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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacttggtctttcagtttttttcttagcttgagtcttcgtttccatcgttttccatatactgatcgatggttttgtttgtctccagATATTGATTCCACAGCTCGAGCCTCTCACCGAGCAGCAGCTTTTAGGAATTTGTAACTTACAGCAGTCGTCACAGCAGGCCGAGGACGCTCTCTCGCAAG

Basic information

species Selaginella moellendorffii
transcript EFJ18699
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ18699 (Selaginella moellendorffii), 3'ss of exon 1
lower sequence: LOC_Os06g15480.2 (Oryza sativa), 3'ss of exon 7
----------------gtacttggtctttcagtttttttcttagcttgagtcttcgtttccatcgttttccatatactgatcgatggttttgtttgtctccagATATTGATTCCACAGCTCGAGCCTCTCACCGAGCAGCAGCTTTTAGGAATTTGTAACTTACAGCAGTCGTCACAGCAGGCCGAGGACGCTCTCTCGCAAG
                ||  |    |   || ||        |||   ||  |  |   | | | ||  ||    | || | |||| | ||||||||   ||| |  |       || || ||||| || || || ||||||||  | || || || ||| | ||||||||||| ||||||||||||||||| || ||||| |
gttttgacacgatcgagtgatcacccacccaattcagcaacaagca-aagaatctgaagctaccattgaccgc-cattg-ttgatgatgttgtttgtg--cagGTTCTTGCCAGCCATCTTGAGCCGCTGACGGATCAGCAGCTGATGGGCATCTGCAACCTGCAGCAGTCGTCGCAGCAGGCCGAGGACGCGCTGTCGCAGG

upper sequence: EFJ18699 (Selaginella moellendorffii), 3'ss of exon 1
lower sequence: LOC_Os10g41640.1 (Oryza sativa), 3'ss of exon 1
-----------gtacttggtctttcagtttttttcttagctt-gagtcttc-gtttccatcgttttccat------atactgatcgatggttttgtttgtctccagATATTGATTCCACAGCTCGAGCCTCTCACCGAGCAGCAGCTTTTAGGAATTTGTAACTTACAGCAGTCGTCACAGCAGGCCGAGGACGCTCTCTCGCAAG
           ||  |    |   || ||   |    |||   || |||   | | |||| |  | | ||      ||  |||| |||| | ||||||||   ||| || |       || || ||||| || ||  | |||||| |  | || || || ||| | ||||||||||| ||||||||||||||||| || || || |
gtttgacacgagtgatcacccacccaattcagtaacaagcaaagaatctgaagctaccattgactgctattgttgaatgatgat-gatgatgttgtttgtg--cagGTACTTGAGAGCCATCTTGAGCCGCTGACGAATCAGCAGTTGATGGGCATCTGCAACCTGCAGCAGTCGTCGCAGCAGGCCGAGGACGCGCTGTCACAGG

upper sequence: EFJ18699 (Selaginella moellendorffii), 3'ss of exon 1
lower sequence: GRMZM2G030877_T01 (Zea mays), 3'ss of exon 10
-----------------gtacttg-gtctttcagtttttttcttagcttgagtcttcgtttccatcgttttccatatactgatcgatggttttgtttgtctccagATATTGATTCCACAGCTCGAGCCTCTCACCGAGCAGCAGCTTTTAGGAATTTGTAACTTACAGCAGTCGTCACAGCAGGCCGAGGACGCTCTCTCGCAAG
                 || |    ||   |||| |||   |||||    ||      ||| ||    || | ||| | |   |||   ||   ||    | |||| | || | || ||||| || || || || ||||||||  |  | || || || | | | |||||||| ||||||||||| ||||| ||||||||||| |
ctaagatcacaagaactgttccaatgtaaatcagatttccccttagtacaagaaga-atttgcag---ttccaataaagtatacga-aattccattctgttgcagACACTGCTGCCCCAGCTAGATCCACTGACAGAGCAGCAAGTGGTCGGCATATGCAGCCTTCAGCAGTCATCACAGCAGGCAGAGGAAGCTCTCTCGCAGG

upper sequence: EFJ18699 (Selaginella moellendorffii), 3'ss of exon 1
lower sequence: GRMZM2G366264_T01 (Zea mays), 3'ss of exon 5
------------------------gtacttggtctttcagtttttttcttagcttgagtcttcgtttccatc--gttttccatatactgatcgatggttttgtttgt--ctccagATATTGATTCCACAGCTCGAGCCTCTCACCGAGCAGCAG---CTTTTAGGAATTTGTAACTTACAGCAGTCGTCACAGCAGGCCGAGGACGCTCTCTCGCAAG
                        |||     ||||    | |    ||          |  |   || |||  ||     || |    |   ||  ||||   |||  || ||||   || | || ||||| || || || ||||||||||||   ||  |||| || || ||| |  ||||||||||||||||||| ||||| |||||||| |   
gtatggattcgtctgataatctgtgtagaacatcttctgatgtcaagctgcctgcactacaccagctcgatcaggtgcctaatctgagtacatataattttccatgttgctgcagACGCTGCTGCCCCAGCTAGACCCCCTGACCGAGCAGCAGCAACTGGTAGGCATATGCAACCTTAAGCAGTCGTCACAGCAGGCAGAGGAAGCTCTCTCCC---

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: 29 (upstream exon), 29 (downstream exon)
Score: 18

GAAAGCCGATGTCTTCCACCTCGTCTCTGGGATGTGGAAAACTCCCGCCGAGAGGTGTTTTATGTGGATGGGTGGCTTCAGGCCATCAGAACTTCTCAAGgtacttggtc ... ttgtctccagATATTGATTCCACAGCTCGAGCCTCTCACCGAGCAGCAGCTTTTAGGAATTTGTAACTTACAGCAGTCGTCACAGCAGGCCGAGGACGCTCTCTCGCAAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agtcttcgtttccatcgttttccatatactgatcgatggttttgtttgtctccagATATTGATTCCACAGCTCGAGCCTCTCACCGAGCAGCAGCTTTTAGGAATTTGTAACTTACAGCAGTCGTCACAGCAGGCCGAGGACGCTCTCTCGCAAG
                          tactgat  putative branch site (score: 18)
                                       ttttgtttgtctcc  putative PPT
                                       ttttgttt  TA-rich tract