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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgtgaagagttactttactttgtcattttctagtggatctttattgcagGTATAATATGCTAGCCCAGAAACTGATATCGCAACCAGTCTTCTCTTTCTGGCTGAATCGCGATGCCTCGGATGAGGAGGACGGCGGTGAAATCGTGTTC

Basic information

species Selaginella moellendorffii
transcript EFJ34434
intron # 4
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|169108566|gb|FE510781.1|FE510781
EST:     CTTGGACTTGGATTCAAAGCGATTTCCATGGGACAGGTTACTCCCGTCTG                         GTATAATATGCTAGCCCAGAAACTGATATCGCAACCAGTCTTCTCTTTCTG
genomic: CTTGGACTTGGATTCAAAGCGATTTCCAAGGGACAGGTTACTCCCGTCTGgtatgtgaag ... tttattgcagGTATAATATGCTAGCCCAGAAACTGATATCGCAACCAGTCTTCTCTTTCTG
EST: gi|169055215|gb|FE461076.1|FE461076
EST:     CTTGGACTTGGATTCAAAGCGATTTCCAAGGGACAGGTTACTCCCGTCTG                         GTATAATATGCTAGCCCAGAAACTGATATCGCAACCAGTCTTCTCTTTCTG
genomic: CTTGGACTTGGATTCAAAGCGATTTCCAAGGGACAGGTTACTCCCGTCTGgtatgtgaag ... tttattgcagGTATAATATGCTAGCCCAGAAACTGATATCGCAACCAGTCTTCTCTTTCTG
EST: gi|169025759|gb|FE433669.1|FE433669
EST:     CTTGGACTTGGATTCAAAGCGATTTCCAAGGGACAGGTTACTCCCGTCTG                         GTATAATATGCTGGCCCAGAAACTGATATCGCAACCAGTCTTCTCTTTCTG
genomic: CTTGGACTTGGATTCAAAGCGATTTCCAAGGGACAGGTTACTCCCGTCTGgtatgtgaag ... tttattgcagGTATAATATGCTAGCCCAGAAACTGATATCGCAACCAGTCTTCTCTTTCTG
EST: gi|169114469|gb|FE516539.1|FE516539
EST:     CTTGGACTTGGATTCAAAGCGATTTCCAAGGGACAGGTTACTCCCGTCTG                         GTATAATATGCTAGCCCAGAAACTGATATCGCAACCAGTCTTCTCTTTCTG
genomic: CTTGGACTTGGATTCAAAGCGATTTCCAAGGGACAGGTTACTCCCGTCTGgtatgtgaag ... tttattgcagGTATAATATGCTAGCCCAGAAACTGATATCGCAACCAGTCTTCTCTTTCTG
EST: gi|169057177|gb|FE464688.1|FE464688
EST:     CTTGGACTTGGATTCAAAGCGATTTCCAAGGGACAGGTTACTCCCGTCTG                         GTATAATATGCTGGCCCAGAAACTGATATCGCAACCAGTCTTCTCTTTCTG
genomic: CTTGGACTTGGATTCAAAGCGATTTCCAAGGGACAGGTTACTCCCGTCTGgtatgtgaag ... tttattgcagGTATAATATGCTAGCCCAGAAACTGATATCGCAACCAGTCTTCTCTTTCTG
EST: gi|169060204|gb|FE467566.1|FE467566
EST:     CTTGGACTTGGATTCAAAGCGATTTCCAAGGGACAGGTTACTCCCGTCTG                         GTATAATATGCTAGCCCAGAAACTGATATCGCAACCAGTCTTCTCTTTCTG
genomic: CTTGGACTTGGATTCAAAGCGATTTCCAAGGGACAGGTTACTCCCGTCTGgtatgtgaag ... tttattgcagGTATAATATGCTAGCCCAGAAACTGATATCGCAACCAGTCTTCTCTTTCTG
EST: gi|169110930|gb|FE509335.1|FE509335
EST:     CTTGGACTTGGATTCAAAGCGATTTCCAAGGGACAGGTTACTCCCGTCTG                         GTATAATATGCTAGCCCAGAAACTGATATCGCAACCAGTCTTCTCTTTCTG
genomic: CTTGGACTTGGATTCAAAGCGATTTCCAAGGGACAGGTTACTCCCGTCTGgtatgtgaag ... tttattgcagGTATAATATGCTAGCCCAGAAACTGATATCGCAACCAGTCTTCTCTTTCTG
EST: gi|169048945|gb|FE456062.1|FE456062
EST:     CTTGGACTTGGATTCAAAGCGATTTCCAAGGGACAGGTTACTCCCGTCTG                         GTATAATATGCTGGCCCAGAAACTGATATCGCAACCAGTCTTCTCTTTCTG
genomic: CTTGGACTTGGATTCAAAGCGATTTCCAAGGGACAGGTTACTCCCGTCTGgtatgtgaag ... tttattgcagGTATAATATGCTAGCCCAGAAACTGATATCGCAACCAGTCTTCTCTTTCTG
EST: gi|169034782|gb|FE445635.1|FE445635
EST:     CTTGGACTTGGATTCAAAGCGATTTCCAAGGGACAGGTTACTCCCGTCTG                         GTATAATATGCTGGCCCAGAAACTGATATCGCAACCAGTCTTCTCTTTCTG
genomic: CTTGGACTTGGATTCAAAGCGATTTCCAAGGGACAGGTTACTCCCGTCTGgtatgtgaag ... tttattgcagGTATAATATGCTAGCCCAGAAACTGATATCGCAACCAGTCTTCTCTTTCTG
EST: gi|169110671|gb|FE509817.1|FE509817
EST:     CTTGGACTTGGATTCAAAGCGATTTCCAAGGGACAGGTTACTCCCGTCTG                         GTATAATATGCTAGCCCAGAAACTGATATCGCAACCAGTCTTCTCTTTCTG
genomic: CTTGGACTTGGATTCAAAGCGATTTCCAAGGGACAGGTTACTCCCGTCTGgtatgtgaag ... tttattgcagGTATAATATGCTAGCCCAGAAACTGATATCGCAACCAGTCTTCTCTTTCTG
EST: gi|169039673|gb|FE448607.1|FE448607
EST:     CTTGGACTTGGATTCAAAGCGATTTCCAAGGGACAGGTTACTCCCGTCTG                         GTATAATATGCTAGCCCAGAAACTGATATCGCAACCAGTCTTCTCTTTCTG
genomic: CTTGGACTTGGATTCAAAGCGATTTCCAAGGGACAGGTTACTCCCGTCTGgtatgtgaag ... tttattgcagGTATAATATGCTAGCCCAGAAACTGATATCGCAACCAGTCTTCTCTTTCTG
EST: gi|169031936|gb|FE440662.1|FE440662
EST:     CTTGGACTTGGATTCAAAGCGATTTCCAAGGGACAGGTTACTCCCGTCTG                         GTATAATATGCTAGCCCAGAAACTGATATCGCAACCAGTCTTCTCTTTCTG
genomic: CTTGGACTTGGATTCAAAGCGATTTCCAAGGGACAGGTTACTCCCGTCTGgtatgtgaag ... tttattgcagGTATAATATGCTAGCCCAGAAACTGATATCGCAACCAGTCTTCTCTTTCTG
EST: gi|169044449|gb|FE451073.1|FE451073
EST:     CTTGGACTTGGATTCAAAGCGATTTCCAAGGGACAGGTTACTCCCGTCTG                         GTATAATATGCTAGCCCAGAAACTGATATCGCAACCAGTCTTCTCTTTCTG
genomic: CTTGGACTTGGATTCAAAGCGATTTCCAAGGGACAGGTTACTCCCGTCTGgtatgtgaag ... tttattgcagGTATAATATGCTAGCCCAGAAACTGATATCGCAACCAGTCTTCTCTTTCTG
EST: gi|169096046|gb|FE500024.1|FE500024
EST:     CTTGGACTTGGATTCAAAGCGATTTCCAAGGGACAGGTTACTCCCGTCTG                         GTATAATATGCTAGCCCAGAAACTGATATCGCAACCAGTCTTCTCTTTCTG
genomic: CTTGGACTTGGATTCAAAGCGATTTCCAAGGGACAGGTTACTCCCGTCTGgtatgtgaag ... tttattgcagGTATAATATGCTAGCCCAGAAACTGATATCGCAACCAGTCTTCTCTTTCTG
EST: gi|169065201|gb|FE474025.1|FE474025
EST:     CTTGGACTTGGATTCAAAGCGATTTCCAAGGGACAGGTTACTCCCGTCTG                         GTATAATATGCTAGCCCAGAAACTGATATCGCAACCAGTCTTCTCTTTCTG
genomic: CTTGGACTTGGATTCAAAGCGATTTCCAAGGGACAGGTTACTCCCGTCTGgtatgtgaag ... tttattgcagGTATAATATGCTAGCCCAGAAACTGATATCGCAACCAGTCTTCTCTTTCTG
EST: gi|169058294|gb|FE466035.1|FE466035
EST:     CTTGGACTTGGATTCAAAGCGATTTCCAAGGGACAGGTTACTCCCGTCTG                         GTATAATATGCTGGCCCAGAAACTGATATCGCAACCAGTCTTCTCTTTCTG
genomic: CTTGGACTTGGATTCAAAGCGATTTCCAAGGGACAGGTTACTCCCGTCTGgtatgtgaag ... tttattgcagGTATAATATGCTAGCCCAGAAACTGATATCGCAACCAGTCTTCTCTTTCTG
EST: gi|169093447|gb|FE495728.1|FE495728
EST:     CTTGGACTTGGATTCAAAGCGATTTCCAAGGGACAGGTTACTCCCGTCTG                         GTATAATATGCTAGCCCAGAAACTGATATCGCAACCAGTCTTCTCTTTCTG
genomic: CTTGGACTTGGATTCAAAGCGATTTCCAAGGGACAGGTTACTCCCGTCTGgtatgtgaag ... tttattgcagGTATAATATGCTAGCCCAGAAACTGATATCGCAACCAGTCTTCTCTTTCTG
EST: gi|169031873|gb|FE438506.1|FE438506
EST:     CTTGGACTTGGATTCAAAGCGATTTCCAAGGGACAGGTTACTCCCGTCTG                         GTATAATATGCTAGCCCAGAAACTGATATCGCAACCAGTCTTCTCTTTCTG
genomic: CTTGGACTTGGATTCAAAGCGATTTCCAAGGGACAGGTTACTCCCGTCTGgtatgtgaag ... tttattgcagGTATAATATGCTAGCCCAGAAACTGATATCGCAACCAGTCTTCTCTTTCTG
EST: gi|169047467|gb|FE455662.1|FE455662
EST:     CTTGGACTTGGATTCAAAGCGATTTCCAAGGGACAGGTTACTCCCGTCTG                         GTATAATATGCTGGCCCAGAAACTGATATCGCAACCAGTCTTCTCTTTCTG
genomic: CTTGGACTTGGATTCAAAGCGATTTCCAAGGGACAGGTTACTCCCGTCTGgtatgtgaag ... tttattgcagGTATAATATGCTAGCCCAGAAACTGATATCGCAACCAGTCTTCTCTTTCTG
EST: gi|169080226|gb|FE488905.1|FE488905
EST:     CTTGGACTTGGATTCAAAGCGATTTCCAAGGGACAGGTTACTCCCGTCTG                         GTATAATATGCTGGCCCAGAAACTGATATCGCAACCAGTCTTCTCTTTCTG
genomic: CTTGGACTTGGATTCAAAGCGATTTCCAAGGGACAGGTTACTCCCGTCTGgtatgtgaag ... tttattgcagGTATAATATGCTAGCCCAGAAACTGATATCGCAACCAGTCTTCTCTTTCTG
EST: gi|169031798|gb|FE438483.1|FE438483
EST:     CTTGGACTTGGATTCAAAGCGATTTCCAAGGGACAGGTTACTCCCGTCTG                         GTATAATATGCTAGCCCAGAAACTGATATCGCAACCAGTCTTCTCTTTCTG
genomic: CTTGGACTTGGATTCAAAGCGATTTCCAAGGGACAGGTTACTCCCGTCTGgtatgtgaag ... tttattgcagGTATAATATGCTAGCCCAGAAACTGATATCGCAACCAGTCTTCTCTTTCTG
EST: gi|169061924|gb|FE470218.1|FE470218
EST:     CTTGGACTTGGATTCAAAGCGATTTCCAAGGGACAGGTTACTCCCGTCTG                         GTATAATATGCTGGCCCAGAAACTGATATCGCAACCAGTCTTCTCTTTCTG
genomic: CTTGGACTTGGATTCAAAGCGATTTCCAAGGGACAGGTTACTCCCGTCTGgtatgtgaag ... tttattgcagGTATAATATGCTAGCCCAGAAACTGATATCGCAACCAGTCTTCTCTTTCTG

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: 104

CAACAAGTGAGCCTGGGCTTGTTTTCCTCGTTGCCAAGTTTGATGGCATCCTTGGACTTGGATTCAAAGCGATTTCCAAGGGACAGGTTACTCCCGTCTGgtatgtgaag ... tttattgcagGTATAATATGCTAGCCCAGAAACTGATATCGCAACCAGTCTTCTCTTTCTGGCTGAATCGCGATGCCTCGGATGAGGAGGACGGCGGTGAAATCGTGTTC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtatgtgaagagttactttactttgtcattttctagtggatctttattgcagGTATAATATGCTAGCCCAGAAACTGATATCGCAACCAGTCTTCTCTTTCTGGCTGAATCGCGATGCCTCGGATGAGGAGGACGGCGGTGAAATCGTGTTC
                                             tctttatt  CT-rich tract
                                          atctttatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgtgaagagttactttactttgtcattttctagtggatctttattgcagGTATAATATGCTAGCCCAGAAACTGATATCGCAACCAGTCTTCTCTTTCTGGCTGAATCGCGATGCCTCGGATGAGGAGGACGGCGGTGAAATCGTGTTC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGGA