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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CCTACTTTCAACAAGAGCGGGGGGCCTTGGAATCAATCTTGCTACTGCAGACACTGTGATTATCTTTGATTCTGATTGGAATCCACAGAATGACCTTCAAgtaagttttctttttgaaaattcacaagtttattccacgttctatgtag

Basic information

species Selaginella moellendorffii
transcript EFJ29460
intron # 18
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ29460 (Selaginella moellendorffii), 5'ss of exon 18
lower sequence: GRMZM2G010342_T01 (Zea mays), 5'ss of exon 18
CCTACTTTCAACAAGAGCGGGGGGCCTTGGAATCAATCTTGCTACTGCAGACACTGTGATTATCTTTGATTCTGATTGGAATCCACAGAATGACCTTCAAgtaagttttct---ttttgaaaattcacaagtttattccacgttctatgtag------------------------------------------------------------------------------
                               || |||||||| |||||||| || ||||| || |||||||| |||||||||||||| ||||| || || ||   |  |||   | |          ||||| | |  |    |  |                                                                                   
------------------------------TATTAATCTTGCAACTGCAGATACAGTGATAATTTTTGATTCAGATTGGAATCCACAAAATGATCTGCAGGTTCTTCCTCTCATTCTCTTCCTCCTGCAAgtgtgtgtctaacttaaaaagatttatttatctttattatgtttttatggttcaatttttgctaggccatgagtagggcacataggattggccaacagga

upper sequence: EFJ29460 (Selaginella moellendorffii), 5'ss of exon 18
lower sequence: GRMZM2G141258_T01 (Zea mays), 5'ss of exon 22
CCTACTTTCAACAAGAGCGGGGGGCCTTGGAATCAATCTTGCTACTGCAGACACTGTGATTATCTTTGATTCTGATTGGAATCCACAGAATGACCTTCAAgtaag-ttttctttttgaaaattcacaagtttattccacgttctatgtag--------------------------------------------------
 ||  | || ||| | || || || ||||| || ||||| || |||||||| || ||||| || |||||||| |||||||||||||| |||||  | || ||    || ||| | |      || |   |  |    |  || | | ||                                                   
TCTTTTATCCACACGTGCCGGAGGACTTGGTATTAATCTAGCAACTGCAGATACAGTGATAATTTTTGATTCAGATTGGAATCCACAAAATGATTTGCAGgttctcttctctctctttcccctcgctcctggaagtgagtttgtgtttaacttgtgaagatttccttatctttcctatgtttcttaatatggctcatttc

upper sequence: EFJ29460 (Selaginella moellendorffii), 5'ss of exon 18
lower sequence: GLYMA02G45000.1 (Glycine max), 5'ss of exon 19
CCTACTTTCAACAAGAGCGGGGGGCCTTGGAATCAATCTTGCTACTGCAGACACTGTGATTATCTTTGATTCTGATTGGAATCCACAGAATGACCTTCAAgta--------agttttctttttgaaaattcacaagtttattccacgttctatgtag----------------
||| ||||||||| | || || || || || |||||||||||||| ||||||||||| || || |||||||||||||||||||| || |||||||| || |||        | ||   ||| | |  | |||  |   ||||    |||   |||                  
CCTTCTTTCAACACGGGCAGGAGGTCTGGGTATCAATCTTGCTACAGCAGACACTGTTATAATATTTGATTCTGATTGGAATCCTCAAAATGACCTGCAGgtattcagctgatttaattttatcattaatcaacaaaatatttggtgtttactgttacttctatgttttttag

upper sequence: EFJ29460 (Selaginella moellendorffii), 5'ss of exon 18
lower sequence: GLYMA14G03780.1 (Glycine max), 5'ss of exon 19
CCTACTTTCAACAAGAGCGGGGGGCCTTGGAATCAATCTTGCTACTGCAGACACTGTGATTATCTTTGATTCTGATTGGAATCCACAGAATGACCTTCAAgtaagttttctttttgaaaattcacaagtttattccacgttctatgtag----------------------------
||| ||||||||| | || || || || || ||||| |||||||| ||||||||||| || || |||||||||||||||||||| || |||||||| || |||  ||    |  |  || || |  |  ||| |||| |   ||  | |                            
CCTTCTTTCAACACGGGCAGGAGGTCTGGGTATCAACCTTGCTACAGCAGACACTGTTATAATATTTGATTCTGATTGGAATCCTCAAAATGACCTGCAGgta--ttcagctgatataattttatta--ttaatccatgaaatagttggtgcttactgttacttttatgtcttttag

upper sequence: EFJ29460 (Selaginella moellendorffii), 5'ss of exon 18
lower sequence: AT2G13370.1 (Arabidopsis thaliana), 5'ss of exon 20
CCTACTTTCAACAAGAGCGGGGGGCCTTGGAATCAATCTTGCTACTGCAGACACTGTGATTATCTTTGATTCTGATTGGAATCCACAGAATGACCTTCAAgtaagttttctttttgaaaattcacaagtttattccacgttctatgtag-----------------------------------------
 || ||||| ||  |||| || || || || |||||||| |||||||| || || ||  |||| ||||| ||||||||||||||||| |||||||| || ||      ||   |  ||  ||   |  |||     |  | || | ||                                          
TCTTCTTTCGACCCGAGCTGGTGGACTGGGTATCAATCTGGCTACTGCTGATACAGTCGTTATATTTGACTCTGATTGGAATCCACAAAATGACCTGCAGgttttgcctccaataaaatttttctacctttggattat-tactctttaatactaaatgttgataatggaatcccaaccctattatatcag

upper sequence: EFJ29460 (Selaginella moellendorffii), 5'ss of exon 18
lower sequence: Vv06s0009g03750.t01 (Vitis vinifera), 5'ss of exon 19
CCTACTTTCAACAAGAGCGGGGGGCCTTGGAATCAATCTTGCTACTGCAGACACTGTGATTATCTTTGATTCTGATTGGAATCCACAGAATGACCTTCAAgta------agttttctttttgaaaattcaca-agtttattccacgtt-ctatgtag-------------------------
||| ||||||||  | || || ||||| || || || ||||| ||||||||||| || ||||| ||||||||||| |||||||| || |||||| | || ||        | | ||  || |     |||   ||||  ||  |  || ||   |                           
CCTCCTTTCAACCCGTGCTGGTGGCCTGGGCATTAACCTTGCAACTGCAGACACAGTTATTATATTTGATTCTGACTGGAATCCCCAAAATGACTTACAGgttttgactggatgtcccttagtttggtcatgtagttggttatatttttctcaattatacttattatagctttatgcactag

upper sequence: EFJ29460 (Selaginella moellendorffii), 5'ss of exon 18
lower sequence: PP1S317_10V6.1 (Physcomitrella patens), 5'ss of exon 20
CCTACTTTCAACAAGAGCGGGGGGCCTTGGAATCAATCTTGCTACTGCAGACACTGTGATTATCTTTGATTCTGATTGGAATCCACAGAATGACCTTCAAgtaagttttcttt---ttgaaaattcacaagtttattccacgttctatgtag------------------------------------------------------------------------------------------------------------------------------
| |||| || ||  | || || ||  | ||||| ||||||||||| ||||||||||| ||||| ||||| || ||||||||||| ||||||||  | || ||  |    |||    |   |  |||  ||||| | | || |   |||  |                                                                                                                               
CTTACTATCTACCCGTGCTGGTGGTTTGGGAATTAATCTTGCTACCGCAGACACTGTCATTATATTTGACTCGGATTGGAATCCCCAGAATGATTTACAGgtttgcccccttaaaatgttaccttcctaagttaagtacatgaagtattgatatactgtatgcgttaagtagatgttgggagaattttgttgcaaactgttgttgcagctcttttgccgcgggcttgaacgttttgttacgaaacaagtgcatgtgctgagaggtttgtttcctgcag

upper sequence: EFJ29460 (Selaginella moellendorffii), 5'ss of exon 18
lower sequence: PP1S93_123V6.1 (Physcomitrella patens), 5'ss of exon 20
CCTACTTTCAACAAGAGCGGGGGGCCTTGGAATCAATCTTGCTACTGCAGACACTGTGATTATCTTTGATTCTGATTGGAATCCACAGAATGACCTTCAAgtaagttttct-----ttttgaaaattcaca-agtt----tattccacgttctatgtag----------------------------------------------------------------------------------------------------------
| || | |||||| |||| || ||  | || || |||||||| |||||||| ||||| ||||| || ||||| ||||||||||| |||||||| || || ||  | || ||     ||||      | | | || |    | ||  | |  |||||||                                                                                                           
CTTATTGTCAACACGAGCTGGTGGTTTAGGCATTAATCTTGCCACTGCAGATACTGTCATTATATTCGATTCGGATTGGAATCCTCAGAATGATCTACAGgtctgcttcctgaaggttttacctgcttaaatagatgaagtgttgtatgcgctatgtaaaaacttaatgaatctgtttaaatggatgctagagttcttcaaccgtctgctttaacatttctttggagtaataactgcatttttctgaaaagcttgtttcctgcag

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: 31 (upstream exon), 25 (downstream exon)
Score: 2

CCTACTTTCAACAAGAGCGGGGGGCCTTGGAATCAATCTTGCTACTGCAGACACTGTGATTATCTTTGATTCTGATTGGAATCCACAGAATGACCTTCAAgtaagttttc ... ttctatgtagGCAATGAGTCGGGCTCATCGTATTGGGCAAGAGTTTGTCGTCAACATTTATCGCTTCGTGACATGTAGAAGTGTCGAGGAAGACATTTTGGAACGCGCAA




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