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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacgaagatcaagcattgggatctttttaaatttacgaggaaattatttaaatccttgttttgtggagcccttacaaatttattgtcatgcagGCAAAAGGCTACAGAGTTGGACCTGTGTATGATGACGTGCTGTCAATGGCTTGGTTCTTCCTTGAGTTGATTGTGAAGTCCATGGCACTTGAGCAATCTC

Basic information

species Physcomitrella patens
transcript PP1S145_21V6.1
intron # 16
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S145_21V6.1 (Physcomitrella patens), 3'ss of exon 16
lower sequence: GRMZM2G462803_T02 (Zea mays), 3'ss of exon 17
------gtacgaagatcaagcattgggatctttttaaatttacgaggaaattatttaaat-ccttgttttgtggagcccttacaaa-tttattgtcatgcagGCAAAAGGCTACAGAGTTGGACCTGTGTATGATGACGTGCTGTCAATGGCTTGGTTCTTCCTTGAGTTGATTGTGAAGTCCATGGCACTTGAGCAATCTC
|| |||| || || | | || ||| | ||||| | | || | | || | ||| | | | ||||| | |||| ||||| || |||||||| |||||||||||||| ||| || ||||||||||||| || || ||| | ||||| || || |||| | | || ||| ||
tcttgcctatgaagg-catccacaacaagtctatttt-tttgaaacataattacatggttgtactgctctcactagtcactacttactcttttgtcttttagGCGAAAGGTTATAGAGTTGGTCCTGTGTATGATGATGTGTTGGCAATGGCTTGGTTTTTTCTGGAGCTTATTGTAAAATCAATGGGATTGGAACAAAGTC

upper sequence: PP1S145_21V6.1 (Physcomitrella patens), 3'ss of exon 16
lower sequence: AT4G16340.1 (Arabidopsis thaliana), 3'ss of exon 17
--------------------------------------------------------------------------------gtacgaag---atcaagcattgggatctttttaa---atttacgaggaaattatttaaatccttgttttgtggagcccttacaaatttattgtcatgcagGCAAAAGGCTACAGAGTTGGACCTGTGTATGATGACGTGCTGTCAATGGCTTGGTTCTTCCTTGAGTTGATTGTGAAGTCCATGGCACTTGAGCAATCTC
|| ||| | ||| | | | | | || | || | | ||| || |||| | || | || || | ||| | | | ||||||| ||||| ||| | ||||||||||| ||||| || || | |||||||| ||||| ||||| ||||||||||| || || |||||| | |||||| | |
gtacaaattgcacacgttgtctggatgaaactactagcttatctttgttctaatgtgatatatatttgtattatacttataaacaaagttgagcaatctccgtgttactgttcagctatctgctttgaattttcttaattatttctcttttgttgatgaacactattactggccttgcagGCCAAAGGTTACCGGGTTGGACCTGTATATGACGATGTATTATCAATGGCGTGGTTTTTCCTCGAGTTGATTGTTAAATCAATGGCATTGGAGCAAGCAC

upper sequence: PP1S145_21V6.1 (Physcomitrella patens), 3'ss of exon 16
lower sequence: Vv11s0016g00100.t01 (Vitis vinifera), 3'ss of exon 17
---gtacgaagatcaagcattgggatctttttaaat-ttacgaggaaattatttaaatc-------cttgttttgtggagcccttacaaatttattgtcatgcagGCAAAAGGCTACAGAGTTGGACCTGTGTATGATGACGTGCTGTCAATGGCTTGGTTCTTCCTTGAGTTGATTGTGAAGTCCATGGCACTTGAGCAATCTC
| | | | || ||| || || | | | | || ||| |||| || ||||||| | | || || | || ||||||| ||||||||| | || || || ||||||||||| || || ||||||||||||| ||||| ||| | ||||| ||||| |||||| | ||||| |||
tggttgctgtgtttaa--atta--attacttcagacactgcatgggcattttttatatgcatctgacttgtttcattcaatgttttcatccatgacttc-tgcagGCTAAAGGCTACCGTGTAGGGCCAGTGTATGATGATGTCTTGGCAATGGCTTGGTTTTTCCTCGAGCTAATTGTCAAGTCAATGGCATTGGAGCAGACTC

upper sequence: PP1S145_21V6.1 (Physcomitrella patens), 3'ss of exon 16
lower sequence: EFJ04870 (Selaginella moellendorffii), 3'ss of exon 17
gtacgaagatcaagcattgggatctttttaaatttacgaggaaattatttaaatccttgttttgtggagcccttacaaatttattgtcatgcagGCAAAAGGCTACAGAGTTGGACCTGTGTATGATGACGTGCTGTCAATGGCTTGGTTCTTCCTTGAGTTGATTGTGAAGTCCATGGCACTTGAGCAATCTC
|| ||| || || | | || | || || ||||||||||||||||| ||||||||||||| ||||||||||||||||||||||||||| | ||| | || |||| || | || ||||| | |||||| ||
--------------------------------------------gtagcagtatcggaacttcgttagcttgtcatgaaatagttttcttgcagGCAAAAGGCTACCGAGTTGGACCTGTATATGATGACGTGCTGTCAATGGCTTGGGTGTTCTTCGAACTGATCGTTAGATCTATGGCTTTAGAGCAAGCTA

upper sequence: PP1S145_21V6.1 (Physcomitrella patens), 3'ss of exon 16
lower sequence: EFJ09916 (Selaginella moellendorffii), 3'ss of exon 16
gtacgaagatcaagcattgggatctttttaaatttacgaggaaattatttaaatccttgttttgtggagcccttacaaatttattgtcatgcagGCAAAAGGCTACAGAGTTGGACCTGTGTATGATGACGTGCTGTCAATGGCTTGGTTCTTCCTTGAGTTGATTGTGAAGTCCATGGCACTTGAGCAATCTC
|| ||| || || | | || | || || ||||||||||||||||| ||||||||||||| ||||||||||||||||||||||||||| | ||| | || |||| || | || ||||| | || ||| ||
--------------------------------------------gtagcagtatcggaacttcgttagcttgtcatgaaatagttttcttgcagGCAAAAGGCTACCGAGTTGGACCTGTATATGATGACGTGCTGTCAATGGCTTGGGTGTTCTTCGAACTGATCGTTAGATCTATGGCTTTAGAACAAGCTA

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: 19 (upstream exon), 17 (downstream exon)
Score: 1

TGTCCAGTATTTGGACTACGCATTTGACGATTTTGGTGGACGCCATGATCCTGTGTATCCTGGTCTCTGCAGTGTTTGGCGTAGTCTTGCTCGCAGCAAGgtacgaagat ... tgtcatgcagGCAAAAGGCTACAGAGTTGGACCTGTGTATGATGACGTGCTGTCAATGGCTTGGTTCTTCCTTGAGTTGATTGTGAAGTCCATGGCACTTGAGCAATCTC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggaaattatttaaatccttgttttgtggagcccttacaaatttattgtcatgcagGCAAAAGGCTACAGAGTTGGACCTGTGTATGATGACGTGCTGTCAATGGCTTGGTTCTTCCTTGAGTTGATTGTGAAGTCCATGGCACTTGAGCAATCTC
                              cccttac  putative branch site (score: 1)
 ttacaaatttattgt  TA-rich tract