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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacaaacgtatgacaaatggtaatccatcgtttgacatgatgggctttccagGTGGAGCGCAATGGCGGCAGCAGCTTTGCACCCGTTTTGGTTGCAGACAATGCAATTTGTGACGAAGTGCGAAGCTTGGAAGAGGATATAGAGATTGCTT

Basic information

species Selaginella moellendorffii
transcript EFJ15634
intron # 8
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|169030089|gb|FE440529.1|FE440529
EST:     ATCGGCCGGTGCTTCATTGAG                         GTGGAGCGCAATGGCGGCAGCAGCTTTGCACCCGTTTTGGTTGCAGACAAT
genomic: ATCGGCCGGTGCTTCATTGAGgtacaaacgt ... ggctttccagGTGGAGCGCAATGGCGGCAGCAGCTTTGCACCCGTTTTGGTTGCAGACAAT
EST: gi|169035624|gb|FE445394.1|FE445394
EST:     TGTGTTTCACACACACTCCGTGCGAGTCTATCGGCCGGTGCTTCATTGAG                         GTGGAGCGCAATGGCGGCAGCAGCTTTGCACCCGTTTTGGTTGCAGACAAT
genomic: TGTGTTTCACACACACTCCGTGCGAGTCTATCGGCCGGTGCTTCATTGAGgtacaaacgt ... ggctttccagGTGGAGCGCAATGGCGGCAGCAGCTTTGCACCCGTTTTGGTTGCAGACAAT
EST: gi|169032876|gb|FE438332.1|FE438332
EST:     TGTGTTTCACACACACTCCGTGCGAGTCTATCGGCCGGTGCTTCATTGAG                         GTGGAGCGCAATGGCGGCAGCAGCTTTGCACCCGTTTTGGTTGCAGACAAT
genomic: TGTGTTTCACACACACTCCGTGCGAGTCTATCGGCCGGTGCTTCATTGAGgtacaaacgt ... ggctttccagGTGGAGCGCAATGGCGGCAGCAGCTTTGCACCCGTTTTGGTTGCAGACAAT
EST: gi|169095903|gb|FE497281.1|FE497281
EST:     TGTGTTTCACACACACTCCGTGCGAGTCTATCGGCCGGTGCTTCATTGAG                         GTGGAGCGCAATGGCGGCAGCAGCTTTG
genomic: TGTGTTTCACACACACTCCGTGCGAGTCTATCGGCCGGTGCTTCATTGAGgtacaaacgt ... ggctttccagGTGGAGCGCAATGGCGGCAGCAGCTTTG
EST: gi|169032875|gb|FE438331.1|FE438331
EST:     TGTGTTTCACACACACTCCGTGCGAGTCTATCGGCCGGTGCTTCATTGAG                         GTGGAGCGCAATGGCGGCAGCAGCTTTGCACCCGTTTTGGTTGCAGACAAT
genomic: TGTGTTTCACACACACTCCGTGCGAGTCTATCGGCCGGTGCTTCATTGAGgtacaaacgt ... ggctttccagGTGGAGCGCAATGGCGGCAGCAGCTTTGCACCCGTTTTGGTTGCAGACAAT
EST: gi|169099314|gb|FE501593.1|FE501593
EST:     TGTGTTTCACACACACTCCGTGCGAGTCTATCGGCCGGTGCTTCATTGAG                         GTGGAGCGCAATGGCGGCAGCAGCTTTGCACCCGTTTTGGTTGCAGACAAT
genomic: TGTGTTTCACACACACTCCGTGCGAGTCTATCGGCCGGTGCTTCATTGAGgtacaaacgt ... ggctttccagGTGGAGCGCAATGGCGGCAGCAGCTTTGCACCCGTTTTGGTTGCAGACAAT
EST: gi|169058648|gb|FE466857.1|FE466857
EST:     TGTGTTTCACACACACTCCGTGCGAGTCTATCGGCCGGTGCTTCATTGAG                         GTGGAGCGCAATGGCGGCAGCAGCTTTGCACCCGTTTTGGTTGCAGACAAT
genomic: TGTGTTTCACACACACTCCGTGCGAGTCTATCGGCCGGTGCTTCATTGAGgtacaaacgt ... ggctttccagGTGGAGCGCAATGGCGGCAGCAGCTTTGCACCCGTTTTGGTTGCAGACAAT
EST: gi|169030797|gb|FE438143.1|FE438143
EST:     TGTGTTTCACACACACTCCGTGCGAGTCTATCGGCCGGTGCTTCATTGAG                         GTGGAGCGCAATGGCGGCAGCAGCTTTGCACCCGTTTTGGTTGCAGACAAT
genomic: TGTGTTTCACACACACTCCGTGCGAGTCTATCGGCCGGTGCTTCATTGAGgtacaaacgt ... ggctttccagGTGGAGCGCAATGGCGGCAGCAGCTTTGCACCCGTTTTGGTTGCAGACAAT
EST: gi|169043052|gb|FE452406.1|FE452406
EST:     TGTGTTTCACACACACTCCGTGCGAGTCTATCGGCCGGTGCTTCATTGAG                         GTGGAGCGCAATGGCGGCAGCAGCTTTGCACCCGTTTTGGTTGCAGACAAT
genomic: TGTGTTTCACACACACTCCGTGCGAGTCTATCGGCCGGTGCTTCATTGAGgtacaaacgt ... ggctttccagGTGGAGCGCAATGGCGGCAGCAGCTTTGCACCCGTTTTGGTTGCAGACAAT
EST: gi|169110840|gb|FE509323.1|FE509323
EST:     TGTGTTTCACACACACTCCGTGCGAGTCTATCGGCCGGTGCTTCATTGAG                         GTGGAGCGCAATGGCGGCAGCAGCTTTGCACCCGTTTTGGTTGCAGACAAT
genomic: TGTGTTTCACACACACTCCGTGCGAGTCTATCGGCCGGTGCTTCATTGAGgtacaaacgt ... ggctttccagGTGGAGCGCAATGGCGGCAGCAGCTTTGCACCCGTTTTGGTTGCAGACAAT
EST: gi|169103571|gb|FE507613.1|FE507613
EST:     TGTGTTTCACACACACTCCGTGCGAGTCTATCGGCCGGTGCTTCATTGAG                         GTGGAGCGCAATGGCGGCAGCAGCTTTGCACCCGTTTTGGTTGCAGACAAT
genomic: TGTGTTTCACACACACTCCGTGCGAGTCTATCGGCCGGTGCTTCATTGAGgtacaaacgt ... ggctttccagGTGGAGCGCAATGGCGGCAGCAGCTTTGCACCCGTTTTGGTTGCAGACAAT
EST: gi|169113874|gb|FE515929.1|FE515929
EST:     TGTGTTTCACACACACTCCGTGCGAGTCTATCGGCCGGTGCTTCATTGAG                         GTGGAGCGCAATGGCGGCAGCAGCTTTGCACCCGTTTTGGTTGCAGACAAT
genomic: TGTGTTTCACACACACTCCGTGCGAGTCTATCGGCCGGTGCTTCATTGAGgtacaaacgt ... ggctttccagGTGGAGCGCAATGGCGGCAGCAGCTTTGCACCCGTTTTGGTTGCAGACAAT
EST: gi|169052045|gb|FE460384.1|FE460384
EST:     TGTGTTTCACACACACTCCGTGCGAGTCTATCGGCCGGTGCTTCATTGAG                         GTGGAGCGCAATGGCGGCAGCAGCTTTGCACCCGTTTTGGTTGCAGACAAT
genomic: TGTGTTTCACACACACTCCGTGCGAGTCTATCGGCCGGTGCTTCATTGAGgtacaaacgt ... ggctttccagGTGGAGCGCAATGGCGGCAGCAGCTTTGCACCCGTTTTGGTTGCAGACAAT
EST: gi|169057609|gb|FE463660.1|FE463660
EST:     TGTGTTTCACACACACTCCGTGCGAGTCTATCGGCCGGTGCTTCATTGAG                         GTGGAGCGCAATGGCGGCAGCAGCTTTGCACCCGTTTTGGTTGCAGACAAT
genomic: TGTGTTTCACACACACTCCGTGCGAGTCTATCGGCCGGTGCTTCATTGAGgtacaaacgt ... ggctttccagGTGGAGCGCAATGGCGGCAGCAGCTTTGCACCCGTTTTGGTTGCAGACAAT
EST: gi|169024640|gb|FE432823.1|FE432823
EST:     TGTGTTTCACACACACTCCGTGCGAGTCTATCGGCCGGTGCTTCATTGAG                         GTGGAGCGCAATGGCGGCAGCAGCTTTGCACCCGTTTTGGTTGCAGACAAT
genomic: TGTGTTTCACACACACTCCGTGCGAGTCTATCGGCCGGTGCTTCATTGAGgtacaaacgt ... ggctttccagGTGGAGCGCAATGGCGGCAGCAGCTTTGCACCCGTTTTGGTTGCAGACAAT
EST: gi|169096098|gb|FE500050.1|FE500050
EST:     TGTGTTTCACACACACTCCGTGCGAGTCTATCGGCCGGTGCTTCATTGAG                         GTGGAGCGCAATGGCGGCAGCAGCTTTGCACCCGTTTTGGTTGCAGACAAT
genomic: TGTGTTTCACACACACTCCGTGCGAGTCTATCGGCCGGTGCTTCATTGAGgtacaaacgt ... ggctttccagGTGGAGCGCAATGGCGGCAGCAGCTTTGCACCCGTTTTGGTTGCAGACAAT
EST: gi|169045539|gb|FE450732.1|FE450732
EST:     TGTGTTTCACACACACTCCGTGCGAGTCTATCGGCCGGTGCTTCATTGAG                         GTGGAGCGCAATGGCGGCAGCAGCTTTGCACCCGTTTTGGTTGCAGACAAT
genomic: TGTGTTTCACACACACTCCGTGCGAGTCTATCGGCCGGTGCTTCATTGAGgtacaaacgt ... ggctttccagGTGGAGCGCAATGGCGGCAGCAGCTTTGCACCCGTTTTGGTTGCAGACAAT
EST: gi|169037499|gb|FE445538.1|FE445538
EST:     TGTGTTTCACACACACTCCGTGCGAGTCTATCGGCCGGTGCTTCATTGAG                         GTGGAGCGCAATGGCGGCAGCAGCTTTGCACCCGTTTTGGTTGCAGACAAT
genomic: TGTGTTTCACACACACTCCGTGCGAGTCTATCGGCCGGTGCTTCATTGAGgtacaaacgt ... ggctttccagGTGGAGCGCAATGGCGGCAGCAGCTTTGCACCCGTTTTGGTTGCAGACAAT

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), 35 (downstream exon)
Score: 44

TCAATCATGGAGCGAAATTGACGCAAACGAAGAGGATGCTGAAGGCAGTTTGTGTTTCACACACACTCCGTGCGAGTCTATCGGCCGGTGCTTCATTGAGgtacaaacgt ... ggctttccagGTGGAGCGCAATGGCGGCAGCAGCTTTGCACCCGTTTTGGTTGCAGACAATGCAATTTGTGACGAAGTGCGAAGCTTGGAAGAGGATATAGAGATTGCTT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtacaaacgtatgacaaatggtaatccatcgtttgacatgatgggctttccagGTGGAGCGCAATGGCGGCAGCAGCTTTGCACCCGTTTTGGTTGCAGACAATGCAATTTGTGACGAAGTGCGAAGCTTGGAAGAGGATATAGAGATTGCTT
                                gtttgac  putative branch site (score: 44)
                                               ctttcc  putative PPT
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacaaacgtatgacaaatggtaatccatcgtttgacatgatgggctttccagGTGGAGCGCAATGGCGGCAGCAGCTTTGCACCCGTTTTGGTTGCAGACAATGCAATTTGTGACGAAGTGCGAAGCTTGGAAGAGGATATAGAGATTGCTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT