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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtactctctctctctctcatatattcatttttcactctcgctctctcgctctctcatacattcatttttcactgtagctttagctctctctctctctctctctctctctctctcccctttgatttcgctgtagctctagtacttctttctaaagcgtttgatttgttggatcaacagGATTCTCGGTGATGTGTTCATGGGGGTATACCATACGGTGTTTGATTTCGGGAACAAACGCATTGGTTTCGCCAAGGCAGTCTGAAAAGACTCTTAATCG

Basic information

species Selaginella moellendorffii
transcript EFJ34432
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ34432 (Selaginella moellendorffii), 3'ss of exon 11
lower sequence: PP1S99_158V6.1 (Physcomitrella patens), 3'ss of exon 12
gtactctctctctctctcatatattcatttttcactctcgctctctcgctctctcatacattcatttttcactgtagctttagctctctctctctctctctctctctctctctcccctttgatttcgctgtagctctagtacttctttc-----taaagcgtttgatttgt-tggatcaacagGATTCTCGGTGATGTGTTCATGGGGGTATACCATACGGTGTTTGATTTCGGGAACAAACGCATTGGTTTCGCCAAGGCAGTCTGAAAAGACTCTTAATCG
|| | | ||| | | | | |||||| | || | | ||| | | |||| | || || | ||| | | |||||||| || |||||||||||||||| |||||||||||||| || ||||||||| | || | || ||||| ||| | | | ||||
----------------------------------------------------------------------------------aatcgtttgttttcttttcatgcaaggcgtttccctttattctctc-acgaatatagaatatttttcaaaattgaattgtgaaacctgtgcacgtgattagGATTCTTGGAGATGTGTTCATGGGGGCTTACCATACGGTGTTCGACTTCGGGAACCAGCGATTGGGCTTCGCTTTGGCTGCTTAGATCCCAAAATAATAT
















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|169048187|gb|FE455459.1|FE455459
EST:     ATTAGTGGCTTTACAGGAATGGACGTCGCTCCTCCAGCCGGCCCACTTTG                         GATTTTCGGTGATGTGTTCATGGGGGTATACCATACGGTGTTTGATTTCGG
genomic: ATTAGTGGCTTTACAGGAATGGACGTCGCTCCTCCAGCCGGCCCAATCTGgtactctctc ... ggatcaacagGATTCTCGGTGATGTGTTCATGGGGGTATACCATACGGTGTTTGATTTCGG
EST: gi|169039488|gb|FE449163.1|FE449163
EST:     ATTAGTGGCTTTACAGGAATGGACGTCGCTCCTCCAGCCGGCCCACTCTG                         GATTCTCGGTGATGTGTTCATGGGGGTATACCATACGGTGTTTGATTTCGG
genomic: ATTAGTGGCTTTACAGGAATGGACGTCGCTCCTCCAGCCGGCCCAATCTGgtactctctc ... ggatcaacagGATTCTCGGTGATGTGTTCATGGGGGTATACCATACGGTGTTTGATTTCGG
EST: gi|169030852|gb|FE439797.1|FE439797
EST:     ATTAGTGGCTTTACAGGAATGGACGTCGCTCCTCCAGCCGGCCCAATCTG                         GATTCTCGGTGATGTGTTCATGGGGGTATACCATACGGTGTTTGATTTCGG
genomic: ATTAGTGGCTTTACAGGAATGGACGTCGCTCCTCCAGCCGGCCCAATCTGgtactctctc ... ggatcaacagGATTCTCGGTGATGTGTTCATGGGGGTATACCATACGGTGTTTGATTTCGG
EST: gi|169043989|gb|FE451575.1|FE451575
EST:     ATTAGTGGCTTTACAGGAATGGACGTCGCTCCTCCAGCCGGCCCACTCTG                         GATTCTCGGTGATGTGTTCATGGGGGTATACCATACGGTGTTTGATTTCGG
genomic: ATTAGTGGCTTTACAGGAATGGACGTCGCTCCTCCAGCCGGCCCAATCTGgtactctctc ... ggatcaacagGATTCTCGGTGATGTGTTCATGGGGGTATACCATACGGTGTTTGATTTCGG
EST: gi|169043990|gb|FE451576.1|FE451576
EST:     ATTAGTGGCTTTACAGGAATGGACGTCGCTCCTCCAGCCGGCCCACTCTG                         GATTCTCGGTGATGTGTTCATGGGGGTATACCATACGGTGTTTGATTTCGG
genomic: ATTAGTGGCTTTACAGGAATGGACGTCGCTCCTCCAGCCGGCCCAATCTGgtactctctc ... ggatcaacagGATTCTCGGTGATGTGTTCATGGGGGTATACCATACGGTGTTTGATTTCGG
EST: gi|169072916|gb|FE482344.1|FE482344
EST:     ATTAGTGGCTTTACAGGAATGGACGTCGCTCCTCCAGCCGGCCCACTCTG                         GATTCTCGGTGATGTGTTCATGGGGGTATACCATACGGTGTTTGATTTCGG
genomic: ATTAGTGGCTTTACAGGAATGGACGTCGCTCCTCCAGCCGGCCCAATCTGgtactctctc ... ggatcaacagGATTCTCGGTGATGTGTTCATGGGGGTATACCATACGGTGTTTGATTTCGG
EST: gi|169043410|gb|FE451854.1|FE451854
EST:     ATTAGTGGCTTTACAGGAATGGACGTCGCTCCTCCAGCCGTCCCAATCTG                         GATTCTCGGTGATGTGTTCATGGGGGTATACCATACGGTGTTTGATTTCGG
genomic: ATTAGTGGCTTTACAGGAATGGACGTCGCTCCTCCAGCCGGCCCAATCTGgtactctctc ... ggatcaacagGATTCTCGGTGATGTGTTCATGGGGGTATACCATACGGTGTTTGATTTCGG
EST: gi|169107735|gb|FE511458.1|FE511458
EST:     ATTAGTGGCTTTACAGGAATGGACGTCGCTCCTCCAGCCGGCCCACTCTG                         GATTCTCGGTGATGTGTTCATGGGGGTATACCATACGGTGTTTGATTTCGG
genomic: ATTAGTGGCTTTACAGGAATGGACGTCGCTCCTCCAGCCGGCCCAATCTGgtactctctc ... ggatcaacagGATTCTCGGTGATGTGTTCATGGGGGTATACCATACGGTGTTTGATTTCGG
EST: gi|169032351|gb|FE440908.1|FE440908
EST:     ATTAGTGGCTTTACAGGAATGGACGTCGCTCCTCCAGCCGGCCCACTCTG                         GATTCTCGGTGATGTGTTCATGGGGGTATACCATACGGTGTTTGATTTCGG
genomic: ATTAGTGGCTTTACAGGAATGGACGTCGCTCCTCCAGCCGGCCCAATCTGgtactctctc ... ggatcaacagGATTCTCGGTGATGTGTTCATGGGGGTATACCATACGGTGTTTGATTTCGG
EST: gi|169108565|gb|FE510780.1|FE510780
EST:     ATTAGTGGCTTTACAGGAATGGACGTCGCTCCTCCAGCCGTCCCAATCTG                         GATTCTCGGTGATGTGTTCATGGGGGTATACCATACGGTGTTTGATTTCGG
genomic: ATTAGTGGCTTTACAGGAATGGACGTCGCTCCTCCAGCCGGCCCAATCTGgtactctctc ... ggatcaacagGATTCTCGGTGATGTGTTCATGGGGGTATACCATACGGTGTTTGATTTCGG

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), 35 (downstream exon)
Score: 95

TACATCTTGCAAGTTGGAGAGGGAGCAGCGGCGCAGTGCATTAGTGGCTTTACAGGAATGGACGTCGCTCCTCCAGCCGGCCCAATCTGgtactctctc ... ggatcaacagGATTCTCGGTGATGTGTTCATGGGGGTATACCATACGGTGTTTGATTTCGGGAACAAACGCATTGGTTTCGCCAAGGCAGTCTGAAAAGACTCTTAATCG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttcgctgtagctctagtacttctttctaaagcgtttgatttgttggatcaacagGATTCTCGGTGATGTGTTCATGGGGGTATACCATACGGTGTTTGATTTCGGGAACAAACGCATTGGTTTCGCCAAGGCAGTCTGAAAAGACTCTTAATCG
                       tttctaaa  TA-rich tract