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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtctactcttggtagaacttgtagtgttaacagtttttatccagGGTGAGAATGCATTACGGTCATCCAGATGTTTTCGATAGAATCTTCCATATAACAAGGGGGGGCATTAGTAAAGCCTCTCGGGTCATAAACATTAGTGAG

Basic information

species Selaginella moellendorffii
transcript EFJ07568
intron # 37
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ07568 (Selaginella moellendorffii), 3'ss of exon 37
lower sequence: LOC_Os03g02756.1 (Oryza sativa), 3'ss of exon 4
-----------------------------------gtaagtctactcttggtaga-acttgtagtgttaacagtttttatccagGGTGAGAATGCATTACGGTCATCCAGATGTTTTCGATAGAATCTTCCATATAACAAGGGGGGGCATTAGTAAAGCCTCTCGGGTCATAAACATTAGTGAG
                                    | ||||   ||  | || | |||   |   ||   | || || | ||| || ||||||||||| || |||||||||||||| |||||||| || |||||||| ||||| || || ||||| ||||| || ||||| || || ||||||
gtaagtgcttttacataatatatattttctatttcatgagtcatttcaagttacatactgtcaacatttggaattcttttgcagAGTAAGAATGCATTATGGCCATCCAGATGTTTTTGATAGAATTTTTCATATAACGAGGGGTGGAATAAGTAAGGCCTCCCGTGTCATCAATATCAGTGAG

upper sequence: EFJ07568 (Selaginella moellendorffii), 3'ss of exon 37
lower sequence: GRMZM2G453794_T01 (Zea mays), 3'ss of exon 3
-----------------------------------------gtaagtctactcttggtagaacttgta-gtgttaacagtttttatccagGGTGAGAATGCATTACGGTCATCCAGATGTTTTCGATAGAATCTTCCATATAACAAGGGGGGGCATTAGTAAAGCCTCTCGGGTCATAAACATTAGTGAG
                                          | ||   |   |  ||  |  |  ||  ||  | |  || || |  || ||||||||||| || ||||||||||||||||| |||||||| || |||||||||||||| || |||||||| ||||||||   ||| || || ||||||
gtaagtgcttttacatagtatgttttctgtttcacatgaggatcagctaaaattgtgtgtagttaatacatgaaaccttttcttttgtagAGTGAGAATGCACTATGGTCATCCAGATGTTTTTGATAGAATTTTTCATATAACAAGGGGTGGAATTAGTAAGGCCTCTCGCAGCATCAATATCAGTGAG

upper sequence: EFJ07568 (Selaginella moellendorffii), 3'ss of exon 37
lower sequence: AT2G36850.1 (Arabidopsis thaliana), 3'ss of exon 38
-------------------------------------------gtaagtctactcttggtagaacttgtagtgttaa------cagtttttatc---cagGGTGAGAATGCATTACGGTCATCCAGATGTTTTCGATAGAATCTTCCATATAACAAGGGGGGGCATTAGTAAAGCCTCTCGGGTCATAAACATTAGTGAG
                                            ||   | ||| |     ||     |||| | ||      ||    | |||   ||| ||  ||||||| || || ||||||||||| ||||||||||| || ||||||||  | || || || || ||||| || || || || ||||| ||||| 
ttcagcactcgttttccggtttattggattgtttttatttaatctattaccactttccagtgacagcttagtttcaatttgttcaaaactaatcttgcagAGTTCGAATGCACTATGGGCATCCAGATGTGTTCGATAGAATATTTCATATAACTCGCGGAGGAATCAGCAAAGCATCCCGTGTTATTAACATCAGTGAA

upper sequence: EFJ07568 (Selaginella moellendorffii), 3'ss of exon 37
lower sequence: Vv06s0004g01200.t01 (Vitis vinifera), 3'ss of exon 35
-----------------------------------------gtaagtctactcttggtagaacttgtagtgttaacagtttttat--ccagGGTGAGAATGCATTACGGTCATCCAGATGTTTTCGATAGAATCTTCCATATAACAAGGGGGGGCATTAGTAAAGCCTCTCGGGTCATAAACATTAGTGAG
                                          | | | ||   |||| | |||| |   ||  | |  |  | ||  |||||||  | |||||||| || |||||||||||||| |||||| | |||||||||||| | || || || || || |||||||| || || ||||||||||| 
gtaagttcatttaattaagcaagcaatttatttgatgtcatatcattttaaatttgggataactggagctgaaatctttaataatggccagGGTTCGTATGCATTATGGCCATCCAGATGTTTTTGATAGAGTTTTCCATATAACACGAGGTGGTATCAGCAAGGCCTCTCGAGTTATCAACATTAGTGAA

upper sequence: EFJ07568 (Selaginella moellendorffii), 3'ss of exon 37
lower sequence: PP1S67_234V6.1 (Physcomitrella patens), 3'ss of exon 39
--------------------------------------------------gtaagtctactcttggtagaacttgtagtgtta--acagtttttatccagGGTGAGAATGCATTACGGTCATCCAGATGTTTTCGATAGAATCTTCCATATAACAAGGGGGGGCATTAGTAAAGCCTCTCGGGTCATAAACATTAGTGAG
                                                      | | |   || |  ||  | |||  |||   |||  |  | | ||||||||| |||||||| |||||||| |||||||| ||| | || ||||||||||||||||| || || || ||| | ||       || ||  | ||||| 
aattatatgtgctgtaaatcgttagttctaatctagtatgactttgccttaggtgccaaggtttcgatgacttcgtatggttgctacatatgatgtgcagGGTGAGGATGCATTATGGTCATCCCGATGTTTTTGATCGTATATTCCATATAACAAGGGGAGGTATCAGCAAACCTTCAAAACAAATTAATCTCAGTGAA

upper sequence: EFJ07568 (Selaginella moellendorffii), 3'ss of exon 37
lower sequence: PP1S40_186V6.2 (Physcomitrella patens), 3'ss of exon 22
--------------------------------------------------------------------------------------------------------------------------------------gtaagtctactcttggtagaacttgtagtgttaa--cagtttttatccagGGTGAGAATGCATTACGGTCATCCAGATGTTTTCGATAGAATCTTCCATATAACAAGGGGGGGCATTAGTAAAGCCTCTCGGGTCATAAACATTAGTGAG
                                                                                                                                      || |    | | | | | ||  |||||   ||||  |   |  |   |||||| |||||||| || |||||||| |||||||||||| | || ||||| ||||||||||| || || || ||| | ||    |  || ||  | ||| | 
gtgagttttctggcaagttctgactattttctgcatatttgttagattgtatatttctttcatatcttcaacctcttaaggataagaaaaagttgtaggggaactcaagaactttgaaaagctttcttgcacatgtcatcaaagtttcgat-gactttgtatgattaattcgcatgctcggcagGGTAAGAATGCACTATGGTCATCCCGATGTTTTCGATCGGATATTCCACATAACAAGGGGAGGTATCAGCAAATCTTCAAAAGAGATCAATCTGAGTAAA

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: 22 (upstream exon), 34 (downstream exon)
Score: 8

TGTATCTTCTTTGGCTTGGTTTATGTCAAGCCAGGAAACTAGTTTTGTTACGTTGGGGCAAAGAGTTCTTGCAAAGCCTCTGAAgtaagtctac ... ttttatccagGGTGAGAATGCATTACGGTCATCCAGATGTTTTCGATAGAATCTTCCATATAACAAGGGGGGGCATTAGTAAAGCCTCTCGGGTCATAAACATTAGTGAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtaagtctactcttggtagaacttgtagtgttaacagtttttatccagGGTGAGAATGCATTACGGTCATCCAGATGTTTTCGATAGAATCTTCCATATAACAAGGGGGGGCATTAGTAAAGCCTCTCGGGTCATAAACATTAGTGAG
                                   tgttaac  putative branch site (score: 8)
                                            tttttatcc  putative PPT
                                     ttaacagtttttat  TA-rich tract