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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatatcatacgatggttttttttttagtttttcctcaaaactttctgcaatgcagGTGCAAAGCGGCTACTGAAATGCGGTCTTGGTGACGATGATCAGTGTATTGAGGATGATTTTACGGCCTG

Basic information

species Selaginella moellendorffii
transcript EFJ14342
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ14342 (Selaginella moellendorffii), 3'ss of exon 6
lower sequence: GRMZM2G086489_T02 (Zea mays), 3'ss of exon 6
------------------------------------------gtatatcatac-gatggttttttttttagtttttcctcaaaactttctgca-atgcagGTGCAAAGCGGCTACTGAAATGCGGTCTTGGTGACGATGATCAGTGTATTGAGGATGATTTTACGGCCTG
                                           |  || ||   | |  ||  |||| | ||  |  ||   || ||  ||   ||  |||||  || || ||  |       || ||||| |||||||||||||| |||||||||||||| || || ||
attagctgccatggtaggtccttcatgatgtagggtttcatgattcatgattttggtatttgattttgttgtcatggcttccaatttcttgtgtatctagGTGGGAAACGTCTTGTTCCTGTTGGCCTTGGAGACGATGATCAGTGCATTGAGGATGATTTCACTGCATG

upper sequence: EFJ14342 (Selaginella moellendorffii), 3'ss of exon 6
lower sequence: Vv18s0001g07630.t01 (Vitis vinifera), 3'ss of exon 6
-------------------------------gtatatcatacgatggttttttttttagtttttcctcaaaact-----ttctgca--------atgcagGTGCAAAGCGGCTACTGAAATGCGGTCTTGGTGACGATGATCAGTGTATTGAGGATGATTTTACGGCCTG
                               |  | |||    ||| ||   |  ||| || |   | ||  |      || || |        || |||| ||||| || ||  |   |   ||||||||||| || |||||||| ||||||||||||||| | || ||
actctggttttgtctattgtcctgtttgtgtgggtttcaattaatgcttaactgattatttgtatttaaagtccataagttttgtatgtcattgattcagGAGCAAAACGTCTTGTTCCAGCTGGTCTTGGTGATGACGATCAGTGCATTGAGGATGATTTTGCTGCTTG
















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|169112293|gb|FE512700.1|FE512700
EST:     GTTGCAGTGGAAGTCGACGAAGCATTGGAGAAGCAAG                         GTGCAAAGCGGCTACTGAAATGCGGTCTTGGTGACGATGATCAGTGTATTG
genomic: GTTGCAGTGGAAGTCGACGAAGCATTGGAGAAGCAAGgtatatcata ... tgcaatgcagGTGCAAAGCGGCTACTGAAATGCGGTCTTGGTGACGATGATCAGTGTATTG
EST: gi|169111964|gb|FE510668.1|FE510668
EST:     GTTGCAGTTGAAGTCGACGAAGCATTGGAGAAGCAAG                         GTGCAAAGCGGCTACTGAAATGCGGTCTTGGTGACGATGATCAGTGTATTG
genomic: GTTGCAGTGGAAGTCGACGAAGCATTGGAGAAGCAAGgtatatcata ... tgcaatgcagGTGCAAAGCGGCTACTGAAATGCGGTCTTGGTGACGATGATCAGTGTATTG
EST: gi|169025173|gb|FE434110.1|FE434110
EST:     GTTGCAGTTGAAGTCGACGAAGCATTGGAGAAGCAAG                         GTGCAAAGCGGCTACTGAAATGCGGTCTTGGTGACGATGATCAGTGTATTG
genomic: GTTGCAGTGGAAGTCGACGAAGCATTGGAGAAGCAAGgtatatcata ... tgcaatgcagGTGCAAAGCGGCTACTGAAATGCGGTCTTGGTGACGATGATCAGTGTATTG
EST: gi|169114245|gb|FE515780.1|FE515780
EST:     GTTGCAGTTGAAGTCGACGAAGCATTGGAGAAGCAAG                         GTGCAAAGCGGCTACTGAAATGCGGTCTTGGTGACGATGATCAGTGTATTG
genomic: GTTGCAGTGGAAGTCGACGAAGCATTGGAGAAGCAAGgtatatcata ... tgcaatgcagGTGCAAAGCGGCTACTGAAATGCGGTCTTGGTGACGATGATCAGTGTATTG
EST: gi|169023113|gb|FE429165.1|FE429165
EST:     GTTGCAGTTGAAGTCGACGAAGCATTGGAGAAGCAAG                         GTGCAAAGCGGCTACTGAAATGCGGTCTTGGTGACGATGATCAGTGTATTG
genomic: GTTGCAGTGGAAGTCGACGAAGCATTGGAGAAGCAAGgtatatcata ... tgcaatgcagGTGCAAAGCGGCTACTGAAATGCGGTCTTGGTGACGATGATCAGTGTATTG
EST: gi|169078171|gb|FE488826.1|FE488826
EST:     GTTGCAGTGGAAGTCGACGAAGCATTGGAGAAGCAAG                         GTGCAAAGCGGCTACTGAAATGCGGTCTTGGTGACGATGATCAGTGTATTG
genomic: GTTGCAGTGGAAGTCGACGAAGCATTGGAGAAGCAAGgtatatcata ... tgcaatgcagGTGCAAAGCGGCTACTGAAATGCGGTCTTGGTGACGATGATCAGTGTATTG
EST: gi|169025078|gb|FE433859.1|FE433859
EST:     GTTGCAGTGGAAGTCGACGAAGCATTGGAGAAGCAAG                         GTGCAAAGCGGCTACTGAAATGCGGTCTTGGTGACGATGATCAGTGTATTG
genomic: GTTGCAGTGGAAGTCGACGAAGCATTGGAGAAGCAAGgtatatcata ... tgcaatgcagGTGCAAAGCGGCTACTGAAATGCGGTCTTGGTGACGATGATCAGTGTATTG

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: 32 (upstream exon), 18 (downstream exon)
Score: 4

GTTGCAGTGGAAGTCGACGAAGCATTGGAGAAGCAAGgtatatcata ... tgcaatgcagGTGCAAAGCGGCTACTGAAATGCGGTCTTGGTGACGATGATCAGTGTATTGAGGATGATTTTACGGCCTG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatatcatacgatggttttttttttagtttttcctcaaaactttctgcaatgcagGTGCAAAGCGGCTACTGAAATGCGGTCTTGGTGACGATGATCAGTGTATTGAGGATGATTTTACGGCCTG
                                        ctttctgc  CT-rich tract
           atggttttttttttag  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatatcatacgatggttttttttttagtttttcctcaaaactttctgcaatgcagGTGCAAAGCGGCTACTGAAATGCGGTCTTGGTGACGATGATCAGTGTATTGAGGATGATTTTACGGCCTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGATG