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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gatttttctttaaaaattgtgctcatctattggattatatcagatcAATGTCATGGACACATTGAGCAGGCTGAGCCATGACACAGACTCGGAAGTCGCGATG

Basic information

species Selaginella moellendorffii
transcript EFJ26022
intron # 18
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ26022 (Selaginella moellendorffii), 3'ss of exon 18
lower sequence: AT2G20580.1 (Arabidopsis thaliana), 3'ss of exon 17
----------------------------------------------------gatttttctttaaaaattgtgct-----catctattggattatatcagatcAATGTCATGGACACATTGAGCAGGCTGAGCCATGACACAGACTCGGAAGTCGCGATG
                                                    |   | |     || | || | |      || | |   |  ||  ||| | | ||| |||||||| |||||| |||| |||||||||||||| |||||||| || |||
gtaaatacttttgtaaatgtagttttactgcacctgcttacaattattagtgggcgtctagagtaatactgggtttttaatatttttcccacaattccagGTGACTGTAATGGACACCTTGAGCCGGCTTAGCCATGACACAGATTCGGAAGTTGCCATG

upper sequence: EFJ26022 (Selaginella moellendorffii), 3'ss of exon 18
lower sequence: AT4G28470.1 (Arabidopsis thaliana), 3'ss of exon 17
-------------------------------------------gatttttct--ttaaaaattgtgct---------catctattggattatatcagatcAATGTCATGGACACATTGAGCAGGCTGAGCCATGACACAGACTCGGAAGTCGCGATG
                                            | ||||||  |||| |||  || |          | || ||  || ||  ||| | | ||| |||||||| |||||||| || |||||||||||||| || ||||| || |||
gtgagtattatttttgcatatctagttttcggcggcgtgcagttacttttctgcttaagaatactgttgttactctctaacttttttataattccagGTGACTGTTATGGACACTTTGAGCAGACTAAGCCATGACACAGATTCAGAAGTTGCAATG

upper sequence: EFJ26022 (Selaginella moellendorffii), 3'ss of exon 18
lower sequence: Vv12s0028g03130.t01 (Vitis vinifera), 3'ss of exon 19
------------------------------------------------gatttttctttaaaaattgtgctcatct-----attggattat----atcagatcAATGTCATGGACACATTGAGCAGGCTGAGCCATGACACAGACTCGGAAGTCGCGATG
                                                  | ||| | | |||||  |||||| ||     | ||| || |    | ||| ||||||| ||||||||||| ||||| || ||||||||||||||  | ||||| || |||
accagttgtgaaagttcaaaattgagggtgtactatatcatgctaatgtctctttttatgaaaatcttgctcacctccttgactgggttgttcttaccagGTCAATGTTATGGACACATTAAGCAGACTTAGCCATGACACAGATACAGAAGTAGCAATG

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|169064751|gb|FE476097.1|FE476097
EST:     TGCCTTTGGCTCTGGGTCTCTTGTCGATTTCGAATCC----G-AAGA-TT                         AATGTCATGGACACATTGAGCAGGCTGAGCCATGACACTGACTCGGAAGTC
genomic: TGCCTTTGGCTCTGGGTCTCTTGTCGATATCGAATCCGAAGGTAAGACTTgatttttctt ... atatcagatcAATGTCATGGACACATTGAGCAGGCTGAGCCATGACACAGACTCGGAAGTC
EST: gi|169025374|gb|FE435988.1|FE435988
EST:     TGCCTTTGGCTCTGGGTCTCTTGTCGATATCGAATCC----G-AAGA-TC                         AATGTCATGGACACATTGAGCAGGCTGAGCCATGACACAGACTCGGAAGTC
genomic: TGCCTTTGGCTCTGGGTCTCTTGTCGATATCGAATCCGAAGGTAAGACTTgatttttctt ... atatcagatcAATGTCATGGACACATTGAGCAGGCTGAGCCATGACACAGACTCGGAAGTC
EST: gi|169088931|gb|FE494443.1|FE494443
EST:     TGCCTTTGGCTCTGGGTCTCTTGTCGATATCGAATCC----G-AAGA-TC                         AATGTCATGGACACATTGAGCAGGCTGAGCCATGACACAGACTCGGAAGTC
genomic: TGCCTTTGGCTCTGGGTCTCTTGTCGATATCGAATCCGAAGGTAAGACTTgatttttctt ... atatcagatcAATGTCATGGACACATTGAGCAGGCTGAGCCATGACACAGACTCGGAAGTC
EST: gi|169019957|gb|FE431022.1|FE431022
EST:     TGCCTTTGGCTCTGGGTCTCTTGTCGATATCGAATCC----G-AAGA-TC                         AATGTCATGGACACATTGAGCAGGCTGAGCCATGACACAGACTCGGAAGTC
genomic: TGCCTTTGGCTCTGGGTCTCTTGTCGATATCGAATCCGAAGGTAAGACTTgatttttctt ... atatcagatcAATGTCATGGACACATTGAGCAGGCTGAGCCATGACACAGACTCGGAAGTC
EST: gi|169080935|gb|FE486104.1|FE486104
EST:     TGCCTTTGGCTCTGGGTCTCTTGTCGATATCGAATCC----G-AAGA-TC                         AATGTCATGGACACATTGAGCAGGCTGAGCCATGACACAGACTCGGAAGTC
genomic: TGCCTTTGGCTCTGGGTCTCTTGTCGATATCGAATCCGAAGGTAAGACTTgatttttctt ... atatcagatcAATGTCATGGACACATTGAGCAGGCTGAGCCATGACACAGACTCGGAAGTC
EST: gi|169030421|gb|FE438677.1|FE438677
EST:     TGCCTTTGGCTCTGGGTCTCTTGTCGATTTCGAATCC----G-AAGA-TT                         AATGTCATGGACACATTGAGCAGGCTGAGCCATGACACTGACTCGGAAGTC
genomic: TGCCTTTGGCTCTGGGTCTCTTGTCGATATCGAATCCGAAGGTAAGACTTgatttttctt ... atatcagatcAATGTCATGGACACATTGAGCAGGCTGAGCCATGACACAGACTCGGAAGTC
EST: gi|169116305|gb|FE517252.1|FE517252
EST:     TGCCTTTGGCTCTGGGTCTCTTGTCGATTTCGAATCC----G-AAGA-TT                         AATGTCATGGACACATTGAGCAGGCTGAGCCATGACACTGACTCGGAAGTC
genomic: TGCCTTTGGCTCTGGGTCTCTTGTCGATATCGAATCCGAAGGTAAGACTTgatttttctt ... atatcagatcAATGTCATGGACACATTGAGCAGGCTGAGCCATGACACAGACTCGGAAGTC
EST: gi|169066440|gb|FE474663.1|FE474663
EST:     TGCCTTTGGCTCTGGGTCTCTTGTCGATTTCGAATCC----G-AAGA-TT                         AATGTCATGGACACATTGAGCAGGCTGAGCCATGACACTGACTCGGAAGTC
genomic: TGCCTTTGGCTCTGGGTCTCTTGTCGATATCGAATCCGAAGGTAAGACTTgatttttctt ... atatcagatcAATGTCATGGACACATTGAGCAGGCTGAGCCATGACACAGACTCGGAAGTC
EST: gi|169097980|gb|FE498777.1|FE498777
EST:     TGCCTTTGGCTCTGGGTCTCTTGTCGATTTCGAATCC----G-AAGA-TT                         AATGTCATGGACACATTGAGCAGGCTGAGCCATGACACTGACTCGGAAGTC
genomic: TGCCTTTGGCTCTGGGTCTCTTGTCGATATCGAATCCGAAGGTAAGACTTgatttttctt ... atatcagatcAATGTCATGGACACATTGAGCAGGCTGAGCCATGACACAGACTCGGAAGTC
EST: gi|169064752|gb|FE476098.1|FE476098
EST:     TGCCTTTGGCTCTGGGTCTCTTGTCGATTTCGAATCCGAAG--A----TT                         AATGTCATGGACACATTGAGCAGGCTGAGCCATGACACTGACTCGGAAGTC
genomic: TGCCTTTGGCTCTGGGTCTCTTGTCGATATCGAATCCGAAGGTAAGACTTgatttttctt ... atatcagatcAATGTCATGGACACATTGAGCAGGCTGAGCCATGACACAGACTCGGAAGTC
EST: gi|169059060|gb|FE468205.1|FE468205
EST:     TGCCTTTGGCTCTGGGTCTCTTGTCGATATCGAATCC----G-AAGA-TC                         AATGTCATGGACACATTGAGCAGGCTGAGCCATGACACAGACTCGGAAGTC
genomic: TGCCTTTGGCTCTGGGTCTCTTGTCGATATCGAATCCGAAGGTAAGACTTgatttttctt ... atatcagatcAATGTCATGGACACATTGAGCAGGCTGAGCCATGACACAGACTCGGAAGTC
EST: gi|169116306|gb|FE517253.1|FE517253
EST:     TGCCTTTGGCTCTGGGTCTCTTGTCGATTTCGAATCC----G-AAGA-TT                         AATGTCATGGACACATTGAGCAGGCTGAGCCATGACACTGACTCGGAAGTC
genomic: TGCCTTTGGCTCTGGGTCTCTTGTCGATATCGAATCCGAAGGTAAGACTTgatttttctt ... atatcagatcAATGTCATGGACACATTGAGCAGGCTGAGCCATGACACAGACTCGGAAGTC
EST: gi|169097109|gb|FE498955.1|FE498955
EST:     TGCCTTTGGCTCTGGGTCTCTTGTCGATTTCGAATCC----G-AAGA-TT                         AATGTCATGGACACATTGAGCAGGCTGAGCCATGACACTGACTCGGAAGTC
genomic: TGCCTTTGGCTCTGGGTCTCTTGTCGATATCGAATCCGAAGGTAAGACTTgatttttctt ... atatcagatcAATGTCATGGACACATTGAGCAGGCTGAGCCATGACACAGACTCGGAAGTC
EST: gi|169064768|gb|FE473735.1|FE473735
EST:     TGCCTTTGGCTCTGGGTCTCTTGTCGATTTCGAATCC----G-AAGA-TT                         AATGTCATGGACACATTGAGCAGGCTGAGCCATGACACTGACTCGGAAGTC
genomic: TGCCTTTGGCTCTGGGTCTCTTGTCGATATCGAATCCGAAGGTAAGACTTgatttttctt ... atatcagatcAATGTCATGGACACATTGAGCAGGCTGAGCCATGACACAGACTCGGAAGTC
EST: gi|169025373|gb|FE435987.1|FE435987
EST:     CTGGGTCTCTTGTCGATATCGAATCC----G-AAGA-TC                         AATGTCATGGACACATTGAGCAGGCTGAGCCATGACACAGACTCGGAAGTC
genomic: CTGGGTCTCTTGTCGATATCGAATCCGAAGGTAAGACTTgatttttctt ... atatcagatcAATGTCATGGACACATTGAGCAGGCTGAGCCATGACACAGACTCGGAAGTC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gatttttctttaaaaattgtgctcatctattggattatatcagatcAATGTCATGGACACATTGAGCAGGCTGAGCCATGACACAGACTCGGAAGTCGCGATG
                           atttttctttaaaaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gatttttctttaaaaattgtgctcatctattggattatatcagatcAATGTCATGGACACATTGAGCAGGCTGAGCCATGACACAGACTCGGAAGTCGCGATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCAG