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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTACTGCAAGTGCGAGATGCCTTACAACCCGGATGATCTTATGGTGCAGTGTGAGGAGTGCAAAGACTGgtaagaatcagtttctctcaaatccaaaagccttggcagcctccgatgaaaaaaatggcag

Basic information

species Selaginella moellendorffii
transcript EFJ26805
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ26805 (Selaginella moellendorffii), 5'ss of exon 3
lower sequence: LOC_Os09g21770.1 (Oryza sativa), 5'ss of exon 3
GTACTGCAAGTGCGAGATGCCTTACAACCCGGATGATCTTATGGTGCAGTGTGAGGAGTGCAAAGACTGgtaagaatcagtttctctcaaatccaaaagccttggcagcctccgatgaaaaaaatggcag------------------------------------------
||||||||||||||||||||| || |||||||||||||| ||||||||||| ||||  ||||| |||||||||  |||| ||     ||     |     | |  | || || |    |   || || |                                           
GTACTGCAAGTGCGAGATGCCGTATAACCCGGATGATCTAATGGTGCAGTGCGAGGGATGCAAGGACTGgtaa--atcacttggggacatccttacctttcata-ctgcatctggctgaccgaagggtatttcatgcccgtcatttttaggaggaagtatcatagactcagt

upper sequence: EFJ26805 (Selaginella moellendorffii), 5'ss of exon 3
lower sequence: LOC_Os08g32620.2 (Oryza sativa), 5'ss of exon 2
-------------------------------GTACTGCAAGTGCGAGATGCCTTACAACCCGGATGATCTTATGGTGCAGTGTGAGGAGTGCAAAGACTGgta---------agaatcagtttctctca-aatccaaa--agccttggcagc----ctccgatgaaaaaa-atggcag----------------------
                                ||||||||||| |||||||| ||||||||||||||||| ||||||||||| || || ||||| ||||||||         | || | |  ||| | |  || ||    || ||    ||      | |  || ||||  |||| |                       
TGCTTGTGTTTTCTTTTTCGTTTTTCTGAAGATACTGCAAGTGTGAGATGCCATACAACCCGGATGATCTCATGGTGCAGTGCGATGACTGCAAGGACTGgtaattccattaataaaccgcctctgttatgatgcatttcagtctatatagtgaatgtacactggaaaatcatggtaacaataatgaaattggcacccat

upper sequence: EFJ26805 (Selaginella moellendorffii), 5'ss of exon 3
lower sequence: LOC_Os08g32620.1 (Oryza sativa), 5'ss of exon 3
GTACTGCAAGTGCGAGATGCCTTACAACCCGGATGATCTTATGGTGCAGTGTGAGGAGTGCAAAGACTGgtaag---------aatcagtttctctca-aatccaaa--agccttggcagcc----tccgatgaaaaaa-atggcag----------------------
 ||||||||||| |||||||| ||||||||||||||||| ||||||||||| || || ||||| |||||||||          || | |  ||| | |  || ||    || ||    ||      | |  || ||||  |||| |                       
ATACTGCAAGTGTGAGATGCCATACAACCCGGATGATCTCATGGTGCAGTGCGATGACTGCAAGGACTGgtaattccattaataaaccgcctctgttatgatgcatttcagtctatatagtgaatgtacactggaaaatcatggtaacaataatgaaattggcacccat

upper sequence: EFJ26805 (Selaginella moellendorffii), 5'ss of exon 3
lower sequence: GRMZM2G091265_T03 (Zea mays), 5'ss of exon 2
-------------------------------GTACTGCAAGTGCGAGATGCCTTACAACCCGGATGATCTTATGGTGCAGTGTGAGGAGTGCAAAGACTGgtaagaatcagt---------------ttctctcaaatccaaaagccttggcagcctccgatg-aaaaaaatggcag-----------------------
                                || |||||||| |||||||| |||||||||||||| || |||||||||||||| |  ||||| ||||||||| |  | ||               ||||| ||       | |  |||  ||      ||  |  |||||  | |                       
TGATCTTATGTGACATTGTTTGTATGTGAAGATATTGCAAGTGTGAGATGCCGTACAACCCGGATGACCTCATGGTGCAGTGTGAAGGATGCAAGGACTGgtaaaatcctgtgaaaactccacacttttctcccattagtgcatgttttgagaggggtttatctagtaaaatcactgtgaaatggctccacattttgccc

upper sequence: EFJ26805 (Selaginella moellendorffii), 5'ss of exon 3
lower sequence: GRMZM2G091265_T05 (Zea mays), 5'ss of exon 3
GTACTGCAAGTGCGAGATGCCTTACAACCCGGATGATCTTATGGTGCAGTGTGAGGAGTGCAAAGACTGgtaagaatcagt---------------ttctctcaaatccaaaagccttg-gcagcctccgatgaaaaaaatggcag-----------------------
 || |||||||| |||||||| |||||||||||||| || |||||||||||||| |  ||||| ||||||||| |  | ||               ||||| ||       | |  ||| |  |  |      |  |||||  | |                       
ATATTGCAAGTGTGAGATGCCGTACAACCCGGATGACCTCATGGTGCAGTGTGAAGGATGCAAGGACTGgtaaaatcctgtgaaaactccacacttttctcccattagtgcatgttttgagaggggtttatctagtaaaatcactgtgaaatggctccacattttgccc

upper sequence: EFJ26805 (Selaginella moellendorffii), 5'ss of exon 3
lower sequence: GRMZM2G091265_T01 (Zea mays), 5'ss of exon 3
GTACTGCAAGTGCGAGATGCCTTACAACCCGGATGATCTTATGGTGCAGTGTGAGGAGTGCAAAGACTGgtaagaatcagt---------------ttctctcaaatccaaaagccttggcagcc-tccgatgaaaaaaatggcag-----------------------
          || |||||||| |||||||||||||| || |||||||||||||| |  ||||| ||||||||| |  | ||               ||||| ||       | |  |||  ||   |      |  |||||  | |                       
----------TGTGAGATGCCGTACAACCCGGATGACCTCATGGTGCAGTGTGAAGGATGCAAGGACTGgtaaaatcctgtgaaaactccacacttttctcccattagtgcatgttttgagaggggtttatctagtaaaatcactgtgaaatggctccacattttgccc

upper sequence: EFJ26805 (Selaginella moellendorffii), 5'ss of exon 3
lower sequence: GRMZM2G119357_T01 (Zea mays), 5'ss of exon 3
GTACTGCAAGTGCGAGATGCCTTACAACCCGGATGATCTTATGGTGCAGTGTGAGGAGTGCAAAGACTGgtaa----gaatcagtttctctcaaatccaaaagccttggca---gcctccgatgaaaaaaatggcag--------------------------------
||| ||||| || |||||||| |||||||||||||| || ||||||||||| || |  ||||| ||||||||     |  ||| |   | |||| |   |   |  ||  |   ||||  | | |    | |    |                                
GTATTGCAAATGTGAGATGCCATACAACCCGGATGACCTCATGGTGCAGTGCGAAGCTTGCAAGGACTGgtacatttgtctcaatgattttcaatttacatttcactgatatttgcctttgttcagtctattttatgcttctacaaagcaaatgctttaaatctctgga

upper sequence: EFJ26805 (Selaginella moellendorffii), 5'ss of exon 3
lower sequence: GLYMA13G34740.1 (Glycine max), 5'ss of exon 3
GTACTGCAAGTGCGAGATGCCTTACAACCCGGATGATCTTATGGTGCAGTGTGAGGAGTGCAAAGACTGgtaagaatcagtttctctcaaatccaaaagcct-tggcagcctccgatgaaaaaaatggcag---------------------------------------
||| |||||||||||||||||||| ||||| ||||| || |||||||||||||||| |||||| || |||||| || |||| | |      |      |  |   |      |   ||  |    |    |                                       
GTATTGCAAGTGCGAGATGCCTTATAACCCAGATGACCTCATGGTGCAGTGTGAGGGGTGCAAGGATTGgtaa-aaccagtatattctgcttttttttgtttactgttattacatttgtgagtggtttttggttgtctggttctctaattttagcattagatgcgttgtt

upper sequence: EFJ26805 (Selaginella moellendorffii), 5'ss of exon 3
lower sequence: GLYMA12G35680.2 (Glycine max), 5'ss of exon 3
GTACTGCAAGTGCGAGATGCCTTACAACCCGGATGATCTTATGGTGCAGTGTGAGGAGTGCAAAGACTGgtaagaatcagtttctctcaaatccaaaagccttggcagcctccgatgaaaaaaatggcag----------------------------------------
||| |||||||||||||||||||| ||||| ||||| || |||||||||||||||| |||||| || |||||| |  |||| | |      | |          |      |   ||  |    |    |                                        
GTATTGCAAGTGCGAGATGCCTTATAACCCAGATGACCTCATGGTGCAGTGTGAGGGGTGCAAGGATTGgtaa-agccagtgtattctgctttctttgtttactgttattacatttgtgagtggtttttggatgtccgggtctctaattttagcattagatgcgttgttt

upper sequence: EFJ26805 (Selaginella moellendorffii), 5'ss of exon 3
lower sequence: GLYMA06G34850.1 (Glycine max), 5'ss of exon 2
GTACTGCAAGTGCGAGATGCCTTACAACCCGGATGATCTTATGGTGCAGTGTGAGGAGTGCAAAGACTGgtaagaatcagtttctctcaaatccaaaagccttgg---cagcctccgatgaaaaaaatggcag------------------------------------
||| ||||| || ||||||||||| |||||||||||||| ||||| || ||||| | |||||| || |||||||| || |||| |    | |      |  | |      |  |  | | |   |  ||| |                                     
GTATTGCAAATGTGAGATGCCTTATAACCCGGATGATCTCATGGTACAATGTGAAGGGTGCAAGGATTGgtaagactcggtttattctgatttactttgtttggagtttggattttgtttatgtatgtggaatttgagaaatagatgttatttactgggttgaagggat

upper sequence: EFJ26805 (Selaginella moellendorffii), 5'ss of exon 3
lower sequence: GLYMA12G20180.1 (Glycine max), 5'ss of exon 3
GTACTGCAAGTGCGAGATGCCTTACAACCCGGATGATCTTATGGTGCAGTGTGAGGAGTGCAAAGACTGgtaagaatcagt---ttctctcaaatccaaaagccttggcagcctccgatgaaaaaaatggcag------------------------------------
||| ||||| || ||||||||||| |||||||||||||| ||||| || ||||| | |||||| || |||||||| || ||   ||||     |       |  ||       |  ||      |  | ||                                      
GTATTGCAAATGTGAGATGCCTTATAACCCGGATGATCTCATGGTACAATGTGAAGGGTGCAAGGATTGgtaagactcggtgtattctgctttactttgttgtgttattgtgtttggagtttggattttgcttatttaggtgtttgtttatgtatgtggaatttgagaa

upper sequence: EFJ26805 (Selaginella moellendorffii), 5'ss of exon 3
lower sequence: GLYMA06G01180.2 (Glycine max), 5'ss of exon 2
GTACTGCAAGTGCGAGATGCCTTACAACCCGGATGATCTTATGGTGCAGTGTGAGGAGTGCAAAGACTGgtaagaatca--------gtttctctcaaatccaaaagccttggcagc--ctccgatgaaaaaaatggcag-----------------------------
||| || || || ||||||||||||||||| ||||| || |||||||| || ||||  ||||  ||||||||||  |||        ||     | |  | |||     |   |  |  ||| | ||       |                                  
GTATTGTAAATGTGAGATGCCTTACAACCCTGATGACCTAATGGTGCAATGCGAGGGCTGCACTGACTGgtaagtttcacatgtaaggtgatatttatcttcaatttattccacgtctgctctgttgttttgttttatgtttctgtatctgttccattttctggactct

upper sequence: EFJ26805 (Selaginella moellendorffii), 5'ss of exon 3
lower sequence: GLYMA04G01140.1 (Glycine max), 5'ss of exon 3
GTACTGCAAGTGCGAGATGCCTTACAACCCGGATGATCTTATGGTGCAGTGTGAGGAGTGCAAAGACTGgtaagaatcagtttctctcaaatccaaaagccttggcagcctccgatgaaaaaaatggcag-----------------------------------------
||| || || || ||||||||||||||||| ||||| || ||||| || |||||||  ||||  ||||||||||  | | | | |           || | ||       |||| ||       ||                                             
GTATTGTAAATGTGAGATGCCTTACAACCCTGATGACCTAATGGTCCAATGTGAGGGCTGCACTGACTGgtaagt-tgaatatgtaaggtgatattaatctttaatttattccg-tgtctgccctgttgttttgttttatgtttctggactctggtatgttcagttctgta

upper sequence: EFJ26805 (Selaginella moellendorffii), 5'ss of exon 3
lower sequence: AT4G22140.2 (Arabidopsis thaliana), 5'ss of exon 3
GTACTGCAAGTGCGAGATGCCTTACAACCCGGATGATCTTATGGTGCAGTGTGAGGAGTGCAAAGACTGgtaagaatcagtttctctcaaatccaaaag---ccttggcagcctccgatgaaaaaaatggcag-----------------------------------------------------------------------
||||||||| || || ||||||||||| || || ||||| |||||||||||||| |  |||||||||||||||   |   | | | ||   |  |  |    ||||    |  |   |  | ||||  | |                                                                         
GTACTGCAAATGTGAAATGCCTTACAATCCAGACGATCTCATGGTGCAGTGTGAAGGCTGCAAAGACTGgtaaatgttgatatttgtcttttttattaacttccttacttgtgtttcaacagaaaagagactatatgtctgtttttaaacttacgtattcttttccaggaattattgataataagcattaattcgctgttgtag

upper sequence: EFJ26805 (Selaginella moellendorffii), 5'ss of exon 3
lower sequence: Vv10s0116g00160.t01 (Vitis vinifera), 5'ss of exon 3
GTACTGCAAGTGCGAGATGCCTTACAACCCGGATGATCTTATGGTGCAGTGTGAGGAGTGCAAAGACTGgtaagaatcagtttctctcaaa-tccaaaagccttggcagcctccgatgaaaaaaatggcag-----------------------------------------
||| ||||| |||||||||||||| ||||| |||||||||||||| ||||| |||| |||||| |||||||||    | | || | | |   |      |  ||  | |     | ||       || ||                                          
GTATTGCAAATGCGAGATGCCTTATAACCCAGATGATCTTATGGTCCAGTGCGAGGGGTGCAAGGACTGgtaa---cctgcttttgttattcttttgttgggtttccggttgttgttgtgttttgtgtcatttcagttttgtatctgattttgtaaaaacatggaaactcaa

upper sequence: EFJ26805 (Selaginella moellendorffii), 5'ss of exon 3
lower sequence: Vv03s0038g00160.t01 (Vitis vinifera), 5'ss of exon 3
GTACTGCAAGTGCGAGATGCCTTACAACCCGGATGATCTTATGGTGCAGTGTGAGGAGTGCAAAGACTGgtaaga-atcagtttctctcaaatccaaaagccttggcagc--ctccgatgaaaaaaatggcag------------------------------------
||| || || |||||||||||||||||||| ||||| || |||||||||||||||| |||||  || |||| ||  ||  | ||    |   |  || |   || |   |   |  | || | | | |    |                                    
GTATTGTAAATGCGAGATGCCTTACAACCCCGATGACCTAATGGTGCAGTGTGAGGGGTGCACTGATTGgtgagttatttgctttggacctgtttaagattttttgtctcaggtttggtggacagattctttgtaacttgatttggattgttcctcagaatatactttt

upper sequence: EFJ26805 (Selaginella moellendorffii), 5'ss of exon 3
lower sequence: Vv12s0059g01180.t01 (Vitis vinifera), 5'ss of exon 3
GTACTGCAAGTGCGAGATGCCTTACAACCCGGATGATCTTATGGTGCAGTGTGAGGAGTGCAAAGACTGgtaagaat----ca-gtttctctcaaatccaaaagccttggcagcc--tccgatgaaaaaaatggcag--------------------------------
||| || ||||||||||||||||| || ||||| || |||||||||||||| || |  ||||| ||||||||    |    ||  ||| |      | ||        |  | |   ||  | ||||  |||| |                                  
GTATTGTAAGTGCGAGATGCCTTATAATCCGGACGACCTTATGGTGCAGTGCGAAGGATGCAAGGACTGgtatacttgttgcatattttttatttgttcagttatgcggaaaactaatcaaaagaaattaatgccctgtacatttgtgaggttttggttttaaatattg

upper sequence: EFJ26805 (Selaginella moellendorffii), 5'ss of exon 3
lower sequence: PP1S171_11V6.1 (Physcomitrella patens), 5'ss of exon 3
GTACTGCAAGTGCGAGATGCCTTACAACCCGGATGATCTTATGGTGCAGTGTGAGGAGTGCAAAGACTGgtaaga---------atcagtttctctcaaatccaaaagccttg------gcagcctccg--atgaaaaaaatggcag----------------------
|||||| ||||||||||||||||||||||| ||  || | ||| || | ||  |    ||||||||||||| |||          ||  |||| ||||      ||   |||       || || || |  ||||   ||||  ||                       
GTACTGTAAGTGCGAGATGCCTTACAACCCCGACCATGTGATGCTGGAATGCAACAGTTGCAAAGACTGgtgagacttcgttgcgtccttttcgctcatcattgaattacttctcagctgcggcttctgttatgacgcaaatctcacatgcgtgaagtatcctccatgt

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: 32 (upstream exon), 28 (downstream exon)
Score: 14

GTACTGCAAGTGCGAGATGCCTTACAACCCGGATGATCTTATGGTGCAGTGTGAGGAGTGCAAAGACTGgtaagaatca ... aaaatggcagGTTTCATCCATCTTGCATCGGACTGCCGGTGGATCAAGTGAAGAAGATGGAGAGCTACTACTGCCCGGATTGCTCTCCGCAAGCACAAGACAAGTCCAAG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTACTGCAAGTGCGAGATGCCTTACAACCCGGATGATCTTATGGTGCAGTGTGAGGAGTGCAAAGACTGgtaagaatcagtttctctcaaatccaaaagccttggcagcctccgatgaaaaaaatggcag

- - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAAG