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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTTTGCCCGAGGTCTGAATGTATCGCTCTCAACCGATGATCCTCTACAAATTCATCTTACTAAAGAGCCTCTTGTTGAAGAGTACAGCATTGCAGCACAGgtgacgcctctgtccgatctgttcttgccgtatctgactgaattcctaatttttagatcatattttcattaatatcatacatttttctgtgtatcag

Basic information

species Physcomitrella patens
transcript PP1S77_89V6.1
intron # 16
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S77_89V6.1 (Physcomitrella patens), 5'ss of exon 16
lower sequence: EFJ17267 (Selaginella moellendorffii), 5'ss of exon 15
TTTTGCCCGAGGTCTGAATGTATCGCTCTCAACCGATGATCCTCTACAAATTCATCTTACTAAAGAGCCTCTTGTTGAAGAGTACAGCATTGCAGCACAGgtgacgcctctgtccgatctgttcttgccgtatctgactgaattcctaatttttagatcatattttcattaatatcatacatttttctgtgtatcag
|||||| || || |||||||| || || || || ||||| |||||||| || ||||||||||| || ||| | |||||||| ||||| |||||||| |||||    |   | |  | |||  | |    |||  | ||| |  |    | |   |  ||  |                                   
TTTTGCTCGCGGGCTGAATGTTTCACTGTCGACGGATGACCCTCTACAGATCCATCTTACTAAGGAACCTTTGGTTGAAGAATACAGTATTGCAGCTCAGgttttactggtttttgttct--tttgattgtaa-taactcagctaaccagtaccatctcgcag----------------------------------

upper sequence: PP1S77_89V6.1 (Physcomitrella patens), 5'ss of exon 16
lower sequence: EFJ30909 (Selaginella moellendorffii), 5'ss of exon 15
TTTTGCCCGAGGTCTGAATGTATCGCTCTCAACCGATGATCCTCTACAAATTCATCTTACTAAAGAGCCTCTTGTTGAAGAGTACAGCATTGCAGCACAGgtgacgcctctgtccgatctgttcttgccgtatctgactgaattcctaatttttagatcatattttcattaatatcatacatttttctgtgtatcag
|||||| || || |||||||| || || || || ||||| |||||||| || ||||||||||| || ||| | |||||||| ||||| ||||| || |||||        | |  | |||  | |    |||  | ||| |  |    | |   |  ||  |                                   
TTTTGCTCGCGGGCTGAATGTTTCACTGTCGACGGATGACCCTCTACAGATACATCTTACTAAGGAACCTTTGGTTGAAGAATACAGTATTGCGGCTCAGgttttattggtttttgttct--tttgattgtaa-taactcagctaaccagtaccatctcgcag----------------------------------
















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|162206778|gb|FC383251.1|FC383251
EST:     TTCATCTTACTAAAGAGCCTCTTGTTGAAGAGTACAGCATTGCAGCACAG                         GTGTGGAAGCTGAGCTCCTGTGACCTCTGTGAAATTGCACGCAATTCTGTT
genomic: TTCATCTTACTAAAGAGCCTCTTGTTGAAGAGTACAGCATTGCAGCACAGgtgacgcctc ... tgtgtatcagGTGTGGAAGCTGAGCTCCTGTGACCTCTGTGAAATTGCACGCAATTCTGTT
EST: gi|162194297|gb|FC369520.1|FC369520
EST:     TTCATCTTACTAAAGAGCCTCTTGTTGAAGAGTACAGCATTGCAGCACAG                         GTGTGGAAGCTGAGCTCCTGTGACCTCTGTGAAATTGCACGCAATTCTGTT
genomic: TTCATCTTACTAAAGAGCCTCTTGTTGAAGAGTACAGCATTGCAGCACAGgtgacgcctc ... tgtgtatcagGTGTGGAAGCTGAGCTCCTGTGACCTCTGTGAAATTGCACGCAATTCTGTT
EST: gi|19779903|gb|BQ039488.1|BQ039488
EST:     TTCATCTTACTAAAGAGCCTCTTGTTGAAGAGTACAGCATTGCAGCACAG                         GTGTGGAAGCTGAGCTCCTGTGACCTCTGTGAAATTGCACGCAATTCTGTT
genomic: TTCATCTTACTAAAGAGCCTCTTGTTGAAGAGTACAGCATTGCAGCACAGgtgacgcctc ... tgtgtatcagGTGTGGAAGCTGAGCTCCTGTGACCTCTGTGAAATTGCACGCAATTCTGTT
EST: gi|162268980|gb|FC445472.1|FC445472
EST:     TACTAAAGAGCCTCTTGTTGAAGAGTACAGCATTGCAGCACAG                         GTGTGGAAGCTGAGCTCCTGTGACCTCTGTGAAATTGCACGCAATTCTGTT
genomic: TACTAAAGAGCCTCTTGTTGAAGAGTACAGCATTGCAGCACAGgtgacgcctc ... tgtgtatcagGTGTGGAAGCTGAGCTCCTGTGACCTCTGTGAAATTGCACGCAATTCTGTT
EST: gi|7147916|gb|AW509838.1|AW509838
EST:     TTCATCTTACTAAAGAGCCTCTTGTTGAAGAGTACAGCATTGCAGCACAG                         GTGTGGAAGCTGAGCTCCTGTGACCTCTGTGAAATTGCACGCAATTCTGTT
genomic: TTCATCTTACTAAAGAGCCTCTTGTTGAAGAGTACAGCATTGCAGCACAGgtgacgcctc ... tgtgtatcagGTGTGGAAGCTGAGCTCCTGTGACCTCTGTGAAATTGCACGCAATTCTGTT
EST: gi|162268981|gb|FC445473.1|FC445473
EST:     TTCATCTTACTAAAGAGCCTCTTGTTGAAGAGTACAGCATTGCAGCACAG                         GTGTGGAAGCTGAGCTCCTGTGACCTCT
genomic: TTCATCTTACTAAAGAGCCTCTTGTTGAAGAGTACAGCATTGCAGCACAGgtgacgcctc ... tgtgtatcagGTGTGGAAGCTGAGCTCCTGTGACCTCT
EST: gi|162206777|gb|FC383250.1|FC383250
EST:     TTCATCTTACTAAAGAGCCTCTTGTTGAAGAGTACAGCATTGCAGCACAG                         GTGTGGAAGCTGAGCTCCTGTGACCTCTGTGAAATTGCACGCAATTCTGTT
genomic: TTCATCTTACTAAAGAGCCTCTTGTTGAAGAGTACAGCATTGCAGCACAGgtgacgcctc ... tgtgtatcagGTGTGGAAGCTGAGCTCCTGTGACCTCTGTGAAATTGCACGCAATTCTGTT
EST: gi|37852950|gb|BJ610958.1|BJ610958
EST:     TTCATCTTACTAAAGAGCCTCTTGTTGAAGAGTACAGCATTGCAGCACAG                         GTGTGGAAGCTGAGCTCCCTGTGACCTCTGTGAAATTGCACGCAATTCTGT
genomic: TTCATCTTACTAAAGAGCCTCTTGTTGAAGAGTACAGCATTGCAGCACAGgtgacgcctc ... tgtgtatcagGTGTGGAAGCTGAGCT-CCTGTGACCTCTGTGAAATTGCACGCAATTCTGT
EST: gi|162171487|gb|FC346762.1|FC346762
EST:     TTCATCTTACTAAAGAGCCTCTTGTTGAAGAGTACAGCATTGCAGCACAG                         GTGTGGAAGCTGAGCTCCTGTGACCTCTGTGAAATTGCACGCAATTCTGTT
genomic: TTCATCTTACTAAAGAGCCTCTTGTTGAAGAGTACAGCATTGCAGCACAGgtgacgcctc ... tgtgtatcagGTGTGGAAGCTGAGCTCCTGTGACCTCTGTGAAATTGCACGCAATTCTGTT
EST: gi|37851047|gb|BJ609055.1|BJ609055
EST:     TTCATCTTACTAAAGAGCCTCTTGTTGAAGAGTACAGCATTGCAGCACAG                         GTGTGGAAGCTGAGCTCCTGTGACCTCTGTGAAATTGCACGCAATTCTGTT
genomic: TTCATCTTACTAAAGAGCCTCTTGTTGAAGAGTACAGCATTGCAGCACAGgtgacgcctc ... tgtgtatcagGTGTGGAAGCTGAGCTCCTGTGACCTCTGTGAAATTGCACGCAATTCTGTT

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: 24 (upstream exon), 35 (downstream exon)
Score: 3

TTTTGCCCGAGGTCTGAATGTATCGCTCTCAACCGATGATCCTCTACAAATTCATCTTACTAAAGAGCCTCTTGTTGAAGAGTACAGCATTGCAGCACAGgtgacgcctc ... tgtgtatcagGTGTGGAAGCTGAGCTCCTGTGACCTCTGTGAAATTGCACGCAATTCTGTTTATCAATCGGGTTTCAATCATAGAACAAAG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TTTTGCCCGAGGTCTGAATGTATCGCTCTCAACCGATGATCCTCTACAAATTCATCTTACTAAAGAGCCTCTTGTTGAAGAGTACAGCATTGCAGCACAGgtgacgcctctgtccgatctgttcttgccgtatctgactgaattcctaatttttagatcatattttcattaatatcatacatttttctgtgtatcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA