Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   		7  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gtacagaattggttttttttgagaggttcgtgttgcataagagtaccgcttttaaattagagagctgattcgaagttggtttcaaatgcggtggttgcagGAGTAATTGAATACGCTGTTGAAAAGAACTCATTAATTGGTGGTGACGACTTCAAGAGCGGTCAAACGAAGATGAAATCCGTTCTAGTGGACTTTCTAGT

Basic information

species Physcomitrella patens
transcript PP1S55_204V6.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S55_204V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: GRMZM2G155242_T01 (Zea mays), 3'ss of exon 5
gtacagaattggttttttttg--agaggttc---gtgttgcataagagtaccgc--ttttaaa---ttagagagctgattcgaagttggtttcaaatgcgg--tggttgcagGAGTAATTGAATACGCTGTTGAAAAGAACTCATTAATTGGTGGTGACGACTTCAAGAGCGGTCAAACGAAGATGAAATCCGTTCTAGTGGACTTTCTAGT
|| |    || | | | ||||  | || |||   |||||||||    || ||    ||| |     ||  |   ||| | | | | |  ||  |  ||  |  || | | |||  | |||||    ||| |  |||| ||||  || ||||||||||||||||||||||| || || || ||||||||||| ||  | || || || || ||
gtgcgtggtttggtgtgtttgcaaaagcttcatggtgttgcatttctgttccaaagtttcatggtgttgtatttctgttccaaggcttattatacctgttgcatgttcgtagGGCTGATTGATCTTGCTATAAAAAACAACTGCTTGATTGGTGGTGACGACTTCAAGAGTGGACAGACCAAGATGAAATCTGTCTTGGTCGATTTCCTTGT

upper sequence: PP1S55_204V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: GRMZM2G392513_T02 (Zea mays), 3'ss of exon 3
---------gtacagaattggttttttttgagaggttcgtgttgcataagagtaccgcttttaaattagagagctgattcgaagttggtttcaaatgcggtggttgcagGAGTAATTGAATACGCTGTTGAAAAGAACTCATTAATTGGTGGTGACGACTTCAAGAGCGGTCAAACGAAGATGAAATCCGTTCTAGTGGACTTTCTAGT
         || |    |  ||||  ||||    ||| |    |  | |  ||   || |||   ||  |   || |||  | ||  ||| ||       || ||| |||  | |||||    ||| |  | || ||||   | || |||||||||||||||||||| || || || ||||||||||| || ||||| || || |||||
aacacttttgtgcctggtgtgtttagtttggtgtgtttgcaaagttttatggtgttgcatttctgttcaaagacttattatacgt--gttgca-------tgtttgtagGGCTGATTGATCTTGCTATCAAGAACAACTGCCTGATCGGTGGTGACGACTTCAAGAGTGGGCAGACCAAGATGAAATCAGTCCTAGTTGAATTCCTAGT

upper sequence: PP1S55_204V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: GRMZM2G392513_T01 (Zea mays), 3'ss of exon 1
gtacagaattggttttttttgagaggttcgtgttgcataagagtaccgcttttaaattagagagctgattcgaagttggtttcaaatgcggtggttgcagGAGTAATTGAATACGCTGTTGAAAAGAACTCATTAATTGGTGGTGACGACTTCAAGAGCGGTCAAACGAAGATGAAATCCGTTCTAGTGGACTTTCTAGT
        |  ||||  ||||    ||| |    |  | |  ||   || |||   ||  |   || |||  | ||  ||| ||       || ||| |||  | |||||    ||| |  | || ||||   | || |||||||||||||||||||| || || || ||||||||||| || ||||| || || |||||
-------gtgtgtttagtttggtgtgtttgcaaagttttatggtgttgcatttctgttcaaagacttattatacgt--gttgca-------tgtttgtagGGCTGATTGATCTTGCTATCAAGAACAACTGCCTGATCGGTGGTGACGACTTCAAGAGTGGGCAGACCAAGATGAAATCAGTCCTAGTTGAATTCCTAGT

upper sequence: PP1S55_204V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: GRMZM2G004528_T03 (Zea mays), 3'ss of exon 5
gtacagaattggttttttttgagaggttcgtgttgcataagagtaccgc-ttttaaattagagagctgattcgaagttggtttcaaatgcggtggttgcagGAGTAATTGAATACGCTGTTGAAAAGAACTCATTAATTGGTGGTGACGACTTCAAGAGCGGTCAAACGAAGATGAAATCCGTTCTAGTGGACTTTCTAGT
        |  ||||  ||||    ||||     |  | |  ||   || | |    | | | | || |||  |   | ||||||       || ||| |||  | |||||    ||| |  | || ||||   | || |||||||||||||||||||| || || || ||||||||||| || || || || ||||| ||
-------gtgtgtttagtttggtgtgttcccaaagttttatggtgttgcatctctgttcaaaaaacttatt--atacttgtttca-------tgtttgtagGGCTGATTGATCTTGCTATCAAGAACAACTGCCTGATCGGTGGTGACGACTTCAAGAGTGGGCAGACCAAGATGAAATCGGTCCTGGTTGATTTTCTTGT

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|40781590|gb|AJ583520.1|AJ583520
EST:     CGAGCAGGTTCCCTTCATCAACGGCAGTCCCCAGAACACATTCGTCCCTG                         GAGTAATTGAATACGCTGTTGAAAAGAACTCATTAATTGGTGGTGACGACT
genomic: CGAGCAGGTTCCCTTCATCAACGGCAGTCCCCAGAACACATTCGTCCCTGgtgaagatcg ... gtggttgcagGAGTAATTGAATACGCTGTTGAAAAGAACTCATTAATTGGTGGTGACGACT
EST: gi|162247857|gb|FC420616.1|FC420616
EST:     CGAGCAGGTTCCCTTCATCAACGGCAGTCCCCAGAACACATTCGTCCCTG                         GAGTAATTGAATACGCTGTTGAAAAGAACTCATTAATTGGTGGTGACGACT
genomic: CGAGCAGGTTCCCTTCATCAACGGCAGTCCCCAGAACACATTCGTCCCTGgtgaagatcg ... gtggttgcagGAGTAATTGAATACGCTGTTGAAAAGAACTCATTAATTGGTGGTGACGACT
EST: gi|162194434|gb|FC368539.1|FC368539
EST:     CGAGCAGGTTCCCTTCATCAACGGCAGTCCCCAGAACACATTCGTCCCTG                         GAGTAATTGAATACGCTGTTGAAAAGAACTCATTAATTGGTGGTGACGACT
genomic: CGAGCAGGTTCCCTTCATCAACGGCAGTCCCCAGAACACATTCGTCCCTGgtgaagatcg ... gtggttgcagGAGTAATTGAATACGCTGTTGAAAAGAACTCATTAATTGGTGGTGACGACT
EST: gi|162165316|gb|FC340817.1|FC340817
EST:     CGAGCAGGTTCCCTTCATCAACGGCAGTCCCCAGAACACATTCGTCCCTG                         GAGTAATTGAATACGCTGTTGAAAAGAACTCATTAATTGGTGGTGACGACT
genomic: CGAGCAGGTTCCCTTCATCAACGGCAGTCCCCAGAACACATTCGTCCCTGgtgaagatcg ... gtggttgcagGAGTAATTGAATACGCTGTTGAAAAGAACTCATTAATTGGTGGTGACGACT
EST: gi|162191433|gb|FC368190.1|FC368190
EST:     CGAGCAGGTTCCCTTCATCAACGGCAGTCCCCAGAACACATTCGTCCCTG                         GAGTAATTGAATACGCTGTTGAAAAGAACTCATTAATTGGTGGTGACGACT
genomic: CGAGCAGGTTCCCTTCATCAACGGCAGTCCCCAGAACACATTCGTCCCTGgtgaagatcg ... gtggttgcagGAGTAATTGAATACGCTGTTGAAAAGAACTCATTAATTGGTGGTGACGACT
EST: gi|162186353|gb|FC361661.1|FC361661
EST:     CGAGCAGGTTCCCTTCATCAACGGCAGTCCCCAGAACACATTCGTCCCTG                         GAGTAATTGAATACGCTGTTGAAAAGAACTCATTAATTGGTGGTGACGACT
genomic: CGAGCAGGTTCCCTTCATCAACGGCAGTCCCCAGAACACATTCGTCCCTGgtgaagatcg ... gtggttgcagGAGTAATTGAATACGCTGTTGAAAAGAACTCATTAATTGGTGGTGACGACT
EST: gi|162194084|gb|FC370259.1|FC370259
EST:     CGAGCAGGTTCCCTTCATCAACGGCAGTCCCCAGAACACATTCGTCCCTG                         GAGTAATTGAATACGCTGTTGAAAAGAACTCATTAATTGGTGGTGACGACT
genomic: CGAGCAGGTTCCCTTCATCAACGGCAGTCCCCAGAACACATTCGTCCCTGgtgaagatcg ... gtggttgcagGAGTAATTGAATACGCTGTTGAAAAGAACTCATTAATTGGTGGTGACGACT
EST: gi|162184403|gb|FC359149.1|FC359149
EST:     CGAGCAGGTTCCCTTCATCAACGGCAGTCCCCAGAACACATTCGTCCCTG                         GAGTAATTGAATACGCTGTTGAAAAGAACTCATTAATTGGTGGTGACGACT
genomic: CGAGCAGGTTCCCTTCATCAACGGCAGTCCCCAGAACACATTCGTCCCTGgtgaagatcg ... gtggttgcagGAGTAATTGAATACGCTGTTGAAAAGAACTCATTAATTGGTGGTGACGACT
EST: gi|162182475|gb|FC357450.1|FC357450
EST:     CGAGCAGGTTCCCTTCATCAACGGCAGTCCCCAGAACACATTCGTCCCTG                         GAGTAATTGAATACGCTGTTGAAAAGAACTCATTAATTGGTGGTGACGACT
genomic: CGAGCAGGTTCCCTTCATCAACGGCAGTCCCCAGAACACATTCGTCCCTGgtgaagatcg ... gtggttgcagGAGTAATTGAATACGCTGTTGAAAAGAACTCATTAATTGGTGGTGACGACT
EST: gi|162175808|gb|FC352110.1|FC352110
EST:     CGAGCAGGTTCCCTTCATCAACGGCAGTCCCCAGAACACATTCGTCCCTG                         GAGTAATTGAATACGCTGTTGAAAAGAACTCATTAATTGGTGGTGACGACT
genomic: CGAGCAGGTTCCCTTCATCAACGGCAGTCCCCAGAACACATTCGTCCCTGgtgaagatcg ... gtggttgcagGAGTAATTGAATACGCTGTTGAAAAGAACTCATTAATTGGTGGTGACGACT
EST: gi|162184271|gb|FC359693.1|FC359693
EST:     CGAGCAGGTTCCCTTCATCAACGGCAGTCCCCAGAACACATTCGTCCCTG                         GAGTAATTGAATACGCTGTTGAAAAGAACTCATTAATTGGTGGTGACGACT
genomic: CGAGCAGGTTCCCTTCATCAACGGCAGTCCCCAGAACACATTCGTCCCTGgtgaagatcg ... gtggttgcagGAGTAATTGAATACGCTGTTGAAAAGAACTCATTAATTGGTGGTGACGACT
EST: gi|162220955|gb|FC396140.1|FC396140
EST:     CGAGCAGGTTCCCTTCATCAACGGCAGTCCCCAGAACACATTCGTCCCTG                         GAGTAATTGAATACGCTGTTGAAAAGAACTCATTAATTGGTGGTGACGACT
genomic: CGAGCAGGTTCCCTTCATCAACGGCAGTCCCCAGAACACATTCGTCCCTGgtgaagatcg ... gtggttgcagGAGTAATTGAATACGCTGTTGAAAAGAACTCATTAATTGGTGGTGACGACT
EST: gi|162151547|gb|FC327260.1|FC327260
EST:     CGAGCAGGTTCCCTTCATCAACGGCAGTCCCCAGAACACATTCGTCCCTG                         GAGTAATTGAATACGCTGTTGAAAAGAACTCATTAATTGGTGGTGACGACT
genomic: CGAGCAGGTTCCCTTCATCAACGGCAGTCCCCAGAACACATTCGTCCCTGgtgaagatcg ... gtggttgcagGAGTAATTGAATACGCTGTTGAAAAGAACTCATTAATTGGTGGTGACGACT
EST: gi|162268155|gb|FC443833.1|FC443833
EST:     CGAGCAGGTTCCCTTCATCAACGGCAGTCCCCAGAACACATTCGTCCCTG                         GAGTAATTGAATACGCTGTTGAAAAGAACTCATTAATTGGTGGTGACGACT
genomic: CGAGCAGGTTCCCTTCATCAACGGCAGTCCCCAGAACACATTCGTCCCTGgtgaagatcg ... gtggttgcagGAGTAATTGAATACGCTGTTGAAAAGAACTCATTAATTGGTGGTGACGACT
EST: gi|162213492|gb|FC389364.1|FC389364
EST:     CGAGCAGGTTCCCTTCATCAACGGCAGTCCCCAGAACACATTCGTCCCTG                         GAGTAATTGAATACGCTGTTGAAAAGAACTCATTAATTGGTGGTGACGACT
genomic: CGAGCAGGTTCCCTTCATCAACGGCAGTCCCCAGAACACATTCGTCCCTGgtgaagatcg ... gtggttgcagGAGTAATTGAATACGCTGTTGAAAAGAACTCATTAATTGGTGGTGACGACT
EST: gi|162156175|gb|FC332550.1|FC332550
EST:     CGAGCAGGTTCCCTTCATCAACGGCAGTCCCCAGAACACATTCGTCCCTG                         GAGTAATTGAATACGCTGTTGAAAAGAACTCATTAATTGGTGGTGACGACT
genomic: CGAGCAGGTTCCCTTCATCAACGGCAGTCCCCAGAACACATTCGTCCCTGgtgaagatcg ... gtggttgcagGAGTAATTGAATACGCTGTTGAAAAGAACTCATTAATTGGTGGTGACGACT
EST: gi|162197484|gb|FC372862.1|FC372862
EST:     CGAGCAGGTTCCCTTCATCAACGGCAGTCCCCAGAACACATTCGTCCCTG                         GAGTAATTGAATACGCTGTTGAAAAGAACTCATTAATTGGTGGTGACGACT
genomic: CGAGCAGGTTCCCTTCATCAACGGCAGTCCCCAGAACACATTCGTCCCTGgtgaagatcg ... gtggttgcagGAGTAATTGAATACGCTGTTGAAAAGAACTCATTAATTGGTGGTGACGACT
EST: gi|162182387|gb|FC357986.1|FC357986
EST:     CCCAGAACACATTCGTCCCTG                         GAGTAATTGAATACGCTGTTGAAAAGAACTCATTAATTGGTGGTGACGACT
genomic: CCCAGAACACATTCGTCCCTGgtgaagatcg ... gtggttgcagGAGTAATTGAATACGCTGTTGAAAAGAACTCATTAATTGGTGGTGACGACT
EST: gi|162194175|gb|FC369687.1|FC369687
EST:     CGAGCAGGTTCCCTTCATCAACGGCAGTCCCCAGAACACATTCGTCCCTG                         GAGTAATTGAATACGCTGTTGAAAAGAACTCATTAATTGGTGGTGACGACT
genomic: CGAGCAGGTTCCCTTCATCAACGGCAGTCCCCAGAACACATTCGTCCCTGgtgaagatcg ... gtggttgcagGAGTAATTGAATACGCTGTTGAAAAGAACTCATTAATTGGTGGTGACGACT
EST: gi|162198718|gb|FC373486.1|FC373486
EST:     AGAACACATTCGTCCCTG                         GAGTAATTGAATACGCTGTTGAAAAGAACTCATTAATTGGTGGTGACGACT
genomic: AGAACACATTCGTCCCTGgtgaagatcg ... gtggttgcagGAGTAATTGAATACGCTGTTGAAAAGAACTCATTAATTGGTGGTGACGACT
EST: gi|162246259|gb|FC421966.1|FC421966
EST:     CGAGCAGGTTCCCTTCATCAACGGCAGTCCCCAGAACACATTCGTCCCTG                         GAGTAATTGAATACGCTGTTGAAAAGAACTCATTAATTGGTGGTGACGACT
genomic: CGAGCAGGTTCCCTTCATCAACGGCAGTCCCCAGAACACATTCGTCCCTGgtgaagatcg ... gtggttgcagGAGTAATTGAATACGCTGTTGAAAAGAACTCATTAATTGGTGGTGACGACT
EST: gi|162222899|gb|FC399361.1|FC399361
EST:     CGAGCAGGTTCCCTTCATCAACGGCAGTCCCCAGAACACATTCGTCCCTG                         GAGTAATTGAATACGCTGTTG
genomic: CGAGCAGGTTCCCTTCATCAACGGCAGTCCCCAGAACACATTCGTCCCTGgtgaagatcg ... gtggttgcagGAGTAATTGAATACGCTGTTG
EST: gi|162218352|gb|FC394526.1|FC394526
EST:     CGAGCAGGTTCCCTTCATCAACGGCAGTCCCCAGAACACATTCGTCCCTG                         GAGTAATTGAATACGCTGTTGAAAAGAACTCATTAATTGGTGGTGACGACT
genomic: CGAGCAGGTTCCCTTCATCAACGGCAGTCCCCAGAACACATTCGTCCCTGgtgaagatcg ... gtggttgcagGAGTAATTGAATACGCTGTTGAAAAGAACTCATTAATTGGTGGTGACGACT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ccgcttttaaattagagagctgattcgaagttggtttcaaatgcggtggttgcagGAGTAATTGAATACGCTGTTGAAAAGAACTCATTAATTGGTGGTGACGACTTCAAGAGCGGTCAAACGAAGATGAAATCCGTTCTAGTGGACTTTCTAGT
                 agctgat  putative branch site (score: 4)
     tttaaattaga  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacagaattggttttttttgagaggttcgtgttgcataagagtaccgcttttaaattagagagctgattcgaagttggtttcaaatgcggtggttgcagGAGTAATTGAATACGCTGTTGAAAAGAACTCATTAATTGGTGGTGACGACTTCAAGAGCGGTCAAACGAAGATGAAATCCGTTCTAGTGGACTTTCTAGT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGTGGA
- - - - - - - - - - - - - - - tgttgca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - caaatgc