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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTCCTTGGCTGATTTGCAAAATGACGAGGACCAGGCTTTCCGCAAGATTAAGCTGAGGGCTGAGGACGTGCAGGGCAAGAATGTTCTCACCAACTTCTGGgtatatttcgtaccctttcatttagggtgtttcatagatgtcttgactactcttcgaaaccagaagtagcgggtgattttgcgccgcattcttgatgtag...

Basic information

species Physcomitrella patens
transcript PP1S92_47V6.1
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S92_47V6.2 (Physcomitrella patens), 5'ss of exon 3
lower sequence: GLYMA11G00890.1 (Glycine max), 5'ss of exon 3
CTCCTTGGCTGATTTGCAAAATGACGAGGACCAGGCTTTCCGCAAGATTAAGCTGAGGGCTGAGGACGTGCAGGGCAAGAATGTTCTCACCAACTTCTGGgtat-atttcgtaccctttcatttagggtgtttcatagatgtcttgactactcttcgaaaccagaagtagcgggtgattttgcgccgcattcttgatgtag
||| ||||||||| | |||   || || |||||  | |||   ||||||    |||| ||||||||||| || || ||||||||||| || ||||||||||||| ||   |       | |||| |      |||  | | |     |     ||  |    |  |  |  |  |  |  |                    
CTCATTGGCTGATCTCCAAGGGGATGAAGACCACTCCTTCAAGAAGATTCGTTTGAGAGCTGAGGACGTTCAAGGGAAGAATGTTCTGACAAACTTCTGGgtatgatggtggctgggcttattttga-----tcactgttattgactcagtgttttaatcttattaagattgtatcttcctag------------------

upper sequence: PP1S92_47V6.2 (Physcomitrella patens), 5'ss of exon 3
lower sequence: Vv14s0030g01810.t01 (Vitis vinifera), 5'ss of exon 4
CTCCTTGGCTGATTTGCAAAATGACGAGGACCAGGCTTTCCGCAAGATTAAGCTGAGGGCTGAGGACGTGCAGGGCAAGAATGTTCTCACCAACTTCTGGgtatatttcgtaccctttcatttagggtgtttcatagatgtcttgactactcttcgaaaccagaagtagcgggt---gattttgcgccgcattcttgatgtag
 ||| |||||||| | || || || ||||| || || | | | |||||    ||||| |||||||| ||||| || |||||||| ||||| |||||||||||      | || | |  || ||||  | |||      | | || | |||      ||     || | | || |    |||||       | | |        
TTCCCTGGCTGATCTTCAGAACGATGAGGATCATGCCTACAGGAAGATCCGACTGAGAGCTGAGGATGTGCAAGGAAAGAATGTCCTCACAAACTTCTGGgtggg---catagcatgacagttagccttttt------ttttttaattacatgcaaaagaggaaaattggggtttctcattttttttaataatttcag-----

upper sequence: PP1S92_47V6.2 (Physcomitrella patens), 5'ss of exon 3
lower sequence: EFJ11589 (Selaginella moellendorffii), 5'ss of exon 4
CTCCTTGGCTGATTTGCAAAATGACGAGGACCAGGCTTTCCGCAAGATTAAGCTGAGGGCTGAGGACGTGCAGGGCAAGAATGTTCTCACCAACTTCTGGgt----atatttcgtaccctttcatttagggtgtttcatagatgtcttgactactcttcgaaaccagaagtagcgggtgattttgcgccgcattcttgatgtag
 ||  | || || ||||| ||||||||||| || || ||||| ||||| ||||| ||||| ||||| || || |||  ||| |||||||| |||||||||||      |||| ||   ||    ||  |   | |||||   ||| || | ||||| |  |                                           
GTCGCTTGCGGACTTGCAGAATGACGAGGATCACGCCTTCCGGAAGATCAAGCTCAGGGCCGAGGATGTCCAAGGCCGGAACGTTCTCACGAACTTCTGGgttagagaattttgttttctccttttgtgctagcttcat---tgttttca-tactcatgcag------------------------------------------

upper sequence: PP1S92_47V6.2 (Physcomitrella patens), 5'ss of exon 3
lower sequence: EFJ09763 (Selaginella moellendorffii), 5'ss of exon 4
CTCCTTGGCTGATTTGCAAAATGACGAGGACCAGGCTTTCCGCAAGATTAAGCTGAGGGCTGAGGACGTGCAGGGCAAGAATGTTCTCACCAACTTCTGGgtatatttcgtaccctttcatttagggtgtttcatagatgtcttgactactcttcgaaaccagaagtagcgggtgattttgcgccgcattcttgatgtag
 ||  |||| || ||||| ||||||||||| || || ||||| ||||| ||||| ||||| ||||| || || |||  ||| |||||||| ||||||||||||       |  | ||||  |     |||      | |  ||| | |  | |      || | ||                                  
GTCGCTGGCGGACTTGCAGAATGACGAGGATCACGCCTTCCGGAAGATCAAGCTCAGGGCCGAGGATGTCCAAGGCCGGAACGTTCTCACGAACTTCTGGgtaagagaattttcttttctctccaattgt------gctagcttcattgttttcatgttcctgcag----------------------------------

upper sequence: PP1S92_47V6.2 (Physcomitrella patens), 5'ss of exon 3
lower sequence: EFJ09804 (Selaginella moellendorffii), 5'ss of exon 4
CTCCTTGGCTGATTTGCAAAATGACGAGGACCAGGCTTTCCGCAAGATTAAGCTGAGGGCTGAGGACGTGCAGGGCAAGAATGTTCTCACCAACTTCTGGgtatatttcgtaccctttcatttagggtgtttcatagatgtcttgactactcttcgaaaccagaagtagcgggtgattttgcgccgcattcttgatgtag
 ||  |||| || ||||| ||||||||||| || || ||||| ||||| ||||| ||||| ||||| || || |||  ||| || ||||| ||||||||||||       |  | ||||  |   | |   |     || |  |   | | |||  |  |  |  | ||                               
GTCGCTGGCGGACTTGCAGAATGACGAGGATCACGCCTTCCGGAAGATCAAGCTCAGGGCCGAGGATGTCCAAGGCCGGAACGTCCTCACGAACTTCTGGgtaagagaattttcttttctctcgtgctagcttcagtatttgattgttccactttcatgctcgt-gcag-------------------------------

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|67571386|gb|BJ944210.1|BJ944210
EST:     AGCTGAGGGCTGAGGACGTGCAGGGCAAGAATGTTCTCACCAACTTCTGG                         GGTATGGATTTAACAACCGACAAGCTGCGGTCCCTTGTGCGCAAGTGGC
genomic: AGCTGAGGGCTGAGGACGTGCAGGGCAAGAATGTTCTCACCAACTTCTGGgtatatttcg ... atatctacagGGTATGGATTTAACAACCGACAAGCTGCGGTCCCTTGTGCGCAAGTGGC
EST: gi|208360419|gb|DC950032.1|DC950032
EST:     AGCTGAGGGCTGAGGACGTGCAGGGCAAGAATGTTCTCACCAACTTCTGG                         GGTATGGATTTAACAACCGACAAGCTGCGGTCCCTTGTGCGCAAGTGGCAG
genomic: AGCTGAGGGCTGAGGACGTGCAGGGCAAGAATGTTCTCACCAACTTCTGGgtatatttcg ... atatctacagGGTATGGATTTAACAACCGACAAGCTGCGGTCCCTTGTGCGCAAGTGGCAG
EST: gi|19790465|gb|BQ041884.1|BQ041884
EST:     AGCTGAGGGCTGAGGACGTGCAGGGCAAGAATGTTCTCACCAACTTCTGG                         GGTATGGATTTAACAACCGACAAGCTGCGGTCCCTTGTGCGCAAGTGGCAG
genomic: AGCTGAGGGCTGAGGACGTGCAGGGCAAGAATGTTCTCACCAACTTCTGGgtatatttcg ... atatctacagGGTATGGATTTAACAACCGACAAGCTGCGGTCCCTTGTGCGCAAGTGGCAG
EST: gi|37851788|gb|BJ609796.1|BJ609796
EST:     AGCTGAGGGCTGAGGACGTGCAGGGCAAGAATGTTCTCACCAACTTCTGG                         GGTATGGATTTAACAACCGACAAGCTGCGGTCCCTTGTGCGCAAGTGGCAG
genomic: AGCTGAGGGCTGAGGACGTGCAGGGCAAGAATGTTCTCACCAACTTCTGGgtatatttcg ... atatctacagGGTATGGATTTAACAACCGACAAGCTGCGGTCCCTTGTGCGCAAGTGGCAG
EST: gi|100450921|gb|CJ974507.1|CJ974507
EST:     AGCTGAGGGCTGAGGACGTGCAGGGCAAGAATGTTCTCACCAACTTCTGG                         GGTATGGATTTAACAACCGACAAGCTGCGGTCCCTTGTGCGCAAGTGGCAG
genomic: AGCTGAGGGCTGAGGACGTGCAGGGCAAGAATGTTCTCACCAACTTCTGGgtatatttcg ... atatctacagGGTATGGATTTAACAACCGACAAGCTGCGGTCCCTTGTGCGCAAGTGGCAG
EST: gi|37826206|gb|BJ584218.1|BJ584218
EST:     AGCTGAGGGCTGAGGACGTGCAGGGCAAGAATGTTCTCACCAACTTCTGG                         GGTATGGATTTAACAACCGACAAGCTGCGGTCCCTTGTGCGCAAGTGGCAG
genomic: AGCTGAGGGCTGAGGACGTGCAGGGCAAGAATGTTCTCACCAACTTCTGGgtatatttcg ... atatctacagGGTATGGATTTAACAACCGACAAGCTGCGGTCCCTTGTGCGCAAGTGGCAG
EST: gi|18347427|gb|BJ179473.1|BJ179473
EST:     AGCTGAGGGCTGAGGACGTGCAGGGCAAGAATGTTCTCACCAACTTCTGG                         GGTATGGATTTAACAACCGACAAGCTGCGGTCCCTTGTGCGCAAGTGGCAG
genomic: AGCTGAGGGCTGAGGACGTGCAGGGCAAGAATGTTCTCACCAACTTCTGGgtatatttcg ... atatctacagGGTATGGATTTAACAACCGACAAGCTGCGGTCCCTTGTGCGCAAGTGGCAG
EST: gi|19777641|gb|BQ039208.1|BQ039208
EST:     AGCTGAGGGCTGAGGACGTGCAGGGCAAGAATGTTCTCACCAACTTCTGG                         GGTATGGATTTAACAACCGACAAGCTGCGGTCCCTTGTGCGCAAGTGGCAG
genomic: AGCTGAGGGCTGAGGACGTGCAGGGCAAGAATGTTCTCACCAACTTCTGGgtatatttcg ... atatctacagGGTATGGATTTAACAACCGACAAGCTGCGGTCCCTTGTGCGCAAGTGGCAG
EST: gi|18347038|gb|BJ179084.1|BJ179084
EST:     AGCTGAGGGCTGAGGACGTGCAGGGCAAGAATGTTCTCACCAACTTCTGG                         GGTATGGATTTAACAACCGACAAGCTGCGGTCCCTTGTGCGCAAGTGGCAG
genomic: AGCTGAGGGCTGAGGACGTGCAGGGCAAGAATGTTCTCACCAACTTCTGGgtatatttcg ... atatctacagGGTATGGATTTAACAACCGACAAGCTGCGGTCCCTTGTGCGCAAGTGGCAG
EST: gi|208372026|gb|DC936226.1|DC936226
EST:     AGCTGAGGGCTGAGGACGTGCAGGGCAAGAATGTTCTCACCAACTTCTGG                         GGTATGGATTTAACAACCGACAAGCTGCGGTCCCTTGTGCGCAAGTGGCAG
genomic: AGCTGAGGGCTGAGGACGTGCAGGGCAAGAATGTTCTCACCAACTTCTGGgtatatttcg ... atatctacagGGTATGGATTTAACAACCGACAAGCTGCGGTCCCTTGTGCGCAAGTGGCAG
EST: gi|162185712|gb|FC361566.1|FC361566
EST:     AGCTGAGGGCTGAGGACGTGCAGGGCAAGAATGTTCTCACCAACTTCTGG                         GGTATGGATTTAACAACCGACAAGCTGCGGTCCCTTGTGCGCAAGTGGCAG
genomic: AGCTGAGGGCTGAGGACGTGCAGGGCAAGAATGTTCTCACCAACTTCTGGgtatatttcg ... atatctacagGGTATGGATTTAACAACCGACAAGCTGCGGTCCCTTGTGCGCAAGTGGCAG
EST: gi|37847269|gb|BJ605277.1|BJ605277
EST:     AGCTGAGGGCTGAGGACGTGCAGGGCAAGAATGTTCTCACCAACTTCTGG                         GGTATGGATTTAACAACCGACAAGCTGCGGTCCCTTGTGCGCAAGTGGCAG
genomic: AGCTGAGGGCTGAGGACGTGCAGGGCAAGAATGTTCTCACCAACTTCTGGgtatatttcg ... atatctacagGGTATGGATTTAACAACCGACAAGCTGCGGTCCCTTGTGCGCAAGTGGCAG
EST: gi|67694711|gb|BJ954944.1|BJ954944
EST:     AGCTGAGGGCTGAGGACGTGCAGGGCAAGAATGTTCTCACCAACTTCTGG                         GGTATGGATTTAACAACCGACAAGCTGCGGTCCCTTGTGCGCAAGTGGCAG
genomic: AGCTGAGGGCTGAGGACGTGCAGGGCAAGAATGTTCTCACCAACTTCTGGgtatatttcg ... atatctacagGGTATGGATTTAACAACCGACAAGCTGCGGTCCCTTGTGCGCAAGTGGCAG
EST: gi|6167400|gb|AW145664.1|AW145664
EST:     AGCTGAGGGCTGAGGACGTGCAGGGCAAGAATGTTCTCACCAACTTCTGG                         GGTATGGATTTAACAACCGACAAGCTGCGGTCCCTTGTGCGCAAGTGGCAG
genomic: AGCTGAGGGCTGAGGACGTGCAGGGCAAGAATGTTCTCACCAACTTCTGGgtatatttcg ... atatctacagGGTATGGATTTAACAACCGACAAGCTGCGGTCCCTTGTGCGCAAGTGGCAG
EST: gi|162261198|gb|FC437215.1|FC437215
EST:     AGCTGAGGGCTGAGGACGTGCAGGGCAAGAATGTTCTCACCAACTTCTGG                         GGTATGGATTTAACAACCGACAAGCTGCGGTCCCTTGTGCGCAAGTGGCAG
genomic: AGCTGAGGGCTGAGGACGTGCAGGGCAAGAATGTTCTCACCAACTTCTGGgtatatttcg ... atatctacagGGTATGGATTTAACAACCGACAAGCTGCGGTCCCTTGTGCGCAAGTGGCAG
EST: gi|162216968|gb|FC393086.1|FC393086
EST:     AGCTGAGGGCTGAGGACGTGCAGGGCAAGAATGTTCTCACCAACTTCTGG                         GGTATGGATTTAACAACCGACAAGCTGCGGTCCCTTGTGCGCAAGTGGCAG
genomic: AGCTGAGGGCTGAGGACGTGCAGGGCAAGAATGTTCTCACCAACTTCTGGgtatatttcg ... atatctacagGGTATGGATTTAACAACCGACAAGCTGCGGTCCCTTGTGCGCAAGTGGCAG
EST: gi|162217884|gb|FC393880.1|FC393880
EST:     AGCTGAGGGCTGAGGACGTGCAGGGCAAGAATGTTCTCACCAACTTCTGG                         GGTATGGATTTAACAACCGACAAGCTGCGGTCCCTTGTGCGCAAGTGGCAG
genomic: AGCTGAGGGCTGAGGACGTGCAGGGCAAGAATGTTCTCACCAACTTCTGGgtatatttcg ... atatctacagGGTATGGATTTAACAACCGACAAGCTGCGGTCCCTTGTGCGCAAGTGGCAG
EST: gi|37844503|gb|BJ602511.1|BJ602511
EST:     AGCTGAGGGCTGAGGACGTGCAGGGCAAGAATGTTCTCACCAACTTCTGG                         GGTATGGATTTAACAACCGACAAGCTGCGGTCCCTTGTGCGCAAGTGGCAG
genomic: AGCTGAGGGCTGAGGACGTGCAGGGCAAGAATGTTCTCACCAACTTCTGGgtatatttcg ... atatctacagGGTATGGATTTAACAACCGACAAGCTGCGGTCCCTTGTGCGCAAGTGGCAG
EST: gi|100360481|gb|BY984147.1|BY984147
EST:     AGCTGAGGGCTGAGGACGTGCAGGGCAAGAATGTTCTCACCAACTTCTGG                         GGTATGGATTTAACAACCGACAAGCTGCGGTCCCTTGTGCGCAAGTGGCAG
genomic: AGCTGAGGGCTGAGGACGTGCAGGGCAAGAATGTTCTCACCAACTTCTGGgtatatttcg ... atatctacagGGTATGGATTTAACAACCGACAAGCTGCGGTCCCTTGTGCGCAAGTGGCAG
EST: gi|18345407|gb|BJ177450.1|BJ177450
EST:     AGCTGAGGGCTGAGGACGTGCAGGGCAAGAATGTTCTCACCAACTTCTGG                         GGTATGGATTTAACAACCGACAAGCTGCGGTCCCTTGTGCGCAAGTGGCAG
genomic: AGCTGAGGGCTGAGGACGTGCAGGGCAAGAATGTTCTCACCAACTTCTGGgtatatttcg ... atatctacagGGTATGGATTTAACAACCGACAAGCTGCGGTCCCTTGTGCGCAAGTGGCAG
EST: gi|18351838|gb|BJ183890.1|BJ183890
EST:     AGCTGAGGGCTGAGGACGTGCAGGGCAAGAATGTTCTCACCAACTTCTGG                         GGTATGGATTTAACAACCGACAAGCTGCGGTCCCTTGTGCGCAAGTGGCAG
genomic: AGCTGAGGGCTGAGGACGTGCAGGGCAAGAATGTTCTCACCAACTTCTGGgtatatttcg ... atatctacagGGTATGGATTTAACAACCGACAAGCTGCGGTCCCTTGTGCGCAAGTGGCAG
EST: gi|18373995|gb|BJ205573.1|BJ205573
EST:     AGCTGAGGGCTGAGGACGTGCAGGGCAAGAATGTTCTCACCAACTTCTGG                         GGTATGGATTTAACAACCGACAAGCTGCGGTCCCTTGTGCGCAAGTGGCAG
genomic: AGCTGAGGGCTGAGGACGTGCAGGGCAAGAATGTTCTCACCAACTTCTGGgtatatttcg ... atatctacagGGTATGGATTTAACAACCGACAAGCTGCGGTCCCTTGTGCGCAAGTGGCAG
EST: gi|162216969|gb|FC393087.1|FC393087
EST:     AGCTGAGGGCTGAGGACGTGCAGGGCAAGAATGTTCTCACCAACTTCTGG                         GGTATGGATTTAACAACCGACAAGCTGCGGTCCCTTGTGCGCAAGTGGCAG
genomic: AGCTGAGGGCTGAGGACGTGCAGGGCAAGAATGTTCTCACCAACTTCTGGgtatatttcg ... atatctacagGGTATGGATTTAACAACCGACAAGCTGCGGTCCCTTGTGCGCAAGTGGCAG
EST: gi|19788665|gb|BQ040844.1|BQ040844
EST:     AGCTGAGGGCTGAGGACGTGCAGGGCAAGAATGTTCTCACCAACTTCTGG                         GGTATGGATTTAACAACCGACAAGCTGCGGTCCCTTGTGCGCAAGTGGCAG
genomic: AGCTGAGGGCTGAGGACGTGCAGGGCAAGAATGTTCTCACCAACTTCTGGgtatatttcg ... atatctacagGGTATGGATTTAACAACCGACAAGCTGCGGTCCCTTGTGCGCAAGTGGCAG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CTCCTTGGCTGATTTGCAAAATGACGAGGACCAGGCTTTCCGCAAGATTAAGCTGAGGGCTGAGGACGTGCAGGGCAAGAATGTTCTCACCAACTTCTGGgtatatttcgtaccctttcatttagggtgtttcatagatgtcttgactactcttcgaaaccagaagtagcgggtgattttgcgccgcattcttgatgtag

- - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA