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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacgctacgagtttatagcacgtcgtgacaaatttgtttgcagGAAAGCAAAGTTGGGGAGCCTTTCTGGGATTCTCCATGGGGACCTGGCCGTCCTGGTTGGCACATCGAGTGCTCGGCTATGGCCAGTGACGTTATTGGGG

Basic information

species Selaginella moellendorffii
transcript EFJ26208
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ26208 (Selaginella moellendorffii), 3'ss of exon 6
lower sequence: PP1S83_56V6.1 (Physcomitrella patens), 3'ss of exon 2
--------------------------------------------------------------------------------------------------------------------gtacg-ctacgagtttatagcacgtcgtgacaaatttgtt-tgcagGAAAGCAAAGTTGGGGAGCCTTTCTGGGATTCTCCATGGGGACCTGGCCGTCCTGGTTGGCACATCGAGTGCTCGGCTATGGCCAGTGACGTTATTGGGG
                                                                                                                    ||  | |     ||| |    | || || ||| ||   |    ||| |||| ||   ||| || ||||  ||||||||||| ||||| || || ||||| || |||||||| ||||| ||||| |||||||||||| |  | || |
gtgagtggtctcaaactggacgtcacgtagggagaaatgagaggagtttgattgctttgatctatattgataaggagctatgtaatgatgtgcagcatggatttgtcagcttgtatgtgtgaccgtttgttgacgcgatgttgtaacatatggatggcccagAAAAGTAAGCCTGGAGAACCTTCATGGGATTCTCCTTGGGGCCCGGGACGTCCAGGCTGGCACATTGAGTGTTCGGCAATGGCCAGTGACATACTGGGTG
















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|169037751|gb|FE442462.1|FE442462
EST:     ACTTCAAAACCAGAAACAAGAAAAACAATAACGACTTCGCGTTATGGAAG                         GAAAGCAAAGTTGGGGAGCCTTTCTGGGATTCCCCATGGGGACCTGGCCGT
genomic: ACTTCAAAACCAGAAACAAGAAAAACAATAACGACTTCGCGTTATGGAAGgtacgctacg ... ttgtttgcagGAAAGCAAAGTTGGGGAGCCTTTCTGGGATTCTCCATGGGGACCTGGCCGT
EST: gi|169071564|gb|FE480477.1|FE480477
EST:     ACTTCAAAACCAGAAACAAGAAAAACAATAACGACTTCGCGTTATGGAAG                         GAAAGCAAAGTTGGGGAGCCTTTCTGGGATTCCCCATGGGGACCTGGCCGT
genomic: ACTTCAAAACCAGAAACAAGAAAAACAATAACGACTTCGCGTTATGGAAGgtacgctacg ... ttgtttgcagGAAAGCAAAGTTGGGGAGCCTTTCTGGGATTCTCCATGGGGACCTGGCCGT
EST: gi|169097407|gb|FE497680.1|FE497680
EST:     ACTTCAAAACCAGAAACAAGAAAAACAATAACGACTTCGCGTTATGGAAG                         GAAAGCAAAGTTGGGGAGCCTTTCTGGGATTCCCCATGGGGACCTGGCCGT
genomic: ACTTCAAAACCAGAAACAAGAAAAACAATAACGACTTCGCGTTATGGAAGgtacgctacg ... ttgtttgcagGAAAGCAAAGTTGGGGAGCCTTTCTGGGATTCTCCATGGGGACCTGGCCGT

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: 10 (upstream exon), 26 (downstream exon)
Score: 1

TAATCCGGCAGCTGTAGGATGTGTTGGTCTGGCTTCTGAGAGTGAAACGAACTTCAAAACCAGAAACAAGAAAAACAATAACGACTTCGCGTTATGGAAGgtacgctacg ... ttgtttgcagGAAAGCAAAGTTGGGGAGCCTTTCTGGGATTCTCCATGGGGACCTGGCCGTCCTGGTTGGCACATCGAGTGCTCGGCTATGGCCAGTGACGTTATTGGGG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtacgctacgagtttatagcacgtcgtgacaaatttgtttgcagGAAAGCAAAGTTGGGGAGCCTTTCTGGGATTCTCCATGGGGACCTGGCCGTCCTGGTTGGCACATCGAGTGCTCGGCTATGGCCAGTGACGTTATTGGGG
                                                      tttgttt  CT-rich tract
                                         aaatttgttt  TA-rich tract