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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GATAACAGAGAAGGTCTTGAATTGCTGAAGACTGCCATTGCGAAGGCTGGCTACACGGACAAGgttacttgatgttgatagcatgtgactcttctatcgttttgggtttaactgcttctggaattcttgtacattagcatctattcctaggagggtcttttttatccacgtacttggtatccgtcgtatttgtggagtctactaaagtcaaagttgcttcgatcaactag

Basic information

species Physcomitrella patens
transcript PP1S1_526V6.1
intron # 10
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S1_526V6.1 (Physcomitrella patens), 5'ss of exon 10
lower sequence: GLYMA16G32960.1 (Glycine max), 5'ss of exon 10
GATAACAGAGAAGGTCTTGAATTGCTGAAGACTGCCATTGCGAAGGCTGGCTACACGGACAAGgtt-acttgatgttgatagcatgtgactcttctatcgttttgggtttaactgctt--ctggaattcttgtacattagcatctattcctaggagggtcttttttatccacgtacttggtatccgtcgtatttgtggagtctactaaagtcaaagttgcttcgatcaactag
|| |||| ||||||||||||| | ||||||||||||||||| || ||||| ||||| |  |||||| | |   |||  |  | || | | | |  |||| | |    | |  ||| ||   |   ||||||  |                                                                                                   
GAAAACAAAGAAGGTCTTGAACTTCTGAAGACTGCCATTGCTAAAGCTGGTTACACTGGAAAGgttgaatctttgtctactgaatctaatt-tagtatcttataacatatggctgattagtttctattcttacag--------------------------------------------------------------------------------------------------

upper sequence: PP1S1_526V6.1 (Physcomitrella patens), 5'ss of exon 10
lower sequence: Vv08s0007g03960.t01 (Vitis vinifera), 5'ss of exon 10
GATAACAGAGAAGGTCTTGAATTGCTGAAGACTGCCATTGCGAAGGCTGGCTACACGGACAAGgttacttgatgttgatagcatgtgactcttctatcgttttgggtttaactgcttctggaattcttgtacattagcatctattcctaggagggtcttttttatccacgtacttggtatccgtcgtatttgtggagtctactaaagtcaaagttgcttcgatcaactag
|| ||||  ||||||||||||||||| ||||| |||||||| ||||| || |||||| |  | || | ||| | |  || |  |   | |||  ||  | |||   || |     |  ||||  |     | | |   |||   |  | |   |                                                                            
GAGAACAAGGAAGGTCTTGAATTGCTCAAGACAGCCATTGCTAAGGCCGGTTACACGAAGGAAgtgagttgttttcaattgtgt-caattctcttaatggttt---ttaatacattgttggagattacaaaaagtgagatcccctttttgtcag----------------------------------------------------------------------------

upper sequence: PP1S1_526V6.1 (Physcomitrella patens), 5'ss of exon 10
lower sequence: EFJ14601 (Selaginella moellendorffii), 5'ss of exon 8
GATAACAGAGAAGGTCTTGAATTGCTGAAGACTGCCATTGCGAAGGCTGGCTACACGGACAAGgttacttgatgttgatagcatgtgactcttctatcgttttgggtttaactgcttctggaattcttgtacattagcatctattcctaggagggtcttttttatccacgtacttggtatccgtcgtatttgtggagtctactaaagtcaaagttgcttcgatcaactag
|| || | ||||||||| ||| || |||||||||| |||| ||||||||||||||| |  |||||            | |  || |  |||||      |     ||  || || ||||                                                                                                               
GAAAATAAAGAAGGTCTGGAACTGTTGAAGACTGCTATTGAGAAGGCTGGCTACACCGGAAAGgtaga--------aacaagatttttctctttacaattacaaagtggaattgattctcag------------------------------------------------------------------------------------------------------------

upper sequence: PP1S1_526V6.1 (Physcomitrella patens), 5'ss of exon 10
lower sequence: EFJ32861 (Selaginella moellendorffii), 5'ss of exon 8
GATAACAGAGAAGGTCTTGAATTGCTGAAGACTGCCATTGCGAAGGCTGGCTACACGGACAAGgttacttgatgttgatagcatgtgactcttctatcgttttgggtttaactgcttctggaattcttgtacattagcatctattcctaggagggtcttttttatccacgtacttggtatccgtcgtatttgtggagtctactaaagtcaaagttgcttcgatcaactag
|| || |  |||||||| ||| || |||||||||| |||| ||||||||||||||| |  |||||            | |   | |  |||||      |     ||  || || ||||                                                                                                               
GAAAATAAGGAAGGTCTGGAACTGTTGAAGACTGCTATTGAGAAGGCTGGCTACACCGGAAAGgtaga--------aacaaggtttttctctttacaattacaaagtggaattgattctcag------------------------------------------------------------------------------------------------------------

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|67724475|gb|BJ974734.1|BJ974734
EST:     AAGACTGCCATTGCGAAGGCTGGCTACACNGACAAG                         GTGGTGATCGGAATGGACGTTGCAGCCTCTGAATTTTACAACGAGAAGGAC
genomic: AAGACTGCCATTGCGAAGGCTGGCTACACGGACAAGgttacttgat ... gatcaactagGTGGTGATCGGAATGGACGTTGCAGCCTCTGAATTTTACAACGAGAAGGAC
EST: gi|162255467|gb|FC431881.1|FC431881
EST:     GTCTTGAATTGCTGAAGACTGCCATTGCGAAAGCTGGCTACACGGACAAG                         GTGGTGATCGGAATGGACG
genomic: GTCTTGAATTGCTGAAGACTGCCATTGCGAAGGCTGGCTACACGGACAAGgttacttgat ... gatcaactagGTGGTGATCGGAATGGACG
EST: gi|67727546|gb|BJ977805.1|BJ977805
EST:     GTCTTGAATTGCTGAAGACTGCCATTGCGAAGGCTGGCTACACGGACAAG                         GTGGTGATCGGAATGGACGTTGCAGCCTCTGAATTTTACAACGAGAAGGAC
genomic: GTCTTGAATTGCTGAAGACTGCCATTGCGAAGGCTGGCTACACGGACAAGgttacttgat ... gatcaactagGTGGTGATCGGAATGGACGTTGCAGCCTCTGAATTTTACAACGAGAAGGAC
EST: gi|162279243|gb|FC455790.1|FC455790
EST:     GTCTTGAATTGCTGAAGACTGCCATTGCGAAGGCTGGCTACACGGACAAG                         GTGGTGATCGGAATGGACGTTGCAGCCTCTGAATTTTACAACGAGAAGGAC
genomic: GTCTTGAATTGCTGAAGACTGCCATTGCGAAGGCTGGCTACACGGACAAGgttacttgat ... gatcaactagGTGGTGATCGGAATGGACGTTGCAGCCTCTGAATTTTACAACGAGAAGGAC
EST: gi|208373227|gb|DC945167.1|DC945167
EST:     CTGGCTACACGGACAAG                         GTGGTGATCGGAATGGACGTTGCAGCCTCTGAATTTTACAACGAGAAGGAC
genomic: CTGGCTACACGGACAAGgttacttgat ... gatcaactagGTGGTGATCGGAATGGACGTTGCAGCCTCTGAATTTTACAACGAGAAGGAC
EST: gi|67724530|gb|BJ974789.1|BJ974789
EST:     GTCTTGAATTGCTGAAGACTGCCATTGCGAAGGCTGGCTACACGGACAAG                         GTGGTGATCGGAATGGACGTTGCAGCCTCTGAATTTTACAACGAGAAGGAC
genomic: GTCTTGAATTGCTGAAGACTGCCATTGCGAAGGCTGGCTACACGGACAAGgttacttgat ... gatcaactagGTGGTGATCGGAATGGACGTTGCAGCCTCTGAATTTTACAACGAGAAGGAC
EST: gi|162273265|gb|FC449246.1|FC449246
EST:     GTCTTGAATTGCTGAAGACTGCCATTGCGAAGGCTGGCTACACGGACAAG                         GTGGTGATCGGAATGGACGTTGCAGCCTCTGAATTTTACAACGAGAAGGAC
genomic: GTCTTGAATTGCTGAAGACTGCCATTGCGAAGGCTGGCTACACGGACAAGgttacttgat ... gatcaactagGTGGTGATCGGAATGGACGTTGCAGCCTCTGAATTTTACAACGAGAAGGAC
EST: gi|162255274|gb|FC431584.1|FC431584
EST:     GTCTTGAATTGCTGAAGACTGCCATTGCGAAGGCTGGCTACACGGACAAG                         GTGGTGATCGGAATGGACGTTGCAGCCTCT
genomic: GTCTTGAATTGCTGAAGACTGCCATTGCGAAGGCTGGCTACACGGACAAGgttacttgat ... gatcaactagGTGGTGATCGGAATGGACGTTGCAGCCTCT
EST: gi|208386819|gb|DC941551.1|DC941551
EST:     GTCTTGAATTGCTGAAGACTGCCATTGCGAAGGCTGGCTACACGGACAAG                         GTGGTGATCGGAATGGACGTTGCAGCCTCTGAATTTTACAACGAGAAGGAC
genomic: GTCTTGAATTGCTGAAGACTGCCATTGCGAAGGCTGGCTACACGGACAAGgttacttgat ... gatcaactagGTGGTGATCGGAATGGACGTTGCAGCCTCTGAATTTTACAACGAGAAGGAC
EST: gi|37827550|gb|BJ585562.1|BJ585562
EST:     CTGAAGACTGCCATTGCGAAGGCTGGCTACACGGACAAG                         GTGGTGATCGGAATGGACGTTGCAGCNTCTGAATTTTACAACGAGAAGGAC
genomic: CTGAAGACTGCCATTGCGAAGGCTGGCTACACGGACAAGgttacttgat ... gatcaactagGTGGTGATCGGAATGGACGTTGCAGCCTCTGAATTTTACAACGAGAAGGAC
EST: gi|100352733|gb|BY945421.1|BY945421
EST:     TCTTTGA-TTGCTGAAGACTGCCATTGCGAAGGCTGGCTACACGGACAAG                         GTGGTGATCGGAATGGACGTTGCAGCCTCTGAA
genomic: TCTT-GAATTGCTGAAGACTGCCATTGCGAAGGCTGGCTACACGGACAAGgttacttgat ... gatcaactagGTGGTGATCGGAATGGACGTTGCAGCCTCTGAA
EST: gi|67724577|gb|BJ974836.1|BJ974836
EST:     GTCTTGAATTGCTGAAGACTGCCATTGCGAAGGCTGGCTACACGGACAAG                         GTGGTGATCGGAATGGACGTTGCAGCCTCTGAATTTTACAACGAGAAGGAC
genomic: GTCTTGAATTGCTGAAGACTGCCATTGCGAAGGCTGGCTACACGGACAAGgttacttgat ... gatcaactagGTGGTGATCGGAATGGACGTTGCAGCCTCTGAATTTTACAACGAGAAGGAC

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 1 RNA-Seqlibrary.


Block sizes: 35 (upstream exon), 35 (downstream exon)
Score: 105

GATAACAGAGAAGGTCTTGAATTGCTGAAGACTGCCATTGCGAAGGCTGGCTACACGGACAAGgttacttgat ... gatcaactagGTGGTGATCGGAATGGACGTTGCAGCCTCTGAATTTTACAACGAGAAGGACAAGTTGTACGACTTGAACTTCAAGGAAGAT




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GATAACAGAGAAGGTCTTGAATTGCTGAAGACTGCCATTGCGAAGGCTGGCTACACGGACAAGgttacttgatgttgatagcatgtgactcttctatcgttttgggtttaactgcttctggaattcttgtacattagcatctattcctaggagggtcttttttatccacgtacttggtatccgtcgtatttgtggagtctactaaagtcaaagttgcttcgatcaactag

- - - - - - - - - - - - CTGAAG
- - - - - - - - - - - -  TGAAGA