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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgacttcatagattgagatcttcttctttcttctttagcttgagtgggagtaactgagattgtttcaataccagGTGGACGAGAGAAGGCTCCGGCTGCGTTTTGTCGAAAGGCCCTGACTTCCACCGATTCGTTTGAGATGTGGGGCGATGGAATGCAGACGCGATCGTTCAC

Basic information

species Selaginella moellendorffii
transcript EFJ18599
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ18599 (Selaginella moellendorffii), 3'ss of exon 3
lower sequence: GRMZM2G124434_T01 (Zea mays), 3'ss of exon 4
------------gtgacttcatagattgagatcttc--ttctttcttctttagcttgagtgggagtaactgagattgtttcaataccagGTGGACGAGAGAAGGCTCCGGCTGCGTTTTGTCGAAAGGCCCTGACTTCCACCGATTCGTTTGAGATGTGGGGCGATGGAATGCAGACGCGATCGTTCAC
                 ||  | |  || |    |    || |     |  | |  |  ||  |  ||       | |||   || ||||||| || |||||||| |||||||| || ||  ||||||| | ||| ||||| ||   |||||||||||||||||||||  | |||||  | || |||||
gtgaacctactaccagttttctgggctgtggctgtgaggtcataacaatccaacg-gcctgataaaaaaatgctctctttgtctatcagGTGGCCGCGAGAAGGCACCGGCTGCCTTCTGCAGAAAGGCTCAGACATCCACGGAGAGGTTTGAGATGTGGGGCGATGGTCTCCAGACCAGGTCCTTCAC

upper sequence: EFJ18599 (Selaginella moellendorffii), 3'ss of exon 3
lower sequence: GLYMA19G43400.1 (Glycine max), 3'ss of exon 4
------------------------------------------gtgacttcatagattga--gatcttcttctttcttcttt-agcttgagtgggagtaactgagattgtttcaatac-cagGTGGACGAGAGAAGGCTCCGGCTGCGTTTTGTCGAAAGGCCCTGACTTCCACCGATTCGTTTGAGATGTGGGGCGATGGAATGCAGACGCGATCGTTCAC
                                           ||| |  ||| | |    ||  ||||| | |   ||||  | || |    |  |         |||||    |   ||||||| | ||||||||||| ||||| |||||||| ||| | || |||||||  |||   |||||||||||||| |||||| |||| ||  |||| |||||
gtatgttcttgactgaattgcaagtttttgcagttgttgtatttgagtcaataaactagtggacattcttttgtagccttttggatttaacaagtttgttgctttgtgttttgtcatatagGTGGAAGGGAGAAGGCTCCTGCTGCTTTTTGTCGCAAGACACTTACTTCCAAAGATCGATTTGAGATGTGGGGAGATGGATTGCAAACAAGATCCTTCAC

upper sequence: EFJ18599 (Selaginella moellendorffii), 3'ss of exon 3
lower sequence: GLYMA10G30400.1 (Glycine max), 3'ss of exon 3
------------------------------------------------gtgacttcatagattgagatcttcttctttctt----ctttagcttgagtgggagtaactgagattgtttcaatac-cagGTGGACGAGAGAAGGCTCCGGCTGCGTTTTGTCGAAAGGCCCTGACTTCCACCGATTCGTTTGAGATGTGGGGCGATGGAATGCAGACGCGATCGTTCAC
                                                 ||  |  || | | |  || || |  |||  |     ||  | || | |  |  |   |    ||||||    |  |||||||| | ||||||||||| ||||| |||||||| || |   | |||||||| |||   |||||||||||||| |||||| |||| || ||||| || ||
gcatgtttttcactgaattgaaagcttttatagttttgactttaccaaatgggtaaattggtagtcattttatattttggtaacctttcggatttaataagtttgtgttttgttgttttgtcatacagGTGGAAGGGAGAAGGCTCCTGCTGCTTTTTGTCGTAAAGTAATCACTTCCACTGATAGATTTGAGATGTGGGGAGATGGATTGCAAACACGATCATTTAC

upper sequence: EFJ18599 (Selaginella moellendorffii), 3'ss of exon 3
lower sequence: AT5G28840.1 (Arabidopsis thaliana), 3'ss of exon 4
-------gtgacttcatagattgagatcttcttctttcttctt--tagcttg--agtgggagtaac-tgagattgtttcaataccagGTGGACGAGAGAAGGCTCCGGCTGCGTTTTGTCGAAAGGCCCTGACTTCCACCGATTCGTTTGAGATGTGGGGCGATGGAATGCAGACGCGATCGTTCAC
            |  | || ||  |  |||  | |   |  ||  | | ||   | ||||| |||  |  | |||  ||||    ||||||| | ||||||||||| ||||| || ||| | ||||| | ||||||||| |||  ||||||||||||||| |||||  | ||||| || || || ||
gtagtatacagataaacagtttccgtactttgtgtgaatgattagttgtttactattgggattaatatttgcttggatcaac-ttagGTGGAAGGGAGAAGGCTCCAGCTGCTTTCTGTAGGAAGGCTCAGACTTCCACTGATAGGTTTGAGATGTGGGGAGATGGGCTTCAGACCCGTTCTTTTAC

upper sequence: EFJ18599 (Selaginella moellendorffii), 3'ss of exon 3
lower sequence: Vv14s0030g02180.t01 (Vitis vinifera), 3'ss of exon 4
----------------------------------------------------------------------------------------gtgacttca--tagattgagatcttcttctttcttctttagcttgagtgggagtaac-tgagattgtttcaataccagGTGGACGAGAGAAGGCTCCGGCTGCGTTTTGTCGAAAGGCCCTGACTTCCACCGATTCGTTTGAGATGTGGGGCGATGGAATGCAGACGCGATCGTTCAC
                                                                                        | |  || |    | || | ||  |      | || ||     | |||     |  | |     | | |   |   ||||||  ||||||||||||| ||||| ||||| |||||||| || |||||||||||   |||||| |||||||| || ||| | || || || || |||||
gtatgctcttaaaagttatggtgattttctacatgtattcgtgattttgtctcttggtcaccgtcaatggtagggagccaagtgcagagaggtttaagcccgctttaaattctaaatcatatttttggatcttagtaattttgtcgttttggtatatttgtcgtagGTGGGAGAGAGAAGGCTCCTGCTGCTTTTTGCCGAAAGGCTCTCACTTCCACCGACAAGTTTGAAATGTGGGGAGACGGACTTCAAACTCGTTCTTTCAC

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|169041899|gb|FE449379.1|FE449379
EST:     CCGCATTGGACGATTCCACAACATCTATGGACCCTTTGGGACCTGGAAAG                         GTGGACGAGAGAAGGCTCCGGCTGCGTTTTGTCGAAAGGCCCTGACTTCCA
genomic: CCGCATTGGACGATTCCACAACATCTATGGACCCTTTGGGACCTGGAAAGgtgacttcat ... tcaataccagGTGGACGAGAGAAGGCTCCGGCTGCGTTTTGTCGAAAGGCCCTGACTTCCA
EST: gi|169064800|gb|FE476120.1|FE476120
EST:     CCGCATTGGACGATTCCACAACATCTATGGACCCTTTGGGACCTGGAAAG                         GTGGACGAGAGAAGGCTCCGGCTGCGTTTTGTCGAAAGGCCCTGACTTCCA
genomic: CCGCATTGGACGATTCCACAACATCTATGGACCCTTTGGGACCTGGAAAGgtgacttcat ... tcaataccagGTGGACGAGAGAAGGCTCCGGCTGCGTTTTGTCGAAAGGCCCTGACTTCCA
EST: gi|169064799|gb|FE476119.1|FE476119
EST:     CCGCATTGGACGATTCCACAACATCTATGGACCCTTTGGGACCTGGAAAG                         GTGGACGAGAGAAGGCTCCGGCTGCGTTTTGTCGAAAGGCCCTGACTTCCA
genomic: CCGCATTGGACGATTCCACAACATCTATGGACCCTTTGGGACCTGGAAAGgtgacttcat ... tcaataccagGTGGACGAGAGAAGGCTCCGGCTGCGTTTTGTCGAAAGGCCCTGACTTCCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttcttctttcttctttagcttgagtgggagtaactgagattgtttcaataccagGTGGACGAGAGAAGGCTCCGGCTGCGTTTTGTCGAAAGGCCCTGACTTCCACCGATTCGTTTGAGATGTGGGGCGATGGAATGCAGACGCGATCGTTCAC
                            gagtaac  putative branch site (score: 2)
                                        ttgtttc  putative PPT
                                           tttcaata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgacttcatagattgagatcttcttctttcttctttagcttgagtgggagtaactgagattgtttcaataccagGTGGACGAGAGAAGGCTCCGGCTGCGTTTTGTCGAAAGGCCCTGACTTCCACCGATTCGTTTGAGATGTGGGGCGATGGAATGCAGACGCGATCGTTCAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GATGGA