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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaagttctctcaatacatagaaaagctttgtttgaaaagatcttattcggttctgacatttgctgctcatgcagGGGTGCTCGTGCTGCTGTTTGGGAGAATTTCAAGGATAATCCTCTCTTTGACATCTCTACCGAGCACCCGATTACGTACTACGAGGACATGCAGCGAGCT

Basic information

species Selaginella moellendorffii
transcript EFJ25836
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ25836 (Selaginella moellendorffii), 3'ss of exon 3
lower sequence: LOC_Os01g70190.1 (Oryza sativa), 3'ss of exon 3
---------------gtaaagttctctcaatacata--gaaaagctttgtt--tgaaaagatcttattc---ggttctgac--atttgctgc---tcatgcagGGGTGCTCGTGCTGCTGTTTGGGAGAATTTCAAGGATAATCCTCTCTTTGACATCTCTACCGAGCACCCGATTACGTACTACGAGGACATGCAGCGAGCT
                |  | | | ||| || | |    | |||| |||||  ||||    | | |  |    ||  |||   |  ||||       |||||| ||||| |||||  | || |||||||| |||||| | |||||||| ||||||||||| || || |||||    || ||||||||||||||||||||  | 
gtgagcaccaagaacatgcaat-cactcgatgcttcctcataagcattgttgatgaattattgtaacccaaaagtcttgatgaacctgctttatgcaatgcagAGGTGCCCGTGCATCGGTGTGGGAGAACTTCAAGAACAATCCTCTTTTTGACATCTCCACAGACCACCCACCAACCTACTACGAGGACATGCAGCGTTCC

upper sequence: EFJ25836 (Selaginella moellendorffii), 3'ss of exon 3
lower sequence: LOC_Os01g70200.1 (Oryza sativa), 3'ss of exon 3
gtaaagttctc--------tcaatacatagaaaagctttgt--ttgaaaagatcttattcggttctgacatttgc---tgctcatgcagGGGTGCTCGTGCTGCTGTTTGGGAGAATTTCAAGGATAATCCTCTCTTTGACATCTCTACCGAGCACCCGATTACGTACTACGAGGACATGCAGCGAGCT
||||| ||  |         ||||||||   |     |  |  |||    |       | |  |||||  |||     ||  |   ||| ||||| || ||  | |||||||||||||||||| | || || || ||||||||||| ||||| |||||    ||||||||||| || |||||| || ||
gtaaattttccgcttatctccaatacatcctatcatctgctcattggctcgtagcatgtggagtctgatgtttctgtatgtcctatcagAGGTGCCCGCGCGTCGGTTTGGGAGAATTTCAAGAACAACCCGCTGTTTGACATCTCAACCGATCACCCACCCACGTACTACGAAGATATGCAGAGATCT

upper sequence: EFJ25836 (Selaginella moellendorffii), 3'ss of exon 3
lower sequence: GRMZM2G448834_T02 (Zea mays), 3'ss of exon 2
-------------------gtaaagttctctcaatac----------atagaaaagctttgtttgaaaagatcttattcggttctgacatttgctgctcatgcagGGGTGCTCGTGCTGCTGTTTGGGAGAATTTCAAGGATAATCCTCTCTTTGACATCTCTACCGAGCACCCGATTACGTACTACGAGGACATGCAGCGAGCT
                   ||  | | |   |||| |          |||| | |  ||| |||  | | ||   ||   | |  |    |       |||||||||| ||||| ||  | || |||||||| |||||||| || || || || |||||||| || |||||||||   ||||||||||||||||||||||| || 
gcaagtcaagtcggctccggtccattccatccaatgccaatgccaatatagtacatgtttatttatatatatgccat---ggttggtggatgatcatgcatgcagGGGCGCTCGCGCGTCGGTGTGGGAGAACTTCAAGGACAACCCGCTGTTCGACATCTCGACGGAGCACCCGTCGACGTACTACGAGGACATGCAGCGCGCC

upper sequence: EFJ25836 (Selaginella moellendorffii), 3'ss of exon 3
lower sequence: GRMZM5G898668_T01 (Zea mays), 3'ss of exon 3
----------------------gtaaagttctctcaatacatagaaaagctttgtttgaaaagatcttattcggttctgacatttgctgctcatgcagGGGTGCTCGTGCTGCTGTTTGGGAGAATTTCAAGGATAATCCTCTCTTTGACATCTCTACCGAGCACCCGATTACGTACTACGAGGACATGCAGCGAGCT
                      ||     | |||   |   ||  |  |  |  |  |       |||        | | || || || | |  ||||||| || || ||  | || |||||||| |||||| | || || ||||| |||||||| || || ||||||   |||||||||||||||||||||||  | 
gtaattaataaatcaactgtctgtctgtctgtctgtctgtctacgagtgagtgatccggcggcggcttccctcaaac-gtcacttacttc-cgcgcagGGGCGCACGCGCGTCGGTCTGGGAGAACTTCAAGAACAACCCGCTCTTCGACATCTCGACGGACCACCCGGCGACGTACTACGAGGACATGCAGCGCTCG

upper sequence: EFJ25836 (Selaginella moellendorffii), 3'ss of exon 3
lower sequence: GRMZM2G059845_T01 (Zea mays), 3'ss of exon 3
--------------------------------------------------gtaaagttctctcaatacatagaaaagctt----tgtttgaaaagatcttattcggttctgac-----atttgctgctca----tgcagGGGTGCTCGTGCTGCTGTTTGGGAGAATTTCAAGGATAATCCTCTCTTTGACATCTCTACCGAGCACCCGATTACGTACTACGAGGACATGCAGCGAGCT
                                                   | ||      ||| |   ||| ||  |||        ||    |  ||     |  | | ||      | | |  | ||    |||||||| || |||||  | || |||||||| |||||| | ||  | || || |||||||| || |||||||||   ||||||||||||||||||||||| || 
gtaccgtagtgctacgagcctgaactacctgacaaaggagtccttagtggatgaatcatcatcactgattagcaagtcttgacgcacctgcgctgcgctgccgtgcgtataactaactgtatacgacgcaacaatgcagGGGCGCCCGTGCGTCGGTGTGGGAGAACTTCAAGAACAACGCGCTGTTCGACATCTCGACGGAGCACCCGCCGACGTACTACGAGGACATGCAGCGCGCC

upper sequence: EFJ25836 (Selaginella moellendorffii), 3'ss of exon 3
lower sequence: GRMZM2G056702_T01 (Zea mays), 3'ss of exon 3
------------------gtaaagttctctcaata--catagaaaagct-ttgtttgaaaagatcttattcggtt--ctgacatttgctgctcatgcagGGGTGCTCGTGCTGCTGTTTGGGAGAATTTCAAGGATAATCCTCTCTTTGACATCTCTACCGAGCACCCGATTACGTACTACGAGGACATGCAGCGAGCT
                     | || ||   || |  | | ||  |||  |||  | |||   || |  |  | |  ||  | | | ||    ||||||||| || |||||  | || |||||||| |||||| | || || ||||| |||||||| || || |||||    ||||||||||||||||||||||| || 
gtacgtcgctaccttcattgcacgtcctaataacaagccttgatgagccattgaatcaaagagtcctgatgtgctacctaccgtatacttacaatgcagGGGCGCCCGTGCATCAGTCTGGGAGAACTTCAAGAACAACCCGCTCTTCGACATCTCAACGGACCACCCACCCACGTACTACGAGGACATGCAGCGTGCC

upper sequence: EFJ25836 (Selaginella moellendorffii), 3'ss of exon 3
lower sequence: GLYMA06G17140.1 (Glycine max), 3'ss of exon 3
-----------------------gtaaagttctctcaatacatagaaaagctttgtttgaa---aagatcttattcggttctgacatttgctgctcatgcagGGGTGCTCGTGCTGCTGTTTGGGAGAATTTCAAGGATAATCCTCTCTTTGACATCTCTACCGAGCACCCGATTACGTACTACGAGGACATGCAGCGAGCT
                        | | | | ||  |  | |  ||| | |  |   |||     | | || |  | |     || ||||   || |  ||| |||||  | || || || |||||||| || ||||| ||||| || |||||||| || || ||||| || |  || ||||||||||||||||| ||||||
tgcatgaagtttggttccatgtcttgatgctttcataccaaaacgaataacaataaatgatcctgaaagctcaaactgactgtacttttgtatctta--cagAGGTGCCAGAGCAGCAGTGTGGGAGAACTTTAAGGACAATCCACTGTTTGACATTTCCACAGAGCATCCAACAACATACTACGAGGACATGCAACGAGCT

upper sequence: EFJ25836 (Selaginella moellendorffii), 3'ss of exon 3
lower sequence: Vv17s0000g00120.t01 (Vitis vinifera), 3'ss of exon 3
--------------gtaaagttctctcaatacat---agaaaagctttgtttgaaaagatctt---attcggttctgacatttgctg----ctcatgcagGGGTGCTCGTGCTGCTGTTTGGGAGAATTTCAAGGATAATCCTCTCTTTGACATCTCTACCGAGCACCCGATTACGTACTACGAGGACATGCAGCGAGCT
               | || || ||  |  |  |   | |  |  ||| |   || |  | ||   || |   | |    |||  ||     |  ||||| || || || || ||||| ||||||||||| || || ||||| || ||||||||||| || |||||||| || || || || ||||||||||| || |||
attgttttttgttccttaatttgtccaatgatctttaatatgaaatttatgccaagatgttttttaatccaactttttttttttttggacatttttgcagAGGCGCACGGGCAGCTGTGTGGGAGAATTTTAAAGACAATCCACTTTTTGACATCTCAACAGAGCACCCAATGACTTATTATGAGGACATGCAACGGGCT

upper sequence: EFJ25836 (Selaginella moellendorffii), 3'ss of exon 3
lower sequence: Vv01s0150g00180.t01 (Vitis vinifera), 3'ss of exon 3
----------------------gtaaagttctctcaat-acatagaaaagctttgtttgaaaagatcttattcggttctgacatttgctgctcat--gcagGGGTGCTCGTGCTGCTGTTTGGGAGAATTTCAAGGATAATCCTCTCTTTGACATCTCTACCGAGCACCCGATTACGTACTACGAGGACATGCAGCGAGCT
                        |  | | | ||  | | ||        || | |||||   |||  | ||   ||| ||  ||     | ||   ||| |||||  | || || ||||||||||| || ||||| || || |||||||||||||| || |||||||| |  || || || || |||||||| || |||
aggaagcaacatcttgtatgatacatggctttgtcttttatattaggtcctttgggttgaatgaatca-actcctatctaactcttttaattgattgacagAGGTGCAAGGGCAGCAGTTTGGGAGAACTTTAAGGACAACCCGCTCTTTGACATCTCCACTGAGCACCCAACGACATATTATGAAGACATGCAACGTGCT

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), 34 (downstream exon)
Score: 34

CCCATCTCATCCCACCGAGCATACCGCGCTCTATCTTCGTCTACTTTCGGGGTCTTTTCTATGACTACGGCAACGATCCGGAAGGAGGCTACTACGCAAGgtaaagttct ... gctcatgcagGGGTGCTCGTGCTGCTGTTTGGGAGAATTTCAAGGATAATCCTCTCTTTGACATCTCTACCGAGCACCCGATTACGTACTACGAGGACATGCAGCGAGCT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gaaaagctttgtttgaaaagatcttattcggttctgacatttgctgctcatgcagGGGTGCTCGTGCTGCTGTTTGGGAGAATTTCAAGGATAATCCTCTCTTTGACATCTCTACCGAGCACCCGATTACGTACTACGAGGACATGCAGCGAGCT
                               ttctgac  putative branch site (score: 34)
           tttgaaaa  TA-rich tract