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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTTGAAGAACTGCAAACTATCTGGAAACTTTTTCAACATACTCTTTAATCTCAATAAATTCGTGGCATTTGAAACCAGGGATCCGTTTTTGATCAGAATGgtaaagcaattcagacagcactatttccatcaaattgagatttgccatatctcagcatgttgcttcaaatccatatcacctactttcaaacgcttcgattcatctcctgataattgttccctggtcatcacatctgcctcgttgacttacctatttgggtcctaaagttccgttccttatggttgcag

Basic information

species Physcomitrella patens
transcript PP1S68_31V6.2
intron # 11
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S68_31V6.2 (Physcomitrella patens), 5'ss of exon 11
lower sequence: GRMZM2G040094_T01 (Zea mays), 5'ss of exon 10
TTTGAAGAACTGCAAACTATCTGGAAACTTTTTCAACATACTCTTTAATCTCAATAAATTCGTGGCATTTGAAACCAGGGATCCGTTTTTGATCAGAATGgtaaagcaattcagacagcactatttccatcaaattgagatttgccatatctca-gcatgttgcttcaaatccatatcacctactttcaaacgcttcgattcatctcctgataattgttccctggtcatcacatctgcctcgttgacttacctatttgggtcctaaagttccgttccttatggttgcag
 ||    |  |||||| | |||||  | || |||||||| ||||||||||| || |||||| ||||||||||| | ||||| || ||  | ||| |    || |  |  |  ||      || ||    | | |       |||  | ||||||        | ||   |    || ||| |    |      |  | || ||    | |                                                                               
CTTCCGAAGGTGCAAATTGTCTGGGCATTTCTTCAACATTCTCTTTAATCTGAACAAATTCATGGCATTTGAAGCTAGGGACCCATTCCTCATCCGCCAAgtgagtcggtcgagttc---cttttcgtgttataccatccattggta-atctcatatgaacagtttgtcacttgtaacacttttgctt---tcccccaatccaagcgcag-------------------------------------------------------------------------------

upper sequence: PP1S68_31V6.2 (Physcomitrella patens), 5'ss of exon 11
lower sequence: AT5G28900.1 (Arabidopsis thaliana), 5'ss of exon 11
TTTGAAGAACTGCAAACTATCTGGAAACTTTTTCAACATACTCTTTAATCTCAATAAATTCGTGGCATTTGAAACCAGGGATCCGTTTTTGATCAGAATGgtaaagcaattcagacagcactatttccatcaaattgagatttgccatatctcagcatgttgcttcaaatccatatcacctactttcaaacgcttcgattcatctcctgataattgttccctggtcatcacatctgcctcgttgacttacctatttgggtcctaaagttccgttccttatggttgcag
  ||||   ||  || || ||||||||| | |||||||| || ||||||||||| |||||  |||||||||||||| ||||||| ||  | ||  |   ||||   | | |||   |       || |  |         ||   || | | |  ||||   |||  ||  ||| ||   || | |||||||    ||  ||                                                                                      
CCTGAAAGGCTCAAAGCTCTCTGGAAACGTCTTCAACATCCTATTTAATCTCAACAAATTTATGGCATTTGAAACCCGGGATCCATTCCTCATTCGTCAGgta---ctaatcatctaatttaccttgctac---------ttcttcacaccaccacatgcgtcttataa--catttc---taatgtcaaacg----gaaacag-------------------------------------------------------------------------------------

upper sequence: PP1S68_31V6.2 (Physcomitrella patens), 5'ss of exon 11
lower sequence: AT5G28850.1 (Arabidopsis thaliana), 5'ss of exon 10
TTTGAAGAACTGCAAACTATCTGGAAACTTTTTCAACATACTCTTTAATCTCAATAAATTCGTGGCATTTGAAACCAGGGATCCGTTTTTGATCAGAATGgtaaagcaattcagacagcactatttccatcaaattgagatttgccatat-ctcagcatgttgcttcaaatccatatcacctactttcaaacgcttcgattcatctcctgataattgttccctggtcatcacatctgcctcgttgacttacctatttgggtcctaaagttccgttccttatggttgcag
  ||||   ||  || || ||||||||| | |||||||| || |||||||| || |||||  |||||||||||||| ||||||||||  | ||  |              ||||  |  |||       | | ||| |   ||||  | | ||   ||   ||   |   |  |      | | | |||||||     |                                                                                          
CCTGAAAGGCTCAAAGCTCTCTGGAAACGTCTTCAACATCCTTTTTAATCTAAACAAATTTATGGCATTTGAAACCCGGGATCCGTTCCTCATTCG--------------TCAGgtactactccacgtttgatattcaaccttgctgttttcttgacacaatgggcctcttataacatttcaaatgtcaaacgaaaacag-----------------------------------------------------------------------------------------

upper sequence: PP1S68_31V6.2 (Physcomitrella patens), 5'ss of exon 11
lower sequence: AT5G44090.1 (Arabidopsis thaliana), 5'ss of exon 11
TTTGAAGAACTGCAAACTATCTGGAAACTTTTTCAACATACTCTTTAATCTCAATAAATTCGTGGCATTTGAAACCAGGGATCCGTTTTTGATCAGAATGgtaaagcaattcagacagcactatttccatcaaattgagatttgccatatctcagcatgttgcttcaaatccatatcacctactttcaaacgcttcgattcatctcctgataattgttccctggtcatcacatctgcctcgttgacttacctatttgggtcctaaagttccgttccttatggttgcag
| ||||    | |||||| ||||||||  ||||||| ||||||||||| || || |||||| |||| ||||||||| | || || ||| | ||  |   ||||||   |      |   |   ||| | ||   ||| | | | | ||   ||     | || || |||    ||  ||  | | |  |    | | ||  |                                                                                      
TCTGAAAGCATCCAAACTTTCTGGAAATATTTTCAATATACTCTTTAACCTGAACAAATTCATGGCGTTTGAAACCCGTGACCCTTTTCTCATTCGTCAGgtaaacataggttttctatagagttttcctccctttg-gttattcaatccttcgtttagctg-ttgaaactgttactactgaatatttattaatgccataaa--------------------------------------------------------------------------------------

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: 32 (upstream exon), 35 (downstream exon)
Score: 16

TTTGAAGAACTGCAAACTATCTGGAAACTTTTTCAACATACTCTTTAATCTCAATAAATTCGTGGCATTTGAAACCAGGGATCCGTTTTTGATCAGAATGgtaaagcaat ... atggttgcagGAAAGGGAAGATCCTACATTGACCGAATGGGACCGATTTGCGCATGCTGAGTACATCCGCCTGGCAATGGAGGAGGACGGTGAGGATGTTTTCATGGATG




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