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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatggcagtttactcgcaatcttctgtcggtactaactcttttcttgtgaaaagGTGTTCCTTTCATCCTAAAAGCTGGAAAAGCCTTGGATACTCGTAAGGCAGAGATTCGTGTCCAATTCAAAGACGTCCCGGGGGATATTTTCAAAT

Basic information

species Selaginella moellendorffii
transcript EFJ21593
intron # 10
splice site 3'
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|169075233|gb|FE481528.1|FE481528
EST:     ACCCACATTCGCCTCGGTGGTGCTGCGAATCCACAATGAGCGTTGGGATG                         GTGTTCCTTTCATCCTAAAAGCTGGAAAAGCCTTGGATACTCGTAAGGCAG
genomic: ACCCACATTCGCCTCGGTGGTGCTGCGAATCCACAATGAGCGTTGGGATGgtatggcagt ... ttgtgaaaagGTGTTCCTTTCATCCTAAAAGCTGGAAAAGCCTTGGATACTCGTAAGGCAG
EST: gi|169031484|gb|FE437194.1|FE437194
EST:     ACCCACATTCGCCTCGGTGGTGCTGCGAATCCACAATGAGCGTTGGGATG                         GTGTTCCTTTCATCCTAAAAGCTGGAAAAGCCTTGGATACTCGTAAGGCAG
genomic: ACCCACATTCGCCTCGGTGGTGCTGCGAATCCACAATGAGCGTTGGGATGgtatggcagt ... ttgtgaaaagGTGTTCCTTTCATCCTAAAAGCTGGAAAAGCCTTGGATACTCGTAAGGCAG
EST: gi|169075232|gb|FE481527.1|FE481527
EST:     ACCCACATTCGCCTCGGTGGTGCTGCGAATCCACAATGAGCGTTGGGATG                         GTGTTCCTTTCATCCTAAAAGCTGGAAAAGCCTTGGATACTCGTAAGGCAG
genomic: ACCCACATTCGCCTCGGTGGTGCTGCGAATCCACAATGAGCGTTGGGATGgtatggcagt ... ttgtgaaaagGTGTTCCTTTCATCCTAAAAGCTGGAAAAGCCTTGGATACTCGTAAGGCAG

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: 26 (upstream exon), 35 (downstream exon)
Score: 15

CAATACGAAGGCTATAGAGACGATCCCACGGTTTCCGATGAGTCATTGACACCCACATTCGCCTCGGTGGTGCTGCGAATCCACAATGAGCGTTGGGATGgtatggcagt ... ttgtgaaaagGTGTTCCTTTCATCCTAAAAGCTGGAAAAGCCTTGGATACTCGTAAGGCAGAGATTCGTGTCCAATTCAAAGACGTCCCGGGGGATATTTTCAAAT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtatggcagtttactcgcaatcttctgtcggtactaactcttttcttgtgaaaagGTGTTCCTTTCATCCTAAAAGCTGGAAAAGCCTTGGATACTCGTAAGGCAGAGATTCGTGTCCAATTCAAAGACGTCCCGGGGGATATTTTCAAAT
                               tactaac  putative branch site (score: 15)
                                 ctaactcttttctt  CT-rich tract
                                        ttttctt  TA-rich tract