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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...agaaacacttcatctgttttactacccgcgtgtttcaatgcattaaatgcttttgtgtagtaggtgggactactattgatgaaagcctgtcttattgcagAACAAGGATGGAGGTTGGGGATTGCACATAGAGGGACACAGTACCATGTTTGGCTCTGTACTGACGTATGTTACACTGCGGATACTTGGTGATGGGCCTG

Basic information

species Physcomitrella patens
transcript PP1S33_211V6.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S33_211V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: LOC_Os02g04710.2 (Oryza sativa), 3'ss of exon 3
agaaacacttcatctgttttactacccgcgtgtttcaatgcattaaatgcttttgtgtagtaggtgggactactattgatgaaagcc-tgtcttattgcagAACAAGGATGGAGGTTGGGGATTGCACATAGAGGGACACAGTACCATGTTTGGCTCTGTACTGACGTATGTTACACTGCGGATACTTGGTGATGGGCCTG
                                | | | | || |   | |  |  || | || ||      | | ||        |  ||| | | || ||||  | |||||||| ||||| |||||||| ||||| ||||| |||||||||||||| |   |||| |||||| |  || |  | ||||| || ||||| |
------------------------gtaagaaatctaattacacttc-tacaatcttgaaataagtaaaggcaatgttttccttttctgtgtgtaagtgtagAATGAAGATGGAGGATGGGGTTTGCACATTGAGGGCCACAGCACCATGTTTGGCTCAGCGTTGACATATGTTTCTTTGAGATTGCTTGGGGAGGGGCCAG

upper sequence: PP1S33_211V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: GRMZM5G821318_T01 (Zea mays), 3'ss of exon 1
agaaacacttcatctgttttactacccgcgtgtttcaatgcattaaatgcttttgtgtagtaggtgggactactattgatgaaagcctgtcttattgcagAACAAGGATGGAGGTTGGGGATTGCACATAGAGGGACACAGTACCATGTTTGGCTCTGTACTGACGTATGTTACACTGCGGATACTTGGTGATGGGCCTG
        |    || ||||| |          || || |  ||   ||||       || |      | |||| |   ||||         || || ||||  | |||||||| |||||||||||||| ||||| ||||| |||||| || |||| |   |||  |||||| |  || || | ||||| ||  | ||  
-------gtaaggctattttattg---ataaacttgaaag--ttgcgtgctgggagagagcaaacttcattactctccctgaata-------taatgtagAATGAAGATGGAGGGTGGGGATTGCACATTGAGGGCCACAGCACCATGCTTAGCTCAGCCTTGAACTATGTTGCTTTGAGGTTGCTTGGGGAGAGCCCAA

upper sequence: PP1S33_211V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: GLYMA15G07110.1 (Glycine max), 3'ss of exon 5
agaaacacttcatctgttttactacccgcgtgtttcaatgc-attaaat---gcttttgtgtagtaggtgggactactattgatgaaagcctgtcttattgcagAACAAGGATGGAGGTTGGGGATTGCACATAGAGGGACACAGTACCATGTTTGGCTCTGTACTGACGTATGTTACACTGCGGATACTTGGTGATGGGCCTG
      |  | || |       |  | | || |  ||  || |||||||     |||| |    | |    ||  |      || ||    |      ||| ||||||| ||||||||||||||| | |||||||| || ||||||| ||||||| || ||  ||| |  ||| |     |||| || ||||| || || ||| 
----ttaagttatataaaactttttcagtgtttcccatagccattaaatctgatttttttcccatggcaatgagcatctaatattaattggtaaacacttgaagAACAAAGATGGAGGTTGGGGACTACACATAGAAGGTCACAGTATCATGTTTTGCACTACACTCAATTATATATGCATGCGAATTCTTGGAGAAGGACCTA

upper sequence: PP1S33_211V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: GLYMA08G03060.1 (Glycine max), 3'ss of exon 3
-----------------------------------------------agaaacacttcatct---gttttactacccgcgtgt---ttcaatgcattaaatgctt------------ttgtgtagtaggtgggactactattgatgaaagcctgtcttattgcagAACAAGGATGGAGGTTGGGGATTGCACATAGAGGGACACAGTACCATGTTTGGCTCTGTACTGACGTATGTTACACTGCGGATACTTGGTGATGGGCCTG
                                               | ||  || | | ||   | |     | |     ||    |  |||||| ||||  |              ||  ||     || | ||| |  |  |   |     |  |    |||||| | |||||||||||||||||||| |||||| | ||||| || |||||||| || |   |||  ||  || |  || | || ||||| || |||||||
gtatatttttatcttgtttcttaagtaatgtaatgcatacaagaatgaaaataacattagctcaggctccggcaactaaaagtaagatttatgcatgaaattttaatttagttccaactgaataacctatgagtctattggttgttgcattgcatgatgagacagAACGAAGATGGAGGTTGGGGATTGCATATAGAGAGTCACAGCACAATGTTTGGGTCAGCGTTGAGCTACATTGCCTTGAGAATTCTTGGAGAAGGGCCTG

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|67716963|gb|BJ967222.1|BJ967222
EST:     TAACTCCAGCCCACCAGAGTGAAATGCGCCGGTACCTTTACAATCATCAG                         AACAAGGATGGAGGTTGGGGATTGCACATAGAGGGACACAGTACCATGTTT
genomic: TAACTCCAGCCCACCAGAGTGAAATGCGCCGGTACCTTTACAATCATCAGgtacttgggt ... cttattgcagAACAAGGATGGAGGTTGGGGATTGCACATAGAGGGACACAGTACCATGTTT
EST: gi|100361183|gb|BY946955.1|BY946955
EST:     TAACTCCAGCCCACCAGAGTGAAATGCGCCGGTACCTTTACAATCATCAG                         AACAAGGATGGAGGTTGGGGATTGCACATAGAGGGACACAGTACCATGTTT
genomic: TAACTCCAGCCCACCAGAGTGAAATGCGCCGGTACCTTTACAATCATCAGgtacttgggt ... cttattgcagAACAAGGATGGAGGTTGGGGATTGCACATAGAGGGACACAGTACCATGTTT
EST: gi|100441769|gb|BY962860.1|BY962860
EST:     TAACTCCAGCCCACCAGAGTGAAATGCGCCGGTACCTTTACAATCATCAG                         AACAAGGATGGAGGTTGGGGATTGCA
genomic: TAACTCCAGCCCACCAGAGTGAAATGCGCCGGTACCTTTACAATCATCAGgtacttgggt ... cttattgcagAACAAGGATGGAGGTTGGGGATTGCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aatgcttttgtgtagtaggtgggactactattgatgaaagcctgtcttattgcagAACAAGGATGGAGGTTGGGGATTGCACATAGAGGGACACAGTACCATGTTTGGCTCTGTACTGACGTATGTTACACTGCGGATACTTGGTGATGGGCCTG
                            tattgat  putative branch site (score: 3)
                                        cctgtctt  putative PPT
                         tactatt  TA-rich tract