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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CCACCGTCGGAGATGCTACCACGGAATGAAACGCTTGGTGGCTATATCTTTGTTTGCAACAATGATACCATGCAAGAGGACCTCAAGCGCCAGCTCTTTGgtaagtcctctctcgttatttctctgtctttcttcgtagctatgactgaaagcttgtttttttttcttttgcgctttcag

Basic information

species Selaginella moellendorffii
transcript EFJ22023
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ22023 (Selaginella moellendorffii), 5'ss of exon 1
lower sequence: LOC_Os05g41930.1 (Oryza sativa), 5'ss of exon 2
CCACCGTCGGAGATGCTACCACGGAATGAAACGCTTGGTGGCTATATCTTTGTTTGCAACAATGATACCATGCAAGAGGACCTCAAGCGCCAGCTCTTTGgtaagtcct----ctctcgttat-ttctctgtc-tttcttcgtagctatgactgaaagcttgtttttttttct-tttgcgctt-tcag----------------------------------------------
||| |    |||||||||||| ||||||||  ||| ||||| ||||||||||||||||||||||| |||||||| ||||| |||||| | ||||| ||||||| ||  |    ||  | |||| ||||   || |  ||| | |  |    | || |     ||  |  | || ||| || |  |||                                               
CCAACAAGTGAGATGCTACCAAGGAATGAAGTGCTCGGTGGATATATCTTTGTTTGCAACAATGACACCATGCAGGAGGATCTCAAGAGGCAGCTTTTTGgtatgtgatccaacttaccttatcttctgaatcatcacttggcatattgttccgagaataaattcatgctgctatttacgatgatcaatatcaaataaccttctgatatataatcatatattgctgttctgcag

upper sequence: EFJ22023 (Selaginella moellendorffii), 5'ss of exon 1
lower sequence: GRMZM2G011923_T01 (Zea mays), 5'ss of exon 2
CCACCGTCGGAGATGCTACCACGGAATGAAACGCTTGGTGGCTATATCTTTGTTTGCAACAATGATACCATGCAAGAGGACCTCAAGCGCCAGCTCTTTGgtaagtcctctctcgtt-atttctctgtctttcttcgtagctatgactgaaagcttgtttttttttcttttgcgctttcag---------------------------------------------------
||  ||   |||||||| ||   ||| |||   |||||||| || |||||||| |||||||| ||||||||||| |||||||||||| | ||||| ||||||| ||| | | |  |  || |  |  | |  |||      |   |  | ||   |  |      ||  ||  | |   ||                                                   
CCGACGAGCGAGATGCTGCCGAAGAACGAAGTCCTTGGTGGGTACATCTTTGTCTGCAACAACGATACCATGCAGGAGGACCTCAAGAGGCAGCTTTTTGgtatgtctttttttttggatcttgccatatcccttgaggaatcaaatggtaactgttctggaaaatcagttttgatcctagcgtatatactaatttggtaatggtgccttaagatctgttgctcttctgcag

upper sequence: EFJ22023 (Selaginella moellendorffii), 5'ss of exon 1
lower sequence: GRMZM2G033117_T01 (Zea mays), 5'ss of exon 2
CCACCGTCGGAGATGCTACCACGGAATGAAACGCTTGGTGGCTATATCTTTGTTTGCAACAATGATACCATGCAAGAGGACCTCAAGCGCCAGCTCTTTGgtaagtcctctctcgttatttctctgtctttcttcgtagctatgactgaaagcttgtttttttttcttttgcgctttcag----------------------------------------------------
||  ||   |||||||||||  ||||||||   |||||||| || |||||||| |||||||| ||||||||||| ||||| |||||| | ||||| ||||||| ||  | || |||   || |     |    |  || || |  ||| |   || ||         | |    |||                                                       
CCGACGAGTGAGATGCTACCGAGGAATGAAGTCCTTGGTGGATACATCTTTGTCTGCAACAACGATACCATGCAGGAGGATCTCAAGAGGCAGCTTTTTGgtatgt--tatcccgtcccttttagaaatcaaatgataactgtt-ctggattttttttaaaaaaaaatatatagttttgatgccagtgtgtaattcgataatggtatctcaagatctattgctcttctgcag

upper sequence: EFJ22023 (Selaginella moellendorffii), 5'ss of exon 1
lower sequence: GLYMA05G36700.1 (Glycine max), 5'ss of exon 1
CCACCGTCGGAGATGCTACCACGGAATGAAACGCTTGGTGGCTATATCTTTGTTTGCAACAATGATACCATGCAAGAGGACCTCAAGCGCCAGCTCTTTGgtaagtcctct------ctcgttatttctctgtctttc--ttcgtagctatgactgaaagcttgtttttttttcttttgcgctttcag------------
||||| || |||   || ||  || |||||||  |||| |||||||||||||||||||||||||||||||||   ||| | |||||| | || ||||| |||| || |  |      || |||    |||  |  | |  ||  ||  | | | ||| |   | |  ||     ||||    || |              
CCACCATCAGAGTCTCTTCCTAGGGATGAAACCATTGGAGGCTATATCTTTGTTTGCAACAATGATACCATGGCTGAGAATCTCAAGAGACAACTCTTCGgtatgttccttaatttccttgttgagactcaattatgcaattgttatatcttattgatacaatatacttcaggttttttaatttcctagtcatacactgg

upper sequence: EFJ22023 (Selaginella moellendorffii), 5'ss of exon 1
lower sequence: GLYMA08G02840.2 (Glycine max), 5'ss of exon 1
CCACCGTCGGAGATGCTACCACGGAATGAAACGCTTGGTGGCTATATCTTTGTTTGCAACAATGATACCATGCAAGAGGACCTCAAGCGCCAGCTCTTTGgtaagtcctctctcgttatttctctgtctttcttcgtagctatgactgaaagcttgtttttttttcttttgcgctttcag----------------------
|| ||  | |||   || ||  ||||||||||  |||| ||||| |||||||||||||||||||||||||||   ||| | |||||| | || |||||||||| ||  ||  |  ||   |   ||    ||      || ||   |  |  ||| || || |    |  |    |  ||                      
CCCCCAGCAGAGTCTCTTCCTAGGAATGAAACCATTGGAGGCTACATCTTTGTTTGCAACAATGATACCATGGCTGAGAATCTCAAGAGACAACTCTTTGgtatgt--tccttaatttcctagttgagactcaattatgcaattgttatattcttattattatcatctaagatactatagacttcaggttttttaattgctg

upper sequence: EFJ22023 (Selaginella moellendorffii), 5'ss of exon 1
lower sequence: GLYMA20G16100.3 (Glycine max), 5'ss of exon 1
CCACCGTCGGAGATGCTACCACGGAATGAAACGCTTGGTGGCTATATCTTTGTTTGCAACAATGATACCATGCAAGAGGACCTCAAGCGCCAGCTCTTTGgtaagtcctctctcgttatttctctgtctttcttcgtagctatgactgaaagcttgtttttttttcttttgcgctttcag--------------------------------------------------------------------------------------------------------------------
||||| || |||   || ||   |||||||||  |||| ||||| |||||||||||||||||||||||||||  |||| | ||| |  | ||||||||||||  |||| ||||| || ||| | | |  || ||     || |   | ||| ||| |||||  ||   |     |  | |                                                                                                                    
CCACCATCAGAGTCTCTGCCTAAGAATGAAACCATTGGAGGCTACATCTTTGTTTGCAACAATGATACCATGGCAGAGAATCTCCAAAGACAGCTCTTTGgtgtgtcccctctccttttttttttcttcttgttttgctctctttatcaaatcttatttttcctttaatctaattcgcggttctctatattttcaataacaataagttgaatcctttgaggaattgatatgtcaagaaattcttcctttctaattctaaattgattttgctgacagatgtttcttgtgctttgtag

upper sequence: EFJ22023 (Selaginella moellendorffii), 5'ss of exon 1
lower sequence: GLYMA13G10640.1 (Glycine max), 5'ss of exon 1
CCACCGTCGGAGATGCTACCACGGAATGAAACGCTTGGTGGCTATATCTTTGTTTGCAACAATGATACCATGCAAGAGGACCTCAAGCGCCAGCTCTTTGgtaagtcctctctcgttatttctctgtctttcttcgtagctatgactgaaagcttgtttttttttcttttg--cgctttcag------------------
||||| || |||   || ||   |||||||||  |||| ||||| ||||||||||||||||| |||||||||  |||| | ||| |  | ||||||||||||| |||| ||||| |  ||| | |   |   ||  |  || |   | ||| ||| |  || || || | |     | || |                  
CCACCATCAGAGTCTCTGCCTAAGAATGAAACCATTGGAGGCTACATCTTTGTTTGCAACAACGATACCATGGCAGAGAATCTCCAAAGACAGCTCTTTGgtatgtcccctctcctctttttttttcttccttttttttctctttatcaaatcttataattgttactatagtctaatctctggttttctatagtttacaa

upper sequence: EFJ22023 (Selaginella moellendorffii), 5'ss of exon 1
lower sequence: AT3G27090.1 (Arabidopsis thaliana), 5'ss of exon 2
CCACCGTCGGAGATGCTACCACGGAATGAAACGCTTGGTGGCTATATCTTTGTTTGCAACAATGATACCATGCAAGAGGACCTCAAGCGCCAGCTCTTTGgtaagtcctctctcgttatttctctgtctttcttcgtagctatgactgaaagcttgtttttttttcttttgcgct----ttcag
||  | |||||||  || ||  ||||||||   |||||||| || ||||||||||||||||||||||| ||||| |||||  | || || || ||||||||||| | | |  |     |||||     |||  |  ||   |  |||| |||    |   |||||   || |       |||||
CCTGCTTCGGAGACTCTTCCGAGGAATGAAGTTCTTGGTGGTTACATCTTTGTTTGCAACAATGATACTATGCAGGAGGATATGAAACGTCACCTCTTTGgtaatttcccaatacccttttctagtgttttactgatattca-aactgcaagtaaataactttttgactttcatcattgttcag

upper sequence: EFJ22023 (Selaginella moellendorffii), 5'ss of exon 1
lower sequence: Vv02s0025g01720.t01 (Vitis vinifera), 5'ss of exon 1
CCACCGTCGGAGATGCTACCACGGAATGAAACGCTTGGTGGCTATATCTTTGTTTGCAACAATGATACCATGCAAGAGGACCTCAAGCGCCAGCTCTTTGgtaagtcctc-------tctcgttatttc--tctgtctttcttcgtagctatgactgaaagcttgttttt--ttttcttttgcgctttcag---------
||||| ||||||   || ||  | ||||| ||  ||||||| || |||||||| |||||||| ||||| ||||||||| | |||||| | ||||||||||||||| || |       | ||  |  |||  | |  | || |||   |   |   |    | ||| || |  || | ||||||| |    |         
CCACCATCGGAGTCTCTCCCCAGAAATGAGACCGTTGGTGGATACATCTTTGTCTGCAACAACGATACTATGCAAGAGAATCTCAAGAGACAGCTCTTTGgtaagcccccgtctctgtttctctgattctatttaccatttttcagtgtccttctttggggtttgattctgattctgttttgcgttggtgggtatctctc

upper sequence: EFJ22023 (Selaginella moellendorffii), 5'ss of exon 1
lower sequence: Vv18s0089g01080.t01 (Vitis vinifera), 5'ss of exon 1
CCACCGTCGGAGATGCTACCACGGAATGAAACGCTTGGTGGCTATATCTTTGTTTGCAACAATGATACCATGCAAGAGGACCTCAAGCGCCAGCTCTTTGgtaagtcctctctcgttatttctctgtc---tttcttcgtagctatgactgaaagcttgtttttttttcttttgcgctttcag-----------------
|| || || |||||||| ||  | |||||  | || || ||||| |||||||| ||||||||||| |||||||||||||| ||    ||||||||||||||| ||  ||||    |    | |  | |     |  ||  |    |   |   |  ||  ||| |||    |  | |||  |                  
CCCCCATCTGAGATGCTTCCCAGAAATGAGGCCCTGGGGGGCTACATCTTTGTGTGCAACAATGACACCATGCAAGAGGATCTTCGCCGCCAGCTCTTTGgtgagctctcttgattctaatataagacaaaagttctcaaaatattattttttatttttatttatttctcataacacttaaaaaaccgaaaatttgtttt

upper sequence: EFJ22023 (Selaginella moellendorffii), 5'ss of exon 1
lower sequence: PP1S168_104V6.2 (Physcomitrella patens), 5'ss of exon 2
CCACCGTCGGAGATGCTACCACGGAATGAAACGCTTGGTGGCTATATCTTTGTTTGCAACAATGATACCATGCAAGAGGACCTCAAGCGCCAGCTCTTTGgtaagtcctctct---cgttatttctctgtctttcttcgtagctatgactga-aagcttgttttttt-----ttcttttgcgctttcag-----------
||| |  | ||| | || || || ||||  || || || || || || ||||||||||| ||||| ||||||||||||||||| || ||||||||||| |||| ||     ||   | ||  || |||| | |   ||  | |      ||  ||||| ||  |         || ||   |  |   |           
CCATCCGCTGAGGTCCTTCCCCGAAATGTCACTCTGGGAGGTTACATATTTGTTTGCAATAATGACACCATGCAAGAGGACCTTAAACGCCAGCTCTTCGgtacgttgcaactatcctttgattttctgccatagatccaatcagcaggtggcaagctggtgatagcacggactcattcatgactcttgtggtggctgta

upper sequence: EFJ22023 (Selaginella moellendorffii), 5'ss of exon 1
lower sequence: PP1S6_446V6.1 (Physcomitrella patens), 5'ss of exon 1
CCACCGTCGGAGATGCTACCACGGAATGAAACGCTTGGTGGCTATATCTTTGTTTGCAACAATGATACCATGCAAGAGGACCTCAAGCGCCAGCTCTTTGgta-agtcctctctcgttatttctctgtctttcttcgtagctatgactgaaagcttgtttttttttct-tttgcgctttcag------------------
|||||  | ||||| || ||| ||||   |||  | || ||||| || ||||| ||||||||||| ||||||||||||||||| ||| | || ||||||||||  |||   ||  |  ||   | | | ||  ||  | | | |   |  |    | | | | | | | |       ||||                   
CCACCTGCAGAGATCCTTCCAAGGAACACAACCTTGGGAGGCTACATATTTGTGTGCAACAATGACACCATGCAAGAGGACCTGAAGAGACAACTCTTTGgtatggtcaattcgtggaatcctttttttttgtttttttgttttttgtttatatatatatatatatatatacatatattcaacaaagtagcatgccttga

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), 35 (downstream exon)
Score: 109

CCACCGTCGGAGATGCTACCACGGAATGAAACGCTTGGTGGCTATATCTTTGTTTGCAACAATGATACCATGCAAGAGGACCTCAAGCGCCAGCTCTTTGgtaagtcctc ... gcgctttcagGCTTGCCTCAAAGGTACCGTGACTCTGTTCGTGCTATCCAGCCGGGCCTGCCTTTGTTTCTTTACAACTATACTACGCACCAGCTTCACGGGGTGTACGA




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CCACCGTCGGAGATGCTACCACGGAATGAAACGCTTGGTGGCTATATCTTTGTTTGCAACAATGATACCATGCAAGAGGACCTCAAGCGCCAGCTCTTTGgtaagtcctctctcgttatttctctgtctttcttcgtagctatgactgaaagcttgtttttttttcttttgcgctttcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTC