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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagaaaactgcaaagtccattaatctcatatttcttggctgcttccagGGAGATCCATTGTTTCAGACTCACGAAAATCTCGAGCACCTGGCAATGATGGAAAGAATTCTCGGTCCCATTCCCAGACGCATAATCGATAACGTAGA

Basic information

species Selaginella moellendorffii
transcript EFJ20929
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ20929 (Selaginella moellendorffii), 3'ss of exon 6
lower sequence: GRMZM2G094039_T06 (Zea mays), 3'ss of exon 7
-------------------gtaagaaaactgcaa--agtccattaatctcatattt--cttggctgcttccagGGAGATCCATTGTTTCAGACTCACGAAAATCTCGAGCACCTGGCAATGATGGAAAGAATTCTCGGTCCCATTCCCAGACGCATAATCGATAACGTAGA
                    | |     ||   |  ||||   ||||    |   |  | |  |   ||  |||| ||  ||||||||||||| ||||| ||||| || ||||| ||||||||||| ||  || | || ||  | ||       || ||    || | |  
gttagatctcttcacacactttatttttctagtaccagtctggtaattgttttcctaacatcacattttttagGGGGAAGCATTGTTTCAGACACACGAGAATCTGGAACACCTAGCAATGATGGAGAGGGTTTTGGGACCTCTACCAGAGGATATGATACGGAAAGCAAG

upper sequence: EFJ20929 (Selaginella moellendorffii), 3'ss of exon 6
lower sequence: GLYMA06G08480.1 (Glycine max), 3'ss of exon 9
------------------------------------------gtaagaaaactgcaaagtccattaatctcatatttcttggctgcttccagGGAGATCCATTGTTTCAGACTCACGAAAATCTCGAGCACCTGGCAATGATGGAAAGAATTCTCGGTCCCATTCCCAGACGCATAATCGATAACGTAGA
                                             |   |||  | |     | |  ||| | || |     ||  |  ||||| ||  |||||||||||||||| |||||  | |||||||||||||||||||||||| || | || || |||||    |  || ||    |      |
gtttgtcttccatatctatcaatatgtattaggcatggcttgaatatggaacaactagtcttagtgttctaa-atgtggaaacttttgacagGGTGAAGCATTGTTTCAGACTCATGAAAACTTGGAGCACCTGGCAATGATGGAAAGAGTTTTGGGACCTATTCCAGAGCATATGATTTGCAGGTCTAA

upper sequence: EFJ20929 (Selaginella moellendorffii), 3'ss of exon 6
lower sequence: GLYMA17G13440.1 (Glycine max), 3'ss of exon 7
--------------------------gtaagaaaactgcaaa---gtccatta------atctcatatttcttggctgc---ttccagGGAGATCCATTGTTTCAGACTCACGAAAATCTCGAGCACCTGGCAATGATGGAAAGAATTCTCGGTCCCATTCCCAGACGCATAATCGATAACGTAGA
                           ||| |||  |    |    ||  |||      ||  |||| ||  ||  |     || ||||| |   | ||||||||||||||||||||| | ||||| || || |||||||||||  | || |||||  | ||    | |||  |  | |  || ||
gtatgtttggctctctcaaatcctgtataaaaaacatatttatccatctcttagattctattccataatttgtgaatttatattacagGGCGGAGCTTTGTTTCAGACTCACGAAAATTTGGAGCATCTTGCCATGATGGAAAGGGTACTTGGTCCATTACCACAGCCCATGTTGAAGAGAGTCGA

upper sequence: EFJ20929 (Selaginella moellendorffii), 3'ss of exon 6
lower sequence: GLYMA05G02740.1 (Glycine max), 3'ss of exon 8
---------------------------------------gtaagaaaactgcaaagtccatta-atctcatatttcttggctgc---ttccagGGAGATCCATTGTTTCAGACTCACGAAAATCTCGAGCACCTGGCAATGATGGAAAGAATTCTCGGTCCCATTCC-CAGACGCATAATCGATAACGTAGA
                                        ||   |      |   |  |||  ||   ||| ||| ||  |     || ||||| ||  | |||||||||||||| |||||| | ||||| || ||||||||||||||  | || ||| |  | || ||||| ||| ||  | |  || ||
gtatgtttggctctttcaaaacctttatacaaagcacatttatccatctcatatcatagattgtattctataattcatgaatttgtattacagGGTGAAGCTTTGTTTCAGACTCATGAAAATTTAGAGCATCTTGCAATGATGGAAAGGGTACTTGGTTCATTACCACAGAC-CATGATGAAGAGAGTCGA

upper sequence: EFJ20929 (Selaginella moellendorffii), 3'ss of exon 6
lower sequence: Vv17s0000g09500.t01 (Vitis vinifera), 3'ss of exon 9
----------------------------------------------gtaagaaaactgcaaagtccattaatctcatatttcttggctgcttccagGGAGATCCATTGTTTCAGACTCACGAAAATCTCGAGCACCTGGCAATGATGGAAAGAATTCTCGGTCCCATTCCCAGACGCATAATCGATAACGTAGA
                                              | |    ||     | ||    | ||   | |||| ||   | |   ||||||||  |||||||||||||||| || ||||| |||||||| || |||||||||||  |  | |||||  | ||    | |||  |  | |  |||||
gtacgtttattaattaaattgcaatgcatgttgtctctttttgtcggcattggaatgatgaggtta--tgatgcaacatttattcattaca--cagGGAGAAGCATTGTTTCAGACTCATGAGAATCTGGAGCACCTTGCCATGATGGAAAGGGTGTTGGGTCCACTGCCGCAGCACATGCTGAAGAGAGTAGA

upper sequence: EFJ20929 (Selaginella moellendorffii), 3'ss of exon 6
lower sequence: PP1S132_58V6.1 (Physcomitrella patens), 3'ss of exon 9
-------------------------------------------------------------------------------------------------------------------------------gtaagaaaactgcaaa-gtccattaatc-tcatatttcttggctgcttccagGGAGATCCATTGTTTCAGACTCACGAAAATCTCGAGCACCTGGCAATGATGGAAAGAATTCTCGGTCCCATTCCCAGACGCATAATCGATAACGTAGA
                                                                                                                                | | |  | || ||| ||   | | |  | | | |  ||| ||  |  ||||| ||| ||||||||||||||||||| ||| | |||||  |||| ||||||||| || |  | ||||| |||||   || ||| ||| | |  | |||
gtatgggattcctatcgccttcctttctcttttatattcctctattatccagtaattccctatactttctcttcaaacttgtaaatttgagaaaatctttgatgtcatagtttttcatgcgaagatgttgaaaccaatgtaaatgtttttcagtggttacagtatttg-cta-tggcagGGTGATGCATTGTTTCAGACTCACGAGAATTTGGAGCATTTGGCTATGATGGAACGAGTCTTAGGTCCTATTCCTGTACACATGATCAAGAGGGCAGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtaagaaaactgcaaagtccattaatctcatatttcttggctgcttccagGGAGATCCATTGTTTCAGACTCACGAAAATCTCGAGCACCTGGCAATGATGGAAAGAATTCTCGGTCCCATTCCCAGACGCATAATCGATAACGTAGA
                        cattaat  putative branch site (score: 3)
                                             ctgcttcc  putative PPT
                         attaatctcatattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagaaaactgcaaagtccattaatctcatatttcttggctgcttccagGGAGATCCATTGTTTCAGACTCACGAAAATCTCGAGCACCTGGCAATGATGGAAAGAATTCTCGGTCCCATTCCCAGACGCATAATCGATAACGTAGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA