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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttactgctattttcttcacgttaaatgttttctaacaccaagctccactacagAGTACTGCTGTTGAAGGTACCATACAGCAGCTTTTCGAAGGCCATCATATGAATTATATTGAATGCATCAATGTGGACTATAAGTCCACTCGAAAGGAAT

Basic information

species Selaginella moellendorffii
transcript EFJ14291
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ14291 (Selaginella moellendorffii), 3'ss of exon 4
lower sequence: LOC_Os01g56490.1 (Oryza sativa), 3'ss of exon 6
-------gtttactgctattttcttcacgttaa------atgttt------tctaacaccaagctc-cactacagAGTACTGCTGTTGAAGGTACCATACAGCAGCTTTTCGAAGGCCATCATATGAATTATATTGAATGCATCAATGTGGACTATAAGTCCACTCGAAAGGAAT
        |||| |  | || | |  | | |||       |||||      | ||  || |  ||| |  | ||| | ||| |||| ||||| || || || ||||| || ||||| |||||||||||||||||||| ||||| ||||| ||||| || || ||  | || ||||
gttggacatttatttttgttatatgtaagataataaatagtgtttcatcaatgtacaactactctctcgattcagGGAACTACTGTGGAAGGGACAATTCAACAGCTATTTGAAGGTCATCATATGAATTATATTGAGTGCATTAATGTTGACTACAAATCTACAAGGAAAGAAT

upper sequence: EFJ14291 (Selaginella moellendorffii), 3'ss of exon 4
lower sequence: GLYMA14G04890.1 (Glycine max), 3'ss of exon 6
-----------------------------------gtttactgctattttcttcacgttaaatgttttctaacaccaagctccactacagAGTACTGCTGTTGAAGGTACCATACAGCAGCTTTTCGAAGGCCATCATATGAATTATATTGAATGCATCAATGTGGACTATAAGTCCACTCGAAAGGAAT
                                    |||  ||  ||    |      |  ||| |   ||      |  |   ||  || | |||| |||||| || || |||||| |||| || ||||| ||||||||||||||||| ||||||||||||||||||||||| || ||| ||||||| |
gtaaaggattatctttggactttcgtacaaaaacatttttgtggaataccgtctcaaattcatgatgatta-tgttcattttgtctttagGGAACTGTTGTTGAGGGAACTATACAGAAGCTATTTGAAGGGCATCATATGAATTATATCGAATGCATCAATGTGGACTATAAATCAACTAGAAAGGAGT

upper sequence: EFJ14291 (Selaginella moellendorffii), 3'ss of exon 4
lower sequence: GLYMA02G43930.1 (Glycine max), 3'ss of exon 6
------------------------------------gtttactgctattttcttcacgttaaatgttttctaacaccaagctccactacagAGTACTGCTGTTGAAGGTACCATACAGCAGCTTTTCGAAGGCCATCATATGAATTATATTGAATGCATCAATGTGGACTATAAGTCCACTCGAAAGGAAT
                                     |||  ||  ||  | |      |  ||| |   ||     ||  |   ||  || | |||| |||||| || || |||||| || | || ||||| ||||||||||| ||||| ||||||||||||||||||||||| || ||| ||||||| |
gtaaaggatgatctttggatgttttgtacacaaacatttttgtggaatactgtctcaaattcatgatgatta-tgttaattttgtctttagGGAACTGTTGTTGAGGGAACTATACAGAAGTTATTTGAAGGGCATCATATGAACTATATCGAATGCATCAATGTGGACTATAAATCAACTAGAAAGGAGT

upper sequence: EFJ14291 (Selaginella moellendorffii), 3'ss of exon 4
lower sequence: GLYMA20G11300.1 (Glycine max), 3'ss of exon 6
-------------------------gtttactgctattttct--------tcacgttaaatgttttctaacaccaagctccactacagAGTACTGCTGTTGAAGGTACCATACAGCAGCTTTTCGAAGGCCATCATATGAATTATATTGAATGCATCAATGTGGACTATAAGTCCACTCGAAAGGAAT
                         ||| |    | || |          |||    ||||| ||  |   |      |   || |||   |||| |||||| || || |||||  || | || ||||| || ||||||||||| ||||||||||||||||| ||||| || || ||| ||||||| |
gtatggcaagagatttggaatgtttgttcatgattcttcttgatgagtgatcataccaaatggttgttg-tatgttatttttcttcagGAAACTGTTGTTGAGGGAACTATACAAAAGTTATTTGAAGGACACCATATGAATTACATTGAATGCATCAATGTAGACTACAAATCAACTAGAAAGGAGT

upper sequence: EFJ14291 (Selaginella moellendorffii), 3'ss of exon 4
lower sequence: GLYMA10G23680.1 (Glycine max), 3'ss of exon 2
-------------------------------------------------------------gtttactgctattttcttcacgttaaatgttttctaacaccaagctccactacagAGTACTGCTGTTGAAGGTACCATACAGCAGCTTTTCGAAGGCCATCATATGAATTATATTGAATGCATCAATGTGGACTATAAGTCCACTCGAAAGGAAT
                                                             || || |  |||  | |        | | |||  |                 ||| | |||| ||| ||||| || ||||||||  | || ||||| || |||||||| |||||||||||||| |||||||| ||||| || ||  | || ||||
gtactggtttttcatgatggctcttattgtcttcttaaaatagcttttactctagatacttgtgtatttttatgatgtcttgaaagattatttgttggggtttcatcttggc-cagGGAACTGTTGTGGAAGGCACTATACAGCAATTGTTTGAAGGACACCATATGAACTATATTGAATGCATAAATGTGGATTATAAATCAACAAGGAAAGAAT

upper sequence: EFJ14291 (Selaginella moellendorffii), 3'ss of exon 4
lower sequence: GLYMA13G16170.1 (Glycine max), 3'ss of exon 6
-------------------------gtttactgctattttct--------tcacgttaaatg-ttttctaacaccaagctccactacagAGTACTGCTGTTGAAGGTACCATACAGCAGCTTTTCGAAGGCCATCATATGAATTATATTGAATGCATCAATGTGGACTATAAGTCCACTCGAAAGGAAT
                         ||| |    |||| |           ||  | ||||| || | |      |   |   || ||| | |||| |||||| || ||||||||  |  | || ||||| || ||||||||||| || |||||||||||||| ||||| || || ||| ||||||| |
gtatggcaagagttttggaatatttgttcatgattattcttgatgggtgaccatatcaaatggttgttttgtgtta--tttgtcttcagGGAACTGTTGTTGAGGGAACCATACAAAAATTATTTGAAGGGCACCATATGAATTACATAGAATGCATCAATGTAGACTACAAATCAACTAGAAAGGAGT

upper sequence: EFJ14291 (Selaginella moellendorffii), 3'ss of exon 4
lower sequence: Vv13s0073g00610.t01 (Vitis vinifera), 3'ss of exon 6
-----------------------------gtttactgctattttcttcacgtt----aaatgttt---tctaacaccaagctccacta---cagAGTACTGCTGTTGAAGGTACCATACAGCAGCTTTTCGAAGGCCATCATATGAATTATATTGAATGCATCAATGTGGACTATAAGTCCACTCGAAAGGAAT
                             |  | | |   || |   || |||    ||||  ||   | | |     |  |  | |    ||| | |||| ||| || ||||| ||||||||| | || ||||| || |||||||| |||||||||||||| |||||||||||||| || ||  |||||||||
gtataggcgcttaacattgccacttgttggacttcagtgcttataagcaagtttgggaaatcattaaatttgattgttatttttaatggctcagGGAACTGTTGTGGAGGGTACTATACAGCAGTTATTTGAAGGGCACCATATGAACTATATTGAATGCATTAATGTGGACTATAAATCAACAAGAAAGGAAT

upper sequence: EFJ14291 (Selaginella moellendorffii), 3'ss of exon 4
lower sequence: Vv06s0009g00960.t01 (Vitis vinifera), 3'ss of exon 6
----gtttactgctattttcttcacgttaaatgttttctaacaccaa---gctccactacagAGTACTGCTGTTGAAGGTACCATACAGCAGCTTTTCGAAGGCCATCATATGAATTATATTGAATGCATCAATGTGGACTATAAGTCCACTCGAAAGGAAT
        |   || || |  |    |||  |   |||| |||   |     | |    ||| | |||| ||| || || || ||||||||| | || ||||| || |||||||| || ||||||||||||||||||||||| || || ||  | ||||| |
gtacaaacatgactgttgttgtggaattatttcagttctgacaattattaagtgcttgccagGGAACTGTTGTGGAGGGCACTATACAGCAGTTATTTGAAGGGCACCATATGAACTACATTGAATGCATCAATGTGGACTACAAATCTACAAGGAAGGAGT

upper sequence: EFJ14291 (Selaginella moellendorffii), 3'ss of exon 4
lower sequence: Vv08s0032g00600.t01 (Vitis vinifera), 3'ss of exon 6
-----------------------gtttactgctattttcttcacgttaaatgttttctaacaccaagctccactacagAGTACTGCTGTTGAAGGTACCATACAGCAGCTTTTCGAAGGCCATCATATGAATTATATTGAATGCATCAATGTGGACTATAAGTCCACTCGAAAGGAAT
                       | || | |   |||||       | || ||||| ||     |   | |   |||| | ||||  || || || || ||||||||| | || ||||| || |||||||| || ||||| ||||||||||||||||| || || ||  |||||||||
gtatatgaggtttaacagctgcagctttcagtatttttcactgttctgaa-gttttttatt-ttatattactggacagGGAACTGTAGTGGAGGGGACAATACAGCAGTTGTTTGAAGGGCACCATATGAACTACATTGAGTGCATCAATGTGGACTACAAATCTACAAGAAAGGAAT

upper sequence: EFJ14291 (Selaginella moellendorffii), 3'ss of exon 4
lower sequence: PP1S104_2V6.1 (Physcomitrella patens), 3'ss of exon 6
----------------------------------------gtttactgctattttcttcacgt-taaatgttttctaacaccaagctcc-act---acagAGTACTGCTGTTGAAGGTACCATACAGCAGCTTTTCGAAGGCCATCATATGAATTATATTGAATGCATCAATGTGGACTATAAGTCCACTCGAAAGGAAT
                                          ||| ||   ||   |  |  | | |    | |  ||   | |  ||| |||     || | || || || || || || |||||  | ||||| ||||||||||||||||||||||| |||||||||||||| || | |||||||||||| ||||| |
gcgttctcggcgttgtggcggttgttgtgcgcgtgaattcagttattgtgcttgggtcaatttgtgagaagtctaaaatttcgatttccgacttacgtagGGCACGGCAGTGGAGGGGACGATACAAAATCTTTTTGAAGGCCATCATATGAATTATATCGAATGCATCAATGTCGATTTTAAGTCCACTCGGAAGGAGT

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|169082131|gb|FE486470.1|FE486470
EST:     TGCAAGAATTGAACCGTGTTTTGTGCGAGAAGCTGGAGGATAAGATGAAG                         AGTACTGCTGTTGAAGGTACCATACAGCAGCTTTTCGAAGGCCATCATATG
genomic: TGCAAGAATTGAACCGTGTTTTGTGCGAGAAGCTGGAGGATAAGATGAAGgtttactgct ... tccactacagAGTACTGCTGTTGAAGGTACCATACAGCAGCTTTTCGAAGGCCATCATATG
EST: gi|169031425|gb|FE437135.1|FE437135
EST:     TGCAAGAATTGAACCGTGTTTTGTGCGAGAAGCTGGAGGATAAGATGAAG                         AGTACTGCTGTTGAAGGTACCATACAGCAGCTTTTCGAAGGCCACCATATG
genomic: TGCAAGAATTGAACCGTGTTTTGTGCGAGAAGCTGGAGGATAAGATGAAGgtttactgct ... tccactacagAGTACTGCTGTTGAAGGTACCATACAGCAGCTTTTCGAAGGCCATCATATG
EST: gi|169032748|gb|FE437775.1|FE437775
EST:     TGCAAGAATTGAACCGTGTTTTGTGCGAGAAGCTGGAGGATAAGATGAAG                         AGTACTGCTGTTGAAGGTACCATACAGCAGCTTTTCGAAGGCCACCATATG
genomic: TGCAAGAATTGAACCGTGTTTTGTGCGAGAAGCTGGAGGATAAGATGAAGgtttactgct ... tccactacagAGTACTGCTGTTGAAGGTACCATACAGCAGCTTTTCGAAGGCCATCATATG

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: 30 (upstream exon), 35 (downstream exon)
Score: 14

GACTAGATCGTTTGGTTGGGATACGTACGATTCGTTTATGCAGCATGATGTGCAAGAATTGAACCGTGTTTTGTGCGAGAAGCTGGAGGATAAGATGAAGgtttactgct ... tccactacagAGTACTGCTGTTGAAGGTACCATACAGCAGCTTTTCGAAGGCCATCATATGAATTATATTGAATGCATCAATGTGGACTATAAGTCCACTCGAAAGGAAT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtttactgctattttcttcacgttaaatgttttctaacaccaagctccactacagAGTACTGCTGTTGAAGGTACCATACAGCAGCTTTTCGAAGGCCATCATATGAATTATATTGAATGCATCAATGTGGACTATAAGTCCACTCGAAAGGAAT
                               ttctaac  putative branch site (score: 14)
                                            ctccact  putative PPT
                      ttaaatgttttctaa  TA-rich tract
















Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtttactgctattttcttcacgttaaatgttttctaacaccaagctccactacagAGTACTGCTGTTGAAGGTACCATACAGCAGCTTTTCGAAGGCCATCATATGAATTATATTGAATGCATCAATGTGGACTATAAGTCCACTCGAAAGGAAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA