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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacgtattgaatacttttgcaagttgaagttttgaaatacacgctattttgaaactagcacatttaatccttaaatcattcatttctttttaattgacaaatttcgtcgacgatcgatcttcatgttatcacttctgtgtgcgcagAATGATTTGAAGAGCCATGTGTGTTGGCATGTCTATGGGCTTCTTTACCGTTCCGACAGGGATTATCGGGAGGCTATTAAGTGCTATCGATGTGCTCTTC

Basic information

species Physcomitrella patens
transcript PP1S67_222V6.2
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S67_222V6.2 (Physcomitrella patens), 3'ss of exon 3
lower sequence: LOC_Os01g43030.2 (Oryza sativa), 3'ss of exon 3
gtacgtattgaatacttttgcaagttgaagttttgaaatacacgctattttgaaactagcacatttaatccttaaatcattcatttctttttaattgacaaatttcg--tcgacgatcgatcttcatgttatcacttctgtgtgcgcagAATGATTTGAAGAGCCATGTGTGTTGGCATGTCTATGGGCTTCTTTACCGTTCCGACAGGGATTATCGGGAGGCTATTAAGTGCTATCGATGTGCTCTTC
                                                          | |  | | |    ||     || | |  |||||  |  | |  || |   |  ||||   ||     || | | ||||   | |  |||||||||| ||||||| |||||||| ||||||||||||||  | ||||| || || ||||| || ||  | || || || || || ||  ||  ||||||  
----------------------------------------------------------gtatgtatgagtgatacggttttgagtatttttttgtctaaatcttacaattgtacgagaaatggaactgattttacttg-atatatgcagAATGATCTGAAGAGTCATGTGTGCTGGCATGTCTATGGCTTGCTTTATCGATCAGACAGAGAATACAGAGAAGCCATAAAATGTTACAGAAATGCTCTGA

upper sequence: PP1S67_222V6.2 (Physcomitrella patens), 3'ss of exon 3
lower sequence: GRMZM2G047093_T01 (Zea mays), 3'ss of exon 3
gtacgtattgaatacttttgcaagttgaagttttgaaatacacgctattttgaaactagcacatttaatccttaaatcattcatttcttt-ttaattgacaaatttcgtcgacgatcgatcttcatgttatcacttctgtgtgcgcagAATGATTTGAAGAGCCATGTGTGTTGGCATGTCTATGGGCTTCTTTACCGTTCCGACAGGGATTATCGGGAGGCTATTAAGTGCTATCGATGTGCTCTTC
                                           | |||     || ||   || | ||| ||    |  || || |  |  |||| ||    |     |  |  |   |     |   ||  | |    | |  |||||||||| ||||||| ||||| ||||||||||| |||||  | ||||| || || || || || ||  | || ||||| || || ||  ||  |||  |  
-------------------------------------------gttatc----aattattgcaatgaattctctg-ttgttgatgtgatgattaaatggggtacaagtttcagaactcagaacta-actaataataaactttttgcagAATGATCTGAAGAGTCATGTCTGTTGGCATGTTTATGGTTTGCTTTATCGGTCAGATAGAGAATACAGAGAAGCTATAAAATGTTACAGAAATGCATTGA

upper sequence: PP1S67_222V6.2 (Physcomitrella patens), 3'ss of exon 3
lower sequence: EFJ36800 (Selaginella moellendorffii), 3'ss of exon 3
gtacgtattgaatacttttgcaagttgaagttttgaaatacacgctattttgaaactagcacatttaatccttaaatcattcatttctttttaattgacaaatttcgtcgacgatcgatcttcatgttatcacttctgtgtgcgcagAATGATTTGAAGAGCCATGTGTGTTGGCATGTCTATGGGCTTCTTTACCGTTCCGACAGGGATTATCGGGAGGCTATTAAGTGCTATCGATGTGCTCTTC
                                                                                    | || |||   ||   ||| |  |  |     |||    ||   |  |  | || ||   ||||| ||| ||||||||||||| || |||||||||||||| ||||| ||||| ||||||||||| || || || ||||| || ||||| ||   ||| ||| 
-----------------------------------------------------------------------------------gtactgtttttctg--taatcttatatatacatgat----atagaacaatgtttg-gtat-cagAACGATGTGAAGAGCCATGTTTGCTGGCATGTCTATGGCCTTCTCTACCGCTCCGACAGGGAATACCGCGAAGCTATAAAATGCTACCGCAATGCGCTTA

upper sequence: PP1S67_222V6.2 (Physcomitrella patens), 3'ss of exon 3
lower sequence: EFJ27872 (Selaginella moellendorffii), 3'ss of exon 3
gtacgtattgaatacttttgcaagttgaagttttgaaatacacgctattttgaaactagcacatttaatccttaaatcattcatttctttttaattgacaaatttcgtcgacgatcgatcttcatgttatcacttctgtgtgcgcagAATGATTTGAAGAGCCATGTGTGTTGGCATGTCTATGGGCTTCTTTACCGTTCCGACAGGGATTATCGGGAGGCTATTAAGTGCTATCGATGTGCTCTTC
                                                                                    | || |||   ||   ||| |  |  |     |||    ||   |  |  | || ||   ||||| ||| ||||||||||||| || |||||||||||||| ||||| ||||| ||||||||||| || || || ||||| || ||||| ||   ||| ||| 
-----------------------------------------------------------------------------------gtactgtttttctg--taatctgatatatacatgat----atagaacaatgtttg-gtat-cagAACGATGTGAAGAGCCATGTTTGCTGGCATGTCTATGGCCTTCTCTACCGCTCCGACAGGGAATACCGCGAAGCTATAAAATGCTACCGCAATGCGCTTA

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|18351120|gb|BJ183171.1|BJ183171
EST:     GCATGGACAGGAAACCTGAGGCTTACGAGCTGGTCCGTAAAGGTTTGAAG                         AATGATTTGAAGAGCCATGTGTGTTGGCATGTCTATGGGCTTCTTTACCGT
genomic: GCATGGACAGGAAACCTGAGGCTTACGAGCTGGTCCGTAAAGGTTTGAAGgtacgtattg ... gtgtgcgcagAATGATTTGAAGAGCCATGTGTGTTGGCATGTCTATGGGCTTCTTTACCGT






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aattgacaaatttcgtcgacgatcgatcttcatgttatcacttctgtgtgcgcagAATGATTTGAAGAGCCATGTGTGTTGGCATGTCTATGGGCTTCTTTACCGTTCCGACAGGGATTATCGGGAGGCTATTAAGTGCTATCGATGTGCTCTTC
 aattgac  putative branch site (score: 3)
                                        cttctgt  putative PPT
     acaaattt  TA-rich tract