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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gttattgaaggattgttggtattttcttaaatttaagcaatctttatcacaattatgtgtcagattgtcatactcttggaatatggatgatgctgtgcagGTGGTCAAAAGAGTAGGGTAGCTTTTGCAAAAATCACTTTCAACAAGCCTCATATATTACTGCTGGATGAGCCATCCAATCACTTG

Basic information

species Physcomitrella patens
transcript PP1S47_97V6.1
intron # 15
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S47_97V6.1 (Physcomitrella patens), 3'ss of exon 15
lower sequence: GLYMA20G16170.1 (Glycine max), 3'ss of exon 14
------------------------------------------------------------gttattga--aggattgttggtattttcttaaatttaagcaatctttatcacaattatgtgtcagattgtcatactcttggaatatggatgatgctgtgc-agGTGGTCAAAAGAGTAGGGTAGCTTTTGCAAAAATCACTTTCAACAAGCCTCATATATTACTGCTGGATGAGCCATCCAATCACTTG
                                                            | || | |   |||   | |||   |  | |  |  ||   || | |||  |  |||||  | | ||| |  ||||  |  ||        || || | | ||||||||| || || ||||| || |||||||| || |||||||| ||||| || ||| || |||| ||||| |||||||||||  ||
gtattgtcttcaaagtcaccataattcataaacaattcgttaatgatttttaagaacagcgataataattgggacactcggtgggtgttgagttgcaatggatatatatttctgttatgaattatatttttttacttctctaa--------attctttactagGTGGTCAGAAAAGCAGGGTTGCCTTTGCAAAGATAACTTTCAAGAAGCCACACATAATATTGCTTGATGAACCATCCAATCATCTG

upper sequence: PP1S47_97V6.1 (Physcomitrella patens), 3'ss of exon 15
lower sequence: GLYMA13G10530.1 (Glycine max), 3'ss of exon 14
-----------------------------------------------------------------gttattgaaggattgttggtattt-tcttaaatttaagcaatctttatcacaattatgtgtcagattgtcatactcttggaatatggatgatgctgtgc-agGTGGTCAAAAGAGTAGGGTAGCTTTTGCAAAAATCACTTTCAACAAGCCTCATATATTACTGCTGGATGAGCCATCCAATCACTTG
                                                                   |||    |||   |||||   | |  ||| ||  |       |      |  | | ||| |     |  || | ||         |  | ||| | | ||||||||| || || ||||| || |||||||| || ||||| || ||||| || ||| || |||| |||||||||||||||||  ||
gtattgtcttcatagtcatcataattcataaacaattcgttaatgttcttttggaacagaaataatgtatgttgggacacttggtgggtgttgtaagttgcaatggatatagatgtacctttctgttatga-attgtatttttacttctctaa--acgctttactagGTGGTCAGAAAAGCAGGGTTGCCTTTGCAAAGATAACTTTTAAGAAGCCACACATAATATTGCTTGATGAGCCATCCAATCATCTG

upper sequence: PP1S47_97V6.1 (Physcomitrella patens), 3'ss of exon 15
lower sequence: EFJ22634 (Selaginella moellendorffii), 3'ss of exon 15
gttattgaaggattgttggtattttcttaaatttaagcaatctttatcacaattatgtgtcagattgtcatactcttggaatatggatgatgctgtgcagGTGGTCAAAAGAGTAGGGTAGCTTTTGCAAAAATCACTTTCAACAAGCCTCATATATTACTGCTGGATGAGCCATCCAATCACTTG
                                                    | |  | | |  || |  |   ||||     |  | | |  | | ||||||| ||||||||| | || ||||||||||||||||| |||||||| || || ||  |  | ||||||||||| || |||||| | 
---------------------------------------------------gtaacatttgaagttcttgtttccttgac---taaaagtttttatacagGTGGGCAAAAGAGTCGTGTCGCTTTTGCAAAAATCACATTCAACAAACCACACATTCTTTTACTGGATGAGCCTTCGAATCACCTT

upper sequence: PP1S47_97V6.1 (Physcomitrella patens), 3'ss of exon 15
lower sequence: EFJ11792 (Selaginella moellendorffii), 3'ss of exon 15
gttattgaaggattgttggtattttcttaaatttaagcaatctttatcacaattatgtgtcagattgtcatactcttggaatatggatgatgctgtgcagGTGGTCAAAAGAGTAGGGTAGCTTTTGCAAAAATCACTTTCAACAAGCCTCATATATTACTGCTGGATGAGCCATCCAATCACTTG
                                                   || |  | | |  |  |  |  || | || ||    |  |  | | ||||||| ||||||||| | || ||||||||||||||||| |||||||| || || ||  |  | ||||||||||| || |||||| | 
-------------------------------------------------gtataacatatgaactacttgt-ttccttgactaaaagtatt--tatacagGTGGGCAAAAGAGTCGTGTCGCTTTTGCAAAAATCACATTCAACAAACCACACATTCTTTTACTGGATGAGCCTTCAAATCACCTT

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|19789030|gb|BQ041056.1|BQ041056
EST:     ATTTGGAATCACGGGCAACCTGGCTTTGCAATCTATGTACACACTTTCAG                         GTGGTCAAAAGAGTAGGGTAGCTTTTGCAAAAATCACTTTCAACAAGCCTC
genomic: ATTTGGAATCACGGGCAACCTGGCTTTGCAATCTATGTACACACTTTCAGgtttgtttct ... tgctgtgcagGTGGTCAAAAGAGTAGGGTAGCTTTTGCAAAAATCACTTTCAACAAGCCTC
EST: gi|162199129|gb|FC375821.1|FC375821
EST:     ATTTGGAATCACGGGCAACCTGGCTTTGCAATCTATGTACACACTTTCAG                         GTGGTCAAAAGAGTAGGGTAGCTTTTGCAAAAATCACTTTCAACAAGCCTC
genomic: ATTTGGAATCACGGGCAACCTGGCTTTGCAATCTATGTACACACTTTCAGgtttgtttct ... tgctgtgcagGTGGTCAAAAGAGTAGGGTAGCTTTTGCAAAAATCACTTTCAACAAGCCTC
EST: gi|37831033|gb|BJ589045.1|BJ589045
EST:     ATTTGGAATCACGGGCAACCTGGCTTTGCAATCTATGTACACACTTTCAG                         GTGGTCAAAAGAGTAGGGTAGCTTTTGCAAAAATCACTTTCAACAAGCCTC
genomic: ATTTGGAATCACGGGCAACCTGGCTTTGCAATCTATGTACACACTTTCAGgtttgtttct ... tgctgtgcagGTGGTCAAAAGAGTAGGGTAGCTTTTGCAAAAATCACTTTCAACAAGCCTC
EST: gi|18341144|gb|BJ173177.1|BJ173177
EST:     ATTTGGAATCACGGGCAACCTGGCTTTGCAATCTATGTACACACTTTCAG                         GTGGTCAAAAGAGTAGGGTAGCTTTTGCAAAAATCACTTTCAACAAGCCTC
genomic: ATTTGGAATCACGGGCAACCTGGCTTTGCAATCTATGTACACACTTTCAGgtttgtttct ... tgctgtgcagGTGGTCAAAAGAGTAGGGTAGCTTTTGCAAAAATCACTTTCAACAAGCCTC
EST: gi|18337417|gb|BJ169441.1|BJ169441
EST:     ATTTGGAATCACGGGCAACCTGGCTTTGCAATCTATGTACACACTTTCAG                         GTGGTCAAAAGAGTAGGGTAGCTTTTGCAAAAATCACTTTCAACAAGCCTC
genomic: ATTTGGAATCACGGGCAACCTGGCTTTGCAATCTATGTACACACTTTCAGgtttgtttct ... tgctgtgcagGTGGTCAAAAGAGTAGGGTAGCTTTTGCAAAAATCACTTTCAACAAGCCTC
EST: gi|37828058|gb|BJ586070.1|BJ586070
EST:     ATTTGGAATCACGGGCAACCTGGCTTTGCAATCTATGTACACACTTTCAG                         GTGGTCAAAAGAGTAGGGTAGCTTTTGCAAAAATCACTTTCAACAAGCCTC
genomic: ATTTGGAATCACGGGCAACCTGGCTTTGCAATCTATGTACACACTTTCAGgtttgtttct ... tgctgtgcagGTGGTCAAAAGAGTAGGGTAGCTTTTGCAAAAATCACTTTCAACAAGCCTC
EST: gi|162187556|gb|FC363818.1|FC363818
EST:     ATTTGGAATCACGGGCAACCTGGCTTTGCAATCTATGTACACACTTTCAG                         GTGGTCAAAAGAGTAGGGTAGCTTTTGCAAAAATCACTTTCAACAAGCCTC
genomic: ATTTGGAATCACGGGCAACCTGGCTTTGCAATCTATGTACACACTTTCAGgtttgtttct ... tgctgtgcagGTGGTCAAAAGAGTAGGGTAGCTTTTGCAAAAATCACTTTCAACAAGCCTC
EST: gi|37836283|gb|BJ594291.1|BJ594291
EST:     ATTTGGAATCACGGGCAACCTGGCTTTGCAATCTATGTACACACTTTCAG                         GTGGTCAAAAGAGTAGGGTAGCTTTTGCAAAAATCACTTTCAACAAGCCTC
genomic: ATTTGGAATCACGGGCAACCTGGCTTTGCAATCTATGTACACACTTTCAGgtttgtttct ... tgctgtgcagGTGGTCAAAAGAGTAGGGTAGCTTTTGCAAAAATCACTTTCAACAAGCCTC
EST: gi|162174579|gb|FC350234.1|FC350234
EST:     ATTTGGAATCACGGGCAACCTGGCTTTGCAATCTATGTACACACTTTCAG                         GTGGTCAAAAGAGTAGGGTAGCTTTTGCAAAAATCACTTTCAACAAGCCTC
genomic: ATTTGGAATCACGGGCAACCTGGCTTTGCAATCTATGTACACACTTTCAGgtttgtttct ... tgctgtgcagGTGGTCAAAAGAGTAGGGTAGCTTTTGCAAAAATCACTTTCAACAAGCCTC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atcacaattatgtgtcagattgtcatactcttggaatatggatgatgctgtgcagGTGGTCAAAAGAGTAGGGTAGCTTTTGCAAAAATCACTTTCAACAAGCCTCATATATTACTGCTGGATGAGCCATCCAATCACTTG
     aattatgt  TA-rich tract
















Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttattgaaggattgttggtattttcttaaatttaagcaatctttatcacaattatgtgtcagattgtcatactcttggaatatggatgatgctgtgcagGTGGTCAAAAGAGTAGGGTAGCTTTTGCAAAAATCACTTTCAACAAGCCTCATATATTACTGCTGGATGAGCCATCCAATCACTTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGGA