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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgatctagaatatgtccagctttttttttacttcagcttcatatatttgctgctgcaataatgcgtgcggcaactagatctctgaggccgcattatcagtaattttggtatgattattgtgctactctagtgctcttatttattttcctttggtttgagtttgtttttgtagGTTCTTTTGAATATGCTCGCAGCATACCATCTCCATGTGAAAACTTACGATAATACACTCATCACAAAGTTTTTTGGTCTTCATCGCATTAAGCCATACG

Basic information

species Physcomitrella patens
transcript PP1S311_23V6.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S311_23V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: GLYMA10G06800.1 (Glycine max), 3'ss of exon 4
gtgatctagaatatgtccagctttttttttacttcagcttcatatatttgctgctgcaataatgcgtgcggcaactagatctctgaggccgcattatcagtaattttggtatgattattgtgctactctagtgctcttat-ttattttcctttggtttgagtttgtttt----tgtagGTTCTTTTGAATATGCTCGCAGCATACCATCTCCATGTGAAAACTTACGATAATACACTCATCACAAAGTTTTTTGGTCTTCATCGCATTAAGCCATACG
                                                                         | | || |    | ||    | || |   ||||| ||||     |||  || ||||| | || ||    ||       |||   | |     ||||    ||||||||||| | |  |||||  |||  || |||| ||||||||| || || ||||||||||| |||||||| ||||||||||| ||  | ||||  || |   
-------------------------------------------------------------------------attggagcat--atgcttagtaatgat--attttagtattcac-ttgctcttctctacttctttttcactaaaaaaaattgtgataaccaaattttgaaatgtagGTTCTTCTAAGAATGCTTCCAGACTATCATCACCATGTGAAGACATATGATAATACACTTATCACAAAATTTTTTGGTCTGCACAGGATTATACCTTCGA

upper sequence: PP1S311_23V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: GLYMA13G20980.1 (Glycine max), 3'ss of exon 4
gtgatctagaatatgtccagctttttttttacttcagcttcatatatttgctgctgcaataatgcgtgcggcaactagatctctgaggccgcattatcagtaattttggtatgattattgtgctactctagtgctc-ttatttattttcctttggtttgagtttgtttt----tgtagGTTCTTTTGAATATGCTCGCAGCATACCATCTCCATGTGAAAACTTACGATAATACACTCATCACAAAGTTTTTTGGTCTTCATCGCATTAAGCCATACG
                                                                            |  ||| ||  ||   ||  |   || | ||   ||| |  || ||    | | ||  ||  |||  | |     |||   |||     ||||    ||||||||||| | |  |||||  |||  || |||| ||||||||| || || ||||||||||| |||||||| ||||||||||| ||  | ||||  || |   
--------------------------------------------------------------------------tcaagtctttggagc-atatattt--tagtgttcacatgctc-ttctgtacttttcgttttcactataaaatacaaattgtaatgaccaaattttgaaatgtagGTTCTTCTAAGAATGCTTCCAGACTATCATCACCATGTGAAGACATATGATAATACACTTATCACAAAATTTTTTGGTCTGCACAGGATTATTCCTTCAA
















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), 31 (downstream exon)
Score: 11

GTTGAGGGAGCTTGTTTCACCTGGAAAGAGTGGCAGCGTATTTTATCTCTCGCATGATGACCGATTCATAATCAAAACAATGAAAAAAGCGGAAGTAAAGgtgatctaga ... gtttttgtagGTTCTTTTGAATATGCTCGCAGCATACCATCTCCATGTGAAAACTTACGATAATACACTCATCACAAAGTTTTTTGGTCTTCATCGCATTAAGCCATACG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgtgctactctagtgctcttatttattttcctttggtttgagtttgtttttgtagGTTCTTTTGAATATGCTCGCAGCATACCATCTCCATGTGAAAACTTACGATAATACACTCATCACAAAGTTTTTTGGTCTTCATCGCATTAAGCCATACG
                                          tttgttttt  CT-rich tract
                  ttatttattttccttt  TA-rich tract