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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaatctaatacaattgtaaacatcggcttgacgatttttttcagGTTGATGATTGATGTTCCTGATGCCGAGAACCGTGCGAAAATTCTCAAAGTTATACTTAGTGACGAGGATCTTTCCCCCGATTTTAACATGGAGGAAGTG

Basic information

species Selaginella moellendorffii
transcript EFJ34631
intron # 13
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|169030971|gb|FE440332.1|FE440332
EST:     AATCGTCCATTCGATCTGGATGAAGCTGTCATACGGAGATTTCCGCGAAG                         GTTGATGATTGATGTTCCTGATGCCGAGAACCGTGCGAAAATTCTCAAAGT
genomic: AATCGTCCATTCGATCTGGATGAAGCTGTCATACGGAGATTTCCGCGAAGgtaaatctaa ... tttttttcagGTTGATGATTGATGTTCCTGATGCCGAGAACCGTGCGAAAATTCTCAAAGT
EST: gi|169043401|gb|FE451338.1|FE451338
EST:     AATCGTCCATTCGATCTGGATGAAGCTGTCATACGGAGATTTCCGCGAAG                         -TTGATGATTGATGTCCCTGATGC
genomic: AATCGTCCATTCGATCTGGATGAAGCTGTCATACGGAGATTTCCGCGAAGgtaaatctaa ... tttttttcagGTTGATGATTGATGTTCCTGATGC
EST: gi|169024270|gb|FE435222.1|FE435222
EST:     AATCGTCCATTCGATCTGGATGAAGCTGTCATACGGAGATTTCCGCGAAG                         GTTGATGATTGATGTTCCTGATGCCGAGAACCGTGCGAAAATTCTCAAAGT
genomic: AATCGTCCATTCGATCTGGATGAAGCTGTCATACGGAGATTTCCGCGAAGgtaaatctaa ... tttttttcagGTTGATGATTGATGTTCCTGATGCCGAGAACCGTGCGAAAATTCTCAAAGT
EST: gi|169052463|gb|FE462271.1|FE462271
EST:     AATCGTCCATTCGATCTGGATGAAGCTGTCATACGGAGATTTCCGCGAAG                         GTTGATGATTGATGTTCCTGATGCCGAGAACCGTGCGAAAATTCTCAAAGT
genomic: AATCGTCCATTCGATCTGGATGAAGCTGTCATACGGAGATTTCCGCGAAGgtaaatctaa ... tttttttcagGTTGATGATTGATGTTCCTGATGCCGAGAACCGTGCGAAAATTCTCAAAGT
EST: gi|169069504|gb|FE480575.1|FE480575
EST:     AATCGTCCATTCGATCTGGATGAAGCTGTCATACGGAGATTTCCGCGAAG                         GTTGATGATTGATGTTCCTGATGCCGAGAACCGTGCGAAAATTCTCAAAGT
genomic: AATCGTCCATTCGATCTGGATGAAGCTGTCATACGGAGATTTCCGCGAAGgtaaatctaa ... tttttttcagGTTGATGATTGATGTTCCTGATGCCGAGAACCGTGCGAAAATTCTCAAAGT
EST: gi|169082585|gb|FE489069.1|FE489069
EST:     AATCGTCCATTCGATCTGGATGAAGCTGTCATACGGAGATTTCCGCGAAG                         GTTGATGATTGATGTTCCTGATGCCGAGAACCGTGCGAAAATTCTCAAAGT
genomic: AATCGTCCATTCGATCTGGATGAAGCTGTCATACGGAGATTTCCGCGAAGgtaaatctaa ... tttttttcagGTTGATGATTGATGTTCCTGATGCCGAGAACCGTGCGAAAATTCTCAAAGT
EST: gi|169115759|gb|FE517345.1|FE517345
EST:     AATCGTCCATTCGATCTGGATGAAGCTGTCATACGGAGATTTCCGCGAAG                         GTTGATGATTGATGTTCCTGATGCCGAGAACCGTGCGAAAATTCTCAAAGT
genomic: AATCGTCCATTCGATCTGGATGAAGCTGTCATACGGAGATTTCCGCGAAGgtaaatctaa ... tttttttcagGTTGATGATTGATGTTCCTGATGCCGAGAACCGTGCGAAAATTCTCAAAGT
EST: gi|169107241|gb|FE504119.1|FE504119
EST:     AATCGTCCATTCGATCTGGATGAAGCTGTCATACGGAGATTTCCGCGAAG                         GTTGATGATTGATGTTCCTGA
genomic: AATCGTCCATTCGATCTGGATGAAGCTGTCATACGGAGATTTCCGCGAAGgtaaatctaa ... tttttttcagGTTGATGATTGATGTTCCTGA
EST: gi|169107240|gb|FE504118.1|FE504118
EST:     AATCGTCCATTCGATCTGGATGAAGCTGTCATACGGAGATTTCCGCGAAG                         GTTGATGATTGATGTTCCTGATGCCGAGAACCGTGCGAAAATTCTCAAAGT
genomic: AATCGTCCATTCGATCTGGATGAAGCTGTCATACGGAGATTTCCGCGAAGgtaaatctaa ... tttttttcagGTTGATGATTGATGTTCCTGATGCCGAGAACCGTGCGAAAATTCTCAAAGT
EST: gi|169070626|gb|FE480085.1|FE480085
EST:     AATCGTCCATTCGATCTGGATGAAGCTGTCATACGGAGATTTCCGCGAAG                         GTTGATGATTGATGTTCCTGATGCCGAGAACCGTGCGAAAATTCTCAAAGT
genomic: AATCGTCCATTCGATCTGGATGAAGCTGTCATACGGAGATTTCCGCGAAGgtaaatctaa ... tttttttcagGTTGATGATTGATGTTCCTGATGCCGAGAACCGTGCGAAAATTCTCAAAGT
EST: gi|169082584|gb|FE489068.1|FE489068
EST:     AATCGTCCATTCGATCTGGATGAAGCTGTCATACGGAGATTTCCGCGAAG                         GTTGATGATTGATGTTCCTGATGCCGAGAACCGTGCGAAAATTCTCAAAGT
genomic: AATCGTCCATTCGATCTGGATGAAGCTGTCATACGGAGATTTCCGCGAAGgtaaatctaa ... tttttttcagGTTGATGATTGATGTTCCTGATGCCGAGAACCGTGCGAAAATTCTCAAAGT
EST: gi|169081354|gb|FE489292.1|FE489292
EST:     AATCGTCCATTCGATCTGGATGAAGCTGTCATACGGAGATTTCCGCGAAG                         GTTGATGATTGATGTTCCTGATGCCGAGAACCGTGCGAAAATTCTCAAAGT
genomic: AATCGTCCATTCGATCTGGATGAAGCTGTCATACGGAGATTTCCGCGAAGgtaaatctaa ... tttttttcagGTTGATGATTGATGTTCCTGATGCCGAGAACCGTGCGAAAATTCTCAAAGT
EST: gi|169076790|gb|FE485833.1|FE485833
EST:     AATCGTCCATTCGATCTGGATGAAGCTGTCATACGGAGATTTCCGCGAAG                         GTTGATGATTGATGTTCCTGATGCCGAGAACCGTGCGAAAATTCTCAAAGT
genomic: AATCGTCCATTCGATCTGGATGAAGCTGTCATACGGAGATTTCCGCGAAGgtaaatctaa ... tttttttcagGTTGATGATTGATGTTCCTGATGCCGAGAACCGTGCGAAAATTCTCAAAGT
EST: gi|169063160|gb|FE471682.1|FE471682
EST:     AATCGTCCATTCGATTTGGATGAAGCTGTCATACGGAGATTTCCGCGAAG                         GTTGATGATTGATGTTCCTGATGCCGAGAACCGTGCGAAAATTCTCAAAGT
genomic: AATCGTCCATTCGATCTGGATGAAGCTGTCATACGGAGATTTCCGCGAAGgtaaatctaa ... tttttttcagGTTGATGATTGATGTTCCTGATGCCGAGAACCGTGCGAAAATTCTCAAAGT
EST: gi|169081355|gb|FE489293.1|FE489293
EST:     AATCGTCCATTCGATCTGGATGAAGCTGTCATACGGAGATTTCCGCGAAG                         GTTGATGATTGATGTTCCTGATGCCGAGAACCGTGCGAAAATTCTCAAAGT
genomic: AATCGTCCATTCGATCTGGATGAAGCTGTCATACGGAGATTTCCGCGAAGgtaaatctaa ... tttttttcagGTTGATGATTGATGTTCCTGATGCCGAGAACCGTGCGAAAATTCTCAAAGT
EST: gi|169092697|gb|FE494926.1|FE494926
EST:     AATCGTCCATTCGATCTGGATGAAGCTGTCATACGGAGATTTCCGCGAAG                         GTTGATGATTGATGTTCCTGATGCCGAGAACCGTGCGAAAATTCTCAAAGT
genomic: AATCGTCCATTCGATCTGGATGAAGCTGTCATACGGAGATTTCCGCGAAGgtaaatctaa ... tttttttcagGTTGATGATTGATGTTCCTGATGCCGAGAACCGTGCGAAAATTCTCAAAGT
EST: gi|169064335|gb|FE471898.1|FE471898
EST:     AATCGTCCATTCGATCTGGATGAAGCTGTCATACGGAGATTTCCGCGAAG                         GTTGATGATTGATGTTCCTGATGCCGAGAACCGTGCGAAAATTCTCAAAGT
genomic: AATCGTCCATTCGATCTGGATGAAGCTGTCATACGGAGATTTCCGCGAAGgtaaatctaa ... tttttttcagGTTGATGATTGATGTTCCTGATGCCGAGAACCGTGCGAAAATTCTCAAAGT
EST: gi|169044544|gb|FE450609.1|FE450609
EST:     AATCGTCCATTCGATCTGGATGAAGCTGTCATACGGAGATTTCCGCGAAG                         GTTGATGATTGATGTTCCTGATGCCGAGAACCGTGCGAAAATTCTCAAAGT
genomic: AATCGTCCATTCGATCTGGATGAAGCTGTCATACGGAGATTTCCGCGAAGgtaaatctaa ... tttttttcagGTTGATGATTGATGTTCCTGATGCCGAGAACCGTGCGAAAATTCTCAAAGT
EST: gi|169034852|gb|FE444041.1|FE444041
EST:     AATCGTCCATTCGATCTGGATGAAGCTGTCATACGGAGATTTCCGCGAAG                         GTTGATGATTGATGTTCCTGATGCCGAGAACCGTGCGAAAATTCTCAAAGT
genomic: AATCGTCCATTCGATCTGGATGAAGCTGTCATACGGAGATTTCCGCGAAGgtaaatctaa ... tttttttcagGTTGATGATTGATGTTCCTGATGCCGAGAACCGTGCGAAAATTCTCAAAGT
EST: gi|169095446|gb|FE497552.1|FE497552
EST:     AATCGTCCATTCGATCTGGATGAAGCTGTCATACGGAGATTTCCGCGAAG                         GTTGATGATTGATGTTCCTGATGCCGAGAACCGTGCGAAAATTCTCAAAGT
genomic: AATCGTCCATTCGATCTGGATGAAGCTGTCATACGGAGATTTCCGCGAAGgtaaatctaa ... tttttttcagGTTGATGATTGATGTTCCTGATGCCGAGAACCGTGCGAAAATTCTCAAAGT

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: 25 (upstream exon), 33 (downstream exon)
Score: 11

ACGGATTAAGAACGCGTGAGAAGGAAAGGGTCATTGTACTGGCAGCAACAAATCGTCCATTCGATCTGGATGAAGCTGTCATACGGAGATTTCCGCGAAGgtaaatctaa ... tttttttcagGTTGATGATTGATGTTCCTGATGCCGAGAACCGTGCGAAAATTCTCAAAGTTATACTTAGTGACGAGGATCTTTCCCCCGATTTTAACATGGAGGAAGTG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtaaatctaatacaattgtaaacatcggcttgacgatttttttcagGTTGATGATTGATGTTCCTGATGCCGAGAACCGTGCGAAAATTCTCAAAGTTATACTTAGTGACGAGGATCTTTCCCCCGATTTTAACATGGAGGAAGTG
                                                     tttttttc  CT-rich tract
          taaatctaatacaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaatctaatacaattgtaaacatcggcttgacgatttttttcagGTTGATGATTGATGTTCCTGATGCCGAGAACCGTGCGAAAATTCTCAAAGTTATACTTAGTGACGAGGATCTTTCCCCCGATTTTAACATGGAGGAAGTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA