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 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagcgcactctttccatatcatatacatattttgcatttcgagcatataatacttagctctgcctctttcgtgctgctttaactgttgaggggtgccaggatttgcgtgacactccagaatcagttacgagaagcgagttttctaactctggttgtaaccgtgtgatacagGAAGCTTACGTTGTTCCCAAGAGGAAGGTTGACGCAGTGGACGGCAGCGCTCTGGCGCAGCGCGTGATCTTCCATGATGGTAGGCTGGTCCAGCTCCCAA

Basic information

species Selaginella moellendorffii
transcript EFJ29816
intron # 1
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|169105846|gb|FE503530.1|FE503530
EST:     TCGGACTCGGCGATCGAGAAACCGACTTCGCCTTCATGTCGCTTTGCAAG                         GGAGCTTACGTTGTTCCCAAG
genomic: TCGGACTCGGCGATCGAGAAACCGACTTCGCCTTCATGTCGCTTTGCAAGgtaagcgcac ... tgtgatacagGAAGCTTACGTTGTTCCCAAG
EST: gi|169033519|gb|FE442071.1|FE442071
EST:     TCGGACTCGGCGATCGAGAAACCGACTTCGCCTTCATGTCGCTTTGCAAG                         GAAGCTTACGTTGTTCCCAAGAGGAAGGTTGACGCAGTGGACGGCAGCGCT
genomic: TCGGACTCGGCGATCGAGAAACCGACTTCGCCTTCATGTCGCTTTGCAAGgtaagcgcac ... tgtgatacagGAAGCTTACGTTGTTCCCAAGAGGAAGGTTGACGCAGTGGACGGCAGCGCT
EST: gi|169051138|gb|FE458685.1|FE458685
EST:     TCGGACTCGGCGATCGAGAAACCGACTTCGCCTTCATGTCGCTTTGCAAG                         GAAGCTTACGTTGTTCCCAAGAGGAAGGTTGACGCAGTGGACGGCAGCGCT
genomic: TCGGACTCGGCGATCGAGAAACCGACTTCGCCTTCATGTCGCTTTGCAAGgtaagcgcac ... tgtgatacagGAAGCTTACGTTGTTCCCAAGAGGAAGGTTGACGCAGTGGACGGCAGCGCT
EST: gi|169022056|gb|FE429091.1|FE429091
EST:     TCGGACTCGGCGATCGAGAAACCGACTTCGCCTTCATGTCGCTTTGCAAG                         GAAGCTTACGTTGTTCCCAAGAGGAAGGTTGACGCAGTGGACGGCAGCGCT
genomic: TCGGACTCGGCGATCGAGAAACCGACTTCGCCTTCATGTCGCTTTGCAAGgtaagcgcac ... tgtgatacagGAAGCTTACGTTGTTCCCAAGAGGAAGGTTGACGCAGTGGACGGCAGCGCT
EST: gi|169067148|gb|FE474916.1|FE474916
EST:     TCGGACTCGGCGATCGAGAAACCGACTTCGCCTTCATGTCGCTTTGCAAG                         GAAGCTTACGTTGTTCCCAAGAGGAAGGTTGACGCAGTGGACGGCAGCGCT
genomic: TCGGACTCGGCGATCGAGAAACCGACTTCGCCTTCATGTCGCTTTGCAAGgtaagcgcac ... tgtgatacagGAAGCTTACGTTGTTCCCAAGAGGAAGGTTGACGCAGTGGACGGCAGCGCT
EST: gi|169045876|gb|FE451732.1|FE451732
EST:     TCGGACTCGGCGATCGAGAAACCGACTTCGCCTTCATGTCGCTTTGCAAG                         GAAGCTTACGTTGTTCCCAAGAGGAAGGTTGACGCAGTGGACGGCAGCGCT
genomic: TCGGACTCGGCGATCGAGAAACCGACTTCGCCTTCATGTCGCTTTGCAAGgtaagcgcac ... tgtgatacagGAAGCTTACGTTGTTCCCAAGAGGAAGGTTGACGCAGTGGACGGCAGCGCT
EST: gi|169065376|gb|FE473485.1|FE473485
EST:     TCGGACTCGGCGATCGAGAAACCGACTTCGCCTTCATGTCGCTTTGCAAG                         GAAGCTTACGTTGTTCCCAAGAGGAAGGTTGACGCAGTGGACGGCAGCGCT
genomic: TCGGACTCGGCGATCGAGAAACCGACTTCGCCTTCATGTCGCTTTGCAAGgtaagcgcac ... tgtgatacagGAAGCTTACGTTGTTCCCAAGAGGAAGGTTGACGCAGTGGACGGCAGCGCT
EST: gi|169047819|gb|FE454675.1|FE454675
EST:     TCGGACTCGGCGATCGAGAAACCGACTTCGCCTTCATGTCGCTTTGCAAG                         GAAGCTTACGTTGTTCCCAAGAGGAAGGTTGACGCAGTGGACGGCAGCGCT
genomic: TCGGACTCGGCGATCGAGAAACCGACTTCGCCTTCATGTCGCTTTGCAAGgtaagcgcac ... tgtgatacagGAAGCTTACGTTGTTCCCAAGAGGAAGGTTGACGCAGTGGACGGCAGCGCT
EST: gi|169110468|gb|FE514151.1|FE514151
EST:     TCGGACTCGGCGATCGAGAAACCGACTTCGCCTTCATGTCGCTTTGCAAG                         GAAGCTTACGTTGTTCCCAAGAGGAAGGTTGACGCAGTGGACGGCAGCGCT
genomic: TCGGACTCGGCGATCGAGAAACCGACTTCGCCTTCATGTCGCTTTGCAAGgtaagcgcac ... tgtgatacagGAAGCTTACGTTGTTCCCAAGAGGAAGGTTGACGCAGTGGACGGCAGCGCT
EST: gi|169082213|gb|FE487007.1|FE487007
EST:     TCGGACTCGGCGATCGAGAAACCGACTTCGCCTTCATGTCGCTTTGCAAG                         GAAGCTTACGTTGTTCCCAAGAGGAAGGTTGACGCAGTGGACGGCAGCGCT
genomic: TCGGACTCGGCGATCGAGAAACCGACTTCGCCTTCATGTCGCTTTGCAAGgtaagcgcac ... tgtgatacagGAAGCTTACGTTGTTCCCAAGAGGAAGGTTGACGCAGTGGACGGCAGCGCT
EST: gi|169068979|gb|FE477710.1|FE477710
EST:     TCGGACTCGGCGATCGAGAAACCGACTTCGCCTTCATGTCGCTTTGCAAG                         GAAGCTTACGTTGTTCCCAAGAGGAAGGTTGACGCAGTGGACGGCAGCGCT
genomic: TCGGACTCGGCGATCGAGAAACCGACTTCGCCTTCATGTCGCTTTGCAAGgtaagcgcac ... tgtgatacagGAAGCTTACGTTGTTCCCAAGAGGAAGGTTGACGCAGTGGACGGCAGCGCT
EST: gi|169068563|gb|FE479686.1|FE479686
EST:     TCGGACTCGGCGATCGAGAAACCGACTTCGCCTTCATGTCGCTTTGCAAG                         GAAGCTTACGTTGTTCCCAAGAGGAAGGTTGACGCAGTGGACGGCAGCGCT
genomic: TCGGACTCGGCGATCGAGAAACCGACTTCGCCTTCATGTCGCTTTGCAAGgtaagcgcac ... tgtgatacagGAAGCTTACGTTGTTCCCAAGAGGAAGGTTGACGCAGTGGACGGCAGCGCT
EST: gi|169077923|gb|FE487798.1|FE487798
EST:     TCGGACTCGGCGATCGAGAAACCGACTTCGCCTTCATGTCGCTTTGCAAG                         GAAGCTTACGTTGTTCCCAAGAGGAAGGTTGACGCAGTGGACGGCAGCGCT
genomic: TCGGACTCGGCGATCGAGAAACCGACTTCGCCTTCATGTCGCTTTGCAAGgtaagcgcac ... tgtgatacagGAAGCTTACGTTGTTCCCAAGAGGAAGGTTGACGCAGTGGACGGCAGCGCT
EST: gi|169021255|gb|FE429616.1|FE429616
EST:     TCGGACTCGGCGATCGAGAAACCGACTTCGCCTTCATGTCGCTTTGCA-G                         GNAAGCTTACGTTGTTCCCAAGAGGAAGGTTGACGCAGTGGACGGCAGCGC
genomic: TCGGACTCGGCGATCGAGAAACCGACTTCGCCTTCATGTCGCTTTGCAAGgtaagcgcac ... tgtgatacagG-AAGCTTACGTTGTTCCCAAGAGGAAGGTTGACGCAGTGGACGGCAGCGC
EST: gi|169050621|gb|FE459663.1|FE459663
EST:     TCGGACTCGGCGATCGAGAAACCGACTTCGCCTTCATGTCGCTTTGCAAG                         GAAGCTTACGTTGTTCCCAAGAGGAAGGTTGACGCAGTGGACGGCAGCGCT
genomic: TCGGACTCGGCGATCGAGAAACCGACTTCGCCTTCATGTCGCTTTGCAAGgtaagcgcac ... tgtgatacagGAAGCTTACGTTGTTCCCAAGAGGAAGGTTGACGCAGTGGACGGCAGCGCT
EST: gi|169054772|gb|FE460568.1|FE460568
EST:     TCGGACTCGGCGATCGAGAAACCGACTTCGCCTTCATGTCGCTTTGCAAG                         GAAGCTTACGTTGTTCCC
genomic: TCGGACTCGGCGATCGAGAAACCGACTTCGCCTTCATGTCGCTTTGCAAGgtaagcgcac ... tgtgatacagGAAGCTTACGTTGTTCCC
EST: gi|169111239|gb|FE510866.1|FE510866
EST:     TCGGACTCGGCGATCGAGAAACCGACTTCGCCTTCATGTCGCTTTGCAAG                         GAAGCTTACGTTGTTCCCAAGAGGAAGGTTGACGCAGTGGACGGCAGCGCT
genomic: TCGGACTCGGCGATCGAGAAACCGACTTCGCCTTCATGTCGCTTTGCAAGgtaagcgcac ... tgtgatacagGAAGCTTACGTTGTTCCCAAGAGGAAGGTTGACGCAGTGGACGGCAGCGCT
EST: gi|169039234|gb|FE448844.1|FE448844
EST:     TCGGACTCGGCGATCGAGAAACCGACTTCGCCTTCATGTCGCTTTGCAAG                         GAAGCTTACGTTGTTCCCAAGAGGAAGGTTGACGCAGTGGACGGCAGCGCT
genomic: TCGGACTCGGCGATCGAGAAACCGACTTCGCCTTCATGTCGCTTTGCAAGgtaagcgcac ... tgtgatacagGAAGCTTACGTTGTTCCCAAGAGGAAGGTTGACGCAGTGGACGGCAGCGCT
EST: gi|169027219|gb|FE435090.1|FE435090
EST:     TCGGACTCGGCGATCGAGAAACCGACTTCGCCTTCATGTCGCTTTGCAAG                         GAAGCTTACGTTGTTCCCAAGAGGAAGGTTGACGCAGTGGACGGCAGCGCT
genomic: TCGGACTCGGCGATCGAGAAACCGACTTCGCCTTCATGTCGCTTTGCAAGgtaagcgcac ... tgtgatacagGAAGCTTACGTTGTTCCCAAGAGGAAGGTTGACGCAGTGGACGGCAGCGCT
EST: gi|169094711|gb|FE491575.1|FE491575
EST:     TCGGACTCGGCGATCGAGAAACCGACTTCGCCTTCATGTCGCTTTGCAAG                         GAAGCTTACGTTGTTCCCAAGAGGAAGGTTGACGCAGTGGACGGCAGCGCT
genomic: TCGGACTCGGCGATCGAGAAACCGACTTCGCCTTCATGTCGCTTTGCAAGgtaagcgcac ... tgtgatacagGAAGCTTACGTTGTTCCCAAGAGGAAGGTTGACGCAGTGGACGGCAGCGCT

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: 33 (upstream exon), 35 (downstream exon)
Score: 39

CAAGAGGACCGCCTTGAAGCTCGAGTTCGTGGACGGGGAGCTTCCCGAGATCGGACTCGGCGATCGAGAAACCGACTTCGCCTTCATGTCGCTTTGCAAGgtaagcgcac ... tgtgatacagGAAGCTTACGTTGTTCCCAAGAGGAAGGTTGACGCAGTGGACGGCAGCGCTCTGGCGCAGCGCGTGATCTTCCATGATGGTAGGCTGGTCCAGCTCCCAA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agaatcagttacgagaagcgagttttctaactctggttgtaaccgtgtgatacagGAAGCTTACGTTGTTCCCAAGAGGAAGGTTGACGCAGTGGACGGCAGCGCTCTGGCGCAGCGCGTGATCTTCCATGATGGTAGGCTGGTCCAGCTCCCAA
                      ttttctaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagcgcactctttccatatcatatacatattttgcatttcgagcatataatacttagctctgcctctttcgtgctgctttaactgttgaggggtgccaggatttgcgtgacactccagaatcagttacgagaagcgagttttctaactctggttgtaaccgtgtgatacagGAAGCTTACGTTGTTCCCAAGAGGAAGGTTGACGCAGTGGACGGCAGCGCTCTGGCGCAGCGCGTGATCTTCCATGATGGTAGGCTGGTCCAGCTCCCAA

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