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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgaacattttgtttgcttgttaagaacctggaaggcatatgccttggtgagaaagcaacatatgaaaatactgattctctgtttacgtttacatcgtcttttttttataaattaacgaatcggtatgttttacagGTTTGAGTGAGGTTGTTGCACTGGAACCTAATGAACAGAACGATGATGGTGATAAACGCACTGTTCCCGTTGACCAGGAAATTAATCATTTGGAGAAACG

Basic information

species Physcomitrella patens
transcript PP1S8_288V6.1
intron # 34
splice site 3'
intron type U2

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|162181732|gb|FC358762.1|FC358762
EST:     GTGTTGTCGTGGAAGAAACAAGAAGTCTTCGAACGAGGAAGTTGTTCCAG                         GTTTGAGTGAGGTTGTTGCACTGGAACCTAATGAACAGAACGATGATGGTG
genomic: GTGTTGTCGTGGAAGAAACAAGAAGTCTTCGAACGAGGAAGTTGTTCCAGgtgaacattt ... tgttttacagGTTTGAGTGAGGTTGTTGCACTGGAACCTAATGAACAGAACGATGATGGTG
EST: gi|162175272|gb|FC351470.1|FC351470
EST:     GTGTTGTCGTGGAAGAAACAAGAAGTCTTCGAACGAGGAAGTTGTTCCAG                         GTTTGAGTGAGGTTGTTGCACTGGAACCTAATGAACAGAACGATGATGGTG
genomic: GTGTTGTCGTGGAAGAAACAAGAAGTCTTCGAACGAGGAAGTTGTTCCAGgtgaacattt ... tgttttacagGTTTGAGTGAGGTTGTTGCACTGGAACCTAATGAACAGAACGATGATGGTG
EST: gi|162189371|gb|FC366529.1|FC366529
EST:     GTGTTGTCGTGGAAGAAACAAGAAGTCTTCGAACGAGGAAGTTGTTCCAG                         GTTTGAGTGAGGTTGTTGCACTGGAACCTAATGAACAGAACGATGATGGTG
genomic: GTGTTGTCGTGGAAGAAACAAGAAGTCTTCGAACGAGGAAGTTGTTCCAGgtgaacattt ... tgttttacagGTTTGAGTGAGGTTGTTGCACTGGAACCTAATGAACAGAACGATGATGGTG
EST: gi|162186820|gb|FC363064.1|FC363064
EST:     GTGTTGTCGTGGAAGAAACAAGAAGTCTTCGAACGAGGAAGTTGTTCCAG                         GTTTGAGTGAGGTTGTTGCACTGGAACCTAATGAACAGAACGATGATGGTG
genomic: GTGTTGTCGTGGAAGAAACAAGAAGTCTTCGAACGAGGAAGTTGTTCCAGgtgaacattt ... tgttttacagGTTTGAGTGAGGTTGTTGCACTGGAACCTAATGAACAGAACGATGATGGTG
EST: gi|18336099|gb|BJ168121.1|BJ168121
EST:     GTGTTGTCGTGGAAGAAACAAGAAGTCTTCGAACGAGGAAGTTGTTCCAG                         GTTTGAGTGAGGTTGTTGCACTGGAACCTAATGAACAGAACGATGATGGTG
genomic: GTGTTGTCGTGGAAGAAACAAGAAGTCTTCGAACGAGGAAGTTGTTCCAGgtgaacattt ... tgttttacagGTTTGAGTGAGGTTGTTGCACTGGAACCTAATGAACAGAACGATGATGGTG
EST: gi|162189370|gb|FC366528.1|FC366528
EST:     GTGTTGTCGTGGAAGAAACAAGAAGTCTTCGAACGAGGAAGTTGTTCCAG                         GTTTGAGTGAGGTTGTTGCACTGGAACCTAATGAACAGAACGATGATGGTG
genomic: GTGTTGTCGTGGAAGAAACAAGAAGTCTTCGAACGAGGAAGTTGTTCCAGgtgaacattt ... tgttttacagGTTTGAGTGAGGTTGTTGCACTGGAACCTAATGAACAGAACGATGATGGTG
EST: gi|162191835|gb|FC367984.1|FC367984
EST:     GTGTTGTCGTGGAAGAAACAAGAAGTCTTCGAACGAGGAAGTTGTTCCAG                         GTTTGAGTGAGGTTGTTGCACTGGAACCTAATGAACAGAACGATGATGGTG
genomic: GTGTTGTCGTGGAAGAAACAAGAAGTCTTCGAACGAGGAAGTTGTTCCAGgtgaacattt ... tgttttacagGTTTGAGTGAGGTTGTTGCACTGGAACCTAATGAACAGAACGATGATGGTG
EST: gi|162208803|gb|FC384939.1|FC384939
EST:     GTGTTGTCGTGGAAGAAACAAGAAGTCTTCGAACGAGGAAGTTGTTCCAG                         GTTTGAGTGAGGTTGTTGCACTGGAACCTAATGAACAGAACGATGATGGTG
genomic: GTGTTGTCGTGGAAGAAACAAGAAGTCTTCGAACGAGGAAGTTGTTCCAGgtgaacattt ... tgttttacagGTTTGAGTGAGGTTGTTGCACTGGAACCTAATGAACAGAACGATGATGGTG
EST: gi|162181320|gb|FC358415.1|FC358415
EST:     GTGTTGTCGTGGAAGAAACAAGAAGTCTTCGAACGAGGAAGTTGTTCCAG                         GTTTGAGTGAGGTTGTTGCACTGGAACCTAATGAACAGAACGATGATGGTG
genomic: GTGTTGTCGTGGAAGAAACAAGAAGTCTTCGAACGAGGAAGTTGTTCCAGgtgaacattt ... tgttttacagGTTTGAGTGAGGTTGTTGCACTGGAACCTAATGAACAGAACGATGATGGTG
EST: gi|37849039|gb|BJ607047.1|BJ607047
EST:     GTGTTGTCGTGGAAGAAACAAGAAGTCTTCGAACGAGGAAGTTGTTCCAG                         GTTTGAGTGAGGTTGTTGCACTGGAACCTAATGAACAGAACGATGATGGTG
genomic: GTGTTGTCGTGGAAGAAACAAGAAGTCTTCGAACGAGGAAGTTGTTCCAGgtgaacattt ... tgttttacagGTTTGAGTGAGGTTGTTGCACTGGAACCTAATGAACAGAACGATGATGGTG
EST: gi|37849985|gb|BJ607993.1|BJ607993
EST:     GTGTTGTCGTGGAAGAAACAAGAAGTCTTCGAACGAGGAAGTTGTTCCAG                         GTTTGAGTGAGGTTGTTGCACTGGAACCTAATGAACAGAACGATGATGGTG
genomic: GTGTTGTCGTGGAAGAAACAAGAAGTCTTCGAACGAGGAAGTTGTTCCAGgtgaacattt ... tgttttacagGTTTGAGTGAGGTTGTTGCACTGGAACCTAATGAACAGAACGATGATGGTG
EST: gi|162197899|gb|FC373953.1|FC373953
EST:     GTGTTGTCGTGGAAGAAACAAGAAGTCTTCGAACGAGGAAGTTGTTCCAG                         GTTTGAGTGAGGTTGTTGCACTGGAACCTAATGAACAGAACGATGATGGTG
genomic: GTGTTGTCGTGGAAGAAACAAGAAGTCTTCGAACGAGGAAGTTGTTCCAGgtgaacattt ... tgttttacagGTTTGAGTGAGGTTGTTGCACTGGAACCTAATGAACAGAACGATGATGGTG
EST: gi|162259196|gb|FC435216.1|FC435216
EST:     GTGTTGTCGTGGAAGAAACAAGAAGTCTTCGAACGAGGAAGTTGTTCCAG                         GTTTGAGTGAGGTTGTTGCACTGGAACCTAATGAACAGAACGATGATGGTG
genomic: GTGTTGTCGTGGAAGAAACAAGAAGTCTTCGAACGAGGAAGTTGTTCCAGgtgaacattt ... tgttttacagGTTTGAGTGAGGTTGTTGCACTGGAACCTAATGAACAGAACGATGATGGTG
EST: gi|162172504|gb|FC348549.1|FC348549
EST:     GTGTTGTCGTGGAAGAAACAAGAAGTCTTCGAACGAGGAAGTTGTTCCAG                         GTTTGAGTGAGGTTGTTGCACTGGAACCTAATGAACAGAACGATGATGGTG
genomic: GTGTTGTCGTGGAAGAAACAAGAAGTCTTCGAACGAGGAAGTTGTTCCAGgtgaacattt ... tgttttacagGTTTGAGTGAGGTTGTTGCACTGGAACCTAATGAACAGAACGATGATGGTG
EST: gi|162153021|gb|FC330051.1|FC330051
EST:     GTGTTGTCGTGGAAGAAACAAGAAGTCTTCGAACGAGGAAGTTGTTCCAG                         GTTTGAGTGAGGTTGTTGCACTGGAACCTAATGAACAGAACGATGATGGTG
genomic: GTGTTGTCGTGGAAGAAACAAGAAGTCTTCGAACGAGGAAGTTGTTCCAGgtgaacattt ... tgttttacagGTTTGAGTGAGGTTGTTGCACTGGAACCTAATGAACAGAACGATGATGGTG
EST: gi|162256238|gb|FC432294.1|FC432294
EST:     GTGTTGTCGTGGAAGAAACAAGAAGTCTTCGAACGAGGAAGTTGTTCCAG                         GTTTGAGTGAGGTTGTTGCACTGGAACCTAATGAACAGAACGATGATGGTG
genomic: GTGTTGTCGTGGAAGAAACAAGAAGTCTTCGAACGAGGAAGTTGTTCCAGgtgaacattt ... tgttttacagGTTTGAGTGAGGTTGTTGCACTGGAACCTAATGAACAGAACGATGATGGTG
EST: gi|37853493|gb|BJ611501.1|BJ611501
EST:     GTGTTGTCGTGGAAGAAACAAGAAGTCTTCGAACGAGGAAGTTGTTCCAG                         GTTTGAGTGAGGTTGTTGCACTGGAACCTAATGGACAGAACGATGATGGTG
genomic: GTGTTGTCGTGGAAGAAACAAGAAGTCTTCGAACGAGGAAGTTGTTCCAGgtgaacattt ... tgttttacagGTTTGAGTGAGGTTGTTGCACTGGAACCTAATGAACAGAACGATGATGGTG
EST: gi|162245992|gb|FC421881.1|FC421881
EST:     GTGTTGTCGTGGAAGAAACAAGAAGTCTTCGAACGAGGAAGTTGTTCCAG                         GTTTGAGTGAGGTTGTTGCACTGGAACCTAATGAACAGAACGATGATGGTG
genomic: GTGTTGTCGTGGAAGAAACAAGAAGTCTTCGAACGAGGAAGTTGTTCCAGgtgaacattt ... tgttttacagGTTTGAGTGAGGTTGTTGCACTGGAACCTAATGAACAGAACGATGATGGTG
EST: gi|162158143|gb|FC333938.1|FC333938
EST:     GAAGAAACAAGAAGTCTTCGAACGAGGAAGTTGTTCCAG                         GTTTGAGTGAGGTTGTTGCACTGGAACCTAATGAACAGAACGATGATGGTG
genomic: GAAGAAACAAGAAGTCTTCGAACGAGGAAGTTGTTCCAGgtgaacattt ... tgttttacagGTTTGAGTGAGGTTGTTGCACTGGAACCTAATGAACAGAACGATGATGGTG
EST: gi|162272382|gb|FC449034.1|FC449034
EST:     GTGTTGTCGTGGAAGAAACAAGAAGTCTTCGAACGAGGAAGT-GTTCCAG                         GTTTGAGTGAGGTTGTTGCACTGG
genomic: GTGTTGTCGTGGAAGAAACAAGAAGTCTTCGAACGAGGAAGTTGTTCCAGgtgaacattt ... tgttttacagGTTTGAGTGAGGTTGTTGCACTGG
EST: gi|162162455|gb|FC338367.1|FC338367
EST:     GTGTTGTCGTGGAAGAAACAAGAAGTCTTCGAACGAGGAAGTTGTTCCAG                         GTTTGAGTGAGGTTGTTGCACTGGAACCTAATGAACAGAACGATGATGGTG
genomic: GTGTTGTCGTGGAAGAAACAAGAAGTCTTCGAACGAGGAAGTTGTTCCAGgtgaacattt ... tgttttacagGTTTGAGTGAGGTTGTTGCACTGGAACCTAATGAACAGAACGATGATGGTG
EST: gi|162272381|gb|FC449033.1|FC449033
EST:     GTGTTGTCGTGGAAGAAACAAGAAGTCTTCGAACGAGGAAGTTGTTCCAG                         GTTTGAGTGAGGTTGTTGCACTGGAACCTAATGAACAGAACGATGATGGTG
genomic: GTGTTGTCGTGGAAGAAACAAGAAGTCTTCGAACGAGGAAGTTGTTCCAGgtgaacattt ... tgttttacagGTTTGAGTGAGGTTGTTGCACTGGAACCTAATGAACAGAACGATGATGGTG
EST: gi|37850518|gb|BJ608526.1|BJ608526
EST:     GTGTTGTCGTGGAAGAAACAAGAAGTCTTCGAACGAGGAAGTTGTTCCAG                         GTTTGAGTGAGGTTGTTGCACTGGAACCTAATGAACAGAACGATGATGGTG
genomic: GTGTTGTCGTGGAAGAAACAAGAAGTCTTCGAACGAGGAAGTTGTTCCAGgtgaacattt ... tgttttacagGTTTGAGTGAGGTTGTTGCACTGGAACCTAATGAACAGAACGATGATGGTG
EST: gi|162155066|gb|FC330860.1|FC330860
EST:     GTGTTGTCGTGGAAGAAACAAGAAGTCTTCGAACGAGGAAGTTGTTCCAG                         GTTTGAGTGAGGTTGTTGCACTGGAACCTAATGAACAGAACGATGATGGTG
genomic: GTGTTGTCGTGGAAGAAACAAGAAGTCTTCGAACGAGGAAGTTGTTCCAGgtgaacattt ... tgttttacagGTTTGAGTGAGGTTGTTGCACTGGAACCTAATGAACAGAACGATGATGGTG
EST: gi|7647881|gb|AW738864.1|AW738864
EST:     GTGTTGTCGTGGAAGAAACAAGAAGTCTTCGAACGAGGAAGTTGTTCCAG                         GTTTGAGTGAGGTTGTTGCACTGGAACCTAATGAACAGAACGATGATGGTG
genomic: GTGTTGTCGTGGAAGAAACAAGAAGTCTTCGAACGAGGAAGTTGTTCCAGgtgaacattt ... tgttttacagGTTTGAGTGAGGTTGTTGCACTGGAACCTAATGAACAGAACGATGATGGTG
EST: gi|162166639|gb|FC343531.1|FC343531
EST:     GTGTTGTCGTGGAAGAAACAAGAAGTCTTCGAACGAGGAAGTTGTTCCAG                         GTTTGAGTGAGGTTGTTGCACTGGAACCTAATGAACAGAACGATGATGGTG
genomic: GTGTTGTCGTGGAAGAAACAAGAAGTCTTCGAACGAGGAAGTTGTTCCAGgtgaacattt ... tgttttacagGTTTGAGTGAGGTTGTTGCACTGGAACCTAATGAACAGAACGATGATGGTG
EST: gi|162249460|gb|FC426444.1|FC426444
EST:     CAAGAAGTCTTCGAACGAGGAAGTTGTTCCAG                         GTTTGAGTGAGGTTGTTGCACTGGAACCTAATGAACAGAACGATGATGGTG
genomic: CAAGAAGTCTTCGAACGAGGAAGTTGTTCCAGgtgaacattt ... tgttttacagGTTTGAGTGAGGTTGTTGCACTGGAACCTAATGAACAGAACGATGATGGTG
EST: gi|162205304|gb|FC380986.1|FC380986
EST:     GTGTTGTCGTGGAAGAAACAAGAAGTCTTCGAACGAGGAAGTTGTTCCAG                         GTTTGAGTGAGGTTGTTGCACTGGAACCTAATGAACAGAACGATGATGGTG
genomic: GTGTTGTCGTGGAAGAAACAAGAAGTCTTCGAACGAGGAAGTTGTTCCAGgtgaacattt ... tgttttacagGTTTGAGTGAGGTTGTTGCACTGGAACCTAATGAACAGAACGATGATGGTG
EST: gi|162256676|gb|FC433194.1|FC433194
EST:     GTGTTGTCGTGGAAGAAACAAGAAGTCTTCGAACGAGGAAGTTGTTCCAG                         GTTTGAGTGAGGTTGTTGCACTGGAACCTAATGAACAGAACGATGATGGTG
genomic: GTGTTGTCGTGGAAGAAACAAGAAGTCTTCGAACGAGGAAGTTGTTCCAGgtgaacattt ... tgttttacagGTTTGAGTGAGGTTGTTGCACTGGAACCTAATGAACAGAACGATGATGGTG

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: 58

TCCAAGTTTGTGCCCGTTCCGAAAAAGCAGTTCCAGCCCAACCTCACTGGGTGTTGTCGTGGAAGAAACAAGAAGTCTTCGAACGAGGAAGTTGTTCCAGgtgaacattt ... tgttttacagGTTTGAGTGAGGTTGTTGCACTGGAACCTAATGAACAGAACGATGATGGTGATAAACGCACTGTTCCCGTTGACCAGGAAATTAATCATTTGGAGAAACG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtttacgtttacatcgtcttttttttataaattaacgaatcggtatgttttacagGTTTGAGTGAGGTTGTTGCACTGGAACCTAATGAACAGAACGATGATGGTGATAAACGCACTGTTCCCGTTGACCAGGAAATTAATCATTTGGAGAAACG
                             aattaac  putative branch site (score: 58)
       tttacatcgtcttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgaacattttgtttgcttgttaagaacctggaaggcatatgccttggtgagaaagcaacatatgaaaatactgattctctgtttacgtttacatcgtcttttttttataaattaacgaatcggtatgttttacagGTTTGAGTGAGGTTGTTGCACTGGAACCTAATGAACAGAACGATGATGGTGATAAACGCACTGTTCCCGTTGACCAGGAAATTAATCATTTGGAGAAACG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAA