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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgaaatgagttctttaactcgcttttatgttactttacctcttaaaacctttttttttgttaaaaacttctccacttgtgaacagatgagggtatctcgtttggatcgcgaagtgtaaaccatgtattggtcaagtgtttcaactctgttcctcgactttctgatctttatgcatatggttcgcctcgtgcaatgcagAAAAGTGATATCAAGTGGGCATCTCGTTGGGATACATATTTATTGATGACAGACGACCAAATCCATTGGTTCTCCATCATTAATTCCCTCATGATTGTGC

Basic information

species Physcomitrella patens
transcript PP1S73_94V6.1
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S73_94V6.1 (Physcomitrella patens), 3'ss of exon 7
lower sequence: LOC_Os08g17370.1 (Oryza sativa), 3'ss of exon 5
gtgaaatgagttctttaactcgcttttatgttactttacctcttaaaacctttttttttgttaaaaacttctccacttgtgaacagatgagggtatctcgtttggatcgcgaagtgtaaaccatgtattggtcaagtgtttcaactctgttcctcgactttctgatctttatgcatatggttcgcctcgtgcaatgcagAAAAGTGATATCAAGTGGGCATCTCGT----TGGGATACATATTTATTGATGACAGACGACCAAATCCATTGGTTCTCCATCATTAATTCCCTCATGATTGTGC
                                   | |  | |     |  ||||||  | |      |||| | ||  ||||  |||    ||| || |     || |   |||||  || |      | |  |||| |   | | |||| | |  || |  |  ||||       ||  |   ||       ||||| | |||||||||||||||||||||||     |||||||| ||| || ||||||| || ||||||||||| ||||| |||||  | |||||||||||||||    
----------------------------------gtgagatatatgtgcacttttttccgatcg----ttctgctctaatgaaatgatcgcagtagctag---aaattgttcagtgtgcacta------gatggagtgctaatattttgttac-catctatgcgtccttt-------tgactattctgtcaatttgcagGAGAGTGATATCAAGTGGGCATCTCGCTGGCTGGGATACCTATCTACTGATGACGGATGACCAAATCCACTGGTTTTCCATTGTGAATTCCCTCATGATT----

upper sequence: PP1S73_94V6.1 (Physcomitrella patens), 3'ss of exon 7
lower sequence: GRMZM2G146951_T01 (Zea mays), 3'ss of exon 6
gtgaaatgagttctttaactcgcttttatgttactttacctcttaaaacctttttttttgttaaaaacttctccacttgtgaacagatgagggtatctcgtttggatcgcgaagtgtaaaccatgtattggtcaagtgtttcaactctgttcctcgactttctgatctttatgcatatggttcgcctcgtgcaatgcagAAAAGTGATATCAAGTGGGCATCTCGTTGGGATACATATTTATTGATGACAGACGACCAAATCCATTGGTTCTCCATCATTAATTCCCTCATGATTGTGC
                                          | | |||       | ||||  |  ||| |    ||   || |  |||  |||       || |   | ||||||        |||  ||  ||  |    | | ||||   |   |||||||    ||    | |   |            || || | || || ||||||||||||||||| ||||| |  ||| ||||||||||||| || || ||||| |||||||| ||  | ||||| ||||||||||| |
-----------------------------------------gtcagaac-------tatgtttgattctttttgtattccaaataagtgattgtagt--agctgtagtactaagtgt------cctataagtggagcatgaatattgtgttttgctcatttctgagaactac---tgtaaatt-----------tgtagGAGAGCGACATCAAGTGGGCATCTCGGTGGGACAGCTATCTATTGATGACAGATGATCAGATCCACTGGTTCTCTATTGTGAATTCTCTCATGATTGTTC

upper sequence: PP1S73_94V6.1 (Physcomitrella patens), 3'ss of exon 7
lower sequence: GRMZM2G409104_T01 (Zea mays), 3'ss of exon 6
gtgaaatgagttctttaactcgcttttatgttactttacctcttaaaacctttttttttgttaaaaacttctccacttgtgaacaga-tgagggtatctcgtttggatcgcgaagtgtaaacc-atgtattggtcaagtgtttcaactctgttcctcgactttctgatctttatgcatatggttcgcct-cgtgcaatgcagAAAAGTGATATCAAGTGGGCATCTCGTTGGGATACATATTTATTGATGACAGACGACCAAATCCATTGGTTCTCCATCATTAATTCCCTCATGATTGTGC
                                          ||  |||  |||||  | || ||  ||| |     | ||| ||   | |  | |        | |      | |||||||| |   || | |    |||||   |  ||      ||  ||| |||   | |   | | ||||   |  ||||  ||||| |||||  ||||||||||||||| || ||||| || ||  |  ||||| |||||||||||||||||||||| || ||  | ||||| || ||||| || |
-------------------------------------gttagtttcaactatttttcatcttgaa--cttttttgtctatgaccaaccttaatgcactataacagaagtctccactgtaaacctacagatagatggtatgttttttccttga-----gaagttcagatgcattt---tttagttcatatgtgtgccgtgcagGAAAGTCCTATCAAGTGGGCATCACGCTGGGACACCTACCTTCTGATGGCAGACGACCAAATCCATTGGTTTTCTATTGTCAATTCACTGATGATAGTCC

upper sequence: PP1S73_94V6.1 (Physcomitrella patens), 3'ss of exon 7
lower sequence: GLYMA08G20640.1 (Glycine max), 3'ss of exon 6
gtgaaatgagttctttaactcgcttttatgttactttacctcttaaaacctttttttttgttaaaaacttctccacttgtgaacagatgagggtatctcgtttggatcgcgaagtgtaaaccatgtattggtcaagtgtttcaactctgttcctcgactttctgat-ctttatgcatatggttcgcctcgtgcaatgcagAAAAGTGATATCAAGTGGGCATCTCGTTGGGATACATATTTATTGATGACAGACGACCAAATCCATTGGTTCTCCATCATTAATTCCCTCATGATTGTGC
                                                                                                       | || ||  | |  || |   |        ||   ||||| |||  ||        || |||| | |||||   |  ||| |          | ||| ||||||||||||| |||||||| || ||||| |||||| | || ||||  || || || ||||| ||||||||||||||||| || || |||||||| |
-------------------------------------------------------------------------------------------------------gtattgctgattaaaatcttggctaccaataaac-tttcacctcatttg-------ttatgatacgttatggcaa--gtttgttggtactttttcagGAAAGTGATATCAAATGGGCATCACGGTGGGACACATATCTTTTAATGAATGATGATCAGATCCACTGGTTCTCCATCATTAACTCTCTGATGATTGTTC

upper sequence: PP1S73_94V6.1 (Physcomitrella patens), 3'ss of exon 7
lower sequence: GLYMA07G01240.1 (Glycine max), 3'ss of exon 6
gtgaaatgagttctttaactcgcttttatgttactttacctcttaaaacctttttttttgttaaaaacttctccacttgtgaacagatgagggtatctcgtttggatcgcgaagtgtaaaccatgtattggtcaagtgtttcaactctgttcctcgactttctgat-ctttatgcatatggttcgcctcgtgcaatgcagAAAAGTGATATCAAGTGGGCATCTCGTTGGGATACATATTTATTGATGACAGACGACCAAATCCATTGGTTCTCCATCATTAATTCCCTCATGATTGTGC
                                                                                                       | || ||  | |  ||| | ||   |  |||    |||  ||    |||    | | | |||| | ||| ||  |  ||| |          | ||| ||||||||||||| |||||||| || ||||| |||||| | || ||||  || || || ||||| ||||||||||||||||| ||  | |||||||| |
-------------------------------------------------------------------------------------------------------gtattgctgatta-aaatcttg-gctactcataaattttcacctcattc----attatatgatacgttaagc-caaagtttgttggtattttttcagGAAAGTGATATCAAATGGGCATCACGGTGGGACACATATCTTTTAATGAATGATGATCAGATCCACTGGTTCTCCATCATTAACTCTTTGATGATTGTTC

upper sequence: PP1S73_94V6.1 (Physcomitrella patens), 3'ss of exon 7
lower sequence: EFJ33415 (Selaginella moellendorffii), 3'ss of exon 6
gtgaaatgagttctttaactcgcttttatgttactttacctcttaaaacctttttttttgttaaaaacttctccacttgtgaacagatgagggtatctcgtttggatcgcgaagtgtaaaccatgtattggtcaagtgtttcaactctgttcctcgactttctgatctttatgcatatggttcgcctcgtgcaatgcagAAAAGTGATATCAAGTGGGCATCTCGTTGGGATACATATTTATTGATGACAGACGACCAAATCCATTGGTTCTCCATCATTAATTCCCTCATGATTGTGC
                                                                                                                                     || |||| |    ||||   |   | ||||| |||  | |    || || |  |        |||| | || |  |  |  ||||| || || |||||||  ||  |  ||||| |||||||||||||||| ||||| || ||||| || ||||||||||| || |
-----------------------------------------------------------------------------------------------------------------------------------gtaactgttacctgcctgtcttttatccttctgttctcaacgtgcctg-tttgttt--------gcagGAGAGCGCCACGAGATGGGCTTCCCGATGGGATATGTACCTTATGATGTCAGACGACCAAATCCACTGGTTTTCTATCATCAACTCCCTCATGATCGTTC

upper sequence: PP1S73_94V6.1 (Physcomitrella patens), 3'ss of exon 7
lower sequence: EFJ09669 (Selaginella moellendorffii), 3'ss of exon 6
gtgaaatgagttctttaactcgcttttatgttactttacctcttaaaacctttttttttgttaaaaacttctccacttgtgaacagatgagggtatctcgtttggatcgcgaagtgtaaaccatgtattggtcaagtgtttcaactctgttcctcgactttctgatctttatgcatatggttcgcctcgtgcaatgcagAAAAGTGATATCAAGTGGGCATCTCGTTGGGATACATATTTATTGATGACAGACGACCAAATCCATTGGTTCTCCATCATTAATTCCCTCATGATTGTGC
                                                                                                                                     || |||| |    ||||   |   | ||||| |||  | |    || || |  |        |||| | || |  |  |  ||||| || || |||||||  ||  |  ||||| |||||||||||||||| ||||| || ||||| || ||||||||||| || |
-----------------------------------------------------------------------------------------------------------------------------------gtaactgttacctgcctgtcttttatccttctgttctcaacgtgcctg-tttgttt--------gcagGAGAGCGCCACGAGATGGGCTTCGCGATGGGATATGTACCTTATGATGTCAGACGACCAAATCCACTGGTTTTCTATCATCAACTCCCTCATGATCGTTC

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|162190467|gb|FC365689.1|FC365689
EST:     AGTTGCTTGAAGACCAGGAAGTGATATTCACTTATGATGTGTCTTTCCAG                         AAAAGTGATATCAAGTGGGCATCTCGTTGGGATACATATTTATTGATGACA
genomic: AGTTGCTTGAAGACCAGGAAGTGATATTCACTTATGATGTGTCTTTCCAGgtgaaatgag ... tgcaatgcagAAAAGTGATATCAAGTGGGCATCTCGTTGGGATACATATTTATTGATGACA
EST: gi|162174574|gb|FC350229.1|FC350229
EST:     AGTTGCTTGAAGACCAGGAAGTGATATTCACTTATGATGTGTCTTTCCAG                         AAAAGTGATATCAAGTGGGCATCTCGTTGGGATACATATTTATTGATGACA
genomic: AGTTGCTTGAAGACCAGGAAGTGATATTCACTTATGATGTGTCTTTCCAGgtgaaatgag ... tgcaatgcagAAAAGTGATATCAAGTGGGCATCTCGTTGGGATACATATTTATTGATGACA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctctgttcctcgactttctgatctttatgcatatggttcgcctcgtgcaatgcagAAAAGTGATATCAAGTGGGCATCTCGTTGGGATACATATTTATTGATGACAGACGACCAAATCCATTGGTTCTCCATCATTAATTCCCTCATGATTGTGC
               ttctgat  putative branch site (score: 3)
                    atctttat  TA-rich tract