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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagttttggtgatcgaattatgtttttttaagtgggctccgcatttggcctaattttgaaatggaaactgaacacgtgtagatcatttggagtaggttcatcttatcctagctattgccacggtttggatgttcaaaaaaaaactgacaggaatttctctttttgcagGATTTTAAAATTCAGAATATTGTTGGTTCATGTGACGTCAAATTCCCTATCCGACTCGAAGGTTTAGCTTACGCTCACGGTCACTTTTCAAGT

Basic information

species Physcomitrella patens
transcript PP1S13_321V6.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S13_321V6.1 (Physcomitrella patens), 3'ss of exon 5
lower sequence: LOC_Os10g29660.2 (Oryza sativa), 3'ss of exon 3
gtaagttttggtgatcgaattatgtttttttaagtgggctccgcatttggcctaattttgaaatggaaactgaacacgtgtagatcatttggagtaggttcatcttatcctagct-attgccacggtttggatgttcaaaaaaaaactgacaggaatttctctttttgcagGATTTTAAAATTCAGAATATTGTTGGTTCATGTGACGTCAAATTCCCTATCCGACTCGAAGGTTTAGCTTACGCTCACGGTCACTTTTCAAGT
                                                                                         |   |    |  | || |    |  | |||   |  | |||    | |  | |  | ||    | | |    | |  |||||||||| || || ||||| ||||||||||||||||| |||||||| ||||| || || || ||  | |||||  |||| ||    || || |||
----------------------------------------------------------------------------------------gtaatgccactctagctcacatcaattcattcagattgattgtccttgcttatatcagcttgacgcattggaacatgatgcagGATTTCAAGATCCAGAACATTGTTGGTTCATGTGATGTCAAATTTCCTATTCGCCTGGAGGGCCTTGCTTATTCTCATGGCGCATTCTCTAGT

upper sequence: PP1S13_321V6.1 (Physcomitrella patens), 3'ss of exon 5
lower sequence: GRMZM2G161418_T05 (Zea mays), 3'ss of exon 6
gtaagttttggtgatcgaattatgtttttttaagtgggctccgcatttggcctaattttgaaatggaaactgaacacgtgtagatcatttggagtaggttcatcttatcctagctattgccacggtttggatgttcaaaaaaaaactgacaggaatttctctttttgcagGATTTTAAAATTCAGAATATTGTTGGTTCATGTGACGTCAAATTCCCTATCCGACTCGAAGGTTTAGCTTACGCTCACGGTCACTTTTCAAGT
                                                                               |||  |  ||   | | | |  |  ||  |||     |||  ||  | || |  |         |  ||  | |    | |  |    ||||||||||| ||||||||||||||||| || ||||| ||||| || || ||  | || || ||  | || ||  |||| |||  ||| ||||||
-------------------------------------------------------------------------------gtaactttttcatacttg-tgtacattgacctgttctttga-acaatatgtacatc--------agttgctaagttgctgttctaagccagGATTTTAAGATTCAGAATATTGTTGGCTCTTGTGATGTCAAGTTTCCAATTAGGCTTGAGGGCCTTGCATATTCTCATGGTGCCTTCTCAAGT

upper sequence: PP1S13_321V6.1 (Physcomitrella patens), 3'ss of exon 5
lower sequence: GLYMA18G44460.1 (Glycine max), 3'ss of exon 5
gtaagttttggtgatcgaattatgtttttttaagtgggctccgcatttggcctaattttgaaatggaaactgaacacgtgtagatcatttggagtaggttcatcttatcctagctattgccacggtttg-gatgttcaaaaaaaaactgacaggaatttctctttttgcagGATTTTAAAATTCAGAATATTGTTGGTTCATGTGACGTCAAATTCCCTATCCGACTCGAAGGTTTAGCTTACGCTCACGGTCACTTTTCAAGT
                                                                 |  ||   |  ||    ||  |||   ||| | ||       |||   |||  |     ||||| |||  |  |   |   ||        ||| |  |  |  |||||||||| ||||||||||||||||| || ||||| || || ||||| || ||||| || ||| | || ||  | || |||   || ||||| 
-----------------------------------------------------------------ggtacaacatccgctctgaaaattgtcagttgttt-------tccactctacagaagtagtttgtgatcattgacttattccttttttttcttttttgtgctttaGGATTTTAAGATTCAGAATATTGTTGGCTCTTGTGATGTAAAGTTCCCCATTCGACTGGAGGGTCTTGCCTATTCCCATGGTGCTTTCTCAAG-

upper sequence: PP1S13_321V6.1 (Physcomitrella patens), 3'ss of exon 5
lower sequence: AT3G13445.1 (Arabidopsis thaliana), 3'ss of exon 6
gtaagttttggtgatcgaattatgtttttttaagtgggctccgcatttggcctaattttgaaatggaaactgaacacgtgtagatcatttggagtaggttcatcttatcc--tagctattgccacggtttggatgttcaaaaaaaaactgacaggaatttctctttttgcagGATTTTAAAATTCAGAATATTGTTGGTTCATGTGACGTCAAATTCCCTATCCGACTCGAAGGTTTAGCTTACGCTCACGGTCACTTTTCAAGT
                                                                             ||  |  |  |||  |     ||   | |||||   |  | ||  |    ||| | |  |   ||| | | | |    | | |  | |  |||||||||| || |||||||||||||| ||||| ||||| ||||||||||||||  |||| |||||| | |||||| |||||| |   || ||||||
-----------------------------------------------------------------------------gtacaatttctttaaacc---ttttccctatccaacattttttttcttacttttgcttatactaaatatattca----attgttacatcctgcagGATTTCAAGATTCAGAATATTGTAGGTTCTTGTGATGTCAAATTCCCTATAAGACTTGAAGGTCTTGCTTACTCTCACGCTGCTTTCTCAAGT

upper sequence: PP1S13_321V6.1 (Physcomitrella patens), 3'ss of exon 5
lower sequence: AT1G55520.1 (Arabidopsis thaliana), 3'ss of exon 6
gtaagttttggtgatcgaattatgtttttttaagtgggctccgcatttggccta-attttgaaatggaaactgaacacgtgtagatcatttg-gagtaggttcatcttatcctagctattgccacggtttggatgttcaaaaaaaaactgacaggaatttctctttttgcagGATTTTAAAATTCAGAATATTGTTGGTTCATGTGACGTCAAATTCCCTATCCGACTCGAAGGTTTAGCTTACGCTCACGGTCACTTTTCAAGT
                 | | || | | | |   |||  |||  ||   ||  | | | ||  ||  |   | | | |   |  |  ||| | | |||  || |||  |    ||  |     ||| | |  |   |   || |||| ||         |  | |||||||||||||||| || ||||| ||||| || |||||||| ||||||||||| ||  | || |||||| | || ||| ||||  ||   || ||||||
---------------gtactcatatgtctctctctgg--tcctgatccagcacacactgtgttattcatttttatctca-atcaacaattcgtgtgtatttttatcgga----aggaaaaattacg-tataaagtctagtaataaaattgctga-----ttacattttgcagGATTTTAAGATACAGAACATTGTAGGCTCATGTGATGTCAAATTCCCCATTAGGCTTGAAGGTCTTGCATACTCTCATAGTGCTTTCTCAAGT

upper sequence: PP1S13_321V6.1 (Physcomitrella patens), 3'ss of exon 5
lower sequence: EFJ36040 (Selaginella moellendorffii), 3'ss of exon 5
gtaagttttggtgatcgaattatgtttttttaagtgggctccgcatttggcctaattttgaaatggaaactgaacacgtgtagatcatttggagtaggttcatcttatcctagctattgccacggtttggatgttcaaaaaaaaactgacaggaatttctctttttgcagGATTTTAAAATTCAGAATATTGTTGGTTCATGTGACGTCAAATTCCCTATCCGACTCGAAGGTTTAGCTTACGCTCACGGTCACTTTTCAAGT
                                                                                                              |    |     ||   |||   ||   |    |||||   || ||  ||  |  | |||||||||||| || ||||| |||||||| || |||||||| || ||||| ||| || | || ||  | || ||||||||||||||||| ||||| 
-----------------------------------------------------------------------------------------------------------gtatgaagacgaaaacacattgtg-gtctgagctcaaact--tagtaacgtccgtgatcgcagGATTTTAAGATCCAGAACATTGTTGGCTCCTGTGACGTTAAGTTCCCGATCAGATTGGAGGGCCTGGCGTACGCTCACGGTCACTTCTCAAGC

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: 23 (upstream exon), 14 (downstream exon)
Score: 2

TATGCTCGAATCATTCAAAAGCTTGGTTTTCCAGCCCAATTCAAGgtaagttttg ... ctttttgcagGATTTTAAAATTCAGAATATTGTTGGTTCATGTGACGTCAAATTCCCTATCCGACTCGAAGGTTTAGCTTACGCTCACGGTCACTTTTCAAGT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attgccacggtttggatgttcaaaaaaaaactgacaggaatttctctttttgcagGATTTTAAAATTCAGAATATTGTTGGTTCATGTGACGTCAAATTCCCTATCCGACTCGAAGGTTTAGCTTACGCTCACGGTCACTTTTCAAGT
                            aactgac  putative branch site (score: 2)
                                        tttctctttttgc  putative PPT
               atgttcaaaaaaaaa  TA-rich tract