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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AATTCTCATTCCCTACTACTTAAATGAGGAATCTAACTGGAGTCTCGACTTCTCCGATGTAAGAAACCAGGTCGTCATTGCAAGGAACAAGAAAATTGTCgtaagtttgtctcttctttcttaagtacgttcattctaagattcctgtaggcag

Basic information

species Selaginella moellendorffii
transcript EFJ30498
intron # 6
splice site 5'
intron type U2

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|169066246|gb|FE475200.1|FE475200
EST:     TCTCCGATGTAAGAAACCAGGTCGTCATTGCAAGGAACAAGAAAATTGTC                         CCCCGAGCTCTAGTGTTCATCAACCCCGGGAATCCCACTGGACAGTGCTTG
genomic: TCTCCGATGTAAGAAACCAGGTCGTCATTGCAAGGAACAAGAAAATTGTCgtaagtttgt ... ctgtaggcagCCCCGAGCTCTAGTGTTCATCAACCCCGGGAATCCCACTGGACAGTGCTTG
EST: gi|169046058|gb|FE453955.1|FE453955
EST:     TCTCCGATGTAAGAAACCAGGTCGTCATTGCAAGGAACAAGAAAATTGTC                         CCCCGAGCTCTAGTGTTCATCAACCCCGGGAATCCCACTGGACAGTGCTTG
genomic: TCTCCGATGTAAGAAACCAGGTCGTCATTGCAAGGAACAAGAAAATTGTCgtaagtttgt ... ctgtaggcagCCCCGAGCTCTAGTGTTCATCAACCCCGGGAATCCCACTGGACAGTGCTTG
EST: gi|169058051|gb|FE463959.1|FE463959
EST:     TCTCCGATGTAAGAAACCAGGTCGTCATTGCAAGGAACAAGAAAATTGTCGC                        
genomic: TCTCCGATGTAAGAAACCAGGTCGTCATTGCAAGGAACAAGAAAATTGT--Cgtaagtttgt ... ctgtaggca
EST: gi|169058051|gb|FE463959.1|FE463959
EST:     TCTCCGATGTAAGAAACCAGGTCGTCATTGCAAGGAACAAGAAAATTGTCGC                        
genomic: TCTCCGATGTAAGAAACCAGGTCGTCATTGCAAGGAACAAGAAAATTGT--Cgtaagtttgt ... ctgtaggca
EST: gi|169058051|gb|FE463959.1|FE463959
EST:     TCTCCGATGTAAGAAACCAGGTCGTCATTGCAAGGAACAAGAAAATTGTCGC                        
genomic: TCTCCGATGTAAGAAACCAGGTCGTCATTGCAAGGAACAAGAAAATTGT--Cgtaagtttgt ... ctgtaggca
EST: gi|169054115|gb|FE462350.1|FE462350
EST:     CTCCGATGNTA-GANACCAGGTCGTCATTGCAAGGAACAAGAAAATTGTC                         CCCCGAGCTCTAGTGTTCATCANCCCCGGGAATCCCACTGGACAGTGCTTG
genomic: CTCCGATG-TAAGAAACCAGGTCGTCATTGCAAGGAACAAGAAAATTGTCgtaagtttgt ... ctgtaggcagCCCCGAGCTCTAGTGTTCATCAACCCCGGGAATCCCACTGGACAGTGCTTG
EST: gi|169059961|gb|FE467323.1|FE467323
EST:     TCTCCGATGTAAGAAACCAGGTCGTCATTGCAAGGAACAAGAAAATTGTC                         CCCCGAGCTCTAGTGTTCATCAACCCCGGGAATCCCACTGGACAGTGCTTG
genomic: TCTCCGATGTAAGAAACCAGGTCGTCATTGCAAGGAACAAGAAAATTGTCgtaagtttgt ... ctgtaggcagCCCCGAGCTCTAGTGTTCATCAACCCCGGGAATCCCACTGGACAGTGCTTG
EST: gi|169056997|gb|FE466224.1|FE466224
EST:     TCTCCGATGTAAGAAACCAGGTCGTCATTGCAAGGAACAAGAAAATTGTC                         CCCCGAGCTCTAGTGTTCATCAACCCCGGGAATCCCACTGGACAGTGCTTG
genomic: TCTCCGATGTAAGAAACCAGGTCGTCATTGCAAGGAACAAGAAAATTGTCgtaagtttgt ... ctgtaggcagCCCCGAGCTCTAGTGTTCATCAACCCCGGGAATCCCACTGGACAGTGCTTG
EST: gi|169100333|gb|FE501130.1|FE501130
EST:     TCTCCGATGTAAGAAACCAGGTCGTCATTGCAAGGAACAAGAAAATTGTC                         CCCCGAGCTCTAGTGTTCATCAACCCCGGGAATCCCACTGGACAGTGCTTG
genomic: TCTCCGATGTAAGAAACCAGGTCGTCATTGCAAGGAACAAGAAAATTGTCgtaagtttgt ... ctgtaggcagCCCCGAGCTCTAGTGTTCATCAACCCCGGGAATCCCACTGGACAGTGCTTG
EST: gi|169035665|gb|FE445435.1|FE445435
EST:     TCTCCGATGTAAGAAACCAGGTCGTCATTGCAAGGAACAAGAAAATTGTC                         CCCCGAGCTCTAGTGTTCATCAACCCCGGGAATCCCACTGGACAGTGCTTG
genomic: TCTCCGATGTAAGAAACCAGGTCGTCATTGCAAGGAACAAGAAAATTGTCgtaagtttgt ... ctgtaggcagCCCCGAGCTCTAGTGTTCATCAACCCCGGGAATCCCACTGGACAGTGCTTG
EST: gi|169098675|gb|FE497249.1|FE497249
EST:     TCTCCGATGTAAGAAACCAGGTCGTCATTGCAAGGAACAAGAAAATTGTC                         CCCCGAGCTCTAGTGTTCATCAACCCCGGGAATCCCACTGGACAGTGCTTG
genomic: TCTCCGATGTAAGAAACCAGGTCGTCATTGCAAGGAACAAGAAAATTGTCgtaagtttgt ... ctgtaggcagCCCCGAGCTCTAGTGTTCATCAACCCCGGGAATCCCACTGGACAGTGCTTG
EST: gi|169078708|gb|FE486516.1|FE486516
EST:     TCTCCGATGTAAGAAACCAGGTCGTCATTGCAAGGAACAAGAAAATTGTCGC                        
genomic: TCTCCGATGTAAGAAACCAGGTCGTCATTGCAAGGAACAAGAAAATTGT--Cgtaagtttgt ... ctgtaggca
EST: gi|169078708|gb|FE486516.1|FE486516
EST:     TCTCCGATGTAAGAAACCAGGTCGTCATTGCAAGGAACAAGAAAATTGTCGC                        
genomic: TCTCCGATGTAAGAAACCAGGTCGTCATTGCAAGGAACAAGAAAATTGT--Cgtaagtttgt ... ctgtaggca
EST: gi|169078708|gb|FE486516.1|FE486516
EST:     TCTCCGATGTAAGAAACCAGGTCGTCATTGCAAGGAACAAGAAAATTGTCGC                        
genomic: TCTCCGATGTAAGAAACCAGGTCGTCATTGCAAGGAACAAGAAAATTGT--Cgtaagtttgt ... ctgtaggca
EST: gi|169111758|gb|FE511957.1|FE511957
EST:     TCTCCGATGTAAGAAACCAGGTCGTCATTGCAAGGAACAAGANAATTGTC                         CCCCGAGCTCTAGTGTTCATCAACCCCGGG
genomic: TCTCCGATGTAAGAAACCAGGTCGTCATTGCAAGGAACAAGAAAATTGTCgtaagtttgt ... ctgtaggcagCCCCGAGCTCTAGTGTTCATCAACCCCGGG
EST: gi|169067097|gb|FE474475.1|FE474475
EST:     TCTCCGATGTAAGAAACCAGGTCGTCATTGCAAGGAACAAGAAAATTGTC                         CCCCGAGCTCTAGTGTTCATCAACCCCGGGGAATCCCACTGGACAGTGCTT
genomic: TCTCCGATGTAAGAAACCAGGTCGTCATTGCAAGGAACAAGAAAATTGTCgtaagtttgt ... ctgtaggcagCCCCGAGCTCTAGTGTTCATCAACCCCGGG-AATCCCACTGGACAGTGCTT
EST: gi|169045644|gb|FE452605.1|FE452605
EST:     TCTCCGATGTAAGAAACCAGGTCGTCATTGCAAGGAACAAGAAAATTGTC                         CCCCGAGCTCTAGTGTTCATCAACCCCGGGAATCCCACTGGACAGTGCTTG
genomic: TCTCCGATGTAAGAAACCAGGTCGTCATTGCAAGGAACAAGAAAATTGTCgtaagtttgt ... ctgtaggcagCCCCGAGCTCTAGTGTTCATCAACCCCGGGAATCCCACTGGACAGTGCTTG
EST: gi|169042323|gb|FE452871.1|FE452871
EST:     TCTCCGATGTAAGAAACCAGGTCGTCATTGCAAGGAACAAGAAAATTGTC                         CCCCGAGCTCTAGTGTTCATCAACCCCGGGAATCCCACTGGACAGTGCTTG
genomic: TCTCCGATGTAAGAAACCAGGTCGTCATTGCAAGGAACAAGAAAATTGTCgtaagtttgt ... ctgtaggcagCCCCGAGCTCTAGTGTTCATCAACCCCGGGAATCCCACTGGACAGTGCTTG
EST: gi|169036858|gb|FE444975.1|FE444975
EST:     TCTCCGATGTAAGAAACCAGGTCGTCATTGCAAGGAACAAGAAAATTGTC                         CCCCGAGCTCTAGTGTTCATCAACCCCGGGAATCCCACTGGACAGTGCTTG
genomic: TCTCCGATGTAAGAAACCAGGTCGTCATTGCAAGGAACAAGAAAATTGTCgtaagtttgt ... ctgtaggcagCCCCGAGCTCTAGTGTTCATCAACCCCGGGAATCCCACTGGACAGTGCTTG
EST: gi|169097504|gb|FE497946.1|FE497946
EST:     TCTCCGATGTAAGAAACCAGGTCGTCATTGCAAGGAACAAGAAAATTGTC                         CCCCGAGCTCTAGTGTTCATCAACCC
genomic: TCTCCGATGTAAGAAACCAGGTCGTCATTGCAAGGAACAAGAAAATTGTCgtaagtttgt ... ctgtaggcagCCCCGAGCTCTAGTGTTCATCAACCC
EST: gi|169106601|gb|FE504636.1|FE504636
EST:     TCTCCGATGTAAGAAACCAGGTCGTCATTGCAAGGAACAAGAAAATTGTC                         CCCCGAGCTCTAGTGTTCATCAACCCCGGGAATCCCACTGGACAGTGCTTG
genomic: TCTCCGATGTAAGAAACCAGGTCGTCATTGCAAGGAACAAGAAAATTGTCgtaagtttgt ... ctgtaggcagCCCCGAGCTCTAGTGTTCATCAACCCCGGGAATCCCACTGGACAGTGCTTG
EST: gi|169065718|gb|FE476206.1|FE476206
EST:     TCTCCGATGTAAGAAACCAGGTCGTCATTGCAAGGAACAAGAAAATTGTC                         CCCCGAGCTCTAGTGTTCATCAACCCCGGGAATCCCACTGGACAGTGCTTG
genomic: TCTCCGATGTAAGAAACCAGGTCGTCATTGCAAGGAACAAGAAAATTGTCgtaagtttgt ... ctgtaggcagCCCCGAGCTCTAGTGTTCATCAACCCCGGGAATCCCACTGGACAGTGCTTG

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 1 RNA-Seqlibrary.


Block sizes: 34 (upstream exon), 28 (downstream exon)
Score: 18

AATTCTCATTCCCTACTACTTAAATGAGGAATCTAACTGGAGTCTCGACTTCTCCGATGTAAGAAACCAGGTCGTCATTGCAAGGAACAAGAAAATTGTCgtaagtttgt ... ctgtaggcagCCCCGAGCTCTAGTGTTCATCAACCCCGGGAATCCCACTGGACAGTGCTTGTCCGTGACTAATCTCCAGGATCTTATTAAGTTTTGCTACAAGGAGAGGC




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AATTCTCATTCCCTACTACTTAAATGAGGAATCTAACTGGAGTCTCGACTTCTCCGATGTAAGAAACCAGGTCGTCATTGCAAGGAACAAGAAAATTGTCgtaagtttgtctcttctttcttaagtacgttcattctaagattcctgtaggcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA