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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttacattcatcacatgtcccaaaaagaagaatttttaactcttctctgtgaattccagTTGCCCAGAGCTTGAGGAACTCGTTCAAGTGTGTCGATCGGCTGGAGCGCTGGGAGCCAGGCTGACTGGAGCCGGATGGGGTGGCTGCGTGGTGGCCCTG

Basic information

species Selaginella moellendorffii
transcript EFJ17214
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ17214 (Selaginella moellendorffii), 3'ss of exon 11
lower sequence: Vv05s0077g00690.t01 (Vitis vinifera), 3'ss of exon 11
-----------------------------------------------gtttacattcatcacatgtcccaaaaagaagaatttttaactcttctctgtgaattccagTTGCCCAGAGCTTGAGGAACTCGTTCAAGTGTGTCGATCGGCTGGAGCGCTGGGAGCCAGGCTGACTGGAGCCGGATGGGGTGGCTGCGTGGTGGCCCTG
                                                 ||   || |||| ||  | || ||||      |||      ||  |||||| |   || ||||||||| | || || || ||  |  | || ||      ||||||||| ||||| ||||| |||||||| ||||||||||| || |  || ||| ||
agtacgtgataaaattactctctgaacaaaaatcctttgcccctaccaattgtgttgatcatattactcataaagg----ctttcctggttttcctgtgatt---agCTGCCCAGAGTTGGAAGAGCTTGTAAAGATTTGCCGGGATAATGGAGCGCTTGGAGCAAGGCTTACTGGAGCTGGATGGGGTGGTTGTGCAGTTGCCTTG
















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|169071789|gb|FE476646.1|FE476646
EST:     AAGCTCATGAACGACAGCCACACTAGCTGCAGCAAACTCTACGAGTGCAG                         TTGCCCAGAGCTTGAGGAACTCGTTCAAGTGTGTCGATCGGCTGGAGCGCT
genomic: AAGCTCATGAACGACAGCCACACTAGCTGCAGCAAACTCTACGAGTGCAGgtttacattc ... tgaattccagTTGCCCAGAGCTTGAGGAACTCGTTCAAGTGTGTCGATCGGCTGGAGCGCT
EST: gi|169019355|gb|FE427665.1|FE427665
EST:     AAGCTCATGAACGACAGCCACACTAGCTGCAGCAAACTCTACGAGTGCAG                         TTGCCCAGAGCTTGAGGAACTCGTTCAAGTGTGTCGATCGGCTGGAGCGCT
genomic: AAGCTCATGAACGACAGCCACACTAGCTGCAGCAAACTCTACGAGTGCAGgtttacattc ... tgaattccagTTGCCCAGAGCTTGAGGAACTCGTTCAAGTGTGTCGATCGGCTGGAGCGCT
EST: gi|169063357|gb|FE472191.1|FE472191
EST:     AAGCTCATGAACGACAGCCACACTAGCTGCAGCAAACTCTACGAGTGCAG                         TTGCCCAGAGCTTGAGGAACTCGTTCAAGTGTGTCGATCGGCTGGAGCGCT
genomic: AAGCTCATGAACGACAGCCACACTAGCTGCAGCAAACTCTACGAGTGCAGgtttacattc ... tgaattccagTTGCCCAGAGCTTGAGGAACTCGTTCAAGTGTGTCGATCGGCTGGAGCGCT
EST: gi|169114901|gb|FE515850.1|FE515850
EST:     AAGCTCATGAACGACAGCCACACTAGCTGCAGCAAACTCTACGAGTGCAG                         TTGCCCAGAGCTTGAGGAACTCGTTCAAGTGTGTCGATCGGCTGGAGCGCT
genomic: AAGCTCATGAACGACAGCCACACTAGCTGCAGCAAACTCTACGAGTGCAGgtttacattc ... tgaattccagTTGCCCAGAGCTTGAGGAACTCGTTCAAGTGTGTCGATCGGCTGGAGCGCT
EST: gi|169063356|gb|FE472190.1|FE472190
EST:     AAGCTCATGAACGACAGCCACACTAGCTGCAGCAAACTCTACGAGTGCAG                         TTGCCCAGAGCTTGAGGAACTCGTTCAAGTGTGTCGATCGGCTGGAGCGCT
genomic: AAGCTCATGAACGACAGCCACACTAGCTGCAGCAAACTCTACGAGTGCAGgtttacattc ... tgaattccagTTGCCCAGAGCTTGAGGAACTCGTTCAAGTGTGTCGATCGGCTGGAGCGCT
EST: gi|169050265|gb|FE458345.1|FE458345
EST:     AAGCTCATGAACGACAGCCACACTAGCTGCAGCAAACTCTACGAGTGCAG                         TTGCCCAGAGCTTGAGGAACTCGTTCAAGTGTGTCGATCGGCTGGAGCGCT
genomic: AAGCTCATGAACGACAGCCACACTAGCTGCAGCAAACTCTACGAGTGCAGgtttacattc ... tgaattccagTTGCCCAGAGCTTGAGGAACTCGTTCAAGTGTGTCGATCGGCTGGAGCGCT

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), 33 (downstream exon)
Score: 9

TGAAGAAGAAGCATTGAAACGGCTTGGAAAGCTCATGAACGACAGCCACACTAGCTGCAGCAAACTCTACGAGTGCAGgtttacattc ... tgaattccagTTGCCCAGAGCTTGAGGAACTCGTTCAAGTGTGTCGATCGGCTGGAGCGCTGGGAGCCAGGCTGACTGGAGCCGGATGGGGTGGCTGCGTGGTGGCCCTG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cattcatcacatgtcccaaaaagaagaatttttaactcttctctgtgaattccagTTGCCCAGAGCTTGAGGAACTCGTTCAAGTGTGTCGATCGGCTGGAGCGCTGGGAGCCAGGCTGACTGGAGCCGGATGGGGTGGCTGCGTGGTGGCCCTG
                             ttttaac  putative branch site (score: 9)
                                   ctcttctctgt  CT-rich tract
                 aaaaagaagaattttt  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtttacattcatcacatgtcccaaaaagaagaatttttaactcttctctgtgaattccagTTGCCCAGAGCTTGAGGAACTCGTTCAAGTGTGTCGATCGGCTGGAGCGCTGGGAGCCAGGCTGACTGGAGCCGGATGGGGTGGCTGCGTGGTGGCCCTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGTGG