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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaacgttcttcctgttttgcacttgtgtttatgatgaattcccagTTGATGAGCAACGGGAGGTACCGGAGTGTCATCCATCGCGTGCAAGTGAACGCGTCGCGTCCCAGGATGTCCATTGCTTGCAACTACAGCTGCTCGTTTG

Basic information

species Selaginella moellendorffii
transcript EFJ14904
intron # 2
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|169033664|gb|FE441904.1|FE441904
EST:     TCGAGCCCATCCCGGGAGCAATCACCATCAACATCAGTGATCTCCTTGAG                         TTGATGAGCAACGGGAGGTACCGGAGTGTCATCCATCGCGTGCAAGTGAAC
genomic: TCGAGCCCATCCCGGGAGCAATCACCATCAACATCAGTGATCTCCTTGAGgtaaacgttc ... gaattcccagTTGATGAGCAACGGGAGGTACCGGAGTGTCATCCATCGCGTGCAAGTGAAC
EST: gi|169057369|gb|FE464750.1|FE464750
EST:     TCGAGCCCATCCCGGGAGCAATCACCATCAACATCAGTGATCTCCTTGAG                         TTGATGAGCAACGGGAGGTACCGGAGTGTCATCCATCGCGTGCAAGTGAAC
genomic: TCGAGCCCATCCCGGGAGCAATCACCATCAACATCAGTGATCTCCTTGAGgtaaacgttc ... gaattcccagTTGATGAGCAACGGGAGGTACCGGAGTGTCATCCATCGCGTGCAAGTGAAC
EST: gi|169054488|gb|FE460297.1|FE460297
EST:     TCGAGCCCATCCCGGGAGCAATCACCATCAACATCAGTGATCTCCTTGAG                         TTGATGAGCAACGGGAGGTACCGGAGTGTCATCCATCGCGTGCAAGTGAAC
genomic: TCGAGCCCATCCCGGGAGCAATCACCATCAACATCAGTGATCTCCTTGAGgtaaacgttc ... gaattcccagTTGATGAGCAACGGGAGGTACCGGAGTGTCATCCATCGCGTGCAAGTGAAC
EST: gi|169109864|gb|FE513911.1|FE513911
EST:     TCGAGCCCATCCCGGGAGCAATCACCATCAACATCAGTGATCTCCTTGAG                         TTGATGAGCAACGGGAGGTACCGGAGTGTCATCCATCGCGTGCAAGTGAAC
genomic: TCGAGCCCATCCCGGGAGCAATCACCATCAACATCAGTGATCTCCTTGAGgtaaacgttc ... gaattcccagTTGATGAGCAACGGGAGGTACCGGAGTGTCATCCATCGCGTGCAAGTGAAC
EST: gi|169049328|gb|FE458239.1|FE458239
EST:     TCGAGCCCATCCCGGGAGCAATCACCATCAACATCAGTGATCTCCTTGAG                         TTGATGAGCAACGGGAGGTACCGGAGTGTCATCCATCGCGTGCAAGTGAAC
genomic: TCGAGCCCATCCCGGGAGCAATCACCATCAACATCAGTGATCTCCTTGAGgtaaacgttc ... gaattcccagTTGATGAGCAACGGGAGGTACCGGAGTGTCATCCATCGCGTGCAAGTGAAC
EST: gi|169071196|gb|FE477860.1|FE477860
EST:     TCGAGCCCATCCCGGGAGCAATCACCATCAACATCAGTGATCTCCTTGAG                         TTGATGAGCAACGGGAGGTACCGGAGTGTCATCCATCGCGTGCAAGTGAAC
genomic: TCGAGCCCATCCCGGGAGCAATCACCATCAACATCAGTGATCTCCTTGAGgtaaacgttc ... gaattcccagTTGATGAGCAACGGGAGGTACCGGAGTGTCATCCATCGCGTGCAAGTGAAC
EST: gi|169043485|gb|FE452618.1|FE452618
EST:     TCGAGCCCATCCCGGGAGCAATCACCATCAACATCAGTGATCTCCTTGAG                         TTGATGAGCAACGGGAGGTACCGGAGTGTCATCCATCGCGTGCAAGTGAAC
genomic: TCGAGCCCATCCCGGGAGCAATCACCATCAACATCAGTGATCTCCTTGAGgtaaacgttc ... gaattcccagTTGATGAGCAACGGGAGGTACCGGAGTGTCATCCATCGCGTGCAAGTGAAC
EST: gi|70669637|gb|DN838214.1|DN838214
EST:     TCGAGCCCATCCCGGGAGCAATCACCATCAACATCAGTGATCTCCTTGAG                         TTGATGAGCAACGGGAGGTACCGGAGTGTCATCCATCGCGTGCAAGTGAAC
genomic: TCGAGCCCATCCCGGGAGCAATCACCATCAACATCAGTGATCTCCTTGAGgtaaacgttc ... gaattcccagTTGATGAGCAACGGGAGGTACCGGAGTGTCATCCATCGCGTGCAAGTGAAC
EST: gi|169071210|gb|FE477861.1|FE477861
EST:     CGAGCCCATCCCGGGAGCAATCACCATCAACATCAGTGATCTCCCTTGAG                         T-GATGAGCAACGGGAGGTA
genomic: CGAGCCCATCCCGGGAGCAATCACCATCAACATCAGTGATCTCC-TTGAGgtaaacgttc ... gaattcccagTTGATGAGCAACGGGAGGTA
EST: gi|169051959|gb|FE460298.1|FE460298
EST:     TCGAGCCCATCCCGGGAGCAATCACCATCAACATCAGTGATCTCCTTGAG                         TTGATGAGCAAC
genomic: TCGAGCCCATCCCGGGAGCAATCACCATCAACATCAGTGATCTCCTTGAGgtaaacgttc ... gaattcccagTTGATGAGCAAC
EST: gi|169107035|gb|FE505980.1|FE505980
EST:     TCGAGCCCATCCCGGGAGCAATCACCATCAACATCAGTGATCTCCTTGAG                         TTGATGAGCAACGGGAGGTACCGGAGTGTCATCCATCGCGTGCAAGTGAAC
genomic: TCGAGCCCATCCCGGGAGCAATCACCATCAACATCAGTGATCTCCTTGAGgtaaacgttc ... gaattcccagTTGATGAGCAACGGGAGGTACCGGAGTGTCATCCATCGCGTGCAAGTGAAC
EST: gi|169107036|gb|FE505981.1|FE505981
EST:     TCGAGCCCATCCCGGGAGCAATCACCATCAACATCAGTGATCTCCTTGAG                         TTGATGAGCAACGGGAGGTACCGGAGTGTCATCCATCGCGTGCAAGTGAAC
genomic: TCGAGCCCATCCCGGGAGCAATCACCATCAACATCAGTGATCTCCTTGAGgtaaacgttc ... gaattcccagTTGATGAGCAACGGGAGGTACCGGAGTGTCATCCATCGCGTGCAAGTGAAC

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: 28 (upstream exon), 31 (downstream exon)
Score: 21

AGATGGTGTTCCCGGCCTCCAAGTTCTCAAGAACAACACCTGGGTGGTCGTCGAGCCCATCCCGGGAGCAATCACCATCAACATCAGTGATCTCCTTGAGgtaaacgttc ... gaattcccagTTGATGAGCAACGGGAGGTACCGGAGTGTCATCCATCGCGTGCAAGTGAACGCGTCGCGTCCCAGGATGTCCATTGCTTGCAACTACAGCTGCTCGTTTG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtaaacgttcttcctgttttgcacttgtgtttatgatgaattcccagTTGATGAGCAACGGGAGGTACCGGAGTGTCATCCATCGCGTGCAAGTGAACGCGTCGCGTCCCAGGATGTCCATTGCTTGCAACTACAGCTGCTCGTTTG
                                                       ttccc  CT-rich tract
                                     tttatgat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaacgttcttcctgttttgcacttgtgtttatgatgaattcccagTTGATGAGCAACGGGAGGTACCGGAGTGTCATCCATCGCGTGCAAGTGAACGCGTCGCGTCCCAGGATGTCCATTGCTTGCAACTACAGCTGCTCGTTTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGCT