaaattatatggtaacctggcttggtatttatgtctgagagagcaagaattgcctcctggccagt--
|||| || || || ||||| ||  | ||| |||||  ||| |||   |||||||||||||| |||||||| ||||| || ||||||||||| |||||||||| |||    | | | | | |      |||  |     ||| | || |  | |   |||||   ||| |||||  | |   |  | || |  | ||  |   
TGGTGGGTCGCGCGCTGCCGACCCCAACCGATGAGCACCCCAAGATCTACCGCATGAAGCTCTGGGCCACCAACGAGGTTCGCGCCAAGTCCAAGTTCTGgtcagtg---cattacacactcgggccgatgct--agcattgtctgattgcgt--tttggttcgtatttctgacggtg-gcgtctcgcttgattgcgcgcag

upper sequence: PP1S56_243V6.3 (Physcomitrella patens), 5'ss of exon 2
lower sequence: AC230013.2_FGT007 (Zea mays), 5'ss of exon 2
TGGTAGGGCGGGCCCTGCCCACTGCCACCAATGAGACCCCGAAGGCTTACCGCATGAAGCTATGGGCCACTAACGAAGTGCGCGCCAAGTCGAAGTTCTGgtaagtcactcttcaaaaaatatttgtgatcttcagaaattatatggtaacctggcttggtatttatgtctgagagagcaagaattgcctcctggccagt---------
|||| ||||| || ||||| ||  ||  | | |||  ||| |||   |||||||||||||| |||||||| |||||||| |||||||||   |||||||||| ||   |  |  | |   | |  |    ||| |    |  | | | |   |  ||| ||  ||| ||  |||    | |  | ||       |  |           
TGGTGGGGCGCGCGCTGCCGACGCCCGGCGACGAGCACCCCAAGATCTACCGCATGAAGCTCTGGGCCACCAACGAAGTCCGCGCCAAGAGCAAGTTCTGgtgagctgccatctata---tctgcgcttcctttatgtttcctgttgaaggatttcttcgt-cttaggtgcgagtcgtcgattaatgtactgctgttatctgtgcgcag

upper sequence: PP1S56_243V6.3 (Physcomitrella patens), 5'ss of exon 2
lower sequence: GRMZM2G126928_T01 (Zea mays), 5'ss of exon 2
TGGTAGGGCGGGCCCTGCCCACTGCCACCAATGAGACCCCGAAGGCTTACCGCATGAAGCTATGGGCCACTAACGAAGTGCGCGCCAAGTCGAAGTTCTGgtaagtcactcttcaaaaaatatttgtgat--cttcagaaattat-atggtaacctggcttggtatttatgtctgag--agagcaagaattgcctcctggccagt------------
|||| ||||| || ||||| ||  ||  | |||||  ||| |||   |||||||||||||| |||||||| ||||| || |||||||||   |||||||||| ||   | |  | |   |||| || |||  ||||||   |  |  | | |   |   ||       || |  ||    |  |    |||  |     |    |            
TGGTGGGGCGCGCGCTGCCGACGCCCGGCGATGAGCACCCCAAGATCTACCGCATGAAGCTCTGGGCCACCAACGAGGTCCGCGCCAAGAGCAAGTTCTGgtgag---cgccgccatctatatgtgcgattccttcaggtttccttgttgaaggattattttccccccattttcgatgcgggtcgtcgattaacgtactgttgttgtgagtgcgcag

upper sequence: PP1S56_243V6.3 (Physcomitrella patens), 5'ss of exon 2
lower sequence: GLYMA13G28830.1 (Glycine max), 5'ss of exon 2
TGGTAGGGCGGGCCCTGCCCACTGCCACCAATGAGACCCCGAAGGCTTACCGCATGAAGCTATGGGCCACTAACGAAGTGCGCGCCAAGTCGAAGTTCTGgtaa-gtcactcttcaaa--aaatatttgtgatcttcagaaattatatg-gtaacctggcttggtatttatg-tctgagagagcaagaattgcctcctggccagt----------------------------------------------
|||| ||| |||| || || || |   |  || ||   ||||||   ||||| |||||||| |||||||| ||||| || ||||||||||| |||||||||||| ||     ||| |    | || || || | ||  || ||  | |  ||||    | || |  |  |   || |||  |        ||  |       |                                                
TGGTCGGGAGGGCTCTCCCAACGGAAGCAGATCAGCATCCGAAGATCTACCGAATGAAGCTCTGGGCCACCAACGAGGTTCGCGCCAAGTCTAAGTTCTGgtaatgttttgtttctattttattagttttgtttttacgagatcctttatgtaat---gttttgcgtcaacaatcggagttaattgcctctgtttttgaattataggttttagtttttttttataattttgtatttttttctttcaattag

upper sequence: PP1S56_243V6.3 (Physcomitrella patens), 5'ss of exon 2
lower sequence: GLYMA15G10220.1 (Glycine max), 5'ss of exon 2
TGGTAGGGCGGGCCCTGCCCACTGCCACCAATGAGACCCCGAAGGCTTACCGCATGAAGCTATGGGCCACTAACGAAGTGCGCGCCAAGTCGAAGTTCTGgtaa------gtcactcttcaaaaa----atatttgtga---tcttcagaaattatatggtaacctggcttggtat-ttatgtctgagagagcaa---gaattgcctcc-tggccagt------------------------------------------------------
|||| ||| |||| || ||||| |   |  || ||  ||| |||   ||||| |||||||| |||||||| ||||| || ||||||||||| ||||||||||||      ||  || || |  |     || ||| |||    ||| |   | | | | |   | ||  ||| | | |||  |   ||  | ||    ||||||||||  |    | |                                                      
TGGTTGGGAGGGCTCTTCCCACGGAAGCAGATCAGCACCCCAAGATCTACCGAATGAAGCTCTGGGCCACCAACGAGGTTCGCGCCAAGTCCAAGTTCTGgtaatgttttgttcctttttattagttttatttttttgagatccttgatttaatgttttgcgccgtgtattgttttcttagtttccagcaatcagattgaattgcctctgttttgaattctagggtttaggggctgtttttataattttgaatttgttttgctttcaattag

upper sequence: PP1S56_243V6.3 (Physcomitrella patens), 5'ss of exon 2
lower sequence: GLYMA17G31430.1 (Glycine max), 5'ss of exon 1
TGGTAGGGCGGGCCCTGCCCACTGCCACCAATGAGACCCCGAAGGCTTACCGCATGAAGCTATGGGCCACTAACGAAGTGCGCGCCAAGTCGAAGTTCTGgtaagtcact----cttcaaaaaatatttgtgatcttcagaaatt--atatggtaacctg-gcttggtatttatgtctgagagagcaagaattgcctcc--tggccagt-----------------------------------------------------------------
|||| ||| |||| || || || |   |  || |   ||| ||    ||||| |||||||| |||||||| ||||| ||  |||||||||| ||||||||||||     |    |||   || |  ||| |  | || |||   |  || |  |    || ||   |||||  | ||| ||    ||  ||| |  | |  | |||  |                                                                 
TGGTTGGGAGGGCTCTTCCTACGGAAGCAGATCAACACCCCAAAATCTACCGGATGAAGCTCTGGGCCACCAACGAGGTTTGCGCCAAGTCCAAGTTCTGgtaatgttttgttcctttttaatagttttattttttttagatgcttgatgtaatgttttgcgccatgtattgttttcttagtttccagaaatcgaattcaattgcctctgtttttgaattctagggtttaggggttgtgttgtataatttcgaatttgttttgctttcaattag

upper sequence: PP1S56_243V6.3 (Physcomitrella patens), 5'ss of exon 2
lower sequence: Vv10s0003g03150.t01 (Vitis vinifera), 5'ss of exon 2
TGGTAGGGCGGGCCCTGCCCACTGCCACCAATGAGACCCCGAAGGCTTACCGCATGAAGCTATGGGCCACTAACGAAGTGCGCGCCAAGTCGAAGTTCTGgtaagtcactcttcaaaaaatatttgtg-atcttcagaaattatat----ggtaacctggcttggtatttatgtctgagagagcaagaattgcctcctggccagt
| || ||| | || || ||  | |  ||| |||||   ||||||   |||||||||||||| |||||||| || || || |||||||| |||||||||||||| ||     | | | ||  || |||| || |   |  ||| | |    |||||   || | ||  |||  ||  | ||      |  |||  ||      || 
TTGTGGGGAGAGCTCTCCCGTCGGAGACCGATGAGCATCCGAAGATCTACCGCATGAAGCTCTGGGCCACAAATGAGGTTCGCGCCAAATCGAAGTTCTGgtatgtggga-tacgataatgatctgtggatttgtggttattgtttaattggtaataaggttcgggttttgagttaggga---tttggtttga-tctgaaatag-

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|208353060|gb|DC926083.1|DC926083
EST:     CGCATGAAGCTATGGGCCACTAACGAAGTGCGCGCCAAGTCGAAGTTCTG                         GTACTTCCTGAGGAAGCTGCAGAAGGTGAAGAAGGCTCACGGCCAACTCCT
genomic: CGCATGAAGCTATGGGCCACTAACGAAGTGCGCGCCAAGTCGAAGTTCTGgtaagtcact ... tcctttgcagGTACTTCCTGAGGAAGCTGCAGAAGGTGAAGAAGGCTCACGGCCAACTCCT
EST: gi|37825472|gb|BJ583538.1|BJ583538
EST:     CGCATGAAGCTATGGGCCACTAACGAAGTGCGCGCCAAGTCGAAGTTCTG                         GTACTTCCTGAGGAAGCTGCAGAAGGTGAAGAAGGCTCACGGCCAACTCCT
genomic: CGCATGAAGCTATGGGCCACTAACGAAGTGCGCGCCAAGTCGAAGTTCTGgtaagtcact ... tcctttgcagGTACTTCCTGAGGAAGCTGCAGAAGGTGAAGAAGGCTCACGGCCAACTCCT
EST: gi|18346362|gb|BJ178405.1|BJ178405
EST:     CGCATGAAGCTATGGGCCACTAACGAAGTGCGCGCCAAGTCGAAGTTCTG                         GTACTTCCTGAGGAAGCTGCAGAAGGTGAAGAAGGCTCACGGCCAACTCCT
genomic: CGCATGAAGCTATGGGCCACTAACGAAGTGCGCGCCAAGTCGAAGTTCTGgtaagtcact ... tcctttgcagGTACTTCCTGAGGAAGCTGCAGAAGGTGAAGAAGGCTCACGGCCAACTCCT
EST: gi|37847485|gb|BJ605493.1|BJ605493
EST:     ACGAAGTGCGCGCCAAGTCGAAGTTCTG                         GTACTTCCTGAGGAAGCTGCAGAAGGTGAAGAAGGCTCACGGCCAACTCCT
genomic: ACGAAGTGCGCGCCAAGTCGAAGTTCTGgtaagtcact ... tcctttgcagGTACTTCCTGAGGAAGCTGCAGAAGGTGAAGAAGGCTCACGGCCAACTCCT
EST: gi|37838414|gb|BJ596422.1|BJ596422
EST:     CGCATGAAGCTATGGGCCACTAACGAAGTGCGCGCCAAGTCGAAGTTCTG                         GTACTTCCTGAGGAAGCTGCAGAAGGTGAAGAAGGCTCACGGCCAACTCCT
genomic: CGCATGAAGCTATGGGCCACTAACGAAGTGCGCGCCAAGTCGAAGTTCTGgtaagtcact ... tcctttgcagGTACTTCCTGAGGAAGCTGCAGAAGGTGAAGAAGGCTCACGGCCAACTCCT
EST: gi|37852027|gb|BJ610035.1|BJ610035
EST:     CGCATGAAGCTATGGGCCACTAACGAAGTGCGCGCCAAGTCGAAGTTCTG                         GTACTTCCTGAGGAAGCTGCAGAAGGTGAAGAAGGCTCACGGCCAACTCCT
genomic: CGCATGAAGCTATGGGCCACTAACGAAGTGCGCGCCAAGTCGAAGTTCTGgtaagtcact ... tcctttgcagGTACTTCCTGAGGAAGCTGCAGAAGGTGAAGAAGGCTCACGGCCAACTCCT
EST: gi|37846767|gb|BJ604775.1|BJ604775
EST:     CGCATGAAGCTATGGGCCACTAACGAAGTGCGCGCCAAGTCGAAGTTCTG                         GTACTTCCTGAGGAAGCTGCAGAAGGTGAAGAAGGCTCACGGCCAACTCCT
genomic: CGCATGAAGCTATGGGCCACTAACGAAGTGCGCGCCAAGTCGAAGTTCTGgtaagtcact ... tcctttgcagGTACTTCCTGAGGAAGCTGCAGAAGGTGAAGAAGGCTCACGGCCAACTCCT
EST: gi|18343070|gb|BJ175108.1|BJ175108
EST:     CGCATGAAGCTATGGGCCACTAACGAAGTGCGCGCCAAGTCGAAGTTCTG                         GTACTTCCTGAGGAAGCTGCAGAAGGTGAAGAAGGCTCACGGCCAACTCCT
genomic: CGCATGAAGCTATGGGCCACTAACGAAGTGCGCGCCAAGTCGAAGTTCTGgtaagtcact ... tcctttgcagGTACTTCCTGAGGAAGCTGCAGAAGGTGAAGAAGGCTCACGGCCAACTCCT
EST: gi|37822224|gb|BJ580290.1|BJ580290
EST:     CGCATGAAGCTATGGGCCACTAACGAAGTGCGCGCCAAGTCGAAGTTCTG                         GTACTTCCTGAGGAAGCTGCAGAAGGTGAAGAAGGCTCACGGCCAACTCCT
genomic: CGCATGAAGCTATGGGCCACTAACGAAGTGCGCGCCAAGTCGAAGTTCTGgtaagtcact ... tcctttgcagGTACTTCCTGAGGAAGCTGCAGAAGGTGAAGAAGGCTCACGGCCAACTCCT
EST: gi|208364358|gb|DC950659.1|DC950659
EST:     CGCATGAAGCTATGGGCCACTAACGAAGTGCGCGCCAAGTCGAAGTTCTG                         GTACTTCCTGAGGAAGCTGCAGAAGGTGAGGAAGGCTCACGGCCAACTCCT
genomic: CGCATGAAGCTATGGGCCACTAACGAAGTGCGCGCCAAGTCGAAGTTCTGgtaagtcact ... tcctttgcagGTACTTCCTGAGGAAGCTGCAGAAGGTGAAGAAGGCTCACGGCCAACTCCT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGGTAGGGCGGGCCCTGCCCACTGCCACCAATGAGACCCCGAAGGCTTACCGCATGAAGCTATGGGCCACTAACGAAGTGCGCGCCAAGTCGAAGTTCTGgtaagtcactcttcaaaaaatatttgtgatcttcagaaattatatggtaacctggcttggtatttatgtctgagagagcaagaattgcctcctggccagt

- - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC