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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTTCCAGGCTGAGATCAACCAGCTTCTCAGTCTCATCATCAACACTTTCTACAGCAACAAGGAGATTTTCTTGCGGGAGCTCATCAGCAATGCCTCGGATgtgagtatttcgcctcgttcttccagttcttgtcaaactctttcttcttctcatgctgcgctgctgtgactccag

Basic information

species Selaginella moellendorffii
transcript EFJ17594
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ17594 (Selaginella moellendorffii), 5'ss of exon 1
lower sequence: LOC_Os09g30412.1 (Oryza sativa), 5'ss of exon 1
GTTCCAGGCTGAGATCAACCAGCTTCTCAGTCTCATCATCAACACTTTCTACAGCAACAAGGAGATTTTCTTGCGGGAGCTCATCAGCAATGCCTCGGATgtgagtattt--cgcctc---gttcttccagttcttgtc---------aaactctttcttcttctcatgctgcgctgctgtgactccag------------
 |||||||| |||||||||||||| ||    |||||||||||||| ||||||  |||||||||||| ||| | || |||||||||  |||  |||| ||||| ||| |    |||| |     |    |   ||| |||         |||    | |||  |    |||| |  ||||||   |  |             
CTTCCAGGCCGAGATCAACCAGCTGCTGTCCCTCATCATCAACACCTTCTACTCCAACAAGGAGATCTTCCTCCGCGAGCTCATCTCCAACTCCTCCGATgtaagtttgcgccgcccccgaaattaatcccctctcgtcgaggaatcgaaatcggtgcttgcttatgtgct-ctttgctgttgttgtacgcgtcgatctgt

upper sequence: EFJ17594 (Selaginella moellendorffii), 5'ss of exon 1
lower sequence: LOC_Os08g39140.2 (Oryza sativa), 5'ss of exon 1
GTTCCAGGCTGAGATCAACCAGCTTCTCAGTCTCATCATCAACACTTTCTACAGCAACAAGGAGATTTTCTTGCGGGAGCTCATCAGCAATGCCTCGGATgtgagtatt-tcgcctcgttcttccagttct-----------tgtcaaa----ctctttcttcttctcat-gctgcgctgctgtgact--ccag------
 |||||||| |||||||||||||| ||    |||||||||||||| ||||||  |||||||||||| ||| | || |||||||||  |||  |||| ||||| |||    |||  |   |  | ||| |||            || | |    || ||| ||  ||  || | |     | | ||     |||       
CTTCCAGGCGGAGATCAACCAGCTGCTGTCGCTCATCATCAACACGTTCTACTCCAACAAGGAGATCTTCCTCCGCGAGCTCATCTCCAACTCCTCCGATgtaagtgccctcggtttactggttcagatctgcacgcgcgcgcgttagaagggcttttttttggtccgattggtagatcggtttgttcacccaatctggt

upper sequence: EFJ17594 (Selaginella moellendorffii), 5'ss of exon 1
lower sequence: GRMZM2G012631_T01 (Zea mays), 5'ss of exon 1
GTTCCAGGCTGAGATCAACCAGCTTCTCAGTCTCATCATCAACACTTTCTACAGCAACAAGGAGATTTTCTTGCGGGAGCTCATCAGCAATGCCTCGGATgtgagtatttcgcctcgttcttccagttcttgtcaaactctttcttcttctcatgctgcgctgctgtgactccag-----------------------------
 |||||||| |||||||||||||| |||   |||||||||||||| ||||||  |||||||||||| ||| |  |||||||||||  |||  |||| |||||||||   |   | || ||  ||||     | |    || |||||||     ||| |   |   || |    ||                             
CTTCCAGGCGGAGATCAACCAGCTGCTCTCGCTCATCATCAACACCTTCTACTCCAACAAGGAGATCTTCCTCAGGGAGCTCATCTCCAACTCCTCCGATgtgagtgggtt-tcacgctcccccagac---ggcccgatcgttcttctctctttgcggttttaaagttaaaatagactactacgtagactagatctgtgcgcta

upper sequence: EFJ17594 (Selaginella moellendorffii), 5'ss of exon 1
lower sequence: GRMZM2G069651_T04 (Zea mays), 5'ss of exon 1
GTTCCAGGCTGAGATCAACCAGCTTCTCAGTCTCATCATCAACACTTTCTACAGCAACAAGGAGATTTTCTTGCGGGAGCTCATCAGCAATGCCTCGGATgtgagt--atttcgcc---tcgttcttccagttcttgtcaaactctttcttcttct----catgctgcgctgc--tgtgactccag--------------
 || |||||||||||||||||||| |||   |||||||||||||| |||||   |||||||||||| ||| | |||||||||||   |||  | || ||||| |||      ||     |||   |    || | | | |   | ||  |  ||       |   || |||    ||||| | ||               
CTTTCAGGCTGAGATCAACCAGCTGCTCTCACTCATCATCAACACCTTCTATTCCAACAAGGAGATCTTCCTCCGGGAGCTCATTTCCAACTCTTCCGATgtaagtccgccccgttaagtcgaagtctgggtgcatcttagtgtgttagtgtttgggcggtaacttgtgctatggtgtgattacacactgcggttaatac

upper sequence: EFJ17594 (Selaginella moellendorffii), 5'ss of exon 1
lower sequence: GRMZM2G069651_T02 (Zea mays), 5'ss of exon 1
GTTCCAGGCTGAGATCAACCAGCTTCTCAGTCTCATCATCAACACTTTCTACAGCAACAAGGAGATTTTCTTGCGGGAGCTCATCAGCAATGCCTCGGATgtgagt--atttcgcc---tcgttcttccagttcttgtcaaactctttcttctt----ctcatgctgcgc--tgctgtgactccag--------------------------------------------------------------------------
 || |||||||||||||||||||| |||   |||||||||||||| |||||   |||||||||||| ||| | |||||||||||   |||  | || ||||| |||      ||     |||   |    || | | | |   | ||  |  ||       |   || ||  || ||||| | ||                                                                           
CTTTCAGGCTGAGATCAACCAGCTGCTCTCACTCATCATCAACACCTTCTATTCCAACAAGGAGATCTTCCTCCGGGAGCTCATTTCCAACTCTTCCGATgtaagtccgccccgttaagtcgaagtctgggtgcatcttagtgtgttagtgtttgggcggtaacttgtgctatggtgtgattacacactgcggttaatactgtttctgacgcttgattttgcgctcctacttggtgctgttttttgtgcgacttctgcag

upper sequence: EFJ17594 (Selaginella moellendorffii), 5'ss of exon 1
lower sequence: GRMZM2G112165_T02 (Zea mays), 5'ss of exon 1
GTTCCAGGCTGAGATCAACCAGCTTCTCAGTCTCATCATCAACACTTTCTACAGCAACAAGGAGATTTTCTTGCGGGAGCTCATCAGCAATGCCTCGGATgtgagt-atttcgcctcgttct---tccagttcttgtcaaactctttcttcttctcat-gctgcgctgctgtgactccag--------------------
 || |||||||||||||||||||| |||   |||||||||||||| ||||||  |||||||||||| ||| | || ||||| |||  |||  | || ||||| ||| |   ||  |   ||    || ||      |  |   |  | ||  |   || | |  | |||  |       |                    
ATTTCAGGCTGAGATCAACCAGCTGCTCTCACTCATCATCAACACCTTCTACTCCAACAAGGAGATCTTCCTCCGCGAGCTTATCTCCAACTCTTCCGATgtaagtgaccccgtttaagtcgaaatctagacgcatttcagtgcgctattagtgatataggttggatgccttactgtttgggcgacgacttgtgctatgg

upper sequence: EFJ17594 (Selaginella moellendorffii), 5'ss of exon 1
lower sequence: GRMZM2G024668_T02 (Zea mays), 5'ss of exon 2
GTTCCAGGCTGAGATCAACCAGCTTCTCAGTCTCATCATCAACACTTTCTACAGCAACAAGGAGATTTTCTTGCGGGAGCTCATCAGCAATGCCTCGGATgtgagtatttcgcctcgttcttccagttcttgtcaaactctttcttcttctcatgctgcgctgctgtgactccag-----------------------------
 |||||||| |||||||||||||| ||    |||||||||||||| ||||||  |||||||||||| ||| |  ||||||||||    ||  |||| ||||||||| |    | || |    |||   |  |   | |    |||  ||      |  || |       |||||                              
CTTCCAGGCGGAGATCAACCAGCTGCTATCGCTCATCATCAACACCTTCTACTCCAACAAGGAGATCTTCCTTAGGGAGCTCATTTCAAACTCCTCCGATgtgagttt----catcctcaccccaacccccgatgaccctcgtctatttgcagaccaccgataacccccctccattcgcgggttctagaagtaagactagatct

upper sequence: EFJ17594 (Selaginella moellendorffii), 5'ss of exon 1
lower sequence: GLYMA08G44590.1 (Glycine max), 5'ss of exon 1
GTTCCAGGCTGAGATCAACCAGCTTCTCAGTCTCATCATCAACACTTTCTACAGCAACAAGGAGATTTTCTTGCGGGAGCTCATCAGCAATGCCTCGGATgtgagtatttcgcctcgttcttccagttcttgtcaaactctttcttctt--ctcatgctgcgctgctgtgactccag-----------------------------
 ||||||||||||||||||||||| |||||||||||||||||||| ||||||  |||||||||||||||| | || || ||||||||||| ||||| |||||  || | |    ||||| |||   | |||| |    | ||||| |||   || || || | |  |||  || ||                              
TTTCCAGGCTGAGATCAACCAGCTCCTCAGTCTCATCATCAACACCTTCTACTCCAACAAGGAGATTTTCCTTCGTGAACTCATCAGCAACGCCTCCGATgtacgtttct----tcgtttttc-gctccttgacttgttgtttctgcttgtttcgtgatgtgtttatgtt-cttcatccgattttattcaactaacatgctttatt

upper sequence: EFJ17594 (Selaginella moellendorffii), 5'ss of exon 1
lower sequence: GLYMA02G47210.1 (Glycine max), 5'ss of exon 1
GTTCCAGGCTGAGATCAACCAGCTTCTCAGTCTCATCATCAACACTTTCTACAGCAACAAGGAGATTTTCTTGCGGGAGCTCATCAGCAATGCCTCGGATgtgagtatttcgcc-----------tcgttcttccagttcttgtcaaactctttcttcttctcatgc-tgcgctgctgtgactccag-------------
 || ||||| |||||||||||||| |||||||| ||||||||||| |||||||||||||||||||| ||  | || |||||||||||||||||||| ||||| ||  ||||  |           | |||||| |  | ||||| |     |||  | ||  |||   | |  | |      | | |             
TTTTCAGGCCGAGATCAACCAGCTCCTCAGTCTAATCATCAACACCTTCTACAGCAACAAGGAGATCTTTCTTCGTGAGCTCATCAGCAATGCCTCTGATgtaagattttcttcctgcttctttcttgttcttacgatccttgttaggtcttttggtatttccatttgttcattacgtcctttactgcgatcgttcttta

upper sequence: EFJ17594 (Selaginella moellendorffii), 5'ss of exon 1
lower sequence: GLYMA08G03690.1 (Glycine max), 5'ss of exon 1
-----------------GTTCCAGGCTGAGATCAACCAGCTTCTCAGTCTCATCATCAACACTTTCTACAGCAACAAGGAGATTTTCTTGCGGGAGCTCATCAGCAATGCCTCGGATgtgagtatttcgcctcgttcttccagttcttgtcaaactct-ttcttcttctcatgctgcgctgc-tgtgactccag-----------------------
                  |||||| | |||||||||||||| || ||||| ||||||||||| |||||||||||||||||||||||| |  | |||||||||||||||||||| ||| | ||  | |    |  |        |  || ||| ||||| || |||   |  |||| ||   | |      || |                       
GAAACTGAGACGTTTGCTTTCCAGTCCGAGATCAACCAGCTCCTTAGTCTTATCATCAACACCTTCTACAGCAACAAGGAGATTTTCCTTAgtgagctcatcagcaatgcctctgatttaagattcttatattatagggttcatgtttatcatactctgtttttccattgttgctccgtaacataacgtccctgtattgtgagaattatgtgggtag

upper sequence: EFJ17594 (Selaginella moellendorffii), 5'ss of exon 1
lower sequence: GLYMA18G08220.1 (Glycine max), 5'ss of exon 1
-GTTCCAGGCTGAGATCAACCAGCTTCTCAGTCTCATCATCAACACTTTCTACAGCAACAAGGAGATTTTCTTGCGGGAGCTCATCAGCAATGCCTCGGATgtgagtatttcgcctcgttcttccagttcttgtcaaactctttcttcttctcatgctgcgctgctgtgactccag---------------------------
  ||||||||||||||||||||||| |||||||||||||||||||| ||||||  ||||||||| || ||| | || || ||||||||||| ||||| ||||| ||| | |    || |   ||   | |||       | | |||  ||  | || |||       ||| ||  |                           
CTTTCCAGGCTGAGATCAACCAGCTCCTCAGTCTCATCATCAACACCTTCTACTCCAACAAGGAAATCTTCCTTCGTGAACTCATCAGCAACGCCTCTGAtgtaagtttcttcgttcttctctcttttccttcct---ttttctctcgttgacttgttgcttctgcttgattcgtgacgtatttgtgtttttcatccaattta

upper sequence: EFJ17594 (Selaginella moellendorffii), 5'ss of exon 1
lower sequence: GLYMA14G01530.1 (Glycine max), 5'ss of exon 1
GTTCCAGGCTGAGATCAACCAGCTTCTCAGTCTCATCATCAACACTTTCTACAGCAACAAGGAGATTTTCTTGCGGGAGCTCATCAGCAATGCCTCGGATgtgagtatttcgcctcgttcttccagttcttgtcaaactctttcttcttctcatg-ctgcgctgctgtgactccag-------------------------
 || ||||| |||||||||||||| |||||||| || |||||||| |||||||||||||||||||| ||  | || |||||||||||||||||||| || || ||  |||   |   | |||      ||| || |  || || |  |  | | | |    |||| ||   ||                            
TTTTCAGGCCGAGATCAACCAGCTCCTCAGTCTAATAATCAACACCTTCTACAGCAACAAGGAGATCTTTCTTCGTGAGCTCATCAGCAATGCCTCTGACgtaagatttttatcg-atccttgttagccttttctatttccttttgttgattacgtccttactgcggtcgttctttatttcatgtttattgctcaaacaca

upper sequence: EFJ17594 (Selaginella moellendorffii), 5'ss of exon 1
lower sequence: Vv00s0194g00030.t01 (Vitis vinifera), 5'ss of exon 1
GTTCCAGGCTGAGATCAACCAGCTTCTCAGTCTCATCATCAACACTTTCTACAGCAACAAGGAGATTTTCTTGCGGGAGCTCATCAGCAATGCCTCGGATgtgagtatttcgcctcgttcttccagttcttgtc-------aaactctttcttcttctcatgctgcgctgctgtgactccag------------------
 |||||||| |||||||||||||| |||||||||||||||||||||||||| |||||||||||||||||| | || ||| ||||||||||| |||| ||||||||| ||  |    |||  |||    ||| ||         |     ||  || |   || |||||   | | |     |                  
ATTCCAGGCGGAGATCAACCAGCTGCTCAGTCTCATCATCAACACTTTCTATAGCAACAAGGAGATTTTCCTTCGTGAGATCATCAGCAATTCCTCCGATgtgagttttcagaacagtttctccttcacttctccttttaaggatctgatcgactgcgtgtgttgcgcgtatttcatgttcgtaatgatgcaatgcgatt

upper sequence: EFJ17594 (Selaginella moellendorffii), 5'ss of exon 1
lower sequence: Vv19s0015g01090.t01 (Vitis vinifera), 5'ss of exon 1
GTTCCAGGCTGAGATCAACCAGCTTCTCAGTCTCATCATCAACACTTTCTACAGCAACAAGGAGATTTTCTTGCGGGAGCTCATCAGCAATGCCTCGGATgtgagtatttcgcctcgttcttccagttcttgtcaaactctttcttcttctcatgctgcgctgctgtgactccag-------------------------
 |||||||||||||||||||| ||  | ||| | ||||||||||| |||||||||||||||||||||||  | || ||||||||||||||| |||| ||||| |||  |   | |  |   |    || |  |||     |   || || |   ||    ||| | |   | | |                         
TTTCCAGGCTGAGATCAACCAACTCTTGAGTTTGATCATCAACACCTTCTACAGCAACAAGGAGATTTTTCTCCGTGAGCTCATCAGCAATTCCTCTGATgtaagtcctatactttttatctttttttttcctcatttaatcagtttttttttcgcgatcctgttttatttgcggctgatctgttctctgttggtttatt

upper sequence: EFJ17594 (Selaginella moellendorffii), 5'ss of exon 1
lower sequence: PP1S291_62V6.1 (Physcomitrella patens), 5'ss of exon 1
GTTCCAGGCTGAGATCAACCAGCTTCTCAGTCTCATCATCAACACTTTCTACAGCAACAAGGAGATTTTCTTGCGGGAGCTCATCAGCAATGCCTCGGATgtgagtatttcg----cctcgttcttcca--gttcttgtcaaac----tctttcttcttctcatgctgcgctgctg-tgactccag--------------
 |||||||| |||||||| ||  |  | ||| | ||||| ||||| ||||| ||||||||||||||||||||||| || |||||||| ||| |||||||||| ||| |||      ||| | |  |  |  |||  ||||  |     ||| | ||  ||   ||| | |  | ||  ||  || |              
TTTCCAGGCGGAGATCAATCAATTGTTGAGTTTGATCATTAACACCTTCTATAGCAACAAGGAGATTTTCTTGCGAGAACTCATCAGTAATTCCTCGGATgtaagtgttttttcacccttgcttgtgtactgtttgtgtctcatcgtgtctctatttgtcatttgcggtggagttggcgaggccggcgtttcccgtagag

upper sequence: EFJ17594 (Selaginella moellendorffii), 5'ss of exon 1
lower sequence: PP1S220_79V6.1 (Physcomitrella patens), 5'ss of exon 1
GTTCCAGGCTGAGATCAACCAGCTTCTCAGTCTCATCATCAACACTTTCTACAGCAACAAGGAGATTTTCTTGCGGGAGCTCATCAGCAATGCCTCGGATgtgagtatttcgcctcgttcttccagttcttgtcaaactctttcttcttctcatgctgcgctgctgtgactccag-----------------------------
 |||||||| |||||||||||| | || ||| | || |||||||||||||||||||||||||| ||||||||  | ||| | ||||| ||  | || ||||| | | | |     | || | | ||||||||  ||  | |   |  |||||| | ||  ||     |    ||                              
CTTCCAGGCGGAGATCAACCAGTTGCTTAGTTTGATTATCAACACTTTCTACAGCAACAAGGAAATTTTCTTAAGAGAGTTGATCAGTAACTCATCCGATgtaattttctttaaac-ttttgcaagttcttg--aatatttgaatcattctca-gttgatctatcagggtcgcattgcgctttaagtctgagaattccagacat

upper sequence: EFJ17594 (Selaginella moellendorffii), 5'ss of exon 1
lower sequence: PP1S258_52V6.1 (Physcomitrella patens), 5'ss of exon 1
GTTCCAGGCTGAGATCAACCAGCTTCTCAGTCTCATCATCAACACTTTCTACAGCAACAAGGAGATTTTCTTGCGGGAGCTCATCAGCAATGCCTCGGATgtgagtatt--------------tcgcct-cgttcttccagttcttgtcaaactctttcttcttctcatgctgcgc-tgctgtgactccag---------
 || ||||| || ||||| ||| | || ||| | ||||||||||| |||||||||||||||||||||||| |||| || || ||||||||| | || ||||| |||  |              || | | || |||||  ||     |   | |      |||     ||    |    |   || ||  |         
CTTTCAGGCGGAAATCAATCAGTTGCTGAGTTTGATCATCAACACCTTCTACAGCAACAAGGAGATTTTCCTGCGAGAACTTATCAGCAATTCTTCTGATgtaagtgctagtgctgacgaaagtcccatgcggtcttcttgtcgggattgtagtggccagtctatctgtgtcatgtgcacgccgattcttggttggtgca

upper sequence: EFJ17594 (Selaginella moellendorffii), 5'ss of exon 1
lower sequence: PP1S220_83V6.1 (Physcomitrella patens), 5'ss of exon 1
GTTCCAGGCTGAGATCAACCAGCTTCTCAGTCTCATCATCAACACTTTCTACAGCAACAAGGAGATTTTCTTGCGGGAGCTCATCAGCAATGCCTCGGATgtgagtatttcgcctcg-------ttcttccagttcttgt--caaactctttcttcttctcatgctgcgctgctgtgactccag----------------
 |||||||| |||||||| ||| |  | ||| | || ||||||||||||||||| ||||||||||| |||||| | || |||||||||||  | || |||||  || |||   || |       || ||  || |  |||  |  |    | |||        | | |  |||  ||||   ||                
TTTCCAGGCGGAGATCAATCAGTTGTTGAGTTTGATTATCAACACTTTCTACAGTAACAAGGAGATATTCTTGAGAGAACTCATCAGCAACTCTTCTGATgtaggtgtttttgcttggaactttttgttgtaggttctgtgcctcagatatgctttagagttggtttctatgcgatgacattagcgatgcccgctaacta

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: 17 (upstream exon), 35 (downstream exon)
Score: 6

GTTCCAGGCTGAGATCAACCAGCTTCTCAGTCTCATCATCAACACTTTCTACAGCAACAAGGAGATTTTCTTGCGGGAGCTCATCAGCAATGCCTCGGATgtgagtattt ... gtgactccagGCTCTCGACAAGATCCGCTTCGAAGGCCTCACTGACAAGAGTAAGCTTGAGAGCCAGCCGGAGCTCTTCATCCACATCATCCCCGACAAGGCCAGCAAGA




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTTCCAGGCTGAGATCAACCAGCTTCTCAGTCTCATCATCAACACTTTCTACAGCAACAAGGAGATTTTCTTGCGGGAGCTCATCAGCAATGCCTCGGATgtgagtatttcgcctcgttcttccagttcttgtcaaactctttcttcttctcatgctgcgctgctgtgactccag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTCA