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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgggctgcttttttcgtcactgtcattgaagcactgctgtcaagctcatgtagaaagtgtagagaagatttcaagctttcgtagattggcagagtgtctttgctccatgattttatagagaagctgcattcttctgttcttgaaagtaattgggttttcctctggcgtggttgacgacttgttttttaatgcagGTTCTTAATCAGGATGATTCACCTCTACTATACAGTCTTGTGTTTGGAGAAGGAGTTGTCAATGATGCTACCTCTGTAGTCTTATTCCGGGCTGTACAGA

Basic information

species Physcomitrella patens
transcript PP1S207_23V6.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S207_23V6.2 (Physcomitrella patens), 3'ss of exon 6
lower sequence: LOC_Os05g05590.1 (Oryza sativa), 3'ss of exon 6
gtgggctgcttttttcgtcactgtcattgaagcactgctgtcaagctcatgtagaaagtgtagagaagatttcaagctttcgtagattggcagagtgtctttgctccatgattttatagagaagctgcattcttctgttcttgaaagtaattgggttttcctctggcgtggttgacgacttgttttttaatgcagGTTCTTAATCAGGATGATTCACCTCTACTATACAGTCTTGTGTTTGGAGAAGGAGTTGTCAATGATGCTACCTCTGTAGTCTTATTCCGGGCTGTACAGA
                                                                                                            |  ||  ||  |    |    |  |  |||  |  ||| | |    |    ||  |       |   | | ||  ||  |  ||||||| ||||| || || ||  |||| ||||| || ||||| || ||||| ||||| ||||||||||||||||| ||||| ||  | ||    ||  |  |  
-----------------------------------------------------------------------------------------------------------gtttttccatttaatgacctgttgttaatgtcttgtaaaatgaaacagcacaccattaa----atatgcaattttgttact--tgcagGTGCTTAACCAAGACGAAACACCCCTACTCTATAGTCTGGTTTTTGGTGAAGGGGTTGTCAATGATGCTACATCTGTTGTGCTCTTTAATGCAATTGAAG

upper sequence: PP1S207_23V6.2 (Physcomitrella patens), 3'ss of exon 6
lower sequence: GLYMA19G42900.1 (Glycine max), 3'ss of exon 5
gtgggctgcttttttcgtcactgtcattgaagcactgctgtcaagctcatgtagaaagtgtagagaagatttcaagctttcgtagattggcagagtgtctttgctccatgattttatagagaagctgcattcttctgttcttgaaagtaattgggttttcctctggcgtggttgacgacttgttttttaatgcagGTTCTTAATCAGGATGATTCACCTCTACTATACAGTCTTGTGTTTGGAGAAGGAGTTGTCAATGATGCTACCTCTGTAGTCTTATTCCGGGCTGTACAGA
                                                                                                               |||   |    |  ||| || |||      |   || ||    | | ||            |||     |   |  |  ||||||| || || ||||||||  ||||| |||| ||||||||||| ||||| || || ||||| ||||||||||| ||||| ||  | ||    ||  || | |
--------------------------------------------------------------------------------------------------------------gtttggaacgatatgtgcctttttcgcaatgtagcagcaacgaaggtgtcaatgctaagtactgaatttataaatgatgttgcagGTGCTAAACCAGGATGAGACACCTTTACTGTACAGTCTTGTATTTGGCGAGGGTGTTGTGAATGATGCTACATCTGTTGTGCTTTTTAATGCAATAAAAA

upper sequence: PP1S207_23V6.2 (Physcomitrella patens), 3'ss of exon 6
lower sequence: GLYMA03G40290.1 (Glycine max), 3'ss of exon 5
gtgggctgcttttttcgtcactgtcattgaagcactgctgtcaagctcatgtagaaagtgtagagaagatttcaagctttcgtagattggcagagtgtctttgctccatgattttatagagaagctgcattcttctgtt-cttgaaagtaattgggttttcctctggcgtggttgacgacttgttttttaatgcagGTTCTTAATCAGGATGATTCACCTCTACTATACAGTCTTGTGTTTGGAGAAGGAGTTGTCAATGATGCTACCTCTGTAGTCTTATTCCGGGCTGTACAGA
                                                                                                               |||   | |  |  ||| || ||| |   | |   || ||    | | ||            |||     |   |  |  ||||||| || || ||||||||  ||||| |||| ||||||||||| ||||| || || ||||| ||||||||||| ||||| ||  | |||   ||  |  | |
--------------------------------------------------------------------------------------------------------------gtttggaacaatatgtgcctttttccgcaacgttgcagcaaccaaggtgtcaatgcttagtactgaacttataaatgatgttgcagGTGCTAAACCAGGATGAGACACCTTTACTGTACAGTCTTGTATTTGGCGAGGGTGTTGTGAATGATGCTACATCTGTGGTGCTTTTCAATGCAATCAAAA

upper sequence: PP1S207_23V6.2 (Physcomitrella patens), 3'ss of exon 6
lower sequence: GLYMA20G37370.1 (Glycine max), 3'ss of exon 6
gtgggctgcttttttcgtcactgtcattgaagcactgctgtcaagctcatgtagaaagtgtagagaagatttcaagctttcgtagattggcagagtgtctttgctccatgattttatagagaagctgcattcttctgttcttgaaagtaattgggttttcctctggcgtggttgacgacttgttttttaatgcagGTTCTTAATCAGGATGATTCACCTCTACTATACAGTCTTGTGTTTGGAGAAGGAGTTGTCAATGATGCTACCTCTGTAGTCTTATTCCGGGCTGTACAGA
                                                                                                                        |||  |  ||| ||    |  |      || |  | | ||       ||   |||     |   |  | |||||||| || |||||||||||  ||||| | || ||||||||||| ||||| || || ||||| ||||||||||| || || ||  | |||   ||  | || |
--------------------------------------------------------------------------------------------------------------------gtttgaaaatatattttttaaattcttccttcaactaaggtatcactgctagttactgaacttataaatgatgatgcagGTGCTAAATCAGGATGAGACACCTTTGCTGTACAGTCTTGTATTTGGGGAGGGTGTTGTGAATGATGCTACATCAGTGGTGCTTTTCAATGCAATCCAAA

upper sequence: PP1S207_23V6.2 (Physcomitrella patens), 3'ss of exon 6
lower sequence: GLYMA10G30020.1 (Glycine max), 3'ss of exon 6
gtgggctgcttttttcgtcactgtcattgaagcactgctgtcaagctcatgtagaaagtgtagagaagatttcaagctttcgtagattggcagagtgtctttgctccatgattttatagagaagctgcattcttctgttcttgaaagtaattgggttttcctctggcgtggttgacgacttgttttttaatgcagGTTCTTAATCAGGATGATTCACCTCTACTATACAGTCTTGTGTTTGGAGAAGGAGTTGTCAATGATGCTACCTCTGTAGTCTTATTCCGGGCTGTACAGA
                                                                                                                  | |  || |  |  ||| ||    |  |      || |  | | ||       ||   |||     |   |  | |||||||| || |||||||||||  ||||| | || ||||||||||| ||||| || || ||||| ||||||||||| || || ||  | |||   ||  | || |
-----------------------------------------------------------------------------------------------------------------gtttgaagcaa-tatatttttaaaattcttccttcaactaaggtatcactgctagttactgaacttataaatgatgatgcagGTGCTAAATCAGGATGAGACACCTTTGCTGTACAGTCTTGTATTTGGGGAGGGTGTTGTGAATGATGCTACATCAGTGGTGCTTTTCAATGCAATCCAAA

upper sequence: PP1S207_23V6.2 (Physcomitrella patens), 3'ss of exon 6
lower sequence: AT3G05030.2 (Arabidopsis thaliana), 3'ss of exon 2
gtgggctgcttttttcgtcactgtcattgaagcactgctgtcaagctcatgtagaaagtgtagagaagatttcaagctttcgtagattggcagagtgtctttgctccatgattttatagagaagctgcattcttctgttcttgaaagtaattgggttttcctctggcgtggttgacgacttgttttttaatgcagGTTCTTAATCAGGATGATTCACCTCTACTATACAGTCTTGTGTTTGGAGAAGGAGTTGTCAATGATGCTACCTCTGTAGTCTTATTCCGGGCTGTACAGA
                                                                                                      |     |||||    |   |       | | |     |    ||  ||  | ||  |   |        |||     |  |||  | || |||||||| ||||| |||||  ||||| | || ||||||||||| |||||||| || ||||| |||||||| || ||||| ||  | |||   ||| | ||||
------------------------------------------------------------------------------------------------------gtaatgtgattcgccaattagcagaagtacatacaggcccagaatcaaa-gtgtaattaacaaaaactcttg----ttcctttggtgatacagGTTCTCAATCAAGATGAGACACCTTTGCTTTACAGTCTTGTATTTGGAGAGGGCGTTGTGAATGATGCCACATCTGTTGTGCTCTTCAATGCTATTCAGA

upper sequence: PP1S207_23V6.2 (Physcomitrella patens), 3'ss of exon 6
lower sequence: Vv05s0020g01960.t01 (Vitis vinifera), 3'ss of exon 6
gtgggctgcttttttcgtcactgtcattgaagcactgctgtcaagctcatgtagaaagtgtagagaagatttcaagctttcgtagattggcagagtgtctttgctccatgattttatagagaagctgcattcttctgttcttgaaagtaattgggttttcctctggcgtggttgacgacttgttttttaatgcagGTTCTTAATCAGGATGATTCACCTCTACTATACAGTCTTGTGTTTGGAGAAGGAGTTGTCAATGATGCTACCTCTGTAGTCTTATTCCGGGCTGTACAGA
                                                                                                        | || |||    |    ||||||   ||  |||||  |     |||  ||      ||    |    |      |   |    |  ||||||| ||||||||||||||  ||||  |||| |||||||| || ||||||||||| ||||| |||||||| || ||||| ||  | |||   ||  | ||||
-------------------------------------------------------------------------------------------------------gtaca-gatggccttactaagctgtgatc--ctgttactagttctaag-ggacaacacttccacaacttatttatccaatccaattgtgcagGTGCTTAATCAGGATGAGACACCCTTACTCTACAGTCTGGTTTTTGGAGAAGGTGTTGTGAATGATGCCACATCTGTGGTGCTTTTCAATGCAATCCAGA

upper sequence: PP1S207_23V6.2 (Physcomitrella patens), 3'ss of exon 6
lower sequence: Vv07s0104g01280.t01 (Vitis vinifera), 3'ss of exon 5
gtgggctgcttttttcgtcactgtcattgaagcactgctgtcaagctcatgtagaaagtgtagagaagatttcaagctttcgtagattggcagagtgtctttgctccatgattttatagagaagctgcattcttctgttct--tgaaagtaattgggttttcctctggcgtggttgacgact-tgttttttaatgcagGTTCTTAATCAGGATGATTCACCTCTACTATACAGTCTTGTGTTTGGAGAAGGAGTTGTCAATGATGCTACCTCTGTAGTCTTATTCCGGGCTGTACAGA
                                                                                                      |       || || |  ||    || ||||| ||    |  ||     ||| |    || ||       |  | | |  |   | |  ||  |||||| || |||||||||||  ||||| | ||||||||||| || ||||| ||||| || || |||||||| || |||||                       
------------------------------------------------------------------------------------------------------gtatagatatcttctcaaggctgtg-attctgcttccataatggggacaatagaacatttct-------gactaaagtttgcatctgatatggcagGTGCTCAATCAGGATGAGACACCTTTGCTATACAGTCTAGTCTTTGGGGAAGGTGTGGTAAATGATGCCACATCTGTG----------------------

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|162190028|gb|FC366602.1|FC366602
EST:     CTCTTGGTACTATTTTCTCCGCTACAGACTCAGTTTGTGTTCTGCAG                         GTTCTTAATCAGGATGATTCACCTCTACTATACAGTCTTGTGTTTGGAGAA
genomic: CTCTTGGTACTATTTTCTCCGCTACAGACTCAGTTTGTGTTCTGCAGgtgggctgct ... tttaatgcagGTTCTTAATCAGGATGATTCACCTCTACTATACAGTCTTGTGTTTGGAGAA






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgaaagtaattgggttttcctctggcgtggttgacgacttgttttttaatgcagGTTCTTAATCAGGATGATTCACCTCTACTATACAGTCTTGTGTTTGGAGAAGGAGTTGTCAATGATGCTACCTCTGTAGTCTTATTCCGGGCTGTACAGA
                                            ttttaat  putative branch site (score: 3)
                                      cttgtttttt  CT-rich tract
                                     acttgttttttaat  TA-rich tract