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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaaatcttagaaagtataaccagccatacctgtgctgacgcggatgcacagGTGCTAGCCATGGACATCAACAGGAAGAATTTTGAGCTCGGCTACCCGTACATGGTGGAAGCCGGCGTGGCTCACAAGATCGATTTCAGGGAAGGACCCG

Basic information

species Selaginella moellendorffii
transcript EFJ11728
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ11728 (Selaginella moellendorffii), 3'ss of exon 3
lower sequence: AT4G34050.2 (Arabidopsis thaliana), 3'ss of exon 1
gtaaaatcttagaaagtataaccagccatacctgtgctgacgcggatgcacagGTGCTAGCCATGGACATCAACAGGAAGAATTTTGAGCTCGGCTACCCGTACATGGTGGAAGCCGGCGTGGCTCACAAGATCGATTTCAGGGAAGGACCCG--------------------------------
                       |     |  | |  |       ||   ||| | || || |||||  |||||||  ||||||  ||  | || |  |||  ||| | | |||||||||| |||||||||||||| ||||||||||| || |                                
-----------------------aattgaaagtttcatcctttttatcatcagattctggctatggatgtcaacagagagaattacgaattgggtttaccgatcattgagaaagccggcgttgCTCACAAGATCGACTTCAGGGAAGGCCCTGCTCTTCCCGTTCTTGATGAAATCGTTGCTGAC

upper sequence: EFJ11728 (Selaginella moellendorffii), 3'ss of exon 3
lower sequence: AT4G34050.1 (Arabidopsis thaliana), 3'ss of exon 2
---------------------------------gtaaaatcttagaaagtataaccagccatacctgtgctgacgcggatgcacagGTGCTAGCCATGGACATCAACAGGAAGAATTTTGAGCTCGGCTACCCGTACATGGTGGAAGCCGGCGTGGCTCACAAGATCGATTTCAGGGAAGGACCCG
                                 |     | ||    |   |    |   | |  |                 ||| | || || |||||  |||||||  ||||||  ||  | || |  |||  ||| | | |||||||||| |||||||||||||| ||||||||||| || |
gtaaatcaatctcttcatcctcctctgttttttggtgggttttgtcgaacttgggaattgaaagtttcatcctttttatcat-cagATTCTGGCTATGGATGTCAACAGAGAGAATTACGAATTGGGTTTACCGATCATTGAGAAAGCCGGCGTTGCTCACAAGATCGACTTCAGGGAAGGCCCTG
















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|169106716|gb|FE506753.1|FE506753
EST:     CTGGTTACTCTCTTCTCAGCACGGCTCTGGCTCTGCCGGAAGATGGAACG                         GTGCTAGCCATGGACATCAACAGGAAGAATTTTGAGCTCGGCTACCCGTAC
genomic: CTGGTTACTCTCTTCTCAGCACGGCTCTGGCTCTGCCGGAAGATGGAACGgtaaaatctt ... ggatgcacagGTGCTAGCCATGGACATCAACAGGAAGAATTTTGAGCTCGGCTACCCGTAC
EST: gi|169066692|gb|FE475448.1|FE475448
EST:     CTGGTTACTCTCTTCTCAGCACGGCTCTGGCTCTGCCGGAAGATGGAACG                         GTGCTAGCCATGGACATCAACAGGAAGAATTTTGAGCTCGGCTACCCGTAC
genomic: CTGGTTACTCTCTTCTCAGCACGGCTCTGGCTCTGCCGGAAGATGGAACGgtaaaatctt ... ggatgcacagGTGCTAGCCATGGACATCAACAGGAAGAATTTTGAGCTCGGCTACCCGTAC
EST: gi|169106715|gb|FE506752.1|FE506752
EST:     CAGCACGGCTCTGGCTCTGCCGGAAGATGGAACG                         GTGCTAGCCATGGACATCAACAGGAAGAATTTTGAGCTCGGCTACCCGTAC
genomic: CAGCACGGCTCTGGCTCTGCCGGAAGATGGAACGgtaaaatctt ... ggatgcacagGTGCTAGCCATGGACATCAACAGGAAGAATTTTGAGCTCGGCTACCCGTAC
EST: gi|169075572|gb|FE481958.1|FE481958
EST:     CTGGTTACTCTCTTCTCAGCACGGCTCTGGCTCTGCCGGAAGATGGAACG                         GTGCTAGCCATGGACATCAACAGGAAGAATTTTGAGCTCGGCTACCCGTAC
genomic: CTGGTTACTCTCTTCTCAGCACGGCTCTGGCTCTGCCGGAAGATGGAACGgtaaaatctt ... ggatgcacagGTGCTAGCCATGGACATCAACAGGAAGAATTTTGAGCTCGGCTACCCGTAC
EST: gi|169059287|gb|FE467468.1|FE467468
EST:     CTGGTTACTCTCTTCTCAGCACGGCTCTGGCTCTGCCGGAAGATGGAACG                         GTGCTAGCCATGGACATCAACAGGAAGAATTTTGAGCTCGGCTACCCGTAC
genomic: CTGGTTACTCTCTTCTCAGCACGGCTCTGGCTCTGCCGGAAGATGGAACGgtaaaatctt ... ggatgcacagGTGCTAGCCATGGACATCAACAGGAAGAATTTTGAGCTCGGCTACCCGTAC
EST: gi|70670609|gb|DN839186.1|DN839186
EST:     CTGGTTACTCTCTTCTCAGCACGGCTCTGGCTCTGCCGGAAGATGGAACG                         GTGCTAGCCATGGACATCAACAGGAAGAACTTTGAGCTCGGCTACCCGTAC
genomic: CTGGTTACTCTCTTCTCAGCACGGCTCTGGCTCTGCCGGAAGATGGAACGgtaaaatctt ... ggatgcacagGTGCTAGCCATGGACATCAACAGGAAGAATTTTGAGCTCGGCTACCCGTAC
EST: gi|169108255|gb|FE513564.1|FE513564
EST:     CTGGTTACTCTCTTCTCAGCACGGCTCTGGCTCTGCCGGAAGATGGAACG                         GTGCTAGCCATGGACATCAACAGGAAGAATTTTGAGCTCGGCTACCCGTAC
genomic: CTGGTTACTCTCTTCTCAGCACGGCTCTGGCTCTGCCGGAAGATGGAACGgtaaaatctt ... ggatgcacagGTGCTAGCCATGGACATCAACAGGAAGAATTTTGAGCTCGGCTACCCGTAC
EST: gi|169107108|gb|FE507262.1|FE507262
EST:     CAGCACGGCTCTGGCTCTGCCGGAAGATGGAACG                         GTGCTAGCCATGGACATCAACAGGAAGAATTTTGAGCTCGGCTACCCGTAC
genomic: CAGCACGGCTCTGGCTCTGCCGGAAGATGGAACGgtaaaatctt ... ggatgcacagGTGCTAGCCATGGACATCAACAGGAAGAATTTTGAGCTCGGCTACCCGTAC
EST: gi|169042315|gb|FE452863.1|FE452863
EST:     CAGCACGGCTTTGGCTTTGCCGGAAGATGGAACG                         GTGCTAGCCATGGACATCAACAGGAAGAATTTTGAGCTCGGCTACCCGTAC
genomic: CAGCACGGCTCTGGCTCTGCCGGAAGATGGAACGgtaaaatctt ... ggatgcacagGTGCTAGCCATGGACATCAACAGGAAGAATTTTGAGCTCGGCTACCCGTAC
EST: gi|169070774|gb|FE477321.1|FE477321
EST:     CTGGTTACTCTCTTCTCAGCACGGCTCTGGCTCTGCCGGAAGATGGAACG                         GTGCTAGCCATGGACATCAACAGGAAGAATTTTGAGCTCGGCTACCCGTAC
genomic: CTGGTTACTCTCTTCTCAGCACGGCTCTGGCTCTGCCGGAAGATGGAACGgtaaaatctt ... ggatgcacagGTGCTAGCCATGGACATCAACAGGAAGAATTTTGAGCTCGGCTACCCGTAC
EST: gi|169065676|gb|FE474344.1|FE474344
EST:     CTGGTTACTCTCTTCTCAGCACGGCTCTGGCTCTGCCGGAAGATGGAACG                         GTGCTAGCCATGGACATCAACAGGAAGAACTTTGAGCTCGGCTACCCGTAC
genomic: CTGGTTACTCTCTTCTCAGCACGGCTCTGGCTCTGCCGGAAGATGGAACGgtaaaatctt ... ggatgcacagGTGCTAGCCATGGACATCAACAGGAAGAATTTTGAGCTCGGCTACCCGTAC
EST: gi|169115443|gb|FE516184.1|FE516184
EST:     CTGGTTACTCTCTTCTCAGCACGGCTCTGGCTCTGCCGGAAGATGGAACG                         GTGCTAGCCATGGACATCAACAGGAAGAATTTTGAGCTCGGCTACCCGTAC
genomic: CTGGTTACTCTCTTCTCAGCACGGCTCTGGCTCTGCCGGAAGATGGAACGgtaaaatctt ... ggatgcacagGTGCTAGCCATGGACATCAACAGGAAGAATTTTGAGCTCGGCTACCCGTAC
EST: gi|169075571|gb|FE481957.1|FE481957
EST:     CTGGTTACTCTCTTCTCAGCACGGCTCTGGCTCTGCCGGAAGATGGAACG                         GTGCTAGCCATGGACATCAACAGGAAGAATTTTGAGCTCGGCTACCCGTAC
genomic: CTGGTTACTCTCTTCTCAGCACGGCTCTGGCTCTGCCGGAAGATGGAACGgtaaaatctt ... ggatgcacagGTGCTAGCCATGGACATCAACAGGAAGAATTTTGAGCTCGGCTACCCGTAC
EST: gi|169107109|gb|FE507263.1|FE507263
EST:     CTGGTTACTCTCTTCTCAGCACGGCTCTGGCTCTGCCGGAAGATGGAACG                         GTGCTAGCCATGGACATCAACAGGAAGAATTTTGAGCTCGGCTACCCGTAC
genomic: CTGGTTACTCTCTTCTCAGCACGGCTCTGGCTCTGCCGGAAGATGGAACGgtaaaatctt ... ggatgcacagGTGCTAGCCATGGACATCAACAGGAAGAATTTTGAGCTCGGCTACCCGTAC
EST: gi|169036115|gb|FE444622.1|FE444622
EST:     CTGGTTACTCTCTTCTCAGCACGGCTCTGGCTCTGCCGGAAGATGGAACG                         GTGCTAGCCATGGACATCAACAGGAAGAATTTTGAGCTCGGCTACCCGTAC
genomic: CTGGTTACTCTCTTCTCAGCACGGCTCTGGCTCTGCCGGAAGATGGAACGgtaaaatctt ... ggatgcacagGTGCTAGCCATGGACATCAACAGGAAGAATTTTGAGCTCGGCTACCCGTAC
EST: gi|169104300|gb|FE503714.1|FE503714
EST:     CTGGTTACTCTCTTCTCAGCACGGCTCTGGCTCTGCCGGAAGATGGAACG                         GTGCTAGCCATGGACATCAACAGGAAGAATTTTGAGCTCGGCTACCCGTAC
genomic: CTGGTTACTCTCTTCTCAGCACGGCTCTGGCTCTGCCGGAAGATGGAACGgtaaaatctt ... ggatgcacagGTGCTAGCCATGGACATCAACAGGAAGAATTTTGAGCTCGGCTACCCGTAC
EST: gi|169115444|gb|FE516185.1|FE516185
EST:     CTGGTTACTCTCTTCTCAGCACGGCTCTGGCTCTGCCGGAAGATGGAACG                         GTGCTAGCCATGGACATCAACAGGAAGAATTTTGAGCTCGGCTACCCGTAC
genomic: CTGGTTACTCTCTTCTCAGCACGGCTCTGGCTCTGCCGGAAGATGGAACGgtaaaatctt ... ggatgcacagGTGCTAGCCATGGACATCAACAGGAAGAATTTTGAGCTCGGCTACCCGTAC
EST: gi|169104299|gb|FE503713.1|FE503713
EST:     CAGCACGGCTCTGGCTCTGCCGGAAGATGGAACG                         GTGCTAGCCATGGACATCAACAGGAAGAATTTTGAGCTCGGCTACCCGTAC
genomic: CAGCACGGCTCTGGCTCTGCCGGAAGATGGAACGgtaaaatctt ... ggatgcacagGTGCTAGCCATGGACATCAACAGGAAGAATTTTGAGCTCGGCTACCCGTAC
EST: gi|169070773|gb|FE477320.1|FE477320
EST:     CTGGTTACTCTCTTCTCAGCACGGCTCTGGCTCTGCCGGAAGATGGAACG                         GTGCTAGCCATGGACATCAACAGGAAGAATTTTGAGCTCGGCTACCCGTAC
genomic: CTGGTTACTCTCTTCTCAGCACGGCTCTGGCTCTGCCGGAAGATGGAACGgtaaaatctt ... ggatgcacagGTGCTAGCCATGGACATCAACAGGAAGAATTTTGAGCTCGGCTACCCGTAC

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: 35 (upstream exon), 34 (downstream exon)
Score: 319

CTTGCTCAAGATGATGAACGCCAAGAAGACAATGGAGATTGGAGTCTACACTGGTTACTCTCTTCTCAGCACGGCTCTGGCTCTGCCGGAAGATGGAACGgtaaaatctt ... ggatgcacagGTGCTAGCCATGGACATCAACAGGAAGAATTTTGAGCTCGGCTACCCGTACATGGTGGAAGCCGGCGTGGCTCACAAGATCGATTTCAGGGAAGGACCCG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtaaaatcttagaaagtataaccagccatacctgtgctgacgcggatgcacagGTGCTAGCCATGGACATCAACAGGAAGAATTTTGAGCTCGGCTACCCGTACATGGTGGAAGCCGGCGTGGCTCACAAGATCGATTTCAGGGAAGGACCCG
                                    tgctgac  putative branch site (score: 319)
                aaagtataa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaaatcttagaaagtataaccagccatacctgtgctgacgcggatgcacagGTGCTAGCCATGGACATCAACAGGAAGAATTTTGAGCTCGGCTACCCGTACATGGTGGAAGCCGGCGTGGCTCACAAGATCGATTTCAGGGAAGGACCCG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG