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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatactaggaaaatccaccgcccgctggttttaacctcttgctgcagATAGAAAAGCAAGAATTTGGTCTGAAGCCCATGAATTGTCCCGGCCATTGTTTACTTTTCCAACACAGGGTCCGTTCATATCGAG

Basic information

species Selaginella moellendorffii
transcript EFJ07136
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ07136 (Selaginella moellendorffii), 3'ss of exon 11
lower sequence: LOC_Os08g19850.1 (Oryza sativa), 3'ss of exon 10
----------------------------------------------------gtaatactaggaaaatccaccgcccgctggtt-ttaacctc-ttgctgcagATAGAAAAGCAAGAATTTGGTCTGAAGCCCATGAATTGTCCCGGCCATTGTTTACTTTTCCAACACAGGGTCCGTTCATATCGAG
                                                    | |  | |    |  |  |   |  | || || ||   ||  ||  ||||||| || || || ||||||||||| ||||| ||||||||||| ||||||||  || | ||  | |||||||| ||||||||  |||
gtaagtctagtgtgcagaggatttgctctgtacatattatagattacattttggatgaattacgatctttattactgggtgcttgttggtcttattcttgcagATTGAGAAACAGGAATTTGGTCTCAAGCCAATGAATTGTCCTGGCCATTGCCTAATGTTTGAGCACAGGGTTCGTTCATACAGAG
















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|169033199|gb|FE441219.1|FE441219
EST:     AACAATCCGGACATGCGGCTCATTATAAAGAANACATGTTCGTCTTCGAG                         ATAGAAAAGCAAGAATTTGGTCTGAAGCCCATGAATTGTCCCGGCCATTGT
genomic: AACAATCCGGACATGCGGCTCATTATAAAGAAAACATGTTCGTCTTCGAGgtaatactag ... cttgctgcagATAGAAAAGCAAGAATTTGGTCTGAAGCCCATGAATTGTCCCGGCCATTGT
EST: gi|169037065|gb|FE442712.1|FE442712
EST:     AACAATCCGGACATGCGGCTCATTATAAAGAAAACATGTTCGTCTTCGAG                         ATAGAAAAGCAAGAATTTGGTCTGAAGCCCATGAATTGTCCCGGCCATTGT
genomic: AACAATCCGGACATGCGGCTCATTATAAAGAAAACATGTTCGTCTTCGAGgtaatactag ... cttgctgcagATAGAAAAGCAAGAATTTGGTCTGAAGCCCATGAATTGTCCCGGCCATTGT
EST: gi|169081171|gb|FE489759.1|FE489759
EST:     AACAATCCGGACATGCGGCTCATTATAAAGAAAACATGTTCGTCTTCGAG                         ATAGAAAAGCAAGAATTTGGTCTGAAGCCCATGAATTGTCCCGGCCATTGT
genomic: AACAATCCGGACATGCGGCTCATTATAAAGAAAACATGTTCGTCTTCGAGgtaatactag ... cttgctgcagATAGAAAAGCAAGAATTTGGTCTGAAGCCCATGAATTGTCCCGGCCATTGT

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), 30 (downstream exon)
Score: 5

GTAGTCACTCCGAACATTTATAACATGAAACTTTGGGAACAATCCGGACATGCGGCTCATTATAAAGAAAACATGTTCGTCTTCGAGgtaatactag ... cttgctgcagATAGAAAAGCAAGAATTTGGTCTGAAGCCCATGAATTGTCCCGGCCATTGTTTACTTTTCCAACACAGGGTCCGTTCATATCGAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtaatactaggaaaatccaccgcccgctggttttaacctcttgctgcagATAGAAAAGCAAGAATTTGGTCTGAAGCCCATGAATTGTCCCGGCCATTGTTTACTTTTCCAACACAGGGTCCGTTCATATCGAG
                                    ttttaac  putative branch site (score: 5)
                                          cctcttgct  CT-rich tract
       taatacta  TA-rich tract