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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgaggaattgaagtcttttggagtttctctaaacgatctcttcctttttctctactgctttatgtagATTTTACAATCACTTCTTCTGGATTTACCCGGACTCTTGTTCTTCACGACGTACACTTTGCTAGTACTCTTCTGGGCTGAGATTTATCACCAG

Basic information

species Selaginella moellendorffii
transcript EFJ23006
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ23006 (Selaginella moellendorffii), 3'ss of exon 3
lower sequence: GRMZM2G171469_T01 (Zea mays), 3'ss of exon 3
-----------gtgaggaattgaagtc---ttttggagtttctctaaacgatctct--tcctttttctctactgctttatgtagATTTTACAATCACTTCTTCTGGATTTACCCGGACTCTTGTTCTTCACGACGTACACTTTGCTAGTACTCTTCTGGGCTGAGATTTATCACCAG
           | ||  | ||  | |    || || || |  |   ||  | || |  |  | | | || |    |   | |||||  | |||    | ||| | ||||| || || ||   |||||||||||| ||| || ||||||| ||||||||||||||||||||  | |||
gtttgtgtcaggagacaagttttatttcgtttctgtagctggttggaaacaactgtagtaatgtgtatcaatacttccttttagATACTTCAACACGTGCTTATTGATTTGCCGGGCCTAGCGTTCTTCACGACCTACGCTCTGCTAGTGCTCTTCTGGGCTGAGATTTACTATCAG
















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|169049297|gb|FE458221.1|FE458221
EST:     CGCCAAGTCCAGTTCCTGGAGCCCCGG                         ATTTTACAATCACTTCTTCTGGATTTACCCGGACTC-TGTTTCTTCACGAC
genomic: CGCCAAGTCCAGTTCCTTGAGCCCCGGgtgaggaatt ... ctttatgtagATTTTACAATCACTTCTTCTGGATTTACCCGGACTCTTG-TTCTTCACGAC
EST: gi|169049298|gb|FE458222.1|FE458222
EST:     GAGCTGTGGTGTTCTTCTTCCGGCGCCAAGTCCAGTTCCTTGAGCCCCGG                         ATTTTACAATCACTTCTTCTGGATTTACCCGGACTCTTGTTCTTCACGACG
genomic: GAGCTGTGGTGTTCTTCTTCCGGCGCCAAGTCCAGTTCCTTGAGCCCCGGgtgaggaatt ... ctttatgtagATTTTACAATCACTTCTTCTGGATTTACCCGGACTCTTGTTCTTCACGACG
EST: gi|169087157|gb|FE493104.1|FE493104
EST:     TCCGGCGCCAAGTCCAGTTCCTTGAGCCCCGG                         ATTTTACAATCACTTCTTCTGGATTTACCCGGACTCTTGTTCTTCACGACG
genomic: TCCGGCGCCAAGTCCAGTTCCTTGAGCCCCGGgtgaggaatt ... ctttatgtagATTTTACAATCACTTCTTCTGGATTTACCCGGACTCTTGTTCTTCACGACG
EST: gi|169087158|gb|FE493105.1|FE493105
EST:     GAGCTGTGGTGTTCTTCTTCCGGCGCCAAGTCCAGTTCCTTGAGCCCCGG                         ATTTTACAATCACTTCTTCTGGATTTACCCGGACTCTTGTTCTTCACGACG
genomic: GAGCTGTGGTGTTCTTCTTCCGGCGCCAAGTCCAGTTCCTTGAGCCCCGGgtgaggaatt ... ctttatgtagATTTTACAATCACTTCTTCTGGATTTACCCGGACTCTTGTTCTTCACGACG

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: 28 (upstream exon), 31 (downstream exon)
Score: 14

TCCGAGCTGTGGTGTTCTTCTTCCGGCGCCAAGTCCAGTTCCTTGAGCCCCGGgtgaggaatt ... ctttatgtagATTTTACAATCACTTCTTCTGGATTTACCCGGACTCTTGTTCTTCACGACGTACACTTTGCTAGTACTCTTCTGGGCTGAGATTTATCACCAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtcttttggagtttctctaaacgatctcttcctttttctctactgctttatgtagATTTTACAATCACTTCTTCTGGATTTACCCGGACTCTTGTTCTTCACGACGTACACTTTGCTAGTACTCTTCTGGGCTGAGATTTATCACCAG
              ctctaaa  putative branch site (score: 14)
                        tctcttcctttttctc  putative PPT
                                              tttatgta  TA-rich tract