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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtagattttcttttttctttttcccaatgcttccctgagttgacgacgaatttgccagGAACTCGACTACCTCGATGGAGCCGTGTCGAATCCTAAAAGACCATTTGCTGCCATCGTTGGAGGCTCCAAGGTGTCGTCCAAGATTGGAGTGATTGAAT

Basic information

species Selaginella moellendorffii
transcript EFJ26731
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ26731 (Selaginella moellendorffii), 3'ss of exon 5
lower sequence: LOC_Os06g45710.1 (Oryza sativa), 3'ss of exon 4
--------------------------------------gtagattttct----tttttctttttcccaatgcttccctgagttgacgacgaatttgccagGAACTCGACTACCTCGATGGAGCCGTGTCGAATCCTAAAAGACCATTTGCTGCCATCGTTGGAGGCTCCAAGGTGTCGTCCAAGATTGGAGTGATTGAAT
                                        ||||||| |    | | |  |  |   ||   ||    |           |     | ||||||| ||||| || | |||||| ||  | || || |||| ||||||||||||||| ||||| || |||||||||||  | |||||||| ||||||||  
ttaaattgtatccgcaatgaattcaagctgtttttccttgagattttttgaaatatgtaatccttttaaaattttgtagtaactgtcctcaccaatctagGAACTTGACTATCTTGTTGGAGCTGTTGCCAACCCCAAAAAACCATTTGCTGCCATTGTTGGTGGATCCAAGGTGTCAACAAAGATTGGGGTGATTGAGA

upper sequence: EFJ26731 (Selaginella moellendorffii), 3'ss of exon 5
lower sequence: LOC_Os05g41640.3 (Oryza sativa), 3'ss of exon 3
-------------------------------------------------------------------------------gtagattttcttttttctttttcccaatgc----ttc----cctga--gttgacgacgaatttgc----cagGAACTCGACTACCTCGATGGAGCCGTGTCGAATCCTAAAAGACCATTTGCTGCCATCGTTGGAGGCTCCAAGGTGTCGTCCAAGATTGGAGTGATTGAAT
                                                                               |||   |||||||| | |      ||||      |||    ||| |  ||| |  |  |||||      ||||| || |||||||| | |||||| || || |  |||||| | ||||||||||||||||| || || || |||||||| ||||||||||| || || ||||
gttactaccgtttcaccttacattttcaagtctgatgcttgaaatttttgaaagctatacctagaccagaaattttagagtaccctttcttttctttcaaaaacaatataaagttctgagcctcaatgtttatcattaatttaaatcacagGAGCTTGACTACCTTGTTGGAGCTGTTTCAAGCCCTAAACGCCCATTTGCTGCCATCGTGGGTGGTTCAAAGGTGTCATCCAAGATTGGGGTTATCGAAT

upper sequence: EFJ26731 (Selaginella moellendorffii), 3'ss of exon 5
lower sequence: GRMZM2G083016_T01 (Zea mays), 3'ss of exon 5
-------------------------------------------------------------------------------------------------------gtagattttcttttttctttttcccaatgcttccctg----agttgacgacg--aatttgccagGAACTCGACTACCTCGATGGAGCCGTGTCGAATCCTAAAAGACCATTTGCTGCCATCGTTGGAGGCTCCAAGGTGTCGTCCAAGATTGGAGTGATTGAAT
                                                                                                        ||  ||  ||||   ||   || ||||     |||     | || || |    ||||||| |||| || |||||||| |  ||||| || || |  |||| | | ||||||||||||||||| || || || |||||||| |||||||| || || |||||||
gttatatttctttttctatgtttacatgttccattttgtaacatagaaactatgaaagatggcatcaaagaaaaacaatgctacataaaacagaaaatagcgattattttcactttcccctcaatctcaatctgatccttttatatttaacaaaatcaatttgc-agGAGCTTGACTACCTTGTCGGAGCTGTTTCAAGCCCTACACGCCCATTTGCTGCCATCGTGGGTGGTTCAAAGGTGTCATCCAAGATCGGGGTTATTGAAT

upper sequence: EFJ26731 (Selaginella moellendorffii), 3'ss of exon 5
lower sequence: GRMZM2G089136_T02 (Zea mays), 3'ss of exon 3
------------------------------------------gtagattttcttttttcttttt--cccaatgcttccctgagttg-acgacgaatttgccagGAACTCGACTACCTCGATGGAGCCGTGTCGAATCCTAAAAGACCATTTGCTGCCATCGTTGGAGGCTCCAAGGTGTCGTCCAAGATTGGAGTGATTGAAT
                                            |||    | |  ||  | |    |  || |||   |   |   |  |  ||||||| |||||||||||||||| |  ||||| || || |  |||||| | || |||||||||||||| || || || |||||||| |||||||| || || ||||| |
gttatctctctatgtctacatgttccattttgtaactctatgaaagacgcccctccttgatctcaatctgatccttttatatctaataaaatcaatttgc-agGAACTCGACTACCTTGTCGGAGCTGTTTCAAGCCCTAAACGCCCTTTTGCTGCCATCGTGGGTGGTTCAAAGGTGTCATCCAAGATCGGGGTTATTGAGT

upper sequence: EFJ26731 (Selaginella moellendorffii), 3'ss of exon 5
lower sequence: GLYMA08G17600.1 (Glycine max), 3'ss of exon 4
--------------------------------------------gtagattttcttttttctttttcccaatgcttccctgagttgacgacgaatttg--ccagGAACTCGACTACCTCGATGGAGCCGTGTCGAATCCTAAAAGACCATTTGCTGCCATCGTTGGAGGCTCCAAGGTGTCGTCCAAGATTGGAGTGATTGAAT
                                            || |  |   || | |  |||   || |   | | |  |||        | |||   |||||||| ||||| || | |||||| ||||| || || || |||||||||||||| |||||||| || || |||||||| |||||||||||||| ||||| |
gtttgtaggaactaggaagtaattgttagcttcattatatgaatgttgggtaatttatgtaatttatgcagtttattcatctgttatttgtttaattgtttcagGAACTTGACTATCTAGTTGGAGCTGTGTCAAACCCCAAGAGACCATTTGCTGCTATCGTTGGTGGGTCAAAGGTGTCTTCCAAGATTGGAGTTATTGAGT

upper sequence: EFJ26731 (Selaginella moellendorffii), 3'ss of exon 5
lower sequence: GLYMA15G41540.1 (Glycine max), 3'ss of exon 3
----------------------------------------gtagattt--tcttttttctttttcccaatgcttccctgagttgacgacgaatttgccagGAACTCGACTACCTCGATGGAGCCGTGTCGAATCCTAAAAGACCATTTGCTGCCATCGTTGGAGGCTCCAAGGTGTCGTCCAAGATTGGAGTGATTGAAT
                                        | | ||||  ||  |     |  |   ||   ||       |  |      || |   ||||||| || ||||| | ||| || || || |  || ||||| |||||||||||||| ||||| || |||||||| || || || |||||||||||||| |
tcaaggaaatgccatttttcattttttaaggaaattatatgcatatttgatcaatcaatatcataataactatttttcacatgcatttttcatgttttagGAACTTGATTACCTTGTTGGGGCGGTATCAAGCCCCAAAAGGCCATTTGCTGCCATTGTTGGTGGTTCCAAGGTCTCATCTAAAATTGGAGTGATTGAGT

upper sequence: EFJ26731 (Selaginella moellendorffii), 3'ss of exon 5
lower sequence: GLYMA15G41550.1 (Glycine max), 3'ss of exon 4
-------------------------------------gtagattttcttttttctttttcccaatgcttc-cctgagttgacgacgaatttgccagGAACTCGACTACCTCGATGGAGCCGTGTCGAATCCTAAAAGACCATTTGCTGCCATCGTTGGAGGCTCCAAGGTGTCGTCCAAGATTGGAGTGATTGAAT
                                      | |  |   | | |  ||| | |   || ||   ||||  |       | | |  ||||| || || || || | ||| || ||||| || || || |||||||||||||| || || || || || |||||||| |||||||||||||| |||||||
gtttgtaggaagtaattgttagcttcattatatatatattgggtaattatgtaatttatacagttgattgatctgatgtatttttaattgtttcagGAGCTTGATTATCTAGTTGGGGCTGTGTCAAACCCCAAGAGACCATTTGCTGCTATTGTCGGTGGATCGAAGGTGTCTTCCAAGATTGGAGTTATTGAAT

upper sequence: EFJ26731 (Selaginella moellendorffii), 3'ss of exon 5
lower sequence: GLYMA08G17610.1 (Glycine max), 3'ss of exon 3
------------------------------------------gtagattttcttttttctttttcccaatgcttccctgagttgacgacgaatttgccagGAACTCGACTACCTCGATGGAGCCGTGTCGAATCCTAAAAGACCATTTGCTGCCATCGTTGGAGGCTCCAAGGTGTCGTCCAAGATTGGAGTGATTGAAT
                                           |  || ||   |     |  |   ||   ||       |  | |    || |   ||||||| || ||||| | ||| || || || || || ||||| |||||||||||||| ||||| || ||||| || || || || |||||||||||||| |
aaggaaacgtcattttttcatttttttatttattgaaattatatgtatatttgatcaatatcataataactatttttcacatatatgctttatgttttagGAACTTGATTACCTTGTTGGGGCAGTATCAAACCCCAAAAGGCCATTTGCTGCCATTGTTGGTGGTTCCAAAGTCTCATCTAAAATTGGAGTGATTGAGT

upper sequence: EFJ26731 (Selaginella moellendorffii), 3'ss of exon 5
lower sequence: AT1G56190.1 (Arabidopsis thaliana), 3'ss of exon 3
------------------------------------------gtagattttcttttttctttttcccaatgcttccctgagttgacgacgaatttgccagGAACTCGACTACCTCGATGGAGCCGTGTCGAATCCTAAAAGACCATTTGCTGCCATCGTTGGAGGCTCCAAGGTGTCGTCCAAGATTGGAGTGATTGAAT
                                           |  |||   || |   |||      |  |     ||  |     |   ||||  |||||  | |||||||| | ||| || || || || || || ||||||||||||||||| || ||||| |||||||| || || ||||||||||| || ||||
ttcaataggtttctcaactgcaatttggaggagtccattgacttgaattgagttatgagtttgaattgaatcacatttggttatcttatatatttcgcagGAGTTGGACTACCTTGTTGGTGCGGTTTCAAACCCAAAGAGACCATTTGCTGCCATTGTGGGAGGTTCCAAGGTCTCATCTAAGATTGGAGTTATCGAAT

upper sequence: EFJ26731 (Selaginella moellendorffii), 3'ss of exon 5
lower sequence: AT3G12780.1 (Arabidopsis thaliana), 3'ss of exon 3
---------------------------gtagattttcttttttctttttcccaatgcttccctgagttgacgacgaatttgcc-----------agGAACTCGACTACCTCGATGGAGCCGTGTCGAATCCTAAAAGACCATTTGCTGCCATCGTTGGAGGCTCCAAGGTGTCGTCCAAGATTGGAGTGATTGAAT
                             ||  ||      |  ||  | | |||| | || |||  |        | ||  |           ||||||| |||||||| | ||| || || || || || || ||||||||||| ||||| || || || ||||| || || |||||||||||||| |||||||
gtaatattttgatagagattattctattcagcattgaagcatcgttgctacaaatggtaccatgaactttttgtttacttctctctacctctatagGAACTGGACTACCTAGTTGGTGCTGTTTCAAACCCAAAGAGACCATTTGCAGCCATAGTGGGTGGTTCCAAAGTCTCATCCAAGATTGGAGTTATTGAAT

upper sequence: EFJ26731 (Selaginella moellendorffii), 3'ss of exon 5
lower sequence: Vv19s0085g00370.t01 (Vitis vinifera), 3'ss of exon 3
--------------------------------gtagattttcttttttctt-----tttcccaatgcttccctgagttgacgacgaatttgc-----cagGAACTCGACTACCTCGATGGAGCCGTGTCGAATCCTAAAAGACCATTTGCTGCCATCGTTGGAGGCTCCAAGGTGTCGTCCAAGATTGGAGTGATTGAAT
                                 ||| ||||||||| | |       |||     | || | |||  | ||      |||        ||||||| |||||||| | |||||| ||||| || || || || ||||||||||| || ||||| ||||| |||||||| || || ||||||||||||||||
cttaatgtatgaagtccaaatagtggctacacctaggttttcttttgtttagaatacttctttgagtttacttgacataacatttgttttctggttttagGAACTTGACTACCTTGTTGGAGCTGTGTCAAACCCCAAGAGGCCATTTGCTGCAATTGTTGGTGGCTCGAAGGTGTCATCGAAAATTGGAGTGATTGAAT

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|169074110|gb|FE483512.1|FE483512
EST:     TCCTC-TGCAAAAG                         GAGCTCGACTACCCT-GATGGAGCTGTGTCGAATCCTAAACGACCATTTGC
genomic: TCCTCTTGCAAAAGgtagattttc ... aatttgccagGAACTCGACTA-CCTCGATGGAGCCGTGTCGAATCCTAAAAGACCATTTGC
EST: gi|169097219|gb|FE498454.1|FE498454
EST:     ACCAAGTTCCTCAAGCCCTCCGTGGCTGGATTCCTCTTGCAAAAG                         GAACTCGACTACCTCGATGGAGCCGTGTCGAATCCTAAAAGACCATTTGCT
genomic: ACCAAGTTCCTCAAGCCCTCCGTGGCTGGATTCCTCTTGCAAAAGgtagattttc ... aatttgccagGAACTCGACTACCTCGATGGAGCCGTGTCGAATCCTAAAAGACCATTTGCT
EST: gi|169110216|gb|FE511624.1|FE511624
EST:     GCGTGACCAAGTTCCTCAAGCCCTCCGTGGCTGGATTCCTCTTGCAAAAG                         GAGCTCGACTACCTTGATGGAGCTGTGTCGAATCCTAAACGACCATTTGCT
genomic: GCGTGACCAAGTTCCTCAAGCCCTCCGTGGCTGGATTCCTCTTGCAAAAGgtagattttc ... aatttgccagGAACTCGACTACCTCGATGGAGCCGTGTCGAATCCTAAAAGACCATTTGCT
EST: gi|169065045|gb|FE475117.1|FE475117
EST:     GCGTGACCAAGTTCCTCAAGCCCTCCGTGGCTGGATTCCTCTTGCAAAAG                         GAACTCGACTACCTCGATGGAGCCGTGTCGAATCCTAAAAGACCATTTGCT
genomic: GCGTGACCAAGTTCCTCAAGCCCTCCGTGGCTGGATTCCTCTTGCAAAAGgtagattttc ... aatttgccagGAACTCGACTACCTCGATGGAGCCGTGTCGAATCCTAAAAGACCATTTGCT
EST: gi|169037059|gb|FE442706.1|FE442706
EST:     GCGTGACCAAGTTCCTCAAGCCCTCCGTGGCTGGATTCCTCTTGCAAAAG                         GAACTCGACTACCTCGATGGAGCCGTGTCGAATCCTAAAAGACCATTTGCT
genomic: GCGTGACCAAGTTCCTCAAGCCCTCCGTGGCTGGATTCCTCTTGCAAAAGgtagattttc ... aatttgccagGAACTCGACTACCTCGATGGAGCCGTGTCGAATCCTAAAAGACCATTTGCT
EST: gi|169071658|gb|FE476580.1|FE476580
EST:     GCGTGACCAAGTTCCTCAAGCCCTCCGTGGCTGGATTCCTCTTGCAAAAG                         GAACTCGACTACCTCGATGGAGCCGTGTCGAATCCTAAAAGACCATTTGCT
genomic: GCGTGACCAAGTTCCTCAAGCCCTCCGTGGCTGGATTCCTCTTGCAAAAGgtagattttc ... aatttgccagGAACTCGACTACCTCGATGGAGCCGTGTCGAATCCTAAAAGACCATTTGCT
EST: gi|169081223|gb|FE489265.1|FE489265
EST:     GCGTGACCAAGTTCCTCAAGCCCTCCGTGGCTGGATTCCTCTTGCAAAAG                         GAGCTCGACTACCTTGATGGAGCTGTGTCGAATCCTAAACGACCATTTGCT
genomic: GCGTGACCAAGTTCCTCAAGCCCTCCGTGGCTGGATTCCTCTTGCAAAAGgtagattttc ... aatttgccagGAACTCGACTACCTCGATGGAGCCGTGTCGAATCCTAAAAGACCATTTGCT

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: 58

CGTGAACGATGCTTTTGGTACCGCTCACAGAGCTCATGCTTCTACCGAGGGCGTGACCAAGTTCCTCAAGCCCTCCGTGGCTGGATTCCTCTTGCAAAAGgtagattttc ... aatttgccagGAACTCGACTACCTCGATGGAGCCGTGTCGAATCCTAAAAGACCATTTGCTGCCATCGTTGGAGGCTCCAAGGTGTCGTCCAAGATTGGAGTGATTGAAT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gattttcttttttctttttcccaatgcttccctgagttgacgacgaatttgccagGAACTCGACTACCTCGATGGAGCCGTGTCGAATCCTAAAAGACCATTTGCTGCCATCGTTGGAGGCTCCAAGGTGTCGTCCAAGATTGGAGTGATTGAAT
                                  agttgac  putative branch site (score: 58)
     tcttttttcttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtagattttcttttttctttttcccaatgcttccctgagttgacgacgaatttgccagGAACTCGACTACCTCGATGGAGCCGTGTCGAATCCTAAAAGACCATTTGCTGCCATCGTTGGAGGCTCCAAGGTGTCGTCCAAGATTGGAGTGATTGAAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGGAG