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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtctctcttttcttctatttttctgctgtgattttgtttgatcttgggaacttgatctagGCTACGGTGGCGATGTTTGGTACCCGCAGCCTCCTCCGAAAGATCACCCATGGCGATCCATGCCAAACAACGCAATGACTCCTCACGTCTCTGGATCGAC

Basic information

species Selaginella moellendorffii
transcript EFJ13636
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ13636 (Selaginella moellendorffii), 3'ss of exon 6
lower sequence: GLYMA13G23790.4 (Glycine max), 3'ss of exon 4
-------------------------------gtctctcttttcttctatttttctgctg-tgattttgt-----ttgatcttgggaacttgatc---tagGCTACGGTGGCGATGTTTGGTACCCGCAGCCTCCTCCGAAAGATCACCCATGGCGATCCATGCCAAACAACGCAATGACTCCTCACGTCTCTGGATCGAC
                               ||  || ||   || ||  || |   |  | ||||||      |   || |     |||  |    |||| ||  |||| |||||||||| ||| |||||  |||| || ||||| |||||||| | |||||||||| | || |||||||||||  | |||||  | ||
tccctaagttctgttatgatcctttgttgttgttactattcctttttaagttgcaattactaattttgccatcctctttcctaatctcttatttctatagGTTATAGTGGTGATGTTTGGTTCCCACAGCCAGCTCCAAAGGATCATCCATGGCGTTACATGCCAAACCATGCCATGACTCCTCATATTTCTGGCACCAC
















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|169029784|gb|FE441017.1|FE441017
EST:     CATGGAAGCAAATGCGGTGGCGGAAGCGTGTAAATCTGGACACCTTGGAG                         GCTACGGTGGCGATGTTTGGTACCCGCAGCCTCCTCCGAAAGATCACCCAT
genomic: CATGGATGCCAATGCGGTGGCGGAAGCGTGTAAATCTGGACACCTTGGAGgtctctcttt ... cttgatctagGCTACGGTGGCGATGTTTGGTACCCGCAGCCTCCTCCGAAAGATCACCCAT
EST: gi|169056514|gb|FE464922.1|FE464922
EST:     CATGGAAGCAAATGCGGTGGCGGAAGCGTGTAAATCTGGACACCTTGGAG                         GCTACGGTGGCGATGTTTGGTACCCGCAGCCTCCTCCGAAAGATCACCCAT
genomic: CATGGATGCCAATGCGGTGGCGGAAGCGTGTAAATCTGGACACCTTGGAGgtctctcttt ... cttgatctagGCTACGGTGGCGATGTTTGGTACCCGCAGCCTCCTCCGAAAGATCACCCAT
EST: gi|169094987|gb|FE493008.1|FE493008
EST:     CATGGATGCCAATGCGGTGGCGGAAGCGTGTAAATCTGGACACCTTGGAG                         GCTACGGTGGCGATGTTTGGTACCCGCAGCCTCCTCCGAAAGATCACCCAT
genomic: CATGGATGCCAATGCGGTGGCGGAAGCGTGTAAATCTGGACACCTTGGAGgtctctcttt ... cttgatctagGCTACGGTGGCGATGTTTGGTACCCGCAGCCTCCTCCGAAAGATCACCCAT
EST: gi|169067792|gb|FE473376.1|FE473376
EST:     CATGGAAGCAAATGCGGTGGCGGAAGCGTGTAAATCTGGACACCTTGGAG                         GCTACGGTGGCGATGTTTGGTACCCGCAGCCTCCTCCGAAAGATCACCCAT
genomic: CATGGATGCCAATGCGGTGGCGGAAGCGTGTAAATCTGGACACCTTGGAGgtctctcttt ... cttgatctagGCTACGGTGGCGATGTTTGGTACCCGCAGCCTCCTCCGAAAGATCACCCAT
EST: gi|169104371|gb|FE503733.1|FE503733
EST:     CATGGATGCCAATGCGGTGGCGGAAGCGTGTAAATCTGGACACCTTGGAG                         GCTACGGTGGCGATGTTTGGTACCCGCAGCCTCCTCCGAAAGATCACCCAT
genomic: CATGGATGCCAATGCGGTGGCGGAAGCGTGTAAATCTGGACACCTTGGAGgtctctcttt ... cttgatctagGCTACGGTGGCGATGTTTGGTACCCGCAGCCTCCTCCGAAAGATCACCCAT
EST: gi|169087508|gb|FE494625.1|FE494625
EST:     CATGGATGCCAATGCGGTGGCGGAAGCGTGTAAATCTGGACACCTTGGAG                         GCTACGGTGGCGATGTTTGGTACCCGCAGCCTCCTCCGAAAGATCACCCAT
genomic: CATGGATGCCAATGCGGTGGCGGAAGCGTGTAAATCTGGACACCTTGGAGgtctctcttt ... cttgatctagGCTACGGTGGCGATGTTTGGTACCCGCAGCCTCCTCCGAAAGATCACCCAT
EST: gi|169079757|gb|FE491166.1|FE491166
EST:     CATGGAAGCAAATGCGGTGGCGGAAGCGTGTAAATCTGGACACCTTGGAG                         GCTACGGTGGCGATGTTTGGTACCCGCAGCCTCCTCCGAAAGATCACCCAT
genomic: CATGGATGCCAATGCGGTGGCGGAAGCGTGTAAATCTGGACACCTTGGAGgtctctcttt ... cttgatctagGCTACGGTGGCGATGTTTGGTACCCGCAGCCTCCTCCGAAAGATCACCCAT
EST: gi|169079758|gb|FE491167.1|FE491167
EST:     CATGGAAGCAAATGCGGTGGCGGAAGCGTGTAAATCTGGACACCTTGGAG                         GCTACGGTGGCGATGTTTGGTACCCGCAGCCTCCTCCGAAAGAT
genomic: CATGGATGCCAATGCGGTGGCGGAAGCGTGTAAATCTGGACACCTTGGAGgtctctcttt ... cttgatctagGCTACGGTGGCGATGTTTGGTACCCGCAGCCTCCTCCGAAAGAT
EST: gi|169060084|gb|FE468694.1|FE468694
EST:     CATGGATGCCAATGCGGTGGCGGAAGCGTGTAAATCTGGACACCTTGGAG                         GCTACGGTGGCGATGTTTGGTACCCGCAGCCTCCTCCGAAAGATCACCCAT
genomic: CATGGATGCCAATGCGGTGGCGGAAGCGTGTAAATCTGGACACCTTGGAGgtctctcttt ... cttgatctagGCTACGGTGGCGATGTTTGGTACCCGCAGCCTCCTCCGAAAGATCACCCAT
EST: gi|169088324|gb|FE492042.1|FE492042
EST:     CATGGATGCCAATGCGGTGGCGGAAGCGTGTAAATCTGGACACCTTGGAG                         GCTACGGTGGCGATGTTTGGTACCCGCAGCCTCCTCCGAAAGATCACCCAT
genomic: CATGGATGCCAATGCGGTGGCGGAAGCGTGTAAATCTGGACACCTTGGAGgtctctcttt ... cttgatctagGCTACGGTGGCGATGTTTGGTACCCGCAGCCTCCTCCGAAAGATCACCCAT
EST: gi|169106399|gb|FE507424.1|FE507424
EST:     CATGGATGCCAATGCGGTGGCGGAAGCGTGTAAATCTGGACACCTTGGAG                         GCTACGGTGGCGATGTTTGGTACCCGCAGCCTCCTCCGAAAGATCACCCAT
genomic: CATGGATGCCAATGCGGTGGCGGAAGCGTGTAAATCTGGACACCTTGGAGgtctctcttt ... cttgatctagGCTACGGTGGCGATGTTTGGTACCCGCAGCCTCCTCCGAAAGATCACCCAT
EST: gi|169101312|gb|FE502507.1|FE502507
EST:     CATGGATGCCAATGCGGTGGCGGAAGCGTGTAAATCTGGACACCTTGGAG                         GCTACGGTGGCGATGTTTGGTACCCGCAGCCTCCTCCGAAAGATCACCCAT
genomic: CATGGATGCCAATGCGGTGGCGGAAGCGTGTAAATCTGGACACCTTGGAGgtctctcttt ... cttgatctagGCTACGGTGGCGATGTTTGGTACCCGCAGCCTCCTCCGAAAGATCACCCAT
EST: gi|169048961|gb|FE454947.1|FE454947
EST:     CATGGATGCCAATGCGGTGGCGGAAGCGTGTAAATCTGGACACCTTGGAG                         GCTACGGTGGCGATGTTTGGTACCCGCAGCCTCCTCCGAAAGATCACCCAT
genomic: CATGGATGCCAATGCGGTGGCGGAAGCGTGTAAATCTGGACACCTTGGAGgtctctcttt ... cttgatctagGCTACGGTGGCGATGTTTGGTACCCGCAGCCTCCTCCGAAAGATCACCCAT

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), 35 (downstream exon)
Score: 68

AGCAAAATGAAGAGAGGTGCGGTTTTAGTGAACAATGCGAGAGGAGCCCTCATGGATGCCAATGCGGTGGCGGAAGCGTGTAAATCTGGACACCTTGGAGgtctctcttt ... cttgatctagGCTACGGTGGCGATGTTTGGTACCCGCAGCCTCCTCCGAAAGATCACCCATGGCGATCCATGCCAAACAACGCAATGACTCCTCACGTCTCTGGATCGAC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcttttcttctatttttctgctgtgattttgtttgatcttgggaacttgatctagGCTACGGTGGCGATGTTTGGTACCCGCAGCCTCCTCCGAAAGATCACCCATGGCGATCCATGCCAAACAACGCAATGACTCCTCACGTCTCTGGATCGAC
                                            acttgat  putative branch site (score: 68)
       ttctattttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtctctcttttcttctatttttctgctgtgattttgtttgatcttgggaacttgatctagGCTACGGTGGCGATGTTTGGTACCCGCAGCCTCCTCCGAAAGATCACCCATGGCGATCCATGCCAAACAACGCAATGACTCCTCACGTCTCTGGATCGAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTCCTC