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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttgtttcaagctcatttcttctctttccttcatacaatgggatttttgttctgtggttccagGTTCCATTTTGTCCAATGGTGGGATCGGAGGTTTTCTCTTCCGAAGTTAAGAAGACCGAAGTTCTCATGGAAAACTTTCGTCGCTCGATCGGCCTGCGTA

Basic information

species Selaginella moellendorffii
transcript EFJ27201
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ27201 (Selaginella moellendorffii), 3'ss of exon 2
lower sequence: GLYMA07G02170.1 (Glycine max), 3'ss of exon 2
-------------------------------gtttgtttcaagctcatttcttctcttt---ccttcatacaa-tgggatttttgttc-tgtggttc--cagGTTCCATTTTGTCCAATGGTGGGATCGGAGGTTTTCTCTTCCGAAGTTAAGAAGACCGAAGTTCTCATGGAAAACTTTCGTCGCTCGATCGGCCTGCGTA
                               |||| |||        | | ||   | |   ||||| | |   ||  | |  ||||  ||    ||  |||||||| || || |||||||| || || || |||| ||| || ||||| ||||||||||| |||||||||||||| ||| | ||  | || || |||||||
gtttccctctcaagactctcattctcgtggtgttttttttttctctgtgttttgattgtgacccttcttgctgctgataataatgtttatgccactctgcagGTTCCTTTCTGCCCAATGGTTGGTTCTGAAGTTTACTCCTCAGAAGTAAAGAAGACCGAGGTTCTCATGGAAAATTTTAGACGGGCCATTGGTCTGCGTA

upper sequence: EFJ27201 (Selaginella moellendorffii), 3'ss of exon 2
lower sequence: AT5G22330.1 (Arabidopsis thaliana), 3'ss of exon 2
--------------------------------------------------------gtttgtttcaagctcatttcttctctttccttcatacaatgggatttttgttctgtggttccagGTTCCATTTTGTCCAATGGTGGGATCGGAGGTTTTCTCTTCCGAAGTTAAGAAGACCGAAGTTCTCATGGAAAACTTTCGTCGCTCGATCGGCCTGCGTA
                                                          |||| | |||||  |||||| |  ||    | ||   |       |||||   |  || ||||||||||| ||||||||||| ||||| ||||||| ||| || || |||||||| || || ||||||||||| || ||| | ||  | || || || ||||
gtaattttggatgtctcattttgtatcttctttgttacattgtttccacatggcttcattgtatgaagcttttttcttttacttttagcttattttatctggattgtttctttcttgcagGTTCCATTCTGTCCAATGGTTGGATCTGAGGTTTACTCATCAGAGGTTAAGAAAACAGAGGTTCTCATGGAGAATTTTAGACGTGCCATTGGTCTACGTA

upper sequence: EFJ27201 (Selaginella moellendorffii), 3'ss of exon 2
lower sequence: PP1S4_73V6.1 (Physcomitrella patens), 3'ss of exon 3
----------------------------gtttgtttcaagctcatttcttct---ctttcct-tcatacaatgggatt----tttgttctgtggttccagGTTCCATTTTGTCCAATGGTGGGATCGGAGGTTTTCTCTTCCGAAGTTAAGAAGACCGAAGTTCTCATGGAAAACTTTCGTCGCTCGATCGGCCTGCGTA
                              |  ||| ||   |   |  |||   | ||||| |  |   || |        |||||  |    || ||||||||||| || |||||||| || || || |||| ||| || |||||||||||||| |||||||| ||||| || || || ||  | || || || ||||
tttgaaagtattgattgaatgctttgaaaatgatttgaaagcctccttctctgggcattcctattgtttcatcgagccatggtttgtattcccttttcagGTTCCATTCTGCCCAATGGTAGGGTCCGAAGTTTACTCATCAGAAGTTAAGAAGACGGAAGTTCTTATGGAGAATTTCCGCCGTGCAATTGGGCTTCGTA

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|169060615|gb|FE467353.1|FE467353
EST:     CCGGGAAAACAGCCATCGCATTGGGCATAGCTCAGGAGCTAGGCAGCAAG                         GTTCCATTTTGTCCAATGGTGGGATCGGAGGTTTTCTCTTCCGAAGTTAAG
genomic: CCGGGAAAACAGCCATCGCATTGGGCATAGCTCAGGAGCTAGGCAGCAAGgtttgtttca ... gtggttccagGTTCCATTTTGTCCAATGGTGGGATCGGAGGTTTTCTCTTCCGAAGTTAAG






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aagctcatttcttctctttccttcatacaatgggatttttgttctgtggttccagGTTCCATTTTGTCCAATGGTGGGATCGGAGGTTTTCTCTTCCGAAGTTAAGAAGACCGAAGTTCTCATGGAAAACTTTCGTCGCTCGATCGGCCTGCGTA
                                  atttttgtt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtttgtttcaagctcatttcttctctttccttcatacaatgggatttttgttctgtggttccagGTTCCATTTTGTCCAATGGTGGGATCGGAGGTTTTCTCTTCCGAAGTTAAGAAGACCGAAGTTCTCATGGAAAACTTTCGTCGCTCGATCGGCCTGCGTA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CATGGA