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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgttactcatagctttaaccttgacaattttatgcaagcgtcgtctttcatgtcataattacaattcagtgatgattttacttccgtttcatgtgtgcagACAAGTAGCGCACACAGCTGGACCTGCTTAGATCTTTACGTATTTGCAACTCCATACCGTGTGACTTGGGATTACTACTTTACTGCTCGCAATCACACTC

Basic information

species Physcomitrella patens
transcript PP1S191_130V6.3
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S191_130V6.3 (Physcomitrella patens), 3'ss of exon 2
lower sequence: LOC_Os01g58114.2 (Oryza sativa), 3'ss of exon 1
tgttactcatagctttaaccttgacaattttatgcaagcg-tcgtctttcatgtcataatta-------caattcagtgatgattttacttccgtttcatgtgtgcagACAAGTAGCGCACACAGCTGGACCTGCTTAGATCTTTACGTATTTGCAACTCCATACCGTGTGACTTGGGATTACTACTTTACTGCTCGCAATCACACTC
      || ||     |   || |    ||| || | |   || | | ||    ||| | ||        | |||| |  ||||  |    | ||| | ||| |||||||||  |  || || |||||||| ||| |||| ||||| || |||||||| ||||| ||||| || |||||||||||||||   | |||  | || || |
-----ttcttaatacaag--ttaattgctttctgaaggttctcatttctctacacatgaatattcttcttatttcactattgatcctgacactgttccttgt-tgcagACAAACAAAGCTCATAGCTGGACTTGCATAGACCTTTATGTGTTTGCAACACCATATCGTGTTACATGGGATTACTACTTTGTAGGTCGTGAGCATACCC

upper sequence: PP1S191_130V6.3 (Physcomitrella patens), 3'ss of exon 2
lower sequence: GRMZM2G139374_T02 (Zea mays), 3'ss of exon 1
tgttactcatagctttaaccttgacaattttatgcaagcgtcgtctttcatg-tcataat--tacaattcagtgatgattttacttccgtttc--atgtgtgcagACAAGTAGCGCACACAGCTGGACCTGCTTAGATCTTTACGTATTTGCAACTCCATACCGTGTGACTTGGGATTACTACTTTACTGCTCGCAATCACACTC
     ||   || | |||  |    ||  || |||        |  | |  | |  |  |  |     | | || || | | |  ||  ||    |  || |||||||   |  |||||||||||||| ||| ||||||| || ||||||||||| |||||| | || || |||||||||||||||   |  ||  | |||||||
----tcttgcag-tgtaatttcagtaaaattctgctcctaattttctgcgcggttgttttcctttgccttaatgttggtctaaaatcgattataaacttgcgcagACATCCAAAGCACACAGCTGGACTTGCATAGATCTGTATGTATTTGCAACACCATACAGAGTTACATGGGATTACTACTTTCTGGGGCGAGAGCACACTC

upper sequence: PP1S191_130V6.3 (Physcomitrella patens), 3'ss of exon 2
lower sequence: Vv19s0090g00100.t01 (Vitis vinifera), 3'ss of exon 1
----tgttactcatagctttaaccttgacaattttatgcaagcgtcgtctttcatgtcataattacaattcagtgatgattttacttccgtttcatgtgtgcagACAAGTAGCGCACACAGCTGGACCTGCTTAGATCTTTACGTATTTGCAACTCCATACCGTGTGACTTGGGATTACTACTTTACTGCTCGCAATCACACTC
     |   ||  | |  |||   |   ||  | ||  | |   | | |         |||| |    || ||   | |  |    | |  || |  ||| |||   ||||  || || || ||||  ||  | || ||||| || ||||||||||||||||  ||||| |||||||||||||||    ||||  | || ||  
gcttggaagcttcttgtattagtataatca--tataccctaatatggccagcagaagaataaattatttttagctttaaaatgctattc--tttacttgttcagGTTAGTAATGCGCATAGTTGGAAGTGTATGGACCTTTATGTCTTTGCAACTCCATACCAAGTGACATGGGATTACTACTTTTTGTCTCGGGAGCATACCG

upper sequence: PP1S191_130V6.3 (Physcomitrella patens), 3'ss of exon 2
lower sequence: Vv19s0090g00130.t01 (Vitis vinifera), 3'ss of exon 1
----tgttactcatagctttaaccttgacaattttatgcaagcgtcgtctttcatgtcataattacaattcagtgatgattttacttccgtttcatgtgtgcagACAAGTAGCGCACACAGCTGGACCTGCTTAGATCTTTACGTATTTGCAACTCCATACCGTGTGACTTGGGATTACTACTTTACTGCTCGCAATCACACTC
     |   ||  | |  |||   |   ||  | ||  | |   | | |         |||  |    || ||   | |  |    | |  || |  ||| |||   ||||| || || || ||||| ||  | || ||||| || ||||||||||||||||  ||||| |||||||||||||||    ||||  | || ||  
gcttggaagcttcttgtattagtataatca--tataccctaatatggccagcagaagaatagattatttttagctttaaaatg--ctactctttacttgttcagGTTAGTAGTGCCCATAGTTGGACATGTATGGACCTTTATGTCTTTGCAACTCCATACCAAGTGACATGGGATTACTACTTTTTGTCTCGGGAGCATACCA

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|100424967|gb|BY976905.1|BY976905
EST:     CTGAGCCNNNNNNNGAAGGTCATAATGGTGGTGGCATTCTTCATATTCGA                         ACAAGTAGCGCACACAGCTGGACCTGCTTAGATCTTTACGTATTTGCAACT
genomic: CTGAGCCAAAAAAAGAAGGTCATAATGGTGGTGGCATTCTTCATATTCGAgtatgtacat ... atgtgtgcagACAAGTAGCGCACACAGCTGGACCTGCTTAGATCTTTACGTATTTGCAACT






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttcatgtcataattacaattcagtgatgattttacttccgtttcatgtgtgcagACAAGTAGCGCACACAGCTGGACCTGCTTAGATCTTTACGTATTTGCAACTCCATACCGTGTGACTTGGGATTACTACTTTACTGCTCGCAATCACACTC
       tcataattacaatt  TA-rich tract