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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagcgtttgctttgcatgatacttgaaacgctcatgagtcccttggtgtcgcagGGTGGCACGTTCACGGTCTCGAACTTGGGTGGACCATTTGGTATCAAACAATTTTGTGCTATCATCAATCCGCCACAGTCGTGCATTCTTGCCGTCGGCA

Basic information

species Selaginella moellendorffii
transcript EFJ13978
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ28117 (Selaginella moellendorffii), 3'ss of exon 11
lower sequence: GRMZM2G161969_T01 (Zea mays), 3'ss of exon 11
---------gtaagc---gtttgctttgcatgatacttgaaacgc---------tcatga------gtcccttggtgtcgcagGGTGGCACGTTCACGGTCTCGAACTTGGGTGGACCATTTGGTATCAAACAATTTTGTGCTATCATCAATCCGCCACAGTCGTGCATTCTTGCCGTCGGCA
         | |  |   || ||||  ||| || |   |||| |           |||||      ||  ||   | |  ||||||||||| |||||| | || |||||||| || || || || ||||||||||| ||||| ||||| ||||| || |||||    ||| | ||  | ||  
gtatatcgtgcatactaggtgtgctaagcaggaaagaagaaatgagaaaaaaaaccatgatatattgttgctgcatttttcagGGTGGCACCTTCACGATATCAAACTTGGGAGGTCCCTTCGGAATCAAACAATTCTGTGCCATCATAAATCCTCCTCAGTCAGCAATTTTGGCTATTGGTT

upper sequence: EFJ28117 (Selaginella moellendorffii), 3'ss of exon 11
lower sequence: GLYMA16G00590.1 (Glycine max), 3'ss of exon 16
-----------------------------------gtaagcgtttgctttgcatgatacttgaaacgctcatgagtcccttggtgtcgcagGGTGGCACGTTCACGGTCTCGAACTTGGGTGGACCATTTGGTATCAAACAATTTTGTGCTATCATCAATCCGCCACAGTCGTGCATTCTTGCCGTCGGCA
                                   || |       | |     | |  || |     |  || ||    | |  |  ||||| || || || || ||  | ||| |||| || ||||||||| |||||||||| ||||| ||||||||||| || ||| |  ||||||||||||| ||  
gtaattagagtttcatgtccattctttattcatctgtgaataacgacctcttgggctggtttatgaatttttgggtggacttgcattacagGGAGGTACATTTACAGTGACTAACCTGGGAGGGCCATTTGGTGTCAAACAATTCTGTGCAATCATCAATCCTCCTCAGGCAGGCATTCTTGCCGTTGGAT

upper sequence: EFJ28117 (Selaginella moellendorffii), 3'ss of exon 11
lower sequence: GLYMA07G03930.2 (Glycine max), 3'ss of exon 16
-----------------------------------gtaagcgtttgctttgcatgatacttgaaacgctcatgagtcccttggtgtcgcagGGTGGCACGTTCACGGTCTCGAACTTGGGTGGACCATTTGGTATCAAACAATTTTGTGCTATCATCAATCCGCCACAGTCGTGCATTCTTGCCGTCGGCA
                                   || |       | |     | |  || |     |  ||  |    | |  |  ||||| || || || || || || ||| |||| || ||||||||| ||| |||||| ||||| ||||||||||| || ||| |  ||||||||||||| ||  
gtaattggagtttcatgtccattctttattcatctgtgaataacgacctcttgggctggtttatgaatttttggcttgaattgcattacagGGAGGTACATTTACAGTGTCTAACCTGGGAGGGCCATTTGGTGTCAGACAATTCTGTGCAATCATCAATCCTCCTCAGGCTGGCATTCTTGCCGTTGGAT

upper sequence: EFJ28117 (Selaginella moellendorffii), 3'ss of exon 11
lower sequence: Vv11s0016g01870.t01 (Vitis vinifera), 3'ss of exon 16
------------------------------gtaagcgtttgcttt--gcatgatacttgaaacgctcatgagtcccttggtgt-cgcagGGTGGCACGTTCACGGTCTCGAACTTGGGTGGACCATTTGGTATCAAACAATTTTGTGCTATCATCAATCCGCCACAGTCGTGCATTCTTGCCGTCGGCA
                               |    | ||| ||    |||| |  || ||| |  | | |    | |  | |  |||||| ||||| || || || ||||||||||| |||||||||||  |||||||||||||||| || |||||||| || || ||  |||| || || || ||  
gtaactgcattaccttctaattggccatcaatggatggttgattgtatcatggtcttttaaatgaacttcatgatcatcatatatgcagGGAGGCACCTTTACTGTTTCGAACTTGGGAGGACCATTTGGAGTCAAACAATTTTGTGCCATAATCAATCCTCCCCAATCCGGCATCCTCGCAGTTGGGT

upper sequence: EFJ28117 (Selaginella moellendorffii), 3'ss of exon 11
lower sequence: Vv09s0002g01800.t01 (Vitis vinifera), 3'ss of exon 17
---------------------------------gtaagcgtttgctttg-catgatacttgaaacgctcatgagtcccttggtgtcgcagGGTGGCACGTTCACGGTCTCGAACTTGGGTGGACCATTTGGTATCAAACAATTTTGTGCTATCATCAATCCGCCACAGTCGTGCATTCTTGCCGTCGGCA
                                 | ||| | | |||  |   | | |  |||||      |  ||||       | |||||| || || || || || || ||  |||| ||||| ||||||||||| ||||| ||||| ||||||||||| || |||||  ||||||| ||| | ||  
gtaaaaattatgtttcaatgttattagttgttggcaagtgatcgctagggtttaacatatgaaaactggcttcgtcctcc----ttgcagGGAGGGACATTTACTGTGTCTAATCTGGGAGGACCCTTTGGTATCAAGCAATTCTGTGCCATCATCAATCCTCCTCAGTCAGGCATTCTAGCCATTGGGT

upper sequence: EFJ28117 (Selaginella moellendorffii), 3'ss of exon 11
lower sequence: PP1S78_56V6.1 (Physcomitrella patens), 3'ss of exon 14
---------------------------------------------gtaagcgtttgctttgcatgatacttgaaacgctcatgagtcccttggtgtcgcagGGTGGCACGTTCACGGTCTCGAACTTGGGTGGACCATTTGGTATCAAACAATTTTGTGCTATCATCAATCCGCCACAGTCGTGCATTCTTGCCGTCGGCA
                                              |     ||| ||| |  |  ||||  |     |  | | | |     |   ||||||||| || || ||  |||| || ||||| ||||| ||||| || |||||||||||||||||||||||||| || ||  |   ||||||||| || || |
attccgtgtttctgtgatttgaagattatgatttttattttttagtttcatttttccttcgttttttactaaatgttttt-taactgcaacaattctgcagGGTGGAACATTTACAATCTCCAATTTGGGAGGACCTTTTGGGATTAAACAATTTTGTGCTATCATCAATCCTCCTCAAGCAGCCATTCTTGCTGTTGGGA

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: 34 (upstream exon), 35 (downstream exon)
Score: 29

GATGCTGATAAGAAAGGGTTGGGAGCTATTTCGGACGATGTAAGAACGTTGGCGGAGAAGGCTAGGGAGAACACACTGAAGCCTAGTGACTACGATgtaagcgttt ... ggtgtcgcagGGTGGCACGTTCACGGTCTCGAACTTGGGTGGACCATTTGGTATCAAACAATTTTGTGCTATCATCAATCCGCCACAGTCGTGCATTCTTGCCGTCGGCA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

taagcgtttgctttgcatgatacttgaaacgctcatgagtcccttggtgtcgcagGGTGGCACGTTCACGGTCTCGAACTTGGGTGGACCATTTGGTATCAAACAATTTTGTGCTATCATCAATCCGCCACAGTCGTGCATTCTTGCCGTCGGCA
                                       tcccttg  CT-rich tract