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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaactacatttttacgttcaagttgaagaagcttgacacgccgagtttttgctgcagGGGTTGGGAATGATCCACGAGAAGATCGCTACTTCAGCATTCCCAAACAG

Basic information

species Selaginella moellendorffii
transcript EFJ22017
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ22017 (Selaginella moellendorffii), 3'ss of exon 11
lower sequence: GRMZM2G103897_T02 (Zea mays), 3'ss of exon 10
------------------------------------------------------gtaactacatttttacgttcaagttgaagaagcttgacacgc--cgagtttttgctg-cagGGGTTGGGAATGATCCACGAGAAGATCGCTACTTCAGCATTCCCAAACAG
                                                      ||  ||  |  | | | |  |   || |   |  ||| | |   |  || |   ||| |||| ||||| |||||||||||||||||||| |||||||| || || ||||| 
gttagttgtctttagtatgaccaaaggaaataaattcaaaaaaaaattacaagtgtcgct-tacatatccttgtagactggaactgaatgaaatgtttctggtgtactctgacagGAGTTGGCAATGATCCACGAGAAGATCGATACTTCAGTATCCCAAAACAA

upper sequence: EFJ22017 (Selaginella moellendorffii), 3'ss of exon 11
lower sequence: AT5G24850.1 (Arabidopsis thaliana), 3'ss of exon 10
------------------------------------------------------gtaactacatttttacgttcaagttgaagaagcttgacacgccgagtttttgc---tgcagGGGTTGGGAATGATCCACGAGAAGATCGCTACTTCAGCATTCCCAAACAG
                                                        ||  | |||   | |   |  ||  ||| | |||| |       || || |   || ||| ||||| ||||||||||| ||||| || ||||||||||||||||| || 
gtaagtactactcatgacacagtttgtgacttgtggttttcaaattcaacattgagaatgagattgaaatggaaactttatagatggttgaaatctgtttttcttaccattgaagGAGTTGGAAATGATCCACGGGAAGACCGGTACTTCAGCATTCCCAAGCAA

upper sequence: EFJ22017 (Selaginella moellendorffii), 3'ss of exon 11
lower sequence: Vv04s0008g02670.t01 (Vitis vinifera), 3'ss of exon 11
-------------------------------------------------------------gtaactacatttttacgttcaagttgaagaagcttgacacgccgagtttttgctgcagGGGTTGGGAATGATCCACGAGAAGATCGCTACTTCAGCATTCCCAAACAG
                                                             | |   |||| | |  |      |  | | |  || | |  |     | ||     ||| ||||||||||| ||| ||||||||||||| |||||||| || || || 
gtgattcacatcacaactaatgtagacatatatccttatgtttttatgtaaatttagatgagaacacacatatctgtgcatctatatatgcattttaatatcctatcctgttttattagGTGTTGGGAATGACCCAAGAGAAGATCGCTATTTCAGCATCCCAAAGCAA

upper sequence: EFJ22017 (Selaginella moellendorffii), 3'ss of exon 11
lower sequence: PP1S488_10V6.1 (Physcomitrella patens), 3'ss of exon 12
----------------------------------------gta-actacatttttacgttcaagttgaagaagcttgacac-gccgagtttttg-ctgcagGGGTTGGGAATGATCCACGAGAAGATCGCTACTTCAGCATTCCCAAACAG
                                         || || || | |  |  ||| |    ||   | |||  || |  |  |   ||  || ||| || || |||||||| |||||||||||||||||||||||||| || |||
agattttcacacccctttgtccttgtattgctaacatcttttacacgacttgtacatcttctaagc-aatctgtttgctactgatgcatcactgattgtagGCGTAGGCAATGATCCTCGAGAAGATCGCTACTTCAGCATTCCAAAGCAG

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), 33 (downstream exon)
Score: 31

GATATGGGGATTGATTGGCGCATGGGAGCCGAGTGGTTTGAATCCTGTCTGCTGGATTACGATCCATGCTCTAACTATGGAAACTGGACGTATGGAGCTGgtaactacat ... tttgctgcagGGGTTGGGAATGATCCACGAGAAGATCGCTACTTCAGCATTCCCAAACAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

actacatttttacgttcaagttgaagaagcttgacacgccgagtttttgctgcagGGGTTGGGAATGATCCACGAGAAGATCGCTACTTCAGCATTCCCAAACAG
                            gcttgac  putative branch site (score: 31)
                                           tttttgct  putative PPT
     attttta  TA-rich tract