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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtcctctttcttttttttctttctttgctcttacaatgcactgactctttcgctttttttttttctcatttattctgtgcagTCTGTTCACGAAGGACGCATTTATCAGCTTAAGTTGTACTGCGACAAAGACTATCCGGATAAGCCACCAAGTGTGCGATTCCATTCGCGAATCAACATGA

Basic information

species Selaginella moellendorffii
transcript EFJ15952
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ15952 (Selaginella moellendorffii), 3'ss of exon 2
lower sequence: GRMZM2G027378_T01 (Zea mays), 3'ss of exon 2
-------gtcctctttctt------ttttttctttctttgctcttacaatgcactgactctttcgctttttttttttctca------tttattctgtgcagTCTGTTCACGAAGGACGCATTTATCAGCTTAAGTTGTACTGCGACAAAGACTATCCGGATAAGCCACCAAGTGTGCGATTCCATTCGCGAATCAACATGA
       ||| ||| |             |  ||||  |    ||||    |  || || | |   || |||       ||      ||| |  |   ||| |||| || || || ||||| || ||||| |||||||  || ||||||||||||||||| |||||||||  |||  ||||||| ||  ||||||||||||
tctgtaggtcttctctaacaacagcgcagtcttttccatagagttacttctc-ttggctatctaatttgtttccacgtccaacaacatttctctttgtcagACTGTACATGAGGGTCGCATCTACCAGCTGAAGTTGTTTTGTGACAAAGACTATCCGGAGAAGCCACCATCTGTCAGATTCCACTCAAGAATCAACATGA

upper sequence: EFJ15952 (Selaginella moellendorffii), 3'ss of exon 2
lower sequence: GRMZM2G071010_T01 (Zea mays), 3'ss of exon 2
-------gtcctctttc-ttttttttctttctttgctcttacaatgcac----tgactctttcgctttttttttt-tctcat----ttattctgtg-cagTCTGTTCACGAAGGACGCATTTATCAGCTTAAGTTGTACTGCGACAAAGACTATCCGGATAAGCCACCAAGTGTGCGATTCCATTCGCGAATCAACATGA
       ||| ||| |          | |||||| |  |     |||      || || | |   || |||     || ||     ||  ||| || ||| |||| || || || ||||| || ||||| |||||||  || ||||| ||||||||||| |||||||||  |||  ||||||| ||  ||||||||||||
tctgtaggtcttctctaacaacagcgcattcttttccatagagttgcttctcttggctatctaatttatttccacgtcccacaacatttctctttgtcagACTGTACATGAGGGTCGCATCTACCAGCTGAAGTTGTTTTGTGACAAGGACTATCCGGAGAAGCCACCATCTGTCAGATTCCACTCAAGAATCAACATGA

upper sequence: EFJ15952 (Selaginella moellendorffii), 3'ss of exon 2
lower sequence: Vv08s0007g02580.t01 (Vitis vinifera), 3'ss of exon 2
-------------------gtcctctttcttttttttctttctttgctcttacaatgcactgactctttcgctttttttttttctcatttattctgtg-cagTCTGTTCACGAAGGACGCATTTATCAGCTTAAGTTGTACTGCGACAAAGACTATCCGGATAAGCCACCAAGTGTGCGATTCCATTCGCGAATCAACATGA
                   ||     || |   ||||   |  |||||  ||       || ||     | | ||    | ||||| |||||| | |  ||| |||| || ||||| ||||| |||||| | ||| ||| ||| |||||||| ||||| || |||||||||||||| || || ||||| || ||||||||||
tagaatgaaatgtactattgttgaggttttggattttgacttcttgctgatatggatagcttacaag--cacattacaatcttctcctttattttttttcagACTGTACATGAAGGTCGCATATATCAGTTGAAGCTGTTCTGTGACAAAGATTATCCAGAGAAGCCACCAAGTGTCCGTTTTCATTCACGGATCAACATGA

upper sequence: EFJ15952 (Selaginella moellendorffii), 3'ss of exon 2
lower sequence: Vv06s0080g01080.t01 (Vitis vinifera), 3'ss of exon 2
-----------------gtcctctttcttttttttctttctttgctctta-caatgcac-tgactctttcgctttttttttttctcatttattctgtgcagTCTGTTCACGAAGGACGCATTTATCAGCTTAAGTTGTACTGCGACAAAGACTATCCGGATAAGCCACCAAGTGTGCGATTCCATTCGCGAATCAACATGA
                   | | || | |  | |    | | | |||  | | || ||      | ||  | |  ||   | | | | ||| | | | |||||||| || ||||| ||||||||||| || ||| | |  || || ||||| |||||||| ||||| || ||||| || |||||||| || ||||||||||
aagattttgtgtttgatagcttattccatcgtgtatcatgtattctcacatctatacatacagattttatgttcattaactattttaattacttttt-cagTCTGTACATGAAGGTCGCATTTATCAACTGAAGCTTTTTTGTGATAAAGATTATCCGGAGAAGCCTCCTAGTGTACGGTTCCATTCACGCATCAACATGA

upper sequence: EFJ15952 (Selaginella moellendorffii), 3'ss of exon 2
lower sequence: PP1S490_20V6.1 (Physcomitrella patens), 3'ss of exon 3
-------------------gtcctctttcttttttttctttctttgctcttacaatgc-actgactctttcgctttttttttttctcatttattctgtgcagTCTGTTCACGAAGGACGCATTTATCAGCTTAAGTTGTACTGCGACAAAGACTATCCGGATAAGCCACCAAGTGTGCGATTCCATTCGCGAATCAACATGA
                    | |  | | |||  ||||   || ||         ||  ||||| | | || |       ||    |  || || ||| ||||| ||||| ||||| || || ||     | ||  ||| ||||||||| ||||| || ||||||||||||| |||  |||||||||| || ||||||||||
ttacttgtgataaaccccatttcattgtttttgatttcgcactctgtctaagttgtgttactgagt-tgtcaccgacacattcaagctcttgtt-tgtacagTCAGTTCATGAAGGTCGTATCTACACATTGAAACTGTTCTGCGACAAGGACTACCCCGATAAGCCACCAACTGTTAGATTCCATTCTCGGATCAACATGA

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: 27 (upstream exon), 35 (downstream exon)
Score: 30

GGAGAAGGGCCTTGGCGATGCGTCTGTGAGCTTGGGCATGGATGACAGTGACGATGTGTACATGTGTTCGTGGACTGGCACAATTCTGGGGCCTAGCAATgtcctctttc ... ttctgtgcagTCTGTTCACGAAGGACGCATTTATCAGCTTAAGTTGTACTGCGACAAAGACTATCCGGATAAGCCACCAAGTGTGCGATTCCATTCGCGAATCAACATGA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctcttacaatgcactgactctttcgctttttttttttctcatttattctgtgcagTCTGTTCACGAAGGACGCATTTATCAGCTTAAGTTGTACTGCGACAAAGACTATCCGGATAAGCCACCAAGTGTGCGATTCCATTCGCGAATCAACATGA
           cactgac  putative branch site (score: 30)
             ctgactctttcgcttt  CT-rich tract
                          tttttttttttctcat  TA-rich tract