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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagcacctggtttttttatgcgacatgtttggaacttgactcgtgtttctacagGTCAGGGAGATGTCAAACGTGTTAATTCTTCCTCGGAGTGCCGATTACAGTGACGATGCGTGGAACGAAATCCGGTTAAAGGCATTTTCTCTGCTGAGGT

Basic information

species Selaginella moellendorffii
transcript EFJ07708
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ07708 (Selaginella moellendorffii), 3'ss of exon 3
lower sequence: LOC_Os03g03460.1 (Oryza sativa), 3'ss of exon 2
--------------------------------------------------gtaagcacctggtttttttatgcgacatgtttggaacttgactcgtgtttctacagGTCAGGGAGATGTCAAACGTGTTAATTCTTCCTCGGAGTGCCGATTACAGTGACGATGCGTGGAACGAAATCCGGTTAAAGGCATTTTCTCTGCTGAGGT
                                                    ||| || ||   || ||  || | ||| | |  |||  | |  | ||   | |||| ||||||||| |||| || |||||||||||||| ||||| || |||||||| || | |||||  |||||  |    || ||| |  |  |  ||  ||
ttttctgcattgctatggtggtgccacttgttcatcatccatcttataaaaaaagaacttg---ttgttcagcaaaatgatggatact--atttat-ttgacatagGTAAGGGAGATGCCAAATGTTTTAATTCTTCCTCGAAGTGCAGACTACAGTGAAGAAGTGTGGATGGAAATAAGAGAGAAAGCAATCACGATATTGCAGT

upper sequence: EFJ07708 (Selaginella moellendorffii), 3'ss of exon 3
lower sequence: GRMZM2G460952_T01 (Zea mays), 3'ss of exon 1
-------------------------------------------------------------------------------------------------------------------------------------------------gtaagcacctggtttttttatgcgacatgtttggaacttgactcgtgtt-tctacagGTCAGGGAGATGTCAAACGTGTTAATTCTTCCTCGGAGTGCCGATTACAGTGACGATGCGTGGAACGAAATCCGGTTAAAGGCATTTTCTCTGCTGAGGT
                                                                                                                                                  | || |  |     |||| | |  ||   | |  ||| ||    |||| | |||||||  |||||||| |||| || ||||||||||| |||||||| || |||||||| || | |||||  |||||  |    || ||| |  || || |   ||
gtgagctgtctatgttgtatccttctggtacaggtgaggagggtgagagttctgggggtggtgaagtaccctcagtgtcaccactaccacaatcacctgtgacccctcaaaattcaagaactcaacctatactttcaggatcttcatcagaaatta--cattttgttcagcaaagtggtgact-gatcattgttgtgtacagGTGCGGGAGATGCCAAATGTTTTAATTCTTCCGCGGAGTGCAGACTACAGTGAAGAAGTGTGGATGGAAATAAGAGAGAAAGCAATAACTATGTTACAGT

upper sequence: EFJ07708 (Selaginella moellendorffii), 3'ss of exon 3
lower sequence: PP1S55_132V6.1 (Physcomitrella patens), 3'ss of exon 3
-------------------------------------------------------------gtaagcacc-tggtttttttatgcgacatgtttggaacttgactcgtgtttctacagGTCAGGGAGATGTCAAACGTGTTAATTCTTCCTCGGAGTGCCGATTACAGTGACGATGCGTGGAACGAAATCCGGTTAAAGGCATTTTCTCTGCTGAGGT
                                                               ||  |   ||| || || ||     || | |   ||||  ||     ||  |||||| ||||| ||| | |||||||| ||||||||||| ||||||||||||||||| || | ||||   || || || |  || ||  | ||| ||||| | |
gtacagcgctatcttcatgtctgctaacagcttcaccatttctactgcatgatgtttaattacaaatagaatggattcttcattaattatttgttcgactt--ctttgtcttgaacagGTGAGGGAAATGCCCAACGTGTTGATTCTTCCTCGCAGTGCCGATTACAGTGAAGAAGTGTGGGCTGAGATACGATGCAAAGCCGTCTCTGTGCTGTGCT

upper sequence: EFJ07708 (Selaginella moellendorffii), 3'ss of exon 3
lower sequence: PP1S35_361V6.1 (Physcomitrella patens), 3'ss of exon 3
----------------------------------------------gtaagcacctggtttttttatg----cgacatgtttggaacttgac-tcgtgtttct---------acagGTCAGGGAGATGTCAAACGTGTTAATTCTTCCTCGGAGTGCCGATTACAGTGACGATGCGTGGAACGAAATCCGGTTAAAGGCATTTTCTCTGCTGAGGT
                                              | | |    |   ||| | |||    | |   ||    ||||  |  |  | |||||         |||||| ||||||||| ||||||| || ||||||||||| ||||| || ||||| || || | ||||  ||| || ||||  |||||  | ||| |||||   |
gtacgtcgctatcttcaactttgcaaatcgcttcccacttcccactgcatggtgtttcatttctaatgaaatcaatgcgtcgttaactaaatgttatatttcttcatcatatacagGTGAGGGAGATGCCAAACGTCTTGATTCTTCCTCGCAGTGCTGACTACAGCGAGGAAGTGTGGGCCGAGATACGGTCCAAGGCCATCTCTGTGCTGTACT

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), 28 (downstream exon)
Score: 13

TCTACTCGACGACTGCGCTGTGAAGCAAGCTCTCATTGACGGCATCATTGCTGGCTGCGCTTTGGATGGCGTCGAAGGTCCGCAATGGCTGGAAGCGTGGgtaagcacct ... gtttctacagGTCAGGGAGATGTCAAACGTGTTAATTCTTCCTCGGAGTGCCGATTACAGTGACGATGCGTGGAACGAAATCCGGTTAAAGGCATTTTCTCTGCTGAGGT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

taagcacctggtttttttatgcgacatgtttggaacttgactcgtgtttctacagGTCAGGGAGATGTCAAACGTGTTAATTCTTCCTCGGAGTGCCGATTACAGTGACGATGCGTGGAACGAAATCCGGTTAAAGGCATTTTCTCTGCTGAGGT
                                  acttgac  putative branch site (score: 13)
                                            tgtttct  putative PPT
           tttttttat  TA-rich tract