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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgcaggcgactgtagaatgttgtcgaatcgtgagttgatcagcactagtgtgaaatctcaaaccatgtcactgaagcaagtgcttgatctgcaggagcagATATCCGGAGTGTGTGTACAGAGGCAGGTATGTATGCCATTCGTGCACGCAGGAAGACTGTGACAGAGAAGGACTTTTTGGAAGCTGTCAACAAGGTCAT

Basic information

species Physcomitrella patens
transcript PP1S152_13V6.2
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S152_13V6.2 (Physcomitrella patens), 3'ss of exon 9
lower sequence: LOC_Os06g09290.1 (Oryza sativa), 3'ss of exon 6
-----tgcaggcgactgtagaatgttg---tcgaatcgtgagttgatc----------agcactagtgtgaaatctcaaaccatgtcactga-----agcaa---gtgcttgatctg-caggagcagATATCCGGAGTGTGTGTACAGAGGCAGGTATGTATGCCATTCGTGCACGCAGGAAGACTGTGACAGAGAAGGACTTTTTGGAAGCTGTCAACAAGGTCAT
     ||| ||  | | | | |||      || | ||    | |  |             || |  | |  || |||      | |  || |      || |   ||| ||| |    |||| || || || ||||||||||| || ||||| || ||||| ||||| || || ||||||||||| |||||||||||||| || ||||| || || || ||      
gtaagtgccgggaattcttgcatgacagaatccagtctctggctagtttctgttccatgtcatttatctttaacctccttttttttttctcacgtttggctatttgtgtttgttggaacagGGGCCGACATACGGAGTGTGTGCACGGAGGCTGGCATGTACGCCATCCGCGCTCGCAGGAAGACGGTGACAGAGAAGGATTTCTTGGACGCGGTGAATAA------

upper sequence: PP1S152_13V6.2 (Physcomitrella patens), 3'ss of exon 9
lower sequence: GRMZM2G181359_T01 (Zea mays), 3'ss of exon 9
----------tgcaggcgactgtagaatgttgtcgaatcg---tgagttgatcagcactagtgtgaaatct----caaaccatgtcactgaagcaagtgcttgatctg------caggagcagATATCCGGAGTGTGTGTACAGAGGCAGGTATGTATGCCATTCGTGCACGCAGGAAGACTGTGACAGAGAAGGACTTTTTGGAAGCTGTCAACAAGGTCAT
          |   ||   | | ||||||||   |  ||    ||| |  ||         ||   | | |     | |  ||     |    ||    |||| | ||      ||||||| |||||  |||| || || ||||| || || ||||||||||||||||| |||||||| || |||||||||||||| ||| | || |||||||| ||      
gtgagttgctttgtggtttcagcagaatgtttgtgtttctgcttgattcaattgatttacttgaagactttgcgatagatgatcaggttctcacatagccttgctttgttactccagGAGCGGATATAAGGAGCGTCTGCACAGAAGCCGGGATGTATGCCATTCGTGCCCGCAGGAAAACGGTGACAGAGAAGGATTTTCTCGATGCTGTCAATAA------

upper sequence: PP1S152_13V6.2 (Physcomitrella patens), 3'ss of exon 9
lower sequence: GRMZM2G110185_T01 (Zea mays), 3'ss of exon 8
tgcaggcgactgtagaatgttgtcgaatcgtgagttgat-cagcactagtgtgaaatctcaaaccatgtcactgaagcaagt-gcttgat-ctgcaggagcagATATCCGGAGTGTGTGTACAGAGGCAGGTATGTATGCCATTCGTGCACGCAGGAAGACTGTGACAGAGAAGGACTTTTTGGAAGCTGTCAACAAGGTCAT
                 ||| ||   ||| ||||| | | | ||  || |     |      | || ||      |     | ||||| | || ||||||| |||||  |||| || || ||||| || || ||||| |||||||| || |||||||| || |||||||| ||||| ||| | || |||||||||||      
----------------gtgtggtttcatc-tgagtggtttctgctttattcgatgacagacgatcaggttctcacattgccttgcttgttgctccagGAGCTGATATAAGGAGCGTTTGCACAGAAGCCGGGATGTACGCCATTCGCGCCCGCAGGAAAACGGTGACAGAAAAGGATTTTCTCGATGCTGTCAACAA------

upper sequence: PP1S152_13V6.2 (Physcomitrella patens), 3'ss of exon 9
lower sequence: GLYMA07G05220.1 (Glycine max), 3'ss of exon 9
tgcaggcgactgtagaatgttgtcgaatcgtgagttgatcagcactagtgtgaaatctc-aaaccatgtcactgaagcaagtgcttg-----atctgcaggagcagATATCCGGAGTGTGTGTACAGAGGCAGGTATGTATGCCATTCGTGCACGCAGGAAGACTGTGACAGAGAAGGACTTTTTGGAAGCTGTCAACAAGGTCAT
|       | |    || | | |   |||     ||| |      |  | |   || || | ||  ||    |     || | |||       ||| ||||||| |||||  ||||||| || ||||| || ||||||||||| || ||||| || ||||||||||| |||||||| |||||  | || || || || ||      
tttttctcatttcctaaagctttgctatccaacattgttgcttcatgctttaggatttctagacattggttttctgataaatactttttgttgtctccagGAGCTGATATAAGGAGTGTATGCACAGAAGCCGGTATGTATGCTATCCGTGCCCGGAGGAAGACTGTAACAGAGAAAGACTTCCTTGATGCAGTAAATAA------

upper sequence: PP1S152_13V6.2 (Physcomitrella patens), 3'ss of exon 9
lower sequence: GLYMA16G01810.1 (Glycine max), 3'ss of exon 9
tgcaggcgac-tgtagaatgttgtcgaatcgtgagttgatcagcacta-gtgtgaaatctcaaaccatgtcactgaagcaagtgcttg-----atctgcaggagcagATATCCGGAGTGTGTGTACAGAGGCAGGTATGTATGCCATTCGTGCACGCAGGAAGACTGTGACAGAGAAGGACTTTTTGGAAGCTGTCAACAAGGTCAT
 |   ||  | ||    |  |||       |  |  |      || |  |||    ||   | ||  ||    |     |  | | |       ||| ||||||| |||||  ||||||| || ||||| || ||||||||||| || ||||| || ||||||||||| |||||||| |||||  | || || || || ||      
-gtgtgcttcatgctagacattggttttctgatacatatctgacattgtgtgcttcatgctagacattggttttctgatagataccttttgttgtctccagGAGCTGATATAAGGAGTGTATGCACAGAAGCCGGTATGTATGCTATCCGTGCCCGGAGGAAGACTGTAACAGAGAAAGACTTCCTTGATGCAGTAAATAA------

upper sequence: PP1S152_13V6.2 (Physcomitrella patens), 3'ss of exon 9
lower sequence: Vv09s0002g00170.t01 (Vitis vinifera), 3'ss of exon 9
-------------------tgcaggcgactgtagaatgttgtcgaatcgtgagttgatcagcactagtgtgaaatctcaaaccatgtcactgaagcaagtgcttgatctgcaggagcagATATCCGGAGTGTGTGTACAGAGGCAGGTATGTATGCCATTCGTGCACGCAGGAAGACTGTGACAGAGAAGGACTTTTTGGAAGCTGTCAACAAGGTCAT
                    ||| |      | | ||  | || | |  ||  ||   | |   || | ||   |||       | |||          |  |  |  | ||||||| || ||  | |||||||| || || || || |||||||| ||||| ||||| |||||||| ||||| |||||||||||  | ||  | || |||||      
gtaaaatacttatctgaagggcacgttgtctttgtatactctccattgatggttttggctgt--tattttgggttcttggtttttctcat----attctttttccacattcagGAGCCGACATAAGAAGTGTGTGCACTGAAGCTGGAATGTATGCTATTCGAGCACGAAGGAAGACAGTGACCGAGAAGGACTTCCTTGATTCAGTGAACAA------

upper sequence: PP1S152_13V6.2 (Physcomitrella patens), 3'ss of exon 9
lower sequence: EDP03835 (Chlamydomonas reinhardtii), 3'ss of exon 11
------------------------------------------------------------------tgcaggcgactgtagaatgttgtcgaatcgtgagt------tgatcagcactagtg----tgaaatctcaaaccatgtcactgaagcaagtgcttgat-ctgcag--gagcagATATCCGGAGT---GTGTGTACAGAGGCAGGTATGTATGCCATTCGTGCACGCAGGAAGACTGTGACAGAGAAGGACTTTTTGGAAGCTGTCAACAAGGTCAT-------
                                                                  || | |||   | |   || |   |   ||   ||        | || |||   ||    | ||| ||      |||||| | ||     ||   | |  ||| |  | ||    |  || ||    || || || ||||| || ||||| || || || || ||| |||| |||||||| ||||||||||| ||||| ||||| |||||||||||       
gtgcggcgaccgcgtgcggccgcaccccgccccaccgcatccctcatcccttgttggaatctgtggtg-acgcgctaggaccttgctcctgccccgccggtatcatgccaccatcacagatgccactcaaaactgtttgtatgtcattaaacattatgaacggtattgctgttgtgcgaccactcgcagGTCGGTTTGCACGGAGGCGGGAATGTACGCTATCCGCGCTCGCCGGAAAACTGTGACGGAGAAGGACTTCTTGGAGGCTGTTAACAAGGTCATCAAGGGC

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|208364215|gb|DC947291.1|DC947291
EST:     GCGAGACATTCGTTTCGAGCTTCTTTCCCGCCTTTGCCCCAATTCAACAG                         G
genomic: GCGAGACATTCGTTTCGAGCTTCTTTCCCGCCTTTGCCCCAATTCAACAGgttctaatct ... gcaggagcag-
EST: gi|208364215|gb|DC947291.1|DC947291
EST:     GCGAGACATTCGTTTCGAGCTTCTTTCCCGCCTTTGCCCCAATTCAACAG                         G
genomic: GCGAGACATTCGTTTCGAGCTTCTTTCCCGCCTTTGCCCCAATTCAACAGgttctaatct ... gcaggagcag-
EST: gi|208368723|gb|DC947956.1|DC947956
EST:     GCGAGACATTCGTTTCGAGCTTCTTTCCCGCCTTTGCCCCAATTCAACAG                         G
genomic: GCGAGACATTCGTTTCGAGCTTCTTTCCCGCCTTTGCCCCAATTCAACAGgttctaatct ... gcaggagcag-
EST: gi|208368723|gb|DC947956.1|DC947956
EST:     GCGAGACATTCGTTTCGAGCTTCTTTCCCGCCTTTGCCCCAATTCAACAG                         G
genomic: GCGAGACATTCGTTTCGAGCTTCTTTCCCGCCTTTGCCCCAATTCAACAGgttctaatct ... gcaggagcag-
EST: gi|162256307|gb|FC432317.1|FC432317
EST:     GCGAGACATTCGTTTCGAGCTTCTTTCCCGCCTTTGCCCCAATTCAACAG                         G
genomic: GCGAGACATTCGTTTCGAGCTTCTTTCCCGCCTTTGCCCCAATTCAACAGgttctaatct ... gcaggagcag-
EST: gi|162256307|gb|FC432317.1|FC432317
EST:     GCGAGACATTCGTTTCGAGCTTCTTTCCCGCCTTTGCCCCAATTCAACAG                         G
genomic: GCGAGACATTCGTTTCGAGCTTCTTTCCCGCCTTTGCCCCAATTCAACAGgttctaatct ... gcaggagcag-
EST: gi|208350436|gb|DC926183.1|DC926183
EST:     GCGAGACATTCGTTTCGAGCTTCTTTCCCGCCTTTGCCCCAATTCAACAG                         G
genomic: GCGAGACATTCGTTTCGAGCTTCTTTCCCGCCTTTGCCCCAATTCAACAGgttctaatct ... gcaggagcag-
EST: gi|208350436|gb|DC926183.1|DC926183
EST:     GCGAGACATTCGTTTCGAGCTTCTTTCCCGCCTTTGCCCCAATTCAACAG                         G
genomic: GCGAGACATTCGTTTCGAGCTTCTTTCCCGCCTTTGCCCCAATTCAACAGgttctaatct ... gcaggagcag-
EST: gi|37847976|gb|BJ605984.1|BJ605984
EST:     GCGAGACATTCGTTTCGAGCTTCTTTCCCGCCTTTGCCCCAATTCAACAG                         ATATCCGGAGTGTGTGTACAGAGGCAGGTATGTATGCCATTCGTGCACGCA
genomic: GCGAGACATTCGTTTCGAGCTTCTTTCCCGCCTTTGCCCCAATTCAACAGgttctaatct ... gcaggagcagATATCCGGAGTGTGTGTACAGAGGCAGGTATGTATGCCATTCGTGCACGCA
EST: gi|67720349|gb|BJ970608.1|BJ970608
EST:     GCGAGACATTCGTTTCGAGCTTCTTTCCCGCCTTTGCCCCAATTCAACAG                         G
genomic: GCGAGACATTCGTTTCGAGCTTCTTTCCCGCCTTTGCCCCAATTCAACAGgttctaatct ... gcaggagcag-
EST: gi|67720349|gb|BJ970608.1|BJ970608
EST:     GCGAGACATTCGTTTCGAGCTTCTTTCCCGCCTTTGCCCCAATTCAACAG                         G
genomic: GCGAGACATTCGTTTCGAGCTTCTTTCCCGCCTTTGCCCCAATTCAACAGgttctaatct ... gcaggagcag-
EST: gi|162267487|gb|FC444238.1|FC444238
EST:     GCGAGACATTCGTTTCGAGCTTCTTTCCCGCCTTTGCCCCAATTCAACAG                         G
genomic: GCGAGACATTCGTTTCGAGCTTCTTTCCCGCCTTTGCCCCAATTCAACAGgttctaatct ... gcaggagcag-
EST: gi|162267487|gb|FC444238.1|FC444238
EST:     GCGAGACATTCGTTTCGAGCTTCTTTCCCGCCTTTGCCCCAATTCAACAG                         G
genomic: GCGAGACATTCGTTTCGAGCTTCTTTCCCGCCTTTGCCCCAATTCAACAGgttctaatct ... gcaggagcag-
EST: gi|208366359|gb|DC947569.1|DC947569
EST:     GCGAGACATTCGTTTCGAGCTTCTTTCCCGCCTTTGCCCCAATTCAACAG                         G
genomic: GCGAGACATTCGTTTCGAGCTTCTTTCCCGCCTTTGCCCCAATTCAACAGgttctaatct ... gcaggagcag-
EST: gi|208366359|gb|DC947569.1|DC947569
EST:     GCGAGACATTCGTTTCGAGCTTCTTTCCCGCCTTTGCCCCAATTCAACAG                         G
genomic: GCGAGACATTCGTTTCGAGCTTCTTTCCCGCCTTTGCCCCAATTCAACAGgttctaatct ... gcaggagcag-
EST: gi|67579074|gb|BJ951225.1|BJ951225
EST:     GCGAGACATTCGTTTCGAGCTTCTTTCCCGCCTTTGCCCCAATTCAACAGGAGCAG                    
genomic: GCGAGACATTCGTTTCGAGCTTCTTTCCCGCCTTTGCCCCAATT---CA--A-CAGgttctaatct ... gcagg
EST: gi|67694853|gb|BJ955086.1|BJ955086
EST:     GCGAGACATTCGTTTCGAGCTTCTTTCCCGCCTTTGCCCCAATTCAACAG                         G
genomic: GCGAGACATTCGTTTCGAGCTTCTTTCCCGCCTTTGCCCCAATTCAACAGgttctaatct ... gcaggagcag-
EST: gi|67694853|gb|BJ955086.1|BJ955086
EST:     GCGAGACATTCGTTTCGAGCTTCTTTCCCGCCTTTGCCCCAATTCAACAG                         G
genomic: GCGAGACATTCGTTTCGAGCTTCTTTCCCGCCTTTGCCCCAATTCAACAGgttctaatct ... gcaggagcag-
EST: gi|67720715|gb|BJ970974.1|BJ970974
EST:     GCGAGACATTCGTTTCGAGCTTCTTTCCCGCCTTTGCCCCAATTCAACAG                         G
genomic: GCGAGACATTCGTTTCGAGCTTCTTTCCCGCCTTTGCCCCAATTCAACAGgttctaatct ... gcaggagcag-
EST: gi|67720715|gb|BJ970974.1|BJ970974
EST:     GCGAGACATTCGTTTCGAGCTTCTTTCCCGCCTTTGCCCCAATTCAACAG                         G
genomic: GCGAGACATTCGTTTCGAGCTTCTTTCCCGCCTTTGCCCCAATTCAACAGgttctaatct ... gcaggagcag-
EST: gi|162257096|gb|FC432556.1|FC432556
EST:     GCGAGACATTCGTTTCGAGCTTCTTTCCCGCCTTTGCCCCAATTCAACAG                         G
genomic: GCGAGACATTCGTTTCGAGCTTCTTTCCCGCCTTTGCCCCAATTCAACAGgttctaatct ... gcaggagcag-
EST: gi|162257096|gb|FC432556.1|FC432556
EST:     GCGAGACATTCGTTTCGAGCTTCTTTCCCGCCTTTGCCCCAATTCAACAG                         G
genomic: GCGAGACATTCGTTTCGAGCTTCTTTCCCGCCTTTGCCCCAATTCAACAGgttctaatct ... gcaggagcag-


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tagtgtgaaatctcaaaccatgtcactgaagcaagtgcttgatctgcaggagcagATATCCGGAGTGTGTGTACAGAGGCAGGTATGTATGCCATTCGTGCACGCAGGAAGACTGTGACAGAGAAGGACTTTTTGGAAGCTGTCAACAAGGTCAT
                                    gcttgat  putative branch site (score: 5)
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgcaggcgactgtagaatgttgtcgaatcgtgagttgatcagcactagtgtgaaatctcaaaccatgtcactgaagcaagtgcttgatctgcaggagcagATATCCGGAGTGTGTGTACAGAGGCAGGTATGTATGCCATTCGTGCACGCAGGAAGACTGTGACAGAGAAGGACTTTTTGGAAGCTGTCAACAAGGTCAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCTG