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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTTATTGTCAACACGAGCTGGTGGTTTAGGCATTAATCTTGCCACTGCAGATACTGTCATTATATTCGATTCGGATTGGAATCCTCAGAATGATCTACAGgtctgcttcctgaaggttttacctgcttaaatagatgaagtgttgtatgcgctatgtaaaaacttaatgaatctgtttaaatggatgctagagttcttcaaccgtctgctttaacatttctttggagtaataactgcatttttctgaaaagcttgtttcctgcag

Basic information

species Physcomitrella patens
transcript PP1S93_123V6.1
intron # 20
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S93_123V6.1 (Physcomitrella patens), 5'ss of exon 20
lower sequence: LOC_Os07g46590.1 (Oryza sativa), 5'ss of exon 8
CTTATTGTCAACACGAGCTGGTGGTTTAGGCATTAATCTTGCCACTGCAGATACTGTCATTATATTCGATTCGGATTGGAATCCTCAGAATGATCTACAGgtctgcttcctgaaggttttacctgcttaaatagatgaagtgttgtatgcgctatgtaaaaacttaatgaatctgtttaaatggatgctagagttcttcaaccgtctgctttaacatttctttggagtaataactgcatttttctgaaaagcttgtttcctgcag
  |  |||| ||||| ||||||||  | || ||||||||||| || |||||||| || || || || ||||| || |||||||| || |||||| |||||||   | ||       | |  |   ||   ||| |||  || ||  ||    | |||     ||| |   |  |  | | ||      | | ||| || ||  || || | | |   |                                               
TCTTCTGTCTACACGTGCTGGTGGGCTTGGTATTAATCTTGCAACAGCAGATACCGTGATCATTTTTGATTCAGACTGGAATCCGCAAAATGATTTACAGgttcccctctc-----tctctctctctctcatatatgg-gttttcaat---ttttgt-----cttgaaagagtttctcatat-----ttcgggtttttgaat-gtgtgatgtcatgctag---------------------------------------------

upper sequence: PP1S93_123V6.1 (Physcomitrella patens), 5'ss of exon 20
lower sequence: GRMZM2G010342_T01 (Zea mays), 5'ss of exon 18
CTTATTGTCAACACGAGCTGGTGGTTTAGGCATTAATCTTGCCACTGCAGATACTGTCATTATATTCGATTCGGATTGGAATCCTCAGAATGATCTACAGgtctgcttcctgaaggttttacctgcttaaatagatgaagtgttgtatgcgctatgtaaaaacttaatgaatctgtttaaatggatgctag--agttcttcaaccgtctgctttaacatttctttggagtaataactgcatttttctgaaaagcttgtttcctgcag
                               ||||||||||| ||||||||||| || || || || ||||| ||||||||||| || |||||||| |||||       || |   | || |      || |   ||      |  |   | | | |  |   ||| |   | | | |   |  ||  | |  ||  | | |   |    | | |  |||       || |                                    
------------------------------TATTAATCTTGCAACTGCAGATACAGTGATAATTTTTGATTCAGATTGGAATCCACAAAATGATCTGCAGGTTCTTCCTCTCATTCTCTTCCTCCTGCAAgtgtgtgtctaacttaaaaagatttatttatctttattatgtttttatggttcaatttttgctaggccatgagtagggcacat-aggattggccaacagga------------------------------------

upper sequence: PP1S93_123V6.1 (Physcomitrella patens), 5'ss of exon 20
lower sequence: GLYMA02G45000.1 (Glycine max), 5'ss of exon 19
CTTATTGTCAACACGAGCTGGTGGTTTAGGCATTAATCTTGCCACTGCAGATACTGTCATTATATTCGATTCGGATTGGAATCCTCAGAATGATCTACAGgtctgcttcctgaaggttttacctgctta--aatagatgaagtgttgtatgcgctatgtaaaaacttaatgaatctgtttaaatggatgctagagttcttcaaccgtctgctttaacatttctttggagtaataactgcatttttctgaaaagcttgtttcctgcag
| |  | |||||||| || || ||| | || || |||||||| || ||||| ||||| || ||||| ||||| |||||||||||||| ||||| || ||||| | |  |     | ||| |  |  | |  |||  |  || | ||   ||     ||| |   ||  |||    | ||||                                                                                      
CCTTCTTTCAACACGGGCAGGAGGTCTGGGTATCAATCTTGCTACAGCAGACACTGTTATAATATTTGATTCTGATTGGAATCCTCAAAATGACCTGCAGgtattcagct----gatttaattttatcattaatcaacaaaatatttggtgtttactgttacttct--atg---ttttttag-------------------------------------------------------------------------------------

upper sequence: PP1S93_123V6.1 (Physcomitrella patens), 5'ss of exon 20
lower sequence: EFJ29460 (Selaginella moellendorffii), 5'ss of exon 18
CTTATTGTCAACACGAGCTGGTGGTTTAGGCATTAATCTTGCCACTGCAGATACTGTCATTATATTCGATTCGGATTGGAATCCTCAGAATGATCTACAGgtctgcttcctgaaggttttacctgcttaaatagatgaagtgttgtatgcgctatgtaaaaacttaatgaatctgtttaaatggatgctagagttcttcaaccgtctgctttaacatttctttggagtaataactgcatttttctgaaaagcttgtttcctgcag
| || | |||||| |||| || ||  | || || |||||||| |||||||| ||||| ||||| || ||||| ||||||||||| |||||||| || || ||  | || ||     ||||      | | | || |    | ||  | |  |||||||                                                                                                           
CCTACTTTCAACAAGAGCGGGGGGCCTTGGAATCAATCTTGCTACTGCAGACACTGTGATTATCTTTGATTCTGATTGGAATCCACAGAATGACCTTCAAgtaagttttct-----ttttgaaaattcaca-agtt----tattccacgttctatgtag----------------------------------------------------------------------------------------------------------

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: 16 (upstream exon), 25 (downstream exon)
Score: 2

CTTATTGTCAACACGAGCTGGTGGTTTAGGCATTAATCTTGCCACTGCAGATACTGTCATTATATTCGATTCGGATTGGAATCCTCAGAATGATCTACAGgtctgcttcc ... tttcctgcagGCAATGAGTAGAGCACATCGTATTGGGCAGCGGGATGTTGTGAATATATATCGTTTTGTAATTAGTCGGAGTGTTGAGGAGGATATTCTCGAGCGGGCGA




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