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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gaaagatttccttttttttctatattcataagctgtcttacacattgctgttggtctctcttccagGTCCAGCTCGCCGAGGCTTTAGAGGAAGAGGGTGCCGATATCATCCAAACAGAGGGTGGAACAGCTTCTACTCCTTCCAAGCCTGGGATCACAGGTCTCA

Basic information

species Selaginella moellendorffii
transcript EFJ22466
intron # 6
splice site 3'
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|169046730|gb|FE456668.1|FE456668
EST:     ACATCACTCTTTCAGTGACGGTGCCACATACTTTGCCACTCGATGAGCAG                         GTCCAGCTCGCCGAGGCTTTAGAGGAAGAGGGTGCCGATATCATCCAAACA
genomic: ACATCACTCTTTCAGTGACGGTGCCACATACTTTGCCACTCGATGAGCAGgaaagatttc ... tctcttccagGTCCAGCTCGCCGAGGCTTTAGAGGAAGAGGGTGCCGATATCATCCAAACA
EST: gi|169070532|gb|FE479809.1|FE479809
EST:     ACATCACTCTTTCAGTGACGGTGCCACATACTTTGCCACTCGATGAGCAG                         GTCCAGCTCGCCGAGGCTTTAGAGGAAGAGGGTGCCGATATCATCCAAACA
genomic: ACATCACTCTTTCAGTGACGGTGCCACATACTTTGCCACTCGATGAGCAGgaaagatttc ... tctcttccagGTCCAGCTCGCCGAGGCTTTAGAGGAAGAGGGTGCCGATATCATCCAAACA
EST: gi|169054264|gb|FE463205.1|FE463205
EST:     ACATCACTCTTTCAGTGACGGTGCCACATACTTTGCCACTCGATGAGCAG                         GTCCAGCTCGCCGAGGCTTTAGAGGAAGAGGGTGCCGATATCATCCAAACA
genomic: ACATCACTCTTTCAGTGACGGTGCCACATACTTTGCCACTCGATGAGCAGgaaagatttc ... tctcttccagGTCCAGCTCGCCGAGGCTTTAGAGGAAGAGGGTGCCGATATCATCCAAACA
EST: gi|169019639|gb|FE427468.1|FE427468
EST:     ACATCACTCTTTCAGTGACGGTGCCACATACTTTGCCACTCGATGAGCAG                         GTCCAGCTCGCCGAGGCTTTAGAGGAAGAGGGTGCCGATATCATCCAAACA
genomic: ACATCACTCTTTCAGTGACGGTGCCACATACTTTGCCACTCGATGAGCAGgaaagatttc ... tctcttccagGTCCAGCTCGCCGAGGCTTTAGAGGAAGAGGGTGCCGATATCATCCAAACA
EST: gi|70670894|gb|DN839471.1|DN839471
EST:     ACATCACTCTTTCAGTGACGGTGCCACATACTTTGCCACTCGATGAGCAG                         GTCCAGCTCGCCGAGGCTTTAGAGGAAGAGGGTGCCGATATCATCCAAACA
genomic: ACATCACTCTTTCAGTGACGGTGCCACATACTTTGCCACTCGATGAGCAGgaaagatttc ... tctcttccagGTCCAGCTCGCCGAGGCTTTAGAGGAAGAGGGTGCCGATATCATCCAAACA
EST: gi|169068421|gb|FE478998.1|FE478998
EST:     ACATCACTCTTTCAGTGACGGTGCCACATACTTTGCCACTCGATGAGCAG                         GTCCAGCTCGCCGAGGCTTTAGAGGAAGAGGGTGCCGATATCATCCAAACA
genomic: ACATCACTCTTTCAGTGACGGTGCCACATACTTTGCCACTCGATGAGCAGgaaagatttc ... tctcttccagGTCCAGCTCGCCGAGGCTTTAGAGGAAGAGGGTGCCGATATCATCCAAACA
EST: gi|169025044|gb|FE434670.1|FE434670
EST:     ACATCACTCTTTCAGTGACGGTGCCACATACTTTGCCACTCGATGAGCAG                         GTCCAGCTCGCCGAGGCTTTAGAGGAAGAGGGTGCCGATATCATCCAAACA
genomic: ACATCACTCTTTCAGTGACGGTGCCACATACTTTGCCACTCGATGAGCAGgaaagatttc ... tctcttccagGTCCAGCTCGCCGAGGCTTTAGAGGAAGAGGGTGCCGATATCATCCAAACA
EST: gi|169106951|gb|FE508834.1|FE508834
EST:     ACATCACTCTTTCAGTGACGGTGCCACATACTTTGCCACTCGATGAGCAG                         GTCCAGCTCGCCGAGGCTTTAGAGGAAGAGGGTGCCGATATCATCCAAACA
genomic: ACATCACTCTTTCAGTGACGGTGCCACATACTTTGCCACTCGATGAGCAGgaaagatttc ... tctcttccagGTCCAGCTCGCCGAGGCTTTAGAGGAAGAGGGTGCCGATATCATCCAAACA
EST: gi|169046729|gb|FE456667.1|FE456667
EST:     ACATCACTCTTTCAGTGACGGTGCCACATACTTTGCCACTCGATGAGCAG                         GTCCAGCTCGCCGAGGCTTTAGAGGAAGAGGGTGCCGATATCATCCAAACA
genomic: ACATCACTCTTTCAGTGACGGTGCCACATACTTTGCCACTCGATGAGCAGgaaagatttc ... tctcttccagGTCCAGCTCGCCGAGGCTTTAGAGGAAGAGGGTGCCGATATCATCCAAACA
EST: gi|169036088|gb|FE445128.1|FE445128
EST:     ACATCACTCTTTCAGTGACGGTGCCACATACTTTGCCACTCGATGAGCAG                         GTCCAGCTCGCCGAGGCTTTAGAGGAAGAGGGTGCCGATATCATCCAAACA
genomic: ACATCACTCTTTCAGTGACGGTGCCACATACTTTGCCACTCGATGAGCAGgaaagatttc ... tctcttccagGTCCAGCTCGCCGAGGCTTTAGAGGAAGAGGGTGCCGATATCATCCAAACA
EST: gi|169060729|gb|FE469755.1|FE469755
EST:     ACATCACTCTTTCAGTGACGGTGCCACATACTTTGCCACTCGATGAGCAG                         GTCCAGCTCGCCGAGGCTTTAGAGGAAGAGGGTGCCGATATCATCCAAACA
genomic: ACATCACTCTTTCAGTGACGGTGCCACATACTTTGCCACTCGATGAGCAGgaaagatttc ... tctcttccagGTCCAGCTCGCCGAGGCTTTAGAGGAAGAGGGTGCCGATATCATCCAAACA
EST: gi|169070531|gb|FE479808.1|FE479808
EST:     ACATCACTCTTTCAGTGACGGTGCCACATACTTTGCCACTCGATGAGCAG                         GTCCAGCTCGCCGAGGCTTTAGAGGAAGAGGGTGCCGATATCATCCAAACA
genomic: ACATCACTCTTTCAGTGACGGTGCCACATACTTTGCCACTCGATGAGCAGgaaagatttc ... tctcttccagGTCCAGCTCGCCGAGGCTTTAGAGGAAGAGGGTGCCGATATCATCCAAACA
EST: gi|169054265|gb|FE463206.1|FE463206
EST:     ACATCACTCTTTCAGTGACGGTGCCACATACTTTGCCACTCGATGAGCAG                         GTCCAGCTCGCCGAGGCTTTAGAGGAAGAGGGTGCCGATATCATCCAAACA
genomic: ACATCACTCTTTCAGTGACGGTGCCACATACTTTGCCACTCGATGAGCAGgaaagatttc ... tctcttccagGTCCAGCTCGCCGAGGCTTTAGAGGAAGAGGGTGCCGATATCATCCAAACA
EST: gi|169019638|gb|FE427467.1|FE427467
EST:     ACATCACTCTTTCAGTGACGGTGCCACATACTTTGCCACTCGATGAGCAG                         GTCCAGCTCGCCGAGGCTTTAGAGGAAGAGGGTGCCGATATCATCCAAACA
genomic: ACATCACTCTTTCAGTGACGGTGCCACATACTTTGCCACTCGATGAGCAGgaaagatttc ... tctcttccagGTCCAGCTCGCCGAGGCTTTAGAGGAAGAGGGTGCCGATATCATCCAAACA
EST: gi|169068959|gb|FE477703.1|FE477703
EST:     ACATCACTCTTTCAGTGACGGTGCCACATACTTTGCCACTCGATGAGCAG                         GTCCAGCTCGCCGAGGCTTTAGAGGAAGAGGGTGCCGATATCATCCAAACA
genomic: ACATCACTCTTTCAGTGACGGTGCCACATACTTTGCCACTCGATGAGCAGgaaagatttc ... tctcttccagGTCCAGCTCGCCGAGGCTTTAGAGGAAGAGGGTGCCGATATCATCCAAACA
EST: gi|169099322|gb|FE502108.1|FE502108
EST:     ACATCACTCTTTCAGTGACGGTGCCACATACTTTGCCACTCGATGAGCAG                         GTCCAGCTCGCCGAGGCTTTAGAGGAAGAGGGTGCCGATATCATCCAAACA
genomic: ACATCACTCTTTCAGTGACGGTGCCACATACTTTGCCACTCGATGAGCAGgaaagatttc ... tctcttccagGTCCAGCTCGCCGAGGCTTTAGAGGAAGAGGGTGCCGATATCATCCAAACA
EST: gi|169042964|gb|FE452318.1|FE452318
EST:     ACATCACTCTTTCAGTGACGGTGCCACATACTTTGCCACTCGATGAGCAG                         GTCCAGCTCGCCGAGGCTTTAGAGGAAGAGGGTGCCGATATCATCCAAACA
genomic: ACATCACTCTTTCAGTGACGGTGCCACATACTTTGCCACTCGATGAGCAGgaaagatttc ... tctcttccagGTCCAGCTCGCCGAGGCTTTAGAGGAAGAGGGTGCCGATATCATCCAAACA
EST: gi|169099321|gb|FE502107.1|FE502107
EST:     ACATCACTCTTTCAGTGACGGTGCCACATACTTTGCCACTCGATGAGCAG                         GTCCAGCTCGCCGAGGCTTTAGAGGAAGAGGGTGCCGATATCATCCAAACA
genomic: ACATCACTCTTTCAGTGACGGTGCCACATACTTTGCCACTCGATGAGCAGgaaagatttc ... tctcttccagGTCCAGCTCGCCGAGGCTTTAGAGGAAGAGGGTGCCGATATCATCCAAACA
EST: gi|169044589|gb|FE450628.1|FE450628
EST:     ACATCACTCTTTCAGTGACGGTGCCACATACTTTGCCACTCGATGAGCAG                         GTCCAGCTCGCCGAGGCTTTAGAGGAAGAGGGTGCCGATATCATCCAAACA
genomic: ACATCACTCTTTCAGTGACGGTGCCACATACTTTGCCACTCGATGAGCAGgaaagatttc ... tctcttccagGTCCAGCTCGCCGAGGCTTTAGAGGAAGAGGGTGCCGATATCATCCAAACA
EST: gi|169042965|gb|FE452319.1|FE452319
EST:     ACATCACTCTTTCAGTGACGGTGCCACATACTTTGCCACTCGATGAGCAG                         GTCCAGCTCGCCGAGGCTTTAGAGGAAGAGGGTGCCGATATCATCCAAACA
genomic: ACATCACTCTTTCAGTGACGGTGCCACATACTTTGCCACTCGATGAGCAGgaaagatttc ... tctcttccagGTCCAGCTCGCCGAGGCTTTAGAGGAAGAGGGTGCCGATATCATCCAAACA
EST: gi|169036087|gb|FE445127.1|FE445127
EST:     ACATCACTCTTTCAGTGACGGTGCCACATACTTTGCCACTCGATGAGCAG                         GTCCAGCTCGCCGAGGCTTTAGAGGAAGAGGGTGCCGATATCATCCAAACA
genomic: ACATCACTCTTTCAGTGACGGTGCCACATACTTTGCCACTCGATGAGCAGgaaagatttc ... tctcttccagGTCCAGCTCGCCGAGGCTTTAGAGGAAGAGGGTGCCGATATCATCCAAACA
EST: gi|169025043|gb|FE434669.1|FE434669
EST:     ACATCACTCTTTCAGTGACGGTGCCACATACTTTGCCACTCGATGAGCAG                         GTCCAGCTCGCCGAGGCTTTAGAGGAAGAGGGTGCCGATATCATCCAAACA
genomic: ACATCACTCTTTCAGTGACGGTGCCACATACTTTGCCACTCGATGAGCAGgaaagatttc ... tctcttccagGTCCAGCTCGCCGAGGCTTTAGAGGAAGAGGGTGCCGATATCATCCAAACA
EST: gi|169060728|gb|FE469754.1|FE469754
EST:     ACATCACTCTTTCAGTGACGGTGCCACATACTTTGCCACTCGATGAGCAG                         GTCCAGCTCGCCGAGGCTTTAGAGGAAGAGGGTGCCGATATCATCCAAACA
genomic: ACATCACTCTTTCAGTGACGGTGCCACATACTTTGCCACTCGATGAGCAGgaaagatttc ... tctcttccagGTCCAGCTCGCCGAGGCTTTAGAGGAAGAGGGTGCCGATATCATCCAAACA
EST: gi|169027095|gb|FE435629.1|FE435629
EST:     ACATCACTCTTTCAGTGACGGTGCCACATACTTTGCCACTCGATGAGCAG                         GTCCAGCTCGCCGAGGCTTTAGAGGAAGAGGGTGCCGATATCATCCAAACA
genomic: ACATCACTCTTTCAGTGACGGTGCCACATACTTTGCCACTCGATGAGCAGgaaagatttc ... tctcttccagGTCCAGCTCGCCGAGGCTTTAGAGGAAGAGGGTGCCGATATCATCCAAACA

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: 35 (upstream exon), 33 (downstream exon)
Score: 48

GTCTTAGAGCTCACTAGAAGAACAAGAGAACTTTTGCCACACATCACTCTTTCAGTGACGGTGCCACATACTTTGCCACTCGATGAGCAGgaaagatttc ... tctcttccagGTCCAGCTCGCCGAGGCTTTAGAGGAAGAGGGTGCCGATATCATCCAAACAGAGGGTGGAACAGCTTCTACTCCTTCCAAGCCTGGGATCACAGGTCTCA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttttttttctatattcataagctgtcttacacattgctgttggtctctcttccagGTCCAGCTCGCCGAGGCTTTAGAGGAAGAGGGTGCCGATATCATCCAAACAGAGGGTGGAACAGCTTCTACTCCTTCCAAGCCTGGGATCACAGGTCTCA
                       gtcttac  putative branch site (score: 48)
                                       ttggtctctcttcc  putative PPT
     tttctatattcataa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gaaagatttccttttttttctatattcataagctgtcttacacattgctgttggtctctcttccagGTCCAGCTCGCCGAGGCTTTAGAGGAAGAGGGTGCCGATATCATCCAAACAGAGGGTGGAACAGCTTCTACTCCTTCCAAGCCTGGGATCACAGGTCTCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA