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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtttattcattcaggagtgaagtggaagctctcttttttcctgatgccactgttcgcctcgtgtagACAATTTTTCTCCCAGTGGTTGGTTTGGTGGATCCGACCACTCTAAAACCGGGTGACCTTGTGGGTGTGAACAAGGACAGCTACTTAATCTTGGATACAC

Basic information

species Selaginella moellendorffii
transcript EFJ37626
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ37626 (Selaginella moellendorffii), 3'ss of exon 3
lower sequence: GLYMA10G29250.1 (Glycine max), 3'ss of exon 3
---------------------------------------gtaagtttattcattcaggagtgaagtggaagctctcttttttcctgatgccac---tgttcgcctcg---tgtagACAATTTTTCTCCCAGTGGTTGGTTTGGTGGATCCGACCACTCTAAAACCGGGTGACCTTGTGGGTGTGAACAAGGACAGCTACTTAATCTTGGATACAC
                                       |  ||   |  |  |||| |    |||  |   | |||||  || |||    |    ||||  | |     || ||||||| ||||| || || |||||  | || || ||   ||   ||||||| ||||| || || ||||| |||||||| || |||||||||||||||||  
gtgacatggacgatgatttcatattatcttattcttttagcgaggaaaagctctcagtacaatagtacatatt-tctttaatcttgagcttaattatgttttcttttgactgcagACAATCTTTCTACCTGTTGTTGGGCTTGTTGACCCTGACAAGTTAAAACCTGGTGATCTGGTTGGTGTTAACAAGGATAGTTACTTAATCTTGGATACCT

upper sequence: EFJ37626 (Selaginella moellendorffii), 3'ss of exon 3
lower sequence: GLYMA20G38030.1 (Glycine max), 3'ss of exon 3
--------------------------------------------------------------------------------gtaagtttattcatt---caggagtgaagtggaagctctcttttt-----tcctga---tgccactgttcgcctcg---tgtagACAATTTTTCTCCCAGTGGTTGGTTTGGTGGATCCGACCACTCTAAAACCGGGTGACCTTGTGGGTGTGAACAAGGACAGCTACTTAATCTTGGATACAC
                                                                                || |  |||| | ||   |  |    |  |   ||  |  ||||       | |||   |   | ||||  | |     || ||||||| ||||| || || |||||  | || || ||   ||   ||||||| ||||| || || ||||| |||||||| || ||||||||||||||||| |
gtgacatggactaggatttcatattgtcatctgatgttcctatatcatagtttaagattgttttatttgttatagttattgttatcttatgcttttaacgaggacaagctcttagtacatttttcggtaaccttgagcttaataatgttttcttttgactgcagACAATCTTTCTACCTGTTGTTGGGCTTGTTGACCCTGACAAGTTAAAACCCGGTGATCTGGTTGGTGTTAACAAGGATAGTTACTTAATCTTGGATACCC
















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|169070059|gb|FE476528.1|FE476528
EST:     ATTCTCAAAGAAAAGGAAAATGCGTCGTGCTCAAGACCTCCACTCGCCAA                         ACAATTTTTCTCCCAGTGGTTGGTTTGGTGGATCCGACCACTCTAAAACCG
genomic: ATTCTCAAAGAAAAGGAAAATGCGTCGTGCTCAAGACCTCCACTCGCCAAgtaagtttat ... cctcgtgtagACAATTTTTCTCCCAGTGGTTGGTTTGGTGGATCCGACCACTCTAAAACCG
EST: gi|169105078|gb|FE505920.1|FE505920
EST:     ATTCTCAAAGAAAAGGAAAATGCGTCGTGCTCAAGACCTCCACTCGCCAA                         ACAATTTTTCTCCCAGTGGTTGGTTTGGTGGATCCGACCACTCTAAAACCG
genomic: ATTCTCAAAGAAAAGGAAAATGCGTCGTGCTCAAGACCTCCACTCGCCAAgtaagtttat ... cctcgtgtagACAATTTTTCTCCCAGTGGTTGGTTTGGTGGATCCGACCACTCTAAAACCG
EST: gi|169074634|gb|FE481189.1|FE481189
EST:     ATTCTCAAAGAAAAGGAAAATGCGTCGTGCTCAAGACCTCCACTCGCCAA                         ACAATTTTTCTCCCAGTGGTTGGTTTGGTGGATCCGACCACTCTAAAACCG
genomic: ATTCTCAAAGAAAAGGAAAATGCGTCGTGCTCAAGACCTCCACTCGCCAAgtaagtttat ... cctcgtgtagACAATTTTTCTCCCAGTGGTTGGTTTGGTGGATCCGACCACTCTAAAACCG

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), 14 (downstream exon)
Score: 8

TGTAAATCCTGAGGATGAAGCTGAGGAAGACGGTGCCAATGTCGATCTCGATTCTCAAAGAAAAGGAAAATGCGTCGTGCTCAAGACCTCCACTCGCCAAgtaagtttat ... cctcgtgtagACAATTTTTCTCCCAGTGGTTGGTTTGGTGGATCCGACCACTCTAAAACCGGGTGACCTTGTGGGTGTGAACAAGGACAGCTACTTAATCTTGGATACAC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

caggagtgaagtggaagctctcttttttcctgatgccactgttcgcctcgtgtagACAATTTTTCTCCCAGTGGTTGGTTTGGTGGATCCGACCACTCTAAAACCGGGTGACCTTGTGGGTGTGAACAAGGACAGCTACTTAATCTTGGATACAC
                           tcctgat  putative branch site (score: 8)
                                         ttcgcctc  putative PPT
                    tctttttt  TA-rich tract