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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagtttatgacttagaactattctattgttcatgaatgtttattagtgtttactgttctcttacatggatatgcactctgcagCGGAGTTGCCGTTGGAATTTCCTGATGGGACTACTCCGGTTATGTCGCGTATATGCATATATGACAGCGCAGTCGGAGGTGGAGTTGGTGTTGGTGCTCC

Basic information

species Physcomitrella patens
transcript PP1S58_197V6.1
intron # 6
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|18342243|gb|BJ174278.1|BJ174278
EST:     CGCTTTCCCTATCCCAGTACAGTACACAGAGTGTTGTCAGCATCGAGAAG                         CGGAGTTGCCGTTGGAATTTCCTGATGGGACTACTC
genomic: CGCTTTCCCTATCCCAGTACAGTACACAGAGTGTTGTCAGCATCGAGAAGgtgagtttat ... cactctgcagCGGAGTTGCCGTTGGAATTTCCTGATGGGACTACTC
EST: gi|100407853|gb|BY955811.1|BY955811
EST:     CGCTTTCCCTATCCCAGTACAGTACACAGAGTGTTGTCAGCATCGAGAAG                         CGGAGTTGCCGTTGGAAATTCCTGATGGGACTACTCCGGTTATGTCGCGTA
genomic: CGCTTTCCCTATCCCAGTACAGTACACAGAGTGTTGTCAGCATCGAGAAGgtgagtttat ... cactctgcagCGGAGTTGCCGTTGGAATTTCCTGATGGGACTACTCCGGTTATGTCGCGTA
EST: gi|208355357|gb|DC929804.1|DC929804
EST:     CGCTTTCCCTATCCCAGTACAGTACACAGAGTGTTGTCAGCATCGAGAAG                         CGGAGTTGCCGTTGGAATTTCCTGATGGGACTACTCCGGTTATGTCGCGTA
genomic: CGCTTTCCCTATCCCAGTACAGTACACAGAGTGTTGTCAGCATCGAGAAGgtgagtttat ... cactctgcagCGGAGTTGCCGTTGGAATTTCCTGATGGGACTACTCCGGTTATGTCGCGTA
EST: gi|162155579|gb|FC331530.1|FC331530
EST:     CGCTTTCCCTATCCCAGTACAGTACACAGAGTGTTGTCAGCATCGAGAAG                         CGGAGTTGCCGTTGGAATTTCCTGATGGGACTACTCCGGTTATGTCGCGTA
genomic: CGCTTTCCCTATCCCAGTACAGTACACAGAGTGTTGTCAGCATCGAGAAGgtgagtttat ... cactctgcagCGGAGTTGCCGTTGGAATTTCCTGATGGGACTACTCCGGTTATGTCGCGTA
EST: gi|67718012|gb|BJ968271.1|BJ968271
EST:     CGCTTTCCCTATCCCAGTACAGTACACAGAGTGTTGTCAGCATCGAGAAG                         CGGAGTTGCCGTTGGAATTTCCTGATGGGACTACTCCGGTTATGTCGCGTA
genomic: CGCTTTCCCTATCCCAGTACAGTACACAGAGTGTTGTCAGCATCGAGAAGgtgagtttat ... cactctgcagCGGAGTTGCCGTTGGAATTTCCTGATGGGACTACTCCGGTTATGTCGCGTA
EST: gi|67578657|gb|BJ950824.1|BJ950824
EST:     CGCTTTCCCTATCCCAGTACAGTACACAGAGTGTTGTCAGCATCGAGAAG                         CGGAGTTGCCGTTGGAATTTCCTGATGGGACTACTCCGGTTATGTCGCGTA
genomic: CGCTTTCCCTATCCCAGTACAGTACACAGAGTGTTGTCAGCATCGAGAAGgtgagtttat ... cactctgcagCGGAGTTGCCGTTGGAATTTCCTGATGGGACTACTCCGGTTATGTCGCGTA
EST: gi|18371944|gb|BJ203546.1|BJ203546
EST:     CGCTTTCCCTATCCCAGTACAGTACACAGAGTGTTGTCAGCATCGAGAAG                         CGGAGTTGCCGTTGGAATTTCCTGATGGGACTACTCCGGTTATGTCGCGTA
genomic: CGCTTTCCCTATCCCAGTACAGTACACAGAGTGTTGTCAGCATCGAGAAGgtgagtttat ... cactctgcagCGGAGTTGCCGTTGGAATTTCCTGATGGGACTACTCCGGTTATGTCGCGTA
EST: gi|100409673|gb|BY956049.1|BY956049
EST:     CGCTTTCCCTATCCCAGTACAGTACACAGAGTGGTGTCAGCATCGAGAAG                         CGGAGTTGCCGTTGGAATTTCCTGATGGGACTACTCCGGGTATGTCGCGTA
genomic: CGCTTTCCCTATCCCAGTACAGTACACAGAGTGTTGTCAGCATCGAGAAGgtgagtttat ... cactctgcagCGGAGTTGCCGTTGGAATTTCCTGATGGGACTACTCCGGTTATGTCGCGTA
EST: gi|100435291|gb|BY979169.1|BY979169
EST:     CGCTCTCCCTATCCCAGTACAGTACACAGAGTGTTGTCAGCATCGAGAAG                         CGGAGTTGCCGTTGGAATTTCCTGATGGGACTACTCCGGTTATGTCGCGTA
genomic: CGCTTTCCCTATCCCAGTACAGTACACAGAGTGTTGTCAGCATCGAGAAGgtgagtttat ... cactctgcagCGGAGTTGCCGTTGGAATTTCCTGATGGGACTACTCCGGTTATGTCGCGTA
EST: gi|100411979|gb|BY956357.1|BY956357
EST:     CGCTTTCCCTATCCCAGTACAGTACACAGAGTGTTGTCAGCATCGAGAAG                         CGGAGTTGCCGTTTGGA-TTTCCTGATGGGACTACTCCGGTTATGTCGCGT
genomic: CGCTTTCCCTATCCCAGTACAGTACACAGAGTGTTGTCAGCATCGAGAAGgtgagtttat ... cactctgcagCGGAGTTGCCGTT-GGAATTTCCTGATGGGACTACTCCGGTTATGTCGCGT

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), 33 (downstream exon)
Score: 9

GGTCTATCATTCGCTTTCCCTATCCCAGTACAGTACACAGAGTGTTGTCAGCATCGAGAAGgtgagtttat ... cactctgcagCGGAGTTGCCGTTGGAATTTCCTGATGGGACTACTCCGGTTATGTCGCGTATATGCATATATGACAGCGCAGTCGGAGGTGGAGTTGGTGTTGGTGCTCC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttcatgaatgtttattagtgtttactgttctcttacatggatatgcactctgcagCGGAGTTGCCGTTGGAATTTCCTGATGGGACTACTCCGGTTATGTCGCGTATATGCATATATGACAGCGCAGTCGGAGGTGGAGTTGGTGTTGGTGCTCC
                             ctcttac  putative branch site (score: 9)
          tttattagtgttta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagtttatgacttagaactattctattgttcatgaatgtttattagtgtttactgttctcttacatggatatgcactctgcagCGGAGTTGCCGTTGGAATTTCCTGATGGGACTACTCCGGTTATGTCGCGTATATGCATATATGACAGCGCAGTCGGAGGTGGAGTTGGTGTTGGTGCTCC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GTGGAG