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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgggaagtttgtgtgctttgtcttgcattctacgcctaaaacttgatattgcagGCGTATCTCTTCAATGACTACTGGGAAGACATTGGAACTATTAAGTCGTTTTTTGACGCTAATCTCGCTCTCACTGCTCAG

Basic information

species Selaginella moellendorffii
transcript EFJ23417
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ23417 (Selaginella moellendorffii), 3'ss of exon 10
lower sequence: LOC_Os03g52460.1 (Oryza sativa), 3'ss of exon 9
------------------------------------------------------------------------------------------------------------------------------------------------gtgggaagtttgtgtgctttgtcttg----cattctacgcctaaaacttgatattgcagGCGTATCTCTTCAATGACTACTGGGAAGACATTGGAACTATTAAGTCGTTTTTTGACGCTAATCTCGCTCTCACTGCTCAG
                                                                                                                                                ||  |||  | |  |      |||      || |     |||| ||||    ||||||||| ||||| |||||||| |||||||||||||| |||||||| || || || ||||| || |||||  ||||  |||  |||
gtaaggatttaacataataagttccatttggtagtgttctctaatattgcactattggcatcagatttacacaaatttattcaataataatactgcatatgtatgatgtattatttattttcttacaatcaacttcagtatcatgtcagaaactagccttgaacatctcaggcacagttgtaacctagaactc---attgcagGCATATCTTTTCAATGATTACTGGGAAGACATAGGAACTATAAAATCATTCTTTGAAGCCAATCTTTCTCTTGCTGAACAG

upper sequence: EFJ23417 (Selaginella moellendorffii), 3'ss of exon 10
lower sequence: GRMZM2G391936_T01 (Zea mays), 3'ss of exon 5
------------------------------------gtgggaagtttgtgt----gctttgtcttgcattctacgcctaaaactt-----gatattgcagGCGTATCTCTTCAATGACTACTGGGAAGACATTGGAACTATTAAGTCGTTTTTTGACGCTAATCTCGCTCTCACTGCTCAG
                                    ||    |   ||  |       |||||    | |||   | | | | |      || ||| ||||| ||||| |||||||| ||||||||||| ||||||||||||||||| || ||||| || || || |||||  |||  |||
actatttgaagacaggcatatcaccatcttagttatgtattcatcctgcctcataatcttgtcccaaaatcttgacttgatattatgatggacatttcagGCTTATCTTTTCAATGATTACTGGGAAGATATTGGAACTATTAAGTCCTTCTTTGAGGCAAACCTTGCTCTTGCTGAACAG

upper sequence: EFJ23417 (Selaginella moellendorffii), 3'ss of exon 10
lower sequence: GLYMA17G01900.1 (Glycine max), 3'ss of exon 9
-----------------------gtgggaagtttgtgtgctt-tgtcttgcattctacgcctaaaacttgatattgcagGCGTATCTCTTCAATGACTACTGGGAAGACATTGGAACTATTAAGTCGTTTTTTGACGCTAATCTCGCTCTCACTGCTCAG
                       |  ||||  || | ||||| ||  || | |     |  | | | ||  ||| |||||| |||||||||||||| |||||||||||||| || ||||| |  || || || || || ||||| || |||||||  || 
gtatgactggaaaaaagcattaaggaggaatcttttttgcttatgatttacctatggtg--tgacaatttgtat-gcagGCTTATCTCTTCAATGATTACTGGGAAGACATAGGGACTATCAGATCCTTCTTCGAGGCAAATCTTGCCCTCACTGAGCAT

upper sequence: EFJ23417 (Selaginella moellendorffii), 3'ss of exon 10
lower sequence: GLYMA07G38820.2 (Glycine max), 3'ss of exon 9
----------------------gtgggaagtttgtgtgctttgtcttgcattctacgcctaaaacttgatattgcagGCGTATCTCTTCAATGACTACTGGGAAGACATTGGAACTATTAAGTCGTTTTTTGACGCTAATCTCGCTCTCACTGCTCAG
                          | | | | | ||| |  |  |  |  |   |  | | | ||  ||| |||||| ||||| |||||||| |||||||||||||| || ||||| |  || || ||||| || ||||| || |||||||  || 
gtatgactggaaaagatcattacaaaggaatctttttgcat-atgatttacccacggtgtgacaatttgtat-gcagGCTTATCTATTCAATGATTACTGGGAAGACATAGGTACTATCAGATCATTCTTTGAGGCAAATCTTGCCCTCACTGAGCAT

upper sequence: EFJ23417 (Selaginella moellendorffii), 3'ss of exon 10
lower sequence: AT5G19220.1 (Arabidopsis thaliana), 3'ss of exon 9
-------------------gtgggaagtttgtgtgctttgtcttgcattctac--gcctaaaacttgatatt----gcagGCGTATCTCTTCAATGACTACTGGGAAGACATTGGAACTATTAAGTCGTTTTTTGACGCTAATCTCGCTCTCACTGCTCAG
                        |  |||  || |  || ||  | || ||       | |||  ||| ||    |||||| |||||||| ||||||||||||||||| || ||||| || |  || || || || || ||||| || |||||||  || 
gtcagtaacattcatattaagcacacatttaagtccaatgactaacgttatatcaagggataacaagattttttgagcagGCTTATCTCTTTAATGACTACTGGGAAGATATAGGAACAATAAGATCTTTCTTCGAGGCGAATCTTGCACTCACTGAGCAT

upper sequence: EFJ23417 (Selaginella moellendorffii), 3'ss of exon 10
lower sequence: PP1S389_5V6.1 (Physcomitrella patens), 3'ss of exon 8
-----------------------------------gtgggaagtttgtgtgctttgtcttgcattctacgcctaa-aact---tgatattg------cagGCGTATCTCTTCAATGACTACTGGGAAGACATTGGAACTATTAAGTCGTTTTTTGACGCTAATCTCGCTCTCACTGCTCAG
                                    || || |||  | | ||   ||     |   |     || ||||   | ||| ||      ||||||||  | || |||||||| |||||||| |||||||| |||||||| || ||||| || ||| | |||||||||||||||
ccaaccttcagatttatagaagattctagatcttcttgagacgttactattctagttcaaaagtgtgagatgcaataactcattaatactgtttgtgcagGCGTACTTGTTTAATGACTATTGGGAAGATATTGGAACCATTAAGTCCTTCTTTGATGCCAATTTAGCTCTCACTGCTCAG

upper sequence: EFJ23417 (Selaginella moellendorffii), 3'ss of exon 10
lower sequence: PP1S347_12V6.1 (Physcomitrella patens), 3'ss of exon 7
-----------------------------------------------gtgggaagtttgtgtgctttgtcttgcattctacgcctaaaacttgatattgcagGCGTATCTCTTCAATGACTACTGGGAAGACATTGGAACTATTAAGTCGTTTTTTGACGCTAATCTCGCTCTCACTGCTCAG
                                                | || || |||      || |||  ||||  |    |     ||| | | |||||| ||| | ||||||||||||||||| || |||||||| || ||||| || ||||| |||||| | ||||| ||| |||||
gcccctgtccatcttatccaaaatttggtgagcatcagctattagttcttggcagattgcagaaattatctgccattaaaattttgt--tttgttttcgcagGCATATTTGTTCAATGACTACTGGGAGGATATTGGAACCATCAAGTCTTTCTTTGATGCTAATTTAGCTCTTACTTCTCAG

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|169019237|gb|FE428150.1|FE428150
EST:     ACTTTGGCTCGGAGATCATTCCCGCTGCAGCGAGCGAGTACAATGTTCAG                         GCGTATCTCTTCAATGACTACTGGGAAGACATTGGAACTATTAAGTCGTTT
genomic: ACTTTGGCTCGGAGATCATTCCCGCTGCAGCGAGCGAGTACAATGTTCAGgtgggaagtt ... gatattgcagGCGTATCTCTTCAATGACTACTGGGAAGACATTGGAACTATTAAGTCGTTT
EST: gi|169034358|gb|FE443131.1|FE443131
EST:     ACTTTGGCTCGGAGATCATTCCCGCTGCAGCGAGCGAGTACAATGTTCAG                         GCGTATCTCTTCAATGACTACTGGGAAGACATTGGAACTATTAAGTCGTTT
genomic: ACTTTGGCTCGGAGATCATTCCCGCTGCAGCGAGCGAGTACAATGTTCAGgtgggaagtt ... gatattgcagGCGTATCTCTTCAATGACTACTGGGAAGACATTGGAACTATTAAGTCGTTT
EST: gi|169065579|gb|FE474832.1|FE474832
EST:     ACTTTGGCTCGGAGATCATTCCCGCTGCAGCGAGCGAGTACAATGTTCAG                         GCGTATCTCTTCAATGACTACTGGGAAGACATTGGAACTATTAAGTCGTTT
genomic: ACTTTGGCTCGGAGATCATTCCCGCTGCAGCGAGCGAGTACAATGTTCAGgtgggaagtt ... gatattgcagGCGTATCTCTTCAATGACTACTGGGAAGACATTGGAACTATTAAGTCGTTT
EST: gi|169034359|gb|FE443132.1|FE443132
EST:     ACTTTGGCTCGGAGATCATTCCCGCTGCAGCGAGCGAGTACAATGTTCAG                         GCGTATCTCTTCAATGACTACTGGGAAGACATTGGAACTATTAAGTCGTTT
genomic: ACTTTGGCTCGGAGATCATTCCCGCTGCAGCGAGCGAGTACAATGTTCAGgtgggaagtt ... gatattgcagGCGTATCTCTTCAATGACTACTGGGAAGACATTGGAACTATTAAGTCGTTT
EST: gi|169074270|gb|FE481930.1|FE481930
EST:     ACTTTGGCTCGGAGATCATTCCCGCTGCAGCGAGCGAGTACAATGTTCAG                         GCGTATCTCTTCAATGACTACTGGGAAGACATTGGAACTATTAAGTCGTTT
genomic: ACTTTGGCTCGGAGATCATTCCCGCTGCAGCGAGCGAGTACAATGTTCAGgtgggaagtt ... gatattgcagGCGTATCTCTTCAATGACTACTGGGAAGACATTGGAACTATTAAGTCGTTT
EST: gi|169040800|gb|FE447851.1|FE447851
EST:     ACTTTGGCTCGGAGATCATTCCCGCTGCAGCGAGCGAGTACAATGTTCAG                         GCGTATCTCTTCAATGACTACTGGGAAGACATTGGAACTATTAAGTCGTTT
genomic: ACTTTGGCTCGGAGATCATTCCCGCTGCAGCGAGCGAGTACAATGTTCAGgtgggaagtt ... gatattgcagGCGTATCTCTTCAATGACTACTGGGAAGACATTGGAACTATTAAGTCGTTT

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: 37

ATGGCGGTATCCTACCTCTAATGACTTTGGCTCGGAGATCATTCCCGCTGCAGCGAGCGAGTACAATGTTCAGgtgggaagtt ... gatattgcagGCGTATCTCTTCAATGACTACTGGGAAGACATTGGAACTATTAAGTCGTTTTTTGACGCTAATCTCGCTCTCACTGCTCAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtgggaagtttgtgtgctttgtcttgcattctacgcctaaaacttgatattgcagGCGTATCTCTTCAATGACTACTGGGAAGACATTGGAACTATTAAGTCGTTTTTTGACGCTAATCTCGCTCTCACTGCTCAG
                                     taaaacttgatatt  TA-rich tract