Skip to another splice site:
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 5'  3'   		2  
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 5'  3'   		6  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TATAAGTTCGAGATGAGCGTCGAGGAAGCCGTGGAGCTGGGAAGACGAGCGATCTATCACGCGACGTTTAGAGATGGAGCCAGCGGAGGAGTTGCGAGCGgtaagctttttttctttcgcttttcatcgctctgagcctgctttgcttccag

Basic information

species Selaginella moellendorffii
transcript EFJ25863
intron # 6
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|70669750|gb|DN838327.1|DN838327
EST:     GATCTATCACGCGACGTTTAGAGATGGAGCCAGCGGAGGAGTTGCGAGCG                         TTTATCACATTGGTCCCCAAGGCTGGAAGAAGATCTCCGGTGACGATGTGA
genomic: GATCTATCACGCGACGTTTAGAGATGGAGCCAGCGGAGGAGTTGCGAGCGgtaagctttt ... ttgcttccagTTTATCACATTGGTCCCCAAGGCTGGAAGAAGATCTCCGGTGACGATGTGA
EST: gi|70670787|gb|DN839364.1|DN839364
EST:     GATCTATCACGCGACGTTTAGAGATGGAGCCAGCGGAGGAGTTGCGAGCG                         TTTATCACATTGGTCCCCAAGGCTGGAAGAAGATCTCCGGTGACGATGTGA
genomic: GATCTATCACGCGACGTTTAGAGATGGAGCCAGCGGAGGAGTTGCGAGCGgtaagctttt ... ttgcttccagTTTATCACATTGGTCCCCAAGGCTGGAAGAAGATCTCCGGTGACGATGTGA
EST: gi|169066324|gb|FE473000.1|FE473000
EST:     GATCTATCACGCGACGTTTAGAGATGGAGCCAGCGGAGGAGTTGCGAGCG                         TTTATCACATTGGT
genomic: GATCTATCACGCGACGTTTAGAGATGGAGCCAGCGGAGGAGTTGCGAGCGgtaagctttt ... ttgcttccagTTTATCACATTGGT
EST: gi|169047645|gb|FE454813.1|FE454813
EST:     GATCTATCACGCGACGTTTAGAGATGGAGCCAGCGGAGGAGTTGCGAGCG                         TTTATCACATTGGTCCCCAAGGCTGGAAGAAGATCTCCGGTGACGATGTGA
genomic: GATCTATCACGCGACGTTTAGAGATGGAGCCAGCGGAGGAGTTGCGAGCGgtaagctttt ... ttgcttccagTTTATCACATTGGTCCCCAAGGCTGGAAGAAGATCTCCGGTGACGATGTGA
EST: gi|169066323|gb|FE472999.1|FE472999
EST:     GATCTATCACGCGACGTTTAGAGATGGAGCCAGCGGAGGAGTTGCGAGCG                         TTTATCACATTGGTCCCCAAGGCTGGAAGAAGATCTCCGGTGACGATGTGA
genomic: GATCTATCACGCGACGTTTAGAGATGGAGCCAGCGGAGGAGTTGCGAGCGgtaagctttt ... ttgcttccagTTTATCACATTGGTCCCCAAGGCTGGAAGAAGATCTCCGGTGACGATGTGA
EST: gi|169062114|gb|FE469173.1|FE469173
EST:     GATCTATCACGCGACGTTTAGAGATGGAGCCAGCGGAGGAGTTGCGAGCG                         TTTATCACATTGGTCCCCAAGGCTGGAAGAAGATCTCCGGTGACGATGTGA
genomic: GATCTATCACGCGACGTTTAGAGATGGAGCCAGCGGAGGAGTTGCGAGCGgtaagctttt ... ttgcttccagTTTATCACATTGGTCCCCAAGGCTGGAAGAAGATCTCCGGTGACGATGTGA
EST: gi|169038991|gb|FE447732.1|FE447732
EST:     GATCTATCACGCGACGTTTAGAGATGGAGCCAGCGGAGGAGTTGCGAGCG                         TTTATCACATTGGTCCCCAAGGCTGGAAGAAGATCTCCGGTGACGATGTGA
genomic: GATCTATCACGCGACGTTTAGAGATGGAGCCAGCGGAGGAGTTGCGAGCGgtaagctttt ... ttgcttccagTTTATCACATTGGTCCCCAAGGCTGGAAGAAGATCTCCGGTGACGATGTGA
EST: gi|169053896|gb|FE460987.1|FE460987
EST:     GATCTATCACGCGACGTTTAGAGATGGAGCCAGCGGAGGAGTTGCGAGCG                         TTTATCACATTGGTCCCCAAGGCTGGAAGAAGATCTCCGGTGACGATGTGA
genomic: GATCTATCACGCGACGTTTAGAGATGGAGCCAGCGGAGGAGTTGCGAGCGgtaagctttt ... ttgcttccagTTTATCACATTGGTCCCCAAGGCTGGAAGAAGATCTCCGGTGACGATGTGA
EST: gi|70669328|gb|DN837905.1|DN837905
EST:     GATCTATCACGCGACGTTTAGAGATGGAGCCAGCGGAGGAGTTGCGAGCG                         TTTATCACATTGGTCCCCTAGGCTGGAAGAAGATCTCCGGTGACGATGTGA
genomic: GATCTATCACGCGACGTTTAGAGATGGAGCCAGCGGAGGAGTTGCGAGCGgtaagctttt ... ttgcttccagTTTATCACATTGGTCCCCAAGGCTGGAAGAAGATCTCCGGTGACGATGTGA
EST: gi|169062115|gb|FE469174.1|FE469174
EST:     GATCTATCACGCGACGTTTAGAGATGGAGCCAGCGGAGGAGTTGCGAGCG                         TTTATCACATTGGTCCCCAAGGCTGGAAGAAGATCTCCGGTGACGATGTGA
genomic: GATCTATCACGCGACGTTTAGAGATGGAGCCAGCGGAGGAGTTGCGAGCGgtaagctttt ... ttgcttccagTTTATCACATTGGTCCCCAAGGCTGGAAGAAGATCTCCGGTGACGATGTGA
EST: gi|169019358|gb|FE427668.1|FE427668
EST:     GATCTATCACGCGACGTTTAGAGATGGAGCCAGCGGAGGAGTTGCGAGCG                         TTTATCACATTGGTCCCCAAGGCTGGA
genomic: GATCTATCACGCGACGTTTAGAGATGGAGCCAGCGGAGGAGTTGCGAGCGgtaagctttt ... ttgcttccagTTTATCACATTGGTCCCCAAGGCTGGA
EST: gi|169019357|gb|FE427667.1|FE427667
EST:     GATCTATCACGCGACGTTTAGAGATGGAGCCAGCGGAGGAGTTGCGAGCG                         TTTATCACATTGGTCCCCAAGGCTGGAAGAAGATCTCCGGTGACGATGTGA
genomic: GATCTATCACGCGACGTTTAGAGATGGAGCCAGCGGAGGAGTTGCGAGCGgtaagctttt ... ttgcttccagTTTATCACATTGGTCCCCAAGGCTGGAAGAAGATCTCCGGTGACGATGTGA
EST: gi|169047646|gb|FE454814.1|FE454814
EST:     GATCTATCACGCGACGTTTAGAGATGGAGCCAGCGGAGGAGTTGCGAGCG                         TTTATCACATTGGTCCCCAAGGCTGGAAGAAGATCTCCGGTGACGATGTGA
genomic: GATCTATCACGCGACGTTTAGAGATGGAGCCAGCGGAGGAGTTGCGAGCGgtaagctttt ... ttgcttccagTTTATCACATTGGTCCCCAAGGCTGGAAGAAGATCTCCGGTGACGATGTGA

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: 49

TATAAGTTCGAGATGAGCGTCGAGGAAGCCGTGGAGCTGGGAAGACGAGCGATCTATCACGCGACGTTTAGAGATGGAGCCAGCGGAGGAGTTGCGAGCGgtaagctttt ... ttgcttccagTTTATCACATTGGTCCCCAAGGCTGGAAGAAGATCTCCGGTGACGATGTGAGTGAGCTACACTATCAGTACTACCCCCCGGAATCACAAGCGTCCGCCCC




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TATAAGTTCGAGATGAGCGTCGAGGAAGCCGTGGAGCTGGGAAGACGAGCGATCTATCACGCGACGTTTAGAGATGGAGCCAGCGGAGGAGTTGCGAGCGgtaagctttttttctttcgcttttcatcgctctgagcctgctttgcttccag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAG