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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGCTTTGCACCCGGAATGGCAGGAGCGCGCTCGCGCCGAGGCCCAGGAAGTCTGCGAAGGTGCCACTCCAGAAGCCGATTCAATCAGCAAGCTCAAGCTGgtaaaggttttacgttactttcgagtttcacgagctcaagctttctttctcatggctag

Basic information

species Selaginella moellendorffii
transcript EFJ06390
intron # 4
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|169068836|gb|FE477177.1|FE477177
EST:     TCTGCGAAGGTGCCACTCCAGAAGCCGATTCAATCAGCAAGCTCAAGCTG                         ATCAACATGATCCTCCACGAAACTCTCCGCCTGTATCCACCGGTGGGGGTG
genomic: TCTGCGAAGGTGCCACTCCAGAAGCCGATTCAATCAGCAAGCTCAAGCTGgtaaaggttt ... tcatggctagATCAACATGATCCTCCACGAAACTCTCCGCCTGTATCCACCGGTGGGGGTG
EST: gi|169055500|gb|FE463818.1|FE463818
EST:     TCTGCGAAGGTGCCACTCCAGAAGCCGATTCAATCAGCAAGCTCAAGCTG                         ATCAACATGATCCTCCACGAAACTCTCCGCCTGTATCCACCGGTGGGGGTG
genomic: TCTGCGAAGGTGCCACTCCAGAAGCCGATTCAATCAGCAAGCTCAAGCTGgtaaaggttt ... tcatggctagATCAACATGATCCTCCACGAAACTCTCCGCCTGTATCCACCGGTGGGGGTG
EST: gi|169078018|gb|FE489375.1|FE489375
EST:     TCTGCGAAGGTGCCACTCCAGAAGCCGATTCAATCAGCAAGCTCAAGCTG                         ATCAACATGATCCTCCACGAAACTCTCCGCCTGTATCCACCGGTGGGGGTG
genomic: TCTGCGAAGGTGCCACTCCAGAAGCCGATTCAATCAGCAAGCTCAAGCTGgtaaaggttt ... tcatggctagATCAACATGATCCTCCACGAAACTCTCCGCCTGTATCCACCGGTGGGGGTG
EST: gi|169042774|gb|FE450451.1|FE450451
EST:     TCTGCGAAGGTGCCACTCCAGAAGCCGATTCAATCAGCAAGCTCAAGCTG                         ATCAACATGATCCTCCACGAAACTCTCCGCCTGTATCCACCGGTGGGGGTG
genomic: TCTGCGAAGGTGCCACTCCAGAAGCCGATTCAATCAGCAAGCTCAAGCTGgtaaaggttt ... tcatggctagATCAACATGATCCTCCACGAAACTCTCCGCCTGTATCCACCGGTGGGGGTG
EST: gi|169096459|gb|FE499189.1|FE499189
EST:     TCTGCGAAGGTGCCACTCCAGAAGCCGATTCAATCAGCAAGCTCAAGCTG                         ATCAACATGATCCTCCACGAAACTCTCCGCCTGTATCCACCGGTGGGGGTG
genomic: TCTGCGAAGGTGCCACTCCAGAAGCCGATTCAATCAGCAAGCTCAAGCTGgtaaaggttt ... tcatggctagATCAACATGATCCTCCACGAAACTCTCCGCCTGTATCCACCGGTGGGGGTG
EST: gi|169077929|gb|FE487804.1|FE487804
EST:     TCTGCGAAGGTGCCACTCCAGAAGCCGATTCAATCAGCAAGCTCAAGCTG                         ATCAACATGATCCTCCACGAAACTCTCCGCCTGTATCCACCGGTGGGGGTG
genomic: TCTGCGAAGGTGCCACTCCAGAAGCCGATTCAATCAGCAAGCTCAAGCTGgtaaaggttt ... tcatggctagATCAACATGATCCTCCACGAAACTCTCCGCCTGTATCCACCGGTGGGGGTG
EST: gi|169061250|gb|FE470363.1|FE470363
EST:     TCTGCGAAGGTGCCACTCCAGAAGCCGATTCAATCAGCAAGCTCAAGCTG                         ATCAACATGATCCTCCACGAAACTCTCCGCCTGTATCCACCGGTGGGGGTG
genomic: TCTGCGAAGGTGCCACTCCAGAAGCCGATTCAATCAGCAAGCTCAAGCTGgtaaaggttt ... tcatggctagATCAACATGATCCTCCACGAAACTCTCCGCCTGTATCCACCGGTGGGGGTG
EST: gi|169078017|gb|FE489374.1|FE489374
EST:     TCTGCGAAGGTGCCACTCCAGAAGCCGATTCAATCAGCAAGCTCAAGCTG                         ATCAACATGATCCTCCACGAAACTCTCCGCCTGTATCCACCGGTGGGGGTG
genomic: TCTGCGAAGGTGCCACTCCAGAAGCCGATTCAATCAGCAAGCTCAAGCTGgtaaaggttt ... tcatggctagATCAACATGATCCTCCACGAAACTCTCCGCCTGTATCCACCGGTGGGGGTG
EST: gi|169057457|gb|FE465761.1|FE465761
EST:     TCTGCGAAGGTGCCACTCCAGAAGCCGATTCAATCAGCAAGCTCAAGCTG                         ATCAACATGATCCTCCACGAAACTCTCCGCCTGTATCCACCGGTGGGGGTG
genomic: TCTGCGAAGGTGCCACTCCAGAAGCCGATTCAATCAGCAAGCTCAAGCTGgtaaaggttt ... tcatggctagATCAACATGATCCTCCACGAAACTCTCCGCCTGTATCCACCGGTGGGGGTG
EST: gi|169061249|gb|FE470362.1|FE470362
EST:     AAGGTGNCACTCCAGAAGCCGATTCAATCAGCAAGCTCAAGCTG                         ATCAACATGATCCTCCACGAAACTCTCCGCCTGTATCCACCGGTGGGGGTG
genomic: AAGGTGCCACTCCAGAAGCCGATTCAATCAGCAAGCTCAAGCTGgtaaaggttt ... tcatggctagATCAACATGATCCTCCACGAAACTCTCCGCCTGTATCCACCGGTGGGGGTG
EST: gi|169088329|gb|FE492047.1|FE492047
EST:     TCTGCGAAGGTGCCACTCCAGAAGCCGATTCAATCAGCAAGCTCAAGCTG                         ATCAACATGATCCTCCACGAAACTCTCCGCCTGTATCCACCGGTGGGGGTG
genomic: TCTGCGAAGGTGCCACTCCAGAAGCCGATTCAATCAGCAAGCTCAAGCTGgtaaaggttt ... tcatggctagATCAACATGATCCTCCACGAAACTCTCCGCCTGTATCCACCGGTGGGGGTG
EST: gi|169062309|gb|FE470499.1|FE470499
EST:     TCTGCGAAGGTGCCACTCCAGAAGCCGATTCAATCAGCAAGCTCAAGCTG                         ATCAACATGATCCTCCACGAAACTCTCCGCCTGTATCCACCGGTGGGGGTG
genomic: TCTGCGAAGGTGCCACTCCAGAAGCCGATTCAATCAGCAAGCTCAAGCTGgtaaaggttt ... tcatggctagATCAACATGATCCTCCACGAAACTCTCCGCCTGTATCCACCGGTGGGGGTG
EST: gi|169062308|gb|FE470498.1|FE470498
EST:     TCTGCGAAGGTGCCACTCCAGAAGCCGATTCAATCAGCAAGCTCAAGCTG                         ATCAACATGATCCTCCACGAAACTCTCCGCCTGTATCCACCGGTGGGGGTG
genomic: TCTGCGAAGGTGCCACTCCAGAAGCCGATTCAATCAGCAAGCTCAAGCTGgtaaaggttt ... tcatggctagATCAACATGATCCTCCACGAAACTCTCCGCCTGTATCCACCGGTGGGGGTG
EST: gi|169068837|gb|FE477178.1|FE477178
EST:     TCTGCGAAGGTGCCACTCCAGAAGCCGATTCAATCAGCAAGCTCAAGCTG                         ATCAACATGATCCTCCACGAAACTCTCCGCCTGTATCCACCGGTGGGGGTG
genomic: TCTGCGAAGGTGCCACTCCAGAAGCCGATTCAATCAGCAAGCTCAAGCTGgtaaaggttt ... tcatggctagATCAACATGATCCTCCACGAAACTCTCCGCCTGTATCCACCGGTGGGGGTG
EST: gi|169078823|gb|FE486553.1|FE486553
EST:     AAGGTGCCACTCCAGAAGCCGATTCAATCAGCAAGCTCAAGCTG                         ATCAACATGATCCTCCACGAAACTCTCCGCCTGTATCCACCGGTGGGGGTG
genomic: AAGGTGCCACTCCAGAAGCCGATTCAATCAGCAAGCTCAAGCTGgtaaaggttt ... tcatggctagATCAACATGATCCTCCACGAAACTCTCCGCCTGTATCCACCGGTGGGGGTG

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), 34 (downstream exon)
Score: 51

TGCTTTGCACCCGGAATGGCAGGAGCGCGCTCGCGCCGAGGCCCAGGAAGTCTGCGAAGGTGCCACTCCAGAAGCCGATTCAATCAGCAAGCTCAAGCTGgtaaaggttt ... tcatggctagATCAACATGATCCTCCACGAAACTCTCCGCCTGTATCCACCGGTGGGGGTGATGATGCGATCGTGCTTCGAGGACACCATACTGGGAGATATCCTCGTCC




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGCTTTGCACCCGGAATGGCAGGAGCGCGCTCGCGCCGAGGCCCAGGAAGTCTGCGAAGGTGCCACTCCAGAAGCCGATTCAATCAGCAAGCTCAAGCTGgtaaaggttttacgttactttcgagtttcacgagctcaagctttctttctcatggctag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG