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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttatttgttgtgttgttttgattttttgaaaaaaattgtaataattttaatttgaagttcactgatcgttttcactttcgtatatgcttcttctttgcagTTTGATTACTTAAAGAGTTTGGAAATAGAGGAGAAGATCAATAAAATTAGATGGTGCCAGACTGCCAATGCCGCTCAGTTTCTACTTTCTACCAATGATA

Basic information

species Physcomitrella patens
transcript PP1S425_2V6.2
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S425_2V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: LOC_Os06g36770.1 (Oryza sativa), 3'ss of exon 3
--------ttat-ttgttgtgttgttttgattttttgaaaaaaattgtaataattttaatttgaagttcactgatcgttttcactttcgtatatgcttcttctttgcagTTTGATTACTTAAAGAGTTTGGAAATAGAGGAGAAGATCAATAAAATTAGATGGTGCCAGACTGCCAATGCCGCTCAGTTTCTACTTTCTACCAATGATA
        |||  || ||||| | |  |  | |||||       ||| | || ||  |  | |||  ||||  |||  | |   |||  |  |   ||||       ||||||||||| | || |||||||||||||||||||||||||| || || || ||||||||||| ||||||    | |  |  || || ||||| |||||||
atgaagcattacattattgtgctatgctcttgttttgttcttgcttgaattacttgcatatggaaactcac--atctatgtttttttgatgaactgttct-------agTTTGATTACCTCAAAAGTTTGGAAATAGAGGAGAAGATCAACAAGATCAGGTGGTGCCAGACAGCCAATAATTCACTCTCCCTTCTGTCTACAAATGATA

upper sequence: PP1S425_2V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: GLYMA13G42800.1 (Glycine max), 3'ss of exon 3
ttatttgttgtgttgttttgattttttgaaaaaaattgtaataattttaatttgaagttcactgatcgttttcactttcgtatatgcttcttctttgcagTTTGATTACTTAAAGAGTTTGGAAATAGAGGAGAAGATCAATAAAATTAGATGGTGCCAGACTGCCAATGCCGCTCAGTTTCTACTTTCTACCAATGATA
           ||  |  | ||||  | |  ||  ||| |  ||  |   | ||      |    ||  | |   | |  | |||| |  || ||| |||||||| ||  | |||||||||||||| || ||||| ||||| ||||| ||||||||||| |  || ||||  || |  || || |||||||| |||||||
-----------gtaatcatcatttggtcagtaatgttgcaccaacatcc-tatgggtcagaagagtcaatatt--tataatgtatgatcattgttt-cagTTTGACTATCTTAAGAGTTTGGAAATTGAAGAGAAAATCAACAAAATCAGATGGTGCCAAATAGCTAATGGTGCCCTCTTCCTTCTTTCTACAAATGATA

upper sequence: PP1S425_2V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: GLYMA08G20830.4 (Glycine max), 3'ss of exon 3
ttatttgttgtgttgttttgattttttgaaaaaaattgtaataattttaatttgaagttcactgatcgttttcactt-tcgtatatgcttcttctttgcagTTTGATTACTTAAAGAGTTTGGAAATAGAGGAGAAGATCAATAAAATTAGATGGTGCCAGACTGCCAATGCCGCTCAGTTTCTACTTTCTACCAATGATA
           ||  |||| | |   ||   ||   ||    || |     |||  |  ||   || |||  || || |   || || || || ||| |||||||| ||  | ||||||||||||||||| ||||| || || ||||| | ||||||||| || |||||||  |||  ||| || || || || |||||||
-----------gtaattttcagtcactggttaatgctgcctgaaat---gcttgtggagcagaaat-gttaacatttatgacatgtgattgttgttt-cagTTTGACTATCTTAAGAGTTTGGAAATAGAAGAGAAAATTAACAAAATCAAATGGTGCCAAACAGCCAATGGTGCTTTGTTCCTTCTATCCACAAATGATA

upper sequence: PP1S425_2V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: AT1G51690.3 (Arabidopsis thaliana), 3'ss of exon 5
ttatttgttgtgttgttttgattttttgaaaaaaattgtaataattttaatttgaagttcactgatcgttttcactttcgtatatgcttcttctttgcagTTTGATTACTTAAAGAGTTTGGAAATAGAGGAGAAGATCAATAAAATTAGATGGTGCCAGACTGCCAATGCCGCTCAGTTTCTACTTTCTACCAATGATA
 |||||| | |  | | ||   || ||            |   ||||   | |    || |    || ||||||   ||   ||| ||| ||     |||||||||||| | ||||||||||| ||||||||||| || || |||||||||||||| || || || ||||  ||||  ||||| || || ||||||||||
gtatttgatttactctgttttcttctta--------ctcagctatttggctataccttttatctgtc-ttttcatgctc---tatccttgtttac--cagTTTGATTACCTCAAGAGTTTGGAGATAGAGGAGAAAATTAACAAAATTAGATGGTGTCAAACAGCAAATGGAGCTCTTTTTCTCCTCTCGACCAATGATA

upper sequence: PP1S425_2V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: AT1G17720.2 (Arabidopsis thaliana), 3'ss of exon 3
ttatttgttgtgttgttttgattttttgaaaaaaattgtaataattttaatttgaagttcactgatcgttttcactttcgtatatgcttcttctttgcagTTTGATTACTTAAAGAGTTTGGAAATAGAGGAGAAGATCAATAAAATTAGATGGTGCCAGACTGCCAATGCCGCTCAGTTTCTACTTTCTACCAATGATA
           ||   ||  |  || | |  | | ||    ||    |||||    ||||  ||| |   |  |    | |   |     |   || |||||||| ||  | ||||||||||| ||||||||||| ||||| ||||| |||||||| ||| | || ||||  ||   |||||| |||||||| || ||||
-----------gtacattaaaacttatcaccagatttcacttacgagtaatt--gtgttccttgagctactcaataagcttgcttttcaatctgtttcagTTTGACTATCTCAAGAGTTTGGAGATAGAGGAGAAAATCAACAAAATCAGATGGTGTCAGCCAGCTAATGGTGCATTGTTTCTGCTTTCTACAAACGATA

upper sequence: PP1S425_2V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: Vv11s0016g02550.t01 (Vitis vinifera), 3'ss of exon 3
ttatttgttgtgttgttttgattttttgaaaaaaattgtaataattttaatttgaagttcactgatcgttttcactttcgtatatgcttcttctttgcagTTTGATTACTTAAAGAGTTTGGAAATAGAGGAGAAGATCAATAAAATTAGATGGTGCCAGACTGCCAATGCCGCTCAGTTTCTACTTTCTACCAATGATA
 |||||  | |  ||| ||| |        ||  |||||| |  |      ||    ||   |  || |  | | | | |  ||| | | |  ||| |||||||||||  | ||||||||||||||||||||||| |||||||| ||||||||||| || || || ||    ||   |||||| || || |||||||| |
gtatttacttttctgtgttgctaacactctaatcattgtagttttcacggatttgtatttttt--tcttactaaatctagactattcgt-tcatttccagTTTGATTATCTCAAGAGTTTGGAAATAGAGGAGAAAATCAATAAGATTAGATGGTGTCAAACAGCTAACAATGCATTGTTTCTTCTCTCCACCAATGACA

upper sequence: PP1S425_2V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: Vv09s0002g02470.t01 (Vitis vinifera), 3'ss of exon 3
---------ttatttgttgtgttgttttga---ttttttgaaaaaaattgtaataattttaatttgaagttcactgatcgttttcactttcgtatatgcttcttctttgcagTTTGATTACTTAAAGAGTTTGGAAATAGAGGAGAAGATCAATAAAATTAGATGGTGCCAGACTGCCAATGCCGCTCAGTTTCTACTTTCTACCAATGATA
         | ||  |||         |||   || |||| |  |   | |  | | |    | |||| |    | || | |  ||| || |  ||| ||   |  |  |||||||| ||  | ||||| ||||||||||||||||| |||||||| || |||||||||||||| || ||||  || | |||||| || ||||| |||||||
gtatttctttcatcagttactcctgcctgaagtttgtttgcaccaccctttgctcactaggctctgaaatgttttaattgatgccacatt-gcttattctctgtgct--cagTTTGACTATCTGAAGAGCTTGGAAATAGAGGAGAAAATCAATAAGATCAGATGGTGCCAGACAGCAAATGGTGCCCTGTTTCTTCTATCTACGAATGATA

upper sequence: PP1S425_2V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: Vv04s0008g00840.t01 (Vitis vinifera), 3'ss of exon 3
----ttatttgttgtgttgttt-tgattttttgaaaaaaattgtaataattttaatttgaagttcactgatcgttttc--actttcgtatatgcttcttc----------tttg----cagTTTGATTACTTAAAGAGTTTGGAAATAGAGGAGAAGATCAATAAAATTAGATGGTGCCAGACTGCCAATGCCGCTCAGTTTCTACTTTCTACCAATGATA
       ||     | | |||| ||  ||  |||  |  |   || |  |||||  |||    ||    ||| ||     ||| | | || |  |||| |          ||||    |||||||| ||  | ||||| |||||||| |||||||| ||||| || ||||||||||| ||||| || ||   ||| | |||||| || || || |||||||
gtgtcctttaagaatttcgtttctgggttgctgatgattaccata-tccttttatcttgtctgtcttccatccttactggactctggaatttaattctgcatttaatatgtttgaattcagTTTGACTATCTCAAGAGCTTGGAAATTGAGGAGAAAATCAACAAGATTAGATGGTGTCAGACAGCTAACAGCGCACTGTTTCTTCTCTCCACTAATGATA

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|162150295|gb|FC326380.1|FC326380
EST:     GGCATCCTGAATATCGATACTCAACTGAGTTTCAAAGTCATGAGCCGGAG                         TTTGATTACTTAAAGAGTTTGGAAATAGAGGAGAAGATCAATAAAATTAGA
genomic: GGCATCCTGAATATCGATACTCAACTGAGTTTCAAAGTCATGAGCCGGAGgtaaatctaa ... ttctttgcagTTTGATTACTTAAAGAGTTTGGAAATAGAGGAGAAGATCAATAAAATTAGA
EST: gi|100389123|gb|BY952327.1|BY952327
EST:     GGCATCCTGAATATCGATACTCAACTGAGTTTCAAAGTCATGAGCCGGAG                         TTTGATTACTTAAAGAGTT
genomic: GGCATCCTGAATATCGATACTCAACTGAGTTTCAAAGTCATGAGCCGGAGgtaaatctaa ... ttctttgcagTTTGATTACTTAAAGAGTT
EST: gi|162255330|gb|FC432056.1|FC432056
EST:     GGCATCCTGAATATCGATACTCAACTGAGTTTCAAAGTCATGAGCCGGAG                         TTTGATTACTTAAAGAGTTTGGAAATAGAGGAGAAGATCAATAAAATTAGA
genomic: GGCATCCTGAATATCGATACTCAACTGAGTTTCAAAGTCATGAGCCGGAGgtaaatctaa ... ttctttgcagTTTGATTACTTAAAGAGTTTGGAAATAGAGGAGAAGATCAATAAAATTAGA
EST: gi|100386449|gb|BY951245.1|BY951245
EST:     GGCATCCTGAATATCGATACTCAACTGAGTTTCAAAGTCATGAGCCGGAG                         TTT-ATTACTTTAAGAGTTTGGAAATA
genomic: GGCATCCTGAATATCGATACTCAACTGAGTTTCAAAGTCATGAGCCGGAGgtaaatctaa ... ttctttgcagTTTGATTACTTAAAGAGTTTGGAAATA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttaatttgaagttcactgatcgttttcactttcgtatatgcttcttctttgcagTTTGATTACTTAAAGAGTTTGGAAATAGAGGAGAAGATCAATAAAATTAGATGGTGCCAGACTGCCAATGCCGCTCAGTTTCTACTTTCTACCAATGATA
              cactgat  putative branch site (score: 3)
                                     tatgcttcttcttt  putative PPT
                                   tatat  TA-rich tract