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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCCAAAAACCTCAAGCTAGCACTCACTGCAGGGATTGGCTCTGACCACATTGACTTGACGGCTGCCTCCAAGGCTGGCATCACAGTCGCAGAAGTCACAGgtagctgactgggcttttcgactctgacccgaccatcaaacacggtctttgcattgacgatctcccag

Basic information

species Selaginella moellendorffii
transcript EFJ13636
intron # 3
splice site 5'
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|169029785|gb|FE441018.1|FE441018
EST:     TGACTTGACGGCTGCCTCCAAGGCTGGCATCACAGTCGCAGAAGTCACAG                         GGTCAAATGTGGTCTCGGTTGCGGAGGACCAGCTCATGCGTGTCTTGATCC
genomic: TGACTTGACGGCTGCCTCCAAGGCTGGCATCACAGTCGCAGAAGTCACAGgtagctgact ... gatctcccagGGTCAAATGTGGTCTCGGTTGCGGAGGACCAGCTCATGCGTGTCTTGATCC
EST: gi|169029784|gb|FE441017.1|FE441017
EST:     TGACTTGACGGCTGCCTNCAAGGCTGGCATCACAGTCGCAGAAGTCACAG                         GGTCAAATGTGGTCTCGGTTGCGGAGGACCAGCTCATGCGTGTCTTGATCC
genomic: TGACTTGACGGCTGCCTCCAAGGCTGGCATCACAGTCGCAGAAGTCACAGgtagctgact ... gatctcccagGGTCAAATGTGGTCTCGGTTGCGGAGGACCAGCTCATGCGTGTCTTGATCC
EST: gi|169106400|gb|FE507425.1|FE507425
EST:     TGACTTGACGGCTGCCTCCAAGGCTGGCATCACAGTCGCAGAAGTCACAG                         GGTCAAATGTGGTCTCGGTTGCGGAGGACCAGCTCATGCGTGTCTTGATCC
genomic: TGACTTGACGGCTGCCTCCAAGGCTGGCATCACAGTCGCAGAAGTCACAGgtagctgact ... gatctcccagGGTCAAATGTGGTCTCGGTTGCGGAGGACCAGCTCATGCGTGTCTTGATCC
EST: gi|169067793|gb|FE473377.1|FE473377
EST:     TGACTTGACGGCTGCCTCCAAGGCTGGCATCACAGTCGCAGAAGTCACAG                         GGTCAAATGTGGTCTCGGTTGCGGAGGACCAGCTCATGCGTGTCTTGATCC
genomic: TGACTTGACGGCTGCCTCCAAGGCTGGCATCACAGTCGCAGAAGTCACAGgtagctgact ... gatctcccagGGTCAAATGTGGTCTCGGTTGCGGAGGACCAGCTCATGCGTGTCTTGATCC
EST: gi|169048962|gb|FE454948.1|FE454948
EST:     TGACTTGACGGCTGCCTCCAAGGCTGGCATCACAGTCGCAGAAGTCACAG                         GGTCAAATGTGGTCTCGGTTGCGGAGGACCAGCTCATGCGTGTCTTGATCC
genomic: TGACTTGACGGCTGCCTCCAAGGCTGGCATCACAGTCGCAGAAGTCACAGgtagctgact ... gatctcccagGGTCAAATGTGGTCTCGGTTGCGGAGGACCAGCTCATGCGTGTCTTGATCC
EST: gi|70670001|gb|DN838578.1|DN838578
EST:     TGACTTGACGGCTGCCTCCAAGGCTGGCATCACAGTCGCAGAAGTCACAG                         GGTCAAATGTGGTCTCGGTTGCGGAGGACCAGCTCATGCGTGTCTTGATCC
genomic: TGACTTGACGGCTGCCTCCAAGGCTGGCATCACAGTCGCAGAAGTCACAGgtagctgact ... gatctcccagGGTCAAATGTGGTCTCGGTTGCGGAGGACCAGCTCATGCGTGTCTTGATCC
EST: gi|169062830|gb|FE472866.1|FE472866
EST:     TGACTTGACGGCTGCCTCCAAGGCTGGCATCACAGTCGCAGAAGTCACAG                         GGTCAAATGTGGTCTCGGTTGCGGAGGACCAGCTCATGCGTGTCTTGATCC
genomic: TGACTTGACGGCTGCCTCCAAGGCTGGCATCACAGTCGCAGAAGTCACAGgtagctgact ... gatctcccagGGTCAAATGTGGTCTCGGTTGCGGAGGACCAGCTCATGCGTGTCTTGATCC
EST: gi|169087508|gb|FE494625.1|FE494625
EST:     TGGCATCACAGTCGCAGAAGTCACAG                         GGTCAAATGTGGTCTCGGTTGCGGAGGACCAGCTCATGCGTGTCTTGATCC
genomic: TGGCATCACAGTCGCAGAAGTCACAGgtagctgact ... gatctcccagGGTCAAATGTGGTCTCGGTTGCGGAGGACCAGCTCATGCGTGTCTTGATCC
EST: gi|169079758|gb|FE491167.1|FE491167
EST:     TGACTTGACGGCTGCCTCCAAGGCTGGCATCACAGTCGCAGAAGTCACAG                         GGTCAAATGTGGTCTCGGTTGCGGAGGACCAGCTCATGCGTGTCTTGATCC
genomic: TGACTTGACGGCTGCCTCCAAGGCTGGCATCACAGTCGCAGAAGTCACAGgtagctgact ... gatctcccagGGTCAAATGTGGTCTCGGTTGCGGAGGACCAGCTCATGCGTGTCTTGATCC
EST: gi|169088324|gb|FE492042.1|FE492042
EST:     TGACTTGACGGCTGCCTCCAAGGCTGGCATCACAGTCGCAGAAGTCACAG                         GGTCAAATGTGGTCTCGGTTGCGGAGGACCAGCTCATGCGTGTCTTGATCC
genomic: TGACTTGACGGCTGCCTCCAAGGCTGGCATCACAGTCGCAGAAGTCACAGgtagctgact ... gatctcccagGGTCAAATGTGGTCTCGGTTGCGGAGGACCAGCTCATGCGTGTCTTGATCC
EST: gi|169101313|gb|FE502508.1|FE502508
EST:     TGACTTGACGGCTGCCTCCAAGGCTGGCATCACAGTCGCAGAAGTCACAG                         GGTCAAATGTGGTCTCGGTTGCGGAGGACCAGCTCATGCGTGTCTTGATCC
genomic: TGACTTGACGGCTGCCTCCAAGGCTGGCATCACAGTCGCAGAAGTCACAGgtagctgact ... gatctcccagGGTCAAATGTGGTCTCGGTTGCGGAGGACCAGCTCATGCGTGTCTTGATCC
EST: gi|169104372|gb|FE503734.1|FE503734
EST:     TGACTTGACGGCTGCCTCCAAGGCTGGCATCACAGTCGCAGAAGTCACAG                         GGTCAAATGTGGTCTCGGTTGCGGAGGACCAGCTCATGCGTGTCTTGATCC
genomic: TGACTTGACGGCTGCCTCCAAGGCTGGCATCACAGTCGCAGAAGTCACAGgtagctgact ... gatctcccagGGTCAAATGTGGTCTCGGTTGCGGAGGACCAGCTCATGCGTGTCTTGATCC
EST: gi|169060085|gb|FE468695.1|FE468695
EST:     TGACTTGACGGCTGCCTCCAAGGCTGGCATCACAGTCGCAGAAGTCACAG                         GGTCAAATGTGGTCTCGGTTGCGGAGGACCAGCTCATGCGTGTCTTGATCC
genomic: TGACTTGACGGCTGCCTCCAAGGCTGGCATCACAGTCGCAGAAGTCACAGgtagctgact ... gatctcccagGGTCAAATGTGGTCTCGGTTGCGGAGGACCAGCTCATGCGTGTCTTGATCC
EST: gi|169078349|gb|FE490382.1|FE490382
EST:     TGACTTGACGGCTGCCTCCAAGGCTGGCATCACAGTCGCAGAAGTCACAG                         GGTCAAATGTGGTCTCGGTTGCGGAGGACCAGCTCATGCGTGTCTTGATCC
genomic: TGACTTGACGGCTGCCTCCAAGGCTGGCATCACAGTCGCAGAAGTCACAGgtagctgact ... gatctcccagGGTCAAATGTGGTCTCGGTTGCGGAGGACCAGCTCATGCGTGTCTTGATCC
EST: gi|169088325|gb|FE492043.1|FE492043
EST:     TGACTTGACGGCTGCCTCCAAGGCTGGCATCACAGTCGCAGAAGTCACAG                         GGTCAAATGTGGTCTCGGTTGCGGAGGACCAGCTCATGCGTGTCTTGATCC
genomic: TGACTTGACGGCTGCCTCCAAGGCTGGCATCACAGTCGCAGAAGTCACAGgtagctgact ... gatctcccagGGTCAAATGTGGTCTCGGTTGCGGAGGACCAGCTCATGCGTGTCTTGATCC

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), 35 (downstream exon)
Score: 56

GCCAAAAACCTCAAGCTAGCACTCACTGCAGGGATTGGCTCTGACCACATTGACTTGACGGCTGCCTCCAAGGCTGGCATCACAGTCGCAGAAGTCACAGgtagctgact ... gatctcccagGGTCAAATGTGGTCTCGGTTGCGGAGGACCAGCTCATGCGTGTCTTGATCCTTCTGCGCAACTATCAGAATGGGTGGACCCAAGTCAACGCTGGCGGCTG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCCAAAAACCTCAAGCTAGCACTCACTGCAGGGATTGGCTCTGACCACATTGACTTGACGGCTGCCTCCAAGGCTGGCATCACAGTCGCAGAAGTCACAGgtagctgactgggcttttcgactctgacccgaccatcaaacacggtctttgcattgacgatctcccag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGT