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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cagcttggctactgtacgaaaaatgcggaattctgtaataaacatagctttctggcgaaaacgatggcgagtcgttgatgttattacttcgttttcgcagGTGTAGATATCAGCATGAATACGCATTTGAAGTCTGTGAAGCTCACTTTGAAGGGAAAGGTTCCTGTGGCTCTCGACCATCTCAGTGTCCGCGGCAACAA

Basic information

species Physcomitrella patens
transcript PP1S37_118V6.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S37_118V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: GRMZM2G416061_T01 (Zea mays), 3'ss of exon 3
cagcttggctactgtacgaaaaatgcggaattctgtaataaacatagctttctggcgaaaacgatggcg-agtcgt-tgatgttattacttcgttttcgcagGTGTAGATATCAGCATGAATACGCATTTGAAGTCTGTGAAGCTCACTTTGAAGGGAAAGGTTCCTGTGGCTCTCGACCATCTCAGTGTCCGCGGCAACAA
    ||    |    |  |||| |         |  |  | |  |  |  |    | | || |||     ||| || |  | | |||  || |  || | |||||| || |||||||||||||| ||| ||||| |||||||||| ||  | || || ||   ||||||  | || || || || |||||  | || |||||
--tttttaacatcccattaaaattctctcccattccatcagattttacagtaatcctagaatgattattcagtagtgtattctgattttttggactttgtagGTGTTGACATCAGCATGAATACTCATCTGAAGACTGTGAAGCTGACACTAAAAGGGAAAAATCCTGTTACCCTTGATCACCTTAGTGTGAGGGGAAACAA
















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|162210344|gb|FC386224.1|FC386224
EST:     GGTATCGATAGAGCTCAAGAATGGAACCATTGTGCACGGTACTATCACAG                         GTGTAGATATCAGCATGAATACGCATTTGAAGTCTGTGAAGCTCACTTTGA
genomic: GGTATCGATAGAGCTCAAGAATGGAACCATTGTGCACGGTACTATCACAGgtatgtgttc ... gttttcgcagGTGTAGATATCAGCATGAATACGCATTTGAAGTCTGTGAAGCTCACTTTGA
EST: gi|208364908|gb|DC947050.1|DC947050
EST:     GGTATCGATAGAGCTCAAGAATGGAACCATTGTGCACGGTACTATCACAG                         GTGTAGATATCAGCATGAATACGCATTTGAAGTCTGTGAAGCTCACTTTGA
genomic: GGTATCGATAGAGCTCAAGAATGGAACCATTGTGCACGGTACTATCACAGgtatgtgttc ... gttttcgcagGTGTAGATATCAGCATGAATACGCATTTGAAGTCTGTGAAGCTCACTTTGA
EST: gi|18345230|gb|BJ177271.1|BJ177271
EST:     GGTATCGATAGAGCTCAAGAATGGAACCATTGTGCACGGTACTATCACAG                         GTGTAGATATCAGCATGAATACGCATTTGAAGTCTGTGAAGCTCACTTTGA
genomic: GGTATCGATAGAGCTCAAGAATGGAACCATTGTGCACGGTACTATCACAGgtatgtgttc ... gttttcgcagGTGTAGATATCAGCATGAATACGCATTTGAAGTCTGTGAAGCTCACTTTGA
EST: gi|162217222|gb|FC391962.1|FC391962
EST:     TATCGATAGAGCTCAAGAATGGAACCATTGTGCACGGTACTATCACAG                         GTGTAGATATCAGCATGAATACGCATTTGAAGTCTGTGAAGCTCACTTTGA
genomic: TATCGATAGAGCTCAAGAATGGAACCATTGTGCACGGTACTATCACAGgtatgtgttc ... gttttcgcagGTGTAGATATCAGCATGAATACGCATTTGAAGTCTGTGAAGCTCACTTTGA
EST: gi|208375129|gb|DC956469.1|DC956469
EST:     GGTATNGATAGAGCTCAAGAATGGAACCATTGTGCACGGTACTATCACAG                         GNGTAGATATCAGCATGAATACGCATTTGAAGTCTGTGAAGCTCACTTTGA
genomic: GGTATCGATAGAGCTCAAGAATGGAACCATTGTGCACGGTACTATCACAGgtatgtgttc ... gttttcgcagGTGTAGATATCAGCATGAATACGCATTTGAAGTCTGTGAAGCTCACTTTGA
EST: gi|208369557|gb|DC932539.1|DC932539
EST:     GGTATCGATAGAGCTCAAGAATGGAACCATTGTGCACGGTACTATCACAG                         GTGTAGATATCAGCATGAATACGCATTTGAAGTCTGTGAAGCTCACTTTGA
genomic: GGTATCGATAGAGCTCAAGAATGGAACCATTGTGCACGGTACTATCACAGgtatgtgttc ... gttttcgcagGTGTAGATATCAGCATGAATACGCATTTGAAGTCTGTGAAGCTCACTTTGA
EST: gi|162217223|gb|FC391963.1|FC391963
EST:     TATCGATAGAGCTCAAGAATGGAACCATTGTGCACGGTACTATCACAG                         GTGTAGATATCAGCATGAATACGCATTTGAAGTCTGTGAAGCTCACTTTGA
genomic: TATCGATAGAGCTCAAGAATGGAACCATTGTGCACGGTACTATCACAGgtatgtgttc ... gttttcgcagGTGTAGATATCAGCATGAATACGCATTTGAAGTCTGTGAAGCTCACTTTGA
EST: gi|208388874|gb|DC932902.1|DC932902
EST:     GGTATCGATAGAGCTCAAGAATGGAACCATTGTGCACGGTACTATCACAG                         GTGTAGATATCAGCATGAATACGCATTTGAAGTCTGTGAAGCTCACTTTGA
genomic: GGTATCGATAGAGCTCAAGAATGGAACCATTGTGCACGGTACTATCACAGgtatgtgttc ... gttttcgcagGTGTAGATATCAGCATGAATACGCATTTGAAGTCTGTGAAGCTCACTTTGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agctttctggcgaaaacgatggcgagtcgttgatgttattacttcgttttcgcagGTGTAGATATCAGCATGAATACGCATTTGAAGTCTGTGAAGCTCACTTTGAAGGGAAAGGTTCCTGTGGCTCTCGACCATCTCAGTGTCCGCGGCAACAA
                           cgttgat  putative branch site (score: 5)
                                         cttcgttttc  putative PPT
                                atgttatta  TA-rich tract