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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtagagaggaatttgtattcgtttgtgccagcactctccctgacaaagtttgcttgacagGTTCGGAAGGTCGGGAAAGTTGTCCGGGCCATATGCATCATGAGCCATCCAATCCCAAACACGAACGATTCCTCGTCAGTTCAAGTTATCCTTCCCCAAA

Basic information

species Selaginella moellendorffii
transcript EFJ11673
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ11673 (Selaginella moellendorffii), 3'ss of exon 9
lower sequence: PP1S100_23V6.1 (Physcomitrella patens), 3'ss of exon 9
------------------------------------------------gtagagaggaat----ttgtat-tcgtttgtgccagcactctccctgacaaagtttgcttga-----cagGTTCGGAAGGTCGGGAAAGTTGTCCGGGCCATATGCATCATGAGCCATCCAATCCCAAACACGAACGATTCCTCGTCAGTTCAAGTTATCCTTCCCCAAA
                                                |||||||  | |    ||  |  | || || |    |     |  ||   ||     | ||      ||||||  |||||||||||| ||||| || || || ||| |||||||||||||||| ||||| || |  || ||    || |||||| | || || || ||||
gtaatttttgtgatttgaaagttgttgctagcagtctatcgtgaacttgtagagaatagtaggcttacacatggtatgggttgacttatgcgatgcataaaaccacctgctcctccagGTTAAGAAGGTCGGGAAGGTTGTGCGCGCTATCTGCTTCATGAGCCATCCAATTCCAAATACTAGTGACTCTGATTCGGTTCAAATAATTCTGCCGCAAA
















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|169057386|gb|FE466821.1|FE466821
EST:     CTGCCAGGACCAAGAAAGTNGTCTGCGATCCTAGCTATGCACGAAACAAG                         GTTCGGAAGGTCGGGAAAGTTGTCCGGGCCATATGCATCATGAGCCATCCA
genomic: CTGCCAGGACCAAGAAAGTTGTCTGCGATCCTAGCTATGCACGAAACAAGgtagagagga ... tgcttgacagGTTCGGAAGGTCGGGAAAGTTGTCCGGGCCATATGCATCATGAGCCATCCA
EST: gi|169038887|gb|FE449604.1|FE449604
EST:     CTGCCAGGACCAAGAAAGTTGTCTGCGATCCTAGCTATGCACGAAACAAG                         GTTCGGAAGGTCGGGAAAGTTGTCCGGGCCATATGCATCATGAGCCATCCA
genomic: CTGCCAGGACCAAGAAAGTTGTCTGCGATCCTAGCTATGCACGAAACAAGgtagagagga ... tgcttgacagGTTCGGAAGGTCGGGAAAGTTGTCCGGGCCATATGCATCATGAGCCATCCA
EST: gi|169070710|gb|FE477309.1|FE477309
EST:     CTGCCAGGACCAAGAAAGTTGTCTGCGATCCTAGCTATGCACGAAACAAG                         GTTCGGAAGGTCGGGAAAGTTGTCCGGGCCATATGCATCATGAGCCATCCA
genomic: CTGCCAGGACCAAGAAAGTTGTCTGCGATCCTAGCTATGCACGAAACAAGgtagagagga ... tgcttgacagGTTCGGAAGGTCGGGAAAGTTGTCCGGGCCATATGCATCATGAGCCATCCA
EST: gi|169093396|gb|FE492700.1|FE492700
EST:     CTGCCAGGACCAAGAAAGTTGTCTGCGATCCTAGCTATGCACGAAACAAG                         GTTCGGAAGGTCGGGAAAGTTGTCCGGGCCATATGCATCATGAGCCATCCA
genomic: CTGCCAGGACCAAGAAAGTTGTCTGCGATCCTAGCTATGCACGAAACAAGgtagagagga ... tgcttgacagGTTCGGAAGGTCGGGAAAGTTGTCCGGGCCATATGCATCATGAGCCATCCA
EST: gi|169092637|gb|FE493657.1|FE493657
EST:     CTGCCAGGACCAAGAAAGTTGTCTGCGATCCTAGCTATGCACGAAACAAG                         GTTCGGAAGGTCGGGAAAGTTGTCCGGGCCATATGCATCATGAGCCATCCA
genomic: CTGCCAGGACCAAGAAAGTTGTCTGCGATCCTAGCTATGCACGAAACAAGgtagagagga ... tgcttgacagGTTCGGAAGGTCGGGAAAGTTGTCCGGGCCATATGCATCATGAGCCATCCA
EST: gi|169038296|gb|FE445308.1|FE445308
EST:     CTGCCAGGACCAAGAAAGTTGTCTGCGATCCTAGCTATGCACGAAACAAG                         GTTCGGAAGGTCGGGAAAGTTGTCCGGGCCATATGCATCATGAGCCATCCA
genomic: CTGCCAGGACCAAGAAAGTTGTCTGCGATCCTAGCTATGCACGAAACAAGgtagagagga ... tgcttgacagGTTCGGAAGGTCGGGAAAGTTGTCCGGGCCATATGCATCATGAGCCATCCA
EST: gi|169092638|gb|FE493658.1|FE493658
EST:     CTGCCAGGACCAAGAAAGTTGTCTGCGATCCTAGCTATGCACGAAACAAG                         GTTCGGAAGGTCGGGAAAGTTGTCCGGGCCATATGCATCATGAGCCATCCA
genomic: CTGCCAGGACCAAGAAAGTTGTCTGCGATCCTAGCTATGCACGAAACAAGgtagagagga ... tgcttgacagGTTCGGAAGGTCGGGAAAGTTGTCCGGGCCATATGCATCATGAGCCATCCA
EST: gi|169083494|gb|FE491925.1|FE491925
EST:     CTGCCAGGACCAAGAAAGTTGTCTGCGATCCTAGCTATGCACGAAACAAG                         GTTCGGAAGGTCGGGAAAGTTGTCCGGGCCATATGCATCATGAGCCATCCA
genomic: CTGCCAGGACCAAGAAAGTTGTCTGCGATCCTAGCTATGCACGAAACAAGgtagagagga ... tgcttgacagGTTCGGAAGGTCGGGAAAGTTGTCCGGGCCATATGCATCATGAGCCATCCA

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: 31 (upstream exon), 29 (downstream exon)
Score: 5

AGAGTTTGACGAGGAAGGCAAGGTTAGAGGCGTCACCTCCGAAGGTGAAACTGCCAGGACCAAGAAAGTTGTCTGCGATCCTAGCTATGCACGAAACAAGgtagagagga ... tgcttgacagGTTCGGAAGGTCGGGAAAGTTGTCCGGGCCATATGCATCATGAGCCATCCAATCCCAAACACGAACGATTCCTCGTCAGTTCAAGTTATCCTTCCCCAAA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gaggaatttgtattcgtttgtgccagcactctccctgacaaagtttgcttgacagGTTCGGAAGGTCGGGAAAGTTGTCCGGGCCATATGCATCATGAGCCATCCAATCCCAAACACGAACGATTCCTCGTCAGTTCAAGTTATCCTTCCCCAAA
                                ccctgac  putative branch site (score: 5)
                                           tttgctt  putative PPT
     atttgtatt  TA-rich tract