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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtctgtttcgttttttcatgtatctcattattgagcttaattttcttttccagTAATCGGCTGAGACTTCTCACTCAGTTTTTGGAGCACCTGGTTAGCGAAGGTAGCCAAGACGTGCATGTGCACAATGCGCTCGGAAAAATTATCATCGAT

Basic information

species Selaginella moellendorffii
transcript EFJ24508
intron # 22
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ24508 (Selaginella moellendorffii), 3'ss of exon 22
lower sequence: LOC_Os11g01380.1 (Oryza sativa), 3'ss of exon 22
---------------------------------------------------------------------gtctgtttcgttttttcatgtatctcattattgagcttaattttcttttccagTAATCGGCTGAGACTTCTCACTCAGTTTTTGGAGCACCTGGTTAGCGAAGGTAGCCAAGACGTGCATGTGCACAATGCGCTCGGAAAAATTATCATCGAT
                                                                       || ||| ||||| |     | |||||  || |     ||||  |||| ||| || || ||  | || || || || |||||||||||| | || ||||| ||||||||||| || |||||||||||||| || |||||||| ||||| || 
gtatgattctttatattatcttgtattccacaaccagattaagggcatgtgcacacgcacacaaacatatgcttttttgttttgttgctgacctcatcttttat----atttcttttttcagGAACCGCCTACGGCTGCTGACACAATTTTTGGAGCACTTAGTGAGCGAGGGTAGCCAAGATGTCCATGTGCACAATGCTCTTGGAAAAATCATCATTGAC

upper sequence: EFJ24508 (Selaginella moellendorffii), 3'ss of exon 22
lower sequence: LOC_Os12g01390.1 (Oryza sativa), 3'ss of exon 22
---------------------------------------------------------------------gtctgtttcgttttttcatgtatctcattattgagcttaattttcttttccagTAATCGGCTGAGACTTCTCACTCAGTTTTTGGAGCACCTGGTTAGCGAAGGTAGCCAAGACGTGCATGTGCACAATGCGCTCGGAAAAATTATCATCGAT
                                                                       || ||| ||||  |     |||||||  || |     ||||  |||| ||| || || ||  | || || || || |||||||||||| | || ||||| ||||||||||| || |||||||||||||| || |||||||| ||||| || 
gtatgattctttatattatcttgtattccacagccagcttaagggcatgtgcacatgcacacaaacatatgcttttttgtttcgttgctgatctcatcttttat----atttcttttttcagGAACCGCCTACGGCTGCTGACACAATTTTTGGAGCACTTAGTGAGCGAGGGTAGCCAAGATGTCCATGTGCACAATGCTCTTGGAAAAATCATCATTGAC

upper sequence: EFJ24508 (Selaginella moellendorffii), 3'ss of exon 22
lower sequence: GRMZM2G057576_T01 (Zea mays), 3'ss of exon 21
---------------------------------------gtctgtttcgttttttcatgtatctcattattgagcttaattttcttttccagTAATCGGCTGAGACTTCTCACTCAGTTTTTGGAGCACCTGGTTAGCGAAGGTAGCCAAGACGTGCATGTGCACAATGCGCTCGGAAAAATTATCATCGAT
                                        |     |    |||| | ||   |||    ||   || | | | | |  ||| || || ||  |  | || ||||| || |||||||| || || || |||||||||||||| |||||||| |||||||| || || ||||| |||||||| 
gtttgaattctttattcctggggtctgcaaagtgacaagtttcacattccctttttaagtggatcacatctg--tttgaatatgtgtatcagGAACCGCCTACGGTTGCTTACTCAATTCTTGGAGCATCTAGTGAGTGAAGGTAGCCAAGATGTGCATGTCCACAATGCTCTTGGGAAAATCATCATCGAC

upper sequence: EFJ24508 (Selaginella moellendorffii), 3'ss of exon 22
lower sequence: GLYMA02G39360.1 (Glycine max), 3'ss of exon 22
-------------gtctgtttcgttttttcatgt-atctcattattgagcttaattttcttttc------cagTAATCGGCTGAGACTTCTCACTCAGTTTTTGGAGCACCTGGTTAGCGAAGGTAGCCAAGACGTGCATGTGCACAATGCGCTCGGAAAAATTATCATCGAT
              ||      |  |   ||  | | |  ||||||     | ||||   ||||      ||| ||||| ||  |  | || ||||||||||||||||| || || || || || ||||| || ||||||||||| ||||| || || ||||||||||| || 
gtgtgcaagttttttccaccctgcatccccaaattaccatattattttttctcatttcactttctatgcgcagAAATCGTCTCCGCTTGCTTACTCAGTTTTTGGAGCATCTTGTAAGTGAGGGAAGCCAGGATGTGCATGTGCATAATGCTCTGGGTAAAATTATCATTGAC

upper sequence: EFJ24508 (Selaginella moellendorffii), 3'ss of exon 22
lower sequence: GLYMA14G37510.1 (Glycine max), 3'ss of exon 20
-------------gtctgtttcgttttttcatgt-atctcattattgagcttaattttcttttc------cagTAATCGGCTGAGACTTCTCACTCAGTTTTTGGAGCACCTGGTTAGCGAAGGTAGCCAAGACGTGCATGTGCACAATGCGCTCGGAAAAATTATCATCGAT
              ||      |  |   ||  | | |  ||||||     | |||    ||||      ||| ||||| ||  |  | || ||||||||||||||||| || || || || || ||||| || |||||||| || ||||| || || ||||||||||| || 
gtgtgcaagttttttccaccctgcatccccaaattaccatattattttttctcattgcactttctatgcgcagAAATCGTCTTCGCTTGCTTACTCAGTTTTTGGAGCATCTTGTAAGTGAGGGAAGCCAGGATGTGCATGTACATAATGCTCTGGGTAAAATTATCATTGAC

upper sequence: EFJ24508 (Selaginella moellendorffii), 3'ss of exon 22
lower sequence: AT3G11130.1 (Arabidopsis thaliana), 3'ss of exon 22
--------------------gtctgtttcgttttttcatg---tatctcattattgagctt--------aattttcttttccagTAATCGGCTGAGACTTCTCACTCAGTTTTTGGAGCACCTGGTTAGCGAAGGTAGCCAAGACGTGCATGTGCACAATGCGCTCGGAAAAATTATCATCGAT
                     |   |||||||  |   |    ||| |  || || ||  |         || |   ||  ||| ||||| ||  | || ||||||||||| |||||||| || ||||| || || |||||||| |||||||| || |||||  | || ||||||||||| || 
gtgcgaacccttttagcatcttgaatttcgttcatatgtatgctattttgttctttaggctctaatatgtatatgtcttctcagAAATCGACTCCGTCTCCTCACTCAGTTCTTGGAGCATCTAGTTAGTGAGGGAAGCCAAGATGTGCATGTCCATAATGCCTTGGGTAAAATTATCATAGAC

upper sequence: EFJ24508 (Selaginella moellendorffii), 3'ss of exon 22
lower sequence: PP1S452_30V6.1 (Physcomitrella patens), 3'ss of exon 22
--------------------------------------gtctgtttcgttttttcatgtatct--cattattgagc-ttaattttct------tttccagTAATCGGCTGAGACTTCTCACTCAGTTTTTGGAGCACCTGGTTAGCGAAGGTAGCCAAGACGTGCATGTGCACAATGCGCTCGGAAAAATTATCATCGAT
                                       |  || ||    ||| |     ||  | |  | |||   | ||    |      |||  || ||||| ||| ||||  | || || || || |||||  |||| || |||||||||||||| ||||||||||||||||| || || || || ||||| |||
atattagaactaggttgcgtttttaaatgtctaaacattttagtgtcacgatttaaacatcctgacgtcgtcgagaactgatgagttgtggggtttatagGAATCGTCTGCGACTGTTGACACAATTCTTAGAGCATTTGGTAAGTGAAGGTAGCCAAGATGTGCATGTGCACAATGCTCTTGGGAAGATCATCATAGAT

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: 34 (upstream exon), 35 (downstream exon)
Score: 27

TTTTAGATGATGAATGTCCTGAGGATTTTATAAAAAATCTCATCCTCTCTGTTCGATCGTTACTACCGGTTGAGCCTCTTGTTGAGCAATGCGAGAAACGgtctgtttcg ... tcttttccagTAATCGGCTGAGACTTCTCACTCAGTTTTTGGAGCACCTGGTTAGCGAAGGTAGCCAAGACGTGCATGTGCACAATGCGCTCGGAAAAATTATCATCGAT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtctgtttcgttttttcatgtatctcattattgagcttaattttcttttccagTAATCGGCTGAGACTTCTCACTCAGTTTTTGGAGCACCTGGTTAGCGAAGGTAGCCAAGACGTGCATGTGCACAATGCGCTCGGAAAAATTATCATCGAT
                                    gcttaat  putative branch site (score: 27)
                                     cttaattttcttttcc  CT-rich tract
                                      ttaattttctttt  TA-rich tract