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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GATATTGTCATGTATGTTAATTCACCTGGTGGTTCTGTCACAGCAGgtaaagcatacatgacagcaatcaaaatcataacatggatttgtttgtttgtttgtttgtttgtttgttttgttttgttttcttttccgctttctgcact...

Basic information

species Physcomitrella patens
transcript PP1S49_191V6.1
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S49_191V6.1 (Physcomitrella patens), 5'ss of exon 5
lower sequence: AT1G02560.1 (Arabidopsis thaliana), 5'ss of exon 5
GATATTGTCATGTATGTTAATTCACCTGGTGGTTCTGTCACAGCAGgtaaagcatacatgacagcaatcaaaatcataacatggatttgtttgtttgtttgtttgtttgtttgttttgttttgttttcttttccgctttctgcact
||||||||||||||||||||||| |||||||| || || ||||| |||||        | ||| |  |    | | ||   |  || | |||    ||||  | |||  |   |  ||  |   || |||| ||            
GATATTGTCATGTATGTTAATTCTCCTGGTGGATCAGTTACAGCTGgtaa--------taacaact-ttgtcagcttactctttatcttttttccggttttatggttaatgactcgtgcatctcttactttacccag---------

upper sequence: PP1S49_191V6.1 (Physcomitrella patens), 5'ss of exon 5
lower sequence: EFJ35520 (Selaginella moellendorffii), 5'ss of exon 4
GATATTGTCATGTATGTTAATTCACCTGGTGGTTCTGTCACAGCAGgtaaagcatacatgacagcaatcaaaatcataacatggatttgtttgtttgtttgtttgtttgtttgttttgttttgttttcttttccgctttctgcact
||||||||||||||||| ||||||||||| ||||| || || || ||||  |  |   |        |      | || |  |   |    |     ||| ||| | | | || |  |                            
GATATTGTCATGTATGTAAATTCACCTGGAGGTTCCGTTACCGCTGgtatggtttttttt-------ttttttccctatcgagttgtcagctaacaatttattt-tctttctgctcag----------------------------
















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|162179727|gb|FC356318.1|FC356318
EST:     GATATTGTCATGTATGTTAATTCACCTGGTGGTTCTGTCACAGCAG                         GAATGGCAATCTTCGACACCATGAGGCATATTCGACCTGATGTGAGCACAG
genomic: GATATTGTCATGTATGTTAATTCACCTGGTGGTTCTGTCACAGCAGgtaaagcata ... attttgacagGAATGGCAATCTTCGACACCATGAGGCATATTCGACCTGATGTGAGCACAG
EST: gi|208382931|gb|DC923503.1|DC923503
EST:     GATATTGTCATGTATGTTAATTCACCTGGTGGTTCTGTCACAGCAG                         GAATGGCAATCTTCGACACCATGAGGCATATTCGACCTGATGTGAGCACAG
genomic: GATATTGTCATGTATGTTAATTCACCTGGTGGTTCTGTCACAGCAGgtaaagcata ... attttgacagGAATGGCAATCTTCGACACCATGAGGCATATTCGACCTGATGTGAGCACAG
EST: gi|162179726|gb|FC356317.1|FC356317
EST:     GATATTGTCATGTATGTTAATTCACCTGGTGGTTCTGTCACAGCAG                         GAATGGCAATCTTCGACACCATGAGGCATATTCGACCTGATGTGAGCACAG
genomic: GATATTGTCATGTATGTTAATTCACCTGGTGGTTCTGTCACAGCAGgtaaagcata ... attttgacagGAATGGCAATCTTCGACACCATGAGGCATATTCGACCTGATGTGAGCACAG
EST: gi|37851229|gb|BJ609237.1|BJ609237
EST:     GATATTGTCATGTATGTTAATTCACCTGGTGGTTCTGTCACAGCAG                         GAATGGCAATCTTCGACACCATGAGGCATATTCGACCTGATGTGAGCACAG
genomic: GATATTGTCATGTATGTTAATTCACCTGGTGGTTCTGTCACAGCAGgtaaagcata ... attttgacagGAATGGCAATCTTCGACACCATGAGGCATATTCGACCTGATGTGAGCACAG
EST: gi|18334691|gb|BJ166708.1|BJ166708
EST:     GATATTGTCATGTATGTTAATTCACCTGGTGGTTCTGTCACAGCAG                         GAATGGCAATCTTCGACACCATGAGGCATATTCGACCTGATGTGAGCACAG
genomic: GATATTGTCATGTATGTTAATTCACCTGGTGGTTCTGTCACAGCAGgtaaagcata ... attttgacagGAATGGCAATCTTCGACACCATGAGGCATATTCGACCTGATGTGAGCACAG
EST: gi|7148089|gb|AW510011.1|AW510011
EST:     GATATTGTCATGTATGTTAATTCACCTGGTGGTTCTGTCACAGCAG                         GAATGGCAATCTTCGACACCATGAGGCATATTCGACCTGATGTGAGCACAG
genomic: GATATTGTCATGTATGTTAATTCACCTGGTGGTTCTGTCACAGCAGgtaaagcata ... attttgacagGAATGGCAATCTTCGACACCATGAGGCATATTCGACCTGATGTGAGCACAG
EST: gi|162159944|gb|FC336197.1|FC336197
EST:     GATATTGTCATGTATGTTAATTCACCTGGTGGTTCTGTCACAGCAG                         GAATGGCAATCTTCGACACCATGAGGCATATTCGACCTGATGTGAGCACAG
genomic: GATATTGTCATGTATGTTAATTCACCTGGTGGTTCTGTCACAGCAGgtaaagcata ... attttgacagGAATGGCAATCTTCGACACCATGAGGCATATTCGACCTGATGTGAGCACAG
EST: gi|18341257|gb|BJ173291.1|BJ173291
EST:     GATATTGTCATGTATGTTAATTCACCTGGTGGTTCTGTCACAGCAG                         GAATGGCAATCTTCGACACCATGAGGCATATTCGACCTGATGTGAGCACAG
genomic: GATATTGTCATGTATGTTAATTCACCTGGTGGTTCTGTCACAGCAGgtaaagcata ... attttgacagGAATGGCAATCTTCGACACCATGAGGCATATTCGACCTGATGTGAGCACAG
EST: gi|208381909|gb|DC923433.1|DC923433
EST:     GATATTGTCATGTATGTTAATTCACCTGGTGGTTCTGTCACAGCAG                         GAATGGCAATCTTCGACACCATGAGGCATATTCGACCTGATGTGAGCACAG
genomic: GATATTGTCATGTATGTTAATTCACCTGGTGGTTCTGTCACAGCAGgtaaagcata ... attttgacagGAATGGCAATCTTCGACACCATGAGGCATATTCGACCTGATGTGAGCACAG
EST: gi|67696515|gb|BJ956748.1|BJ956748
EST:     GATATTGTCATGTATGTTAATTCACCTGGTGGTTCTGTCACAGCAG                         GAATGGCAATCTTCGACACCATGAGGCATATTCGACCTGATGTGAGCACAG
genomic: GATATTGTCATGTATGTTAATTCACCTGGTGGTTCTGTCACAGCAGgtaaagcata ... attttgacagGAATGGCAATCTTCGACACCATGAGGCATATTCGACCTGATGTGAGCACAG
EST: gi|208380837|gb|DC923319.1|DC923319
EST:     GATATTGTCATGTATGTTAATTCACCTGGTGGTTCTGTCACAGCAG                         GAATGGCAATCTTCGACACCATGAGGCATATTCGACCTGATGTGAGCACAG
genomic: GATATTGTCATGTATGTTAATTCACCTGGTGGTTCTGTCACAGCAGgtaaagcata ... attttgacagGAATGGCAATCTTCGACACCATGAGGCATATTCGACCTGATGTGAGCACAG
EST: gi|37836163|gb|BJ594171.1|BJ594171
EST:     GATATTGTCATGTATGTTAATTCACCTGGTGGTTCTGTCACAGCAG                         GAATGGCAATCTTCGACACCATGAGGCATATTCGACCTGATGTGAGCACAG
genomic: GATATTGTCATGTATGTTAATTCACCTGGTGGTTCTGTCACAGCAGgtaaagcata ... attttgacagGAATGGCAATCTTCGACACCATGAGGCATATTCGACCTGATGTGAGCACAG
EST: gi|162268713|gb|FC445210.1|FC445210
EST:     GATATTGTCATGTATGTTAATTCACCTGGTGGTTCTGTCACAGCAG                         GAATGGCAATCTTCGACACCATGAGGCATATTCGACCTGATGTGAGCACAG
genomic: GATATTGTCATGTATGTTAATTCACCTGGTGGTTCTGTCACAGCAGgtaaagcata ... attttgacagGAATGGCAATCTTCGACACCATGAGGCATATTCGACCTGATGTGAGCACAG
EST: gi|208372169|gb|DC947972.1|DC947972
EST:     GATATTGTCATGTATGTTAATTCACCTGGTGGTTCTGTCACAGCAG                         GAATGGCAATCTTCGACACCATGAGGCATATTCGACCTGATGTGAGCACAG
genomic: GATATTGTCATGTATGTTAATTCACCTGGTGGTTCTGTCACAGCAGgtaaagcata ... attttgacagGAATGGCAATCTTCGACACCATGAGGCATATTCGACCTGATGTGAGCACAG
EST: gi|37851336|gb|BJ609344.1|BJ609344
EST:     GATATTGTCATGTATGTTAATTCACCTGGTGGTTCTGTCACAGCAG                         GAATGGCAATCTTCGACACCATGAGGCATATTCGACCTGATGTGAGCACAG
genomic: GATATTGTCATGTATGTTAATTCACCTGGTGGTTCTGTCACAGCAGgtaaagcata ... attttgacagGAATGGCAATCTTCGACACCATGAGGCATATTCGACCTGATGTGAGCACAG
EST: gi|162259738|gb|FC436744.1|FC436744
EST:     GATATTGTCATGTATGTTAATTCACCTGGTGGTTCTGTCACAGCAG                         GAATGGCAATCTTCGACACCATGAGGCATATTCGACCTGATGTGAGCACAG
genomic: GATATTGTCATGTATGTTAATTCACCTGGTGGTTCTGTCACAGCAGgtaaagcata ... attttgacagGAATGGCAATCTTCGACACCATGAGGCATATTCGACCTGATGTGAGCACAG

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: 34 (upstream exon), 34 (downstream exon)
Score: 20

GATATTGTCATGTATGTTAATTCACCTGGTGGTTCTGTCACAGCAGgtaaagcata ... attttgacagGAATGGCAATCTTCGACACCATGAGGCATATTCGACCTGATGTGAGCACAGTCTGTGTTGGGCTTGCAGCCAG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GATATTGTCATGTATGTTAATTCACCTGGTGGTTCTGTCACAGCAGgtaaagcatacatgacagcaatcaaaatcataacatggatttgtttgtttgtttgtttgtttgtttgttttgttttgttttcttttccgctttctgcact

- - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aatcaaaa