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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTACTTCAAGGGTCCTGAGCTGCTGGTTGATCTTCAAGATTATGATTACTCTCTCGACATGTGGAGCTTGGGGTGCATGTTTGCCGGCATGgtaaatttaattccaagttcaatatttcgatggtccttgattatcacagtttgtcgctacgttgatttgctttttggtttagtttttgagcttgattctcgttaaacaggtgaattgaagtgattgcag

Basic information

species Physcomitrella patens
transcript PP1S165_119V6.2
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S165_119V6.1 (Physcomitrella patens), 5'ss of exon 6
lower sequence: LOC_Os03g55389.1 (Oryza sativa), 5'ss of exon 5
GTACTTCAAGGGTCCTGAGCTGCTGGTTGATCTTCAAGATTATGATTACTCTCTCGACATGTGGAGCTTGGGGTGCATGTTTGCCGGCATGgtaaatttaattccaagttcaatatttcgatggtccttgattatcacagtttgtcgctacgttgatttgctttttggtttagtttttgagcttgattctcgttaaacaggtgaattgaagtgattgcag
||| |||||||| |||||||| || |||||| | |||||||||||||| ||| | |||||||||||| | || ||||||||||| || ||||||  | |   |  ||    || || |||   |||   |   ||  | |  | ||  ||   |  | |  | ||     ||  | |   |  |||     |||||     ||   ||| |         
GTATTTCAAGGGGCCTGAGCTTCTTGTTGATTTGCAAGATTATGATTATTCTTTGGACATGTGGAGCCTTGGTTGCATGTTTGCTGGGATGgtatgtgtggctgtaa----aaaatatcgcctgtctaggtcaatgtctggatatc--taatgtactattgtattgataataagtctgacgtctgaactcagttaactgtatgctatgatgcag------

upper sequence: PP1S165_119V6.1 (Physcomitrella patens), 5'ss of exon 6
lower sequence: LOC_Os07g02350.1 (Oryza sativa), 5'ss of exon 5
GTACTTCAAGGGTCCTGAGCTGCTGGTTGATCTTCAAGATTATGATTACTCTCTCGACATGTGGAGCTTGGGGTGCATGTTTGCCGGCATGgtaaatttaattccaagttcaatatttcgatggtccttgattatcacagtttgtcgctacgttgatttgctttttggtttagttt-ttgagcttgattctcgttaaacaggtgaattgaagtgattgcag
|||||||||||| |||||||| || |||||  | ||||||||||| |||||| | |||||||||||  | || ||||||||||| || ||||||    | |     |  |  |||  |   |  | ||   ||     | |||||        ||  ||  | | |     | ||   ||    ||||||  | |||  | |||  |||   ||| |||||
GTACTTCAAGGGACCTGAGCTTCTTGTTGACTTGCAAGATTATGACTACTCTTTGGACATGTGGAGTCTTGGTTGCATGTTTGCTGGAATGgta----ttaccatgacatttatacattactttttctcatttcatcaattttgtaatgcaactgcctttttctataaaagaattaactggtgctgattc--gctaataatgtg--ttgt--tgagtgcag

upper sequence: PP1S165_119V6.1 (Physcomitrella patens), 5'ss of exon 6
lower sequence: GRMZM5G845755_T02 (Zea mays), 5'ss of exon 5
GTACTTCAAGGGTCCTGAGCTGCTGGTTGATCTTCAAGATTATGATTACTCTCTCGACATGTGGAGCTTGGGGTGCATGTTTGCCGGCATGgtaaatttaattccaagttcaatatttcgatggtccttgattatcacagtttgtcgctacgttgatttgctttttggtttagtttttgagcttgattctcgttaaacaggtgaattgaagtgattgcag
||||||||||||||||||||| || |||||  | |||||||||||||||||||| |||||||||||  |||| ||||||||||| || ||||||   |||    || |   | |||  | ||   |  | || ||| |  ||| | | ||  ||  | || ||  |  |  |  |    |   | | |||  || | ||  ||   |    || ||||||
GTACTTCAAGGGTCCTGAGCTTCTTGTTGACTTGCAAGATTATGATTACTCTCTGGACATGTGGAGTCTGGGCTGCATGTTTGCTGGAATGgta---ttacccacacgactattatacctatttgctgtcat-atccctttttttag-tat-ttcttgtgattccttatagacatgaccaatattaatct-atttatcatatgctgt----tggttgcag

upper sequence: PP1S165_119V6.1 (Physcomitrella patens), 5'ss of exon 6
lower sequence: GRMZM5G845755_T01 (Zea mays), 5'ss of exon 4
---------GTACTTCAAGGGTCCTGAGCTGCTGGTTGATCTTCAAGATTATGATTACTCTCTCGACATGTGGAGCTTGGGGTGCATGTTTGCCGGCATGgtaaatttaattccaagttcaatatttcgatggtccttgattatcacagtttgtcgctacgttgatttgctttttggtttagtttttgagcttgattctcgttaaacaggtgaattgaagtgattgcag
         ||||||||||||||||||||| || |||||  | |||||||||||||||||||| |||||||||||  |||| ||||||||||| || ||||||   |||    || |   | |||  | ||   |  | || ||| |  ||| | | ||  ||  | || ||  |  |  |  |    |   | | |||  || | ||  ||   |    || ||||||
GGAATTCAGGTACTTCAAGGGTCCTGAGCTTCTTGTTGACTTGCAAGATTATGATTACTCTCTGGACATGTGGAGTCTGGGCTGCATGTTTGCTGGAATGgta---ttacccacacgactattatacctatttgctgtcat-atccctttttttag-tat-ttcttgtgattccttatagacatgaccaatattaatct-atttatcatatgctgt----tggttgcag

upper sequence: PP1S165_119V6.1 (Physcomitrella patens), 5'ss of exon 6
lower sequence: GRMZM2G143602_T01 (Zea mays), 5'ss of exon 5
GTACTTCAAGGGTCCTGAGCTGCTGGTTGATCTTCAAGATTATGATTACTCTCTCGACATGTGGAGCTTGGGGTGCATGTTTGCCGGCATGgtaaatttaattccaagttcaatatttcgatggtccttgattatcacagtttgtcgctacgttgatttgctttttggtttagtttttgagcttgattctcgttaaacaggtgaattgaagtgattgcag
|||||||||||| |||||||| || |||||  | |||||||||||||||||| | |||||||||||  |||| ||||||||||| || ||||||  ||||    ||   | | |||| |       | |  ||    |  | |   | ||   |  |||| | | |      |||| | |     ||    | ||  | | |    ||   |||||||||
GTACTTCAAGGGGCCTGAGCTTCTTGTTGACTTGCAAGATTATGATTACTCTTTGGACATGTGGAGTCTGGGCTGCATGTTTGCTGGGATGgta--tttacccaca---ttactattcca------cctatttgctgccatatcctgatatcctcctttggtatctctgacggtttcttatagaaataactggta--ctgatttgctgttctgattgcag

upper sequence: PP1S165_119V6.1 (Physcomitrella patens), 5'ss of exon 6
lower sequence: GRMZM2G047855_T01 (Zea mays), 5'ss of exon 5
GTACTTCAAGGGTCCTGAGCTGCTGGTTGATCTTCAAGATTATGATTACTCTCTCGACATGTGGAGCTTGGGGTGCATGTTTGCCGGCATGgta----------aatttaattccaagttcaatattt-------cgatggtccttgat------tatcacagtttgtcgctacgttgatttgctttttggtttagtttttgagcttgattctcgttaaacaggtgaattgaagtgattgcag---
||| |||||||| ||||| || || |||||| | ||||| |||||||| ||| | |||||||||||  | || ||||||||||| || ||||||          | |    |  | || | |||| |        | || |   ||||       ||  ||  || | | | | |  ||||  | ||||| |  |||  || ||     || |    | | | ||    |||  ||||||| |   
GTATTTCAAGGGACCTGAACTCCTTGTTGATTTACAAGACTATGATTATTCTTTGGACATGTGGAGTCTTGGTTGCATGTTTGCTGGAATGgtatgtacacaaaagtgctgtctctaggttaatactattggacacaattgggtttgacattctgtaatactattggacacgatggggattgacattttg-tcaagtgcttcagtggttttttacccatatatgtttgctgac-tgattgctgcag

upper sequence: PP1S165_119V6.1 (Physcomitrella patens), 5'ss of exon 6
lower sequence: GRMZM2G141903_T01 (Zea mays), 5'ss of exon 5
GTACTTCAAGGGTCCTGAGCTGCTGGTTGATCTTCAAGATTATGATTACTCTCTCGACATGTGGAGCTTGGGGTGCATGTTTGCCGGCATGgtaaatttaattccaagttcaatatttcgatggtccttgattatcacagtttgtcgctacgttgatttgctttttggtttagtttttgagcttgattctcgttaaacaggtgaattga--agtgattgcag
||| |||||||| ||||| || || |||||| | ||||| |||||||| ||| | |||||||||||  | || ||||||||||| || ||||||  |  |  |  || | |  |   |   |      |      |||| |||   |    |  | ||  | |||||     | ||| | | ||  || |   || | | ||    |||    ||  |||||
GTATTTCAAGGGACCTGAACTCCTTGTTGATTTACAAGACTATGATTATTCTTTAGACATGTGGAGTCTTGGTTGCATGTTTGCTGGAATGgtatgtacatgtaaaaatgctctccctaccttaatactatcagacacaatttaggggggag--ggttgacattttgtcagtgctttcgtgttt--ttttacctatatatgtttgctgactgatggctgcag

upper sequence: PP1S165_119V6.1 (Physcomitrella patens), 5'ss of exon 6
lower sequence: GLYMA05G22320.1 (Glycine max), 5'ss of exon 5
GTACTTCAAGGGTCCTGAGCTGCTGGTTGATCTTCAAGATTATGATTACTCTCTCGACATGTGGAGCTTGGGGTGCATGTTTGCCGGCATGgtaaat-------ttaattccaagttcaatatttcgatggtccttgattatcac--agtttgtcgctacgttgatttgctttttggtttagtttttgagcttgattctcgttaaacaggtgaattgaagtgattgcag----------------------------------------------------
 || ||||| ||||||||||| || |||||||||||||| |||||||||||||| ||  | |||||  | || || |||||||| || |||||||||       ||   | ||||| |||| |||  ||  | | |  || |  |   |||| ||  | |   |||   | ||    | | | |||   || ||||   |   ||         ||||||| ||  |||                                                    
ATATTTCAAAGGTCCTGAGCTTCTTGTTGATCTTCAAGACTATGATTACTCTCTAGATTTATGGAGTCTTGGTTGTATGTTTGCTGGGATGgtaaatggttcactttccttcaagtgcaatttttatattatacattgttttggcctggtttttcctttctgagataaaccttagaatcttgatttactgcatgatatac--caatttctccttttgaagtcat-acaggtttaaatctcctcccctgcttgcctcatgcttgtgtttttactttttacag

upper sequence: PP1S165_119V6.1 (Physcomitrella patens), 5'ss of exon 6
lower sequence: GLYMA17G17520.2 (Glycine max), 5'ss of exon 5
GTACTTCAAGGGTCCTGAGCTGCTGGTTGATCTTCAAGATTATGATTACTCTCTCGACATGTGGAGCTTGGGGTGCATGTTTGCCGGCATGgtaaatttaattccaagttcaatatttcgatggtccttgattatcacagtttgtcgctacgttgatttgctttttggtttagtttttgag-cttgattctcgtta-aacaggtgaattgaagtgattgcag------------------------------------------------------------
 || ||||| ||||| ||||| || |||||||||||||| |||||||||||||| ||  | |||||  | || || |||||||| || |||||||||     | ||  |||  |     |    |  || ||||| |||  ||||     | | | | | | |||  | | |   || ||  ||| ||   | | |  | || | ||||       ||| ||                                                            
ATATTTCAAAGGTCCCGAGCTTCTTGTTGATCTTCAAGACTATGATTACTCTCTAGATTTATGGAGTCTTGGTTGTATGTTTGCTGGGATGgtaaat---ggttcactttccttcaaatgcaatttttttattattaca--ttgtttaggcctggttcttcctttgagataaaccttagaatctttatctacttcatgatagatcaatttctccttttgaagtcatacagatttaaatctcctcccctgcttgcctcatgcttgtgtatttacgttttacag

upper sequence: PP1S165_119V6.1 (Physcomitrella patens), 5'ss of exon 6
lower sequence: EFJ20478 (Selaginella moellendorffii), 5'ss of exon 5
GTACTTCAAGGGTCCTGAGCTGCTGGTTGATCTTCAAGATTATGATTACTCTCTCGACATGTGGAGCTTGGGGTGCATGTTTGCCGGCATGgtaaatttaattccaagt--tcaatatttcgatggtccttgattatcacagtttgtcgctacgttgatttgctttttggtttagtttttgagcttgattctcgttaaacaggtgaattgaagtgattgcag
 |||||||| ||||| |||||||| || || || || || || |||||||||||||||||||||||| | || |||||||| || || ||||| | | |  |  |   |  |   || ||       ||   |   ||||||                                                                                
ATACTTCAAAGGTCCGGAGCTGCTTGTGGACCTGCAGGACTACGATTACTCTCTCGACATGTGGAGCCTAGGCTGCATGTTCGCTGGAATGgtgagtcttttgtctgatcattcgtacttgctaacgccccaagcttcacag--------------------------------------------------------------------------------

Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|37852401|gb|BJ610409.1|BJ610409
EST:     ATGATTACTCTCTCGACATGTGGAGCTTGGGGTGCATGTTTGCCGGCATG                         ATATTTCGGAAGGAGCCATTCTTTTATGGGCATGACAATTATGATCAACTT
genomic: ATGATTACTCTCTCGACATGTGGAGCTTGGGGTGCATGTTTGCCGGCATGgtaaatttaa ... gtgattgcagATATTTCGGAAGGAGCCATTCTTTTATGGGCATGACAATTATGATCAACTT
EST: gi|37844002|gb|BJ602010.1|BJ602010
EST:     ATGATTACTCTCTCGACATGTGGAGCTTGGGGTGCATGTTTGCCGGCATG                         ATATTTCGGAAGGAGCCATTCTTTTTATGGGCATGACAATTATGATCAACT
genomic: ATGATTACTCTCTCGACATGTGGAGCTTGGGGTGCATGTTTGCCGGCATGgtaaatttaa ... gtgattgcagATATTTCGGAAGGAGCCATTC-TTTTATGGGCATGACAATTATGATCAACT
EST: gi|162267952|gb|FC444033.1|FC444033
EST:     ATGATTACTCTCTCGACATGTGGAGCTTGGGGTGCATGTTTGCCGGCATG                         ATATTTCGGAAGGAGCCATTCTTTTATGGGCATGACAATTATGATCAACTT
genomic: ATGATTACTCTCTCGACATGTGGAGCTTGGGGTGCATGTTTGCCGGCATGgtaaatttaa ... gtgattgcagATATTTCGGAAGGAGCCATTCTTTTATGGGCATGACAATTATGATCAACTT
EST: gi|208397887|gb|DC916642.1|DC916642
EST:     ATGATTACTCTCTCGACATGTGGAGCTTGGGGTGCATGTTTGCCGGCATG                         ATATTTCGGAAGGAGCCATTCTTTTATGGGCATGACAATTATGATCAACTT
genomic: ATGATTACTCTCTCGACATGTGGAGCTTGGGGTGCATGTTTGCCGGCATGgtaaatttaa ... gtgattgcagATATTTCGGAAGGAGCCATTCTTTTATGGGCATGACAATTATGATCAACTT
EST: gi|37852940|gb|BJ610948.1|BJ610948
EST:     ATGATTACTCTCTCGACATGTGGAGCTTGGGGTGCATGTTTGCCGGCATG                         ATATTTCGGAAGGAGCCATTCTTTTATGGGCATGACAATTATGATCAACTT
genomic: ATGATTACTCTCTCGACATGTGGAGCTTGGGGTGCATGTTTGCCGGCATGgtaaatttaa ... gtgattgcagATATTTCGGAAGGAGCCATTCTTTTATGGGCATGACAATTATGATCAACTT
EST: gi|67698003|gb|BJ958236.1|BJ958236
EST:     ATGATTACTCTCTCGACATGTGGAGCTTGGGGTGCATGTTTGCCGGCATG                         ATATTTCGGAAGGAGCCATTCTTTTATGGGCATGACAATTATGATCAACTT
genomic: ATGATTACTCTCTCGACATGTGGAGCTTGGGGTGCATGTTTGCCGGCATGgtaaatttaa ... gtgattgcagATATTTCGGAAGGAGCCATTCTTTTATGGGCATGACAATTATGATCAACTT
EST: gi|208397217|gb|DC920860.1|DC920860
EST:     ATGATTACTCTCTCGACATGTGGAGCTTGGGGTGCATGTTTGCCGGCATG                         ATATTTCGGAAGGAGCCATTCTTTTATGGGCATGACAATTATGATCAACTT
genomic: ATGATTACTCTCTCGACATGTGGAGCTTGGGGTGCATGTTTGCCGGCATGgtaaatttaa ... gtgattgcagATATTTCGGAAGGAGCCATTCTTTTATGGGCATGACAATTATGATCAACTT
EST: gi|162153012|gb|FC330042.1|FC330042
EST:     ATGATTACTCTCTCGACATGTGGAGCTTGGGGTGCATGTTTGCCGGCATG                         ATATTTCGGAAGGAGCCATTCTTTTATGGGCATGACAATTATGATCAACTT
genomic: ATGATTACTCTCTCGACATGTGGAGCTTGGGGTGCATGTTTGCCGGCATGgtaaatttaa ... gtgattgcagATATTTCGGAAGGAGCCATTCTTTTATGGGCATGACAATTATGATCAACTT
EST: gi|162153011|gb|FC330041.1|FC330041
EST:     ATGATTACTCTCTCGACATGTGGAGCTTGGGGTGCATGTTTGCCGGCATG                         ATATTTCGGAAGGAGCCATTCTTTTATGGGCATGACAATTATGATCAACTT
genomic: ATGATTACTCTCTCGACATGTGGAGCTTGGGGTGCATGTTTGCCGGCATGgtaaatttaa ... gtgattgcagATATTTCGGAAGGAGCCATTCTTTTATGGGCATGACAATTATGATCAACTT
EST: gi|37847708|gb|BJ605716.1|BJ605716
EST:     ATGATTACTCTCTCGACATGTGGAGCTTGGGGTGCATGTTTGCCGGCATG                         ATATTTCGGAAGGAGCCATTCTTTTATGGGCATGACAATTATGATCAACTT
genomic: ATGATTACTCTCTCGACATGTGGAGCTTGGGGTGCATGTTTGCCGGCATGgtaaatttaa ... gtgattgcagATATTTCGGAAGGAGCCATTCTTTTATGGGCATGACAATTATGATCAACTT

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: 30 (upstream exon), 35 (downstream exon)
Score: 14

GTACTTCAAGGGTCCTGAGCTGCTGGTTGATCTTCAAGATTATGATTACTCTCTCGACATGTGGAGCTTGGGGTGCATGTTTGCCGGCATGgtaaatttaa ... gtgattgcagATATTTCGGAAGGAGCCATTCTTTTATGGGCATGACAATTATGATCAACTTGTGAAGATTGCTAAG




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Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTACTTCAAGGGTCCTGAGCTGCTGGTTGATCTTCAAGATTATGATTACTCTCTCGACATGTGGAGCTTGGGGTGCATGTTTGCCGGCATGgtaaatttaattccaagttcaatatttcgatggtccttgattatcacagtttgtcgctacgttgatttgctttttggtttagtttttgagcttgattctcgttaaacaggtgaattgaagtgattgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCTT