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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagctgacttttctattttcttttgtccctactatggcattggtgcttccttcccacattaagaagggttgaaataagttttgcttttgatttttgacttttgattttttcaatttttttatccttttcgaagtgtcttgatcttgagctctttgattggttaacttgaatgtgcagTTGGATATTATGGATAGAGGAACAGATGCGCGGAATTTTCTTCTAGGAAATGTCATTCCATTACGACTTGGCTATATTGGGGTTGTAAACAGGAGCCAAG

Basic information

species Physcomitrella patens
transcript PP1S49_216V6.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S49_216V6.1 (Physcomitrella patens), 3'ss of exon 5
lower sequence: LOC_Os01g69130.1 (Oryza sativa), 3'ss of exon 3
gtaagctgacttttctattttcttttgtccctactatggcattggtgcttccttcccacattaagaagggttgaaataagttttgcttttgatttttgacttttgattttttcaatttttttatccttttcgaagtgtcttgatcttgagctctttgattggttaacttgaatgtgcagTTGGATATTATGGATAGAGGAACAGATGCGCGGAATTTTCTTCTAGGAAATGTCATTCCATTACGACTTGGCTATATTGGGGTTGTAAACAGGAGCCAAG
                                                                            |      || | |||| ||||   | | ||||   | ||   || | | | |  |  |||| |    | |   | |||| | ||   |    | |   | ||| |||| || ||||| || || |||||||| || || |||||  | |||||||| |||||||||||||| |||||| |||| || |||||| | || ||| 
--------------------------------------------------------------------------gtttgaccctggtcttgagttttttgtctggattaaat-aagcattgtgttcatacc--agtgacccagttt---gatcttggcttcacttctattatcttccagCTGGACATAATGGACAGGGGCACAGATGCTCGTAACTTTCTGTTGGGAAATGTGATTCCATTACGACTAGGCTATGTTGGTGTGGTAAACCGCAGTCAAC

upper sequence: PP1S49_216V6.1 (Physcomitrella patens), 3'ss of exon 5
lower sequence: GRMZM2G180335_T01 (Zea mays), 3'ss of exon 3
gtaagctgacttttctattttcttttgtccctactatggcattggtgcttccttcccacattaagaagggttgaaataagttttgcttttgatttttgacttttgattttttcaatttttttatccttttcgaagtgtcttgatcttgagctctttgattggttaacttgaatgtgcagTTGGATATTATGGATAGAGGAACAGATGCGCGGAATTTTCTTCTAGGAAATGTCATTCCATTACGACTTGGCTATATTGGGGTTGTAAACAGGAGCCAAG
                                                                               |||||  |||       | | |||  ||  |  || |||    ||||| |      |||     ||         |||  || |    |      | ||||||||||| ||||| || || || ||||| ||||| ||||| || |||||||| || || |||  |||||||||| |||| ||||| ||| | |||||  
-------------------------------------------------------------------------------gtttttttttcctcgccttaatttctatgcta-cattttggccatcctatctctcctgtgccactcaatgcagtcttgtctgatgttgtgtttcttccagTTGGATATAATGGACAGGGGCACTGATGCCCGGAACTTTCTGCTGGGAAATGTGATCCCCTTAAAACTTGGCTATGTTGGTGTTGTTAACCGCAGCCAGC

upper sequence: PP1S49_216V6.1 (Physcomitrella patens), 3'ss of exon 5
lower sequence: GLYMA08G07160.1 (Glycine max), 3'ss of exon 3
gtaagctgacttttctattttcttttgtccctactatggcattggtgcttccttcccacattaagaagggttgaaataagttttgcttttgatttttgacttttgattttttcaatttttttatccttttcgaagtgtcttgatcttgagctctttgattggttaacttgaatgtgcagTTGGATATTATGGATAGAGGAACAGATGCGCGGAATTTTCTTCTAGGAAATGTCATTCCATTACGACTTGGCTATATTGGGGTTGTAAACAGGAGCCAAG
                                                                        | |  | ||| |  |  || ||||| |  | |||   |||     || | |    | | |  |||| |   | |   |     ||   || |   |||  |    |||||||||| ||||||||||| || |||||||||||| |  | |||||||| || |||||  | |||||||| ||| | || ||||| ||  | || ||||
------------------------------------------------------------------------gtataatgttgtagtactg-tttttaatgtgtgaacgttt-----ttgtgaagtgtgttgtggtgtttctgtttactgacaagtgtgggggtgtgttgtgt---tagTTGGATATCATGGATAGAGGCACTGATGCGCGGAATCTGTTGCTAGGAAAAGTTATTCCCCTCCGACTTGGTTATGTCGGTGTTGTGAATCGTAGTCAAG

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|162155641|gb|FC331254.1|FC331254
EST:     CTCGAACCATTGGGGTTATTACCAAA                         TTGGATATTATGGATAGAGGAACAGATGCGCGGAATTTTCTTCTAGGAAAT
genomic: CTCGAACCATTGGGGTTATTACCAAAgtaagctgac ... gaatgtgcagTTGGATATTATGGATAGAGGAACAGATGCGCGGAATTTTCTTCTAGGAAAT






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ccttttcgaagtgtcttgatcttgagctctttgattggttaacttgaatgtgcagTTGGATATTATGGATAGAGGAACAGATGCGCGGAATTTTCTTCTAGGAAATGTCATTCCATTACGACTTGGCTATATTGGGGTTGTAAACAGGAGCCAAG
                                    ggttaac  putative branch site (score: 3)
                             tttgatt  TA-rich tract