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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaaatatctctctgtgttcgtcgagaaaaagcttgaaacttatcgttttcttgccttagATGGGATACTCCTATCCACGTTGATGCTGCCAGTGGAGGATTCATCGCTCCATTCCTCTATCCAGATTTGGAGTGGGATTTTCGATTGCCTCTTGTCAAG

Basic information

species Selaginella moellendorffii
transcript EFJ18071
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ18071 (Selaginella moellendorffii), 3'ss of exon 4
lower sequence: GLYMA08G09660.1 (Glycine max), 3'ss of exon 3
------------------------------------------------------------gtaaaatatctctctgtgttcgt-cgagaaaaagcttgaaacttatcgttttcttgccttagATGGGATACTCCTATCCACGTTGATGCTGCCAGTGGAGGATTCATCGCTCCATTCCTCTATCCAGATTTGGAGTGGGATTTTCGATTGCCTCTTGTCAAG
                                                             | |  || || |   |  || |     ||   |||| |  ||| || | || |     |||||||||||| ||||| || || |||||||| ||||| || || || ||||||||||| |||||||| || || ||||||||| || | ||  | || |||
gtaagtaaattaatgtaccactaattacctctctattcactaattcaactatcttcactgttcacttagcttttcattgtcatgtactaatttgcttta--cttgtcatattata--tatagATGGGATACACCTATTCATGTGGATGCTGCAAGTGGTGGCTTTATTGCTCCATTCCTTTATCCAGAGTTAGAATGGGATTTTAGACTCCCATTGGTGAAG

upper sequence: EFJ18071 (Selaginella moellendorffii), 3'ss of exon 4
lower sequence: GLYMA08G09670.1 (Glycine max), 3'ss of exon 3
-----------------------gtaaaatatctct-ctgtgttcgtcgagaaaaagcttgaaacttatcgttt-tcttgcct----tagATGGGATACTCCTATCCACGTTGATGCTGCCAGTGGAGGATTCATCGCTCCATTCCTCTATCCAGATTTGGAGTGGGATTTTCGATTGCCTCTTGTCAAG
                        | |||||| | | ||| | |   |   |    |    ||     |   || ||    |     |||||||||||| ||||| ||||| |||||||| ||||| || || || ||||||||||| ||||||||  | || ||||||||  || | ||  | || |||
gtaatgaattgatattccactaattcaaatatttttactgggctttcctttaccttgtactaattgctttacttgtcacatcaatgatagATGGGATACGCCTATTCACGTGGATGCTGCAAGTGGTGGGTTTATTGCTCCATTCCTATATCCAGAGCTAGAATGGGATTTCAGACTCCCATTGGTGAAG

upper sequence: EFJ18071 (Selaginella moellendorffii), 3'ss of exon 4
lower sequence: GLYMA14G39170.1 (Glycine max), 3'ss of exon 5
--------------------------------------------------------gtaaaatatctctctgtgttcgtcgagaaaaagcttgaaacttatcgttttcttgccttagATGGGATACTCCTATCCACGTTGATGCTGCCAGTGGAGGATTCATCGCTCCATTCCTCTATCCAGATTTGGAGTGGGATTTTCGATTGCCTCTTGTCAAG
                                                         |||  ||  |   | |   | | ||    |    ||||| | ||  ||         ||||||||| ||||| || || || ||||| |||||||| |||||||| || || || |||||||| ||  | |||||||||||||| ||||| || || |||
gtttgtattgcacatattgattgagtcttaactgcttcctattttgtgaacctagtttaaggtactttaatttagacttggaattgacatgtgaaattaattattgg-------tagATGGGACACTCCAATTCATGTGGATGCAGCCAGTGGTGGATTCATTGCACCTTTTCTCTATCCTGAGCTTGAGTGGGATTTTCGGTTGCCACTAGTGAAG

upper sequence: EFJ18071 (Selaginella moellendorffii), 3'ss of exon 4
lower sequence: GLYMA02G40840.1 (Glycine max), 3'ss of exon 4
---------------------------------------------------------gtaaaatatctctctgtgttcgtcgagaaaaagcttgaaacttatcgttttcttgccttagATGGGATACTCCTATCCACGTTGATGCTGCCAGTGGAGGATTCATCGCTCCATTCCTCTATCCAGATTTGGAGTGGGATTTTCGATTGCCTCTTGTCAAG
                                                          |||  ||| |   | |   | | ||    |    ||||| | ||  ||   |      |||||||| ||||| || || || |||||||||||||| |||||||| || || || || ||||||||  | || ||||| ||||| ||||| || || |||
gtttgtattgcacatattgattgagtctttactgcttcctattttgtgaactaaagtttaaggtattttaatttagacttggaattgacatgtgaaattaattattgggt------agATGGGACACTCCAATTCATGTGGATGCTGCCAGTGGGGGATTCATTGCACCTTTTCTTTATCCAGAGCTTGAATGGGACTTTCGGTTGCCACTAGTGAAG

upper sequence: EFJ18071 (Selaginella moellendorffii), 3'ss of exon 4
lower sequence: Vv01s0011g06600.t01 (Vitis vinifera), 3'ss of exon 4
-------------------------------gtaaaatatc----tctctgtgttcgtcgagaaaaa--------gcttgaaacttatcgttttcttgcctt--agATGGGATACTCCTATCCACGTTGATGCTGCCAGTGGAGGATTCATCGCTCCATTCCTCTATCCAGATTTGGAGTGGGATTTTCGATTGCCTCTTGTCAAG
                                 | ||| |     ||| ||   || ||   |  ||        | |      || | ||||| ||  | |  ||||||||||| || || || |||||||| || ||||| |||||||| || |||||||| ||||| ||  |||||||||| || ||  | ||  | || |||
gtatataatcactcttctaccaacatttagttcagaattttgaaatctttgaagtcttccgaattaatatgctctgttcctttttttttgtttttttttcctgcagATGGGATACCCCAATTCATGTTGATGCAGCTAGTGGTGGATTCATTGCACCATTCCTTTATCCGGAACTGGAGTGGGACTTCCGCCTTCCATTGGTGAAG

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|169031371|gb|FE441187.1|FE441187
EST:     GACGTGAAGCTCCTCAACGAGCTCTTGGNNNNNNNGAACAAAGAAACTGG                         ATGGGATACTCCTATCCACGTTGATGCTGCCAGTGGAGGATTCATCGCTCC
genomic: GACGTGAAGCTCCTCAACGAGCTCTTGGAAAAAAAGAACAAAGAAACTGGgtaaaatatc ... cttgccttagATGGGATACTCCTATCCACGTTGATGCTGCCAGTGGAGGATTCATCGCTCC
EST: gi|169042692|gb|FE451511.1|FE451511
EST:     GACGTGAAGCTCCTCAACGAGCTCTTGGNNNNNNNGAACAAAGAAACTGG                         ATGGGATACTCCTATCCACGTTGATGCTGCCAGTG
genomic: GACGTGAAGCTCCTCAACGAGCTCTTGGAAAAAAAGAACAAAGAAACTGGgtaaaatatc ... cttgccttagATGGGATACTCCTATCCACGTTGATGCTGCCAGTG
EST: gi|169053855|gb|FE460946.1|FE460946
EST:     GACGTGAAGCTCCTCAACGAGCTCTTGGNNNNNNNGAACAAAGAAACTGG                         ATGGGATACTCCTATCCACGTTGATGCTGCCAGTGGAGGATTCATCGCTCC
genomic: GACGTGAAGCTCCTCAACGAGCTCTTGGAAAAAAAGAACAAAGAAACTGGgtaaaatatc ... cttgccttagATGGGATACTCCTATCCACGTTGATGCTGCCAGTGGAGGATTCATCGCTCC
EST: gi|169019233|gb|FE428146.1|FE428146
EST:     ACGTGAAGCTCCTCAACGAGCTCTTGGNNNNNNNNGAACAAAGAAACTGG                         ATGGGATACTCCTATCCACGTTGATGCTGCCAGTGGAGGATTCATCGCTCC
genomic: ACGTGAAGCTCCTCAACGAGCTCTTGGAAAAAAA-GAACAAAGAAACTGGgtaaaatatc ... cttgccttagATGGGATACTCCTATCCACGTTGATGCTGCCAGTGGAGGATTCATCGCTCC
EST: gi|169063238|gb|FE472696.1|FE472696
EST:     GACGTGAAGCTCCTCAACGAGCTCTTGGNNNNNNNGAACAAAGAAACTGG                         ATGGGATACTCCTATCCACGTTGATGCTGCCAGTGGAGGATTCATCGCTCC
genomic: GACGTGAAGCTCCTCAACGAGCTCTTGGAAAAAAAGAACAAAGAAACTGGgtaaaatatc ... cttgccttagATGGGATACTCCTATCCACGTTGATGCTGCCAGTGGAGGATTCATCGCTCC
EST: gi|169026893|gb|FE434244.1|FE434244
EST:     GACGTGAAGCTCCTCAACGAGCTCTTGGNNNNNNNGAACAAAGACACTGG                         ATGGAATACTCCTATCCACGTTGATGCCGCCAGTGGAGGATTCATCGCTCC
genomic: GACGTGAAGCTCCTCAACGAGCTCTTGGAAAAAAAGAACAAAGAAACTGGgtaaaatatc ... cttgccttagATGGGATACTCCTATCCACGTTGATGCTGCCAGTGGAGGATTCATCGCTCC
EST: gi|169108572|gb|FE510787.1|FE510787
EST:     GACGTGAAGCTCCTCAACGAGCTCTTGGNNNNNNNGAACAAAGAAACTGG                         ATGGGATACTCCTATCCACGTTGATGCTGCCAGTGGAGGATTCATCGCTCC
genomic: GACGTGAAGCTCCTCAACGAGCTCTTGGAAAAAAAGAACAAAGAAACTGGgtaaaatatc ... cttgccttagATGGGATACTCCTATCCACGTTGATGCTGCCAGTGGAGGATTCATCGCTCC
EST: gi|169072350|gb|FE480249.1|FE480249
EST:     GACGTGAAGCTCCTCAACGAGCTCTTGGAAAAAA-GAACAAAGAAACTGG                         ATGGGATACTCCTATCCACGTTGATGCTGCCAGTGGAGGATTCATCGCTCC
genomic: GACGTGAAGCTCCTCAACGAGCTCTTGGAAAAAAAGAACAAAGAAACTGGgtaaaatatc ... cttgccttagATGGGATACTCCTATCCACGTTGATGCTGCCAGTGGAGGATTCATCGCTCC
EST: gi|169049329|gb|FE458240.1|FE458240
EST:     GACGTGAAGCTCCTCAACGAGCTCTTGGNNNNNNNGAACAAAGAAACTGG                         ATGGGATACTCCTATCCACGTTGATGCTGCCAGTGGAGGATTCATCGCTCC
genomic: GACGTGAAGCTCCTCAACGAGCTCTTGGAAAAAAAGAACAAAGAAACTGGgtaaaatatc ... cttgccttagATGGGATACTCCTATCCACGTTGATGCTGCCAGTGGAGGATTCATCGCTCC
EST: gi|169064341|gb|FE471904.1|FE471904
EST:     GACGTGAAGCTCCTCAACGAGCTCTTGGNNNNNNNGAACAAAGAAACTGG                         ATGGGATACTCCTATCCACGTTGATGCTGCCAGTGGAGGATTCATCGCTCC
genomic: GACGTGAAGCTCCTCAACGAGCTCTTGGAAAAAAAGAACAAAGAAACTGGgtaaaatatc ... cttgccttagATGGGATACTCCTATCCACGTTGATGCTGCCAGTGGAGGATTCATCGCTCC
EST: gi|169030244|gb|FE440580.1|FE440580
EST:     GACGTGAAGCTCCTCAACGAGCTCTTGGNNNNNNNGAACAAAGAAACTGG                         ATGGGATACTCCTATCCACGTTGATGCTGCCAGTGGAGGATTCATCGCTCC
genomic: GACGTGAAGCTCCTCAACGAGCTCTTGGAAAAAAAGAACAAAGAAACTGGgtaaaatatc ... cttgccttagATGGGATACTCCTATCCACGTTGATGCTGCCAGTGGAGGATTCATCGCTCC
EST: gi|169027576|gb|FE432750.1|FE432750
EST:     GACGTGAAGCTCCTCAACGAGCTCTTGGNNNNNNNGAACAAAGAAACTGG                         ATGGGATACTCCTATCCACGTTGATGCTGCCAGTGGAGGATTCATCGCTCC
genomic: GACGTGAAGCTCCTCAACGAGCTCTTGGAAAAAAAGAACAAAGAAACTGGgtaaaatatc ... cttgccttagATGGGATACTCCTATCCACGTTGATGCTGCCAGTGGAGGATTCATCGCTCC
EST: gi|169098884|gb|FE502281.1|FE502281
EST:     GAACAAAGACACTGG                         ATGGAATACTCCTATCCACGTTGATGCCGCCAGTGGAGGATTCATCGCTCC
genomic: GAACAAAGAAACTGGgtaaaatatc ... cttgccttagATGGGATACTCCTATCCACGTTGATGCTGCCAGTGGAGGATTCATCGCTCC
EST: gi|169045970|gb|FE451241.1|FE451241
EST:     GACGTGAAGCTCCTCAACGAGCTCTTGGNNNNNNNGAACAAAGAAACTGG                         ATGGGATACTCCTATCCACGTTGATGCTGCCAGTGGAGGATTCATCGCTCC
genomic: GACGTGAAGCTCCTCAACGAGCTCTTGGAAAAAAAGAACAAAGAAACTGGgtaaaatatc ... cttgccttagATGGGATACTCCTATCCACGTTGATGCTGCCAGTGGAGGATTCATCGCTCC
EST: gi|169075987|gb|FE482854.1|FE482854
EST:     GACGTGAAGCTCCTCAACGAGCTCTTGGNNNNNNNGAACAAAGAAACTGG                         ATGGGATACTCCTATCCACGTTGATGCTGCCAGTGGAGGATTCATCGCTCC
genomic: GACGTGAAGCTCCTCAACGAGCTCTTGGAAAAAAAGAACAAAGAAACTGGgtaaaatatc ... cttgccttagATGGGATACTCCTATCCACGTTGATGCTGCCAGTGGAGGATTCATCGCTCC

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), 35 (downstream exon)
Score: 106

CCATTTGCATTGCAGCCATCCTTGGTTCCACTTACAACGGAGAGTTCGAAGACGTGAAGCTCCTCAACGAGCTCTTGGAAAAAAAGAACAAAGAAACTGGgtaaaatatc ... cttgccttagATGGGATACTCCTATCCACGTTGATGCTGCCAGTGGAGGATTCATCGCTCCATTCCTCTATCCAGATTTGGAGTGGGATTTTCGATTGCCTCTTGTCAAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatctctctgtgttcgtcgagaaaaagcttgaaacttatcgttttcttgccttagATGGGATACTCCTATCCACGTTGATGCTGCCAGTGGAGGATTCATCGCTCCATTCCTCTATCCAGATTTGGAGTGGGATTTTCGATTGCCTCTTGTCAAG
                                      tcgttttcttgcctt  CT-rich tract
                               aaacttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaaatatctctctgtgttcgtcgagaaaaagcttgaaacttatcgttttcttgccttagATGGGATACTCCTATCCACGTTGATGCTGCCAGTGGAGGATTCATCGCTCCATTCCTCTATCCAGATTTGGAGTGGGATTTTCGATTGCCTCTTGTCAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG