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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtcttggctttcacttggacatagatttctatttcttagtggtgtttctggcagATTTGTGGAGATCATGGCTCCGGTGTTTTCCAGGAATGCTTGGAGATGCGTGTGGCATATGATACAAAACGATTTGGTACACGGTTGGGGCCTCGACTTC

Basic information

species Selaginella moellendorffii
transcript EFJ06933
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ06933 (Selaginella moellendorffii), 3'ss of exon 9
lower sequence: GLYMA19G08270.1 (Glycine max), 3'ss of exon 9
-----------------------------------gtaagtcttggctttcacttggacatagatttcta-------tttcttagtggtgtttctggcagATTTGTGGAGATCATGGCTCCGGTGTTTTCCAGGAATGCTTGGAGATGCGTGTGGCATATGATACAAAACGATTTGGTACACGGTTGGGGCCTCGACTTC
                                   || ||  |        |      || |  | ||||       |||   | | |   || |  ||||||||| |||||||||||||| || ||||||||  |||| ||| | || |||||||| ||||||||                                  
acttaataacatgcacctttctttctttctgtcttgtgagcttctaaagggatcatatcaaatgtatctaacatagctttgacacttgaaattttctcagATTTGTTGAGATCATGGCTCCTGTATTTTCCAGAGATGCATGGCGTTGTGTGTGGCACATGATACAG---------------------------------

upper sequence: EFJ06933 (Selaginella moellendorffii), 3'ss of exon 9
lower sequence: AT1G13000.2 (Arabidopsis thaliana), 3'ss of exon 10
----gtaagtcttggctttcact---tggacatagatttctat----ttcttagtggtgt------ttctggcagATTTGTGGAGATCATGGCTCCGGTGTTTTCCAGGAATGCTTGGAGATGCGTGTGGCATATGATACAAAACGATTTGGTACACGGTTGGGGCCTCGACTTC
    |||          |||| |      |||||||| | ||      ||||  |    |      ||||  ||| ||| | ||||| |||||||| || || || ||  |||| ||| | ||||||||||||||||| || ||||||||||| ||||||||||| || || |||
gtacgtagtctcaaatgttcattacaaaaacatagatctatacagtactcttgattccatgtaatattcttacagGTTTATAGAGATTATGGCTCCAGTATTCTCAAGAGATGCATGGCGTTGCGTGTGGCATATGATTCAGAACGATTTGGTTCACGGTTGGGGTCTTGATTTC

upper sequence: EFJ06933 (Selaginella moellendorffii), 3'ss of exon 9
lower sequence: AT1G67850.2 (Arabidopsis thaliana), 3'ss of exon 10
---------------------------------gtaagtcttggctttcacttggacatag--atttctatttcttagtggtgtttctg---gcagATTTGTGGAGATCATGGCTCCGGTGTTTTCCAGGAATGCTTGGAGATGCGTGTGGCATATGATACAAAACGATTTGGTACACGGTTGGGGCCTCGACTTC
                                 ||  || ||  | |  |   |||  ||   | |        || |||   ||       ||||||| || |||||||||||||| || ||||| || ||||| ||| |||||||||||||| |||| ||                                  
gtatgtagaagcctttctttttacccgttttgagttggtttttccctataacaggaactaaccagtatcgaacttttgtgtcattcaaaaatgcagATTCGTAGAGATCATGGCTCCTGTATTTTCAAGAAATGCCTGGCGATGCGTGTGGCATGTGATCCAG---------------------------------

upper sequence: EFJ06933 (Selaginella moellendorffii), 3'ss of exon 9
lower sequence: PP1S129_53V6.1 (Physcomitrella patens), 3'ss of exon 10
---------------------------------------------------------gtaagtcttggctttcacttggacat-agatttctatttcttagtggtgtttctggcagATTTGTGGAGATCATGGCTCCGGTGTTTTCCAGGAATGCTTGGAGATGCGTGTGGCATATGATACAAAACGATTTGGTACACGGTTGGGGCCTCGACTTC
                                                         ||     ||  || ||  || |   |  | | | || |||||  |  |  | ||| ||||||||| |||||||||||||| ||||||||  | || || ||| | ||| | ||| | || |||||                                  
gtaataagtcaacctgtatttagttagtgattcgtgtcttaccttcctcctttggtcgttgaaatttactgtctgttagttgttgggtatttacttcttgtt--taatactg-cagATTTGTTGAGATCATGGCTCCTGTGTTTTCACGAAAAGCATGGCGTTGCATCTGGTACATAATACAG---------------------------------

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|169033291|gb|FE441605.1|FE441605
EST:     GAAAGGCCAGGATGGTGCGCAGACGGTCCGGAAAAGCCACCTTGTGCTGC                         ATTTGTGGAGATCATGGCTCCGGTGTTTTCCAGGAATGCTTGGAGATGCGT
genomic: GAAAGGCCAGGATGGTGCGCAGACGGTCCGGAAAAGCCACCTTGTGCTGCgtaagtcttg ... tttctggcagATTTGTGGAGATCATGGCTCCGGTGTTTTCCAGGAATGCTTGGAGATGCGT




















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: 33 (upstream exon), 35 (downstream exon)
Score: 5

GGACGCTGAGGAAAGGCCAGGATGGTGCGCAGACGGTCCGGAAAAGCCACCTTGTGCTGCgtaagtcttg ... tttctggcagATTTGTGGAGATCATGGCTCCGGTGTTTTCCAGGAATGCTTGGAGATGCGTGTGGCATATGATACAAAACGATTTGGTACACGGTTGGGGCCTCGACTTC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agtcttggctttcacttggacatagatttctatttcttagtggtgtttctggcagATTTGTGGAGATCATGGCTCCGGTGTTTTCCAGGAATGCTTGGAGATGCGTGTGGCATATGATACAAAACGATTTGGTACACGGTTGGGGCCTCGACTTC
                                           tgtttct  CT-rich tract
                     atagatttctattt  TA-rich tract