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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacgtactcgtgccgttatttccttgtatttcagtttgcactgcttctggtctgtgagtagctcattttcaggataagtccactgcaaatattttttcttgttgaattcctcccttttatccctacatgtggaatgttgtgtttctggtgccctggaaatgtactgagtacatgaaatggatcgaaatgcgtttcagTTCATCCAGAGACTTGGAATCCAATGTGGTCTGTTTCAAG

Basic information

species Physcomitrella patens
transcript PP1S366_17V6.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S366_17V6.1 (Physcomitrella patens), 3'ss of exon 5
lower sequence: GRMZM2G177276_T01 (Zea mays), 3'ss of exon 5
gtacgtactcgtgccgttatttccttgtatttcagtttgcactgcttctggtctgtgagtagctcattttcaggataagtccactgcaaatattttttcttgttgaattcctcccttttatccctacatgtggaatgttg-tgtttctggtgccctggaaatgtactgagtacatgaaatggatcgaaatgcgtttcagTTCATCCAGAGACTTGGAATCCAATGTGGTCTGTTTCAAG
                                                                                                               |   || |   | | | |||||| | | | || || || |    |      |  ||||    |||      ||   ||||  || |||||||||| ||  ||||||||||||||||||||||| ||||
--------------------------------------------------------------------------------------------------------------gtaagttctgaacttgcttgtggattatagatgcttttgttattatta----gctctgaaataatgctcattattacaatgttttgcagTTCATCCTGAATCTTGGAATCCAATGTGGTCTGTTGCAAG

upper sequence: PP1S366_17V6.1 (Physcomitrella patens), 3'ss of exon 5
lower sequence: GLYMA07G05170.2 (Glycine max), 3'ss of exon 5
gtacgtactcgtgccgttatttccttgtatttcagtttgcactgcttctggtctgtgagtagctcattttcaggataagtccactgcaaatattttttcttgttgaattcctcccttttatccctacatgtggaatgttgtgtttctggtgccctggaaatgtactgagtacatgaaatggatcgaaatgcgtttcagTTCATCCAGAGACTTGGAATCCAATGTGGTCTGTTTCAAG
                                                                                                |   |||  ||    |   || | |     ||      |  | || |     ||  ||   |     | | | ||  |     ||||         || ||||||||||||| | ||||||||| ||||||||||| |||||
------------------------------------------------------------------------------------------------tgactgt--aagctattttttctgttgtagcacaaaacaattagtatcatgagtaacccatattacaatttaatatttctgcgggatttgctacttttgcagTTCATCCAGAAAGTTGGAATCCCATGTGGTCTGTATCAAG

upper sequence: PP1S366_17V6.1 (Physcomitrella patens), 3'ss of exon 5
lower sequence: GLYMA07G05170.1 (Glycine max), 3'ss of exon 6
gtacgtactcgtgccgttatttccttgtatttcagtttgcactgcttctggtctgtgagtagctcattttcaggataagtccactgcaaatattttttcttgttgaattcctcccttttatccctacatgtggaatgttgtgtttctggtgccctggaaatgtactgagtacatgaaatggatcgaaatgcgtttcagTTCATCCAGAGACTTGGAATCCAATGTGGTCTGTTTCAAG
                                                                                                         ||    |   || | |     ||      |  | || |     ||  ||   |     | | | ||  |     ||||         || ||||||||||||| | ||||||||| ||||||||||| |||||
-------------------------------------------------------------------------------------------------------gtaagctattttttctgttgtagcacaaaacaattagtatcatgagtaacccatattacaatttaatatttctgcgggatttgctacttttgcagTTCATCCAGAAAGTTGGAATCCCATGTGGTCTGTATCAAG

upper sequence: PP1S366_17V6.1 (Physcomitrella patens), 3'ss of exon 5
lower sequence: GLYMA16G01680.1 (Glycine max), 3'ss of exon 6
gtacgtactcgtgccgttatttccttgtatttcagtttgcactgcttctggtctgtgagtagctcattttcaggataagtccactgcaaatattttttcttgttgaattcctcccttttatccctacatgtggaatgttgtgtttctggtgccctggaaatgta-ctgagtacatgaaatggatcgaaatgcgtttcagTTCATCCAGAGACTTGGAATCCAATGTGGTCTGTTTCAAG
                                                                                                         || | |||  || | |     ||      |  | || |     ||   |    | |  |  | | ||  |      |||         || ||||||||||||| | ||||||||| ||||||||||| |||||
-------------------------------------------------------------------------------------------------------gtaagttctcttttctgttgtagcacaaaacaattagtatcatgagttaacccatattacaatttaatatttctgcacgatttgctacttttgcagTTCATCCAGAAAGTTGGAATCCCATGTGGTCTGTATCAAG

upper sequence: PP1S366_17V6.1 (Physcomitrella patens), 3'ss of exon 5
lower sequence: EFJ16846 (Selaginella moellendorffii), 3'ss of exon 5
gtacgtactcgtgccgttatttccttgtatttcagtttgcactgcttctggtctgtgagtagctcattttcaggataagtccactgcaaatattttttcttgttgaattcctcccttttatccctacatgtggaatgttgtgtttctggtgccctggaaatgtactgagtacatgaaatggatcgaaatgcgttt--------cagTTCATCCAGAGACTTGGAATCCAATGTGGTCTGTTTCAAG
                                                                                                                                                               | | |   ||  | ||   | | ||  | || || |        |||||||||||||||||||||||||||||||||| ||||||||
-------------------------------------------------------------------------------------------------------------------------------------------------------------gtaagcatcaagcgcttgtttttgctctcattgtgtgttcttctcgcagTTCATCCAGAGACTTGGAATCCAATGTGGTCAGTTTCAAG

upper sequence: PP1S366_17V6.1 (Physcomitrella patens), 3'ss of exon 5
lower sequence: EFJ32150 (Selaginella moellendorffii), 3'ss of exon 5
gtacgtactcgtgccgttatttccttgtatttcagtttgcactgcttctggtctgtgagtagctcattttcaggataagtccactgcaaatattttttcttgttgaattcctcccttttatccctacatgtggaatgttgtgtttctggtgccctggaaatgtactgagtacatgaaatggatcgaaatgcgtttcagTTCATCCAGAGACTTGGAATCCAATGTGGTCTGTTTCAAG
                                                                                                                                                    ||   |   ||  |         | |   || |   |   | | |  |||||||||||||||||||||||||||||||||| ||||||||
----------------------------------------------------------------------------------------------------------------------------------------------------gtaagcatcaatcgcttatttctcctctcattgtgtgttcttc-tcgcagTTCATCCAGAGACTTGGAATCCAATGTGGTCAGTTTCAAG

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|208387466|gb|DC949251.1|DC949251
EST:     AAATGGGCGATTTGCAACTCAGAAGCGGATCTGTATGTCTATGAGTGATT                         TTCATCCAGAGACTTGGAATCCAATGTGGTCTGTTTCAAG
genomic: AAATGGGCGATTTGCAACTCAGAAGCGGATCTGTATGTCTATGAGTGATTgtacgtactc ... tgcgtttcagTTCATCCAGAGACTTGGAATCCAATGTGGTCTGTTTCAAG
EST: gi|208347731|gb|DC925604.1|DC925604
EST:     TATGAGTGA-T                         TTCATCCAGAGACTTGGAATCCCATGTGGTCTGTTTCNAG
genomic: TATGAGTGATTgtacgtactc ... tgcgtttcagTTCATCCAGAGACTTGGAATCCAATGTGGTCTGTTTCAAG
EST: gi|162277893|gb|FC454356.1|FC454356
EST:     AAATGGGCGATTTGCAACTCAGAAGCGGATCTGTATGTCTATGAGTGATT                         TTCATCCAGAGACTTGGAATCCAATGTGGTCTGTTTCAAG
genomic: AAATGGGCGATTTGCAACTCAGAAGCGGATCTGTATGTCTATGAGTGATTgtacgtactc ... tgcgtttcagTTCATCCAGAGACTTGGAATCCAATGTGGTCTGTTTCAAG
EST: gi|37829048|gb|BJ587060.1|BJ587060
EST:     ACTCAGAAGCGGATCTGTATGTCTATGAGTGATT                         TTCATCCAGAGACTTGGAACCCAATGTGGTCTGTTTCAAG
genomic: ACTCAGAAGCGGATCTGTATGTCTATGAGTGATTgtacgtactc ... tgcgtttcagTTCATCCAGAGACTTGGAATCCAATGTGGTCTGTTTCAAG
EST: gi|208368770|gb|DC951336.1|DC951336
EST:     AAATGGGCGATTTGCAACTCAGAAGCGGATCTGTATGTCTATGAGTGATT                         TTCATCCAGAGACTTGGAATCCAATGTGGTCTGTTTCAAG
genomic: AAATGGGCGATTTGCAACTCAGAAGCGGATCTGTATGTCTATGAGTGATTgtacgtactc ... tgcgtttcagTTCATCCAGAGACTTGGAATCCAATGTGGTCTGTTTCAAG
EST: gi|208365980|gb|DC955499.1|DC955499
EST:     AAATGGGCGATTTGCAACTCAGAAGCGGATCTGTATGTCTATGAGTGATT                         TTCATCCAGAGACTTGGAATCCAATGTGGTCTGTTTCAAG
genomic: AAATGGGCGATTTGCAACTCAGAAGCGGATCTGTATGTCTATGAGTGATTgtacgtactc ... tgcgtttcagTTCATCCAGAGACTTGGAATCCAATGTGGTCTGTTTCAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttctggtgccctggaaatgtactgagtacatgaaatggatcgaaatgcgtttcagTTCATCCAGAGACTTGGAATCCAATGTGGTCTGTTTCAAG
              aaatgta  TA-rich tract