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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cgtcttcactttttgtgctttcctaattttccttacgaatgcaaggaccaaatagatagtaatttctttttctgatctgcgtggtgatgatgctgtgtagATTTGGACAGCCTATCAAAGTTAATTGGGCATATGCAAGCGGGCAGAGAGAGGATACTACAG

Basic information

species Physcomitrella patens
transcript PP1S84_50V6.2
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S84_50V6.2 (Physcomitrella patens), 3'ss of exon 5
lower sequence: LOC_Os07g42380.1 (Oryza sativa), 3'ss of exon 4
cgtcttcactttttgtgctttcctaattttccttacgaatgcaaggaccaaatagatagtaatttctttttctgatc-tgcgtggtgatgatgctgtgtagATTTGGACAGCCTATCAAAGTTAATTGGGCATATGCAAGCGGGCAGAGAGAGGATACTACAG
       |        ||| | |  ||||    ||        | |   || ||  |  |  |||||       | |   | | |     |     |  || ||||| |||| ||||| |||||||||||||||||| || |||||||| ||||| || ||||
-----gtaagagaaaagctattc--atttctgctagtttgttgaagcttaattatgtttttttttctccccaaaaacactcattgaagaaaaatgatacagTTTTGGGCAGCTTATCAGAGTTAATTGGGCATATGCTAGTGGGCAGAGGGAGGACACAACAG

upper sequence: PP1S84_50V6.2 (Physcomitrella patens), 3'ss of exon 5
lower sequence: GLYMA16G01230.1 (Glycine max), 3'ss of exon 4
cgtcttcactttttgtgctttcctaattttccttacgaatgcaaggaccaaatagatagtaatttctttttctgatctgcgtggtgatgatgctgtgtagATTTGGACAGCCTATCAAAGTTAATTGGGCATATGCAAGCGGGCAGAGAGAGGATACTACAG
                       ||| | |   |    |          |||| |||  | ||||  | |||| || |   |       ||||| || |||||||| ||||||||||||||||||||||||||||| || || ||||||||||||||  |||
----------------------gtaagtgttgctctttagatttatgttaaattgatt-tcattttgtattctaattttaatt----caatgctttgcagATTTGGGCAGCCTATCAAAGTTAATTGGGCATATGCGAGTGGTCAGAGAGAGGATACGTCAG

upper sequence: PP1S84_50V6.2 (Physcomitrella patens), 3'ss of exon 5
lower sequence: GLYMA07G04640.1 (Glycine max), 3'ss of exon 4
cgtcttcactttttgtgctttcctaattttccttacgaatgcaaggaccaaatagatagtaatttctttttctgatctgcgtggtgatgatgctgtgtagATTTGGACAGCCTATCAAAGTTAATTGGGCATATGCAAGCGGGCAGAGAGAGGATACTACAG
                       ||| | |   |   ||          |||| |||   | ||| | ||     |||   |       ||||| || |||||||| ||||||||||||||||||||||||||||| || || ||||||||||||||  |||
----------------------gtaagtgttgctgttaagatttatgttaaattgatttcattttgtgttcaaattctaatt-----caatgctttgcagATTTGGGCAGCCTATCAAAGTTAATTGGGCATATGCTAGTGGTCAGAGAGAGGATACGTCAG

upper sequence: PP1S84_50V6.2 (Physcomitrella patens), 3'ss of exon 5
lower sequence: AT1G54080.2 (Arabidopsis thaliana), 3'ss of exon 4
cgtcttcactttttgtgctttcctaattttccttacgaatgcaaggaccaaatagatagtaatttctttttctgatctgcgtggtgatgatgctgtgtagATTTGGACAGCCTATCAAAGTTAATTGGGCATATGCAAGCGGGCAGAGAGAGGATACTACAG
              ||      ||||  ||  |     ||||   ||  |   |  |  |   |   || ||| |  |   |  |  ||    |    ||||||||||||||||| |||||||||||||| |||||||  || || || || |||||  || 
--------------gtaagaatctaacattgatacttcatgctttgattagtcaatttattcatgtgttctcttagat-tataatattgg-atttcacagATTTGGACAGCCTATGAAAGTTAATTGGGCGTATGCAACTGGTCAAAGGGAAGATACATCAA

upper sequence: PP1S84_50V6.2 (Physcomitrella patens), 3'ss of exon 5
lower sequence: AT3G14100.1 (Arabidopsis thaliana), 3'ss of exon 4
--cgtcttcactttttgtgctttcctaattttccttacgaatgcaaggaccaaatagatagtaatttctttttctgatctgcgtggtgatgatgctgtgtagATTTGGACAGCCTATCAAAGTTAATTGGGCATATGCAAGCGGGCAGAGAGAGGATACTACAG
        || ||||  |  ||||||   | ||||               |  || | | | |   | || ||  | |     |  |  |   | | |  || |||||||||||||||||||| |||||||| ||||| |  || ||||| || |||||  || 
gtaaggaacaattttcatagtttccttcctctcctctt------------cttatcgttcgaatgcttttgtttaggtt---ataatcgtcgagtt-tacagGTTTGGACAGCCTATCAAAGTCAATTGGGCGTATGCCACTGGTCAGAGGGAAGATACATCAA

upper sequence: PP1S84_50V6.2 (Physcomitrella patens), 3'ss of exon 5
lower sequence: Vv11s0016g00700.t01 (Vitis vinifera), 3'ss of exon 4
cgtcttcactttttgtgctttcctaattttccttacgaatgcaaggaccaaatagat-----agtaatttctttttctgatctgcgtggtgatgatgctgtgtagATTTGGACAGCCTATCAAAGTTAATTGGGCATATGCAAGCGGGCAGAGAGAGGATACTACAG
                                    | | | |   | |  ||||||     | | | || ||   ||  | |   |    ||| |  | || || ||||| ||||| ||||||||||||||||||||||| ||  | ||||||||||||||  |||
------------------------------------gtaagtagaaatccgatagatttctaactgactttttccactcctgtatcttaacatgttagtttgcagGTTTGGTCAGCCAATCAAAGTTAATTGGGCATATGCTAGTAGTCAGAGAGAGGATACATCAG

upper sequence: PP1S84_50V6.2 (Physcomitrella patens), 3'ss of exon 5
lower sequence: Vv09s0002g00880.t01 (Vitis vinifera), 3'ss of exon 4
cgtcttcactttttgtgctttcctaattttccttacgaatgcaaggaccaaatagatagtaatttctttttctgatctgcgtggtgatgatgctgtgtagATTTGGACAGCCTATCAAAGTTAATTGGGCATATGCAAGCGGGCAGAGAGAGGATACTACAG
          |     |    | | |||||  ||    |||  |    ||  | |  | |  ||||| || || || |            |  | || || ||||| ||||||||||||||||||||||||||||| || || || || ||||| ||  |||
---------gtaagaagaacccttgatttttattt---atgtta----catgttgggatttgtttctgttgctcatttt----------gtaatttgcagGTTTGGGCAGCCTATCAAAGTTAATTGGGCATATGCTAGTGGTCAAAGGGAGGACACATCAG

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|162254430|gb|FC430656.1|FC430656
EST:     GACCATATTTATGCTGCAGTAGCATTAACTACTCTAAATGGCAGACTAAT                         ATTTGGACAGCCTATCAAAGTTAATTGGGCATATGCAAGCGGGCAGAGAGA
genomic: GACCATATTTATGCTGCAGTAGCATTAACTACTCTAAATGGCAGACTAATgtacgttcca ... tgctgtgtagATTTGGACAGCCTATCAAAGTTAATTGGGCATATGCAAGCGGGCAGAGAGA
EST: gi|100358593|gb|BY965724.1|BY965724
EST:     GACCATATTTATGCTGCAGTAGCATTAACTACTCTAAATGGCAGACTAAT                         ATTTGGACAGCCTATCNAAGTTAATTGGGCATATGCAAGCGGGCAGA
genomic: GACCATATTTATGCTGCAGTAGCATTAACTACTCTAAATGGCAGACTAATgtacgttcca ... tgctgtgtagATTTGGACAGCCTATCAAAGTTAATTGGGCATATGCAAGCGGGCAGA
EST: gi|100407206|gb|BY974055.1|BY974055
EST:     GACCATATTTATGCTGCAGTAGCATTAACTACTCTAAATGGCAGACTAAT                         ATTTGGACAGCCTATCACAGTTAATTGGGCATATGCAAG
genomic: GACCATATTTATGCTGCAGTAGCATTAACTACTCTAAATGGCAGACTAATgtacgttcca ... tgctgtgtagATTTGGACAGCCTATCAAAGTTAATTGGGCATATGCAAG
EST: gi|162277159|gb|FC453381.1|FC453381
EST:     GACCATATTTATGCTGCAGTAGCATTAACTACTCTAAATGGCAGACTAAT                         ATTTGGACAGCCTATCAAAGTTAATTGGGCATATGCAAGCGGGCAGAGAGA
genomic: GACCATATTTATGCTGCAGTAGCATTAACTACTCTAAATGGCAGACTAATgtacgttcca ... tgctgtgtagATTTGGACAGCCTATCAAAGTTAATTGGGCATATGCAAGCGGGCAGAGAGA
EST: gi|162152881|gb|FC328975.1|FC328975
EST:     GACCATATTTATGCTGCAGTAGCATTAACTACTCTAAATGGCAGACTAAT                         ATTTGGACAGCCTATCAAAGTTAATTGGGCATATGCAAGCGGGCAGAGAGA
genomic: GACCATATTTATGCTGCAGTAGCATTAACTACTCTAAATGGCAGACTAATgtacgttcca ... tgctgtgtagATTTGGACAGCCTATCAAAGTTAATTGGGCATATGCAAGCGGGCAGAGAGA
EST: gi|162261365|gb|FC437798.1|FC437798
EST:     GACCATATTTATGCTGCAGTAGCATTAACTACTCTAAATGGCAGACTAAT                         ATTTGGACAGCCTATCAAAGTTAATTGGGCATATGCAAGCGGGCAGAGAGA
genomic: GACCATATTTATGCTGCAGTAGCATTAACTACTCTAAATGGCAGACTAATgtacgttcca ... tgctgtgtagATTTGGACAGCCTATCAAAGTTAATTGGGCATATGCAAGCGGGCAGAGAGA
EST: gi|100377715|gb|BY986366.1|BY986366
EST:     GACCATATTTATGCTGCAGTAGCATTAACTACTCTAAATGGCAGACTAAT                         ATTTGGACAGCCTATCANAGTTAATTGGGCATATGCAAGCGGGCAGAGAGA
genomic: GACCATATTTATGCTGCAGTAGCATTAACTACTCTAAATGGCAGACTAATgtacgttcca ... tgctgtgtagATTTGGACAGCCTATCAAAGTTAATTGGGCATATGCAAGCGGGCAGAGAGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gaccaaatagatagtaatttctttttctgatctgcgtggtgatgatgctgtgtagATTTGGACAGCCTATCAAAGTTAATTGGGCATATGCAAGCGGGCAGAGAGAGGATACTACAG
                        ttctgat  putative branch site (score: 3)
     aatagatagtaatttc  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cgtcttcactttttgtgctttcctaattttccttacgaatgcaaggaccaaatagatagtaatttctttttctgatctgcgtggtgatgatgctgtgtagATTTGGACAGCCTATCAAAGTTAATTGGGCATATGCAAGCGGGCAGAGAGAGGATACTACAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAT