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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCGGCTGGACAGCAAGGGCAAGATCGTGTGCTCACTGGTGGTGGCGCTCAGTGTCTTCTCGGCGATTCTTGGCTTCTCGGCCGAGGGCGAGCGCGTCAGGgtatgtgtgattcgatttcttcccgttcttgccctattctcgctcttcctctcgattcttggctggatttcctagaagctgggcttttctcgattggatt...

Basic information

species Selaginella moellendorffii
transcript EFJ19063
intron # 1
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|169056931|gb|FE465469.1|FE465469
EST:     GTGTCTTCTCGGCGATTCTTGGCTTCTCGGCCGAGGGCGAGCGCGTCAGG                         CCCGACGAGGTGCGTCGCGTCAATGGGGCGTGTACATATCCCAAGAGCTCG
genomic: GTGTCTTCTCGGCGATTCTTGGCTTCTCGGCCGAGGGCGAGCGCGTCAGGgtatgtgtga ... ccaagcgaagCCCGATGAGGTCCGTCGCGTCAATGGAGCGTGTACATATCCCAAGAGCTCG
EST: gi|169056930|gb|FE465468.1|FE465468
EST:     GTGTCTTCTCGGCGATTCTTGGCTTCTCGGCCGAGGGCGAGCGCGTCAGG                         CCCGACGAGGTGCGTCGCGTCAATGGGGCGTGTACATATCCCAAGAGCTCG
genomic: GTGTCTTCTCGGCGATTCTTGGCTTCTCGGCCGAGGGCGAGCGCGTCAGGgtatgtgtga ... ccaagcgaagCCCGATGAGGTCCGTCGCGTCAATGGAGCGTGTACATATCCCAAGAGCTCG
EST: gi|169062191|gb|FE469198.1|FE469198
EST:     GTGTCTTCTCGGCGATTCTTGGCTTCTCGGCCGAGGGCGAGCGCGTCAGG                         CCCGATGAGGTCCGTCGCGTCAATGGAGCGTGTACATATCCCAAGAGCTCG
genomic: GTGTCTTCTCGGCGATTCTTGGCTTCTCGGCCGAGGGCGAGCGCGTCAGGgtatgtgtga ... ccaagcgaagCCCGATGAGGTCCGTCGCGTCAATGGAGCGTGTACATATCCCAAGAGCTCG
EST: gi|169114521|gb|FE516591.1|FE516591
EST:     GTGTCTTCTCGGCGATTCTTGGCTTCTCGGCCGAGGGCGAGCGCGTCAGG                         CCCGACGAGGTGCGTCGCGTCAATGGGGCGTGTACATATCCCAAGAGCTCG
genomic: GTGTCTTCTCGGCGATTCTTGGCTTCTCGGCCGAGGGCGAGCGCGTCAGGgtatgtgtga ... ccaagcgaagCCCGATGAGGTCCGTCGCGTCAATGGAGCGTGTACATATCCCAAGAGCTCG
EST: gi|169104530|gb|FE508130.1|FE508130
EST:     CCGAGGGCGAGCGCGTCAGG                         CCCGATGAGGTCCGTCGCGTCAATGGAGCGTGTACATATCCCAAGAGCTCG
genomic: CCGAGGGCGAGCGCGTCAGGgtatgtgtga ... ccaagcgaagCCCGATGAGGTCCGTCGCGTCAATGGAGCGTGTACATATCCCAAGAGCTCG
EST: gi|169058254|gb|FE464994.1|FE464994
EST:     GTGTCTTCTCGGCGATTCTTGGCTTCTCGGCCGAGGGCGAGCGCGTCAGG                         CCCGACGAGGTGCGTCGCGTCAATGGGGCGTGTACATATCCCAAGAGCTCG
genomic: GTGTCTTCTCGGCGATTCTTGGCTTCTCGGCCGAGGGCGAGCGCGTCAGGgtatgtgtga ... ccaagcgaagCCCGATGAGGTCCGTCGCGTCAATGGAGCGTGTACATATCCCAAGAGCTCG
EST: gi|169108573|gb|FE510788.1|FE510788
EST:     GTGTCTTCTCGGCGATTCTTGGCTTCTCGGCCGAGGGCGAGCGCGTCAGG                         CCCGATGAGGTCCGTCGCGTCAATGGAGCGTGTACATATCCCAAGAGCTCG
genomic: GTGTCTTCTCGGCGATTCTTGGCTTCTCGGCCGAGGGCGAGCGCGTCAGGgtatgtgtga ... ccaagcgaagCCCGATGAGGTCCGTCGCGTCAATGGAGCGTGTACATATCCCAAGAGCTCG
EST: gi|169075536|gb|FE482546.1|FE482546
EST:     GATTCTTGGCTTCTCGGCCGAGGGCGAGCGCGTCAGG                         CCCGATGAGGTCCGTCGCGTCAATGGAGCGTGTACATATCCCAAGAGCTCG
genomic: GATTCTTGGCTTCTCGGCCGAGGGCGAGCGCGTCAGGgtatgtgtga ... ccaagcgaagCCCGATGAGGTCCGTCGCGTCAATGGAGCGTGTACATATCCCAAGAGCTCG
EST: gi|169108574|gb|FE510789.1|FE510789
EST:     GTGTCTTCTCGGCGATTCTTGGCTTCTCGGCCGAGGGCGAGCGCGTCAGG                         CCCGATGAGGTCCGTCGCGTCAATGGAGCGTGTACATATCCCAAGAGCTCG
genomic: GTGTCTTCTCGGCGATTCTTGGCTTCTCGGCCGAGGGCGAGCGCGTCAGGgtatgtgtga ... ccaagcgaagCCCGATGAGGTCCGTCGCGTCAATGGAGCGTGTACATATCCCAAGAGCTCG

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: 34 (upstream exon), 35 (downstream exon)
Score: 12

GCGGCTGGACAGCAAGGGCAAGATCGTGTGCTCACTGGTGGTGGCGCTCAGTGTCTTCTCGGCGATTCTTGGCTTCTCGGCCGAGGGCGAGCGCGTCAGGgtatgtgtga ... ccaagcgaagCCCGATGAGGTCCGTCGCGTCAATGGAGCGTGTACATATCCCAAGAGCTCGGCGTTGGGTCTTGGAATCAGCGCGGCGCTCTTCCTCCTCGCCGCCCAAG




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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
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---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCGGCTGGACAGCAAGGGCAAGATCGTGTGCTCACTGGTGGTGGCGCTCAGTGTCTTCTCGGCGATTCTTGGCTTCTCGGCCGAGGGCGAGCGCGTCAGGgtatgtgtgattcgatttcttcccgttcttgccctattctcgctcttcctctcgattcttggctggatttcctagaagctgggcttttctcgattggatt

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tttcttc
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- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ttctcgc
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