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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GACTGATAAACCCATGCCTAGAGGAGAAATTGTCATTGGCGGCCCCAGTGTTACATTGGGATACTTCAAGAACCAGGGGAAGACGGATGAAGATTACAAGgtacaacttttcagtttccttgaagcgttcatgtttaattcgtttttttgtgaag

Basic information

species Selaginella moellendorffii
transcript EFJ26722
intron # 8
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|169062087|gb|FE469679.1|FE469679
EST:     TTACATTGGGATACTTCAAGAACCAGGGGAAGACGGATGAAGATTACAAG                         GTTGACGAGAGGGGCATGAGATGGTTCTACACTGGTGACATTGGACAGTTC
genomic: TTACATTGGGATACTTCAAGAACCAGGGGAAGACGGATGAAGATTACAAGgtacaacttt ... ttttgtgaagGTTGACGAGAGGGGCATGAGATGGTTCTACACTGGTGACATTGGACAATTC
EST: gi|169098530|gb|FE498534.1|FE498534
EST:     TTACATTGGGATACTTCAAGAACCAGGGGAAGACGGATGAAGATTACAAG                         GTTGACGAGAGGGGCATGAGATGGTTCTACACTGGTGACATTGGACAGTTC
genomic: TTACATTGGGATACTTCAAGAACCAGGGGAAGACGGATGAAGATTACAAGgtacaacttt ... ttttgtgaagGTTGACGAGAGGGGCATGAGATGGTTCTACACTGGTGACATTGGACAATTC
EST: gi|169102589|gb|FE508568.1|FE508568
EST:     TTACATTGGGATACTTCAAGAACCAGGGGAAGACGGATGAAGATTACAAG                         GTTGACGAGAGGGGCATGAGATGGTTCTACACTGGTGACATTGGACAGTTC
genomic: TTACATTGGGATACTTCAAGAACCAGGGGAAGACGGATGAAGATTACAAGgtacaacttt ... ttttgtgaagGTTGACGAGAGGGGCATGAGATGGTTCTACACTGGTGACATTGGACAATTC
EST: gi|169020953|gb|FE429340.1|FE429340
EST:     TTACATTGGGATACTTCAAGAACCAGGGGAAGACGGATGAAGATTACAAG                         GTTGACGAGAGGGGCATGAGATGGTTCTACACTGGTGACATTGGACAATTC
genomic: TTACATTGGGATACTTCAAGAACCAGGGGAAGACGGATGAAGATTACAAGgtacaacttt ... ttttgtgaagGTTGACGAGAGGGGCATGAGATGGTTCTACACTGGTGACATTGGACAATTC
EST: gi|169062086|gb|FE469678.1|FE469678
EST:     TTACATTGGGATACTTCAAGAACCAGGGGAAGACGGATGAAGATTACAAG                         GTTGACGAGAGGGGCATGAGATGGTTCTACACTGGTGACATTGGACAGTTC
genomic: TTACATTGGGATACTTCAAGAACCAGGGGAAGACGGATGAAGATTACAAGgtacaacttt ... ttttgtgaagGTTGACGAGAGGGGCATGAGATGGTTCTACACTGGTGACATTGGACAATTC
EST: gi|169081832|gb|FE487445.1|FE487445
EST:     TTACATTGGGATACTTCAAGAACCAGGGGAAGACGGATGAAGATTACAAG                         GTTGACGAGAGGGGCATGAGATGGTTCTACACTGGTGACATTGGACAGTTC
genomic: TTACATTGGGATACTTCAAGAACCAGGGGAAGACGGATGAAGATTACAAGgtacaacttt ... ttttgtgaagGTTGACGAGAGGGGCATGAGATGGTTCTACACTGGTGACATTGGACAATTC
EST: gi|169088887|gb|FE492865.1|FE492865
EST:     TTACATTGGGATACTTCAAGAACCAGGGGAAGACGGATGAAGATTACAAG                         GTTGACGAGAGGGGCATGAGATGGTTCTACACTGGTGACATTGGACAGTTC
genomic: TTACATTGGGATACTTCAAGAACCAGGGGAAGACGGATGAAGATTACAAGgtacaacttt ... ttttgtgaagGTTGACGAGAGGGGCATGAGATGGTTCTACACTGGTGACATTGGACAATTC
EST: gi|169098740|gb|FE500252.1|FE500252
EST:     TTACATTGGGATACTTCAAGAACCAGGGGAAGACGGATGAAGATTACAAG                         GTTGACGAGAGGGGCATGAGATGGTTCTACACTGGTGACATTGGACAGTTC
genomic: TTACATTGGGATACTTCAAGAACCAGGGGAAGACGGATGAAGATTACAAGgtacaacttt ... ttttgtgaagGTTGACGAGAGGGGCATGAGATGGTTCTACACTGGTGACATTGGACAATTC
EST: gi|169113590|gb|FE514501.1|FE514501
EST:     TTACATTGGGATTCTTCAAGATCCAGGGGAAGACGGATGATGATTACAAG                         GTTGACGAGAGGGGCATGAGATGGTTCTACACTGGTGACATTGGACAATTC
genomic: TTACATTGGGATACTTCAAGAACCAGGGGAAGACGGATGAAGATTACAAGgtacaacttt ... ttttgtgaagGTTGACGAGAGGGGCATGAGATGGTTCTACACTGGTGACATTGGACAATTC
EST: gi|169054875|gb|FE463479.1|FE463479
EST:     TTACATTGGGATACTTCAAGAACCAGGGGAAGACGGATGAAGATTACAAG                         GTTGACGAGAGGGGCATGAGATGGTTCTACACTGGTGACATTGGACAGTTC
genomic: TTACATTGGGATACTTCAAGAACCAGGGGAAGACGGATGAAGATTACAAGgtacaacttt ... ttttgtgaagGTTGACGAGAGGGGCATGAGATGGTTCTACACTGGTGACATTGGACAATTC
EST: gi|169113591|gb|FE514502.1|FE514502
EST:     TTACATTGGGATACTTCAAGAACCAGGGGAAGACGGATGAAGATTACCAG                         GTTGACGAGAGGGGCATGAGATGGTTCTACACTGGTGACATTGGACAATTC
genomic: TTACATTGGGATACTTCAAGAACCAGGGGAAGACGGATGAAGATTACAAGgtacaacttt ... ttttgtgaagGTTGACGAGAGGGGCATGAGATGGTTCTACACTGGTGACATTGGACAATTC

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: 18

GACTGATAAACCCATGCCTAGAGGAGAAATTGTCATTGGCGGCCCCAGTGTTACATTGGGATACTTCAAGAACCAGGGGAAGACGGATGAAGATTACAAGgtacaacttt ... ttttgtgaagGTTGACGAGAGGGGCATGAGATGGTTCTACACTGGTGACATTGGACAATTCCATCCCGATGGTTGCTTAGAAATTGTAGACCGGAAGAAGGACATTGTTA




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GACTGATAAACCCATGCCTAGAGGAGAAATTGTCATTGGCGGCCCCAGTGTTACATTGGGATACTTCAAGAACCAGGGGAAGACGGATGAAGATTACAAGgtacaacttttcagtttccttgaagcgttcatgtttaattcgtttttttgtgaag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA