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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTATTCCATCTCCAGAGCTATTACGCTTCCAGTTCTCTGTGCCTCTGGATTGAGTGCAGTGACAGCTCCAATGGCGATCACTGCTGGCGCTTCTGGAGTGgtaatcttagcatcaagcgtttcttcttcttcgtttttaacgtttgcaccatttcttccag

Basic information

species Selaginella moellendorffii
transcript EFJ22466
intron # 8
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|169046730|gb|FE456668.1|FE456668
EST:     TGAGTGCAGTGACAGCTCCAATGGCGATCACTGCTGGCGCTTCTGGAGTG                         GGCATTGGCTCAGCTGTGAACAAACTANACAGCCAACTTTGCA-TGGTGGC
genomic: TGAGTGCAGTGACAGCTCCAATGGCGATCACTGCTGGCGCTTCTGGAGTGgtaatcttag ... tttcttccagGGCATTGGCTCAGCTGTGAACAAACTAAACAGCCAACTT-GCAATGGTGGC
EST: gi|169070532|gb|FE479809.1|FE479809
EST:     TGAGTGCAGTGACAGCTCCAATGGCGATCACTGCTGGCGCTTCTGGAGTG                         GGCATTGGCTCAGCTGTGAACAAACTGAAACAGCCA-CTTGCAATGGTGGC
genomic: TGAGTGCAGTGACAGCTCCAATGGCGATCACTGCTGGCGCTTCTGGAGTGgtaatcttag ... tttcttccagGGCATTGGCTCAGCTGTGAACAAACT-AAACAGCCAACTTGCAATGGTGGC
EST: gi|169054264|gb|FE463205.1|FE463205
EST:     TGAGTGCAGTGACAGCTCCAATGGCGATCACTGCTGGCGCTTCTGGAGTG                         GGCATTGGCTCAGCTGTGAACAAACTAAACAGCCAACTTGCAATGGTGGCG
genomic: TGAGTGCAGTGACAGCTCCAATGGCGATCACTGCTGGCGCTTCTGGAGTGgtaatcttag ... tttcttccagGGCATTGGCTCAGCTGTGAACAAACTAAACAGCCAACTTGCAATGGTGGCG
EST: gi|169019639|gb|FE427468.1|FE427468
EST:     TGAGTGCAGTGACAGCTCCCATGGCGATCACTGCTGGCGCTTCTGGAGTG                         GGCATTGGCTCAGCTGTGAACAAACTAAACAG
genomic: TGAGTGCAGTGACAGCTCCAATGGCGATCACTGCTGGCGCTTCTGGAGTGgtaatcttag ... tttcttccagGGCATTGGCTCAGCTGTGAACAAACTAAACAG
EST: gi|70670894|gb|DN839471.1|DN839471
EST:     TGAGTGCAGTGACAGCTCCAATGGCGATCACTGCTGGCGCTTCTGGAGTG                         GGCAT-GGNCTCAGCTGTGAACAAACT
genomic: TGAGTGCAGTGACAGCTCCAATGGCGATCACTGCTGGCGCTTCTGGAGTGgtaatcttag ... tttcttccagGGCATTGG-CTCAGCTGTGAACAAACT
EST: gi|169068421|gb|FE478998.1|FE478998
EST:     TGAGTGCAGTGACAGCTCCAATGGCGATCACTGCTGGCGCTTCTGGAGTG                         GGCATTGGCTCAGCTGTGAACAAACTGAACAGCCAACTTGCAATGGTGGCG
genomic: TGAGTGCAGTGACAGCTCCAATGGCGATCACTGCTGGCGCTTCTGGAGTGgtaatcttag ... tttcttccagGGCATTGGCTCAGCTGTGAACAAACTAAACAGCCAACTTGCAATGGTGGCG
EST: gi|169025044|gb|FE434670.1|FE434670
EST:     TGAGTGCAGTGACAGCTCCAATGGCGATCACTGCTGGCGCTTCTGGAGTG                         GGCATTGGCTCAGCTGTGAACAAACTGAACAGCNCA-CTTGCAA
genomic: TGAGTGCAGTGACAGCTCCAATGGCGATCACTGCTGGCGCTTCTGGAGTGgtaatcttag ... tttcttccagGGCATTGGCTCAGCTGTGAACAAACTAAACAGC-CAACTTGCAA
EST: gi|169106951|gb|FE508834.1|FE508834
EST:     TGAGTGCAGTGACAGCTCCAATGGCGATCACTGCTGGCGCTTCTGGAGTG                         GGCATTGGCTCAGCTGTGAACAAACTAAACAGCCAACTTGCAATGGTGGCG
genomic: TGAGTGCAGTGACAGCTCCAATGGCGATCACTGCTGGCGCTTCTGGAGTGgtaatcttag ... tttcttccagGGCATTGGCTCAGCTGTGAACAAACTAAACAGCCAACTTGCAATGGTGGCG
EST: gi|169046729|gb|FE456667.1|FE456667
EST:     TGAGTGCAGTGACAGCTCCAATGGCGATCACTGCTGGCGCTTCTGGAGTG                         GGCATTGGCTCAGCTGTGAACAAACTAAACAGCCAACTTGCAATGGTGGCG
genomic: TGAGTGCAGTGACAGCTCCAATGGCGATCACTGCTGGCGCTTCTGGAGTGgtaatcttag ... tttcttccagGGCATTGGCTCAGCTGTGAACAAACTAAACAGCCAACTTGCAATGGTGGCG
EST: gi|169036088|gb|FE445128.1|FE445128
EST:     TGAGTGCAGTGACAGCTCCNATGGCGATCACTGCTGGCGCTTCTGGAGTG                         NGCATTGGCTCAGCTGTGAACAA
genomic: TGAGTGCAGTGACAGCTCCAATGGCGATCACTGCTGGCGCTTCTGGAGTGgtaatcttag ... tttcttccagGGCATTGGCTCAGCTGTGAACAA
EST: gi|169060729|gb|FE469755.1|FE469755
EST:     TGAGTGCAGTGACAGCTCCNATGGCGATCACTGCTGGCGCTTCTGGAGTG                         GGCATTGGCTCAGCTGTGAACAAACTGAACAG
genomic: TGAGTGCAGTGACAGCTCCAATGGCGATCACTGCTGGCGCTTCTGGAGTGgtaatcttag ... tttcttccagGGCATTGGCTCAGCTGTGAACAAACTAAACAG
EST: gi|169070531|gb|FE479808.1|FE479808
EST:     TGAGTGCAGTGACAGCTCCAATGGCGATCACTGCTGGCGCTTCTGGAGTG                         GGCATTGGCTCAGCTGTGAACAAACTGAACAGCCAACTTGCAATGGTGGCG
genomic: TGAGTGCAGTGACAGCTCCAATGGCGATCACTGCTGGCGCTTCTGGAGTGgtaatcttag ... tttcttccagGGCATTGGCTCAGCTGTGAACAAACTAAACAGCCAACTTGCAATGGTGGCG
EST: gi|169019638|gb|FE427467.1|FE427467
EST:     TGAGTGCAGTGACAGCTCCAATGGCGATCACTGCTGGCGCTTCTGGAGTG                         GGCATTGGCTCAGCTGTGAACAAACTAAACAGCCAACTTGCAATGGTGGCG
genomic: TGAGTGCAGTGACAGCTCCAATGGCGATCACTGCTGGCGCTTCTGGAGTGgtaatcttag ... tttcttccagGGCATTGGCTCAGCTGTGAACAAACTAAACAGCCAACTTGCAATGGTGGCG
EST: gi|169068959|gb|FE477703.1|FE477703
EST:     TGAGTGCAGTGACAGCTCCAATGGCGATCACTGCTGGCGCTTCTGGAGTG                         GGCATTGGCTCAGCTGTGAACAAACTGAACAGCCAACTTGCAATGGTGGCG
genomic: TGAGTGCAGTGACAGCTCCAATGGCGATCACTGCTGGCGCTTCTGGAGTGgtaatcttag ... tttcttccagGGCATTGGCTCAGCTGTGAACAAACTAAACAGCCAACTTGCAATGGTGGCG
EST: gi|169099322|gb|FE502108.1|FE502108
EST:     TGAGTGCAGTGACAGCTCCAATGGCGATCACTGCTGGCGCTTCTGGAGTG                         GGCATTGGCTCAGCTGTG
genomic: TGAGTGCAGTGACAGCTCCAATGGCGATCACTGCTGGCGCTTCTGGAGTGgtaatcttag ... tttcttccagGGCATTGGCTCAGCTGTG
EST: gi|169042964|gb|FE452318.1|FE452318
EST:     TGAGTGCAGTGACAGCTCCAATGGCGATCACTGCTGGCGCTTCTGGAGTG                         GGCATTGGCTCAGCTGTGAACAAACTAAACAGCCAACTTGCAATGGTGGCG
genomic: TGAGTGCAGTGACAGCTCCAATGGCGATCACTGCTGGCGCTTCTGGAGTGgtaatcttag ... tttcttccagGGCATTGGCTCAGCTGTGAACAAACTAAACAGCCAACTTGCAATGGTGGCG
EST: gi|169099321|gb|FE502107.1|FE502107
EST:     TGAGTGCAGTGACAGCTCCAATGGCGATCACTGCTGGCGCTTCTGGAGTG                         GGCATTGGCTCAGCTGTGAACAAACTGAACAGCCAACTTGCAATGGTGGCG
genomic: TGAGTGCAGTGACAGCTCCAATGGCGATCACTGCTGGCGCTTCTGGAGTGgtaatcttag ... tttcttccagGGCATTGGCTCAGCTGTGAACAAACTAAACAGCCAACTTGCAATGGTGGCG
EST: gi|169042965|gb|FE452319.1|FE452319
EST:     TGAGTGCAGTGACAGCTCCAATGGCGATCACTGCTGGCGCTTCTGGAGTG                         GGCATTGGCTCAGCTGTGAACAAAACTAA-CAGCCCACTTNGCAA
genomic: TGAGTGCAGTGACAGCTCCAATGGCGATCACTGCTGGCGCTTCTGGAGTGgtaatcttag ... tttcttccagGGCATTGGCTCAGCTGTGAACAAA-CTAAACAGCCAACTT-GCAA
EST: gi|169036087|gb|FE445127.1|FE445127
EST:     TGAGTGCAGTGACAGCTCCAATGGCGATCACTGCTGGCGCTTCTGGAGTG                         GGCATTGGCTCAGCTGTGAACAAACTGAACAGCCAACTTGCAATGGTGGCG
genomic: TGAGTGCAGTGACAGCTCCAATGGCGATCACTGCTGGCGCTTCTGGAGTGgtaatcttag ... tttcttccagGGCATTGGCTCAGCTGTGAACAAACTAAACAGCCAACTTGCAATGGTGGCG
EST: gi|169025043|gb|FE434669.1|FE434669
EST:     TGAGTGCAGTGACAGCTCCAATGGCGATCACTGCTGGCGCTTCTGGAGTG                         GGCATTGGCTCAGCTGTGAACAAACTGAACAGCCAACTTGCAATGGTGGCG
genomic: TGAGTGCAGTGACAGCTCCAATGGCGATCACTGCTGGCGCTTCTGGAGTGgtaatcttag ... tttcttccagGGCATTGGCTCAGCTGTGAACAAACTAAACAGCCAACTTGCAATGGTGGCG
EST: gi|169060728|gb|FE469754.1|FE469754
EST:     TGAGTGCAGTGACAGCTCCAATGGCGATCACTGCTGGCGCTTCTGGAGTG                         GGCATTGGCTCAGCTGTGAACAAACTGAACAGCCAACTTGCAATGGTGGCG
genomic: TGAGTGCAGTGACAGCTCCAATGGCGATCACTGCTGGCGCTTCTGGAGTGgtaatcttag ... tttcttccagGGCATTGGCTCAGCTGTGAACAAACTAAACAGCCAACTTGCAATGGTGGCG
EST: gi|169027095|gb|FE435629.1|FE435629
EST:     TGAGTGCAGTGACAGCTCCAATGGCGATCACTGCTGGCGCTTCTGGAGTG                         NGCATTGGCTCAGCTGTGAACAAACT
genomic: TGAGTGCAGTGACAGCTCCAATGGCGATCACTGCTGGCGCTTCTGGAGTGgtaatcttag ... tttcttccagGGCATTGGCTCAGCTGTGAACAAACT

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), 35 (downstream exon)
Score: 51

GTATTCCATCTCCAGAGCTATTACGCTTCCAGTTCTCTGTGCCTCTGGATTGAGTGCAGTGACAGCTCCAATGGCGATCACTGCTGGCGCTTCTGGAGTGgtaatcttag ... tttcttccagGGCATTGGCTCAGCTGTGAACAAACTAAACAGCCAACTTGCAATGGTGGCGACTGTTCGCAGCATTGCGGATGCAATGGGACTAGAACCATCCACTGAAA




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTATTCCATCTCCAGAGCTATTACGCTTCCAGTTCTCTGTGCCTCTGGATTGAGTGCAGTGACAGCTCCAATGGCGATCACTGCTGGCGCTTCTGGAGTGgtaatcttagcatcaagcgtttcttcttcttcgtttttaacgtttgcaccatttcttccag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTC