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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GACTCTCTTCGGTACTCGGTGCGAGAGTGGTTTATCTTGAGATCATGAAGCCATACGCAGAAGCAGTACTATATAGgtttgtactgtttctatttgctgtagtttgacacgaaattaattgcag

Basic information

species Selaginella moellendorffii
transcript EFJ33842
intron # 15
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|169029830|gb|FE441037.1|FE441037
EST:     GTGGTTTATCTTGAGATCATGAAGCCATACGCAGAAGCAGTACTATATAG                         TGGCGGTCGCTCTAATGGTGGGAACGAACTACCAATTTTTGATAGTCCATT
genomic: GTGGTTTATCTTGAGATCATGAAGCCATACGCAGAAGCAGTACTATATAGgtttgtactg ... ttaattgcagTGGCGGTCGCTCTAATGGTGGGAACGAACTACCAATTTTTGATAGTCCATT
EST: gi|169067871|gb|FE473416.1|FE473416
EST:     GTGGTTTATCTTGAGATCATGAAGCCATACGCAGAAGCAGTACTATATAG                         TGGCGGTCGCTCTAATGGTGGGAACGAACTACCAATTTTTGATAGTCCATT
genomic: GTGGTTTATCTTGAGATCATGAAGCCATACGCAGAAGCAGTACTATATAGgtttgtactg ... ttaattgcagTGGCGGTCGCTCTAATGGTGGGAACGAACTACCAATTTTTGATAGTCCATT
EST: gi|169055550|gb|FE464583.1|FE464583
EST:     GTGGTTTATCTTGAGATCATGAAGCCATACGCAGAAGCAGTACTATATAG                         TGGCGGTCGCTCTAATGGTGGGAACGAACTACCAATTTTTGATAGTCCATT
genomic: GTGGTTTATCTTGAGATCATGAAGCCATACGCAGAAGCAGTACTATATAGgtttgtactg ... ttaattgcagTGGCGGTCGCTCTAATGGTGGGAACGAACTACCAATTTTTGATAGTCCATT
EST: gi|169049893|gb|FE458609.1|FE458609
EST:     GTGGTTTATCTTGAGATCATGAAGCCATACGCAGAAGCAGTACTATATAG                         TGGCGGTCGCTCTAATGGTGGGAACGAACTACCAATTTTTGATAGTCCATT
genomic: GTGGTTTATCTTGAGATCATGAAGCCATACGCAGAAGCAGTACTATATAGgtttgtactg ... ttaattgcagTGGCGGTCGCTCTAATGGTGGGAACGAACTACCAATTTTTGATAGTCCATT
EST: gi|169099114|gb|FE502836.1|FE502836
EST:     GTGGTTTATCTTGAGATCATGAAGCCATACGCAGAAGCAGTACTATATAG                         TGGCGGTCGCTCTAATGGTGGGAACGAACTACCAATTTTTGATAGTCCATT
genomic: GTGGTTTATCTTGAGATCATGAAGCCATACGCAGAAGCAGTACTATATAGgtttgtactg ... ttaattgcagTGGCGGTCGCTCTAATGGTGGGAACGAACTACCAATTTTTGATAGTCCATT
EST: gi|169068100|gb|FE477390.1|FE477390
EST:     GTGGTTTATCTTGAGATCATGAAGCCATACGCAGAAGCAGTACTATATAG                         TGGCGGTCGCTCTAATGGTGGGAACGAACTACCAATTTTTGATAGTCCATT
genomic: GTGGTTTATCTTGAGATCATGAAGCCATACGCAGAAGCAGTACTATATAGgtttgtactg ... ttaattgcagTGGCGGTCGCTCTAATGGTGGGAACGAACTACCAATTTTTGATAGTCCATT
EST: gi|169038685|gb|FE450156.1|FE450156
EST:     TGAGATCATGAAGCCATACGCAGAAGCAGTACTATATAG                         TGGCGGTCGCTCTAATGGTGGGAACGAACTACCAATTTTTGATAGTCCATT
genomic: TGAGATCATGAAGCCATACGCAGAAGCAGTACTATATAGgtttgtactg ... ttaattgcagTGGCGGTCGCTCTAATGGTGGGAACGAACTACCAATTTTTGATAGTCCATT
EST: gi|169019820|gb|FE426907.1|FE426907
EST:     GTGGTTTATCTTGAGATCATGAAGCCATACGCAGAAGCAGTACTATATAG                         TGGCGGTCGCTCTAATGGTGGGAACGAACTACCAATTTTTGATAGTCCATT
genomic: GTGGTTTATCTTGAGATCATGAAGCCATACGCAGAAGCAGTACTATATAGgtttgtactg ... ttaattgcagTGGCGGTCGCTCTAATGGTGGGAACGAACTACCAATTTTTGATAGTCCATT
EST: gi|169082975|gb|FE488497.1|FE488497
EST:     GTGGTTTATCTTGAGATCATGAAGCCATACGCAGAAGCAGTACTATATAG                         TGGTGGTCGCTCTAATGGTGGGAACGAACTACCAATTTTTGATAGTCCATT
genomic: GTGGTTTATCTTGAGATCATGAAGCCATACGCAGAAGCAGTACTATATAGgtttgtactg ... ttaattgcagTGGCGGTCGCTCTAATGGTGGGAACGAACTACCAATTTTTGATAGTCCATT
EST: gi|169102500|gb|FE503903.1|FE503903
EST:     GTGGTTTATCTTGAGATCATGAAGCCATACGCAGAAGCAGTACTATATAG                         TGGCGGTCGCTCTAATGGTGGGAACGAACTACCAATTTTTGATAGTCCATT
genomic: GTGGTTTATCTTGAGATCATGAAGCCATACGCAGAAGCAGTACTATATAGgtttgtactg ... ttaattgcagTGGCGGTCGCTCTAATGGTGGGAACGAACTACCAATTTTTGATAGTCCATT

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), 34 (downstream exon)
Score: 16

GACTCTCTTCGGTACTCGGTGCGAGAGTGGTTTATCTTGAGATCATGAAGCCATACGCAGAAGCAGTACTATATAGgtttgtactg ... ttaattgcagTGGCGGTCGCTCTAATGGTGGGAACGAACTACCAATTTTTGATAGTCCATTGCATTCTCAGGCTGAGGTCAAGCTCCATCAACTTTTACGTGAGATGCAC




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GACTCTCTTCGGTACTCGGTGCGAGAGTGGTTTATCTTGAGATCATGAAGCCATACGCAGAAGCAGTACTATATAGgtttgtactgtttctatttgctgtagtttgacacgaaattaattgcag

- - - - - - - - - - - - - - - - - - - GAGATC
- - - - - - - - - - - - - - - - - - -  AGATCA
- - - - - - - - - - - - - - - - - - - - - -  TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC